Fri May 10 20:02:30 UTC 2024 I: starting to build pyranges/trixie/armhf on jenkins on '2024-05-10 20:02' Fri May 10 20:02:30 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_31/4863/console.log Fri May 10 20:02:30 UTC 2024 I: Downloading source for trixie/pyranges=0.0.111+ds-7 --2024-05-10 20:02:30-- http://deb.debian.org/debian/pool/main/p/pyranges/pyranges_0.0.111%2bds-7.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2428 (2.4K) [text/prs.lines.tag] Saving to: ‘pyranges_0.0.111+ds-7.dsc’ 0K .. 100% 264M=0s 2024-05-10 20:02:30 (264 MB/s) - ‘pyranges_0.0.111+ds-7.dsc’ saved [2428/2428] Fri May 10 20:02:30 UTC 2024 I: pyranges_0.0.111+ds-7.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: pyranges Binary: python3-pyranges Architecture: all Version: 0.0.111+ds-7 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Étienne Mollier Homepage: https://github.com/biocore-ntnu/pyranges Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/pyranges Vcs-Git: https://salsa.debian.org/med-team/pyranges.git Testsuite: autopkgtest-pkg-python Build-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 Package-List: python3-pyranges deb python optional arch=all Checksums-Sha1: 3591cd303505955df6c34eec755d51f27bd38e5b 3288424 pyranges_0.0.111+ds.orig.tar.xz bbf602d834d8e2ce67c1029b2e561f00d39e8589 83796 pyranges_0.0.111+ds-7.debian.tar.xz Checksums-Sha256: b22a50cb9e0109c8c14720385a5e87bef029f491d4f3e02dbe492866802144d1 3288424 pyranges_0.0.111+ds.orig.tar.xz e03b1b53d8cc25d6e94ac62b0dc6eb455e56a8ab0c6018a106c43b07e36c429e 83796 pyranges_0.0.111+ds-7.debian.tar.xz Files: 2c48870491f89e171b4aeeaa5b3b216a 3288424 pyranges_0.0.111+ds.orig.tar.xz 31ddf7357517790430841c5fdcf32de1 83796 pyranges_0.0.111+ds-7.debian.tar.xz Dgit: 334ec47f92336819696f8e033c7c690a17174f2f debian archive/debian/0.0.111+ds-7 https://git.dgit.debian.org/pyranges -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmXYxM0UHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdol0Q//b9TWLQmeyLiC7Ugi1QqlvOflrQCx 46DBSrymgC8Q043RiOd5i/Kx6nmsoy58mifXRndO09oTWQAw4lMbGM3q/nMmDid2 2jHDcN5SwFsP7fWj2diIQDJ4vcMRU6twAFDPwKX+yJD08X4f2PTLYJsKptqvoRLP 4by1J0TR1rU5jjrqeQCzaR2jCGEIOSSk6CZJ9N+1T+7KvHQ1pqS345AVS6zzluza l/ppJVV+wviWPSabBGzfhZ4lTrXjWUqEewfgswJV5RGtOSa3cZxwgXUdn6KFyFYW 4Zd5BsnWJ/VWMSUlOoIfO6EN+ghH8MQ/kzzkWFhSyngdsL7VrTWt0fWlc1kvMKDS GwzexnKN/XNHYV1V9vozrWWubRmlMZMJXTad+po+lNbAPOLGd7T+bP93x2l/Ftm0 GkdPitN8Y9EJquxG2wF40wtzQfmoi8AfuI28s7mB1aFlfsVmC5Z/z/ZwDsZ5craU f4zLjdipsCsKLHAaSi6ded35M+pNIrMpCbwmzjY2kxdhVLWCPhnlhMzKrqxWknLN YKcUs0olHOyGIjwoq+5U8o6ZQuMYLwY9+3kizyobgJ/AYaxvOgXi9LgbaBmhG/2I pmn2LdFudnjKvmSckJzQSuIZowpeZwL5USqyD8JCDxQn1Cc3J+B0ZO2TBMBUpTkv rP3I2BS8O18Kx4M= =JH6d -----END PGP SIGNATURE----- Fri May 10 20:02:30 UTC 2024 I: Checking whether the package is not for us Fri May 10 20:02:30 UTC 2024 I: Starting 1st build on remote node virt64c-armhf-rb.debian.net. Fri May 10 20:02:30 UTC 2024 I: Preparing to do remote build '1' on virt64c-armhf-rb.debian.net. Sat May 11 14:02:59 UTC 2024 I: Deleting $TMPDIR on virt64c-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri May 10 08:02:41 -12 2024 I: pbuilder-time-stamp: 1715371361 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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: Copying source file I: copying [pyranges_0.0.111+ds-7.dsc] I: copying [./pyranges_0.0.111+ds.orig.tar.xz] I: copying [./pyranges_0.0.111+ds-7.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Feb 23 16:16:13 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-7.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-7.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/12935/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='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='d8ada2e076e744ba8c5fdae2f1444ff2' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' 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='12935' 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.x5Dq4uVh/pbuilderrc_MEGC --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.x5Dq4uVh/b1 --logfile b1/build.log pyranges_0.0.111+ds-7.dsc' SUDO_GID='113' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt64c 6.1.0-21-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 10 18:08 /bin -> usr/bin I: user script /srv/workspace/pbuilder/12935/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: armhf 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 ... 19445 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} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} librtmp1{a} libssh2-1t64{a} libsub-override-perl{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-dateutil{a} python3-distutils{a} python3-execnet{a} python3-hypothesis{a} python3-iniconfig{a} python3-lib2to3{a} python3-minimal{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-tz{a} python3.11{a} python3.11-minimal{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 libltdl-dev libmail-sendmail-perl 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, 94 newly installed, 0 to remove and 0 not upgraded. Need to get 51.7 MB of archives. After unpacking 214 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf libpython3.11-minimal armhf 3.11.9-1 [805 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf libexpat1 armhf 2.6.2-1 [83.5 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf python3.11-minimal armhf 3.11.9-1 [1600 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf python3-minimal armhf 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf libreadline8t64 armhf 8.2-4 [145 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf libpython3.11-stdlib armhf 3.11.9-1 [1704 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf python3.11 armhf 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf libpython3-stdlib armhf 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian trixie/main armhf python3 armhf 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf libpython3.12-minimal armhf 3.12.3-1 [795 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf python3.12-minimal armhf 3.12.3-1 [1783 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.22 [22.4 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-3 [314 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf libmagic1t64 armhf 1:5.45-3 [98.1 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-3 [42.0 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.21-14+b1 [157 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 22 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-4 [1090 kB] Get: 23 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.40-8 [85.6 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.7-2 [33.3 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.12.1-1 [1375 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf autoconf all 2.71-3 [332 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf autopoint all 0.21-14 [496 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf bedtools armhf 2.31.1+dfsg-2 [578 kB] Get: 32 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.15.3 [88.0 kB] Get: 33 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-7 [517 kB] Get: 34 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 35 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian trixie/main armhf libsub-override-perl all 0.10-1 [10.6 kB] Get: 37 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 38 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 39 http://deb.debian.org/debian trixie/main armhf libelf1t64 armhf 0.191-1+b1 [183 kB] Get: 40 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 41 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-4+b1 [9070 kB] Get: 42 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.9.14+dfsg-1.3+b3 [598 kB] Get: 43 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.21-14+b1 [1230 kB] Get: 44 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 45 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 46 http://deb.debian.org/debian trixie/main armhf debhelper all 13.15.3 [901 kB] Get: 47 http://deb.debian.org/debian trixie/main armhf python3-pkg-resources all 68.1.2-2 [241 kB] Get: 48 http://deb.debian.org/debian trixie/main armhf python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 49 http://deb.debian.org/debian trixie/main armhf python3-distutils all 3.12.3-1 [131 kB] Get: 50 http://deb.debian.org/debian trixie/main armhf python3-setuptools all 68.1.2-2 [468 kB] Get: 51 http://deb.debian.org/debian trixie/main armhf dh-python all 6.20240422 [107 kB] Get: 52 http://deb.debian.org/debian trixie/main armhf libblas3 armhf 3.12.0-3 [108 kB] Get: 53 http://deb.debian.org/debian trixie/main armhf libbrotli1 armhf 1.1.0-2+b3 [284 kB] Get: 54 http://deb.debian.org/debian trixie/main armhf libcom-err2 armhf 1.47.1~rc2-1 [21.8 kB] Get: 55 http://deb.debian.org/debian trixie/main armhf libkrb5support0 armhf 1.20.1-6+b1 [30.6 kB] Get: 56 http://deb.debian.org/debian trixie/main armhf libk5crypto3 armhf 1.20.1-6+b1 [75.5 kB] Get: 57 http://deb.debian.org/debian trixie/main armhf libkeyutils1 armhf 1.6.3-3 [7908 B] Get: 58 http://deb.debian.org/debian trixie/main armhf libkrb5-3 armhf 1.20.1-6+b1 [290 kB] Get: 59 http://deb.debian.org/debian trixie/main armhf libgssapi-krb5-2 armhf 1.20.1-6+b1 [112 kB] Get: 60 http://deb.debian.org/debian trixie/main armhf libnghttp2-14 armhf 1.61.0-1+b1 [64.1 kB] Get: 61 http://deb.debian.org/debian trixie/main armhf libpsl5t64 armhf 0.21.2-1.1 [55.6 kB] Get: 62 http://deb.debian.org/debian trixie/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b4 [53.2 kB] Get: 63 http://deb.debian.org/debian trixie/main armhf libssh2-1t64 armhf 1.11.0-4.1+b2 [198 kB] Get: 64 http://deb.debian.org/debian trixie/main armhf libcurl3t64-gnutls armhf 8.7.1-3 [384 kB] Get: 65 http://deb.debian.org/debian trixie/main armhf libdeflate0 armhf 1.20-1 [35.9 kB] Get: 66 http://deb.debian.org/debian trixie/main armhf libgfortran5 armhf 14-20240330-1 [264 kB] Get: 67 http://deb.debian.org/debian trixie/main armhf libhtscodecs2 armhf 1.6.0-1+b1 [61.3 kB] Get: 68 http://deb.debian.org/debian trixie/main armhf libhts3t64 armhf 1.19+ds-1.1+b1 [395 kB] Get: 69 http://deb.debian.org/debian trixie/main armhf liblapack3 armhf 3.12.0-3 [1803 kB] Get: 70 http://deb.debian.org/debian trixie/main armhf libncurses6 armhf 6.4+20240414-1 [81.8 kB] Get: 71 http://deb.debian.org/debian trixie/main armhf libpython3.12-stdlib armhf 3.12.3-1 [1808 kB] Get: 72 http://deb.debian.org/debian trixie/main armhf python3.12 armhf 3.12.3-1 [659 kB] Get: 73 http://deb.debian.org/debian trixie/main armhf python3-all armhf 3.11.8-1 [1056 B] Get: 74 http://deb.debian.org/debian trixie/main armhf python3-attr all 23.2.0-2 [65.5 kB] Get: 75 http://deb.debian.org/debian trixie/main armhf python3-six all 1.16.0-6 [16.3 kB] Get: 76 http://deb.debian.org/debian trixie/main armhf python3-dateutil all 2.9.0-2 [79.4 kB] Get: 77 http://deb.debian.org/debian trixie/main armhf python3-execnet all 2.1.1-1 [40.2 kB] Get: 78 http://deb.debian.org/debian trixie/main armhf python3-sortedcontainers all 2.4.0-2 [31.9 kB] Get: 79 http://deb.debian.org/debian trixie/main armhf python3-hypothesis all 6.100.4-1 [314 kB] Get: 80 http://deb.debian.org/debian trixie/main armhf python3-iniconfig all 1.1.1-2 [6396 B] Get: 81 http://deb.debian.org/debian trixie/main armhf python3-natsort all 8.0.2-2 [39.0 kB] Get: 82 http://deb.debian.org/debian trixie/main armhf python3-numpy armhf 1:1.26.4+ds-8 [4132 kB] Get: 83 http://deb.debian.org/debian trixie/main armhf python3-ncls armhf 0.0.63-hotfix+ds-1+b4 [437 kB] Get: 84 http://deb.debian.org/debian trixie/main armhf python3-packaging all 24.0-1 [45.5 kB] Get: 85 http://deb.debian.org/debian trixie/main armhf python3-tz all 2024.1-2 [30.9 kB] Get: 86 http://deb.debian.org/debian trixie/main armhf python3-pandas-lib armhf 2.1.4+dfsg-8 [7001 kB] Get: 87 http://deb.debian.org/debian trixie/main armhf python3-pandas all 2.1.4+dfsg-8 [3015 kB] Get: 88 http://deb.debian.org/debian trixie/main armhf python3-pluggy all 1.5.0-1 [26.9 kB] Get: 89 http://deb.debian.org/debian trixie/main armhf python3-tabulate all 0.8.10-1 [38.8 kB] Get: 90 http://deb.debian.org/debian trixie/main armhf python3-pyrle armhf 0.0.33-4.1 [313 kB] Get: 91 http://deb.debian.org/debian trixie/main armhf python3-pytest all 7.4.4-3 [239 kB] Get: 92 http://deb.debian.org/debian trixie/main armhf python3-pytest-xdist all 3.5.0-1 [42.1 kB] Get: 93 http://deb.debian.org/debian trixie/main armhf python3-sorted-nearest armhf 0.0.39+dfsg-2 [488 kB] Get: 94 http://deb.debian.org/debian trixie/main armhf samtools armhf 1.19.2-1+b1 [614 kB] Fetched 51.7 MB in 2s (34.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:armhf. (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 ... 19445 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_armhf.deb ... Unpacking libpython3.11-minimal:armhf (3.11.9-1) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.6.2-1_armhf.deb ... Unpacking libexpat1:armhf (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_armhf.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:armhf (3.11.9-1) ... Setting up libexpat1:armhf (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... 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 ... 19761 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_armhf.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:armhf. Preparing to unpack .../5-libreadline8t64_8.2-4_armhf.deb ... Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8 to /lib/arm-linux-gnueabihf/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8.2 to /lib/arm-linux-gnueabihf/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8 to /lib/arm-linux-gnueabihf/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8.2 to /lib/arm-linux-gnueabihf/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:armhf (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:armhf. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_armhf.deb ... Unpacking libpython3.11-stdlib:armhf (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_armhf.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:armhf. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_armhf.deb ... Unpacking libpython3-stdlib:armhf (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (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 ... 20753 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.8-1_armhf.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package libpython3.12-minimal:armhf. Preparing to unpack .../01-libpython3.12-minimal_3.12.3-1_armhf.deb ... Unpacking libpython3.12-minimal:armhf (3.12.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../02-python3.12-minimal_3.12.3-1_armhf.deb ... Unpacking python3.12-minimal (3.12.3-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../03-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.45-3_armhf.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:armhf. Preparing to unpack .../05-libmagic1t64_1%3a5.45-3_armhf.deb ... Unpacking libmagic1t64:armhf (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../06-file_1%3a5.45-3_armhf.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../07-gettext-base_0.21-14+b1_armhf.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../08-libuchardet0_0.0.8-1+b1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../09-groff-base_1.23.0-4_armhf.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../10-bsdextrautils_2.40-8_armhf.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../11-libpipeline1_1.5.7-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../12-man-db_2.12.1-1_armhf.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. 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Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:armhf. Preparing to unpack .../26-libelf1t64_0.191-1+b1_armhf.deb ... Unpacking libelf1t64:armhf (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../27-dwz_0.15-1+b2_armhf.deb ... Unpacking dwz (0.15-1+b2) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../28-libicu72_72.1-4+b1_armhf.deb ... Unpacking libicu72:armhf (72.1-4+b1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../29-libxml2_2.9.14+dfsg-1.3+b3_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../30-gettext_0.21-14+b1_armhf.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../31-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... 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Selecting previously unselected package dh-python. Preparing to unpack .../38-dh-python_6.20240422_all.deb ... Unpacking dh-python (6.20240422) ... Selecting previously unselected package libblas3:armhf. Preparing to unpack .../39-libblas3_3.12.0-3_armhf.deb ... Unpacking libblas3:armhf (3.12.0-3) ... Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../40-libbrotli1_1.1.0-2+b3_armhf.deb ... Unpacking libbrotli1:armhf (1.1.0-2+b3) ... Selecting previously unselected package libcom-err2:armhf. Preparing to unpack .../41-libcom-err2_1.47.1~rc2-1_armhf.deb ... Unpacking libcom-err2:armhf (1.47.1~rc2-1) ... Selecting previously unselected package libkrb5support0:armhf. Preparing to unpack .../42-libkrb5support0_1.20.1-6+b1_armhf.deb ... Unpacking libkrb5support0:armhf (1.20.1-6+b1) ... Selecting previously unselected package libk5crypto3:armhf. Preparing to unpack .../43-libk5crypto3_1.20.1-6+b1_armhf.deb ... Unpacking libk5crypto3:armhf (1.20.1-6+b1) ... Selecting previously unselected package libkeyutils1:armhf. Preparing to unpack .../44-libkeyutils1_1.6.3-3_armhf.deb ... Unpacking libkeyutils1:armhf (1.6.3-3) ... Selecting previously unselected package libkrb5-3:armhf. Preparing to unpack .../45-libkrb5-3_1.20.1-6+b1_armhf.deb ... Unpacking libkrb5-3:armhf (1.20.1-6+b1) ... Selecting previously unselected package libgssapi-krb5-2:armhf. Preparing to unpack .../46-libgssapi-krb5-2_1.20.1-6+b1_armhf.deb ... Unpacking libgssapi-krb5-2:armhf (1.20.1-6+b1) ... Selecting previously unselected package libnghttp2-14:armhf. Preparing to unpack .../47-libnghttp2-14_1.61.0-1+b1_armhf.deb ... Unpacking libnghttp2-14:armhf (1.61.0-1+b1) ... Selecting previously unselected package libpsl5t64:armhf. Preparing to unpack .../48-libpsl5t64_0.21.2-1.1_armhf.deb ... Unpacking libpsl5t64:armhf (0.21.2-1.1) ... Selecting previously unselected package librtmp1:armhf. Preparing to unpack .../49-librtmp1_2.4+20151223.gitfa8646d.1-2+b4_armhf.deb ... 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Preparing to unpack .../73-python3-pandas-lib_2.1.4+dfsg-8_armhf.deb ... Unpacking python3-pandas-lib:armhf (2.1.4+dfsg-8) ... Selecting previously unselected package python3-pandas. Preparing to unpack .../74-python3-pandas_2.1.4+dfsg-8_all.deb ... Unpacking python3-pandas (2.1.4+dfsg-8) ... Selecting previously unselected package python3-pluggy. Preparing to unpack .../75-python3-pluggy_1.5.0-1_all.deb ... Unpacking python3-pluggy (1.5.0-1) ... Selecting previously unselected package python3-tabulate. Preparing to unpack .../76-python3-tabulate_0.8.10-1_all.deb ... Unpacking python3-tabulate (0.8.10-1) ... Selecting previously unselected package python3-pyrle. Preparing to unpack .../77-python3-pyrle_0.0.33-4.1_armhf.deb ... Unpacking python3-pyrle (0.0.33-4.1) ... Selecting previously unselected package python3-pytest. Preparing to unpack .../78-python3-pytest_7.4.4-3_all.deb ... Unpacking python3-pytest (7.4.4-3) ... Selecting previously unselected package python3-pytest-xdist. Preparing to unpack .../79-python3-pytest-xdist_3.5.0-1_all.deb ... Unpacking python3-pytest-xdist (3.5.0-1) ... Selecting previously unselected package python3-sorted-nearest. Preparing to unpack .../80-python3-sorted-nearest_0.0.39+dfsg-2_armhf.deb ... Unpacking python3-sorted-nearest (0.0.39+dfsg-2) ... Selecting previously unselected package samtools. Preparing to unpack .../81-samtools_1.19.2-1+b1_armhf.deb ... Unpacking samtools (1.19.2-1+b1) ... Setting up libhtscodecs2:armhf (1.6.0-1+b1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:armhf (1.5.7-2) ... Setting up libkeyutils1:armhf (1.6.3-3) ... Setting up libicu72:armhf (72.1-4+b1) ... Setting up bsdextrautils (2.40-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:armhf (1.1.0-2+b3) ... Setting up libmagic1t64:armhf (1:5.45-3) ... Setting up libpython3.12-minimal:armhf (3.12.3-1) ... Setting up libpsl5t64:armhf (0.21.2-1.1) ... Setting up libnghttp2-14:armhf (1.61.0-1+b1) ... Setting up libdeflate0:armhf (1.20-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:armhf (1.47.1~rc2-1) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:armhf (0.191-1+b1) ... Setting up libkrb5support0:armhf (1.20.1-6+b1) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Fri May 10 20:05:05 UTC 2024. Universal Time is now: Fri May 10 20:05:05 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:armhf (3.12.0-3) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libncurses6:armhf (6.4+20240414-1) ... Setting up autopoint (0.21-14) ... Setting up libk5crypto3:armhf (1.20.1-6+b1) ... Setting up libgfortran5:armhf (14-20240330-1) ... Setting up autoconf (2.71-3) ... Setting up dwz (0.15-1+b2) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:armhf (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... Setting up libkrb5-3:armhf (1.20.1-6+b1) ... Setting up libssh2-1t64:armhf (1.11.0-4.1+b2) ... Setting up readline-common (8.2-4) ... Setting up libxml2:armhf (2.9.14+dfsg-1.3+b3) ... Setting up bedtools (2.31.1+dfsg-2) ... 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 (1.13.1-1) ... Setting up python3.12-minimal (3.12.3-1) ... Setting up liblapack3:armhf (3.12.0-3) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:armhf (1.20.1-6+b1) ... Setting up libreadline8t64:armhf (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-4) ... Setting up libpython3.12-stdlib:armhf (3.12.3-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:armhf (3.11.9-1) ... Setting up python3.12 (3.12.3-1) ... Setting up libcurl3t64-gnutls:armhf (8.7.1-3) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libhts3t64:armhf (1.19+ds-1.1+b1) ... Setting up libpython3-stdlib:armhf (3.11.8-1) ... Setting up python3.11 (3.11.9-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up python3-sortedcontainers (2.4.0-2) ... Setting up python3-tz (2024.1-2) ... Setting up python3-natsort (8.0.2-2) ... Setting up samtools (1.19.2-1+b1) ... Setting up python3-six (1.16.0-6) ... Setting up python3-packaging (24.0-1) ... 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-lib2to3 (3.12.3-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.3-1) ... python3.12: can't get files for byte-compilation Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-attr (23.2.0-2) ... Setting up python3-setuptools (68.1.2-2) ... Setting up python3-pytest (7.4.4-3) ... Setting up python3-hypothesis (6.100.4-1) ... Setting up python3-tabulate (0.8.10-1) ... Setting up python3-all (3.11.8-1) ... Setting up python3-numpy (1:1.26.4+ds-8) ... Setting up python3-ncls (0.0.63-hotfix+ds-1+b4) ... Setting up dh-python (6.20240422) ... Setting up python3-pytest-xdist (3.5.0-1) ... Setting up python3-pandas-lib:armhf (2.1.4+dfsg-8) ... Setting up python3-sorted-nearest (0.0.39+dfsg-2) ... Setting up python3-pandas (2.1.4+dfsg-8) ... Setting up python3-pyrle (0.0.33-4.1) ... Processing triggers for libc-bin (2.38-7) ... 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-7_source.changes dpkg-buildpackage: info: source package pyranges dpkg-buildpackage: info: source version 0.0.111+ds-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf 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-armv7l' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it I: pybuild base:311: python3.11 setup.py clean 'build/bdist.linux-armv7l' does not exist -- can't clean it 'build/scripts-3.11' 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 I: pybuild base:311: python3.11 setup.py config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3.12 setup.py build 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/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/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/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/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' '/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' 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 4 ============================= test session starts ============================== platform linux -- Python 3.12.3, pytest-7.4.4, 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: hypothesis-6.100.4, xdist-3.5.0 created: 4/4 workers 4 workers [531 items] scheduling tests via LoadScheduling tests/test_binary.py::test_set_intersect[False] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain2-method_chain2] tests/test_binary.py::test_nearest[downstream-False-opposite] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain35-method_chain35] [gw1] [ 0%] FAILED tests/test_binary.py::test_nearest[downstream-False-opposite] tests/test_binary.py::test_jaccard[False] [gw0] [ 0%] FAILED tests/test_binary.py::test_set_intersect[False] [gw3] [ 0%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain2-method_chain2] tests/test_binary.py::test_set_intersect[same] [gw2] [ 0%] 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_chain3-method_chain3] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain36-method_chain36] [gw3] [ 0%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain3-method_chain3] [gw1] [ 1%] FAILED tests/test_binary.py::test_jaccard[False] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain4-method_chain4] tests/test_binary.py::test_jaccard[same] [gw2] [ 1%] 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] [gw0] [ 1%] FAILED tests/test_binary.py::test_set_intersect[same] tests/test_binary.py::test_set_union[False] [gw1] [ 1%] FAILED tests/test_binary.py::test_jaccard[same] tests/test_binary.py::test_join[False] [gw3] [ 1%] 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] [gw2] [ 2%] 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] [gw0] [ 2%] FAILED tests/test_binary.py::test_set_union[False] tests/test_binary.py::test_set_union[same] [gw3] [ 2%] 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] [gw0] [ 2%] FAILED tests/test_binary.py::test_set_union[same] tests/test_binary.py::test_overlap[False] [gw2] [ 2%] 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] [gw3] [ 3%] 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_chain7-method_chain7] [gw1] [ 3%] PASSED tests/test_binary.py::test_join[False] tests/test_binary.py::test_join[same] [gw2] [ 3%] 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] [gw0] [ 3%] PASSED tests/test_binary.py::test_overlap[False] tests/test_binary.py::test_overlap[same] [gw3] [ 3%] 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] [gw1] [ 3%] PASSED tests/test_binary.py::test_join[same] tests/test_binary.py::test_join[opposite] [gw2] [ 4%] 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] [ 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] [gw0] [ 4%] PASSED tests/test_binary.py::test_overlap[same] tests/test_binary.py::test_overlap[opposite] [gw3] [ 4%] 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] [gw2] [ 4%] 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] [ 5%] PASSED tests/test_binary.py::test_join[opposite] tests/test_binary.py::test_reldist [gw3] [ 5%] 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] [gw0] [ 5%] PASSED tests/test_binary.py::test_overlap[opposite] tests/test_binary.py::test_intersect[False] [gw2] [ 5%] 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_chain43-method_chain43] [gw3] [ 5%] 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] [gw1] [ 6%] PASSED tests/test_binary.py::test_reldist tests/test_binary.py::test_k_nearest[downstream-False-opposite-last] [gw0] [ 6%] PASSED tests/test_binary.py::test_intersect[False] tests/test_binary.py::test_intersect[same] [gw2] [ 6%] 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] [gw3] [ 6%] 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] [ 6%] 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] [gw1] [ 6%] FAILED tests/test_binary.py::test_k_nearest[downstream-False-opposite-last] tests/test_binary.py::test_k_nearest[downstream-False-same-last] [gw3] [ 7%] 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] [gw1] [ 7%] FAILED tests/test_binary.py::test_k_nearest[downstream-False-same-last] tests/test_binary.py::test_k_nearest[downstream-False-False-last] [gw2] [ 7%] 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] [gw2] [ 7%] 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] [gw0] [ 7%] PASSED tests/test_binary.py::test_intersect[same] tests/test_binary.py::test_intersect[opposite] [gw3] [ 8%] 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] [gw1] [ 8%] FAILED tests/test_binary.py::test_k_nearest[downstream-False-False-last] tests/test_binary.py::test_k_nearest[downstream-True-opposite-last] [gw2] [ 8%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain47-method_chain47] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain48-method_chain48] [gw3] [ 8%] 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] [gw2] [ 8%] 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] [gw3] [ 9%] 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] [gw1] [ 9%] FAILED tests/test_binary.py::test_k_nearest[downstream-True-opposite-last] tests/test_binary.py::test_k_nearest[downstream-True-same-last] [gw0] [ 9%] PASSED tests/test_binary.py::test_intersect[opposite] tests/test_binary.py::test_coverage[False] [gw2] [ 9%] 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] [gw1] [ 9%] FAILED tests/test_binary.py::test_k_nearest[downstream-True-same-last] tests/test_binary.py::test_k_nearest[downstream-True-False-last] [gw3] [ 9%] 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] [gw3] [ 10%] 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_chain19-method_chain19] [gw0] [ 10%] FAILED tests/test_binary.py::test_coverage[False] tests/test_binary.py::test_coverage[same] [gw2] [ 10%] 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] [gw1] [ 10%] FAILED tests/test_binary.py::test_k_nearest[downstream-True-False-last] tests/test_binary.py::test_k_nearest[upstream-False-opposite-last] [gw3] [ 10%] 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] [gw2] [ 11%] 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] [gw3] [ 11%] 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] [gw0] [ 11%] FAILED tests/test_binary.py::test_coverage[same] tests/test_binary.py::test_coverage[opposite] [gw1] [ 11%] FAILED tests/test_binary.py::test_k_nearest[upstream-False-opposite-last] tests/test_binary.py::test_k_nearest[upstream-False-same-last] [gw3] [ 11%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain21-method_chain21] [gw0] [ 12%] FAILED tests/test_binary.py::test_coverage[opposite] [gw2] [ 12%] 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_chain22-method_chain22] tests/test_binary.py::test_subtraction[same] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain53-method_chain53] [gw1] [ 12%] FAILED tests/test_binary.py::test_k_nearest[upstream-False-same-last] tests/test_binary.py::test_k_nearest[upstream-False-False-last] [gw0] [ 12%] FAILED tests/test_binary.py::test_subtraction[same] tests/test_binary.py::test_subtraction[opposite] [gw2] [ 12%] 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] [gw1] [ 12%] FAILED tests/test_binary.py::test_k_nearest[upstream-False-False-last] tests/test_binary.py::test_k_nearest[upstream-True-opposite-last] [gw3] [ 13%] 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] [gw0] [ 13%] FAILED tests/test_binary.py::test_subtraction[opposite] tests/test_binary.py::test_subtraction[False] [gw2] [ 13%] 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_chain55-method_chain55] [gw3] [ 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] [gw1] [ 13%] FAILED tests/test_binary.py::test_k_nearest[upstream-True-opposite-last] tests/test_binary.py::test_k_nearest[upstream-True-same-last] [gw0] [ 14%] FAILED tests/test_binary.py::test_subtraction[False] tests/test_binary.py::test_nearest[None-True-False] [gw2] [ 14%] 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] [gw3] [ 14%] 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] [gw1] [ 14%] FAILED tests/test_binary.py::test_k_nearest[upstream-True-same-last] tests/test_binary.py::test_k_nearest[upstream-True-False-last] [gw2] [ 14%] 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] [gw0] [ 15%] FAILED tests/test_binary.py::test_nearest[None-True-False] tests/test_binary.py::test_nearest[None-True-same] [gw3] [ 15%] 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] [gw1] [ 15%] FAILED tests/test_binary.py::test_k_nearest[upstream-True-False-last] tests/test_binary.py::test_k_nearest[None-False-opposite-last] [gw2] [ 15%] 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] [gw0] [ 15%] FAILED tests/test_binary.py::test_nearest[None-True-same] tests/test_binary.py::test_nearest[None-True-opposite] [gw3] [ 16%] 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] [gw1] [ 16%] FAILED tests/test_binary.py::test_k_nearest[None-False-opposite-last] tests/test_binary.py::test_k_nearest[None-False-same-last] [gw1] [ 16%] FAILED tests/test_binary.py::test_k_nearest[None-False-same-last] tests/test_binary.py::test_k_nearest[None-False-False-last] [gw2] [ 16%] 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] [gw0] [ 16%] FAILED tests/test_binary.py::test_nearest[None-True-opposite] tests/test_binary.py::test_nearest[None-False-False] [gw3] [ 16%] 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] [gw1] [ 17%] FAILED tests/test_binary.py::test_k_nearest[None-False-False-last] tests/test_binary.py::test_k_nearest[None-True-opposite-last] [gw0] [ 17%] FAILED tests/test_binary.py::test_nearest[None-False-False] tests/test_binary.py::test_nearest[None-False-same] [gw2] [ 17%] 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] [gw3] [ 17%] 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] [gw0] [ 17%] FAILED tests/test_binary.py::test_nearest[None-False-same] tests/test_binary.py::test_nearest[None-False-opposite] [gw1] [ 18%] FAILED tests/test_binary.py::test_k_nearest[None-True-opposite-last] tests/test_binary.py::test_k_nearest[None-True-same-last] [gw2] [ 18%] 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] [gw3] [ 18%] 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] [gw1] [ 18%] FAILED tests/test_binary.py::test_k_nearest[None-True-same-last] [gw0] [ 18%] FAILED tests/test_binary.py::test_nearest[None-False-opposite] tests/test_binary.py::test_k_nearest[None-True-False-last] tests/test_binary.py::test_nearest[upstream-True-False] [gw3] [ 19%] 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_chain31-method_chain31] [gw2] [ 19%] 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] [ 19%] FAILED tests/test_binary.py::test_k_nearest[None-True-False-last] tests/test_binary.py::test_k_nearest_1_vs_nearest [gw0] [ 19%] FAILED tests/test_binary.py::test_nearest[upstream-True-False] tests/test_binary.py::test_nearest[upstream-True-same] [gw2] [ 19%] 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] [ 19%] 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] [gw1] [ 20%] FAILED tests/test_binary.py::test_k_nearest_1_vs_nearest tests/test_change_chromosome_custom.py::test_change_chromosomes [gw1] [ 20%] PASSED tests/test_change_chromosome_custom.py::test_change_chromosomes tests/test_concat.py::test_concat_stranded_unstranded [gw1] [ 20%] PASSED tests/test_concat.py::test_concat_stranded_unstranded tests/test_concat.py::test_concat_unstranded_unstranded [gw1] [ 20%] PASSED tests/test_concat.py::test_concat_unstranded_unstranded tests/test_concat.py::test_concat_unstranded_stranded [gw1] [ 20%] PASSED tests/test_concat.py::test_concat_unstranded_stranded tests/test_count_overlaps.py::test_strand_vs_strand_same [gw3] [ 21%] 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] [gw1] [ 21%] 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] [ 21%] FAILED tests/test_binary.py::test_nearest[upstream-True-same] tests/test_binary.py::test_nearest[upstream-True-opposite] [gw2] [ 21%] 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] [gw1] [ 21%] 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] [ 22%] 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] [gw0] [ 22%] FAILED tests/test_binary.py::test_nearest[upstream-True-opposite] tests/test_binary.py::test_nearest[upstream-False-False] [gw3] [ 22%] 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_chain116-method_chain116] [gw3] [ 22%] 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] [gw0] [ 22%] FAILED tests/test_binary.py::test_nearest[upstream-False-False] tests/test_binary.py::test_nearest[upstream-False-same] [gw2] [ 22%] 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] [gw1] [ 23%] 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_chain68-method_chain68] [gw2] [ 23%] 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] [gw2] [ 23%] PASSED 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_chain67-method_chain67] [gw2] [ 23%] 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_chain158-method_chain158] [gw0] [ 23%] FAILED tests/test_binary.py::test_nearest[upstream-False-same] tests/test_binary.py::test_nearest[upstream-False-opposite] [gw3] [ 24%] 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] [gw3] [ 24%] 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] [gw1] [ 24%] 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] [gw1] [ 24%] 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] [gw2] [ 24%] 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] [gw0] [ 25%] FAILED tests/test_binary.py::test_nearest[upstream-False-opposite] tests/test_binary.py::test_nearest[downstream-True-False] [gw3] [ 25%] 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] [ 25%] 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] [gw2] [ 25%] 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] [gw0] [ 25%] FAILED tests/test_binary.py::test_nearest[downstream-True-False] tests/test_binary.py::test_nearest[downstream-True-same] [gw3] [ 25%] 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] [gw2] [ 26%] 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] [gw1] [ 26%] 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] [gw0] [ 26%] FAILED tests/test_binary.py::test_nearest[downstream-True-same] tests/test_binary.py::test_nearest[downstream-True-opposite] [gw3] [ 26%] 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] [gw2] [ 26%] 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] [gw1] [ 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] [gw0] [ 27%] FAILED tests/test_binary.py::test_nearest[downstream-True-opposite] tests/test_binary.py::test_nearest[downstream-False-False] [gw3] [ 27%] 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_chain123-method_chain123] [gw2] [ 27%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain162-method_chain162] [gw1] [ 27%] 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_chain163-method_chain163] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain74-method_chain74] [gw0] [ 28%] FAILED tests/test_binary.py::test_nearest[downstream-False-False] tests/test_binary.py::test_nearest[downstream-False-same] [gw2] [ 28%] 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] [gw0] [ 28%] FAILED tests/test_binary.py::test_nearest[downstream-False-same] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain195-method_chain195] [gw0] [ 28%] 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] [gw3] [ 28%] 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] [gw1] [ 29%] 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] [gw2] [ 29%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain164-method_chain164] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain165-method_chain165] [gw2] [ 29%] 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] [gw0] [ 29%] 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] [gw3] [ 29%] 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] [gw1] [ 29%] 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] [gw2] [ 30%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain166-method_chain166] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain167-method_chain167] [gw0] [ 30%] 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_chain198-method_chain198] [gw2] [ 30%] 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] [gw3] [ 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] [gw1] [ 30%] 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_chain77-method_chain77] [gw0] [ 31%] 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] [gw2] [ 31%] 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] [gw3] [ 31%] 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] [gw1] [ 31%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain77-method_chain77] [gw0] [ 31%] 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_chain78-method_chain78] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain200-method_chain200] [gw2] [ 32%] 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] [gw3] [ 32%] 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] [gw3] [ 32%] 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] [gw0] [ 32%] 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] [gw1] [ 32%] 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] [gw1] [ 32%] 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] [gw2] [ 33%] 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] [gw0] [ 33%] 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] [gw3] [ 33%] 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] [gw2] [ 33%] 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] [gw1] [ 33%] 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] [gw3] [ 34%] 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] [gw1] [ 34%] 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] [gw0] [ 34%] 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] [ 34%] 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] [gw2] [ 34%] 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] [gw1] [ 35%] 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] [gw3] [ 35%] 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] [gw0] [ 35%] 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] [gw1] [ 35%] 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] [gw3] [ 35%] 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] [gw2] [ 35%] 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] [gw0] [ 36%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain204-method_chain204] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain205-method_chain205] [gw1] [ 36%] 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] [gw3] [ 36%] 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] [gw0] [ 36%] 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] [gw1] [ 36%] 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] [gw2] [ 37%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain174-method_chain174] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain175-method_chain175] [gw3] [ 37%] 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] [gw0] [ 37%] 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] [gw2] [ 37%] 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_chain176-method_chain176] [gw1] [ 37%] 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] [gw0] [ 38%] 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] [gw3] [ 38%] 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_chain137-method_chain137] [gw2] [ 38%] 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] [ 38%] 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] [gw2] [ 38%] 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] [gw0] [ 38%] 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_chain209-method_chain209] [gw2] [ 39%] PASSED 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] [gw2] [ 39%] 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] [gw3] [ 39%] 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] [gw1] [ 39%] 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] [gw0] [ 39%] 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] [gw2] [ 40%] 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] [gw3] [ 40%] 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] [gw2] [ 40%] 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] [gw1] [ 40%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain89-method_chain89] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain90-method_chain90] [gw0] [ 40%] 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] [ 41%] 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] [ 41%] 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] [gw1] [ 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] [gw0] [ 41%] 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] [gw0] [ 41%] 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] [gw0] [ 41%] PASSED 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] [gw3] [ 42%] 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] [gw0] [ 42%] 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] [gw2] [ 42%] 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] [gw1] [ 42%] 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] [gw3] [ 42%] 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] [ 43%] 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] [gw3] [ 43%] 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_chain143-method_chain143] [gw2] [ 43%] 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] [gw0] [ 43%] 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] [gw1] [ 43%] 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_chain93-method_chain93] [gw1] [ 44%] 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] [gw2] [ 44%] 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_chain186-method_chain186] [gw3] [ 44%] 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] [gw0] [ 44%] 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] [gw3] [ 44%] 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] [gw1] [ 45%] 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] [gw1] [ 45%] 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] [gw2] [ 45%] 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_chain187-method_chain187] [gw3] [ 45%] 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] [gw1] [ 45%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain96-method_chain96] [gw0] [ 45%] 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_chain97-method_chain97] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain219-method_chain219] [gw3] [ 46%] 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] [ 46%] 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] [gw2] [ 46%] 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] [gw0] [ 46%] 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] [gw3] [ 46%] 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] [gw1] [ 47%] 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] [gw2] [ 47%] 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] [gw3] [ 47%] 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] [gw1] [ 47%] 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] [gw0] [ 47%] 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] [gw2] [ 48%] 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] [gw3] [ 48%] 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_chain150-method_chain150] [gw1] [ 48%] 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] [gw0] [ 48%] 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] [gw2] [ 48%] 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] [gw3] [ 48%] 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] [gw2] [ 49%] 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] [gw1] [ 49%] 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] [gw0] [ 49%] 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] [gw3] [ 49%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain151-method_chain151] [gw1] [ 49%] 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] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain152-method_chain152] [gw2] [ 50%] 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] [gw0] [ 50%] 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] [gw2] [ 50%] 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] [gw3] [ 50%] 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] [gw1] [ 50%] 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] [gw0] [ 51%] 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] [gw2] [ 51%] 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_chain228-method_chain228] [gw2] [ 51%] 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_chain229-method_chain229] [gw3] [ 51%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain153-method_chain153] [gw1] [ 51%] 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_chain154-method_chain154] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain105-method_chain105] [gw0] [ 51%] 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] [gw2] [ 52%] 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] [gw0] [ 52%] 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] [gw2] [ 52%] 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] [gw3] [ 52%] 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] [gw1] [ 52%] 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] [gw2] [ 53%] 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_chain232-method_chain232] [gw3] [ 53%] 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] [gw1] [ 53%] 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] [gw0] [ 53%] 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_chain256-method_chain256] [gw2] [ 53%] 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] [gw1] [ 54%] 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_chain108-method_chain108] [gw3] [ 54%] 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] [gw0] [ 54%] 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] [gw2] [ 54%] 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] [gw1] [ 54%] 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] [gw3] [ 54%] 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_chain281-method_chain281] [gw0] [ 55%] 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] [ 55%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain234-method_chain234] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain235-method_chain235] [gw3] [ 55%] 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] [gw1] [ 55%] 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] [gw0] [ 55%] 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] [gw2] [ 56%] 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] [gw1] [ 56%] 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] [gw0] [ 56%] 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] [gw3] [ 56%] 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] [gw1] [ 56%] 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] [gw2] [ 57%] 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] [gw3] [ 57%] 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] [gw0] [ 57%] 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] [gw0] [ 57%] 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] [gw0] [ 57%] PASSED 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_chain263-method_chain263] [gw1] [ 58%] 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] [gw2] [ 58%] 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_chain238-method_chain238] [gw0] [ 58%] 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] [gw3] [ 58%] 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_chain285-method_chain285] [gw1] [ 58%] 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] [gw2] [ 58%] 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] [gw1] [ 59%] 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] [gw3] [ 59%] 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] [gw0] [ 59%] 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] [gw0] [ 59%] 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] [gw3] [ 59%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain286-method_chain286] [gw2] [ 60%] 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_chain287-method_chain287] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain240-method_chain240] [gw1] [ 60%] 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_chain303-method_chain303] [gw2] [ 60%] 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] [ 60%] 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] [gw2] [ 60%] PASSED 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] [gw2] [ 61%] 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] [gw3] [ 61%] 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] [gw1] [ 61%] 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_chain304-method_chain304] [gw0] [ 61%] 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] [gw2] [ 61%] 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] [gw2] [ 61%] 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] [gw1] [ 62%] 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] [gw3] [ 62%] 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] [gw3] [ 62%] 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] [gw0] [ 62%] 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] [gw2] [ 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] [ 63%] 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] [gw3] [ 63%] 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] [gw0] [ 63%] 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] [gw3] [ 63%] 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_chain292-method_chain292] [gw1] [ 63%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain306-method_chain306] [gw2] [ 64%] 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_chain307-method_chain307] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain247-method_chain247] [gw0] [ 64%] 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_chain271-method_chain271] [gw3] [ 64%] 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] [gw1] [ 64%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain307-method_chain307] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain308-method_chain308] [gw2] [ 64%] 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] [gw3] [ 64%] 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] [ 65%] 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] [ 65%] 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] [gw2] [ 65%] 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] [gw3] [ 65%] 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] [gw1] [ 65%] 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_chain310-method_chain310] [gw2] [ 66%] 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] [gw1] [ 66%] 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] [gw0] [ 66%] 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] [gw3] [ 66%] 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] [gw2] [ 66%] 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] [gw0] [ 67%] 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] [gw1] [ 67%] 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] [gw1] [ 67%] 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] [gw3] [ 67%] 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] [gw2] [ 67%] 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] [gw0] [ 67%] 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] [ 68%] 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] [gw1] [ 68%] 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] [gw0] [ 68%] PASSED 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] [gw1] [ 68%] 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] [ 68%] 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_chain278-method_chain278] [gw3] [ 69%] 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_chain298-method_chain298] [gw2] [ 69%] 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] [gw0] [ 69%] 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] [gw1] [ 69%] 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_chain316-method_chain316] [gw3] [ 69%] 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] [gw0] [ 70%] 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] [gw2] [ 70%] 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] [gw3] [ 70%] 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] [gw0] [ 70%] 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_chain322-method_chain322] [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] [gw2] [ 70%] 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_chain255-method_chain255] [gw2] [ 71%] 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_chain339-method_chain339] [gw3] [ 71%] 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_chain301-method_chain301] [gw1] [ 71%] 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] [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] [gw3] [ 71%] 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] [gw1] [ 72%] 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] [gw0] [ 72%] 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] [gw2] [ 72%] 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_chain340-method_chain340] [gw0] [ 72%] 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] [gw2] [ 72%] 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] [gw3] [ 73%] 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_chain354-method_chain354] [gw1] [ 73%] 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] [gw2] [ 73%] 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_chain342-method_chain342] [gw0] [ 73%] 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_chain326-method_chain326] [gw2] [ 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] [gw0] [ 74%] 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] [gw3] [ 74%] 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] [ 74%] 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_chain321-method_chain321] [gw2] [ 74%] 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_chain344-method_chain344] [gw0] [ 74%] 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] [gw3] [ 74%] 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_chain356-method_chain356] [gw0] [ 75%] 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] [gw1] [ 75%] 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_chain367-method_chain367] [gw2] [ 75%] 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] [gw3] [ 75%] 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] [gw0] [ 75%] 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] [gw1] [ 76%] 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] [gw2] [ 76%] 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] [gw3] [ 76%] 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] [gw0] [ 76%] 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_chain331-method_chain331] [gw1] [ 76%] 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_chain369-method_chain369] [gw2] [ 77%] 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] [ 77%] 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] [gw3] [ 77%] 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_chain360-method_chain360] [gw0] [ 77%] 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] [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_chain348-method_chain348] [gw1] [ 77%] 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] [gw0] [ 78%] 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] [gw3] [ 78%] 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] [gw3] [ 78%] 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] [gw2] [ 78%] 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] [gw1] [ 78%] 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] [gw0] [ 79%] 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] [gw2] [ 79%] 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] [gw3] [ 79%] 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_chain363-method_chain363] [gw1] [ 79%] 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_chain372-method_chain372] [gw3] [ 79%] 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] [gw0] [ 80%] 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] [gw2] [ 80%] 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] [gw1] [ 80%] 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] [gw3] [ 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] [gw1] [ 80%] 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] [gw0] [ 80%] 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_chain336-method_chain336] [gw2] [ 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_chain352-method_chain352] [gw3] [ 81%] 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_chain366-method_chain366] [gw0] [ 81%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain336-method_chain336] [gw2] [ 81%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain352-method_chain352] [gw1] [ 81%] 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_chain337-method_chain337] 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_chain375-method_chain375] [gw3] [ 82%] 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_chain378-method_chain378] [gw1] [ 82%] 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] [gw2] [ 82%] 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_chain388-method_chain388] [gw0] [ 82%] 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] [gw3] [ 82%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain378-method_chain378] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain379-method_chain379] [gw0] [ 83%] 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_chain396-method_chain396] [gw1] [ 83%] 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] [gw1] [ 83%] 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_chain403-method_chain403] [gw2] [ 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_chain389-method_chain389] [gw3] [ 83%] 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] [gw0] [ 83%] 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_chain397-method_chain397] [gw2] [ 84%] 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] [gw1] [ 84%] 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_chain404-method_chain404] [gw0] [ 84%] 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] [gw3] [ 84%] 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_chain381-method_chain381] [gw2] [ 84%] 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] [gw1] [ 85%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain404-method_chain404] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain405-method_chain405] [gw2] [ 85%] 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] [ 85%] 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_chain382-method_chain382] [gw0] [ 85%] 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_chain399-method_chain399] [gw1] [ 85%] 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_chain406-method_chain406] [gw2] [ 86%] 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_chain393-method_chain393] [gw0] [ 86%] 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] [gw3] [ 86%] 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_chain383-method_chain383] [gw2] [ 86%] 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] [gw1] [ 86%] 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_chain407-method_chain407] [gw0] [ 87%] 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_chain401-method_chain401] [gw3] [ 87%] 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] [gw2] [ 87%] 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_chain395-method_chain395] [gw1] [ 87%] 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_chain408-method_chain408] [gw0] [ 87%] 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_chain402-method_chain402] [gw3] [ 87%] 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_chain385-method_chain385] [gw1] [ 88%] 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_chain409-method_chain409] [gw2] [ 88%] 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_chain410-method_chain410] [gw0] [ 88%] 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_chain416-method_chain416] [gw2] [ 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_chain411-method_chain411] [gw3] [ 88%] 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] [gw1] [ 89%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain409-method_chain409] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain421-method_chain421] [gw0] [ 89%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain416-method_chain416] [gw3] [ 89%] 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_chain417-method_chain417] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain387-method_chain387] [gw2] [ 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_chain412-method_chain412] [gw3] [ 89%] 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_chain425-method_chain425] [gw2] [ 90%] 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_chain413-method_chain413] [gw1] [ 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_chain422-method_chain422] [gw1] [ 90%] 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_chain423-method_chain423] [gw0] [ 90%] 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_chain418-method_chain418] [gw2] [ 90%] 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_chain414-method_chain414] [gw3] [ 90%] 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_chain426-method_chain426] [gw3] [ 91%] 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] [gw1] [ 91%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain423-method_chain423] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain424-method_chain424] [gw2] [ 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_chain415-method_chain415] [gw1] [ 91%] 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_chain429-method_chain429] [gw0] [ 91%] 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_chain419-method_chain419] [gw3] [ 92%] 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_chain428-method_chain428] [gw1] [ 92%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain429-method_chain429] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain430-method_chain430] [gw2] [ 92%] 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_chain432-method_chain432] [gw3] [ 92%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain428-method_chain428] [gw0] [ 92%] 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_chain435-method_chain435] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain420-method_chain420] [gw1] [ 93%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain430-method_chain430] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain431-method_chain431] [gw2] [ 93%] FAILED 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] [gw3] [ 93%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain435-method_chain435] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain436-method_chain436] [gw0] [ 93%] 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_chain438-method_chain438] [gw3] [ 93%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain436-method_chain436] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain437-method_chain437] [gw0] [ 93%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain438-method_chain438] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain439-method_chain439] [gw1] [ 94%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain431-method_chain431] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain440-method_chain440] [gw2] [ 94%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain433-method_chain433] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain434-method_chain434] [gw1] [ 94%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain440-method_chain440] tests/test_genomicfeatures.py::test_introns_single [gw1] [ 94%] FAILED tests/test_genomicfeatures.py::test_introns_single tests/test_io.py::test_read_gff3 [gw1] [ 94%] PASSED tests/test_io.py::test_read_gff3 tests/test_io.py::test_read_bed [gw1] [ 95%] PASSED tests/test_io.py::test_read_bed tests/test_pickle.py::test_pickle [gw1] [ 95%] PASSED tests/test_pickle.py::test_pickle tests/test_stranded.py::test_stranded [gw1] [ 95%] PASSED tests/test_stranded.py::test_stranded tests/test_stranded.py::test_unstrand [gw1] [ 95%] PASSED tests/test_stranded.py::test_unstrand tests/test_unary.py::test_merge[True] [gw0] [ 95%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain439-method_chain439] tests/test_getset_attr.py::test_getsetattr_with_str [gw0] [ 96%] PASSED tests/test_getset_attr.py::test_getsetattr_with_str tests/test_unary.py::test_cluster[True] [gw3] [ 96%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain437-method_chain437] tests/test_getset_attr.py::test_getsetattr [gw3] [ 96%] PASSED tests/test_getset_attr.py::test_getsetattr tests/test_getset_attr.py::test_getsetattr_fails [gw3] [ 96%] PASSED tests/test_getset_attr.py::test_getsetattr_fails tests/test_unary.py::test_cluster_by[True] [gw1] [ 96%] FAILED tests/test_unary.py::test_merge[True] tests/test_unary.py::test_merge[False] [gw2] [ 96%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain434-method_chain434] tests/test_io.py::test_read_gtf [gw2] [ 97%] PASSED tests/test_io.py::test_read_gtf tests/test_unary.py::test_merge_by[False] [gw0] [ 97%] FAILED tests/test_unary.py::test_cluster[True] tests/test_unary.py::test_cluster[False] [gw1] [ 97%] FAILED tests/test_unary.py::test_merge[False] tests/test_unary.py::test_merge_by[True] [gw0] [ 97%] FAILED tests/test_unary.py::test_cluster[False] tests/test_unary.py::test_init[True] [gw0] [ 97%] PASSED tests/test_unary.py::test_init[True] tests/test_unary.py::test_getitem [gw0] [ 98%] PASSED tests/test_unary.py::test_getitem tests/test_unary.py::test_summary [gw0] [ 98%] FAILED tests/test_unary.py::test_summary tests/data/test_data.py::test_all_data [gw0] [ 98%] PASSED tests/data/test_data.py::test_all_data tests/windows/test_windows.py::test_windows [gw0] [ 98%] FAILED tests/windows/test_windows.py::test_windows tests/windows/test_windows.py::test_windows2 [gw0] [ 98%] FAILED tests/windows/test_windows.py::test_windows2 [gw2] [ 99%] PASSED tests/test_unary.py::test_merge_by[False] tests/test_unary.py::test_windows [gw2] [ 99%] FAILED tests/test_unary.py::test_windows [gw1] [ 99%] PASSED tests/test_unary.py::test_merge_by[True] tests/test_unary.py::test_init[False] [gw1] [ 99%] PASSED tests/test_unary.py::test_init[False] [gw3] [ 99%] PASSED tests/test_unary.py::test_cluster_by[True] tests/test_unary.py::test_cluster_by[False] [gw3] [100%] PASSED tests/test_unary.py::test_cluster_by[False] =================================== FAILURES =================================== ___________________ test_nearest[downstream-False-opposite] ____________________ [gw1] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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 | 1376776 | 1382668 | a | 0 | + | | | chr1 | 590594 | 593923 | 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 | 196872 | 197132 | 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 106 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicFYtBCoAwEAMzG7BU68GDCL7D/3+sF1MIzMwhvJMPyZddOqAnBNzVYt0k9sfSKUfXhLZaQGVasrBGfj+DyAIV') 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 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | 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 104 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2QAA0YGBGDEEGIEAACLAAY=') 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/tmp6lc_7y0b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6lc_7y0b/f2.bed) bedtools bedtools bedtools bedtools 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/tmpbtyl1bp0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbtyl1bp0/f2.bed) bedtools bedtools bedtools bedtools 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/tmpxjz9o6bc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxjz9o6bc/f2.bed) bedtools bedtools bedtools bedtools 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/tmp1fh0s8eg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1fh0s8eg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqoazns0w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqoazns0w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfndii050/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfndii050/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphw_6uasy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphw_6uasy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfxyvak5w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfxyvak5w/f2.bed) bedtools bedtools bedtools bedtools 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/tmpk8b85od6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk8b85od6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp72sevg5c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp72sevg5c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf9hfvzq8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf9hfvzq8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2dbulvr4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2dbulvr4/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_9d8_2zk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_9d8_2zk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprlixgrju/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprlixgrju/f2.bed) bedtools bedtools bedtools bedtools 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/tmp3znjp89w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3znjp89w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpklzyduj3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpklzyduj3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6y9s7o_2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6y9s7o_2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvgkwpajr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvgkwpajr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp918021x2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp918021x2/f2.bed) bedtools bedtools bedtools bedtools 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/tmproyndkb7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmproyndkb7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf1vtusm0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf1vtusm0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzgrf2csk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzgrf2csk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy2s3ny1z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy2s3ny1z/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwss3m6gf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwss3m6gf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbvd0hsat/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbvd0hsat/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu59tx8r6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu59tx8r6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz72l2e8a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz72l2e8a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpak1ik7gq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpak1ik7gq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr3meb267/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr3meb267/f2.bed) bedtools bedtools bedtools bedtools 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/tmp5478jbvy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5478jbvy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjvfuc5vt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjvfuc5vt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoudqah78/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoudqah78/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp29_kbh9f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp29_kbh9f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9nbmxxj5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9nbmxxj5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4yyyz4rp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4yyyz4rp/f2.bed) bedtools bedtools bedtools bedtools 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/tmpxb7lbf9k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxb7lbf9k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpooo1yj2x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpooo1yj2x/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9ui5ucej/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9ui5ucej/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm2ug7sbb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm2ug7sbb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0_rcftko/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0_rcftko/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplcc8vuoj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplcc8vuoj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp89poq6b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp89poq6b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpks_ie268/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpks_ie268/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx486jgcn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx486jgcn/f2.bed) bedtools bedtools bedtools bedtools 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/tmpv5dzgad7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv5dzgad7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1zh_lgks/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1zh_lgks/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbx6c99d2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbx6c99d2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpghlz4zlu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpghlz4zlu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxfd2d06b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxfd2d06b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoaul5j0m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoaul5j0m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpigbv2khx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpigbv2khx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp50vxvesa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp50vxvesa/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaqxtbb5i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaqxtbb5i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpofvi_7kr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpofvi_7kr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjp95pw9m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjp95pw9m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphdwhiqjz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphdwhiqjz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp94bh72fn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp94bh72fn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6wrsiw11/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6wrsiw11/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_set_intersect[False] ___________________________ [gw0] linux -- Python 3.12.3 /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., 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('6.100.4', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') 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/tmpqr_0y3uv/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqr_0y3uv/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpjckn2tlh/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjckn2tlh/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpaqpgh175/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpaqpgh175/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmprrd4is7m/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprrd4is7m/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpyqve28y2/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpyqve28y2/f2.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_qpgv41b/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_qpgv41b/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp8czeqjtb/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8czeqjtb/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpinjpodpl/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpinjpodpl/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpume2e__b/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpume2e__b/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpcue19a0f/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcue19a0f/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpsz0m9ury/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpsz0m9ury/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpldarerii/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpldarerii/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmplrhetf0r/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmplrhetf0r/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpx4gkpzdn/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpx4gkpzdn/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp4p3yn66k/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4p3yn66k/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp6aioeitw/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6aioeitw/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp1b8zusix/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1b8zusix/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp2t9oyhz_/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2t9oyhz_/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp9n4chf62/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9n4chf62/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpgei913i6/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgei913i6/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp60nej3_d/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp60nej3_d/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpic47twgx/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpic47twgx/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpi472bsjl/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpi472bsjl/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpza6cd8w9/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpza6cd8w9/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpsvherrvm/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpsvherrvm/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp5k2d1olm/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5k2d1olm/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpqpb31rb2/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqpb31rb2/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmprmema857/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprmema857/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpkyalahnx/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkyalahnx/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpoaeqsddz/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpoaeqsddz/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpi1ekv4sp/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpi1ekv4sp/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpz7lmmcvm/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpz7lmmcvm/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp1epcrz85/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1epcrz85/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp2fzf392n/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2fzf392n/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpj5fwj470/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpj5fwj470/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmph031edhb/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmph031edhb/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpklkmpsn7/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpklkmpsn7/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpkihs5i_8/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkihs5i_8/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpox885ia9/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpox885ia9/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpnwhy79cd/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnwhy79cd/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpo6pvgmrd/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpo6pvgmrd/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpqda4wfqn/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqda4wfqn/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpg1inr34_/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpg1inr34_/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpeftxl70d/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpeftxl70d/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmptqocrnq7/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmptqocrnq7/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpgh_z7hp9/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgh_z7hp9/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpad3owhaz/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpad3owhaz/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpw_vfehqn/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpw_vfehqn/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpsxg5_63u/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpsxg5_63u/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpbyfeah14/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbyfeah14/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpc1l4ezti/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpc1l4ezti/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpp9ur168f/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpp9ur168f/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp1_k4hieb/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1_k4hieb/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpxqb77cm4/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpxqb77cm4/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpkb_9ar8y/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkb_9ar8y/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp3oco9q7y/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3oco9q7y/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp6ggk4wh5/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6ggk4wh5/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp4av9tepf/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4av9tepf/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp7_aqp3t3/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7_aqp3t3/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp2u1xv0oo/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2u1xv0oo/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp1fvozen4/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1fvozen4/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpa92ucnv3/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpa92ucnv3/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpggq171n9/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpggq171n9/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp873f_lkw/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp873f_lkw/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpha6e3pea/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpha6e3pea/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmps9rstheh/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmps9rstheh/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpfd7dcsru/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpfd7dcsru/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmppurppb_6/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppurppb_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/tmp7zbm9ae5/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7zbm9ae5/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmprqsisj8d/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprqsisj8d/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmphs4o_zdn/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphs4o_zdn/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpdotbzi8r/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdotbzi8r/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpind9ta8y/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpind9ta8y/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp0osy2is6/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0osy2is6/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpygvyzufc/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpygvyzufc/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmps81oqkzh/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmps81oqkzh/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpzr67y1k3/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzr67y1k3/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpqs0j4w58/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqs0j4w58/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp9cyi7fdh/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9cyi7fdh/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpqgtv7y8i/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqgtv7y8i/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmph7sxkxaq/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmph7sxkxaq/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp2t62u5be/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2t62u5be/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmplbrn280w/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmplbrn280w/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpm81cyuz9/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpm81cyuz9/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpyh5i5wd8/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpyh5i5wd8/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp8elwskhl/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8elwskhl/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpv9otqrej/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpv9otqrej/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpbdt_ybv1/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbdt_ybv1/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpsy67w5xm/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpsy67w5xm/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpymj75jpc/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpymj75jpc/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp4ykrot65/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4ykrot65/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpm2sht965/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpm2sht965/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpcvqqiw9u/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcvqqiw9u/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpcmorpmev/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcmorpmev/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpa9g9vuf5/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpa9g9vuf5/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp8xz9drdz/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8xz9drdz/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp6a27bs64/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6a27bs64/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmptx21aipw/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmptx21aipw/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_three_in_a_row[strandedness_chain2-method_chain2] ____________ [gw3] linux -- Python 3.12.3 /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 172 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('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') Empty PyRanges ('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') ('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') 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') 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') ---------------------------------- 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_chain35-method_chain35] ___________ [gw2] linux -- Python 3.12.3 /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/pyranges.py:4162 E (and 127 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('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') ('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') 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') ---------------------------------- 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_chain3-method_chain3] ____________ [gw3] linux -- Python 3.12.3 /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, # 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 182 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('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') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('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') ('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') 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') 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') _____________________________ test_jaccard[False] ______________________________ [gw1] linux -- Python 3.12.3 /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., 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('6.100.4', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') 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_chain36-method_chain36] ___________ [gw2] linux -- Python 3.12.3 /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, # 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: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('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('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') ('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') 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') ___________________________ test_set_intersect[same] ___________________________ [gw0] linux -- Python 3.12.3 /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 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 E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') 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/tmpd9vcihri/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpd9vcihri/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmprsw2j61g/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprsw2j61g/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpeaymhm3a/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpeaymhm3a/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpk7d6mhxy/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpk7d6mhxy/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpzx6hiqbl/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzx6hiqbl/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpe1ob5ug1/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpe1ob5ug1/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp22_oftms/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp22_oftms/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpsyg9qq66/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpsyg9qq66/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp7orr1ct9/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7orr1ct9/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp4qz4ciz3/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4qz4ciz3/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp2mdpg4t7/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2mdpg4t7/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp1qz7mv2v/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1qz7mv2v/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpiojys1yo/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpiojys1yo/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpbx466qum/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbx466qum/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpk_xrs02g/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpk_xrs02g/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpfctw6qip/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpfctw6qip/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpfseu3vdt/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpfseu3vdt/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpmxea38vz/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmxea38vz/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpi991obfn/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpi991obfn/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmplpo0u8b5/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmplpo0u8b5/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpp55cwj38/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpp55cwj38/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp2hntce0e/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2hntce0e/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpydyw3chc/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpydyw3chc/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpeqco4nb4/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpeqco4nb4/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpg_d1cyeq/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpg_d1cyeq/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp5pjwxpm9/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5pjwxpm9/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpq8vi0t0n/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpq8vi0t0n/f2.bed | bedtools 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_d9vzv9e/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_d9vzv9e/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpw3b997l2/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpw3b997l2/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp4j5k0woo/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4j5k0woo/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpkep3mm8a/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkep3mm8a/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmphdf7suk5/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphdf7suk5/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpv3u12m96/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpv3u12m96/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpo738tha1/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpo738tha1/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpwnp6fk0t/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpwnp6fk0t/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp9bsv6qhi/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9bsv6qhi/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpdpvgcrl4/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdpvgcrl4/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp6ug_p1q2/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6ug_p1q2/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpt0jlpqfv/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpt0jlpqfv/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp7lj9ytru/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7lj9ytru/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp97lnt_d_/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp97lnt_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/tmpx5b9mcc0/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpx5b9mcc0/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp1wisatqp/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1wisatqp/f2.bed | bedtools 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_zjkh0/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpeg_zjkh0/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpmu741e67/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmu741e67/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpucgzau69/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpucgzau69/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpu0_duxtn/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpu0_duxtn/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp2n7wegq8/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2n7wegq8/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpnehdf_zf/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnehdf_zf/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpkz_nyfgl/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkz_nyfgl/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmps8llnb19/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmps8llnb19/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpfg80v4y8/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpfg80v4y8/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpqsgqbpc2/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqsgqbpc2/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpuqbe9mhl/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpuqbe9mhl/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp4mxrirkb/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4mxrirkb/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpe20aric3/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpe20aric3/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpiq0z9ac3/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpiq0z9ac3/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp0dufb8vg/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0dufb8vg/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpnsp3c8g1/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnsp3c8g1/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpzpq5s5bg/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzpq5s5bg/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpourpsz4a/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpourpsz4a/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp1ypqv26j/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1ypqv26j/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpjx_aimxk/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjx_aimxk/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpdginl4qb/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdginl4qb/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp1a72msai/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1a72msai/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp2ls6zdhc/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2ls6zdhc/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpjuxa3wp0/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjuxa3wp0/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpsjv36cbf/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpsjv36cbf/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpiillmv5j/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpiillmv5j/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpkfoelw9_/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkfoelw9_/f2.bed | bedtools 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_1l5ikhi/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_1l5ikhi/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmphxoo9rqz/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphxoo9rqz/f2.bed | bedtools 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__i873x8/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp__i873x8/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpe8x8pvnf/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpe8x8pvnf/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpm4tnc1pc/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpm4tnc1pc/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmplr29l_04/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmplr29l_04/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpo_zn0a30/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpo_zn0a30/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpi9s87t6r/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpi9s87t6r/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpdnq6py2t/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdnq6py2t/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp7wl3caik/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7wl3caik/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpysymkde5/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpysymkde5/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpdl4zwd03/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdl4zwd03/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpmb959k2u/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmb959k2u/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpd4oygxzz/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpd4oygxzz/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpbc214hhn/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbc214hhn/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpijcvszmv/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpijcvszmv/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpy7yg6tu9/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpy7yg6tu9/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp9ocmaqnr/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9ocmaqnr/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpiuxblf13/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpiuxblf13/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpi89qp73o/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpi89qp73o/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp0agg88vt/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0agg88vt/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpv3oee6ow/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpv3oee6ow/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmppkrcw6nw/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppkrcw6nw/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp2r8r6_aa/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2r8r6_aa/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmppk8824mi/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppk8824mi/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpaaar06so/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpaaar06so/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp7dt14xof/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7dt14xof/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpk_5h30e_/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpk_5h30e_/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpmq4v9tg_/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmq4v9tg_/f2.bed | bedtools 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_upaqrb/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8_upaqrb/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmplv8pbfye/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmplv8pbfye/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp0j4ut647/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0j4ut647/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmptvdyft2m/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmptvdyft2m/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpl5r4meq5/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpl5r4meq5/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpiv6d1nkx/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpiv6d1nkx/f2.bed | bedtools 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_jiyobev/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_jiyobev/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpk8asuja2/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpk8asuja2/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpjmm9jwzi/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjmm9jwzi/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp606van4d/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp606van4d/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpt95_wagk/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpt95_wagk/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpu1iy5gev/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpu1iy5gev/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmph1nxeyrc/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmph1nxeyrc/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpj25uazlo/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpj25uazlo/f2.bed | bedtools 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_s3fkjfu/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_s3fkjfu/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpkxq9tnmj/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkxq9tnmj/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmppj4v34zj/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppj4v34zj/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmptzz1eku1/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmptzz1eku1/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpbqxnjrg9/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbqxnjrg9/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp3idzzgia/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3idzzgia/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpsowz054h/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpsowz054h/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp5hm1fv9r/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5hm1fv9r/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp7euxixbe/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7euxixbe/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp76rt_wwc/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp76rt_wwc/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpk2nsciwi/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpk2nsciwi/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpuqmg8wqk/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpuqmg8wqk/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmppgdtl1cs/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppgdtl1cs/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp9y9sntjg/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9y9sntjg/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpo0w32t6v/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpo0w32t6v/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpkxk4eap3/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkxk4eap3/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpmwkvgbtl/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmwkvgbtl/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp4r1ciqwp/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4r1ciqwp/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpu24bvnbv/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpu24bvnbv/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpa02sf485/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpa02sf485/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpbu0vmyao/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbu0vmyao/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpkb4icylb/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkb4icylb/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpupiziim5/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpupiziim5/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp226pg47m/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp226pg47m/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpoh1827ek/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpoh1827ek/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpq0mx3j3b/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpq0mx3j3b/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp3cpnouqs/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3cpnouqs/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp123jll_q/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp123jll_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/tmpe4m0q18_/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpe4m0q18_/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpg5dtpmcm/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpg5dtpmcm/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmptwv2n06p/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmptwv2n06p/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp3fxeupz4/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3fxeupz4/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp9_kss8hm/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9_kss8hm/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpc0n0x4vb/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpc0n0x4vb/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpr0wu70_4/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpr0wu70_4/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpf8_jbt91/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpf8_jbt91/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpk_eljzg0/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpk_eljzg0/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpof1a9lfo/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpof1a9lfo/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp3b2a7vqq/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3b2a7vqq/f2.bed | bedtools merge -s -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_jaccard[same] ______________________________ [gw1] linux -- Python 3.12.3 /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 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 E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') 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_chain4-method_chain4] ____________ [gw3] linux -- Python 3.12.3 /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('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('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') 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') 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') 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') ---------------------------------- 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_chain37-method_chain37] ___________ [gw2] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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('6.100.4', 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') ('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') 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') 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') Empty PyRanges ('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') ('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') 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') ---------------------------------- 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_union[False] _____________________________ [gw0] linux -- Python 3.12.3 /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., 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('6.100.4', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd cat /tmp/tmptmt6ur08/f1.bed /tmp/tmptmt6ur08/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4zd_s8ka/f1.bed /tmp/tmp4zd_s8ka/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdk4bgxp_/f1.bed /tmp/tmpdk4bgxp_/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpcrp10y7s/f1.bed /tmp/tmpcrp10y7s/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgpx3h3so/f1.bed /tmp/tmpgpx3h3so/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbpjujnx0/f1.bed /tmp/tmpbpjujnx0/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbq5ka1pi/f1.bed /tmp/tmpbq5ka1pi/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp9wovod7w/f1.bed /tmp/tmp9wovod7w/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpexbcgib4/f1.bed /tmp/tmpexbcgib4/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp5lv0rp06/f1.bed /tmp/tmp5lv0rp06/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp12eo723t/f1.bed /tmp/tmp12eo723t/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3cduft6e/f1.bed /tmp/tmp3cduft6e/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpf5knf683/f1.bed /tmp/tmpf5knf683/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpuhyspl8n/f1.bed /tmp/tmpuhyspl8n/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3tvyanh_/f1.bed /tmp/tmp3tvyanh_/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0k4orx8l/f1.bed /tmp/tmp0k4orx8l/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxl6euagw/f1.bed /tmp/tmpxl6euagw/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4jg9e8kn/f1.bed /tmp/tmp4jg9e8kn/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp117g80bt/f1.bed /tmp/tmp117g80bt/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmphfgbh9ul/f1.bed /tmp/tmphfgbh9ul/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdh88xwgr/f1.bed /tmp/tmpdh88xwgr/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3ul1bgka/f1.bed /tmp/tmp3ul1bgka/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgmrzrqs8/f1.bed /tmp/tmpgmrzrqs8/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp76seb89u/f1.bed /tmp/tmp76seb89u/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpjtnjmd93/f1.bed /tmp/tmpjtnjmd93/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp469gxeyu/f1.bed /tmp/tmp469gxeyu/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1kbozt9v/f1.bed /tmp/tmp1kbozt9v/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpthud0la0/f1.bed /tmp/tmpthud0la0/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpd869xqhf/f1.bed /tmp/tmpd869xqhf/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpioc4wqpe/f1.bed /tmp/tmpioc4wqpe/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpb9hc4st6/f1.bed /tmp/tmpb9hc4st6/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpa8wp_gge/f1.bed /tmp/tmpa8wp_gge/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpc2308092/f1.bed /tmp/tmpc2308092/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmppk791cdo/f1.bed /tmp/tmppk791cdo/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpsaaor_4l/f1.bed /tmp/tmpsaaor_4l/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmppdaiciru/f1.bed /tmp/tmppdaiciru/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp5whpnu9h/f1.bed /tmp/tmp5whpnu9h/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmporyqmrgl/f1.bed /tmp/tmporyqmrgl/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2s3uh05g/f1.bed /tmp/tmp2s3uh05g/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpflo1g0f2/f1.bed /tmp/tmpflo1g0f2/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpyx22klk8/f1.bed /tmp/tmpyx22klk8/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpysnbd85d/f1.bed /tmp/tmpysnbd85d/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpd5berbny/f1.bed /tmp/tmpd5berbny/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmplr4nej63/f1.bed /tmp/tmplr4nej63/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpa40gdw6p/f1.bed /tmp/tmpa40gdw6p/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpf9j5ntro/f1.bed /tmp/tmpf9j5ntro/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpsxadbwqq/f1.bed /tmp/tmpsxadbwqq/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpko5cz5sg/f1.bed /tmp/tmpko5cz5sg/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpz_5jso8f/f1.bed /tmp/tmpz_5jso8f/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpamkrllka/f1.bed /tmp/tmpamkrllka/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpjv6unpy2/f1.bed /tmp/tmpjv6unpy2/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpv8fvyx8_/f1.bed /tmp/tmpv8fvyx8_/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpympkhmti/f1.bed /tmp/tmpympkhmti/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdob8k0w0/f1.bed /tmp/tmpdob8k0w0/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvblvryb4/f1.bed /tmp/tmpvblvryb4/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2_xcxz24/f1.bed /tmp/tmp2_xcxz24/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpt_mn96cd/f1.bed /tmp/tmpt_mn96cd/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpv_6k98mv/f1.bed /tmp/tmpv_6k98mv/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp9q1dbxgv/f1.bed /tmp/tmp9q1dbxgv/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_ng3k81r/f1.bed /tmp/tmp_ng3k81r/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpr96ijrzc/f1.bed /tmp/tmpr96ijrzc/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpqig7k22a/f1.bed /tmp/tmpqig7k22a/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpkleqa0fu/f1.bed /tmp/tmpkleqa0fu/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpid2df9pa/f1.bed /tmp/tmpid2df9pa/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpf26yyolx/f1.bed /tmp/tmpf26yyolx/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpn9qhz5dj/f1.bed /tmp/tmpn9qhz5dj/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_chain5-method_chain5] ____________ [gw3] linux -- Python 3.12.3 /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 184 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('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') ('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') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('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_set_union[same] _____________________________ [gw0] linux -- Python 3.12.3 /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 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 E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd cat /tmp/tmpxnlx7p84/f1.bed /tmp/tmpxnlx7p84/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_95ebt1h/f1.bed /tmp/tmp_95ebt1h/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpaubmpmu0/f1.bed /tmp/tmpaubmpmu0/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdqdf86uf/f1.bed /tmp/tmpdqdf86uf/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpylgkm8n0/f1.bed /tmp/tmpylgkm8n0/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4v7ch7z7/f1.bed /tmp/tmp4v7ch7z7/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmps7l43t35/f1.bed /tmp/tmps7l43t35/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpcewujtd1/f1.bed /tmp/tmpcewujtd1/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8jt8c12v/f1.bed /tmp/tmp8jt8c12v/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpomc51qr4/f1.bed /tmp/tmpomc51qr4/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpr_pqztyo/f1.bed /tmp/tmpr_pqztyo/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpt6m3qb78/f1.bed /tmp/tmpt6m3qb78/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptgtgtei5/f1.bed /tmp/tmptgtgtei5/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpp7467shs/f1.bed /tmp/tmpp7467shs/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpe41g7uud/f1.bed /tmp/tmpe41g7uud/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmphsmpor_d/f1.bed /tmp/tmphsmpor_d/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0i1q7jde/f1.bed /tmp/tmp0i1q7jde/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmph01_4fed/f1.bed /tmp/tmph01_4fed/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8977aug3/f1.bed /tmp/tmp8977aug3/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpt98g117h/f1.bed /tmp/tmpt98g117h/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmppjxd709j/f1.bed /tmp/tmppjxd709j/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpoz25_lo5/f1.bed /tmp/tmpoz25_lo5/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpa_duaol3/f1.bed /tmp/tmpa_duaol3/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpqn4sfwzg/f1.bed /tmp/tmpqn4sfwzg/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpd8by3uyz/f1.bed /tmp/tmpd8by3uyz/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpt_uvxwjv/f1.bed /tmp/tmpt_uvxwjv/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp5d3y0lym/f1.bed /tmp/tmp5d3y0lym/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpt0wln56f/f1.bed /tmp/tmpt0wln56f/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwkhdu6nx/f1.bed /tmp/tmpwkhdu6nx/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp5crrw__9/f1.bed /tmp/tmp5crrw__9/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpavury12s/f1.bed /tmp/tmpavury12s/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp216kbo6x/f1.bed /tmp/tmp216kbo6x/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpr3b1by_7/f1.bed /tmp/tmpr3b1by_7/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpze2lm580/f1.bed /tmp/tmpze2lm580/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpe_pq7e5s/f1.bed /tmp/tmpe_pq7e5s/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3m88opsu/f1.bed /tmp/tmp3m88opsu/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpq4_nr252/f1.bed /tmp/tmpq4_nr252/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmps30x3t3s/f1.bed /tmp/tmps30x3t3s/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3ssby2wa/f1.bed /tmp/tmp3ssby2wa/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpw5i1wufg/f1.bed /tmp/tmpw5i1wufg/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp7au2cz4i/f1.bed /tmp/tmp7au2cz4i/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp88z9_bpe/f1.bed /tmp/tmp88z9_bpe/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpj34di8zn/f1.bed /tmp/tmpj34di8zn/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_45a3rkm/f1.bed /tmp/tmp_45a3rkm/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmphbwqc3c5/f1.bed /tmp/tmphbwqc3c5/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvgsh5f1v/f1.bed /tmp/tmpvgsh5f1v/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpe6c8a239/f1.bed /tmp/tmpe6c8a239/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpjutxddok/f1.bed /tmp/tmpjutxddok/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp816wiexx/f1.bed /tmp/tmp816wiexx/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpo2thytua/f1.bed /tmp/tmpo2thytua/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1obxxu0o/f1.bed /tmp/tmp1obxxu0o/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4g3eehjw/f1.bed /tmp/tmp4g3eehjw/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpamvyvm8g/f1.bed /tmp/tmpamvyvm8g/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpqa3fnxwr/f1.bed /tmp/tmpqa3fnxwr/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0xs62d73/f1.bed /tmp/tmp0xs62d73/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpc5cvh9rd/f1.bed /tmp/tmpc5cvh9rd/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpl3iva2cr/f1.bed /tmp/tmpl3iva2cr/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1fwlvcga/f1.bed /tmp/tmp1fwlvcga/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpnmd4s0p7/f1.bed /tmp/tmpnmd4s0p7/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpu03_28p6/f1.bed /tmp/tmpu03_28p6/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp911i66xg/f1.bed /tmp/tmp911i66xg/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpu2mhbpdz/f1.bed /tmp/tmpu2mhbpdz/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp9f_xz_m1/f1.bed /tmp/tmp9f_xz_m1/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpewtdt67t/f1.bed /tmp/tmpewtdt67t/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2l_0mmpk/f1.bed /tmp/tmp2l_0mmpk/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4smn_0np/f1.bed /tmp/tmp4smn_0np/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxw3eju0r/f1.bed /tmp/tmpxw3eju0r/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmplgujjsb6/f1.bed /tmp/tmplgujjsb6/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwiqma4u5/f1.bed /tmp/tmpwiqma4u5/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpenahvn6a/f1.bed /tmp/tmpenahvn6a/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpz2cwbpvi/f1.bed /tmp/tmpz2cwbpvi/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpc6o60w5k/f1.bed /tmp/tmpc6o60w5k/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp__smritr/f1.bed /tmp/tmp__smritr/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpn3gqpap_/f1.bed /tmp/tmpn3gqpap_/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpyxl4gmjr/f1.bed /tmp/tmpyxl4gmjr/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxvobqqs4/f1.bed /tmp/tmpxvobqqs4/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8uy7p5dj/f1.bed /tmp/tmp8uy7p5dj/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp5gqz59uf/f1.bed /tmp/tmp5gqz59uf/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmphyqjidb_/f1.bed /tmp/tmphyqjidb_/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp486kgn52/f1.bed /tmp/tmp486kgn52/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpuuwx76ii/f1.bed /tmp/tmpuuwx76ii/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpqxt40uys/f1.bed /tmp/tmpqxt40uys/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpo5erznsx/f1.bed /tmp/tmpo5erznsx/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4s60nynl/f1.bed /tmp/tmp4s60nynl/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpj04gbe0z/f1.bed /tmp/tmpj04gbe0z/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpeiavz2ut/f1.bed /tmp/tmpeiavz2ut/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpt9a1ajf0/f1.bed /tmp/tmpt9a1ajf0/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgxpebqhr/f1.bed /tmp/tmpgxpebqhr/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp7ldwchz2/f1.bed /tmp/tmp7ldwchz2/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgqg2p17u/f1.bed /tmp/tmpgqg2p17u/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1wn8wdr5/f1.bed /tmp/tmp1wn8wdr5/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpz3grzjtu/f1.bed /tmp/tmpz3grzjtu/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpp6adlkkm/f1.bed /tmp/tmpp6adlkkm/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpqr77_svd/f1.bed /tmp/tmpqr77_svd/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpybqrzsx9/f1.bed /tmp/tmpybqrzsx9/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmperm0ey6w/f1.bed /tmp/tmperm0ey6w/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp88xfgpf5/f1.bed /tmp/tmp88xfgpf5/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpide2jc26/f1.bed /tmp/tmpide2jc26/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmprkc55r1u/f1.bed /tmp/tmprkc55r1u/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvb0noczm/f1.bed /tmp/tmpvb0noczm/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp62wl_kna/f1.bed /tmp/tmp62wl_kna/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpml58tu6z/f1.bed /tmp/tmpml58tu6z/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxc7wmtrj/f1.bed /tmp/tmpxc7wmtrj/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3jecl24k/f1.bed /tmp/tmp3jecl24k/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpm3kmos1g/f1.bed /tmp/tmpm3kmos1g/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmppmovp47x/f1.bed /tmp/tmppmovp47x/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmppx77zoh8/f1.bed /tmp/tmppx77zoh8/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpn3v8jf0z/f1.bed /tmp/tmpn3v8jf0z/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpeissh4mk/f1.bed /tmp/tmpeissh4mk/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp27tc05f7/f1.bed /tmp/tmp27tc05f7/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp001hzd_u/f1.bed /tmp/tmp001hzd_u/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp9y6qm2x7/f1.bed /tmp/tmp9y6qm2x7/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfxoogr8k/f1.bed /tmp/tmpfxoogr8k/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpl114xaxe/f1.bed /tmp/tmpl114xaxe/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpi1hl1coy/f1.bed /tmp/tmpi1hl1coy/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpf23zfwj7/f1.bed /tmp/tmpf23zfwj7/f2.bed | bedtools sort | bedtools merge -s -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_chain38-method_chain38] ___________ [gw2] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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 | 3517667 | 3527666 | 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 | 1771266 | 1772088 | a | 0 | + | | | chr1 | 1771266 | 1772088 | a | 0 | + | | | chr1 | 1771266 | 1772088 | a | 0 | + | | | chr1 | 1771266 | 1772088 | a | 0 | - | | | chr1 | 1771266 | 1772088 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 5 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('6.100.4', b'AARYCA8CAAgAAQAIABQ1rOIABQB/Jw4ABQABAAABdMIWIlmqDU4z+RVkAQMpTHABBAwAABoBAAQAKgQncNS8BwUxdAANAB8AAR8AARsHAQAkOxcDNRoFAAAOBwQAFgIAAAE=') 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, | ) | 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('6.100.4', 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') 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 | 257 | 4158 | a | 0 | ... | | chr1 | 257 | 4513 | a | 0 | ... | | chr1 | 257 | 8558 | a | 0 | ... | | chr1 | 257 | 6068 | a | 0 | ... | | chr1 | 257 | 9597 | 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 ('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') 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') 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') 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') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('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_three_in_a_row[strandedness_chain6-method_chain6] ____________ [gw3] linux -- Python 3.12.3 /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, # 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 181 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('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') 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') 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') 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') 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') ___________ test_three_in_a_row[strandedness_chain39-method_chain39] ___________ [gw2] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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('6.100.4', 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') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('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') ('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') 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') ('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') ('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') 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') 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') ('subtract', 'intersect') ('subtract', 'intersect') ('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') 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') 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') ---------------------------------- 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_chain7-method_chain7] ____________ [gw3] linux -- Python 3.12.3 /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, 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:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3.12/typing.py:1195 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('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('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') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('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') 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') ___________ test_three_in_a_row[strandedness_chain40-method_chain40] ___________ [gw2] linux -- Python 3.12.3 /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: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=('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('6.100.4', 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 | 1 | 2 | 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') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 5123 | 5125 | a | 0 | + | | chrX | 5123 | 5125 | 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') ('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') 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') 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') 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') Empty PyRanges ('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') Empty PyRanges ('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') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('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_chain8-method_chain8] ____________ [gw3] linux -- Python 3.12.3 /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, 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/python3.12/typing.py:1195 E (and 106 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('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') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('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') 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') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('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_chain9-method_chain9] ____________ [gw3] linux -- Python 3.12.3 /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, # 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 63 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('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') 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') 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') 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') 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') ___________ test_three_in_a_row[strandedness_chain41-method_chain41] ___________ [gw2] linux -- Python 3.12.3 /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 | 1282 | 2051 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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: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('6.100.4', b'AAABAAABAgcGAgABBAAAAQAAAQABAAUBAAIDAAAAAA==') 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') 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') 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') 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') ('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') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('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') ---------------------------------- 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_chain10-method_chain10] ___________ [gw3] linux -- Python 3.12.3 /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, # 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:575 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('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') 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') 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') 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') 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') ___________ test_three_in_a_row[strandedness_chain42-method_chain42] ___________ [gw2] linux -- Python 3.12.3 /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, # 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 271 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', 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') 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') ('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') 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') ('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') ('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') 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') 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') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('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') ('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') ('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') 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') ___________ test_three_in_a_row[strandedness_chain11-method_chain11] ___________ [gw3] linux -- Python 3.12.3 /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, # 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 63 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('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') Empty PyRanges ('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') ('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') 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') 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') ___________ test_three_in_a_row[strandedness_chain43-method_chain43] ___________ [gw2] linux -- Python 3.12.3 /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, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 7 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AXicY2BAAFYGNAAUAAAAkwAL') 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') 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') 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') 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 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('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') ('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') 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') ---------------------------------- 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_chain12-method_chain12] ___________ [gw3] linux -- Python 3.12.3 /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 104 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured 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('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('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_k_nearest[downstream-False-opposite-last] ________________ [gw1] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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 | 131365 | 131374 | 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 | 141826 | 142087 | 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('6.100.4', b'AAEfBAIDAAABAAUCASQAAQAIAAEBWwUM5AAAAAAAIQIqAQAGAQQAAA==') 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('6.100.4', 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/tmpp37hsfek/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp37hsfek/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpv25d1h9l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv25d1h9l/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpq5eor5y1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq5eor5y1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpi_1urk9h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi_1urk9h/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp178qv8q2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp178qv8q2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpo7tztngs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo7tztngs/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpgghdy3na/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgghdy3na/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpcx1hvvyr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcx1hvvyr/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/tmprj340tm8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprj340tm8/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/tmp4z8xzdi6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4z8xzdi6/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/tmpmqrhpu_x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmqrhpu_x/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/tmpt9ju1hyt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt9ju1hyt/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/tmpne4y2w6i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpne4y2w6i/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/tmp327ojts0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp327ojts0/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/tmpg7lza85a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg7lza85a/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/tmpd1gu41oo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd1gu41oo/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/tmpfc7rml0o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfc7rml0o/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/tmpp_s5_kum/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp_s5_kum/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/tmpzf90eoa5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzf90eoa5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpk04jyq3j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk04jyq3j/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/tmp59zhcp3s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp59zhcp3s/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/tmp2tmjy9tw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2tmjy9tw/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/tmpueeelwvb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpueeelwvb/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/tmp3w0b7fc8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3w0b7fc8/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/tmpfthizynr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfthizynr/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/tmp91pvj4yc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp91pvj4yc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpdjh8z5ck/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdjh8z5ck/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/tmp0rtyytxp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0rtyytxp/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/tmp5l5ado77/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5l5ado77/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/tmp35tmcfi8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp35tmcfi8/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/tmp3a5rx6fn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3a5rx6fn/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/tmplceobhys/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplceobhys/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/tmp3ussijy6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3ussijy6/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/tmpkp85shcl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkp85shcl/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/tmp5gwsyzeh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5gwsyzeh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpf2g5hq1h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf2g5hq1h/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpxjv40iwa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxjv40iwa/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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_wwwyl5d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_wwwyl5d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpv73qwtqc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv73qwtqc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpk5qdfl5j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk5qdfl5j/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpwymv1zx_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwymv1zx_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp09c9xnn9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp09c9xnn9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpf24xh6jt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf24xh6jt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpw4a06bko/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw4a06bko/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp4kv4j1db/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4kv4j1db/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpu642bybf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu642bybf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp2x_wqz78/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2x_wqz78/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/tmpl71rptyt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl71rptyt/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/tmpgfx70kfh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgfx70kfh/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/tmp911usg5w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp911usg5w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpfv6ws848/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfv6ws848/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/tmps5an3wm1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps5an3wm1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp4zglhks8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4zglhks8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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_97f_va0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_97f_va0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp1wa2zknz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1wa2zknz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpel94s7xj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpel94s7xj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp1z1ydld3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1z1ydld3/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/tmpdwrvwlkp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdwrvwlkp/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/tmpfivm1d_9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfivm1d_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 -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuhq4h37a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuhq4h37a/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/tmpqngok14i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqngok14i/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpm1jriqc7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm1jriqc7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpj4p9v154/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj4p9v154/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpcbr8z47_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcbr8z47_/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/tmp2z65i_gl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2z65i_gl/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/tmps588qr99/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps588qr99/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/tmpi12jv11q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi12jv11q/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/tmp9aa2aocf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9aa2aocf/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/tmp4i7rvgcm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4i7rvgcm/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/tmpz5bba37r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz5bba37r/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/tmpf56gk004/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf56gk004/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/tmp1taqtbd_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1taqtbd_/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/tmphuxaddx0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphuxaddx0/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/tmpi22ncfjf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi22ncfjf/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/tmpx0ill_tn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx0ill_tn/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/tmp8xnx_k3z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8xnx_k3z/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/tmpv1482va6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv1482va6/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/tmpbo2jy7lc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbo2jy7lc/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/tmpxeigl6ph/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxeigl6ph/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/tmp96hp2503/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp96hp2503/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/tmp4ldluo2s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ldluo2s/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/tmp7ohdo4r5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7ohdo4r5/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/tmpnyyk2rt9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnyyk2rt9/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/tmpjg0nd0jx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjg0nd0jx/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_d3icym/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa_d3icym/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/tmpyedu0e_1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyedu0e_1/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/tmpcobxvdnb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcobxvdnb/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/tmpc8lon2fo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc8lon2fo/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/tmphmf_1fr5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphmf_1fr5/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/tmpy89b97ge/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy89b97ge/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/tmpo2po8m87/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo2po8m87/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/tmpw4j233iu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw4j233iu/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/tmp4ps8hbju/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ps8hbju/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_462pa5w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_462pa5w/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/tmpdjvi2158/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdjvi2158/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/tmpa2cem7wp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa2cem7wp/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/tmp6tywexbi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6tywexbi/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/tmpgjj6fb05/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgjj6fb05/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/tmpc0m67ks3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc0m67ks3/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/tmp43hqp0hm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp43hqp0hm/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/tmpxt6vizi1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxt6vizi1/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/tmp37zsbh1b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp37zsbh1b/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/tmph_hoo5su/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph_hoo5su/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/tmpeh_2kqtk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeh_2kqtk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpdknfmoqj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdknfmoqj/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_57qyu5b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_57qyu5b/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/tmpzmdatyiz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzmdatyiz/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/tmp9lovgwba/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9lovgwba/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_sl5l2u0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_sl5l2u0/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/tmprlw04hnr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprlw04hnr/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/tmp976o_iqm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp976o_iqm/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/tmp1bs1scem/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1bs1scem/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/tmpbar7yjoq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbar7yjoq/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/tmpx6_1qlay/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx6_1qlay/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/tmpx7tibnct/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx7tibnct/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/tmpg9197hpm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg9197hpm/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/tmph18chjwh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph18chjwh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpv9n_lp02/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv9n_lp02/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/tmp2ofxbqz_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2ofxbqz_/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/tmp3f6bqx8r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3f6bqx8r/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/tmpmh9hugfc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmh9hugfc/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/tmpodbo65up/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpodbo65up/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/tmpml3b915p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpml3b915p/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/tmp2lekchmz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2lekchmz/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. ---------------------------------- 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_chain13-method_chain13] ___________ [gw3] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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:575 E /usr/lib/python3/dist-packages/pandas/core/common.py:140 E (and 62 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('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') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('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') ('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') 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') 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') ---------------------------------- 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] __________________ [gw1] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1901059 | 1901572 | a | 0 | - | | | chr1 | 1901059 | 1901572 | a | 0 | - | | | chr2 | 1901059 | 1901572 | a | 0 | - | | | chr11 | 1901059 | 1901572 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 4 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 | 65540 | 65542 | 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('6.100.4', b'AXicYxRSWJvAmsa0fS5rHQMDIzszAwiwMTMwsjIwcDEwMrDLMjExMDAxCAOFGRmZGeSYgIIMYA4DMy9DHUgJEAMA/gsEpg==') 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('6.100.4', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') 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/tmpi28ld29_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi28ld29_/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/tmp8gimz3fr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8gimz3fr/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/tmp73hg81xi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp73hg81xi/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/tmp4je83qxk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4je83qxk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpi442cq9_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi442cq9_/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/tmpszyneuba/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpszyneuba/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/tmpflpj699d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpflpj699d/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/tmpxbynsous/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxbynsous/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/tmpoev2p0dd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoev2p0dd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp92fw_7qi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp92fw_7qi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpt9k92ptt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt9k92ptt/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/tmpe8xlji7e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe8xlji7e/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/tmpzhwbzbuo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzhwbzbuo/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/tmpl0tx8jis/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl0tx8jis/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/tmpdtycuf2x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdtycuf2x/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/tmp42zb0x4u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp42zb0x4u/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/tmp7qs73h88/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7qs73h88/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/tmpsjv99yq4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsjv99yq4/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/tmpe2jv_4ao/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe2jv_4ao/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/tmpug8hu7b0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpug8hu7b0/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/tmpvsm0ff9y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvsm0ff9y/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/tmp8a2g9_xi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8a2g9_xi/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/tmp85p3onoe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp85p3onoe/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/tmpwy_6l5ga/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwy_6l5ga/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/tmpey60o2n3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpey60o2n3/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/tmpn8rar7k9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn8rar7k9/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/tmpff7fa3v8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpff7fa3v8/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/tmppdxymghw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppdxymghw/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/tmpw0lvupjf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw0lvupjf/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/tmp18ned1az/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp18ned1az/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/tmp3iyx6swf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3iyx6swf/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/tmpbpeomiw_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbpeomiw_/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/tmpuebhdom9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuebhdom9/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/tmprjcph8q6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprjcph8q6/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/tmpiw788q1j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiw788q1j/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/tmp1y1r_tks/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1y1r_tks/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/tmpfzdj3vsj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfzdj3vsj/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/tmpq5tlv1bw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq5tlv1bw/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/tmpk5zr9red/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk5zr9red/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/tmp1wv68xot/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1wv68xot/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/tmpsyr5q3gx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsyr5q3gx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpjt5jd30m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjt5jd30m/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/tmph2f04ddt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph2f04ddt/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/tmpghtxh45u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpghtxh45u/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/tmptd9c93xx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptd9c93xx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp871o76y8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp871o76y8/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/tmp1wps4lmh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1wps4lmh/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_gdpkkh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa_gdpkkh/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/tmp7t9f7819/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7t9f7819/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpsdgchd0g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsdgchd0g/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/tmpbswmrl00/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbswmrl00/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpsamkfopg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsamkfopg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpy06xivbn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy06xivbn/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/tmpc6j1j4dv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc6j1j4dv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpfc8nvwcv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfc8nvwcv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpvst4a3_h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvst4a3_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 -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd4uory7x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd4uory7x/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/tmpzax4m7dm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzax4m7dm/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/tmpqy9q7rib/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqy9q7rib/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/tmpym6hweoh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpym6hweoh/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/tmp68iw5gwu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp68iw5gwu/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/tmpmpy_ysyl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmpy_ysyl/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/tmpnmgy_e38/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnmgy_e38/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/tmpzg75pcjm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzg75pcjm/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/tmpgvi5v5a0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgvi5v5a0/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/tmp0p7adz46/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0p7adz46/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/tmp2uq9g3a6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2uq9g3a6/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/tmpddh00kbs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpddh00kbs/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpf8b0juc_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf8b0juc_/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/tmp86x3orl2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp86x3orl2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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_vbt9k9i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_vbt9k9i/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/tmpw6bp7uq7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw6bp7uq7/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/tmponms7acc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmponms7acc/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/tmpzvuao0en/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzvuao0en/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/tmpbu2dmjbx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbu2dmjbx/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/tmpqrlp8_wv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqrlp8_wv/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/tmpyqcoz959/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyqcoz959/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp416cxgcm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp416cxgcm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp9i_i5vn0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9i_i5vn0/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/tmpk3o9tml6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk3o9tml6/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/tmpeewwi924/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeewwi924/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp925hx3h0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp925hx3h0/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/tmp1r72mno3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1r72mno3/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/tmpep81oi8a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpep81oi8a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpenmpy8kt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpenmpy8kt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmprat10bya/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprat10bya/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/tmp2oay5_gq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2oay5_gq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpfo2egulr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfo2egulr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpaafbiqw9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaafbiqw9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpriw_tf3k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpriw_tf3k/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpczbtfwj4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpczbtfwj4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp1r7frgvl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1r7frgvl/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/tmpt_3rz0b8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt_3rz0b8/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/tmpci22chv9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpci22chv9/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/tmp0k1j20ew/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0k1j20ew/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpwyydkwdr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwyydkwdr/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/tmpwjkmsetz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwjkmsetz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp43be2kcj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp43be2kcj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpruyj8inv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpruyj8inv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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_1hk2b5i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_1hk2b5i/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/tmpl8e_tesr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl8e_tesr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpr_6u0ypp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr_6u0ypp/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/tmp89alwor6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp89alwor6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpfkasm2dj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfkasm2dj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpnlt1xdil/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnlt1xdil/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpvrbmm4_q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvrbmm4_q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpc_wcfoyv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc_wcfoyv/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/tmpxhtk95b4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxhtk95b4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpdn_jvc7k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdn_jvc7k/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp3wh4noda/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3wh4noda/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/tmpj8_m_9q8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj8_m_9q8/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/tmp1o3a74i9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1o3a74i9/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/tmp4o55xxgj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4o55xxgj/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 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 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 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 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 chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr9 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on 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 chr9 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on 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 chr9 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr9 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr9 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr9 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr9 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr9 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on 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 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 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. ---------------------------------- 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_chain45-method_chain45] ___________ [gw2] linux -- Python 3.12.3 /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 | 9527809 | 9537069 | a | 0 | + | E | chr1 | 9527809 | 9537069 | a | 0 | + | E | chr1 | 9527809 | 9531930 | a | 0 | + | E | chr1 | 208645 | 217905 | a | 0 | + | E | chr1 | 9527809 | 9528891 | a | 0 | + | E | chr1 | 9527809 | 9527860 | a | 0 | + | E | chr1 | 9527809 | 9528581 | 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 | 208645 | 209158 | a | 0 | + | E | chr1 | 464239 | 464752 | a | 0 | + | E | chr1 | 1114668 | 1115181 | a | 0 | + | E | chr1 | 1114668 | 1115181 | a | 0 | + | E | chr1 | 1114668 | 1115181 | a | 0 | + | E | chr1 | 1114668 | 1124142 | a | 0 | + | E | chr1 | 1114668 | 1115184 | 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 gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1967625 | 1969681 | a | 0 | - | E | chr2 | 1967625 | 1969681 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 2 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('6.100.4', b'AXicY6qZMa2ehWfBwu3T9tcwW9bt42NnDdvDFCPkr8Vsf2a/uuuxelZP9uvbGRkUJrqwszMzMgAhEzuzObM+C0PpxCQGNiZLAQkBNmZmZiY2ViZ2Nhs2RVY1BiMOFjUWSzY2RRZVVms2XSYGBRVtRnZ2VgYGBhYJoIUsCnAL2XBYGAax0IaFUYOB0V6NkYnRmV00j5XBZCvvU7DlgkzajKzMqox8bFlMzAwMTCCzrRj4DzIxM1qxMXAyMjIyAB3LICjHxsHAwMHODuIDAAsOKpc=') 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') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9473856 | 9478090 | a | 0 | ... | | chr1 | 2314001 | 2323845 | a | 0 | ... | | chr3 | 7858325 | 7863347 | a | 0 | ... | | chr7 | 4285767 | 4291178 | a | 0 | ... | | chr8 | 5164000 | 5169022 | a | 0 | ... | | chrY | 1845 | 9075 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 17 columns from 5 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') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3840714 | 3842489 | a | 0 | ... | | chr1 | 9527980 | 9534205 | a | 0 | ... | | chr1 | 7463050 | 7465271 | a | 0 | ... | | chr1 | 464239 | 468273 | a | 0 | ... | | chr1 | 222863 | 231220 | a | 0 | ... | | chr1 | 1468566 | 1469529 | a | 0 | ... | | chr1 | 9527980 | 9537574 | 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') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3840714 | 3842489 | a | 0 | ... | | chr1 | 9527980 | 9534205 | a | 0 | ... | | chr1 | 7463050 | 7465271 | a | 0 | ... | | chr1 | 464239 | 468273 | a | 0 | ... | | chr1 | 222863 | 231220 | a | 0 | ... | | chr1 | 1468566 | 1469529 | a | 0 | ... | | chr1 | 9527980 | 9537574 | 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') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') 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) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr8 | 1686252 | 1688050 | a | 0 | ... | | chr8 | 21 | 4119 | a | 0 | ... | | chr8 | 394503 | 396301 | a | 0 | ... | | chr8 | 828394 | 836633 | 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') ('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') 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') 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') 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') ('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') ('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') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') 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') ('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') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('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') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') 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') ('join', 'nearest') ('join', 'nearest') ('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') 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_chain14-method_chain14] ___________ [gw3] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 983041 | 984066 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2562 | 4355 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AAEAAQAOAAABAF8PAAAAIgQAAAAAAQEpVikEA3QBAQcDDB0AAQABAAAGAAoBAAQHAAAB') 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') 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') 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') ('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') 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') ('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') ---------------------------------- 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-False-last] __________________ [gw1] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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 | 135171 | 142342 | a | 0 | - | | | chr1 | 135171 | 135173 | a | 0 | - | | | chr1 | 135171 | 135173 | 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 | 5889 | 13319 | 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 39 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AAFdKV1UAUDX/xKX3iIDZd23FIoxPwARAQEAAQAKAhACAgMAABwCAB4AAQEBAQABAQALAgEAAAEBAAMAFwAAAQABHQUACgABAA==') 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 38 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') 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/tmpccwp8ine/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpccwp8ine/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_ir1tnmf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_ir1tnmf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpfzv7ukp4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfzv7ukp4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv4y3ra5f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv4y3ra5f/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_sngvfh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo_sngvfh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplfqen3qh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplfqen3qh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8394bann/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8394bann/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsrdqccsu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsrdqccsu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuu8tpqmq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuu8tpqmq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5l9a6o9v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5l9a6o9v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpwuno7f83/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwuno7f83/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpm_qc2g0s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm_qc2g0s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpnmgd1135/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnmgd1135/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmxwa3v7q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmxwa3v7q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpro5oqx8x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpro5oqx8x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpreuozobo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpreuozobo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp03agrc__/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp03agrc__/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkkh3q3a8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkkh3q3a8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprcxwaz77/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprcxwaz77/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy9e980dj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy9e980dj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn5faafjm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn5faafjm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphetcc14j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphetcc14j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt0nwrgey/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt0nwrgey/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp71oyaqzy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp71oyaqzy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgmwe5lgp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgmwe5lgp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi4bpy6zd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi4bpy6zd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplz6hiikj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplz6hiikj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp_4gpt71/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp_4gpt71/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb1tadpyr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb1tadpyr/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_g491lh6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_g491lh6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4ryek3fl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ryek3fl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4iy_datq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4iy_datq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv_t30qtr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv_t30qtr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf41_ekig/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf41_ekig/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4d1zqv1c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4d1zqv1c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2vsnh78w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2vsnh78w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmfgz05t5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmfgz05t5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp83ri8pmk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp83ri8pmk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4_3jznp2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4_3jznp2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplkucn2yz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplkucn2yz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjwb5u5_g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjwb5u5_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 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp51ttu_cy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp51ttu_cy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpbyy18dtq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbyy18dtq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpptg8gumv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpptg8gumv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7750oqtj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7750oqtj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyrttubx1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyrttubx1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo66zaap7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo66zaap7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8esg34di/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8esg34di/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp10na9ntw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp10na9ntw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwlnvw3ee/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwlnvw3ee/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp545oq2u5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp545oq2u5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdwtqk_56/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdwtqk_56/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjof6crvo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjof6crvo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpzv1tbki5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzv1tbki5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiabsmmec/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiabsmmec/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoflywexh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoflywexh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8tiw6y2x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8tiw6y2x/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp__j_k0kh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp__j_k0kh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpee8_qvzf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpee8_qvzf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpfcitqwg6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfcitqwg6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpixrfh9t7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpixrfh9t7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp_s9e_wj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp_s9e_wj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp47fap0os/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp47fap0os/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppxrzla8i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppxrzla8i/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpj_olkmuq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj_olkmuq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjbe4qo_1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjbe4qo_1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbk1kt3hy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbk1kt3hy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp09kkbo42/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp09kkbo42/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5sw86xzf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5sw86xzf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqe8tc4cr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqe8tc4cr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0cdzzhct/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0cdzzhct/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps3uz6mrf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps3uz6mrf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpikqhfpzt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpikqhfpzt/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_7s174l6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_7s174l6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplzsav7zf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplzsav7zf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7okr635i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7okr635i/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpqrx4qsr3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqrx4qsr3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl5nc_84s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl5nc_84s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpxs9na4p4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxs9na4p4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmph4wua_a1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph4wua_a1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwxdm3b3w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwxdm3b3w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphwshkxy0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphwshkxy0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9e74mj_2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9e74mj_2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsoa_egjy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsoa_egjy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp03kyg30l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp03kyg30l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7xme7xuz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7xme7xuz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpna5qexe5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpna5qexe5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp8ni97s7_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8ni97s7_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpk1dan44p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk1dan44p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpgnzfu64p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgnzfu64p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2eehl4qx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2eehl4qx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfkcci7nv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfkcci7nv/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. ---------------------------------- 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_chain47-method_chain47] ___________ [gw2] linux -- Python 3.12.3 /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, 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:369 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', 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') ('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') ('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') 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') 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') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('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') 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') ('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') ('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') ('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') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', '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_chain15-method_chain15] ___________ [gw3] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 720920 | 720931 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | 2033666 | 2039305 | a | 0 | + | E | chr1 | 197377 | 203016 | a | 0 | - | E | chr1 | 327940 | 328456 | a | 0 | - | E | chr1 | 459030 | 464669 | a | 0 | - | E | chr1 | 134913 | 140552 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 5 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 103 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicFYtdCoJgFETn3Js/JGLgZ0mQPbog1+BjDy1AW4Gv0XK7HzMwcDgjHpVKawXqGUREanTTS+eAaVvfpOM+saTZ2RXs8/vuwsDyq3GPmQqcTJ41+KVi4DRal3UshGuZ7egf8+UHfQ==') 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') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('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') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('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') ('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') ('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') 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') 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') ---------------------------------- 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] _________________ [gw1] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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='downstream', | overlap=True, | strandedness='opposite', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 131589 | 132635 | 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 | 3604488 | 3604768 | a | 0 | - | | | chr1 | 3604488 | 3604768 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 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('6.100.4', b'AXicY2RgZmRkgEImJhYGBiYWUQYGRtb8TxWM3jWZESBxIGBgiDFnYGfgZRRnYAQAXtQEWw==') 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='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 | - | | | 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., | ) | 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('6.100.4', b'AXicY2RgYGBkZAABRiADyoQAGAdZDAABlQAM') 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/tmpki_ix84e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpki_ix84e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp28gtogxt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp28gtogxt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp9lo17sed/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9lo17sed/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn3945n0t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn3945n0t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw_vw9td3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw_vw9td3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy89x20aq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy89x20aq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvnsp0nbc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvnsp0nbc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0jy85xva/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0jy85xva/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzgr4g8ev/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzgr4g8ev/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4ttg9oc_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ttg9oc_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv3o57guw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv3o57guw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsthhjglj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsthhjglj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp0a02byis/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0a02byis/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5fwb966p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5fwb966p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqjz9rnww/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqjz9rnww/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpysyi0ww7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpysyi0ww7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpao094p2y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpao094p2y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjklp6zpk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjklp6zpk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsamrynhm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsamrynhm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmzix21m8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmzix21m8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6c3jw818/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6c3jw818/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpr8lvt73p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr8lvt73p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdk31vd6h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdk31vd6h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5png4ns6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5png4ns6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpackdjioj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpackdjioj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9arlrkys/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9arlrkys/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnu10nitq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnu10nitq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaougxfqs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaougxfqs/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9mnx3_g4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9mnx3_g4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl0d4tae2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl0d4tae2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9z13koxl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9z13koxl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv5yfc80k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv5yfc80k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb0wguy7r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb0wguy7r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbw35x21q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbw35x21q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp01y6srd3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp01y6srd3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcet2lct1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcet2lct1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp31db5y74/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp31db5y74/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsysutd9h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsysutd9h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4jgg1u3k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4jgg1u3k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp69vt6zi7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp69vt6zi7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvdanhfh7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvdanhfh7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8lcdyf_d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8lcdyf_d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqwwphdnj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqwwphdnj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6f68z1r8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6f68z1r8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjhoo3m5z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjhoo3m5z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpim4aeomz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpim4aeomz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy2z33r0e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy2z33r0e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr8gi5jyr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr8gi5jyr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmplexndeyy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplexndeyy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmaoiealj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmaoiealj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmptmnuko_i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptmnuko_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 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr4q0uvko/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr4q0uvko/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpjjpiwzkq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjjpiwzkq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9i0wj5dh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9i0wj5dh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl22_j85y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl22_j85y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpctvjous6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpctvjous6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxoq5rr6d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxoq5rr6d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfu9onyg2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfu9onyg2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpjfa136ht/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjfa136ht/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2s_cqccn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2s_cqccn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5qxzual_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5qxzual_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpzfe4xs7l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzfe4xs7l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyk1t4al6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyk1t4al6/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_gqi7w0q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_gqi7w0q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9reacvdh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9reacvdh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3hsf4nic/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3hsf4nic/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9n4azxzr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9n4azxzr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp96bkkej7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp96bkkej7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpackv4gz6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpackv4gz6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp2vm5r79r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2vm5r79r/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpifd2nfhq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpifd2nfhq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp3clsp_bb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3clsp_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 -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmphqjufw71/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphqjufw71/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp2wwiwsyx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2wwiwsyx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpr85zw8mq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr85zw8mq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpcb55_27g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcb55_27g/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpjm12rgeo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjm12rgeo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp2u03ww5p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2u03ww5p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp7wlh0bgb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7wlh0bgb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7w3gjyn5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7w3gjyn5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpbs5qrutb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbs5qrutb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp9k9i28sd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9k9i28sd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpdey3iq_u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdey3iq_u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpg7kt6uce/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg7kt6uce/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp2jhwdaq9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2jhwdaq9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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_w65w63j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_w65w63j/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpx7ph53cp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx7ph53cp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp90ciw40l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp90ciw40l/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpwf2tfufe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwf2tfufe/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk5znlzbd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk5znlzbd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpf1b1azcx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf1b1azcx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpw4kvfshq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw4kvfshq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmprqao57kq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprqao57kq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpdb9m5973/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdb9m5973/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpc5kcnyte/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc5kcnyte/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpgn4te1m0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgn4te1m0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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_axshbiy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_axshbiy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp2d2t6h5c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2d2t6h5c/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpeqhgbq29/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeqhgbq29/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp9b8en_0f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9b8en_0f/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpkiy5vhu7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkiy5vhu7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmps5u5bbj4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps5u5bbj4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmphjjhh1__/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphjjhh1__/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp17ytl4fg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp17ytl4fg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpra26sopq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpra26sopq/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 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 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. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. 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_chain49-method_chain49] ___________ [gw2] linux -- Python 3.12.3 /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 226 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('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') ('set_union', 'set_union') ('set_union', 'set_union') ('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') 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') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('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_k_nearest[downstream-True-same-last] ___________________ [gw1] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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='same', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 196870 | 197128 | a | 0 | - | | | chr2 | 196870 | 197128 | 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) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 131073 | 131331 | 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('6.100.4', b'AXicY2S+/yqKOU6ZUZWd2ZGBjYGBEQgYGHiYGVlBTAYQh4ERDBnYmBgY2BmYgEK8QC4ArOYDZQ==') 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='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 40 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') 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/tmpljsu8kp_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpljsu8kp_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbgiiutyf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbgiiutyf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpv7blpgjg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv7blpgjg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuv552v92/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuv552v92/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa7pd9wir/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa7pd9wir/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpguiqw7ij/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpguiqw7ij/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy1v41tlw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy1v41tlw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8fsjk6ww/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8fsjk6ww/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn3ic8j4r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn3ic8j4r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqoo035my/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqoo035my/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpkgnpmjp5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkgnpmjp5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp3nxwar54/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3nxwar54/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp5yausaza/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5yausaza/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd671d9vm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd671d9vm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1grpp1vb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1grpp1vb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp5izpw3c3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5izpw3c3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3fojeb9w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3fojeb9w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0xxxwq96/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0xxxwq96/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_y8ujdys/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_y8ujdys/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5s8m222m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5s8m222m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp04_1_8xo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp04_1_8xo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp01tc6ckf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp01tc6ckf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwsvmnujd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwsvmnujd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcyhjxz_l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcyhjxz_l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6y3jur0x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6y3jur0x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdwstax7c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdwstax7c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo7etnstf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo7etnstf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6imvqohx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6imvqohx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj98sl6c6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj98sl6c6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnth1zpxl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnth1zpxl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3r44wz2_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3r44wz2_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp81bdjjqy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp81bdjjqy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm3fk90v9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm3fk90v9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvv9_kgxp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvv9_kgxp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpob73vpyr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpob73vpyr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkzxjc2dc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkzxjc2dc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwhuvr383/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwhuvr383/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmprhyuvry4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprhyuvry4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaa8iwja_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaa8iwja_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaxqs8dfc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaxqs8dfc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpirwfmmfp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpirwfmmfp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwpsfnmso/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwpsfnmso/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzj8z4rhd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzj8z4rhd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpujm2s1er/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpujm2s1er/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmphtys0dq6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphtys0dq6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp0_8pi02z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0_8pi02z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp839f568i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp839f568i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnl9mg17h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnl9mg17h/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpjf4z_rqs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjf4z_rqs/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp1fb5u2bc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1fb5u2bc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgw4im7qn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgw4im7qn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyriu9wxj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyriu9wxj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsj3zzrg4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsj3zzrg4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnukkp20p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnukkp20p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo0b8p5wn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo0b8p5wn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp539n5cqo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp539n5cqo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4xai5uma/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4xai5uma/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpzvu011ky/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzvu011ky/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmprg0abfn5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprg0abfn5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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_gt8sts2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_gt8sts2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp0wpp39tt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0wpp39tt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpxhjgnd2h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxhjgnd2h/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpjfv3jbhy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjfv3jbhy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpll4or5ck/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpll4or5ck/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp1rv3yu5i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1rv3yu5i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr_olk74i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr_olk74i/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_ykn1ye/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz_ykn1ye/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjgwr14pb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjgwr14pb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkbdwmxpz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkbdwmxpz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpf3hfmd0q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf3hfmd0q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpju_nfrgn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpju_nfrgn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5mk_eaxy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5mk_eaxy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy446sjqd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy446sjqd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpl6ba245o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl6ba245o/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgctf3el6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgctf3el6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmppmo7v1sx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppmo7v1sx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpt6r3qm5c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt6r3qm5c/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpfp11tnzb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfp11tnzb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpivf4k3eg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpivf4k3eg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmphxaa_tgg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphxaa_tgg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmplwkg9ezh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplwkg9ezh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpz9kzu_79/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz9kzu_79/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_4kq_u3a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_4kq_u3a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpng8jmudl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpng8jmudl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmptm84amp1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptm84amp1/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_08pjt4k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_08pjt4k/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpi16i3idx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi16i3idx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmphqh9zc35/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphqh9zc35/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdt8joo2x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdt8joo2x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw702o454/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw702o454/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpyyubndfu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyyubndfu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpmie4hhgj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmie4hhgj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8dkl91lt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8dkl91lt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpqvk6tm8h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqvk6tm8h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp08oxbte/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp08oxbte/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp4e8jb38w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4e8jb38w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpl6j2u8sx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl6j2u8sx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpnyz8nrqt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnyz8nrqt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp5w_n18e3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5w_n18e3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpjfhxbdbg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjfhxbdbg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpmrlr9_u7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmrlr9_u7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpnsrtqyi0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnsrtqyi0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp4fgmzg4a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4fgmzg4a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0fzjr2d0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0fzjr2d0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnl7085px/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnl7085px/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 chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. 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_chain17-method_chain17] ___________ [gw3] linux -- Python 3.12.3 /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 | 68 | 335 | a | 0 | - | E | chr2 | 68 | 335 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 2 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 | 68 | 70 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | chr2 | 786442 | 790290 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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/join.py:104 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:106 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:12 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:14 E (and 42 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY4kVkVzDaCDOa8PAzMjACEQMIOTMwM/IxcDIChblYYCJ8jOAFDCygTgMICF+HgZOBgZ+dgZGAKfqAx0=') 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') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') 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 | 8379524 | 8386386 | a | 0 | ... | | chr1 | 2110676 | 2116095 | a | 0 | ... | | chr1 | 8869181 | 8877738 | a | 0 | ... | | chr1 | 8940144 | 8943702 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr6 | 9092318 | 9101168 | a | 0 | ... | | chr6 | 3744436 | 3752353 | a | 0 | ... | | chr12 | 2980565 | 2984779 | a | 0 | ... | | chr19 | 7357186 | 7366520 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 4 chromosomes. For 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') ('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') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('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') 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') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') 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') ('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') ('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_coverage[False] _____________________________ [gw0] linux -- Python 3.12.3 /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., 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('6.100.4', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') 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/tmp1f367b9s/f1.bed -b /tmp/tmp1f367b9s/f2.bed Chromosome Start End Name Score Strand 0 chr1 9590310 9593715 a 0 + 1 chr1 9819040 9828368 a 0 - 2 chr1 979154 986080 a 0 - 3 chr2 5508960 5515558 a 0 + 4 chr10 718263 718943 a 0 + 5 chr10 4405509 4406347 a 0 + 6 chr10 299045 305912 a 0 + 7 chr10 9819040 9825369 a 0 - 8 chr17 9534898 9534935 a 0 + 9 chr19 2 4339 a 0 - 10 chrM 2243775 2245507 a 0 - Chromosome Start End Name Score Strand 0 chr1 1127337 1133853 a 0 + 1 chr1 9521763 9527490 a 0 - 2 chr1 1994621 1996467 a 0 - 3 chr14 9578313 9586141 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp6c6g64xu/f1.bed -b /tmp/tmp6c6g64xu/f2.bed Chromosome Start End Name Score Strand 0 chr1 3474690 3474691 a 0 + 1 chr1 3673099 3673100 a 0 - 2 chr1 3474690 3475985 a 0 - 3 chr1 3474690 3478024 a 0 - Chromosome Start End Name Score Strand 0 chr1 6231042 6240805 a 0 + 1 chr15 5935486 5940241 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpa301sd08/f1.bed -b /tmp/tmpa301sd08/f2.bed Chromosome Start End Name Score Strand 0 chr1 3474690 3474691 a 0 + 1 chr1 3673099 3673100 a 0 - 2 chr1 3474690 3475985 a 0 - 3 chr1 3474690 3478024 a 0 - Chromosome Start End Name Score Strand 0 chr1 6231042 6240805 a 0 - 1 chr15 2 9765 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpicq2s4ul/f1.bed -b /tmp/tmpicq2s4ul/f2.bed Chromosome Start End Name Score Strand 0 chr1 3474690 3474691 a 0 + 1 chr1 3673099 3673100 a 0 - 2 chr1 3474690 3475985 a 0 - 3 chr1 3474690 3478024 a 0 - Chromosome Start End Name Score Strand 0 chr1 6231042 6240805 a 0 - 1 chr15 2 9765 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpefsxrqtq/f1.bed -b /tmp/tmpefsxrqtq/f2.bed Chromosome Start End Name Score Strand 0 chr1 3474690 3474691 a 0 + 1 chr1 3673099 3673100 a 0 - 2 chr1 3474690 3475985 a 0 - 3 chr1 3474690 3478024 a 0 - Chromosome Start End Name Score Strand 0 chr1 6231042 6240805 a 0 - 1 chr15 2 9765 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpnaxbsv7l/f1.bed -b /tmp/tmpnaxbsv7l/f2.bed Chromosome Start End Name Score Strand 0 chr1 6231042 6240805 a 0 - 1 chr15 2 9765 a 0 - Chromosome Start End Name Score Strand 0 chr1 6231042 6240805 a 0 - 1 chr15 2 9765 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpvah7xj9b/f1.bed -b /tmp/tmpvah7xj9b/f2.bed Chromosome Start End Name Score Strand 0 chr1 6231042 6240805 a 0 - 1 chr15 2 9765 a 0 + Chromosome Start End Name Score Strand 0 chr1 6231042 6240805 a 0 - 1 chr15 2 9765 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp23aag133/f1.bed -b /tmp/tmp23aag133/f2.bed Chromosome Start End Name Score Strand 0 chr1 7885852 7887004 a 0 + 1 chr1 9999999 10000001 a 0 + 2 chr1 1511491 1513255 a 0 + 3 chr1 579407 585752 a 0 - 4 chr1 147017 151732 a 0 - 5 chr1 8834075 8839595 a 0 - 6 chr17 2457047 2458282 a 0 + Chromosome Start End Name Score Strand 0 chr1 7009237 7015690 a 0 + 1 chr2 9999999 10001021 a 0 - 2 chr4 1981031 1987877 a 0 + 3 chr5 7194408 7195874 a 0 - 4 chrY 3519607 3524457 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp68m9r55q/f1.bed -b /tmp/tmp68m9r55q/f2.bed Chromosome Start End Name Score Strand 0 chr1 7885852 7887004 a 0 + 1 chr1 9999999 10000001 a 0 + 2 chr1 1511491 1513255 a 0 + 3 chr1 579407 585752 a 0 - 4 chr1 147017 151732 a 0 - 5 chr1 8834075 8839595 a 0 - 6 chr17 2457047 2458282 a 0 + Chromosome Start End Name Score Strand 0 chr1 7009237 7015690 a 0 + 1 chr2 9999999 10001021 a 0 - 2 chr4 1981031 1987877 a 0 + 3 chr5 7194408 7195874 a 0 - 4 chrY 3519607 3524457 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp_jur499l/f1.bed -b /tmp/tmp_jur499l/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/tmp85qk6zhb/f1.bed -b /tmp/tmp85qk6zhb/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/tmpxu15ba4f/f1.bed -b /tmp/tmpxu15ba4f/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/tmpcnyv6vpj/f1.bed -b /tmp/tmpcnyv6vpj/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/tmpe6gbb59e/f1.bed -b /tmp/tmpe6gbb59e/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/tmp6wkgqgz5/f1.bed -b /tmp/tmp6wkgqgz5/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/tmpdjb68008/f1.bed -b /tmp/tmpdjb68008/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/tmpute6sav3/f1.bed -b /tmp/tmpute6sav3/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/tmprwsyp_9t/f1.bed -b /tmp/tmprwsyp_9t/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/tmprg1ggzf5/f1.bed -b /tmp/tmprg1ggzf5/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/tmpo3dn8x5s/f1.bed -b /tmp/tmpo3dn8x5s/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/tmp5s6qgfut/f1.bed -b /tmp/tmp5s6qgfut/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/tmpjyzk47hz/f1.bed -b /tmp/tmpjyzk47hz/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/tmpe2sx4n2f/f1.bed -b /tmp/tmpe2sx4n2f/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/tmpkcjhujhe/f1.bed -b /tmp/tmpkcjhujhe/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/tmp_r_1alh6/f1.bed -b /tmp/tmp_r_1alh6/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/tmp_2bexl0v/f1.bed -b /tmp/tmp_2bexl0v/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/tmpapouhije/f1.bed -b /tmp/tmpapouhije/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/tmpx85_qa_y/f1.bed -b /tmp/tmpx85_qa_y/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/tmp_5d86cse/f1.bed -b /tmp/tmp_5d86cse/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/tmpbu7nulpa/f1.bed -b /tmp/tmpbu7nulpa/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/tmp4zujqk26/f1.bed -b /tmp/tmp4zujqk26/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/tmpxg4sridt/f1.bed -b /tmp/tmpxg4sridt/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/tmpu5bzz60h/f1.bed -b /tmp/tmpu5bzz60h/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/tmpmz1dxqaj/f1.bed -b /tmp/tmpmz1dxqaj/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/tmp9ro8f2tc/f1.bed -b /tmp/tmp9ro8f2tc/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/tmp3s2z3avx/f1.bed -b /tmp/tmp3s2z3avx/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/tmp0b3opv0n/f1.bed -b /tmp/tmp0b3opv0n/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4259423 4266396 a 0 - 1 chr1 9008517 9011028 a 0 - 2 chr1 10000000 10010000 a 0 - 3 chr1 9716977 9724100 a 0 - 4 chr4 1716545 1724554 a 0 + 5 chr7 6397107 6397350 a 0 - 6 chr8 7318694 7328694 a 0 + 7 chr15 3529003 3535423 a 0 - 8 chr17 3007259 3014315 a 0 + 9 chr20 9716977 9722864 a 0 - 10 chrX 6062387 6071513 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp6x50i9ql/f1.bed -b /tmp/tmp6x50i9ql/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 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/tmpqg1np9he/f1.bed -b /tmp/tmpqg1np9he/f2.bed Chromosome Start End Name Score Strand 0 chr1 257 258 a 0 + 1 chr1 257 258 a 0 + 2 chr1 257 258 a 0 + Chromosome Start End Name Score Strand 0 chr5 4596268 4599688 a 0 - 1 chr7 6240419 6242704 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp_7hrjqky/f1.bed -b /tmp/tmp_7hrjqky/f2.bed Chromosome Start End Name Score Strand 0 chr1 257 258 a 0 + 1 chr1 257 258 a 0 + 2 chr1 257 258 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmps60vimu9/f1.bed -b /tmp/tmps60vimu9/f2.bed Chromosome Start End Name Score Strand 0 chr1 9272794 9272795 a 0 + Chromosome Start End Name Score Strand 0 chr1 11499 19118 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp2qhtl4rc/f1.bed -b /tmp/tmp2qhtl4rc/f2.bed Chromosome Start End Name Score Strand 0 chr1 9272794 9272795 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpbucgzury/f1.bed -b /tmp/tmpbucgzury/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7504447 7514245 a 0 + 1 chr1 8899557 8907428 a 0 + 2 chr1 2086315 2087652 a 0 - 3 chr1 728218 738118 a 0 - 4 chr1 948605 957421 a 0 - 5 chr10 6649745 6649806 a 0 + 6 chr10 5579539 5584608 a 0 - 7 chr17 35329 45229 a 0 - 8 chr20 1753472 1757016 a 0 + 9 chr20 4152265 4154101 a 0 - 10 chrX 2414157 2415908 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp873bj691/f1.bed -b /tmp/tmp873bj691/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 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/tmpbtly6g6r/f1.bed -b /tmp/tmpbtly6g6r/f2.bed 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 1499053 1504645 a 0 + 1 chr11 5427884 5433349 a 0 + 2 chr11 721809 724945 a 0 - 3 chr15 1499053 1506606 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpfp10ntlo/f1.bed -b /tmp/tmpfp10ntlo/f2.bed 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_disyc3j/f1.bed -b /tmp/tmp_disyc3j/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 + Chromosome Start End Name Score Strand 0 chr1 5311356 5313440 a 0 + 1 chr1 8262326 8269102 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp_o4l9y5n/f1.bed -b /tmp/tmp_o4l9y5n/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 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp5dg3fr68/f1.bed -b /tmp/tmp5dg3fr68/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 595 a 0 + 1 chr1 1 595 a 0 + 2 chr1 1 595 a 0 - Chromosome Start End Name Score Strand 0 chr1 9989353 9995850 a 0 + 1 chr1 3468698 3474902 a 0 + 2 chr1 4817751 4819908 a 0 - 3 chr15 9999999 10006011 a 0 + 4 chr18 2907405 2909131 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpf4o7btqa/f1.bed -b /tmp/tmpf4o7btqa/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 595 a 0 + 1 chr1 1 595 a 0 + 2 chr1 1 595 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpe9d63l1d/f1.bed -b /tmp/tmpe9d63l1d/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1301798 1303251 a 0 + 1 chr1 543874 550883 a 0 + 2 chr1 5841410 5842863 a 0 - 3 chr1 522339 523792 a 0 - 4 chr1 822733 824186 a 0 - 5 chr8 6449369 6450822 a 0 + 6 chrM 3716659 3718112 a 0 - 7 chrX 9063268 9064721 a 0 + 8 chrX 2116795 2117817 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpclihppjf/f1.bed -b /tmp/tmpclihppjf/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 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/tmpac75o_4c/f1.bed -b /tmp/tmpac75o_4c/f2.bed 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 9551 a 0 + 1 chr1 8802193 8810411 a 0 + 2 chr1 7312137 7319829 a 0 + 3 chr1 7097173 7099203 a 0 - 4 chr1 8751406 8758975 a 0 - 5 chr16 2301655 2308702 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpzxgp37vk/f1.bed -b /tmp/tmpzxgp37vk/f2.bed 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/tmpjqb2nckh/f1.bed -b /tmp/tmpjqb2nckh/f2.bed 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 4212367 4219411 a 0 + 1 chr1 4635184 4642492 a 0 + 2 chr6 10000000 10004529 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpcvp1xbpu/f1.bed -b /tmp/tmpcvp1xbpu/f2.bed 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/tmpvo1c6nfd/f1.bed -b /tmp/tmpvo1c6nfd/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 564 a 0 + 1 chr1 1 564 a 0 - 2 chr1 1 564 a 0 - Chromosome Start End Name Score Strand 0 chr1 5550187 5555605 a 0 + 1 chr1 6121902 6123906 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmplge50xys/f1.bed -b /tmp/tmplge50xys/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 564 a 0 + 1 chr1 1 564 a 0 - 2 chr1 1 564 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpmq5buvk7/f1.bed -b /tmp/tmpmq5buvk7/f2.bed 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 8349343 8352343 a 0 + 1 chr1 5809579 5818307 a 0 - 2 chrM 4676111 4684276 a 0 - 3 chrX 1761629 1768001 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp6_c65v8u/f1.bed -b /tmp/tmp6_c65v8u/f2.bed 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/tmp8chgcz0q/f1.bed -b /tmp/tmp8chgcz0q/f2.bed Chromosome Start End Name Score Strand 0 chr1 65537 65539 a 0 + Chromosome Start End Name Score Strand 0 chr1 1850231 1853920 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp0i72k0hy/f1.bed -b /tmp/tmp0i72k0hy/f2.bed Chromosome Start End Name Score Strand 0 chr1 65537 65539 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp6h2mv8zr/f1.bed -b /tmp/tmp6h2mv8zr/f2.bed Chromosome Start End Name Score Strand 0 chr1 257 258 a 0 + 1 chr1 257 258 a 0 + 2 chr1 257 258 a 0 + Chromosome Start End Name Score Strand 0 chr1 6361938 6369416 a 0 - 1 chr1 802371 807722 a 0 - 2 chr1 1854241 1855501 a 0 - 3 chr1 2422733 2427963 a 0 - 4 chr8 744916 749065 a 0 - 5 chr11 2222524 2231283 a 0 - 6 chr15 1908277 1911389 a 0 - 7 chr15 2148090 2150508 a 0 - 8 chr16 2884931 2889259 a 0 - 9 chr20 8455065 8460595 a 0 - 10 chr21 2601360 2601910 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpfvr1vqqc/f1.bed -b /tmp/tmpfvr1vqqc/f2.bed Chromosome Start End Name Score Strand 0 chr1 257 258 a 0 + 1 chr1 257 258 a 0 + 2 chr1 257 258 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpytm5niqn/f1.bed -b /tmp/tmpytm5niqn/f2.bed 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 2016106 2019136 a 0 + 1 chr1 8426731 8426778 a 0 + 2 chr1 5407658 5412116 a 0 + 3 chr1 8956809 8956856 a 0 - 4 chr1 6467404 6472659 a 0 - 5 chr4 4872674 4875946 a 0 + 6 chr8 2 9853 a 0 + 7 chr10 2835550 2844644 a 0 - 8 chr19 726111 726158 a 0 + 9 chr22 1029640 1029687 a 0 + 10 chrY 8568581 8568628 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpbg53rixa/f1.bed -b /tmp/tmpbg53rixa/f2.bed 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/tmpo9p1oy24/f1.bed -b /tmp/tmpo9p1oy24/f2.bed 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 636816 644103 a 0 + 1 chr1 7842644 7843175 a 0 - 2 chr7 8759449 8759905 a 0 - 3 chr10 7914019 7923449 a 0 + 4 chr13 581652 582650 a 0 - 5 chr20 7914019 7921472 a 0 + 6 chr20 8538260 8545294 a 0 - 7 chr20 7914019 7923960 a 0 - 8 chr22 1964578 1964580 a 0 - 9 chrM 8630497 8631505 a 0 + 10 chrM 7914019 7915837 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmphkcqeghp/f1.bed -b /tmp/tmphkcqeghp/f2.bed 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/tmppuwc1g_y/f1.bed -b /tmp/tmppuwc1g_y/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8532918 8542918 a 0 - 1 chr8 8252686 8260221 a 0 + 2 chr20 6218832 6228832 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpvi4b908u/f1.bed -b /tmp/tmpvi4b908u/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 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/tmp9gke6b53/f1.bed -b /tmp/tmp9gke6b53/f2.bed Chromosome Start End Name Score Strand 0 chr3 4292098 4292099 a 0 - Chromosome Start End Name Score Strand 0 chr1 6713432 6722688 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpw4vbypay/f1.bed -b /tmp/tmpw4vbypay/f2.bed Chromosome Start End Name Score Strand 0 chr3 4292098 4292099 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpfo4qwnib/f1.bed -b /tmp/tmpfo4qwnib/f2.bed Chromosome Start End Name Score Strand 0 chr22 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2 4852 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpyatjxuib/f1.bed -b /tmp/tmpyatjxuib/f2.bed Chromosome Start End Name Score Strand 0 chr22 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/tmp3ot4bizq/f1.bed -b /tmp/tmp3ot4bizq/f2.bed 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 10000000 10007040 a 0 + 1 chr1 9878548 9885043 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpjtax31vu/f1.bed -b /tmp/tmpjtax31vu/f2.bed 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/tmpa8wund7c/f1.bed -b /tmp/tmpa8wund7c/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3933287 3934665 a 0 + 1 chr1 8873108 8874791 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp5wc_bkr0/f1.bed -b /tmp/tmp5wc_bkr0/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 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/tmpl7bobzto/f1.bed -b /tmp/tmpl7bobzto/f2.bed 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 5853131 5859950 a 0 + 1 chr1 1904097 1911974 a 0 - 2 chr15 1888282 1892974 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmprh9vz1wn/f1.bed -b /tmp/tmprh9vz1wn/f2.bed 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/tmp0954pi9z/f1.bed -b /tmp/tmp0954pi9z/f2.bed 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 chr12 6258595 6260924 a 0 - 1 chrX 4805857 4814287 a 0 - 2 chrY 9824606 9827690 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpghgyniwj/f1.bed -b /tmp/tmpghgyniwj/f2.bed 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/tmpbsweuyyw/f1.bed -b /tmp/tmpbsweuyyw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 200 a 0 + 1 chr1 1 200 a 0 - 2 chr1 1 200 a 0 - 3 chr1 1 200 a 0 - Chromosome Start End Name Score Strand 0 chr1 7930728 7936973 a 0 + 1 chr1 7918287 7923549 a 0 + 2 chr1 8802644 8807514 a 0 - 3 chr1 8802644 8807305 a 0 - 4 chr1 2324528 2332564 a 0 - 5 chr3 2617171 2621009 a 0 - 6 chr4 8912412 8918325 a 0 - 7 chr11 5358215 5360186 a 0 - 8 chr12 8802644 8811526 a 0 - 9 chr18 4614265 4619196 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp4eutf79l/f1.bed -b /tmp/tmp4eutf79l/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 200 a 0 + 1 chr1 1 200 a 0 - 2 chr1 1 200 a 0 - 3 chr1 1 200 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp5oplinxa/f1.bed -b /tmp/tmp5oplinxa/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 7987 a 0 + 1 chr1 1 7987 a 0 + 2 chr1 1 7987 a 0 - Chromosome Start End Name Score Strand 0 chr1 753311 757582 a 0 - 1 chr20 4700883 4701051 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp0nmh19yz/f1.bed -b /tmp/tmp0nmh19yz/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 7987 a 0 + 1 chr1 1 7987 a 0 + 2 chr1 1 7987 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpjn6hmd_6/f1.bed -b /tmp/tmpjn6hmd_6/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1871138 1877530 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpc_fv0xyd/f1.bed -b /tmp/tmpc_fv0xyd/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 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/tmpbfjeme34/f1.bed -b /tmp/tmpbfjeme34/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 + Chromosome Start End Name Score Strand 0 chr1 4672968 4679647 a 0 + 1 chr18 5619264 5629028 a 0 + 2 chrM 2060956 2065845 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpsxwpxddw/f1.bed -b /tmp/tmpsxwpxddw/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/tmp9nng9x2o/f1.bed -b /tmp/tmp9nng9x2o/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_chain50-method_chain50] ___________ [gw2] linux -- Python 3.12.3 /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/python3.12/typing.py:1195 E (and 122 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('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') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('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') 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') ---------------------------------- 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] __________________ [gw1] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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 | 917506 | 917764 | a | 0 | - | | | chr1 | 917506 | 917764 | 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 | 327942 | 332248 | a | 0 | + | | | chr1 | 66562 | 66619 | a | 0 | + | | | chr1 | 786444 | 790750 | a | 0 | + | | | chr1 | 11780 | 16086 | a | 0 | + | | | chr1 | 11780 | 13081 | a | 0 | + | | | chr1 | 11780 | 16086 | a | 0 | + | | | chr1 | 11780 | 16086 | a | 0 | + | | | chr20 | 11780 | 16086 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 8 rows and 6 columns from 2 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('6.100.4', b'AAEgHceTBRuzqmxp7TIAAAEAAQ4AAQABAQEAAQEABwEBBwYAAQABAgAAAAIDTQcBBwMmxQFMYkj6AxvQEReXH1MFVmApMgJ2fRVZAC8AABMbBgEAAQUBKQUBBQcDAQwACwYCAQEEAQA+AC4DCAUdBRQEAgEAOAB3MgIQ0QAA') 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('6.100.4', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') 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/tmpz52j48_m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz52j48_m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpep6dq_ta/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpep6dq_ta/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw9xz8lfn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw9xz8lfn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsfqpiwsd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsfqpiwsd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1w3uyvjm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1w3uyvjm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo18mop7j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo18mop7j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1bdhwjwg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1bdhwjwg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnco621e4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnco621e4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmppo6ca5vm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppo6ca5vm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1e2wv6ov/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1e2wv6ov/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyxwp6c_n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyxwp6c_n/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzad3wnhi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzad3wnhi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp96oyt5su/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp96oyt5su/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2s0i_m2r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2s0i_m2r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaw5m4sgq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaw5m4sgq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbco6q6ki/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbco6q6ki/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr497gksw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr497gksw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwpy1uy02/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwpy1uy02/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjnu8os59/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjnu8os59/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk43slqhf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk43slqhf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmphcgqsqld/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphcgqsqld/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4m9mi6ho/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4m9mi6ho/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxj2ogt72/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxj2ogt72/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcj00kp7a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcj00kp7a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6w8vyt7o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6w8vyt7o/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv7zmmi2p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv7zmmi2p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz2p1lpkz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz2p1lpkz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9px81wxy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9px81wxy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmplntsm_j2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplntsm_j2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr9vbkcy9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr9vbkcy9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8g46t87t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8g46t87t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpams2eeb1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpams2eeb1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyzfjmm7e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyzfjmm7e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvt2yd7_a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvt2yd7_a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7nbco8tp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7nbco8tp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi_g64ult/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi_g64ult/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzyau0f_q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzyau0f_q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3ezw7t6g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3ezw7t6g/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0iie0ado/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0iie0ado/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy10bzwfn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy10bzwfn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwdhcm15l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwdhcm15l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcedzvze9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcedzvze9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1f6zpd26/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1f6zpd26/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw9sfi0hc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw9sfi0hc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp85u86ox7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp85u86ox7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpvq6wbmhb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvq6wbmhb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp762g4zki/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp762g4zki/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbwb0rfx_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbwb0rfx_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwu8ufg6q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwu8ufg6q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp_e34e9e8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_e34e9e8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1p_7tgpm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1p_7tgpm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp44tza9c3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp44tza9c3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp028u6rjx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp028u6rjx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmptnmttccp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptnmttccp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbif1vxxc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbif1vxxc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpac1suaid/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpac1suaid/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjsipu3du/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjsipu3du/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoaid1rbk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoaid1rbk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_oieg9eg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_oieg9eg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq3a782ro/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq3a782ro/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmptp0jhn5y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptp0jhn5y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp16phn98/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp16phn98/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuuuhzdvs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuuuhzdvs/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp_ag45qzx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_ag45qzx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpalr9xrpn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpalr9xrpn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp38gih3q3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp38gih3q3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjibfm2bs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjibfm2bs/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe_pbj6iw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe_pbj6iw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp5p_ec95o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5p_ec95o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmphsbocyvw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphsbocyvw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpaj3qsdjm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaj3qsdjm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwq27pnjv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwq27pnjv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw5__qwa4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw5__qwa4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpemm_fu_h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpemm_fu_h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4ncjtfyn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ncjtfyn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6ic9qq2b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6ic9qq2b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoj6ar8ch/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoj6ar8ch/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpheo8xlg6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpheo8xlg6/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 chr19 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 chr3 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 chr3 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. 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_chain19-method_chain19] ___________ [gw3] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 3134 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | 462141 | 462203 | a | 0 | + | E | chr13 | 462141 | 463166 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 2 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('6.100.4', b'AXicY2BgYGBkYGBmOQWiQJiRgYkBBHhsGBgZ/RgLrzCGCirKAtkMPCBpdl4bkEJbRkZbFpAyAIgBBDs=') 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') 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') 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') 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') 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') 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') ('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') ('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') ('overlap', 'subtract') Empty PyRanges ('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') 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') ('overlap', 'subtract') ('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') ('overlap', 'subtract') ('overlap', '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_chain51-method_chain51] ___________ [gw2] linux -- Python 3.12.3 /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 182 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('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') 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') 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') 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') _____________________________ test_coverage[same] ______________________________ [gw0] linux -- Python 3.12.3 /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., 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('6.100.4', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') 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/tmp1ew2y1zm/f1.bed -b /tmp/tmp1ew2y1zm/f2.bed Chromosome Start End Name Score Strand 0 chr1 7919621 7919645 a 0 + 1 chr1 3715481 3725188 a 0 + 2 chr1 7926263 7931707 a 0 + 3 chr1 7018769 7024583 a 0 + 4 chr1 4090866 4097048 a 0 - 5 chr1 3057139 3059919 a 0 - 6 chr1 9511043 9518436 a 0 - 7 chr9 9158571 9160064 a 0 - 8 chr16 9457993 9463636 a 0 - 9 chr18 2767770 2773433 a 0 - 10 chrY 4018394 4026808 a 0 + Chromosome Start End Name Score Strand 0 chr1 6609865 6612623 a 0 + 1 chr1 3351682 3354340 a 0 + 2 chr1 6187087 6188928 a 0 - 3 chr1 8619718 8628347 a 0 - 4 chr1 8358995 8368312 a 0 - 5 chr8 9991743 10001641 a 0 + 6 chr12 2261536 2269150 a 0 + 7 chr13 1 5474 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpea_tok64/f1.bed -b /tmp/tmpea_tok64/f2.bed Chromosome Start End Name Score Strand 0 chr1 7919621 7919645 a 0 + 1 chr1 3715481 3725188 a 0 + 2 chr1 7926263 7931707 a 0 + 3 chr1 7018769 7024583 a 0 + 4 chr1 4090866 4097048 a 0 - 5 chr1 3057139 3059919 a 0 - 6 chr1 9511043 9518436 a 0 - 7 chr9 9158571 9160064 a 0 - 8 chr16 9457993 9463636 a 0 - 9 chr18 2767770 2773433 a 0 - 10 chrY 4018394 4026808 a 0 + Chromosome Start End Name Score Strand 0 chr1 7919621 7919645 a 0 + 1 chr1 3715481 3725188 a 0 + 2 chr1 7926263 7931707 a 0 + 3 chr1 7018769 7024583 a 0 + 4 chr1 4090866 4097048 a 0 - 5 chr1 3057139 3059919 a 0 - 6 chr1 9511043 9518436 a 0 - 7 chr9 9158571 9160064 a 0 - 8 chr16 9457993 9463636 a 0 - 9 chr18 2767770 2773433 a 0 - 10 chrY 4018394 4026808 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpv_mnqa8_/f1.bed -b /tmp/tmpv_mnqa8_/f2.bed Chromosome Start End Name Score Strand 0 chr1 7018769 7024583 a 0 + 1 chr1 7919621 7919645 a 0 - 2 chr1 4090866 4097048 a 0 - 3 chr1 3715481 3725188 a 0 - 4 chr1 7926263 7931707 a 0 - 5 chr1 3057139 3059919 a 0 - 6 chr1 9511043 9518436 a 0 - 7 chr9 9158571 9160064 a 0 - 8 chr16 9457993 9463636 a 0 + 9 chr18 2767770 2773433 a 0 + 10 chrY 4018394 4026808 a 0 + Chromosome Start End Name Score Strand 0 chr1 9961474 9962357 a 0 - 1 chr1 262411 263294 a 0 - 2 chr1 9511043 9511926 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpdhgk79ci/f1.bed -b /tmp/tmpdhgk79ci/f2.bed Chromosome Start End Name Score Strand 0 chr1 3057139 3059919 a 0 + 1 chr1 7018769 7024583 a 0 + 2 chr1 7919621 7919645 a 0 - 3 chr1 4090866 4097048 a 0 - 4 chr1 227831 237538 a 0 - 5 chr1 7926263 7931707 a 0 - 6 chr1 9992 17385 a 0 - 7 chr9 9158571 9160064 a 0 - 8 chr16 5326902 5333047 a 0 + 9 chr18 2767770 2773433 a 0 + 10 chrY 4018394 4020716 a 0 + Chromosome Start End Name Score Strand 0 chr1 9961474 9962357 a 0 - 1 chr1 262411 263294 a 0 - 2 chr1 9511043 9511926 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpdbmkw39u/f1.bed -b /tmp/tmpdbmkw39u/f2.bed Chromosome Start End Name Score Strand 0 chr1 3057139 3059919 a 0 + 1 chr1 7018769 7024583 a 0 + 2 chr1 7919621 7919645 a 0 - 3 chr1 4090866 4097048 a 0 - 4 chr1 227831 237538 a 0 - 5 chr1 7926263 7931707 a 0 - 6 chr1 9992 17385 a 0 - 7 chr9 9158571 9160064 a 0 - 8 chr16 5326902 5333047 a 0 + 9 chr18 2767770 2773433 a 0 + 10 chrY 4018394 4020716 a 0 + Chromosome Start End Name Score Strand 0 chr1 196868 201221 a 0 - 1 chr1 1442563 1442595 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp4hit34or/f1.bed -b /tmp/tmp4hit34or/f2.bed Chromosome Start End Name Score Strand 0 chr1 7919621 7919645 a 0 + 1 chr1 4090866 4097048 a 0 + 2 chr1 227831 237538 a 0 + 3 chr1 7926263 7931707 a 0 + 4 chr1 3057139 3059919 a 0 + 5 chr1 7018769 7024583 a 0 + 6 chr1 9992 17385 a 0 + 7 chr9 9158571 9160064 a 0 - 8 chr16 5326902 5333047 a 0 + 9 chr18 2767770 2773433 a 0 + 10 chrY 4018394 4020716 a 0 + Chromosome Start End Name Score Strand 0 chr1 1639682 1643533 a 0 - 1 chr2 1639690 1639750 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp2flue9dh/f1.bed -b /tmp/tmp2flue9dh/f2.bed Chromosome Start End Name Score Strand 0 chr1 7919621 7919645 a 0 + 1 chr1 4090866 4097048 a 0 + 2 chr1 227831 237538 a 0 + 3 chr1 7926263 7931707 a 0 + 4 chr1 3057139 3059919 a 0 + 5 chr1 7018769 7024583 a 0 + 6 chr1 9992 17385 a 0 + 7 chr9 9158571 9160064 a 0 - 8 chr16 5326902 5333047 a 0 + 9 chr18 2767770 2773433 a 0 + 10 chrY 4018394 4020716 a 0 + Chromosome Start End Name Score Strand 0 chr1 1639682 1643533 a 0 - 1 chr2 1639690 1639750 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpn_1gqhya/f1.bed -b /tmp/tmpn_1gqhya/f2.bed Chromosome Start End Name Score Strand 0 chr1 6245765 6246914 a 0 + 1 chr1 1977223 1977224 a 0 + 2 chr1 7043796 7049124 a 0 - 3 chr1 9030086 9034767 a 0 - 4 chr9 3352471 3355224 a 0 + 5 chr21 3094788 3101306 a 0 + 6 chrM 1491257 1492953 a 0 + Chromosome Start End Name Score Strand 0 chr1 5738835 5748835 a 0 + 1 chr1 1174974 1177307 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp9ee3k4d6/f1.bed -b /tmp/tmp9ee3k4d6/f2.bed Chromosome Start End Name Score Strand 0 chr1 6245765 6246914 a 0 + 1 chr1 1977223 1977224 a 0 + 2 chr1 7043796 7049124 a 0 - 3 chr1 9030086 9034767 a 0 - 4 chr9 3352471 3355224 a 0 + 5 chr21 3094788 3101306 a 0 + 6 chrM 1491257 1495938 a 0 + Chromosome Start End Name Score Strand 0 chr1 5738835 5748835 a 0 + 1 chr1 1174974 1177307 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp3omfc6i5/f1.bed -b /tmp/tmp3omfc6i5/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/tmp0n56w3c4/f1.bed -b /tmp/tmp0n56w3c4/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/tmpbymrilu8/f1.bed -b /tmp/tmpbymrilu8/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/tmpavfr4g11/f1.bed -b /tmp/tmpavfr4g11/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/tmpd45mqx2k/f1.bed -b /tmp/tmpd45mqx2k/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/tmpxbh7ck_5/f1.bed -b /tmp/tmpxbh7ck_5/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/tmp7_r8wgib/f1.bed -b /tmp/tmp7_r8wgib/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/tmp7epmx6jb/f1.bed -b /tmp/tmp7epmx6jb/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/tmphbmf4llu/f1.bed -b /tmp/tmphbmf4llu/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/tmp1rbk7pw5/f1.bed -b /tmp/tmp1rbk7pw5/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/tmps9gam6b7/f1.bed -b /tmp/tmps9gam6b7/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/tmpq8h_28m1/f1.bed -b /tmp/tmpq8h_28m1/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/tmpyrj1odlf/f1.bed -b /tmp/tmpyrj1odlf/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/tmpqs1rhe7_/f1.bed -b /tmp/tmpqs1rhe7_/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/tmpjvfrz8dh/f1.bed -b /tmp/tmpjvfrz8dh/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/tmp6olg2bh6/f1.bed -b /tmp/tmp6olg2bh6/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/tmpq6xoruxo/f1.bed -b /tmp/tmpq6xoruxo/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/tmple89nrap/f1.bed -b /tmp/tmple89nrap/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/tmpiktnit79/f1.bed -b /tmp/tmpiktnit79/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/tmp25ti3b_c/f1.bed -b /tmp/tmp25ti3b_c/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/tmp_sj94eb6/f1.bed -b /tmp/tmp_sj94eb6/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/tmpotj0alrc/f1.bed -b /tmp/tmpotj0alrc/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/tmpr5tsg7a1/f1.bed -b /tmp/tmpr5tsg7a1/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/tmpr1g_41eq/f1.bed -b /tmp/tmpr1g_41eq/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/tmp7_pwrf_t/f1.bed -b /tmp/tmp7_pwrf_t/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/tmputcxktm3/f1.bed -b /tmp/tmputcxktm3/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/tmpf3bmh5wp/f1.bed -b /tmp/tmpf3bmh5wp/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/tmp83vdhb27/f1.bed -b /tmp/tmp83vdhb27/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 1697369 1700119 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpe4ozuvtl/f1.bed -b /tmp/tmpe4ozuvtl/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/tmp08lhaqbx/f1.bed -b /tmp/tmp08lhaqbx/f2.bed Chromosome Start End Name Score Strand 0 chr1 65537 65538 a 0 + 1 chr1 65537 65538 a 0 + Chromosome Start End Name Score Strand 0 chr1 8465411 8470950 a 0 + 1 chr1 1441807 1442712 a 0 + 2 chr1 8465411 8471714 a 0 + 3 chr1 8465411 8470894 a 0 + 4 chr1 8465411 8465412 a 0 + 5 chr1 8465411 8465794 a 0 - 6 chr1 3430591 3440591 a 0 - 7 chr17 10511 16892 a 0 - 8 chr18 4196824 4199674 a 0 + 9 chr18 9815376 9820071 a 0 - 10 chr20 8465411 8471905 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp58099grh/f1.bed -b /tmp/tmp58099grh/f2.bed Chromosome Start End Name Score Strand 0 chr1 65537 65538 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 -s -a /tmp/tmpjl966htg/f1.bed -b /tmp/tmpjl966htg/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 907168 911681 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpw76m_npb/f1.bed -b /tmp/tmpw76m_npb/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 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/tmpfncj7qdh/f1.bed -b /tmp/tmpfncj7qdh/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 + Chromosome Start End Name Score Strand 0 chr1 2564606 2570599 a 0 + 1 chr1 9441137 9441618 a 0 + 2 chr1 4176790 4182141 a 0 + 3 chr1 6335011 6340362 a 0 + 4 chr1 5444565 5449916 a 0 + 5 chr1 7371869 7377220 a 0 + 6 chr1 9999999 10009910 a 0 - 7 chr4 1579541 1586479 a 0 - 8 chr6 687859 691826 a 0 + 9 chr6 1905817 1915327 a 0 + 10 chr7 90541 97825 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp9q_3hcfl/f1.bed -b /tmp/tmp9q_3hcfl/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 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpd3g354e6/f1.bed -b /tmp/tmpd3g354e6/f2.bed 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 6693657 6697926 a 0 + 1 chr1 2916237 2917437 a 0 + 2 chr1 958135 962404 a 0 - 3 chr1 418892 423161 a 0 - 4 chr5 4928881 4933150 a 0 - 5 chr6 8017978 8025547 a 0 + 6 chr6 4154128 4160678 a 0 - 7 chr13 8981881 8986150 a 0 + 8 chr18 8940150 8941664 a 0 + 9 chr19 9408120 9412389 a 0 + 10 chr21 5458189 5468189 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpqe22ajvo/f1.bed -b /tmp/tmpqe22ajvo/f2.bed 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/tmpsunybfg1/f1.bed -b /tmp/tmpsunybfg1/f2.bed 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 10000000 10009512 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpedsvmu7z/f1.bed -b /tmp/tmpedsvmu7z/f2.bed 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/tmp0ickwpoe/f1.bed -b /tmp/tmp0ickwpoe/f2.bed 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 6998325 6998652 a 0 + 1 chr1 6244690 6249037 a 0 + 2 chr1 5682080 5686077 a 0 + 3 chr1 6483192 6489788 a 0 + 4 chr1 5761700 5766050 a 0 + 5 chr1 596883 600279 a 0 + 6 chr1 8601330 8603581 a 0 + 7 chr1 806796 810840 a 0 + 8 chr1 5461914 5465524 a 0 - 9 chr1 2797727 2801724 a 0 - 10 chr5 8460297 8469090 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpebs3i8nv/f1.bed -b /tmp/tmpebs3i8nv/f2.bed 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/tmptmpr0rdn/f1.bed -b /tmp/tmptmpr0rdn/f2.bed 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 9016325 9024333 a 0 + 1 chr11 1192386 1193525 a 0 + 2 chr13 3486394 3494388 a 0 + 3 chr21 1380768 1384719 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpfugaor8l/f1.bed -b /tmp/tmpfugaor8l/f2.bed 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/tmpr3mtyrt3/f1.bed -b /tmp/tmpr3mtyrt3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 10001 a 0 + 1 chr1 1 10001 a 0 + 2 chr1 1 10001 a 0 + Chromosome Start End Name Score Strand 0 chr1 8132440 8132441 a 0 - 1 chr1 2876854 2886854 a 0 - 2 chr3 1171873 1173034 a 0 + 3 chr4 4313099 4313268 a 0 + 4 chr5 7556342 7563501 a 0 + 5 chr6 4129426 4129902 a 0 - 6 chr8 3717686 3726889 a 0 + 7 chr11 3560515 3565423 a 0 + 8 chr14 2196263 2204134 a 0 + 9 chr18 7468679 7473869 a 0 + 10 chrX 768356 776454 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpsss13jfn/f1.bed -b /tmp/tmpsss13jfn/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 10001 a 0 + 1 chr1 1 10001 a 0 + 2 chr1 1 10001 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp1u989w7n/f1.bed -b /tmp/tmp1u989w7n/f2.bed 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 chr7 4758258 4759878 a 0 - 1 chr7 1196945 1200269 a 0 - 2 chr15 10000000 10002389 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp2iiq6am0/f1.bed -b /tmp/tmp2iiq6am0/f2.bed 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/tmppg8gh3o4/f1.bed -b /tmp/tmppg8gh3o4/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 + Chromosome Start End Name Score Strand 0 chr1 1904008 1904908 a 0 + 1 chr1 9359935 9363138 a 0 + 2 chr1 1735106 1738704 a 0 + 3 chr1 6195924 6203257 a 0 + 4 chr7 1721938 1731070 a 0 - 5 chr8 632885 638201 a 0 - 6 chr13 1428376 1437880 a 0 - 7 chr14 8466540 8466835 a 0 + 8 chr17 1363294 1365399 a 0 - 9 chr18 9899727 9905043 a 0 - 10 chr22 6014509 6019825 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpjxj8pb4r/f1.bed -b /tmp/tmpjxj8pb4r/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 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp0refyoj1/f1.bed -b /tmp/tmp0refyoj1/f2.bed Chromosome Start End Name Score Strand 0 chr15 1 2 a 0 + 1 chr17 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2198625 2203521 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpywgz7jx9/f1.bed -b /tmp/tmpywgz7jx9/f2.bed Chromosome Start End Name Score Strand 0 chr15 1 2 a 0 + 1 chr17 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/tmp1pry5kpn/f1.bed -b /tmp/tmp1pry5kpn/f2.bed Chromosome Start End Name Score Strand 0 chr1 8718625 8718626 a 0 + Chromosome Start End Name Score Strand 0 chr1 46 6503 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpw_6wv_18/f1.bed -b /tmp/tmpw_6wv_18/f2.bed Chromosome Start End Name Score Strand 0 chr1 8718625 8718626 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_g068ue_/f1.bed -b /tmp/tmp_g068ue_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1997228 1998221 a 0 + 1 chr1 8780107 8784269 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpgy_g7ln0/f1.bed -b /tmp/tmpgy_g7ln0/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/tmpf3ed_biu/f1.bed -b /tmp/tmpf3ed_biu/f2.bed 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 9760254 9765866 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp2xwe_196/f1.bed -b /tmp/tmp2xwe_196/f2.bed 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/tmp_74okcrj/f1.bed -b /tmp/tmp_74okcrj/f2.bed Chromosome Start End Name Score Strand 0 chr5 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr8 9088061 9088801 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpuym_nogn/f1.bed -b /tmp/tmpuym_nogn/f2.bed Chromosome Start End Name Score Strand 0 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/tmpc9tsdva5/f1.bed -b /tmp/tmpc9tsdva5/f2.bed Chromosome Start End Name Score Strand 0 chr1 6477271 6477272 a 0 + Chromosome Start End Name Score Strand 0 chr1 125 10125 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpv9djkwo4/f1.bed -b /tmp/tmpv9djkwo4/f2.bed Chromosome Start End Name Score Strand 0 chr1 6477271 6477272 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpltojvzkf/f1.bed -b /tmp/tmpltojvzkf/f2.bed 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 4190282 4197966 a 0 + 1 chr1 8750831 8760252 a 0 + 2 chr1 903917 911287 a 0 + 3 chr1 4580426 4588452 a 0 + 4 chr1 321886 324581 a 0 + 5 chr1 4016743 4022376 a 0 - 6 chr1 8722116 8728809 a 0 - 7 chr6 7081181 7089594 a 0 + 8 chr9 7498581 7506124 a 0 + 9 chr22 800933 807739 a 0 - 10 chrY 6828137 6837950 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp18i7j1t8/f1.bed -b /tmp/tmp18i7j1t8/f2.bed 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/tmp0t041w7s/f1.bed -b /tmp/tmp0t041w7s/f2.bed 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 7417499 7419758 a 0 + 1 chr1 5034594 5037174 a 0 - 2 chr3 3749905 3757615 a 0 - 3 chr12 630950 640060 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpthzplpsb/f1.bed -b /tmp/tmpthzplpsb/f2.bed 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/tmpotvrgvnt/f1.bed -b /tmp/tmpotvrgvnt/f2.bed 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 1443218 1448533 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpnihrujel/f1.bed -b /tmp/tmpnihrujel/f2.bed 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/tmpeof6e01i/f1.bed -b /tmp/tmpeof6e01i/f2.bed 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 5298702 5308403 a 0 + 1 chr1 8956639 8957870 a 0 + 2 chr3 5183442 5189640 a 0 - 3 chrY 7756785 7766785 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpg6w6h8z2/f1.bed -b /tmp/tmpg6w6h8z2/f2.bed 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/tmprbccckwv/f1.bed -b /tmp/tmprbccckwv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 5221 a 0 + 1 chr1 1 5221 a 0 + 2 chr1 1 5221 a 0 + Chromosome Start End Name Score Strand 0 chr1 4802381 4809677 a 0 + 1 chr1 9244918 9254712 a 0 + 2 chr1 1762788 1770100 a 0 - 3 chr1 2124898 2129261 a 0 - 4 chr10 5088574 5093419 a 0 + 5 chr21 2664503 2664588 a 0 + 6 chr21 2514798 2520885 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp9r4c4nia/f1.bed -b /tmp/tmp9r4c4nia/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 5221 a 0 + 1 chr1 1 5221 a 0 + 2 chr1 1 5221 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpbq5gngk1/f1.bed -b /tmp/tmpbq5gngk1/f2.bed Chromosome Start End Name Score Strand 0 chr1 257 258 a 0 + 1 chr1 257 258 a 0 + Chromosome Start End Name Score Strand 0 chr1 3189831 3191902 a 0 + 1 chr1 4197048 4200050 a 0 + 2 chr1 9356404 9361429 a 0 + 3 chr1 4498426 4507243 a 0 + 4 chr14 4567157 4575653 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpfenebp1h/f1.bed -b /tmp/tmpfenebp1h/f2.bed Chromosome Start End Name Score Strand 0 chr1 257 258 a 0 + 1 chr1 257 258 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp3kr670jj/f1.bed -b /tmp/tmp3kr670jj/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 7674756 7679174 a 0 + 1 chr11 1727780 1732198 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpyw9gfl36/f1.bed -b /tmp/tmpyw9gfl36/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/tmpzw0zxe19/f1.bed -b /tmp/tmpzw0zxe19/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 8206 a 0 + 1 chr1 1 8206 a 0 + 2 chr1 1 8206 a 0 - Chromosome Start End Name Score Strand 0 chr1 5334863 5343839 a 0 - 1 chr8 9144289 9147648 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpp2v85u6b/f1.bed -b /tmp/tmpp2v85u6b/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 8206 a 0 + 1 chr1 1 8206 a 0 + 2 chr1 1 8206 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpk6zjbuqp/f1.bed -b /tmp/tmpk6zjbuqp/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5447048 5453366 a 0 + 1 chr1 6264073 6270177 a 0 - 2 chr1 3648782 3649238 a 0 - 3 chr1 4120533 4123877 a 0 - 4 chr1 6467156 6476628 a 0 - 5 chr3 8603458 8604295 a 0 - 6 chr10 99192 106405 a 0 - 7 chr13 8145534 8150295 a 0 - 8 chr15 4367367 4373465 a 0 + 9 chrM 4355762 4361885 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpkq6v_os7/f1.bed -b /tmp/tmpkq6v_os7/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 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/tmpai6257fc/f1.bed -b /tmp/tmpai6257fc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 5703 a 0 + 1 chr1 1 5703 a 0 - 2 chr1 1 5703 a 0 - Chromosome Start End Name Score Strand 0 chr1 7876193 7885996 a 0 + 1 chr1 9750857 9755849 a 0 + 2 chr1 4603204 4612726 a 0 + 3 chr1 8907709 8912668 a 0 + 4 chr1 9897425 9900482 a 0 + 5 chr1 7626505 7628681 a 0 - 6 chr6 8472948 8482470 a 0 - 7 chr8 9219111 9228677 a 0 - 8 chr9 371892 375632 a 0 + 9 chr14 1052280 1055632 a 0 + 10 chr18 9028801 9033499 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp984pgs_t/f1.bed -b /tmp/tmp984pgs_t/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 5703 a 0 + 1 chr1 1 5703 a 0 - 2 chr1 1 5703 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmprha99zrm/f1.bed -b /tmp/tmprha99zrm/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1477294 1483941 a 0 + 1 chr1 6205454 6215285 a 0 - 2 chr1 9729275 9729541 a 0 - 3 chrM 8548772 8557840 a 0 - 4 chrY 1709569 1715512 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp3t2o1oh_/f1.bed -b /tmp/tmp3t2o1oh_/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 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/tmp4w9jbewy/f1.bed -b /tmp/tmp4w9jbewy/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 + Chromosome Start End Name Score Strand 0 chr1 679254 682806 a 0 + 1 chr1 679254 686687 a 0 + 2 chr1 679254 682806 a 0 + 3 chr1 679254 682806 a 0 - 4 chr7 679254 685405 a 0 - 5 chr21 679254 686362 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpwpq5dj5b/f1.bed -b /tmp/tmpwpq5dj5b/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 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp7wuxe9lp/f1.bed -b /tmp/tmp7wuxe9lp/f2.bed 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 3527594 3531074 a 0 - 1 chr18 5264716 5270014 a 0 + 2 chr18 6363459 6368798 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp1wm7y0_z/f1.bed -b /tmp/tmp1wm7y0_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 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp_4rv61r7/f1.bed -b /tmp/tmp_4rv61r7/f2.bed Chromosome Start End Name Score Strand 0 chr18 4702210 4702211 a 0 - Chromosome Start End Name Score Strand 0 chr1 3805331 3810019 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpsy8_1xz_/f1.bed -b /tmp/tmpsy8_1xz_/f2.bed Chromosome Start End Name Score Strand 0 chr18 4702210 4702211 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpy5p5cpm7/f1.bed -b /tmp/tmpy5p5cpm7/f2.bed 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 7350552 7357472 a 0 + 1 chr1 420443 427363 a 0 + 2 chr1 4447188 4454108 a 0 - 3 chr1 4609150 4616070 a 0 - 4 chr1 321765 328685 a 0 - 5 chr5 8277318 8284238 a 0 - 6 chr14 984531 991451 a 0 - 7 chr14 5336452 5343372 a 0 - 8 chr15 7379924 7386844 a 0 - 9 chr16 6141126 6148046 a 0 + 10 chr22 8461487 8468407 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp1quh21h4/f1.bed -b /tmp/tmp1quh21h4/f2.bed 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/tmpnpye3suw/f1.bed -b /tmp/tmpnpye3suw/f2.bed 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 7369373 7374502 a 0 + 1 chr1 9534089 9542351 a 0 - 2 chr1 9395682 9405382 a 0 - 3 chr1 7556107 7566107 a 0 - 4 chr1 154008 155243 a 0 - 5 chr1 4175783 4183961 a 0 - 6 chr2 9999999 10006503 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpg1h8yrpa/f1.bed -b /tmp/tmpg1h8yrpa/f2.bed 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/tmp7ns09p2p/f1.bed -b /tmp/tmp7ns09p2p/f2.bed Chromosome Start End Name Score Strand 0 chr1 257 258 a 0 + 1 chr1 257 258 a 0 + 2 chr2 257 258 a 0 + Chromosome Start End Name Score Strand 0 chr1 7211520 7217325 a 0 + 1 chr1 8596349 8602984 a 0 + 2 chr1 9302795 9305828 a 0 - 3 chr1 1 1548 a 0 - 4 chr15 8042184 8046676 a 0 - 5 chr16 1 879 a 0 - 6 chr22 3734705 3743437 a 0 + 7 chrX 1 9162 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp52djz3hq/f1.bed -b /tmp/tmp52djz3hq/f2.bed Chromosome Start End Name Score Strand 0 chr1 257 258 a 0 + 1 chr1 257 258 a 0 + 2 chr2 257 258 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp078i077d/f1.bed -b /tmp/tmp078i077d/f2.bed Chromosome Start End Name Score Strand 0 chr1 257 258 a 0 + 1 chr1 257 258 a 0 + Chromosome Start End Name Score Strand 0 chr1 8884890 8887889 a 0 + 1 chr1 4791041 4796976 a 0 - 2 chr22 6540874 6549564 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp0w0jco_8/f1.bed -b /tmp/tmp0w0jco_8/f2.bed Chromosome Start End Name Score Strand 0 chr1 257 258 a 0 + 1 chr1 257 258 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpvxw1sci0/f1.bed -b /tmp/tmpvxw1sci0/f2.bed 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 9825992 9833726 a 0 - 1 chr1 8384652 8390350 a 0 - 2 chr2 106937 110436 a 0 + 3 chr15 3600505 3606203 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpqczw1bas/f1.bed -b /tmp/tmpqczw1bas/f2.bed 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/tmpteyra3q7/f1.bed -b /tmp/tmpteyra3q7/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1829418 1830495 a 0 + 1 chr1 1352135 1356903 a 0 + 2 chr1 9900893 9909284 a 0 + 3 chr1 4392446 4396725 a 0 - 4 chr1 5613412 5618729 a 0 - 5 chr3 4599211 4602809 a 0 - 6 chr9 1914636 1916737 a 0 - 7 chr19 1 8642 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpzlke934p/f1.bed -b /tmp/tmpzlke934p/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 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/tmp3lpw7e4d/f1.bed -b /tmp/tmp3lpw7e4d/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr14 2243297 2246987 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp76i7_osg/f1.bed -b /tmp/tmp76i7_osg/f2.bed Chromosome Start End Name Score Strand 0 chr2 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/tmprxka6gsv/f1.bed -b /tmp/tmprxka6gsv/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 + Chromosome Start End Name Score Strand 0 chr1 32539 32541 a 0 + 1 chr1 1783698 1793602 a 0 - 2 chr6 1088673 1093953 a 0 + 3 chr9 8548698 8552268 a 0 + 4 chr9 487886 497809 a 0 + 5 chr12 5961792 5967019 a 0 + 6 chr16 4360555 4367923 a 0 + 7 chr16 6549348 6552596 a 0 - 8 chr17 9948207 9949401 a 0 + 9 chr19 3422054 3427492 a 0 - 10 chrX 2391940 2401312 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpn5oi64_m/f1.bed -b /tmp/tmpn5oi64_m/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 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpx5ugxrcw/f1.bed -b /tmp/tmpx5ugxrcw/f2.bed 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 2 759 a 0 + 1 chr1 3884876 3891091 a 0 + 2 chr1 2 759 a 0 - 3 chr1 2647399 2648156 a 0 - 4 chr1 829118 836833 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpn2pp14cw/f1.bed -b /tmp/tmpn2pp14cw/f2.bed 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/tmprk1mgso2/f1.bed -b /tmp/tmprk1mgso2/f2.bed Chromosome Start End Name Score Strand 0 chr1 65537 65538 a 0 + 1 chr1 2 3 a 0 + Chromosome Start End Name Score Strand 0 chr1 5761963 5768932 a 0 + 1 chr1 1213907 1222052 a 0 - 2 chr1 2 562 a 0 - 3 chr1 3801766 3809406 a 0 - 4 chr5 2 7104 a 0 + 5 chrM 1214880 1215699 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp8mg46ua8/f1.bed -b /tmp/tmp8mg46ua8/f2.bed Chromosome Start End Name Score Strand 0 chr1 65537 65538 a 0 + 1 chr1 2 3 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpqewk_lrp/f1.bed -b /tmp/tmpqewk_lrp/f2.bed 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 6160289 6168713 a 0 + 1 chr1 2549660 2557842 a 0 + 2 chr1 6225304 6231926 a 0 + 3 chr1 1498855 1505090 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpsbzoz9xf/f1.bed -b /tmp/tmpsbzoz9xf/f2.bed 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/tmpqpw37bk8/f1.bed -b /tmp/tmpqpw37bk8/f2.bed 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 9107034 9111130 a 0 + 1 chr1 4513031 4521161 a 0 + 2 chr3 2795634 2803600 a 0 - 3 chr5 2795634 2796518 a 0 - 4 chrY 3803106 3807202 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmptwn1xpd3/f1.bed -b /tmp/tmptwn1xpd3/f2.bed 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/tmpjovpfhom/f1.bed -b /tmp/tmpjovpfhom/f2.bed 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 6654746 6664746 a 0 + 1 chr1 7627388 7637388 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpfv5dzg59/f1.bed -b /tmp/tmpfv5dzg59/f2.bed 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/tmps8bip9b3/f1.bed -b /tmp/tmps8bip9b3/f2.bed 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 756085 758347 a 0 + 1 chr13 756085 765038 a 0 - 2 chr14 7103724 7109968 a 0 - 3 chr16 756085 762561 a 0 - 4 chr17 3084645 3093542 a 0 + 5 chr18 756085 757436 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmplc3a2s1h/f1.bed -b /tmp/tmplc3a2s1h/f2.bed 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/tmpn7rryc_v/f1.bed -b /tmp/tmpn7rryc_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 9487255 9496673 a 0 + 1 chr1 6013350 6015450 a 0 + 2 chr1 2464256 2467187 a 0 - 3 chr1 1965239 1973501 a 0 - 4 chr3 1088683 1089561 a 0 + 5 chr5 2566415 2576414 a 0 - 6 chr6 769965 775229 a 0 - 7 chr11 2806593 2816546 a 0 - 8 chr16 6081214 6082949 a 0 + 9 chrM 9841812 9842056 a 0 + 10 chrX 5152632 5161491 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpoep88qb5/f1.bed -b /tmp/tmpoep88qb5/f2.bed 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/tmpk1h4rlyj/f1.bed -b /tmp/tmpk1h4rlyj/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/tmpxoth596h/f1.bed -b /tmp/tmpxoth596h/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_k_nearest[upstream-False-opposite-last] _________________ [gw1] linux -- Python 3.12.3 /usr/bin/python3.12 nearest_how = 'upstream', 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: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='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:171 E (and 40 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', 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 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp40w293y2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp40w293y2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpb4wpjzw9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb4wpjzw9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpq80dltnb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq80dltnb/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/tmp2bc3d_rl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2bc3d_rl/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/tmps6ov8i6w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps6ov8i6w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmptxdmm_mx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptxdmm_mx/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/tmpxvyjtire/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxvyjtire/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp8fsrnr6_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8fsrnr6_/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/tmpegdadccg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpegdadccg/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/tmph81yyxcu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph81yyxcu/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/tmp9q5v0ud1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9q5v0ud1/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/tmpao9pzm3d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpao9pzm3d/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/tmpho1u8txx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpho1u8txx/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/tmpd2hqkrld/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd2hqkrld/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_sm5jpum/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_sm5jpum/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/tmp0qf1yarr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0qf1yarr/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/tmpt18hchh0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt18hchh0/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/tmpqd3webnh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqd3webnh/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/tmpk_sei8j7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk_sei8j7/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/tmpwzgv_vcv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwzgv_vcv/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/tmp2yat1o5e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2yat1o5e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpjgygg7og/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjgygg7og/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpq_wka_94/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq_wka_94/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpbu08zw5g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbu08zw5g/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/tmpioiv86hp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpioiv86hp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpuw1olsba/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuw1olsba/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/tmp6du9w3cu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6du9w3cu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp5cqmuoww/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5cqmuoww/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmplr9kr70n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplr9kr70n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpkyej9qe1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkyej9qe1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpf5jn7lxw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf5jn7lxw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp47uktmg8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp47uktmg8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpe098a9sp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe098a9sp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpfuvv9hi6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfuvv9hi6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpkqro0zrc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkqro0zrc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp5nwcg71z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5nwcg71z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpbh6gti3m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbh6gti3m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpbrxyy7tk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbrxyy7tk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp9tvhm5fm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9tvhm5fm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp3uf59ibh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3uf59ibh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmphz7x5ctq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphz7x5ctq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpyqdj_zcl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyqdj_zcl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpf28b_x8s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf28b_x8s/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/tmp6flbcl4e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6flbcl4e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp3eu0l_ku/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3eu0l_ku/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/tmpv5_58aqv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv5_58aqv/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/tmpjzsmqz6r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjzsmqz6r/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmplwr1hkgv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplwr1hkgv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp5711e_2v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5711e_2v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpl8d17qxi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl8d17qxi/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/tmpdxovl_gh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdxovl_gh/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/tmpwjvj06dr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwjvj06dr/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/tmpn3quan_s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn3quan_s/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/tmp1icuryyu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1icuryyu/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/tmpwfe1bwrx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwfe1bwrx/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/tmpkfnl2cfc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkfnl2cfc/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/tmpcyyqxchr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcyyqxchr/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/tmphvv0fp7c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphvv0fp7c/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/tmpsfj9yjh7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsfj9yjh7/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/tmp8ev9a939/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8ev9a939/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/tmptr678y6n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptr678y6n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpvc0w0jmd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvc0w0jmd/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/tmp3i4h5m37/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3i4h5m37/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/tmpzj9gxf7l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzj9gxf7l/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/tmp2wzqcd1d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2wzqcd1d/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/tmp4zda9ohh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4zda9ohh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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_0juamuj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_0juamuj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp0s6ag9fp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0s6ag9fp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpvnp9ib5e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvnp9ib5e/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/tmps2ruiy3n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps2ruiy3n/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/tmpt6tod4bn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt6tod4bn/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/tmp6nrpe7kx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6nrpe7kx/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/tmpamthvzb6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpamthvzb6/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/tmp21dpy7py/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp21dpy7py/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpq8qrqdih/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq8qrqdih/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/tmpeb9xfhfp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeb9xfhfp/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/tmp7jr7lsj1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7jr7lsj1/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/tmpslf1ml70/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpslf1ml70/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpwb0sb6ty/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwb0sb6ty/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpg8k76qyo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg8k76qyo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpr18od3c3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr18od3c3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp6bao9hid/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6bao9hid/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpflq81lhe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpflq81lhe/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/tmpd1jzvdxr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd1jzvdxr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmprxdai6ly/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprxdai6ly/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpcgjlzohq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcgjlzohq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpo66lbpz9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo66lbpz9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpp2pw8qy2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp2pw8qy2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpgmi4d31w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgmi4d31w/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/tmp1pu67zun/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1pu67zun/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/tmpvdxxi9yl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvdxxi9yl/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/tmppnaw0c3t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppnaw0c3t/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_jbqkrx6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_jbqkrx6/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/tmp4tl8hq0c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4tl8hq0c/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/tmp4uugthgr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4uugthgr/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/tmpwgdlufuj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwgdlufuj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpmxkfe5_o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmxkfe5_o/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/tmpkspffg0w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkspffg0w/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/tmpf6spkbkk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf6spkbkk/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/tmpfc13s6sh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfc13s6sh/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/tmpvwoth6pz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvwoth6pz/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. ---------------------------------- 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_chain21-method_chain21] ___________ [gw3] linux -- Python 3.12.3 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('nearest', '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=('nearest', '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 249 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('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') ('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') 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') ('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') 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') 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') 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_coverage[opposite] ____________________________ [gw0] linux -- Python 3.12.3 /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., 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('6.100.4', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') 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/tmpwnwgxaqi/f1.bed -b /tmp/tmpwnwgxaqi/f2.bed Chromosome Start End Name Score Strand 0 chr18 3094288 3097063 a 0 - Chromosome Start End Name Score Strand 0 chr1 4393450 4393452 a 0 + 1 chr1 8966632 8976124 a 0 - 2 chr9 2027841 2027843 a 0 + 3 chr12 6122566 6125002 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpyz7odcuj/f1.bed -b /tmp/tmpyz7odcuj/f2.bed Chromosome Start End Name Score Strand 0 chr18 3094288 3097063 a 0 - Chromosome Start End Name Score Strand 0 chr1 4393450 4393452 a 0 + 1 chr1 8966632 8976124 a 0 - 2 chr9 2027841 2027843 a 0 + 3 chr12 2027841 2030277 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpyj8odypu/f1.bed -b /tmp/tmpyj8odypu/f2.bed Chromosome Start End Name Score Strand 0 chr18 3094288 3097063 a 0 - Chromosome Start End Name Score Strand 0 chr1 4393450 4393452 a 0 + 1 chr1 8966632 8976124 a 0 - 2 chr9 2027841 2027843 a 0 + 3 chr12 2027841 2030277 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpeu6o_b6o/f1.bed -b /tmp/tmpeu6o_b6o/f2.bed Chromosome Start End Name Score Strand 0 chr18 3094288 3097063 a 0 - Chromosome Start End Name Score Strand 0 chr1 8966632 8976124 a 0 - 1 chr1 4393450 4393452 a 0 - 2 chr9 2027841 2027843 a 0 + 3 chr12 2027841 2030277 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp241fuejd/f1.bed -b /tmp/tmp241fuejd/f2.bed Chromosome Start End Name Score Strand 0 chr18 3094288 3097063 a 0 - Chromosome Start End Name Score Strand 0 chr2 65548 66415 a 0 - 1 chr19 529155 530022 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpt_he_jvo/f1.bed -b /tmp/tmpt_he_jvo/f2.bed Chromosome Start End Name Score Strand 0 chr18 3094288 3097063 a 0 - Chromosome Start End Name Score Strand 0 chr2 65548 66415 a 0 - 1 chr19 529155 530022 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpfj0rw6_1/f1.bed -b /tmp/tmpfj0rw6_1/f2.bed Chromosome Start End Name Score Strand 0 chr18 3094288 3097063 a 0 - Chromosome Start End Name Score Strand 0 chr18 3094288 3097063 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpgp0ly9i2/f1.bed -b /tmp/tmpgp0ly9i2/f2.bed Chromosome Start End Name Score Strand 0 chr1 6334804 6341331 a 0 + 1 chr11 3712463 3718850 a 0 - 2 chr13 1303685 1310212 a 0 - 3 chr15 8631776 8638303 a 0 + 4 chr15 9746230 9752757 a 0 + 5 chr15 382964 384817 a 0 - 6 chr15 6413193 6419720 a 0 - 7 chr15 5688865 5695392 a 0 - Chromosome Start End Name Score Strand 0 chr1 6760420 6764655 a 0 + 1 chr1 6877624 6881800 a 0 - 2 chr1 6760420 6764590 a 0 - 3 chr8 9052156 9062156 a 0 - 4 chr8 5564613 5572510 a 0 - 5 chr13 65164 69048 a 0 - 6 chr15 6760420 6762363 a 0 - 7 chr22 744904 747428 a 0 - 8 chr22 6149904 6159035 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmplqwt_43v/f1.bed -b /tmp/tmplqwt_43v/f2.bed Chromosome Start End Name Score Strand 0 chr1 6334804 6341331 a 0 + 1 chr11 3712463 3718850 a 0 - 2 chr13 1303685 1310212 a 0 - 3 chr15 8631776 8638303 a 0 + 4 chr15 9746230 9752757 a 0 + 5 chr15 382964 384817 a 0 - 6 chr15 6413193 6419720 a 0 - 7 chr15 5688865 5695392 a 0 - Chromosome Start End Name Score Strand 0 chr1 6760420 6762235 a 0 + 1 chr1 6877624 6878138 a 0 + 2 chr1 6760420 6766062 a 0 + 3 chr8 9052156 9052205 a 0 + 4 chr8 5564613 5565126 a 0 - 5 chr13 65164 72598 a 0 - 6 chr15 6760420 6760934 a 0 - 7 chr22 744904 745171 a 0 - 8 chr22 6149904 6157593 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp24_z66sk/f1.bed -b /tmp/tmp24_z66sk/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/tmpw2zkx3_d/f1.bed -b /tmp/tmpw2zkx3_d/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/tmpz86crdba/f1.bed -b /tmp/tmpz86crdba/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/tmplm9stitq/f1.bed -b /tmp/tmplm9stitq/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/tmp1qdbi7ee/f1.bed -b /tmp/tmp1qdbi7ee/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/tmp2wbw801q/f1.bed -b /tmp/tmp2wbw801q/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/tmpopxfa9ci/f1.bed -b /tmp/tmpopxfa9ci/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/tmp1tz0_qw5/f1.bed -b /tmp/tmp1tz0_qw5/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/tmpiuuy79hp/f1.bed -b /tmp/tmpiuuy79hp/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/tmp0_6l6ldj/f1.bed -b /tmp/tmp0_6l6ldj/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/tmplgoh3nhs/f1.bed -b /tmp/tmplgoh3nhs/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/tmpgm2agnr0/f1.bed -b /tmp/tmpgm2agnr0/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/tmp1q72fxtj/f1.bed -b /tmp/tmp1q72fxtj/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/tmpg2pc1bj_/f1.bed -b /tmp/tmpg2pc1bj_/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/tmpod12xlkj/f1.bed -b /tmp/tmpod12xlkj/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/tmprh3dlegh/f1.bed -b /tmp/tmprh3dlegh/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/tmpwanmbnj_/f1.bed -b /tmp/tmpwanmbnj_/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/tmpemco9d_a/f1.bed -b /tmp/tmpemco9d_a/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/tmpx4odr5vf/f1.bed -b /tmp/tmpx4odr5vf/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/tmp4cy5rd5d/f1.bed -b /tmp/tmp4cy5rd5d/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/tmpkihf5ab8/f1.bed -b /tmp/tmpkihf5ab8/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/tmpiogcsw9k/f1.bed -b /tmp/tmpiogcsw9k/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/tmpv2gvfq1w/f1.bed -b /tmp/tmpv2gvfq1w/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/tmptwy4u27x/f1.bed -b /tmp/tmptwy4u27x/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/tmpicwz16wg/f1.bed -b /tmp/tmpicwz16wg/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/tmpbh7cosw4/f1.bed -b /tmp/tmpbh7cosw4/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/tmpyz8jo8b4/f1.bed -b /tmp/tmpyz8jo8b4/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/tmpkbe32s9a/f1.bed -b /tmp/tmpkbe32s9a/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chrY 6992394 6995978 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp8yyfhotg/f1.bed -b /tmp/tmp8yyfhotg/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 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/tmp2frsoigf/f1.bed -b /tmp/tmp2frsoigf/f2.bed Chromosome Start End Name Score Strand 0 chr1 6408085 6408086 a 0 + Chromosome Start End Name Score Strand 0 chr1 25637 30756 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp6tg3ptrr/f1.bed -b /tmp/tmp6tg3ptrr/f2.bed Chromosome Start End Name Score Strand 0 chr1 6408085 6408086 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpzlnrmgkt/f1.bed -b /tmp/tmpzlnrmgkt/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 7998962 8008007 a 0 - 1 chr4 1763152 1766898 a 0 + 2 chr4 7673284 7677037 a 0 - 3 chr4 2393968 2401241 a 0 - 4 chr4 3127792 3127896 a 0 - 5 chr4 1763152 1769690 a 0 - 6 chr4 1763152 1767141 a 0 - 7 chr4 6127714 6132903 a 0 - 8 chr4 2730317 2733585 a 0 - 9 chr4 4006223 4011363 a 0 - 10 chr4 6341988 6346334 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpgpm7_q4c/f1.bed -b /tmp/tmpgpm7_q4c/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/tmp4rktqulj/f1.bed -b /tmp/tmp4rktqulj/f2.bed 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 6795602 6800706 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp_9upuw0s/f1.bed -b /tmp/tmp_9upuw0s/f2.bed 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/tmpuzc20qx0/f1.bed -b /tmp/tmpuzc20qx0/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 + Chromosome Start End Name Score Strand 0 chr1 5399331 5406989 a 0 + 1 chr1 4213801 4218672 a 0 + 2 chr1 7215279 7219093 a 0 + 3 chr1 2355346 2357341 a 0 + 4 chr1 5448493 5454549 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp6icfq0jm/f1.bed -b /tmp/tmp6icfq0jm/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 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpkij7ntn4/f1.bed -b /tmp/tmpkij7ntn4/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 8999204 9000361 a 0 + 1 chr1 4657516 4665685 a 0 + 2 chr1 7339513 7347013 a 0 - 3 chr3 1435404 1439305 a 0 - 4 chr5 3806002 3807543 a 0 - 5 chr6 5549959 5557536 a 0 - 6 chr7 6079913 6087216 a 0 - 7 chr8 1925149 1933042 a 0 - 8 chr14 1435404 1438494 a 0 - 9 chr18 1772450 1779154 a 0 - 10 chr20 1435404 1436474 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp6vix9tfw/f1.bed -b /tmp/tmp6vix9tfw/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/tmpqsr7wkrt/f1.bed -b /tmp/tmpqsr7wkrt/f2.bed 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 4986394 4991489 a 0 + 1 chr1 5168222 5168223 a 0 + 2 chr1 9999999 10006480 a 0 + 3 chr1 9416839 9417723 a 0 - 4 chr1 377768 379655 a 0 - 5 chr4 4196672 4205746 a 0 - 6 chr20 3151311 3153492 a 0 - 7 chr22 7449912 7454840 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp79no09ds/f1.bed -b /tmp/tmp79no09ds/f2.bed 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/tmp607je_b4/f1.bed -b /tmp/tmp607je_b4/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 4397 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp4sq3ptn6/f1.bed -b /tmp/tmp4sq3ptn6/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 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/tmp344exo1w/f1.bed -b /tmp/tmp344exo1w/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr6 3789036 3791430 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpp_af0wi9/f1.bed -b /tmp/tmpp_af0wi9/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 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/tmpeccs6h2w/f1.bed -b /tmp/tmpeccs6h2w/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2413757 2423756 a 0 - 1 chr1 8615146 8623186 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpux414sah/f1.bed -b /tmp/tmpux414sah/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 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/tmprf2d2jed/f1.bed -b /tmp/tmprf2d2jed/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 9030 a 0 + 1 chr1 1 9030 a 0 - Chromosome Start End Name Score Strand 0 chr1 2311684 2317644 a 0 + 1 chr1 4688634 4697872 a 0 - 2 chr1 2311684 2320893 a 0 - 3 chr1 2050215 2055191 a 0 - 4 chr1 3656359 3661606 a 0 - 5 chr5 8017665 8026768 a 0 + 6 chr14 7429537 7435309 a 0 + 7 chr16 9602274 9609775 a 0 + 8 chr18 7233026 7234239 a 0 + 9 chr18 4239397 4246747 a 0 - 10 chrM 11303 13778 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp2gicg960/f1.bed -b /tmp/tmp2gicg960/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 9030 a 0 + 1 chr1 1 9030 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp8u6cov1s/f1.bed -b /tmp/tmp8u6cov1s/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6423534 6425551 a 0 + 1 chr1 4148407 4151765 a 0 - 2 chr4 2684636 2692778 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp6b7zap79/f1.bed -b /tmp/tmp6b7zap79/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 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/tmp5rh3a63r/f1.bed -b /tmp/tmp5rh3a63r/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6498471 6504139 a 0 + 1 chr1 3812747 3818486 a 0 + 2 chr1 10000000 10006264 a 0 + 3 chr1 566512 568636 a 0 + 4 chr1 9160883 9170883 a 0 + 5 chr1 440222 442480 a 0 - 6 chr4 8242087 8248803 a 0 - 7 chr12 7015350 7025101 a 0 - 8 chr14 4503826 4513432 a 0 - 9 chr18 8350331 8352163 a 0 + 10 chr20 5668296 5670515 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmppcah7hso/f1.bed -b /tmp/tmppcah7hso/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 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/tmpomcqfe_l/f1.bed -b /tmp/tmpomcqfe_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 5537584 5539533 a 0 + 1 chr1 2757825 2759774 a 0 + 2 chr1 1538813 1541738 a 0 - 3 chr1 4645992 4648123 a 0 - 4 chr1 2253815 2255764 a 0 - 5 chr1 1181479 1183428 a 0 - 6 chr2 7237768 7239717 a 0 + 7 chr13 5951395 5958529 a 0 - 8 chr15 6426537 6428486 a 0 - 9 chr22 1538813 1546745 a 0 + 10 chrY 5998297 6000246 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpqkru9kzb/f1.bed -b /tmp/tmpqkru9kzb/f2.bed 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/tmp4wt_t7jf/f1.bed -b /tmp/tmp4wt_t7jf/f2.bed Chromosome Start End Name Score Strand 0 chr1 2 3 a 0 + 1 chr1 65537 65538 a 0 + Chromosome Start End Name Score Strand 0 chr1 2229511 2238388 a 0 + 1 chr1 2944002 2954002 a 0 + 2 chr1 7672580 7677461 a 0 - 3 chr3 9813682 9823088 a 0 + 4 chr3 5024675 5033599 a 0 + 5 chr3 8393369 8397104 a 0 - 6 chr6 1196892 1202931 a 0 - 7 chr10 5631129 5633527 a 0 + 8 chr12 3498906 3503029 a 0 - 9 chr14 9486403 9493382 a 0 - 10 chrX 478316 484035 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpq9c18nmb/f1.bed -b /tmp/tmpq9c18nmb/f2.bed Chromosome Start End Name Score Strand 0 chr1 2 3 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 -S -a /tmp/tmpbf40u5bp/f1.bed -b /tmp/tmpbf40u5bp/f2.bed 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 1331444 1337262 a 0 - 1 chr20 3797801 3799871 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpbdn0r_ct/f1.bed -b /tmp/tmpbdn0r_ct/f2.bed 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/tmpjlm6ubc6/f1.bed -b /tmp/tmpjlm6ubc6/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7424938 7430907 a 0 + 1 chr17 9146789 9156204 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpgw36ctnb/f1.bed -b /tmp/tmpgw36ctnb/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 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/tmpyvg6h3tc/f1.bed -b /tmp/tmpyvg6h3tc/f2.bed 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 chr8 7344110 7349358 a 0 - 1 chr20 122973 128181 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp1z9ibs9s/f1.bed -b /tmp/tmp1z9ibs9s/f2.bed 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/tmpujkwc_u7/f1.bed -b /tmp/tmpujkwc_u7/f2.bed 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 10000000 10003215 a 0 + 1 chr1 8597916 8598665 a 0 - 2 chr1 8597916 8600812 a 0 - 3 chr11 7375510 7382876 a 0 - 4 chr13 7497482 7500252 a 0 + 5 chr16 7258002 7261702 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpd79olg0l/f1.bed -b /tmp/tmpd79olg0l/f2.bed 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/tmpj2lvdjap/f1.bed -b /tmp/tmpj2lvdjap/f2.bed Chromosome Start End Name Score Strand 0 chr8 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2701769 2706984 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp18w3vxjz/f1.bed -b /tmp/tmp18w3vxjz/f2.bed Chromosome Start End Name Score Strand 0 chr8 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/tmpbdj7iowx/f1.bed -b /tmp/tmpbdj7iowx/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr10 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5317731 5319626 a 0 + 1 chr1 1650369 1651344 a 0 + 2 chr1 8548794 8555918 a 0 + 3 chr1 8222811 8226488 a 0 - 4 chr16 6362606 6366427 a 0 - 5 chr20 670257 677381 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp7yuef57q/f1.bed -b /tmp/tmp7yuef57q/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr10 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/tmpyp9a28ys/f1.bed -b /tmp/tmpyp9a28ys/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 3223 a 0 + 1 chr1 1 3223 a 0 - 2 chr1 1 3223 a 0 - Chromosome Start End Name Score Strand 0 chr1 1490825 1499182 a 0 - 1 chr8 3109442 3117892 a 0 - 2 chr12 194662 201620 a 0 + 3 chr18 2 8170 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpw_6y2611/f1.bed -b /tmp/tmpw_6y2611/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 3223 a 0 + 1 chr1 1 3223 a 0 - 2 chr1 1 3223 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmps3ymj4sg/f1.bed -b /tmp/tmps3ymj4sg/f2.bed Chromosome Start End Name Score Strand 0 chr12 2616578 2616579 a 0 - Chromosome Start End Name Score Strand 0 chr1 6482469 6482471 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp8tizn86m/f1.bed -b /tmp/tmp8tizn86m/f2.bed Chromosome Start End Name Score Strand 0 chr12 2616578 2616579 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmppmjds057/f1.bed -b /tmp/tmppmjds057/f2.bed Chromosome Start End Name Score Strand 0 chr1 65537 65539 a 0 + Chromosome Start End Name Score Strand 0 chr1 7902377 7904040 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp952isbya/f1.bed -b /tmp/tmp952isbya/f2.bed Chromosome Start End Name Score Strand 0 chr1 65537 65539 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpn88ickib/f1.bed -b /tmp/tmpn88ickib/f2.bed 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 2528120 2529324 a 0 + 1 chr1 9999831 10000893 a 0 - 2 chr6 9375672 9381335 a 0 + 3 chr8 4538080 4545923 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp5qnl8k6v/f1.bed -b /tmp/tmp5qnl8k6v/f2.bed 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/tmpar23_6y0/f1.bed -b /tmp/tmpar23_6y0/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4399841 4401959 a 0 + 1 chr3 2822894 2832893 a 0 - 2 chr10 7927284 7930983 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmphj2htdaf/f1.bed -b /tmp/tmphj2htdaf/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 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/tmpbe51sib2/f1.bed -b /tmp/tmpbe51sib2/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 + Chromosome Start End Name Score Strand 0 chr1 9666858 9671842 a 0 - 1 chr13 1618234 1620169 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmptl0x6tye/f1.bed -b /tmp/tmptl0x6tye/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 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpslk1id0q/f1.bed -b /tmp/tmpslk1id0q/f2.bed Chromosome Start End Name Score Strand 0 chr1 1928702 1928703 a 0 + Chromosome Start End Name Score Strand 0 chr1 15039 15860 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpni4uj9q1/f1.bed -b /tmp/tmpni4uj9q1/f2.bed Chromosome Start End Name Score Strand 0 chr1 1928702 1928703 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpxnd0rzay/f1.bed -b /tmp/tmpxnd0rzay/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 9856 a 0 + 1 chr1 1 9856 a 0 - Chromosome Start End Name Score Strand 0 chr1 1214488 1224487 a 0 + 1 chr1 1214488 1222336 a 0 + 2 chr7 1214488 1220914 a 0 - 3 chr19 1214488 1220664 a 0 + 4 chr22 1214488 1215136 a 0 + 5 chrY 1214488 1223037 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpiuzo4tqa/f1.bed -b /tmp/tmpiuzo4tqa/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 9856 a 0 + 1 chr1 1 9856 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpo_09z9tf/f1.bed -b /tmp/tmpo_09z9tf/f2.bed 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 chr4 2 9039 a 0 + 1 chr19 6785506 6791397 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpge71gftr/f1.bed -b /tmp/tmpge71gftr/f2.bed 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/tmp9zjk757l/f1.bed -b /tmp/tmp9zjk757l/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 + Chromosome Start End Name Score Strand 0 chr1 5736288 5746287 a 0 + 1 chr1 4015912 4022030 a 0 + 2 chr1 5508304 5508341 a 0 + 3 chr1 7338695 7348331 a 0 - 4 chr15 653066 653612 a 0 + 5 chr19 8834572 8837684 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp1_shbwmx/f1.bed -b /tmp/tmp1_shbwmx/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 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp9xwdqyds/f1.bed -b /tmp/tmp9xwdqyds/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4002607 4011246 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpz3o0947p/f1.bed -b /tmp/tmpz3o0947p/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 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/tmp13yg5amq/f1.bed -b /tmp/tmp13yg5amq/f2.bed 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 131626 139698 a 0 + 1 chr1 2974327 2983629 a 0 + 2 chr1 4667210 4676512 a 0 - 3 chr1 7842380 7851682 a 0 - 4 chr2 1418248 1427550 a 0 - 5 chr11 1167850 1176380 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmptvx19lto/f1.bed -b /tmp/tmptvx19lto/f2.bed 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/tmpp3sthkl4/f1.bed -b /tmp/tmpp3sthkl4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 1842 a 0 + 1 chr1 1 1842 a 0 - Chromosome Start End Name Score Strand 0 chr1 7443738 7446400 a 0 - 1 chr1 3077705 3085136 a 0 - 2 chr1 1 9641 a 0 - 3 chr5 2228188 2232274 a 0 + 4 chr9 2228188 2237828 a 0 - 5 chr14 6228291 6232055 a 0 - 6 chr16 9351374 9361014 a 0 + 7 chr16 8751911 8759201 a 0 + 8 chr16 3071475 3081115 a 0 - 9 chr16 9855722 9865362 a 0 - 10 chr21 2228188 2237828 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpi0wnrw4n/f1.bed -b /tmp/tmpi0wnrw4n/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 1842 a 0 + 1 chr1 1 1842 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpq4sp3mdo/f1.bed -b /tmp/tmpq4sp3mdo/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 + Chromosome Start End Name Score Strand 0 chr1 2718311 2725380 a 0 + 1 chr1 9999999 10001309 a 0 + 2 chr1 4095330 4099932 a 0 - 3 chr1 5675151 5684046 a 0 - 4 chr1 7626729 7635127 a 0 - 5 chr3 8898822 8898823 a 0 - 6 chr8 2336828 2338823 a 0 + 7 chr8 1258832 1266502 a 0 - 8 chr15 7626729 7634997 a 0 + 9 chrM 7626729 7633192 a 0 + 10 chrY 7626729 7629219 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpygeugroh/f1.bed -b /tmp/tmpygeugroh/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 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpqyqp7_1x/f1.bed -b /tmp/tmpqyqp7_1x/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4201167 4201249 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp7redja92/f1.bed -b /tmp/tmp7redja92/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + 3 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/tmp4_6soxeg/f1.bed -b /tmp/tmp4_6soxeg/f2.bed 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 7732538 7735918 a 0 + 1 chr1 6285727 6293941 a 0 + 2 chr1 4804191 4804307 a 0 + 3 chr20 1614885 1623044 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpvo7br_ob/f1.bed -b /tmp/tmpvo7br_ob/f2.bed 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/tmp6bkqo83o/f1.bed -b /tmp/tmp6bkqo83o/f2.bed Chromosome Start End Name Score Strand 0 chr1 65537 65538 a 0 + 1 chr1 65537 65538 a 0 + Chromosome Start End Name Score Strand 0 chr1 3310622 3316584 a 0 + 1 chr1 6755596 6758532 a 0 + 2 chr1 9370516 9371825 a 0 - 3 chr8 6797163 6798793 a 0 - 4 chr14 169139 178912 a 0 - 5 chr18 918979 927302 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpviuw38ie/f1.bed -b /tmp/tmpviuw38ie/f2.bed Chromosome Start End Name Score Strand 0 chr1 65537 65538 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 -S -a /tmp/tmpzp0u2nm_/f1.bed -b /tmp/tmpzp0u2nm_/f2.bed 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 6486190 6488944 a 0 + 1 chr1 5250982 5252243 a 0 + 2 chr1 5548395 5553680 a 0 - 3 chr1 8228523 8233639 a 0 - 4 chr11 8584282 8587652 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpjquem7tj/f1.bed -b /tmp/tmpjquem7tj/f2.bed 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/tmp8cadb4tj/f1.bed -b /tmp/tmp8cadb4tj/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 chr2 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9844903 9850540 a 0 + 1 chr10 3777752 3784416 a 0 - 2 chr12 9844903 9852593 a 0 + 3 chr13 9844903 9849087 a 0 - 4 chr21 6342034 6346366 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp8wrralh0/f1.bed -b /tmp/tmp8wrralh0/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + 1 chr2 1 2 a 0 + 2 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/tmpjxn3vyv0/f1.bed -b /tmp/tmpjxn3vyv0/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/tmpx03m36_p/f1.bed -b /tmp/tmpx03m36_p/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_chain52-method_chain52] ___________ [gw2] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('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') Empty PyRanges ('set_union', 'nearest') Empty 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'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') 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') ---------------------------------- 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-same-last] ___________________ [gw1] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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='same', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 788994 | 789252 | a | 0 | - | | | chr1 | 3484509 | 3484767 | a | 0 | - | | | chr1 | 985108 | 985366 | a | 0 | - | | | chr1 | 527627 | 529421 | a | 0 | - | | | ... | ... | ... | ... | ... | ... | | | chr1 | 3671310 | 3671568 | a | 0 | - | | | chr1 | 788994 | 789252 | a | 0 | - | | | chr1 | 788994 | 789252 | a | 0 | - | | | chr1 | 69379 | 69637 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 11 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 | 786689 | 790030 | a | 0 | + | | | chr1 | 786689 | 790288 | a | 0 | - | | | chr1 | 786689 | 790030 | a | 0 | - | | | chr7 | 786689 | 790030 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 4 rows and 6 columns from 2 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 46 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicDcpBK4RBGAfw/3+emWfenXlnJrE3J8LqzZ7QprSlHJzloJx8AXcHrBOupL1IyceQcpEoN84oJfId+J1/7N08rxx8/brl6bsfTh7Nf9j+6vWt3Tk9GRf/+TC4X7/cGFzp5uvh23D2jPvD8z07YrenuAtA8uPL8ffF2tzTOzqAKqGgF7fQbKUgLCa6UqWwJCb6fs+lSM22yX7Gtko1iqYOVIdO7ekcKhKkstviYpgoFu3Q9YzBOhQDHRMa0P0nxJqooDkLwFQnYSXBUEALa4yoGGkb4A8nrCQQ') 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='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('6.100.4', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') 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/tmpi3qxsjpm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi3qxsjpm/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/tmp0ti7p9he/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0ti7p9he/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpd31rkirf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd31rkirf/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/tmpjhynd6we/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjhynd6we/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/tmpvtyqto2z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvtyqto2z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp7sa4ptm2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7sa4ptm2/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/tmp3_auhef6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3_auhef6/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/tmpdnjboxx5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdnjboxx5/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/tmp2htbxx_w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2htbxx_w/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/tmp8xcvr66l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8xcvr66l/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmprpqgdoc0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprpqgdoc0/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/tmp7l6745_y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7l6745_y/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/tmp6oidyhkw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6oidyhkw/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/tmpgmymva63/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgmymva63/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/tmp32ksdp99/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp32ksdp99/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/tmpo7k1rgg3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo7k1rgg3/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/tmpob74g180/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpob74g180/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/tmpo1l4_2fh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo1l4_2fh/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/tmphuy5zdfb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphuy5zdfb/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/tmpavdlvkjn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpavdlvkjn/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/tmpcvz37bj9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcvz37bj9/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/tmpya0ctkbj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpya0ctkbj/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/tmpkrdwzmw6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkrdwzmw6/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/tmprcsdc2a0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprcsdc2a0/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/tmphu2vj8w_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphu2vj8w_/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/tmp3uik1hnk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3uik1hnk/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/tmp8xz14l__/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8xz14l__/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/tmpe4o1zsz4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe4o1zsz4/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/tmpszyz2o7y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpszyz2o7y/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/tmpfx7oefse/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfx7oefse/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/tmpm82xdib4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm82xdib4/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/tmpk5bnhe45/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk5bnhe45/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/tmpphfm84af/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpphfm84af/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/tmp0ecm5k5j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0ecm5k5j/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/tmpfeowgveh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfeowgveh/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/tmpfc__ua94/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfc__ua94/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/tmpcobutsxj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcobutsxj/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/tmpd2w0b1in/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd2w0b1in/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/tmp8ndc5h79/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8ndc5h79/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/tmpk8cm0tm7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk8cm0tm7/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/tmpg_utlf5g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg_utlf5g/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/tmp5kfcyci7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5kfcyci7/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/tmp3otzhdon/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3otzhdon/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/tmpb66hwxos/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb66hwxos/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/tmpma1t6rxi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpma1t6rxi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp2kxrk0xe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2kxrk0xe/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpk3kw6eav/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk3kw6eav/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/tmphfb8kflb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphfb8kflb/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/tmpuo_cipzk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuo_cipzk/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/tmpwqp2joms/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwqp2joms/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/tmpcg83fsn3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcg83fsn3/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/tmp68cyx03x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp68cyx03x/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/tmphc_z_z53/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphc_z_z53/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/tmpkbo4syz5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkbo4syz5/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/tmpxog59wk_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxog59wk_/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/tmpkfylt__3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkfylt__3/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_rujx0j1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_rujx0j1/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/tmpihae4lo0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpihae4lo0/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/tmphtd_0dwm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphtd_0dwm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp0j79giih/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0j79giih/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/tmp8hv_fdd2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8hv_fdd2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpp2gi0yyh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp2gi0yyh/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/tmpojkozz7a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpojkozz7a/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/tmpv8gpsuyg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv8gpsuyg/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/tmpgy6a1lmj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgy6a1lmj/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/tmpztucm_6x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpztucm_6x/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/tmp99r5m35o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp99r5m35o/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/tmp08i084ys/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp08i084ys/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/tmpwejdk1d1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwejdk1d1/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/tmp7iba81_h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7iba81_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/tmpr3kitm28/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr3kitm28/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/tmpzoqp8gts/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzoqp8gts/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/tmpktm2mlub/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpktm2mlub/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/tmpsog1b2v6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsog1b2v6/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/tmpese4hiqm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpese4hiqm/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/tmpl9ue8l0p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl9ue8l0p/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/tmp55swrmd3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp55swrmd3/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/tmp1a0hu6cu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1a0hu6cu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp5y650a6r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5y650a6r/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/tmpbe6vjvgt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbe6vjvgt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp1fzcm5c9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1fzcm5c9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpo4tg1v8g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo4tg1v8g/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/tmpm5l8d8ea/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm5l8d8ea/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpo0dbmeku/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo0dbmeku/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/tmptfdwo5os/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptfdwo5os/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/tmpqelkvrgi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqelkvrgi/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/tmpsqey_bna/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsqey_bna/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/tmp5vkx9ln2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5vkx9ln2/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/tmpdn0l00pb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdn0l00pb/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/tmpc5648buo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc5648buo/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/tmp83wdw_i5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp83wdw_i5/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/tmpwrrga3jf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwrrga3jf/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/tmppnukn6np/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppnukn6np/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/tmpynmsj91e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpynmsj91e/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/tmp5jis8ipj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5jis8ipj/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/tmpibk0__gv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpibk0__gv/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/tmp2fs6vm7d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2fs6vm7d/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/tmpce_hdyvm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpce_hdyvm/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/tmp67c5yw0i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp67c5yw0i/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/tmphgtqbb41/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphgtqbb41/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/tmpev893_wm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpev893_wm/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/tmpvs4rmac8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvs4rmac8/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/tmpnfyy7e8w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnfyy7e8w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp54a5ftqj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp54a5ftqj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpdwcxusbv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdwcxusbv/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/tmpz4yw1to1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz4yw1to1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmptt73h6_o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptt73h6_o/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/tmpjiaj4hg1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjiaj4hg1/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_toqtjvt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_toqtjvt/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/tmpgepp31qc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgepp31qc/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/tmpx00s_15d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx00s_15d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpnuc4i4q6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnuc4i4q6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpid1vplkx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpid1vplkx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp2kubla3t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2kubla3t/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp1lz2fk9i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1lz2fk9i/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/tmp4ytgywhe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ytgywhe/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/tmp6iqck0h0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6iqck0h0/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 chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 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 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 chr8 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 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. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on 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 chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. 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_subtraction[same] ____________________________ [gw0] linux -- Python 3.12.3 /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 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 E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') 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/tmppirx_l7b/f1.bed -b /tmp/tmppirx_l7b/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp5iil2pjo/f1.bed -b /tmp/tmp5iil2pjo/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp1y8s7h_e/f1.bed -b /tmp/tmp1y8s7h_e/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpblxkv65k/f1.bed -b /tmp/tmpblxkv65k/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp4gohtxv4/f1.bed -b /tmp/tmp4gohtxv4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpzgezs8i7/f1.bed -b /tmp/tmpzgezs8i7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp3itdys3b/f1.bed -b /tmp/tmp3itdys3b/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpg3ffptt_/f1.bed -b /tmp/tmpg3ffptt_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpny4pc2qx/f1.bed -b /tmp/tmpny4pc2qx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpmyj7xurm/f1.bed -b /tmp/tmpmyj7xurm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp6vovv962/f1.bed -b /tmp/tmp6vovv962/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpiu52q3qq/f1.bed -b /tmp/tmpiu52q3qq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp0sy4utvy/f1.bed -b /tmp/tmp0sy4utvy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp75v7emj2/f1.bed -b /tmp/tmp75v7emj2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp_l9k4iet/f1.bed -b /tmp/tmp_l9k4iet/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp1s24j1nb/f1.bed -b /tmp/tmp1s24j1nb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp_yitsjgm/f1.bed -b /tmp/tmp_yitsjgm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpfoiplb9z/f1.bed -b /tmp/tmpfoiplb9z/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpyty0xy7t/f1.bed -b /tmp/tmpyty0xy7t/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp5m_989y8/f1.bed -b /tmp/tmp5m_989y8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmprro3vtw3/f1.bed -b /tmp/tmprro3vtw3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpv46wil57/f1.bed -b /tmp/tmpv46wil57/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpcolkykc1/f1.bed -b /tmp/tmpcolkykc1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpiqdal95a/f1.bed -b /tmp/tmpiqdal95a/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmppsgb666x/f1.bed -b /tmp/tmppsgb666x/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmplbttrria/f1.bed -b /tmp/tmplbttrria/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpctwxkrus/f1.bed -b /tmp/tmpctwxkrus/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmph4gvynjg/f1.bed -b /tmp/tmph4gvynjg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpg8jg77a9/f1.bed -b /tmp/tmpg8jg77a9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpvrcozppp/f1.bed -b /tmp/tmpvrcozppp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpixzfzy8s/f1.bed -b /tmp/tmpixzfzy8s/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpy5oal4dy/f1.bed -b /tmp/tmpy5oal4dy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp9q91r9rf/f1.bed -b /tmp/tmp9q91r9rf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpfbkmp5fj/f1.bed -b /tmp/tmpfbkmp5fj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpdfy3xuz0/f1.bed -b /tmp/tmpdfy3xuz0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmprs19hqvy/f1.bed -b /tmp/tmprs19hqvy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmppa79x0_0/f1.bed -b /tmp/tmppa79x0_0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpqijzdtrh/f1.bed -b /tmp/tmpqijzdtrh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpng11jp1g/f1.bed -b /tmp/tmpng11jp1g/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpo9uw96jk/f1.bed -b /tmp/tmpo9uw96jk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpfmo58t3j/f1.bed -b /tmp/tmpfmo58t3j/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp98numqp_/f1.bed -b /tmp/tmp98numqp_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpqjj57v2a/f1.bed -b /tmp/tmpqjj57v2a/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpgkx_nhrk/f1.bed -b /tmp/tmpgkx_nhrk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpyxejlxiw/f1.bed -b /tmp/tmpyxejlxiw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpamltd0n1/f1.bed -b /tmp/tmpamltd0n1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp1vyx1o5_/f1.bed -b /tmp/tmp1vyx1o5_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpxucxfr8p/f1.bed -b /tmp/tmpxucxfr8p/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp_x4yo_m8/f1.bed -b /tmp/tmp_x4yo_m8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpgpzl_akn/f1.bed -b /tmp/tmpgpzl_akn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpw2egy5f2/f1.bed -b /tmp/tmpw2egy5f2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp_2lfxkt4/f1.bed -b /tmp/tmp_2lfxkt4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp7l1olw2w/f1.bed -b /tmp/tmp7l1olw2w/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp_d7m018q/f1.bed -b /tmp/tmp_d7m018q/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpk91_75ng/f1.bed -b /tmp/tmpk91_75ng/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp6g6kabfp/f1.bed -b /tmp/tmp6g6kabfp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmplev8aym8/f1.bed -b /tmp/tmplev8aym8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp8cxtfndx/f1.bed -b /tmp/tmp8cxtfndx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpi0w7hdya/f1.bed -b /tmp/tmpi0w7hdya/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp6elj2eeu/f1.bed -b /tmp/tmp6elj2eeu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpxf3wrgc5/f1.bed -b /tmp/tmpxf3wrgc5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp84cyil8f/f1.bed -b /tmp/tmp84cyil8f/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmph8j_wvj5/f1.bed -b /tmp/tmph8j_wvj5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp9443waw4/f1.bed -b /tmp/tmp9443waw4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpz0a6hd0s/f1.bed -b /tmp/tmpz0a6hd0s/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmps_w9w81z/f1.bed -b /tmp/tmps_w9w81z/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpp_kgo_un/f1.bed -b /tmp/tmpp_kgo_un/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpc_8q9yn2/f1.bed -b /tmp/tmpc_8q9yn2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmphq8vebut/f1.bed -b /tmp/tmphq8vebut/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp7b3thgjt/f1.bed -b /tmp/tmp7b3thgjt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp2skdcxjg/f1.bed -b /tmp/tmp2skdcxjg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp_x9l3x5d/f1.bed -b /tmp/tmp_x9l3x5d/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpqzi1q141/f1.bed -b /tmp/tmpqzi1q141/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp7zrhqsz0/f1.bed -b /tmp/tmp7zrhqsz0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpidrbb_vl/f1.bed -b /tmp/tmpidrbb_vl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp__ccs__6/f1.bed -b /tmp/tmp__ccs__6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpue2m7abd/f1.bed -b /tmp/tmpue2m7abd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp1o1semxy/f1.bed -b /tmp/tmp1o1semxy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp94mpjj_a/f1.bed -b /tmp/tmp94mpjj_a/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpngq1yoco/f1.bed -b /tmp/tmpngq1yoco/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp9c84132d/f1.bed -b /tmp/tmp9c84132d/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpqsm7zpq4/f1.bed -b /tmp/tmpqsm7zpq4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp_muck3wj/f1.bed -b /tmp/tmp_muck3wj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp4grdxycz/f1.bed -b /tmp/tmp4grdxycz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpw2mxmle_/f1.bed -b /tmp/tmpw2mxmle_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpraqu5b3e/f1.bed -b /tmp/tmpraqu5b3e/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpqs5b9wv3/f1.bed -b /tmp/tmpqs5b9wv3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpfebuokhx/f1.bed -b /tmp/tmpfebuokhx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpxal8zcq_/f1.bed -b /tmp/tmpxal8zcq_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpfwe_t602/f1.bed -b /tmp/tmpfwe_t602/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpois0ju0i/f1.bed -b /tmp/tmpois0ju0i/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp_umyqiyp/f1.bed -b /tmp/tmp_umyqiyp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp9p09n8bm/f1.bed -b /tmp/tmp9p09n8bm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp1wyr4980/f1.bed -b /tmp/tmp1wyr4980/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpxqygwfnv/f1.bed -b /tmp/tmpxqygwfnv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp12_7tqul/f1.bed -b /tmp/tmp12_7tqul/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp5hca_bsm/f1.bed -b /tmp/tmp5hca_bsm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmph918aumm/f1.bed -b /tmp/tmph918aumm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpf9b8ks4u/f1.bed -b /tmp/tmpf9b8ks4u/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp3iax_pfw/f1.bed -b /tmp/tmp3iax_pfw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp67cyigys/f1.bed -b /tmp/tmp67cyigys/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpn0616mxf/f1.bed -b /tmp/tmpn0616mxf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp__tikj5p/f1.bed -b /tmp/tmp__tikj5p/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp5kets0hx/f1.bed -b /tmp/tmp5kets0hx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpxy1_9si9/f1.bed -b /tmp/tmpxy1_9si9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpbx8rwjcf/f1.bed -b /tmp/tmpbx8rwjcf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpug60lxv9/f1.bed -b /tmp/tmpug60lxv9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpclkd7qbg/f1.bed -b /tmp/tmpclkd7qbg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpqhtahh4p/f1.bed -b /tmp/tmpqhtahh4p/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpbe89s5ip/f1.bed -b /tmp/tmpbe89s5ip/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpkkyz23v7/f1.bed -b /tmp/tmpkkyz23v7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp60gw7avj/f1.bed -b /tmp/tmp60gw7avj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpshk_q4a2/f1.bed -b /tmp/tmpshk_q4a2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpquw_juh8/f1.bed -b /tmp/tmpquw_juh8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpw6jzi2m6/f1.bed -b /tmp/tmpw6jzi2m6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpjzqej_qx/f1.bed -b /tmp/tmpjzqej_qx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpnlyg7pjp/f1.bed -b /tmp/tmpnlyg7pjp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpxhh7ko52/f1.bed -b /tmp/tmpxhh7ko52/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpukug0u4i/f1.bed -b /tmp/tmpukug0u4i/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpcf3chruv/f1.bed -b /tmp/tmpcf3chruv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpcrap6ill/f1.bed -b /tmp/tmpcrap6ill/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp08eel0zx/f1.bed -b /tmp/tmp08eel0zx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp5k35sa58/f1.bed -b /tmp/tmp5k35sa58/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp40s594tu/f1.bed -b /tmp/tmp40s594tu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmppi_zkn_2/f1.bed -b /tmp/tmppi_zkn_2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpd_edzxq1/f1.bed -b /tmp/tmpd_edzxq1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpvj_bqh0g/f1.bed -b /tmp/tmpvj_bqh0g/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpi6g3vdw6/f1.bed -b /tmp/tmpi6g3vdw6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpc7yd329n/f1.bed -b /tmp/tmpc7yd329n/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpfknbiyeu/f1.bed -b /tmp/tmpfknbiyeu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpdsyqllbn/f1.bed -b /tmp/tmpdsyqllbn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpbeud7aom/f1.bed -b /tmp/tmpbeud7aom/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpesh39cac/f1.bed -b /tmp/tmpesh39cac/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp002_om9f/f1.bed -b /tmp/tmp002_om9f/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp0fp3mac7/f1.bed -b /tmp/tmp0fp3mac7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpb2f25515/f1.bed -b /tmp/tmpb2f25515/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp2bq93e24/f1.bed -b /tmp/tmp2bq93e24/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp0h29usm1/f1.bed -b /tmp/tmp0h29usm1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpvnmrw357/f1.bed -b /tmp/tmpvnmrw357/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp2t9b7ep9/f1.bed -b /tmp/tmp2t9b7ep9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpfjurn3yy/f1.bed -b /tmp/tmpfjurn3yy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmphhdnu5q5/f1.bed -b /tmp/tmphhdnu5q5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpns1xvnew/f1.bed -b /tmp/tmpns1xvnew/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpnzhgtzn3/f1.bed -b /tmp/tmpnzhgtzn3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpz_6ntr_3/f1.bed -b /tmp/tmpz_6ntr_3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpopmxzm6z/f1.bed -b /tmp/tmpopmxzm6z/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpw9idu3n_/f1.bed -b /tmp/tmpw9idu3n_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp8euuf9zm/f1.bed -b /tmp/tmp8euuf9zm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpjg87wurn/f1.bed -b /tmp/tmpjg87wurn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp9uk9qbrb/f1.bed -b /tmp/tmp9uk9qbrb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp_wwi7sd2/f1.bed -b /tmp/tmp_wwi7sd2/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_chain53-method_chain53] ___________ [gw2] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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 181 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('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') 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') 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') 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') 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') ---------------------------------- 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-False-last] ___________________ [gw1] linux -- Python 3.12.3 /usr/bin/python3.12 nearest_how = 'upstream', 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: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=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:171 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/k_nearest.py:19 E (and 36 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') 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 -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxvsdxe9h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxvsdxe9h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4k4r1ugu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4k4r1ugu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphaf878ye/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphaf878ye/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg_z7zm41/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg_z7zm41/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvi6gpdne/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvi6gpdne/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg9ptdcz4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg9ptdcz4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpep63nk3d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpep63nk3d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp38le7chn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp38le7chn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplcna49ey/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplcna49ey/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwq4ul4nr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwq4ul4nr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt7yjmdys/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt7yjmdys/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxxq_dnxc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxxq_dnxc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbm2ke1l5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbm2ke1l5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfv01w64u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfv01w64u/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpeay9tk7u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeay9tk7u/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4wgfh8m_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4wgfh8m_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr5rydpl9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr5rydpl9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpieco5lna/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpieco5lna/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8ijdbeez/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8ijdbeez/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpws22iy8h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpws22iy8h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6qxc_ced/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6qxc_ced/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprj_agg76/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprj_agg76/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaem7yxz5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaem7yxz5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmvrjus0e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmvrjus0e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0uu3wsic/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0uu3wsic/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptthfnnc5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptthfnnc5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppg9x7wky/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppg9x7wky/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe_bitary/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe_bitary/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1vjoid7i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1vjoid7i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5kw4c9qv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5kw4c9qv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuy1bdhhn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuy1bdhhn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf76ctd0_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf76ctd0_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwsocgbvq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwsocgbvq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbk2t1fn8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbk2t1fn8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7fppsc3z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7fppsc3z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppegi4dhf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppegi4dhf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0vxd6jtm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0vxd6jtm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa_mbuskz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa_mbuskz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz0lr6deu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz0lr6deu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpni4bnmli/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpni4bnmli/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpa47glcgp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa47glcgp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpteq1e46_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpteq1e46_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2k9zez3c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2k9zez3c/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpca5i50p2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpca5i50p2/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. ___________ test_three_in_a_row[strandedness_chain22-method_chain22] ___________ [gw3] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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 | 7258617 | 7259131 | a | 0 | + | | | chr1 | 6820213 | 6820727 | a | 0 | - | | | chr1 | 4846671 | 4847185 | a | 0 | - | | | chr17 | 5269226 | 5269740 | a | 0 | - | | | chrM | 5269226 | 5269740 | 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 | 1509378 | 1509635 | a | 0 | - | | | chr1 | 590855 | 591631 | a | 0 | - | | | chr1 | 590855 | 590877 | a | 0 | - | | | chr1 | 590855 | 591368 | a | 0 | - | | | chr1 | 1049345 | 1049367 | a | 0 | - | | | chr1 | 590855 | 590888 | a | 0 | - | | | chr1 | 590855 | 591887 | a | 0 | - | | | chr1 | 590855 | 590877 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 8 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) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr2 | 196638 | 198180 | 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('6.100.4', b'AXicFY/PR8NxHMaf9/vz472p73xnZtN8a4eUSIeZ2Wk6pWiJVMREMXVJh0n0B0SnqEvXkVVGXUvZUtNp1C1Ru42o05KiQ9/xeA6P1/PwsPudoI/Paqs3nXk8tLnV3ZrQ5ObOHo/nD+bM0llq5bzQ+XvKdoYWKtdHDZ6YHqvD0yRA3DM6YnVIDMKWqF9RUIwwXERpeS1cChtrlNMebR7fVy4bb8+B1MbtjysUtTo59TUzoIqzxXfM59RwjMlj0kSKHFBcFECcqu2r7Vcy3qk1EWkxF9pls/57km/eWF+ireH0YI7UYj1LpYeqKV6Vue/ud+viBQkALOQ7abgKAooFaERDgto6NqRFK2R6GDGfABmNpCBLUMLKbzGi/iE/h8MsAqdLcXfI6+LW+IPAP16QQBo=') 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, | 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 135 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', 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') 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') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('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') ('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') ('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') ('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') 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') ('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') 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_subtraction[opposite] __________________________ [gw0] linux -- Python 3.12.3 /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 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 E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') 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/tmpx5bi5ht5/f1.bed -b /tmp/tmpx5bi5ht5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpzq3py7nu/f1.bed -b /tmp/tmpzq3py7nu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpbn9qp8_k/f1.bed -b /tmp/tmpbn9qp8_k/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp7mddmebn/f1.bed -b /tmp/tmp7mddmebn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmplo6ytl54/f1.bed -b /tmp/tmplo6ytl54/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmptu4_bo32/f1.bed -b /tmp/tmptu4_bo32/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpm6p7nxbt/f1.bed -b /tmp/tmpm6p7nxbt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpr23_no4k/f1.bed -b /tmp/tmpr23_no4k/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpzqlbq2km/f1.bed -b /tmp/tmpzqlbq2km/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpi3pwq3kc/f1.bed -b /tmp/tmpi3pwq3kc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpiromzj7n/f1.bed -b /tmp/tmpiromzj7n/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpnet3lgdl/f1.bed -b /tmp/tmpnet3lgdl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpenaxs_g7/f1.bed -b /tmp/tmpenaxs_g7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpax351bdx/f1.bed -b /tmp/tmpax351bdx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpo1jk1tlt/f1.bed -b /tmp/tmpo1jk1tlt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpa73qmxrl/f1.bed -b /tmp/tmpa73qmxrl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpkcmfg5ze/f1.bed -b /tmp/tmpkcmfg5ze/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp2i8ruytd/f1.bed -b /tmp/tmp2i8ruytd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpjrvi_617/f1.bed -b /tmp/tmpjrvi_617/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpghztvkeu/f1.bed -b /tmp/tmpghztvkeu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpsh46d7bw/f1.bed -b /tmp/tmpsh46d7bw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp9lcm1ud7/f1.bed -b /tmp/tmp9lcm1ud7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp01fky538/f1.bed -b /tmp/tmp01fky538/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp32hmm90q/f1.bed -b /tmp/tmp32hmm90q/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpj58km6p1/f1.bed -b /tmp/tmpj58km6p1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmphxyhahnr/f1.bed -b /tmp/tmphxyhahnr/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp8ecgtezp/f1.bed -b /tmp/tmp8ecgtezp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpvmhdlkas/f1.bed -b /tmp/tmpvmhdlkas/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp5f1ouawt/f1.bed -b /tmp/tmp5f1ouawt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpqnedcfiy/f1.bed -b /tmp/tmpqnedcfiy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpnk_5evfs/f1.bed -b /tmp/tmpnk_5evfs/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpdrddz7xr/f1.bed -b /tmp/tmpdrddz7xr/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmptbwoatkn/f1.bed -b /tmp/tmptbwoatkn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp_j4k4_dm/f1.bed -b /tmp/tmp_j4k4_dm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpw7kezj4g/f1.bed -b /tmp/tmpw7kezj4g/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpjg1vdtf7/f1.bed -b /tmp/tmpjg1vdtf7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp9_v2jum2/f1.bed -b /tmp/tmp9_v2jum2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp4u99jnrv/f1.bed -b /tmp/tmp4u99jnrv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmph3youl7s/f1.bed -b /tmp/tmph3youl7s/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpzluya06u/f1.bed -b /tmp/tmpzluya06u/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpehrlg_j9/f1.bed -b /tmp/tmpehrlg_j9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp6oyndfnm/f1.bed -b /tmp/tmp6oyndfnm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpzoq00rhj/f1.bed -b /tmp/tmpzoq00rhj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpmm_cx4gg/f1.bed -b /tmp/tmpmm_cx4gg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp64dwse9e/f1.bed -b /tmp/tmp64dwse9e/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpdb_d0zi2/f1.bed -b /tmp/tmpdb_d0zi2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpvb79r919/f1.bed -b /tmp/tmpvb79r919/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpqsebcf5v/f1.bed -b /tmp/tmpqsebcf5v/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpskjnumda/f1.bed -b /tmp/tmpskjnumda/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpl3_mcknt/f1.bed -b /tmp/tmpl3_mcknt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpm_g19vka/f1.bed -b /tmp/tmpm_g19vka/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmplh0izo_f/f1.bed -b /tmp/tmplh0izo_f/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpyon60pjq/f1.bed -b /tmp/tmpyon60pjq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp_xef3ffh/f1.bed -b /tmp/tmp_xef3ffh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpnowxlca0/f1.bed -b /tmp/tmpnowxlca0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpuv3yzeqo/f1.bed -b /tmp/tmpuv3yzeqo/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmps3p021hv/f1.bed -b /tmp/tmps3p021hv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpnkx1_oce/f1.bed -b /tmp/tmpnkx1_oce/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpwq8kzhab/f1.bed -b /tmp/tmpwq8kzhab/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp8a048s43/f1.bed -b /tmp/tmp8a048s43/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp2ram3t1f/f1.bed -b /tmp/tmp2ram3t1f/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpkt_2x_da/f1.bed -b /tmp/tmpkt_2x_da/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp5w_9zm7i/f1.bed -b /tmp/tmp5w_9zm7i/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpbg9ypol2/f1.bed -b /tmp/tmpbg9ypol2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp_5e91791/f1.bed -b /tmp/tmp_5e91791/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpn5lmk6ju/f1.bed -b /tmp/tmpn5lmk6ju/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmppf1iotra/f1.bed -b /tmp/tmppf1iotra/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpbl45zp6e/f1.bed -b /tmp/tmpbl45zp6e/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp_pehopn8/f1.bed -b /tmp/tmp_pehopn8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpkwq5zsc_/f1.bed -b /tmp/tmpkwq5zsc_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp4vr4md45/f1.bed -b /tmp/tmp4vr4md45/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmph0ayb3ib/f1.bed -b /tmp/tmph0ayb3ib/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp2nzjxijy/f1.bed -b /tmp/tmp2nzjxijy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpt4vu0soy/f1.bed -b /tmp/tmpt4vu0soy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpeoz6ubfm/f1.bed -b /tmp/tmpeoz6ubfm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpt1_7uwk9/f1.bed -b /tmp/tmpt1_7uwk9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpeytrnkwr/f1.bed -b /tmp/tmpeytrnkwr/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpzdkmb7xu/f1.bed -b /tmp/tmpzdkmb7xu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpf5ryst8b/f1.bed -b /tmp/tmpf5ryst8b/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpe0cy0pex/f1.bed -b /tmp/tmpe0cy0pex/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpn6pg6yt1/f1.bed -b /tmp/tmpn6pg6yt1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpwq21eaj0/f1.bed -b /tmp/tmpwq21eaj0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmps0h7o8gf/f1.bed -b /tmp/tmps0h7o8gf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp7ue9hkos/f1.bed -b /tmp/tmp7ue9hkos/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpc1jvft5a/f1.bed -b /tmp/tmpc1jvft5a/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpex9_vp96/f1.bed -b /tmp/tmpex9_vp96/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpllhzd2hs/f1.bed -b /tmp/tmpllhzd2hs/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp3i172pc8/f1.bed -b /tmp/tmp3i172pc8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp_oypdsw4/f1.bed -b /tmp/tmp_oypdsw4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpwfn4wqo8/f1.bed -b /tmp/tmpwfn4wqo8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp7xe_48qe/f1.bed -b /tmp/tmp7xe_48qe/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpw7ho75bm/f1.bed -b /tmp/tmpw7ho75bm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp5miywxhd/f1.bed -b /tmp/tmp5miywxhd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpbgtegggg/f1.bed -b /tmp/tmpbgtegggg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp7nc54gp_/f1.bed -b /tmp/tmp7nc54gp_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpg1wpvwzn/f1.bed -b /tmp/tmpg1wpvwzn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp80es39i_/f1.bed -b /tmp/tmp80es39i_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpmpt9g618/f1.bed -b /tmp/tmpmpt9g618/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpbkqnvx8i/f1.bed -b /tmp/tmpbkqnvx8i/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpac0zc94a/f1.bed -b /tmp/tmpac0zc94a/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpj87xtfxh/f1.bed -b /tmp/tmpj87xtfxh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp0vc8f2q9/f1.bed -b /tmp/tmp0vc8f2q9/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_chain54-method_chain54] ___________ [gw2] linux -- Python 3.12.3 /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/python3.12/typing.py:1195 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('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('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') ('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') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('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_chain23-method_chain23] ___________ [gw3] linux -- Python 3.12.3 /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 | 3080484 | 3086125 | a | 0 | + | E | chr1 | 3080484 | 3086125 | a | 0 | + | E | chr1 | 2097665 | 2103306 | a | 0 | + | E | chr1 | 3080484 | 3086125 | a | 0 | + | E | chr1 | 3080484 | 3086125 | a | 0 | - | E | chr7 | 3080484 | 3086125 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 6 rows and 6 columns from 2 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 | 257 | 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 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('6.100.4', b'AXicY+ZJNixhDHldqKzxKp7NKO+bJLPctA+vWJQr4q8wy+nsu8YgxMrAxsrKwMDAyMSkwMTAIKHPqMzAIMbBzszIwMAW/6iCgYOBkYGfkQEEGaCYmQ/EYGRhZGKwYWBmBACEvA9u') 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') ('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') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9393849 | 9402852 | a | 0 | ... | | chr1 | 9393849 | 9401460 | a | 0 | ... | | chr1 | 8597782 | 8598280 | 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 ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('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') ('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') ('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') ('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') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('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_k_nearest[upstream-True-opposite-last] __________________ [gw1] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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 | 5373960 | 5378402 | 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 | 8015641 | 8016219 | 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('6.100.4', b'AAFgR6eIAAABAAlSAAcAXBFZAQABAAFnhnzCAAEAAQABAER6TxgAAQBeAkEAAAA=') 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) | | |--------------+-----------+-----------+------------+-----------+--------------| | | 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 39 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2SAAEYGBGDEFGMEAACRAAY=') 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/tmpr6rgzu2s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr6rgzu2s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpy1mzdtsx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy1mzdtsx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpn6zm076l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn6zm076l/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpc12dlfkk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc12dlfkk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp4fzghyo7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4fzghyo7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpm20m_fqb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm20m_fqb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmptqhmeomg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptqhmeomg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpr098umq8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr098umq8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpkaw69004/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkaw69004/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpuh5ejphz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuh5ejphz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpfqz09h4k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfqz09h4k/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpjk3k6xww/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjk3k6xww/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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_i9ls3oh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_i9ls3oh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp0aj3sbed/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0aj3sbed/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmplc_l40q5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplc_l40q5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp5stysnk2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5stysnk2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpk1gytuat/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk1gytuat/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3838x0g9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3838x0g9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0v4t15jj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0v4t15jj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmprjzw4b0v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprjzw4b0v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpy9ykru7i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy9ykru7i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj7k0i496/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj7k0i496/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuz2k8w0u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuz2k8w0u/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcjub7sch/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcjub7sch/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3g0stw2e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3g0stw2e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn6yf75ax/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn6yf75ax/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6ax697jp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6ax697jp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9j6k5jkc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9j6k5jkc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpeeg5iv52/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeeg5iv52/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy3ggl44e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy3ggl44e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmplpnz2634/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplpnz2634/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc662hpuu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc662hpuu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuz47sjah/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuz47sjah/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmphp9l_bn6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphp9l_bn6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyiqz83bj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyiqz83bj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsyic90ya/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsyic90ya/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpoc0vy9ie/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoc0vy9ie/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp3enaj3mq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3enaj3mq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1reuzfcj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1reuzfcj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2sj3rv13/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2sj3rv13/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp38th7kq7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp38th7kq7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmphgi9t08a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphgi9t08a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxkraa8lo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxkraa8lo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdq_cpht8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdq_cpht8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf7x9ibdy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf7x9ibdy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpen4oxh1f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpen4oxh1f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpag1lnhah/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpag1lnhah/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpci9crnxc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpci9crnxc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp15wnfs1t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp15wnfs1t/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpmmew0qnd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmmew0qnd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp80nyfoc7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp80nyfoc7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr3aong0_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr3aong0_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdefkp5xg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdefkp5xg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkyj4jari/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkyj4jari/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7sgydcyy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7sgydcyy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp78c941nc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp78c941nc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyj97jb0i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyj97jb0i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqrf03hw1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqrf03hw1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3ekzusoy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3ekzusoy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkdihexzy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkdihexzy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwdwhq82c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwdwhq82c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpet9a18sb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpet9a18sb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsbf4f5r2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsbf4f5r2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmplpm6wgmo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplpm6wgmo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu_izdgq0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu_izdgq0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgujiird2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgujiird2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqjj7gj0f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqjj7gj0f/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpsy94scyv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsy94scyv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7169_1jw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7169_1jw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpbzj3i5lm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbzj3i5lm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkrtgsim5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkrtgsim5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp5ao0pifu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5ao0pifu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpga8r6rdk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpga8r6rdk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzfkj1b5r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzfkj1b5r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpovi_dirs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpovi_dirs/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3iz7ru2l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3iz7ru2l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3npif0ru/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3npif0ru/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcqjrg3je/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcqjrg3je/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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_yjvvlqd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_yjvvlqd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmprjj6_1rz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprjj6_1rz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpicrij6we/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpicrij6we/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7mjox6z6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7mjox6z6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpclz5jh2v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpclz5jh2v/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo35uwk9f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo35uwk9f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkkl5eusd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkkl5eusd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpkbnx_k3l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkbnx_k3l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd25oo5hm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd25oo5hm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfc9qpiq0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfc9qpiq0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpzchq7s2z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzchq7s2z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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_h3e49y3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_h3e49y3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpc8bry5fl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc8bry5fl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp4_1r6hzs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4_1r6hzs/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpie7rt9jl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpie7rt9jl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpqs687709/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqs687709/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpyqh_ie6z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyqh_ie6z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpufhuzhvr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpufhuzhvr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpxh0fzei9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxh0fzei9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpozke9py9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpozke9py9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0pmuntfe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0pmuntfe/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0_lqd8si/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0_lqd8si/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzlgeqydo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzlgeqydo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp6_rx2ur5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6_rx2ur5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp7vfjup17/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7vfjup17/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp014clpv1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp014clpv1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp9s5cq2aa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9s5cq2aa/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpp0ry72ga/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp0ry72ga/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpm7pa3xlt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm7pa3xlt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp8ox7itqj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8ox7itqj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp08srcnsg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp08srcnsg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpc4uu2f5a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc4uu2f5a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpr9tv_kkt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr9tv_kkt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp53ttx_jd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp53ttx_jd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxhff85fp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxhff85fp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnp5_vu7m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnp5_vu7m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpral_lm17/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpral_lm17/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzrk5ybbk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzrk5ybbk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmphrc8ka9r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphrc8ka9r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwfb19kuy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwfb19kuy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr9tmo54o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr9tmo54o/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg1ev94q3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg1ev94q3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwdgd541r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwdgd541r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqq9vp3wg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqq9vp3wg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3sd5s38z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3sd5s38z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvkc19oi0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvkc19oi0/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 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 chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on 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 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 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 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 chr2 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_subtraction[False] ____________________________ [gw0] linux -- Python 3.12.3 /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., 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('6.100.4', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') 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/tmp_9onxf2o/f1.bed -b /tmp/tmp_9onxf2o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp49__ldrv/f1.bed -b /tmp/tmp49__ldrv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpbnkga9g2/f1.bed -b /tmp/tmpbnkga9g2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmplvywikp9/f1.bed -b /tmp/tmplvywikp9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpsg96_uk1/f1.bed -b /tmp/tmpsg96_uk1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpdqp1oo_l/f1.bed -b /tmp/tmpdqp1oo_l/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpcdi_6lis/f1.bed -b /tmp/tmpcdi_6lis/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpqwlbm1m7/f1.bed -b /tmp/tmpqwlbm1m7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpfrc3j_bl/f1.bed -b /tmp/tmpfrc3j_bl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpkh62mr1f/f1.bed -b /tmp/tmpkh62mr1f/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmplalc32vl/f1.bed -b /tmp/tmplalc32vl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpji6lp7n1/f1.bed -b /tmp/tmpji6lp7n1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpamyyqgia/f1.bed -b /tmp/tmpamyyqgia/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpxdqu9b_w/f1.bed -b /tmp/tmpxdqu9b_w/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpy4_4xstu/f1.bed -b /tmp/tmpy4_4xstu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp77gtykgm/f1.bed -b /tmp/tmp77gtykgm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpnsb5u_di/f1.bed -b /tmp/tmpnsb5u_di/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp6l8b712o/f1.bed -b /tmp/tmp6l8b712o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp2_1hhjnf/f1.bed -b /tmp/tmp2_1hhjnf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp3ij95p93/f1.bed -b /tmp/tmp3ij95p93/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp81t29nor/f1.bed -b /tmp/tmp81t29nor/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpmxddt558/f1.bed -b /tmp/tmpmxddt558/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpt_q6a36c/f1.bed -b /tmp/tmpt_q6a36c/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp8jrcayjd/f1.bed -b /tmp/tmp8jrcayjd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpv65ty5o1/f1.bed -b /tmp/tmpv65ty5o1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp_yctuv9y/f1.bed -b /tmp/tmp_yctuv9y/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpih0yjz1e/f1.bed -b /tmp/tmpih0yjz1e/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpilsx8pzj/f1.bed -b /tmp/tmpilsx8pzj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp865kn1va/f1.bed -b /tmp/tmp865kn1va/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpx7sf2dvd/f1.bed -b /tmp/tmpx7sf2dvd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp1jgww9na/f1.bed -b /tmp/tmp1jgww9na/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpwa5dmekv/f1.bed -b /tmp/tmpwa5dmekv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpt9m1ggdo/f1.bed -b /tmp/tmpt9m1ggdo/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpms_82btp/f1.bed -b /tmp/tmpms_82btp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp91it692y/f1.bed -b /tmp/tmp91it692y/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpmgk2pwqi/f1.bed -b /tmp/tmpmgk2pwqi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp5rpl3j7o/f1.bed -b /tmp/tmp5rpl3j7o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp_w1g963y/f1.bed -b /tmp/tmp_w1g963y/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpr2zw7g1c/f1.bed -b /tmp/tmpr2zw7g1c/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpznreqgw9/f1.bed -b /tmp/tmpznreqgw9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp4dno7axv/f1.bed -b /tmp/tmp4dno7axv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpt98n77oa/f1.bed -b /tmp/tmpt98n77oa/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpie8n1tjr/f1.bed -b /tmp/tmpie8n1tjr/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpf44m5udc/f1.bed -b /tmp/tmpf44m5udc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpp9rdex_l/f1.bed -b /tmp/tmpp9rdex_l/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpm0oafc9l/f1.bed -b /tmp/tmpm0oafc9l/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpzqupquiu/f1.bed -b /tmp/tmpzqupquiu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpc1nlntb_/f1.bed -b /tmp/tmpc1nlntb_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpogx_eaoq/f1.bed -b /tmp/tmpogx_eaoq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpjozle1qx/f1.bed -b /tmp/tmpjozle1qx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpwwjs8g8z/f1.bed -b /tmp/tmpwwjs8g8z/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp286ynp2z/f1.bed -b /tmp/tmp286ynp2z/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpazllb3nu/f1.bed -b /tmp/tmpazllb3nu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp6j5sh06s/f1.bed -b /tmp/tmp6j5sh06s/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpabqhwotx/f1.bed -b /tmp/tmpabqhwotx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpvpqzedab/f1.bed -b /tmp/tmpvpqzedab/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpb1abnjg3/f1.bed -b /tmp/tmpb1abnjg3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp3yzlp1aq/f1.bed -b /tmp/tmp3yzlp1aq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpy3hhwjye/f1.bed -b /tmp/tmpy3hhwjye/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmph15wl76g/f1.bed -b /tmp/tmph15wl76g/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpbqo41f7m/f1.bed -b /tmp/tmpbqo41f7m/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpcnpvcvw2/f1.bed -b /tmp/tmpcnpvcvw2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpq6epo4s6/f1.bed -b /tmp/tmpq6epo4s6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp3q28psft/f1.bed -b /tmp/tmp3q28psft/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpk6c9dil8/f1.bed -b /tmp/tmpk6c9dil8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmptv22a_wx/f1.bed -b /tmp/tmptv22a_wx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpff4xorbh/f1.bed -b /tmp/tmpff4xorbh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpt8754cfx/f1.bed -b /tmp/tmpt8754cfx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp8t04vqkz/f1.bed -b /tmp/tmp8t04vqkz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpa2y4tctq/f1.bed -b /tmp/tmpa2y4tctq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp97klsrx_/f1.bed -b /tmp/tmp97klsrx_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp_d9_sghz/f1.bed -b /tmp/tmp_d9_sghz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpbpv68asi/f1.bed -b /tmp/tmpbpv68asi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmplsqo42z4/f1.bed -b /tmp/tmplsqo42z4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp20oc9e19/f1.bed -b /tmp/tmp20oc9e19/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpw2_hevuo/f1.bed -b /tmp/tmpw2_hevuo/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp48607gzg/f1.bed -b /tmp/tmp48607gzg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmptnz_9ubz/f1.bed -b /tmp/tmptnz_9ubz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmprzp839pr/f1.bed -b /tmp/tmprzp839pr/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpdgt401mg/f1.bed -b /tmp/tmpdgt401mg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmppk37dt19/f1.bed -b /tmp/tmppk37dt19/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpmtpoe9_6/f1.bed -b /tmp/tmpmtpoe9_6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp8rt8_8o5/f1.bed -b /tmp/tmp8rt8_8o5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpo61gehd3/f1.bed -b /tmp/tmpo61gehd3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpi4ytdjls/f1.bed -b /tmp/tmpi4ytdjls/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpie4qxgxz/f1.bed -b /tmp/tmpie4qxgxz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpiax272i5/f1.bed -b /tmp/tmpiax272i5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp3dwuedqo/f1.bed -b /tmp/tmp3dwuedqo/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmphyhsbg7y/f1.bed -b /tmp/tmphyhsbg7y/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp3wzcpmwg/f1.bed -b /tmp/tmp3wzcpmwg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpllmjm5by/f1.bed -b /tmp/tmpllmjm5by/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpnqit8x50/f1.bed -b /tmp/tmpnqit8x50/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpu4td1xxf/f1.bed -b /tmp/tmpu4td1xxf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpg2pnq7n_/f1.bed -b /tmp/tmpg2pnq7n_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmphse1dhqe/f1.bed -b /tmp/tmphse1dhqe/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpyv91m4j3/f1.bed -b /tmp/tmpyv91m4j3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp4gwuvzkj/f1.bed -b /tmp/tmp4gwuvzkj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpx2fl8iqm/f1.bed -b /tmp/tmpx2fl8iqm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp69zxbgx4/f1.bed -b /tmp/tmp69zxbgx4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpb3tqkwu9/f1.bed -b /tmp/tmpb3tqkwu9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpv0ca5ts4/f1.bed -b /tmp/tmpv0ca5ts4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmprk1570ic/f1.bed -b /tmp/tmprk1570ic/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpj4wutpzv/f1.bed -b /tmp/tmpj4wutpzv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp86i6d364/f1.bed -b /tmp/tmp86i6d364/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpmscxdyv9/f1.bed -b /tmp/tmpmscxdyv9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpu6mf0w28/f1.bed -b /tmp/tmpu6mf0w28/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp0hqg_jgg/f1.bed -b /tmp/tmp0hqg_jgg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpjumxesyi/f1.bed -b /tmp/tmpjumxesyi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpnc3mlz_1/f1.bed -b /tmp/tmpnc3mlz_1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmprc0mr4qj/f1.bed -b /tmp/tmprc0mr4qj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpo9ulcsz0/f1.bed -b /tmp/tmpo9ulcsz0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpqq2_bgll/f1.bed -b /tmp/tmpqq2_bgll/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpf3yhzs5d/f1.bed -b /tmp/tmpf3yhzs5d/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp070dg272/f1.bed -b /tmp/tmp070dg272/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp0erk4s29/f1.bed -b /tmp/tmp0erk4s29/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpu826ti66/f1.bed -b /tmp/tmpu826ti66/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpwkz7da11/f1.bed -b /tmp/tmpwkz7da11/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmps0yaxxzn/f1.bed -b /tmp/tmps0yaxxzn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpsec0q3do/f1.bed -b /tmp/tmpsec0q3do/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp_hsmp7f6/f1.bed -b /tmp/tmp_hsmp7f6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpxqvn_7ie/f1.bed -b /tmp/tmpxqvn_7ie/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_chain55-method_chain55] ___________ [gw2] linux -- Python 3.12.3 /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 181 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('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') Empty PyRanges ('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') ('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') 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') 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') ---------------------------------- 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_chain24-method_chain24] ___________ [gw3] linux -- Python 3.12.3 /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 | 770 | 777 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | 131073 | 132688 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 170 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2RkYAAjRgZmRgZWBjYGRkZ101iIKBMDAwMLmx9IEgwYORgYJBkBH2wBUQ==') 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') 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') ('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') ('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') 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') ('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') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('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_k_nearest[upstream-True-same-last] ____________________ [gw1] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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='same', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 71426 | 72201 | a | 0 | - | | | chr1 | 71426 | 72201 | a | 0 | - | | | chr1 | 71426 | 72201 | a | 0 | - | | | chr3 | 71426 | 72201 | a | 0 | - | | | chrY | 71426 | 72201 | 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 | 65567 | 65824 | 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('6.100.4', b'AAFm4Tm5jO87BwYPNjEOBG8Wt0kGWzCKgwINav99ABkAAAIBBgIBCgcDAQEBAQUCCwQAFwAABQEXAQAAAwYAAQEBAQMDAAAAAAAGAQAeBgAEAQAAAQABAA==') 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='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('6.100.4', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') 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/tmpur1m8whc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpur1m8whc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4u3vljyo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4u3vljyo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqgd4z2j1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqgd4z2j1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp02wk5ooi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp02wk5ooi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5_rawbrp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5_rawbrp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiz83kp23/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiz83kp23/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk8oindqg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk8oindqg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8oljrz00/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8oljrz00/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp472hpzen/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp472hpzen/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpwbgx6f81/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwbgx6f81/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmprrradokl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprrradokl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1c2zjzfj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1c2zjzfj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnxt0w2t2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnxt0w2t2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2hwg602g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2hwg602g/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpatj5r19b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpatj5r19b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjt9aubpe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjt9aubpe/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8lqj0zte/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8lqj0zte/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoeuum4_k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoeuum4_k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3yic3bbc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3yic3bbc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbe1ssfc1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbe1ssfc1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmph2kiomr6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph2kiomr6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxwd2sd9z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxwd2sd9z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmptzmuc5mx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptzmuc5mx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9hludhm0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9hludhm0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6c6ajayf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6c6ajayf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfy0bcfh4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfy0bcfh4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaq_7o7j9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaq_7o7j9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbi2toxrq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbi2toxrq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp69lz386f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp69lz386f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk2zzib2t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk2zzib2t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3ngw8pah/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3ngw8pah/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzli8rnww/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzli8rnww/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb9d3hooh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb9d3hooh/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_mirum06/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_mirum06/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoivq2nee/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoivq2nee/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp94a46xc9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp94a46xc9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3nvy8vru/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3nvy8vru/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz5cuj9n_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz5cuj9n_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp457ex8rq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp457ex8rq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpap9bgija/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpap9bgija/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpup48l831/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpup48l831/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxrt6x8wa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxrt6x8wa/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbf2bidj5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbf2bidj5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmptr48xzqt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptr48xzqt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwgrjoy_t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwgrjoy_t/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpheg0vll2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpheg0vll2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp606t7s9_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp606t7s9_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpusoh863j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpusoh863j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmps2e35nl2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps2e35nl2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpc3jivo2a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc3jivo2a/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_mh0hr7v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_mh0hr7v/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmprhp0j8ju/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprhp0j8ju/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_f8pioqy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_f8pioqy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp5olbi0fm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5olbi0fm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp6c251b2b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6c251b2b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpbt3i5cxw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbt3i5cxw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpqog2nemu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqog2nemu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp3bzo__7_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3bzo__7_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp0q070hvz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0q070hvz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3xns02tt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3xns02tt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpszcjrnmw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpszcjrnmw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm1uxf990/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm1uxf990/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjjbx5pi7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjjbx5pi7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy_f1fdm0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy_f1fdm0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmmsdbhtz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmmsdbhtz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp81ox5i_e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp81ox5i_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/tmp1imm_gdg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1imm_gdg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmptdog120k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptdog120k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7aw_rqe8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7aw_rqe8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpbf0gjju9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbf0gjju9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmphduvtj1t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphduvtj1t/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpt3o98bh2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt3o98bh2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpoojzpfdg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoojzpfdg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq7e75u_y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq7e75u_y/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpa1e34ycx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa1e34ycx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpz69w5939/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz69w5939/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpxeuzu3cb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxeuzu3cb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpmldw6g4s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmldw6g4s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpwbgmhdgt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwbgmhdgt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpbg7dnloc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbg7dnloc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp45hdb0hx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp45hdb0hx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8uakcm6v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8uakcm6v/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgya_jcei/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgya_jcei/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpldxsufh_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpldxsufh_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpznfj1sm2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpznfj1sm2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzahg3b3n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzahg3b3n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmps7u0hy2a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps7u0hy2a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpanvfaz6p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpanvfaz6p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpfmbu4gjt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfmbu4gjt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpvozdah1z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvozdah1z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp11yqjter/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp11yqjter/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmph4mhgesc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph4mhgesc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp0k2fawau/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0k2fawau/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpnrtk5h1s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnrtk5h1s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpnyrgdd1p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnyrgdd1p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpo1uo_cls/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo1uo_cls/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp2i3ipa65/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2i3ipa65/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcc88ldx9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcc88ldx9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp0xg222_4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0xg222_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 -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwpgikp5d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwpgikp5d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvjwm40qp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvjwm40qp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmptnanhro5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptnanhro5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa_d9spf9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa_d9spf9/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 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 chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on 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 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_chain56-method_chain56] ___________ [gw2] linux -- Python 3.12.3 /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/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/python3.12/typing.py:1195 E (and 114 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('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') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('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') 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') 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') ---------------------------------- 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-False] _________________________ [gw0] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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 | 131073 | 131599 | 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 59 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2QAA0YGBGAUZITyGZmAhAATLwMjAAKDADo=') 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 1209, in assert_frame_equal | assert_series_equal( | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 918, 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 414, in assert_attr_equal | raise_assert_detail(obj, msg, left_attr, right_attr) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 598, 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 461 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') 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/tmp0lvbk1pq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0lvbk1pq/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/tmpxzog2xck/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxzog2xck/f2.bed) bedtools bedtools bedtools bedtools 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/tmptzb39hus/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptzb39hus/f2.bed) bedtools bedtools bedtools bedtools 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/tmpch5_wkfa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpch5_wkfa/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy86os1dk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy86os1dk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwirj_op8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwirj_op8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 27697 30930 + 0 1 chr1 769594 777675 - 0 2 chr1 3802025 3805905 - 0 3 chr1 4889731 4891604 + 0 4 chr1 5450959 5460918 + 0 5 chr1 7862313 7865546 + 0 6 chr1 8761750 8771637 - 0 7 chr12 6301694 6306920 + 0 8 chr15 1568206 1570771 + 0 9 chr6 4281166 4284399 - 0 10 chrM 9999999 10003232 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7862313 | 7865546 | a | 0 | ... | | chr1 | 27697 | 30930 | a | 0 | ... | | chr1 | 4889731 | 4891604 | a | 0 | ... | | chr1 | 5450959 | 5460918 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr6 | 4281166 | 4284399 | a | 0 | ... | | chr12 | 6301694 | 6306920 | a | 0 | ... | | chr15 | 1568206 | 1570771 | a | 0 | ... | | chrM | 9999999 | 10003232 | 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 1 chr1 27697 30930 + 0 4 chr1 769594 777675 - 0 9 chr15 1568206 1570771 + 0 5 chr1 3802025 3805905 - 0 7 chr6 4281166 4284399 - 0 2 chr1 4889731 4891604 + 0 3 chr1 5450959 5460918 + 0 8 chr12 6301694 6306920 + 0 0 chr1 7862313 7865546 + 0 6 chr1 8761750 8771637 - 0 10 chrM 9999999 10003232 + 0 df2 Chromosome Start End Strand Distance 0 chr1 27697 30930 + 0 1 chr1 769594 777675 - 0 8 chr15 1568206 1570771 + 0 2 chr1 3802025 3805905 - 0 9 chr6 4281166 4284399 - 0 3 chr1 4889731 4891604 + 0 4 chr1 5450959 5460918 + 0 7 chr12 6301694 6306920 + 0 5 chr1 7862313 7865546 + 0 6 chr1 8761750 8771637 - 0 10 chrM 9999999 10003232 + 0 Actual Chromosome Start End Strand Distance 0 chr1 27697 30930 + 0 1 chr1 769594 777675 - 0 2 chr1 3802025 3805905 - 0 3 chr1 4889731 4891604 + 0 4 chr1 5450959 5460918 + 0 5 chr1 7862313 7865546 + 0 6 chr1 8761750 8771637 - 0 7 chr12 6301694 6306920 + 0 8 chr15 1568206 1570771 + 0 9 chr6 4281166 4284399 - 0 10 chrM 9999999 10003232 + 0 Expected Chromosome Start End Strand Distance 0 chr1 27697 30930 + 0 1 chr1 769594 777675 - 0 2 chr1 3802025 3805905 - 0 3 chr1 4889731 4891604 + 0 4 chr1 5450959 5460918 + 0 5 chr1 7862313 7865546 + 0 6 chr1 8761750 8771637 - 0 7 chr12 6301694 6306920 + 0 8 chr15 1568206 1570771 + 0 9 chr6 4281166 4284399 - 0 10 chrM 9999999 10003232 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object 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 -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuebcpzs5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuebcpzs5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9ds9mssq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9ds9mssq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmpedm0ik/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmpedm0ik/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjihfcr9p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjihfcr9p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplyu74bqa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplyu74bqa/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/tmpnkd663b7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnkd663b7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpap4nej5h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpap4nej5h/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/tmpag59wse4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpag59wse4/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/tmpkdz4b7oe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkdz4b7oe/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/tmp1rx0y1_7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1rx0y1_7/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/tmpcrgza0tc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcrgza0tc/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/tmp9r7e0fxl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9r7e0fxl/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/tmp720838_j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp720838_j/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/tmptlpzabgy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptlpzabgy/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/tmpsuf8sjbx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsuf8sjbx/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/tmp29f5b_z0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp29f5b_z0/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/tmpxsocpkap/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxsocpkap/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/tmp6iamlpmg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6iamlpmg/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/tmpfay1kmz2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfay1kmz2/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/tmph4e1fss5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph4e1fss5/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/tmpstoky3zs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpstoky3zs/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/tmpb1jjise3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb1jjise3/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/tmp7w7f00l8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7w7f00l8/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/tmphaq98nhs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphaq98nhs/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/tmpp23e39to/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp23e39to/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/tmpk9cixkpe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk9cixkpe/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/tmpxhp86m8q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxhp86m8q/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/tmpdxkrwv4b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdxkrwv4b/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/tmpuwfhk31r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuwfhk31r/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/tmp8oh9exbd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8oh9exbd/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/tmpehdxmtm_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpehdxmtm_/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/tmp_gkxmmwu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_gkxmmwu/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/tmpd9k6a73j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd9k6a73j/f2.bed) bedtools bedtools bedtools bedtools 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/tmp9q4a8bi4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9q4a8bi4/f2.bed) bedtools bedtools bedtools bedtools 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/tmppp6k_1bs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppp6k_1bs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpny42mca7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpny42mca7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxnbn6ft0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxnbn6ft0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe2jdqo48/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe2jdqo48/f2.bed) bedtools bedtools bedtools bedtools 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/tmppgc5tmwa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppgc5tmwa/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_fkjics_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_fkjics_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplvtg5af7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplvtg5af7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprr_56bqb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprr_56bqb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphxrjr_u6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphxrjr_u6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5cb_plzp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5cb_plzp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqgcswb1c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqgcswb1c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzzngxol2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzzngxol2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5ghm5zxv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5ghm5zxv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbtpzylyf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbtpzylyf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgf7qinub/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgf7qinub/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_ozdfjzw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_ozdfjzw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi1as9a2e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi1as9a2e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppkullgl6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppkullgl6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpps4t0_76/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpps4t0_76/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpljg0qwpn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpljg0qwpn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk_g4kc64/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk_g4kc64/f2.bed) bedtools bedtools bedtools bedtools 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/tmpty69g8cm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpty69g8cm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbll66ksc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbll66ksc/f2.bed) bedtools bedtools bedtools bedtools 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/tmpro70_25t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpro70_25t/f2.bed) bedtools bedtools bedtools bedtools 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/tmpkbpqiplf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkbpqiplf/f2.bed) bedtools bedtools bedtools bedtools 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/tmp89gkzfkj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp89gkzfkj/f2.bed) bedtools bedtools bedtools bedtools 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/tmpjb0rv9do/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjb0rv9do/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 374 7841 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 374 | 7841 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on 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 374 7841 - 0 df2 Chromosome Start End Strand Distance 0 chr1 374 7841 - 0 Actual Chromosome Start End Strand Distance 0 chr1 374 7841 - 0 Expected Chromosome Start End Strand Distance 0 chr1 374 7841 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object 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/tmp7uey9j8p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7uey9j8p/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 10000 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 10000 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on 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 10000 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 10000 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 10000 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 10000 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object 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/tmpa_bdpp3u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa_bdpp3u/f2.bed) bedtools bedtools bedtools bedtools 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/tmpl20vc059/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl20vc059/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 10000 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 10000 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on 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 10000 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 10000 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 10000 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 10000 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object 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/tmplwdijj70/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplwdijj70/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoxjc7es5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoxjc7es5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpya0mlr8z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpya0mlr8z/f2.bed) bedtools bedtools bedtools bedtools 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/tmps3muet5r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps3muet5r/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl71kdvzr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl71kdvzr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0n_82eq9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0n_82eq9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqvos16af/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqvos16af/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_chain25-method_chain25] ___________ [gw3] linux -- Python 3.12.3 /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 | 65795 | 66053 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | 257 | 2819 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AXicY2RmZmRgYGBkYGJkZALSQA6jGwOIBBHMYIqfC6QExGdl4AcKAAAOzQCS') 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') 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') ('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') ('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') ('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') 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') ('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_k_nearest[upstream-True-False-last] ___________________ [gw1] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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 | 2641589 | 2646968 | a | 0 | - | | | chr2 | 459385 | 459440 | a | 0 | + | | | chr6 | 2229284 | 2230345 | a | 0 | + | | | chr6 | 75523 | 81141 | a | 0 | - | | | chr6 | 8578065 | 8586770 | a | 0 | - | | | chr6 | 2229284 | 2233920 | a | 0 | - | | | chr20 | 220268 | 226420 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 7 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 | 711289 | 721061 | a | 0 | + | | | chr1 | 460080 | 469852 | a | 0 | + | | | chr19 | 786945 | 796717 | a | 0 | + | | | chr19 | 6019926 | 6029698 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 4 rows and 6 columns from 2 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 41 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicFc69SoJhFAfw8z/POc8BEV8/MMKXDL/SzF4DScqsaIigwa0hdG7pBmxp6C4KgsaWmrqIgqC1bCqcaurjAnrbf8MPu4P1FS6Mghuj4f3jZPrzveafDPWHk/fttxfOVRevUSv6C186//xFq0cqpH0zolxHUdKGIxBpEiHqDEq50XEGmyaVq8uPs2m6gBmIK98eRsbjntEGoFuNwV3RZN7VDKGWDE2QK0vFY6/93NyPEvmvjrmIuquy3D8tU1pqdDRrIt5H2TDw0CDPcE6EQ6lSoGgxFR0R0NCd+Fd3cKakTCmLt4BHlqHxM6tspm0Xh/mfJyZjpjQlOeNk+HpA1F1YyjPNEflY4w8T1SoV') 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 36 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') 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/tmp1o6onvpn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1o6onvpn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_69c4qyc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_69c4qyc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmptfdpmy7i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptfdpmy7i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvdtuc22u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvdtuc22u/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmplqrllw7h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplqrllw7h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdt36u8q3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdt36u8q3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6x_t32y3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6x_t32y3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy2ff9x0r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy2ff9x0r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_qv1bpm8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_qv1bpm8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_6qtwquw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_6qtwquw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0izl1742/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0izl1742/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxu17vu2_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxu17vu2_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6cccu5cu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6cccu5cu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk_4k9745/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk_4k9745/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0hp86jd9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0hp86jd9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_cxyx0b9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_cxyx0b9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9rgahvjb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9rgahvjb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdo1hzf53/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdo1hzf53/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmo87dzjx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmo87dzjx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3lvn6zma/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3lvn6zma/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9qs9tfvo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9qs9tfvo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpks29kzfb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpks29kzfb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw8ip943k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw8ip943k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiyg69mzc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiyg69mzc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0bgq842w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0bgq842w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp86sx1cfu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp86sx1cfu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd_j5wq4t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd_j5wq4t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfunu16a_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfunu16a_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw0v3ul06/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw0v3ul06/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7bouyfab/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7bouyfab/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn5ehohq9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn5ehohq9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj2jun1e1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj2jun1e1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp12a8lgjz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp12a8lgjz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0kve79r_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0kve79r_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmppmu6rksg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppmu6rksg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2kjnt019/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2kjnt019/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm283rt04/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm283rt04/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8h22c00e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8h22c00e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpedlelgr7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpedlelgr7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq6jq50lq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq6jq50lq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk8tylm5m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk8tylm5m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmps6g8_ql6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps6g8_ql6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpltp6ed7n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpltp6ed7n/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmppejsf603/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppejsf603/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqlt9fcq7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqlt9fcq7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy5e4kjrd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy5e4kjrd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqd17wo9_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqd17wo9_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5hmqdhvs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5hmqdhvs/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpeu3o7h2x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeu3o7h2x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq3ragg3_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq3ragg3_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdvesyr_h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdvesyr_h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8eyuxgnj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8eyuxgnj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_3e9_uyr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_3e9_uyr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz4xgu3a1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz4xgu3a1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6lf4m5jv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6lf4m5jv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpngqypw2e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpngqypw2e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmputiq6umb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmputiq6umb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmppiqa1knd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppiqa1knd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqsouzxmn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqsouzxmn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqzi9boor/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqzi9boor/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmptwog4bqk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptwog4bqk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi852zaw3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi852zaw3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfcksc078/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfcksc078/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd08yutiw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd08yutiw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp8v48bph8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8v48bph8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmplv21uljx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplv21uljx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpknl9fylz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpknl9fylz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7a8e9_er/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7a8e9_er/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3k4l3n_l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3k4l3n_l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6pkgpbf2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6pkgpbf2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuant5lfn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuant5lfn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6ps046qt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6ps046qt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv3p6wa7i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv3p6wa7i/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpu8hp65cy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu8hp65cy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp51wfgccz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp51wfgccz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxrarqmvu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxrarqmvu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9168ro7u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9168ro7u/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpar43mz06/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpar43mz06/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi7p7my5z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi7p7my5z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxrh99fmv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxrh99fmv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpef8ro2y1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpef8ro2y1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpydkxby70/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpydkxby70/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2ybnt4ut/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2ybnt4ut/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1fs3h09l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1fs3h09l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2sn07yu8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2sn07yu8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdgtruv1j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdgtruv1j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaem9t36z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaem9t36z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpejrquq8_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpejrquq8_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp2kp18qoy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2kp18qoy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbjojtqay/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbjojtqay/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcj79gpf4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcj79gpf4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpnculhugc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnculhugc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpmcy655vp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmcy655vp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpt2gkuqkk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt2gkuqkk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmps0ywwqk5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps0ywwqk5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp08f810w9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp08f810w9/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 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 chr1 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 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 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 chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on 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 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 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. ---------------------------------- 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_chain57-method_chain57] ___________ [gw2] linux -- Python 3.12.3 /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/python3.12/typing.py:1195 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 104 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('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') ('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') 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') ---------------------------------- 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] _________________________ [gw0] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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 | 1029889 | 1029891 | 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 | 2485816 | 2495589 | 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('6.100.4', b'AXicY5TxmyfCwMDIw+DLv50ByGBgZAERDFVADhuQ5mLwUH1nDqSY1HQY+IACAIZbBNA=') 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 1209, in assert_frame_equal | assert_series_equal( | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 918, 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 414, in assert_attr_equal | raise_assert_detail(obj, msg, left_attr, right_attr) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 598, 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 458 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') 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/tmp2b5co8wl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2b5co8wl/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/tmpf5qjs4pd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf5qjs4pd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpst5vusnp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpst5vusnp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl69rdsub/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl69rdsub/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjaykwmvy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjaykwmvy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppdjpu1h_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppdjpu1h_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu82pmbny/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu82pmbny/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppxy7od74/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppxy7od74/f2.bed) bedtools bedtools bedtools bedtools 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/tmp1sb4abbv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1sb4abbv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl54u8hlp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl54u8hlp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfem2hlaa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfem2hlaa/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/tmpufc9rj6k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpufc9rj6k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp44cbvi9g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp44cbvi9g/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/tmp8ya5zav3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8ya5zav3/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/tmprd0xvb4f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprd0xvb4f/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/tmpp4tfa5xs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp4tfa5xs/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/tmpmup216d0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmup216d0/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/tmp7s60y5y4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7s60y5y4/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/tmpv3aqlbik/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv3aqlbik/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/tmpydlc26h0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpydlc26h0/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/tmpdf0nc601/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdf0nc601/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/tmp7mai3qzq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7mai3qzq/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/tmp8p_y4c4g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8p_y4c4g/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/tmp69mfcxl2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp69mfcxl2/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/tmpefwq8e_b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpefwq8e_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 -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptx8ixlrl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptx8ixlrl/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/tmp4y3o97p5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4y3o97p5/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/tmpagrb_hdt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpagrb_hdt/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/tmp0z7rdht0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0z7rdht0/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/tmpmodyagu7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmodyagu7/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/tmpovp7kfwn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpovp7kfwn/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/tmpen7fbt1z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpen7fbt1z/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/tmpdbip026h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdbip026h/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/tmpw0x_wjj_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw0x_wjj_/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/tmpq__j11yv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq__j11yv/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/tmpb_2bb6cb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb_2bb6cb/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/tmpmelforzx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmelforzx/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/tmp5w0q680_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5w0q680_/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/tmp75gamx26/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp75gamx26/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7qozn1y7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7qozn1y7/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/tmp2zz46yu3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2zz46yu3/f2.bed) bedtools bedtools bedtools bedtools 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/tmpgzp7l042/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgzp7l042/f2.bed) bedtools bedtools bedtools bedtools 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/tmp39axgyw4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp39axgyw4/f2.bed) bedtools bedtools bedtools bedtools 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/tmp7ev8crrp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7ev8crrp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0z1u_s28/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0z1u_s28/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa5qai8gb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa5qai8gb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp1czjfs4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp1czjfs4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5am1cw9c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5am1cw9c/f2.bed) bedtools bedtools bedtools bedtools 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/tmp0nwlz8dx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0nwlz8dx/f2.bed) bedtools bedtools bedtools bedtools 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/tmpjjc91rsv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjjc91rsv/f2.bed) bedtools bedtools bedtools bedtools 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/tmpqh4sdxk3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqh4sdxk3/f2.bed) bedtools bedtools bedtools bedtools 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/tmp4nc_k17z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4nc_k17z/f2.bed) bedtools bedtools bedtools bedtools 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_fmgohep/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_fmgohep/f2.bed) bedtools bedtools bedtools bedtools 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/tmpxwhz29f2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxwhz29f2/f2.bed) bedtools bedtools bedtools bedtools 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/tmpelg70v41/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpelg70v41/f2.bed) bedtools bedtools bedtools bedtools 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/tmppikzv9fm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppikzv9fm/f2.bed) bedtools bedtools bedtools bedtools 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/tmpsicvjvow/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsicvjvow/f2.bed) bedtools bedtools bedtools bedtools 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/tmpgm8ku_44/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgm8ku_44/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0_1s_bnt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0_1s_bnt/f2.bed) bedtools bedtools bedtools bedtools 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/tmpfp6mu1yd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfp6mu1yd/f2.bed) bedtools bedtools bedtools bedtools 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/tmp9teka5jl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9teka5jl/f2.bed) bedtools bedtools bedtools bedtools 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/tmpt1mjc67d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt1mjc67d/f2.bed) bedtools bedtools bedtools bedtools 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/tmpshim9mcw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpshim9mcw/f2.bed) bedtools bedtools bedtools bedtools 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/tmplhjsqynz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplhjsqynz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpluelc6xy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpluelc6xy/f2.bed) bedtools bedtools bedtools bedtools 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/tmp3p50564s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3p50564s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmk6zulun/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmk6zulun/f2.bed) bedtools bedtools bedtools bedtools 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/tmpzwr7dnqp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzwr7dnqp/f2.bed) bedtools bedtools bedtools bedtools 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/tmpq6nvvyqo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq6nvvyqo/f2.bed) bedtools bedtools bedtools bedtools 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/tmp7vlxvr7v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7vlxvr7v/f2.bed) bedtools bedtools bedtools bedtools 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_1s6xfjl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_1s6xfjl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz67cqx5l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz67cqx5l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi6ohgj47/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi6ohgj47/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfsjj30x9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfsjj30x9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8wibkr0o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8wibkr0o/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_chain26-method_chain26] ___________ [gw3] linux -- Python 3.12.3 /usr/bin/python3.12 strandedness_chain = ('same', False), method_chain = ('nearest', '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=('nearest', '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 135 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- 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') ('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') 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') 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') 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') 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') 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') ---------------------------------- 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[None-False-opposite-last] ___________________ [gw1] linux -- Python 3.12.3 /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 | chr1 | 65794 | 71680 | a | 0 | + | E | chr1 | 65794 | 65795 | 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 +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AXicY2SQ3fuXMTLBn5uBgZGBEQQYGMT+MnAyAAGjs/5LI5A4HDACALWIBZ8=') 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/tmp96swuzq4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp96swuzq4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp00g9hh0r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp00g9hh0r/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpm7zbxruh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm7zbxruh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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_qczgtz0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_qczgtz0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpp7jymbnc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp7jymbnc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp728bv20w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp728bv20w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr8fsav1s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr8fsav1s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzzxj_9nk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzzxj_9nk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpof_f7vh9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpof_f7vh9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpch0str6l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpch0str6l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfay6egnv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfay6egnv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppnzyn4fx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppnzyn4fx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmphozeeizm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphozeeizm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpikft99fw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpikft99fw/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_pei5jkd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_pei5jkd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpbbphhyo1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbbphhyo1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp7b4otex6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7b4otex6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmptddzimoy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptddzimoy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpprwyj4fj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpprwyj4fj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4xi6zfh3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4xi6zfh3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu15ml8za/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu15ml8za/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjsqny0rg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjsqny0rg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpck267586/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpck267586/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpy7gbdowx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy7gbdowx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmptrwjoa4g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptrwjoa4g/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdsatgrvh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdsatgrvh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpvdtw64b0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvdtw64b0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpkwtqekts/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkwtqekts/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpe8r_dme1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe8r_dme1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpjaq5of5u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjaq5of5u/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_j5lcgz3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_j5lcgz3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppaamkwoy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppaamkwoy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsws4iqtp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsws4iqtp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1ewuxfuz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1ewuxfuz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuci7jj_e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuci7jj_e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfgv8_mcu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfgv8_mcu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprdw2bg5j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprdw2bg5j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8al2ewcl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8al2ewcl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjcvecmb6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjcvecmb6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz62eoj8j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz62eoj8j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyk58m0bi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyk58m0bi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz3j6qn21/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz3j6qn21/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_l74gwa6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_l74gwa6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpejhjplwt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpejhjplwt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp97ht6p0v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp97ht6p0v/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpelg1zcrm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpelg1zcrm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmz6r7skd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmz6r7skd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppj7jxwbj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppj7jxwbj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm6iu854a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm6iu854a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc9cwjsf2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc9cwjsf2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpantb_4ni/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpantb_4ni/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjgzgok9g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjgzgok9g/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmph_w2l4ys/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph_w2l4ys/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5yp1odxj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5yp1odxj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppamr9ig8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppamr9ig8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsbf7sg5l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsbf7sg5l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7vw53rhz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7vw53rhz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvogtcznh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvogtcznh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9tm2rog1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9tm2rog1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3ej6zemg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3ej6zemg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwdd4pxd3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwdd4pxd3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps_cmh18b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps_cmh18b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv9pnmur4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv9pnmur4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpomhubroj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpomhubroj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprz6jwany/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprz6jwany/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0klzpkse/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0klzpkse/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi_15qh31/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi_15qh31/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw6gvu2l6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw6gvu2l6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp8mdliphn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8mdliphn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgbt7ws1h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgbt7ws1h/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_aj7ohpp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_aj7ohpp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgj1k6_qh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgj1k6_qh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbn83lebx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbn83lebx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprccpm22p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprccpm22p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphtz0ylk6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphtz0ylk6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp4txks593/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4txks593/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv071rvds/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv071rvds/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3jrgphie/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3jrgphie/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp7jc8r_8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp7jc8r_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 -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd1dqj4n7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd1dqj4n7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf5d19fbo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf5d19fbo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyrjbyl7b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyrjbyl7b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppln_gaw8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppln_gaw8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjm700vf2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjm700vf2/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. ---------------------------------- 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[None-False-same-last] _____________________ [gw1] linux -- Python 3.12.3 /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 39 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') 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/tmpi0074wm3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi0074wm3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzyys9sz1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzyys9sz1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpou6ht9kn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpou6ht9kn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpsgqr7ex9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsgqr7ex9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp3ma96hwh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3ma96hwh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp010s_v2d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp010s_v2d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7xyfbbva/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7xyfbbva/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps7xnvyab/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps7xnvyab/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgzg8d26q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgzg8d26q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpyd5_ir8z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyd5_ir8z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp81uchpg_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp81uchpg_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9qjjjy6u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9qjjjy6u/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpukp451f6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpukp451f6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5xwidrwj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5xwidrwj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpygyulv_s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpygyulv_s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgqdji7ko/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgqdji7ko/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1iczr834/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1iczr834/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpot0c_e0e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpot0c_e0e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq8r4cmdx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq8r4cmdx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdu84oc9_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdu84oc9_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpylmxpoi1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpylmxpoi1/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_2bwbjag/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_2bwbjag/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9mriyqhk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9mriyqhk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqq5zp0uz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqq5zp0uz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8jort9ls/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8jort9ls/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp385u9cu3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp385u9cu3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgy3lvy9p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgy3lvy9p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmperv972/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmperv972/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprzwlebvr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprzwlebvr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm82zaxnn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm82zaxnn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkmh9zhsr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkmh9zhsr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7algrbcu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7algrbcu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsky9awiw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsky9awiw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfc0cgo2n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfc0cgo2n/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbt6xhvky/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbt6xhvky/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8nsb4qa6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8nsb4qa6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyc5e2hlw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyc5e2hlw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp67wbx0vj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp67wbx0vj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpj8aa4rg8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj8aa4rg8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7112v337/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7112v337/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3judnedq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3judnedq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7l0obkty/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7l0obkty/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8vxxjjeq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8vxxjjeq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnnbegxfh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnnbegxfh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp4krqtg55/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4krqtg55/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzstfiq3x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzstfiq3x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprd5_5da_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprd5_5da_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuz4oavx0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuz4oavx0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpp5n0dmb8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp5n0dmb8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3l6ww5n4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3l6ww5n4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmps6drjqtr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps6drjqtr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmptp_08g0f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptp_08g0f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp79ykehlm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp79ykehlm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb7ui2bmg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb7ui2bmg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2hy122if/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2hy122if/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpapra0v4w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpapra0v4w/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. ___________ test_three_in_a_row[strandedness_chain58-method_chain58] ___________ [gw2] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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 63 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('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') 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') 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') ('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') 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') ---------------------------------- 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] _______________________ [gw0] linux -- Python 3.12.3 /usr/bin/python3.12 nearest_how = None, overlap = True, 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=True, E strandedness='opposite', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65795 | 65797 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | 131088 | 135279 | a | 0 | - | E | chr1 | 131088 | 135279 | 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/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 124 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2TkYGJgYGBkBCJGIAtIAwkdgcxNjA7CTzpAApxMDPwM8gJxjCBFAEm/A9o=') 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 -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsxw1r6zi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsxw1r6zi/f2.bed) bedtools bedtools bedtools bedtools 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/tmp0tansez2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0tansez2/f2.bed) bedtools bedtools bedtools bedtools 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_bdc8eey/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_bdc8eey/f2.bed) bedtools bedtools bedtools bedtools 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/tmp4a8ad9xp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4a8ad9xp/f2.bed) bedtools bedtools bedtools bedtools 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/tmpwin_hbus/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwin_hbus/f2.bed) bedtools bedtools bedtools bedtools 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/tmpkv01olyk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkv01olyk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcc9c73js/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcc9c73js/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa1nbk5xx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa1nbk5xx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4ddlrbon/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ddlrbon/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpds3v4har/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpds3v4har/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp58qspytm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp58qspytm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa24k23aa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa24k23aa/f2.bed) bedtools bedtools bedtools bedtools 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/tmpu3tebi09/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu3tebi09/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgqj8bl3f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgqj8bl3f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnlxestxx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnlxestxx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbjjkop7j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbjjkop7j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzysb0qcp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzysb0qcp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd5_4j4ci/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd5_4j4ci/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpun8whlta/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpun8whlta/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_m9iecxm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_m9iecxm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfxkdrqt7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfxkdrqt7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvnvdv2x1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvnvdv2x1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeaefdlqc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeaefdlqc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprusd5gth/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprusd5gth/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfh0ea7af/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfh0ea7af/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprhaor86_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprhaor86_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprs0l_kch/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprs0l_kch/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp45ov6vru/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp45ov6vru/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9r7tdd_5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9r7tdd_5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnhex70cr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnhex70cr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpizzamnty/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpizzamnty/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpucugbsq0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpucugbsq0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgmhl83w4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgmhl83w4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk4wt93b7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk4wt93b7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7960bjt6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7960bjt6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6ywhu0zc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6ywhu0zc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb2y766ch/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb2y766ch/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuu05n9eo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuu05n9eo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1uiy0v91/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1uiy0v91/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3z6ixp4x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3z6ixp4x/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy3jf1nvs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy3jf1nvs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvgugef6g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvgugef6g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpisd54oh2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpisd54oh2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmipom2n8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmipom2n8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpate_jk7x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpate_jk7x/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprectqpgy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprectqpgy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp32wav94l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp32wav94l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyt8mg33c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyt8mg33c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkmw68l4z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkmw68l4z/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyggo0jnz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyggo0jnz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwf4vgt3u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwf4vgt3u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpesnkem2z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpesnkem2z/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvw3a45_i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvw3a45_i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp063ugs95/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp063ugs95/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyy4o_ux2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyy4o_ux2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp203zwiv3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp203zwiv3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps028la5q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps028la5q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt0a0qrgf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt0a0qrgf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpve5ylgo3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpve5ylgo3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwxli93w5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwxli93w5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgdue8gb_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgdue8gb_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3vpo7biu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3vpo7biu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt4kqcb41/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt4kqcb41/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1yua2jot/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1yua2jot/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3sdlozmc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3sdlozmc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeyxqs7b8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeyxqs7b8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk4njcgkg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk4njcgkg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1cvkds22/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1cvkds22/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz9ysflrz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz9ysflrz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy9utf3lz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy9utf3lz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6mliuev0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6mliuev0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvjkpkgcr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvjkpkgcr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl83awj_9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl83awj_9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpea_g2crl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpea_g2crl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwpixw70o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwpixw70o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxetd55c_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxetd55c_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppo5288ac/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppo5288ac/f2.bed) bedtools bedtools bedtools bedtools 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/tmpqbnhddw2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqbnhddw2/f2.bed) bedtools bedtools bedtools bedtools 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/tmp0_r6i1sw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0_r6i1sw/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_chain27-method_chain27] ___________ [gw3] linux -- Python 3.12.3 /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 | 1050374 | 1058153 | a | 0 | - | E | chr10 | 1050374 | 1058153 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 2 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 | 4128770 | 4129283 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 182 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AAUDR5TgARsfWE4ADQEACQYAAQAAABAHBQAmHmIPAwABDgADAQAAAQAPJwMADwkAAAADPwABAAACAAABAAEAAgABAAQAAQ==') 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') 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') ('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') ('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') 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') 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') ('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') Empty PyRanges ('nearest', 'join') 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') ('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_k_nearest[None-False-False-last] _____________________ [gw1] linux -- Python 3.12.3 /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('6.100.4', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') 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/tmpblj8imem/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpblj8imem/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpettjz7vp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpettjz7vp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps1hvnalo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps1hvnalo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6f42be0f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6f42be0f/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpk1r2pyh7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk1r2pyh7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2b8egdl4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2b8egdl4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgwh_hchq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgwh_hchq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8xp9aeid/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8xp9aeid/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptlcadax8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptlcadax8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1goq23eo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1goq23eo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp25j8gx1g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp25j8gx1g/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppl3shdst/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppl3shdst/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxjpq4nu3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxjpq4nu3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvdy1fptl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvdy1fptl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw1bsqn1b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw1bsqn1b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1d48pbmw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1d48pbmw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpihernajj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpihernajj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppsndlhw0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppsndlhw0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_s19uhw9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_s19uhw9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2irhdvi3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2irhdvi3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1csjtea1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1csjtea1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpivudz8uy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpivudz8uy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplb3gtf7s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplb3gtf7s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyojcgc9q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyojcgc9q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2oukpwt6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2oukpwt6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd9rd_v5v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd9rd_v5v/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1_7gn3uq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1_7gn3uq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwc0_9wva/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwc0_9wva/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjxipja6p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjxipja6p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp53s447wb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp53s447wb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6o8gccio/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6o8gccio/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp0lj5rzl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp0lj5rzl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpav31vs9x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpav31vs9x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg6syqx3x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg6syqx3x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpskl9im17/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpskl9im17/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw9grnrt0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw9grnrt0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvtt4zi0q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvtt4zi0q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp478ej7th/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp478ej7th/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpp6zc4a14/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp6zc4a14/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp3bl4qemz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3bl4qemz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpwg3l20rg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwg3l20rg/f2.bed) ----------------------------- Captured stderr call ----------------------------- 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. ________________________ test_nearest[None-False-False] ________________________ [gw0] linux -- Python 3.12.3 /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('6.100.4', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') 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/tmpn9flfnfx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn9flfnfx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpayt0yzn5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpayt0yzn5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiuzn_4f1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiuzn_4f1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp679xzq80/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp679xzq80/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn18q0ilc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn18q0ilc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpedha5m72/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpedha5m72/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6mos30w0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6mos30w0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg_jsqf6z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg_jsqf6z/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpauxwz2o2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpauxwz2o2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9tdz6z0j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9tdz6z0j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5nzt16zm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5nzt16zm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0dley_mr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0dley_mr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu_zqi6hj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu_zqi6hj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp93p0n56w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp93p0n56w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1b2dzx7a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1b2dzx7a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxcd638l4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxcd638l4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpod0xftlp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpod0xftlp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp964ievdd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp964ievdd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptls1769j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptls1769j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmknj985x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmknj985x/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu2bp22h2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu2bp22h2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8z8j2p_k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8z8j2p_k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpluctihk_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpluctihk_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8h336m_w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8h336m_w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq77q2rwn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq77q2rwn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpss2oyibk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpss2oyibk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzkra3_vz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzkra3_vz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxxxql1qc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxxxql1qc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzyb58_qy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzyb58_qy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptb71a3ve/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptb71a3ve/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkpd6bd04/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkpd6bd04/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoxjyucgg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoxjyucgg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpig3bpi3o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpig3bpi3o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9t4oa743/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9t4oa743/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9wjy4avn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9wjy4avn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgy3mwsda/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgy3mwsda/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9ehwka9i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9ehwka9i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7jzz27x_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7jzz27x_/f2.bed) bedtools bedtools bedtools bedtools 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/tmpex42fonz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpex42fonz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqm7ybxuf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqm7ybxuf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyt16z6on/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyt16z6on/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmproahrh2p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmproahrh2p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7z7kqw9d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7z7kqw9d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvcwm7l4u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvcwm7l4u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8hkx6m4y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8hkx6m4y/f2.bed) bedtools bedtools bedtools bedtools 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/tmparcpyawo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmparcpyawo/f2.bed) bedtools bedtools bedtools bedtools 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/tmpywhq49vd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpywhq49vd/f2.bed) ___________ test_three_in_a_row[strandedness_chain59-method_chain59] ___________ [gw2] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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:575 E /usr/lib/python3/dist-packages/pandas/core/common.py:140 E (and 62 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('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') 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') 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') 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') 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') ---------------------------------- 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_chain28-method_chain28] ___________ [gw3] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr7 | 196865 | 196867 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 162856 | 167977 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 216 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicYxXVZQABNgYGZkYGDiCLEcxnVOdn4GUEirEwcoL5DMxMNeoMDCJANgAfAwFv') 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') ('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') 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') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('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_nearest[None-False-same] _________________________ [gw0] linux -- Python 3.12.3 /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 102 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') 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/tmp_dm7qg1x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_dm7qg1x/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxvo623mu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxvo623mu/f2.bed) bedtools bedtools bedtools bedtools 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/tmphoic3ey0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphoic3ey0/f2.bed) bedtools bedtools bedtools bedtools 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/tmputg7fzdz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmputg7fzdz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc1wodbqe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc1wodbqe/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6n8xn1gc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6n8xn1gc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp04nwniq3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp04nwniq3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj5y42nr3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj5y42nr3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj5n2dpq4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj5n2dpq4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgzb7vweg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgzb7vweg/f2.bed) bedtools bedtools bedtools bedtools 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/tmpxp75uvfd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxp75uvfd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp53obmh9f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp53obmh9f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaiqen91y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaiqen91y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfl58zvpl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfl58zvpl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmq3wgde2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmq3wgde2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpya7yulai/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpya7yulai/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyq0sykn8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyq0sykn8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8fodjbl_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8fodjbl_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7zji9k59/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7zji9k59/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2nd25y7j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2nd25y7j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo4jks42n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo4jks42n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp23uc6ts6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp23uc6ts6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph4dscxnh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph4dscxnh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9l416ndp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9l416ndp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpskfen9ls/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpskfen9ls/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfn6hn9kh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfn6hn9kh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzrfk8pl1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzrfk8pl1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppsbnmkyw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppsbnmkyw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl12di88c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl12di88c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfv8tthtt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfv8tthtt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpppoyr14k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpppoyr14k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpso3qsnic/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpso3qsnic/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpugiaytv2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpugiaytv2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0c2ipvbz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0c2ipvbz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp92zwk32g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp92zwk32g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2ed0a4ez/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2ed0a4ez/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpejcqxnut/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpejcqxnut/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqcuv05v5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqcuv05v5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyzdvhdr6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyzdvhdr6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp78aco_la/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp78aco_la/f2.bed) bedtools bedtools bedtools bedtools 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/tmpe63__z1a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe63__z1a/f2.bed) bedtools bedtools bedtools bedtools 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/tmphr6ljmax/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphr6ljmax/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8_4at6ac/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8_4at6ac/f2.bed) bedtools bedtools bedtools bedtools 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/tmpe1m1ocv3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe1m1ocv3/f2.bed) ___________________ test_k_nearest[None-True-opposite-last] ____________________ [gw1] linux -- Python 3.12.3 /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 | 65550 | 65573 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | 27905 | 27906 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AAEBAAEGAAAAAAAPAQANAAAAFgAAAVEp+VwAAAEABwBtAABbAAAAAQ==') 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/tmp4bm3ud93/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4bm3ud93/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp3idf7nj5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3idf7nj5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp0nxks0r2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0nxks0r2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv1niolkf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv1niolkf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp961io2r6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp961io2r6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbvbfejh_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbvbfejh_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv1de38s5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv1de38s5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwm60gyrk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwm60gyrk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmts9zrm2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmts9zrm2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmptns5csw6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptns5csw6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpc94_nnz7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc94_nnz7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpknjk2gpg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpknjk2gpg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj304gjtx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj304gjtx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmps74661gx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps74661gx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpit_0fd91/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpit_0fd91/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpz2_o1rns/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz2_o1rns/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe510jhdo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe510jhdo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp7k9e3xzz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7k9e3xzz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpnidh_vbn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnidh_vbn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp5zfvd3e_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5zfvd3e_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp0x8n79k2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0x8n79k2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmppg48srg4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppg48srg4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpts70dxo0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpts70dxo0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpalh8i87m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpalh8i87m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjjym_r5s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjjym_r5s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0tvqekyk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0tvqekyk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_s_sdywv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_s_sdywv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpt39wmoll/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt39wmoll/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpngmj2672/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpngmj2672/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkq8obmfi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkq8obmfi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmphp3jy476/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphp3jy476/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7iil5uir/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7iil5uir/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmprrsmqf0b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprrsmqf0b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpibl4ym9_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpibl4ym9_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnu9pv85c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnu9pv85c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0hzk2m6c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0hzk2m6c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2f50hivu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2f50hivu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmppwmzqg49/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppwmzqg49/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq9fgt5ua/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq9fgt5ua/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2zf9jctm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2zf9jctm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk_gk5z1z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk_gk5z1z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaacx85ln/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaacx85ln/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3xz1wc9z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3xz1wc9z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbzgd9vjs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbzgd9vjs/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5ozb4bh0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5ozb4bh0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpatd923rf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpatd923rf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjzwiku88/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjzwiku88/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmphx4_h1vy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphx4_h1vy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_ud9lqk1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_ud9lqk1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7ozvoxe0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7ozvoxe0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcuf78py0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcuf78py0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpal4d29fo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpal4d29fo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg76cg6nv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg76cg6nv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzo0buieg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzo0buieg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpadwkqtop/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpadwkqtop/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmptysyaog7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptysyaog7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnz9s3fcw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnz9s3fcw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp8_6n87w8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8_6n87w8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp90i4pzdh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp90i4pzdh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp87s9rm5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp87s9rm5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpth_1evye/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpth_1evye/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. ---------------------------------- 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] ___________ [gw2] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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 65 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('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') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('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') 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') 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') ---------------------------------- 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_chain29-method_chain29] ___________ [gw3] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 5633 | 5890 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 9 | 1034 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 103 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2fWWrGhJPrBTwYOBkYGIBJjAJEgwKTJysDDyGTLyFxiH80CFGRkYGdgYgAqZOBgAasBABfyBgg=') 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') ('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') 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') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', '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_k_nearest[None-True-same-last] ______________________ [gw1] linux -- Python 3.12.3 /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('6.100.4', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') 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/tmpwxd0ahv2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwxd0ahv2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcf7usjko/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcf7usjko/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmptpw8sjbn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptpw8sjbn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa5943i_s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa5943i_s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmppjns4nci/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppjns4nci/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp9yfyg92/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp9yfyg92/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5ejjwfwm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5ejjwfwm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaeg87ui2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaeg87ui2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpkua4m5yv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkua4m5yv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4ishwthr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ishwthr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7u2tqfin/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7u2tqfin/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvwmxnv49/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvwmxnv49/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu2e9jn2b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu2e9jn2b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvf_xtn12/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvf_xtn12/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpckcksh5p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpckcksh5p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiw3j0unr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiw3j0unr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl56wkeui/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl56wkeui/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsy9s11z9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsy9s11z9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxnh10nrh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxnh10nrh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcf687rua/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcf687rua/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2dbvlkn6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2dbvlkn6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpog0x8xnm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpog0x8xnm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2wa5lzxa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2wa5lzxa/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzlp6dvn8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzlp6dvn8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq3c3h2_n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq3c3h2_n/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmprrjl0k7g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprrjl0k7g/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgoywvxng/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgoywvxng/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkn7iaoj2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkn7iaoj2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp17tu8nmk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp17tu8nmk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmrtwo5b_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmrtwo5b_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqwo1hhsl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqwo1hhsl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdkuhmjbm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdkuhmjbm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmplq_f5h9v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplq_f5h9v/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjygur5qx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjygur5qx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuzagdqzp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuzagdqzp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4i5qhhah/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4i5qhhah/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzww_6z14/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzww_6z14/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1tq39xhd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1tq39xhd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi6w1tb6o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi6w1tb6o/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp646b8oq2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp646b8oq2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9_0h5srv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9_0h5srv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp99a2nod1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp99a2nod1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpao67yz6t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpao67yz6t/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpr59nh5c2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr59nh5c2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcplhwwau/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcplhwwau/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdsd82fzp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdsd82fzp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpi153rnri/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi153rnri/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. ______________________ test_nearest[None-False-opposite] _______________________ [gw0] linux -- Python 3.12.3 /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 102 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2QAA0YGBGDEEGIEAACLAAY=') 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/tmpnb_0vobp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnb_0vobp/f2.bed) bedtools bedtools bedtools bedtools 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/tmp6o_cqow7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6o_cqow7/f2.bed) bedtools bedtools bedtools bedtools 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/tmpmxlzlpr5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmxlzlpr5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv19krv7o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv19krv7o/f2.bed) bedtools bedtools bedtools bedtools 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_hrpo29a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_hrpo29a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3mqbuslq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3mqbuslq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2winy51s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2winy51s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppvya8pn7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppvya8pn7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptfok0698/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptfok0698/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyn_2_4z0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyn_2_4z0/f2.bed) bedtools bedtools bedtools bedtools 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/tmpy_kr1r2g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy_kr1r2g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0d8pctdf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0d8pctdf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpahnz8i8c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpahnz8i8c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpttv73c67/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpttv73c67/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwcprr30u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwcprr30u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpinx85720/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpinx85720/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpokq4z1my/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpokq4z1my/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgq5pj1c4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgq5pj1c4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph6hvqvun/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph6hvqvun/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1y2f2mi_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1y2f2mi_/f2.bed) bedtools bedtools bedtools bedtools 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/tmp3u0jvyzn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3u0jvyzn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3ce7cvnm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3ce7cvnm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1j2aamcu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1j2aamcu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp56cmuxv5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp56cmuxv5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkcr2nwtd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkcr2nwtd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpneskp2_n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpneskp2_n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqlf_l26_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqlf_l26_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpljsx82dw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpljsx82dw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgcc5q0wx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgcc5q0wx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqc0q0dhv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqc0q0dhv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm1nb29sv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm1nb29sv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprf8o3xoc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprf8o3xoc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphpv75us6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphpv75us6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprcs39mef/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprcs39mef/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprkfcjw19/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprkfcjw19/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjureezkq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjureezkq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsfn53wqx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsfn53wqx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdi36gamb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdi36gamb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6ux_h2d9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6ux_h2d9/f2.bed) bedtools bedtools bedtools bedtools 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/tmphoeir6d7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphoeir6d7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6_a3l7eb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6_a3l7eb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6764j4uy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6764j4uy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm680scyd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm680scyd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0pf_1jb1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0pf_1jb1/f2.bed) bedtools bedtools bedtools bedtools 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/tmpg9nk7cl6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg9nk7cl6/f2.bed) bedtools bedtools bedtools bedtools 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/tmpaxmm648j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaxmm648j/f2.bed) bedtools bedtools bedtools bedtools 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/tmpgqpuh5ci/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgqpuh5ci/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw0e96d2h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw0e96d2h/f2.bed) bedtools bedtools bedtools bedtools 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/tmpwrs7gire/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwrs7gire/f2.bed) bedtools bedtools bedtools bedtools 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/tmpleb3f8g8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpleb3f8g8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps8tjodrm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps8tjodrm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_xgsy0zk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_xgsy0zk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuanle4ua/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuanle4ua/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5zwmvghu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5zwmvghu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjyycni1a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjyycni1a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdm2jp6tr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdm2jp6tr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7xq73oi4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7xq73oi4/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_chain61-method_chain61] ___________ [gw2] linux -- Python 3.12.3 /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/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/python3.12/typing.py:1195 E (and 101 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('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') ('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') 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') ---------------------------------- 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[None-True-False-last] _____________________ [gw1] linux -- Python 3.12.3 /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 36 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') 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/tmpgob8l1ot/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgob8l1ot/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj9ckjhgr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj9ckjhgr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy86pb7zi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy86pb7zi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpab2f7eti/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpab2f7eti/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmprnqv9g46/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprnqv9g46/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuqy8z_j0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuqy8z_j0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe0mncv03/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe0mncv03/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmphjd85i64/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphjd85i64/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx8p27qst/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx8p27qst/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp5ntgmfs1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5ntgmfs1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp5hqrf9he/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5hqrf9he/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgyg0824b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgyg0824b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmphcu2op2a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphcu2op2a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk9054_co/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk9054_co/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpheeyc6zv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpheeyc6zv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgqumzwla/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgqumzwla/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5uheyvek/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5uheyvek/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0fh43bz3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0fh43bz3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcybq2w9o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcybq2w9o/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvls_4fgc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvls_4fgc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1u7cesn3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1u7cesn3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_wxncggm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_wxncggm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy4ixc4l4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy4ixc4l4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbjqy7gd2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbjqy7gd2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkhmzb__3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkhmzb__3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbucyuqqa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbucyuqqa/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb9mimu2h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb9mimu2h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6c97g5ub/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6c97g5ub/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmptvac9m87/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptvac9m87/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv_u90o6v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv_u90o6v/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_3kp8_ke/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_3kp8_ke/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjm6as82b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjm6as82b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz1aobtm3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz1aobtm3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9rilmwkh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9rilmwkh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpedfn74au/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpedfn74au/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbu4guju6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbu4guju6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyiu1hbrl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyiu1hbrl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmplvani_7q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplvani_7q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcz1opz14/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcz1opz14/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkt6f9qe0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkt6f9qe0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmpa6yxj88y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa6yxj88y/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty 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/tmp100uqw4k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp100uqw4k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb5aad642/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb5aad642/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp84zit9ts/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp84zit9ts/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmps8jf66q_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps8jf66q_/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 chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrY than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. 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_nearest[upstream-True-False] _______________________ [gw0] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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='upstream', | overlap=True, | strandedness=False, | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 11017 | 19371 | a | 0 | + | | | chr1 | 806819 | 808868 | a | 0 | + | | | chr1 | 1248521 | 1251119 | a | 0 | + | | | chr2 | 10765 | 10808 | a | 0 | + | | | ... | ... | ... | ... | ... | ... | | | chr18 | 806819 | 808621 | a | 0 | + | | | chr18 | 2608859 | 2615576 | a | 0 | + | | | chr18 | 9876908 | 9879726 | a | 0 | + | | | chr18 | 931541 | 934367 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 11 rows and 6 columns from 5 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 | 91863 | 98196 | a | 0 | + | | | chr11 | 460048 | 460609 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 2 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 157 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY0y7Zhnbtc+IKWLPrNn6VWZMBsald9kZFfI4o5k4r2vM6fV3ZQp2NRdkdd0X+yzXQJGdLfqU0t31by6/lr7E057AVLFK4ZL+92fMyVybvFgM11y+s2FbodxrOQZxDgZuMwZGDgYebl4mBkZxBmYGfjZGfX5edkYLDj5efk4GVkUOBgZBOV5Gjo0/2LgZiy3ZOYV5OaQY2VgVPissnLZ1tRg3N6MduwyXKp/ZFQ4GEwZtDkYuAW5OUz5WfkY+Pj4GSyYZBi0efiY5bpZ49XO3bHjZudlZ+VkZWHn8F4GMNQQZy4wwlqFYYaEYq7Yu3Fi2EMLGSiEbq8TByMDAyMnIx8oIVgrkMXAx8DMxcDMwMgJZvIyMYKUMjGnXGHgZ7IyYJPZwMepbAUOVAagFpBwAb5A/kg==') 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 1209, in assert_frame_equal | assert_series_equal( | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 918, 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 414, in assert_attr_equal | raise_assert_detail(obj, msg, left_attr, right_attr) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 598, 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 499 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') 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/tmp1hpsyb7a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1hpsyb7a/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/tmp8x1f6sip/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8x1f6sip/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame 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/tmp3j9nw13n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3j9nw13n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa5f434a4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa5f434a4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3766026 3771286 - 0 1 chr1 8958457 8960866 + 0 2 chr1 9139825 9149666 + 0 3 chr11 9876908 9883579 - 0 4 chr21 806819 815289 + 0 5 chr21 3565936 3567772 - 0 6 chr21 7907343 7914581 - 0 7 chr8 806819 815590 + 0 8 chrX 2608859 2617084 - 0 9 chrY 931541 941226 + 0 10 chrY 6379441 6384226 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9139825 | 9149666 | a | 0 | ... | | chr1 | 8958457 | 8960866 | a | 0 | ... | | chr1 | 3766026 | 3771286 | a | 0 | ... | | chr8 | 806819 | 815590 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr21 | 806819 | 815289 | a | 0 | ... | | chr21 | 3565936 | 3567772 | a | 0 | ... | | chr21 | 7907343 | 7914581 | a | 0 | ... | | chrX | 2608859 | 2617084 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 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 ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 5 chr21 806819 815289 + 0 3 chr8 806819 815590 + 0 10 chrY 931541 941226 + 0 8 chrX 2608859 2617084 - 0 6 chr21 3565936 3567772 - 0 2 chr1 3766026 3771286 - 0 9 chrY 6379441 6384226 + 0 7 chr21 7907343 7914581 - 0 1 chr1 8958457 8960866 + 0 0 chr1 9139825 9149666 + 0 4 chr11 9876908 9883579 - 0 df2 Chromosome Start End Strand Distance 4 chr21 806819 815289 + 0 7 chr8 806819 815590 + 0 9 chrY 931541 941226 + 0 8 chrX 2608859 2617084 - 0 5 chr21 3565936 3567772 - 0 0 chr1 3766026 3771286 - 0 10 chrY 6379441 6384226 + 0 6 chr21 7907343 7914581 - 0 1 chr1 8958457 8960866 + 0 2 chr1 9139825 9149666 + 0 3 chr11 9876908 9883579 - 0 Actual Chromosome Start End Strand Distance 0 chr1 3766026 3771286 - 0 1 chr1 8958457 8960866 + 0 2 chr1 9139825 9149666 + 0 3 chr11 9876908 9883579 - 0 4 chr21 806819 815289 + 0 5 chr21 3565936 3567772 - 0 6 chr21 7907343 7914581 - 0 7 chr8 806819 815590 + 0 8 chrX 2608859 2617084 - 0 9 chrY 931541 941226 + 0 10 chrY 6379441 6384226 + 0 Expected Chromosome Start End Strand Distance 0 chr1 3766026 3771286 - 0 1 chr1 8958457 8960866 + 0 2 chr1 9139825 9149666 + 0 3 chr11 9876908 9883579 - 0 4 chr21 806819 815289 + 0 5 chr21 3565936 3567772 - 0 6 chr21 7907343 7914581 - 0 7 chr8 806819 815590 + 0 8 chrX 2608859 2617084 - 0 9 chrY 931541 941226 + 0 10 chrY 6379441 6384226 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object 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 -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8s2t3r91/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8s2t3r91/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkhbn4d1l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkhbn4d1l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2gd3b_n7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2gd3b_n7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy9f0fpje/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy9f0fpje/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa1fpsmdq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa1fpsmdq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0mgkbnk1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0mgkbnk1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp76h4vgym/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp76h4vgym/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/tmp267vvx75/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp267vvx75/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgooy54zc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgooy54zc/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/tmpu63s03we/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu63s03we/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/tmpl3ssdpog/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl3ssdpog/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/tmp3ou5jswb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3ou5jswb/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/tmp9m_58ndb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9m_58ndb/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/tmpatppyi2_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpatppyi2_/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/tmpsuvo34ri/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsuvo34ri/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/tmpad174p_x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpad174p_x/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/tmp7x2d9nyk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7x2d9nyk/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/tmpd4ci1wvl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd4ci1wvl/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/tmp5oeuvah4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5oeuvah4/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/tmp_ii13pty/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_ii13pty/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/tmp7qs9ox8z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7qs9ox8z/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/tmpfm_6xr4u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfm_6xr4u/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/tmptz7r_gwa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptz7r_gwa/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/tmpndxcfns5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpndxcfns5/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/tmptodjaakl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptodjaakl/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/tmpqe9jwcyn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqe9jwcyn/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/tmpwzmn3nlj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwzmn3nlj/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/tmp1kxkqg1z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1kxkqg1z/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/tmpa8lnov__/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa8lnov__/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/tmp7_iyjzg7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7_iyjzg7/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/tmpunav1ner/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpunav1ner/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/tmprs6pv53g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprs6pv53g/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/tmprw7gdxhx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprw7gdxhx/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/tmplyitzmhc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplyitzmhc/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/tmpihbxmw6g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpihbxmw6g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9qdzsbx5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9qdzsbx5/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_chain62-method_chain62] ___________ [gw2] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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:575 E /usr/lib/python3/dist-packages/pandas/core/common.py:140 E (and 62 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('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') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('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') ('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') 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') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', '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_chain31-method_chain31] ___________ [gw3] linux -- Python 3.12.3 /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 | 9380340 | 9383569 | a | 0 | - | E | chr1 | 9134099 | 9134101 | 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 | 5761 | a | 0 | - | E | chr1 | 9134099 | 9135383 | 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 | 65893 | 66663 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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/join.py:104 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:106 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:12 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:14 E (and 43 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY0xNtbnMVLi55mXr7g0MTAyMrAwsQMjOyMjAyZj0039qd4IQNyMfIy8jPz9PQb/iZx7GOgZGZkZ+HgZl/Ts8c0BaGBkYGfgYeEE02LTSw40GLnsF8ZjGyMDFAAQsDBJi9WwgA1iZgSTYICYGViDJANLAmMIgzQwUAwAxexh4') 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') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') 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') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') 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') ('intersect', 'nearest') ('intersect', 'nearest') ('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') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') 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') 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_k_nearest_1_vs_nearest __________________________ [gw1] linux -- Python 3.12.3 /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 38 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:24: ValueError ---------------------------------- 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-same] _______________________ [gw0] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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 | 1049348 | 1050885 | a | 0 | - | | | chr1 | 985144 | 986681 | a | 0 | - | | | chr1 | 1049348 | 1050117 | a | 0 | - | | | chr1 | 66604 | 68141 | a | 0 | - | | | ... | ... | ... | ... | ... | ... | | | chr1 | 1049348 | 1051911 | a | 0 | - | | | chr1 | 1049348 | 1050885 | a | 0 | - | | | chr1 | 1049348 | 1050885 | a | 0 | - | | | chr1 | 1049348 | 1050885 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 11 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 | 59393 | 69207 | a | 0 | - | | | chr1 | 524296 | 534110 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 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 131 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicFY69agJRFIRnzrn33PVnvQpZIZA0GhdEsTHBQs2+giABH8EmkM4nsLP3JdKkzRNtkzbVFl4ZGJiB4Ruuv1oT3ZdNw+P4cvUF6tyf9pM/MpUqu0Mlfvv/rYvPM9Q8Bs4c+gikB4xgDBRPxXPGNzwqJccYy2Dsxk6b7wBbJuKqTZR5zFZPrqCbmbxIbvTyoMoeShsFaF9V1BTb0G0LxNKUeL07NYGSkLhlhoAh6hRmv9Of8sOTMaOlC8QNyCoV3A==') 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 | 1897672 | 1900625 | a | 0 | + | | | chr4 | 4130114 | 4136158 | a | 0 | + | | | chr4 | 6601464 | 6608887 | a | 0 | - | | | chr18 | 6081954 | 6088954 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 4 rows and 6 columns from 3 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('6.100.4', b'AXicY2QAA0YGBGC04c/5wxyxwchU8sEMtqid0YKmabLMxpzL3RnYGRgExZgYZYCqmPkZeGPOLhRhCr1vGCfz5bgoI+fF1Sn2rI6sjKKMXIx8TPIyzAopu74DjfYwDpcOF2TgZxLi7hBhEGDUFZ/NwyjPXSnzj5UBaJY0IwMXgzgzIxMzNxMDAwA+dBiH') 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 1209, in assert_frame_equal | assert_series_equal( | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 918, 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 414, in assert_attr_equal | raise_assert_detail(obj, msg, left_attr, right_attr) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 598, 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 471 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', 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/tmpjjcb03zd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjjcb03zd/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/tmpce8jupyh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpce8jupyh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr7z7ibzk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr7z7ibzk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmp7amzboy6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7amzboy6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp20giu82l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp20giu82l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt1j78eaa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt1j78eaa/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3otk5ezu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3otk5ezu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmpzypkymg9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzypkymg9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 66604 68141 - 0 1 chr1 132160 133697 - 0 2 chr1 985144 986681 - 0 3 chr1 1049348 1050117 - 0 4 chr1 1049348 1050885 - 0 5 chr1 1049348 1050885 - 0 6 chr1 1049348 1050885 - 0 7 chr1 1049348 1050885 - 0 8 chr1 1049348 1051911 - 0 9 chr1 1311492 1313029 - 0 10 chr7 401928 403465 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1049348 | 1050885 | a | 0 | ... | | chr1 | 985144 | 986681 | a | 0 | ... | | chr1 | 1049348 | 1050117 | a | 0 | ... | | chr1 | 66604 | 68141 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1049348 | 1051911 | a | 0 | ... | | chr1 | 1049348 | 1050885 | a | 0 | ... | | chr1 | 1049348 | 1050885 | a | 0 | ... | | chr1 | 1049348 | 1050885 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 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 3 chr1 66604 68141 - 0 5 chr1 132160 133697 - 0 10 chr7 401928 403465 - 0 1 chr1 985144 986681 - 0 2 chr1 1049348 1050117 - 0 0 chr1 1049348 1050885 - 0 7 chr1 1049348 1050885 - 0 8 chr1 1049348 1050885 - 0 9 chr1 1049348 1050885 - 0 6 chr1 1049348 1051911 - 0 4 chr1 1311492 1313029 - 0 df2 Chromosome Start End Strand Distance 0 chr1 66604 68141 - 0 1 chr1 132160 133697 - 0 10 chr7 401928 403465 - 0 2 chr1 985144 986681 - 0 3 chr1 1049348 1050117 - 0 4 chr1 1049348 1050885 - 0 5 chr1 1049348 1050885 - 0 6 chr1 1049348 1050885 - 0 7 chr1 1049348 1050885 - 0 8 chr1 1049348 1051911 - 0 9 chr1 1311492 1313029 - 0 Actual Chromosome Start End Strand Distance 0 chr1 66604 68141 - 0 1 chr1 132160 133697 - 0 2 chr1 985144 986681 - 0 3 chr1 1049348 1050117 - 0 4 chr1 1049348 1050885 - 0 5 chr1 1049348 1050885 - 0 6 chr1 1049348 1050885 - 0 7 chr1 1049348 1050885 - 0 8 chr1 1049348 1051911 - 0 9 chr1 1311492 1313029 - 0 10 chr7 401928 403465 - 0 Expected Chromosome Start End Strand Distance 0 chr1 66604 68141 - 0 1 chr1 132160 133697 - 0 2 chr1 985144 986681 - 0 3 chr1 1049348 1050117 - 0 4 chr1 1049348 1050885 - 0 5 chr1 1049348 1050885 - 0 6 chr1 1049348 1050885 - 0 7 chr1 1049348 1050885 - 0 8 chr1 1049348 1051911 - 0 9 chr1 1311492 1313029 - 0 10 chr7 401928 403465 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object 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 -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5le7icys/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5le7icys/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpezntedag/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpezntedag/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9z2a7_zi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9z2a7_zi/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/tmp71_zcvyc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp71_zcvyc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpurqp_n42/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpurqp_n42/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplq6fw5vx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplq6fw5vx/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/tmpfa4o8xed/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfa4o8xed/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/tmpov1bznq3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpov1bznq3/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/tmpfwuv5a0c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfwuv5a0c/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/tmpb14uhi5a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb14uhi5a/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/tmp0xcm714t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0xcm714t/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/tmpcl9c_9nk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcl9c_9nk/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/tmpk96g71rf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk96g71rf/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/tmphlllrfvv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphlllrfvv/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/tmpedb357jq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpedb357jq/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/tmpz7zsyh5i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz7zsyh5i/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/tmp57afzo9n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp57afzo9n/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/tmp_k89houp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_k89houp/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/tmphegxw5bh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphegxw5bh/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/tmpqqo_ah56/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqqo_ah56/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/tmph2gvn4og/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph2gvn4og/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/tmpzscwielj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzscwielj/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/tmpurk8j7xn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpurk8j7xn/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/tmpico35k_m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpico35k_m/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/tmpkmvx7hza/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkmvx7hza/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/tmpqwg62u85/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqwg62u85/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/tmpf5g8uxbx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf5g8uxbx/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/tmp3k9luyv2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3k9luyv2/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/tmpxlonvh1l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxlonvh1l/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/tmp9jsvxokx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9jsvxokx/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/tmpr1ldldcj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr1ldldcj/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/tmpv1h0hraa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv1h0hraa/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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_7gky5sm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_7gky5sm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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_6a4deon/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_6a4deon/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvmjhugcq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvmjhugcq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpumz6k4p0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpumz6k4p0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxxe6evxc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxxe6evxc/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_chain63-method_chain63] ___________ [gw2] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2991240 | 2991753 | a | 0 | + | E | chr1 | 7944169 | 7944682 | a | 0 | + | E | chr1 | 3338118 | 3338631 | 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=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr2 | 16 | 786 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 74 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY4ryruxgzTQrPcDOKsLEyMDAwMjMwKu7pF2KgZeRpdL8BSMDFxPHpadbjd63MjDwMDEwAVUwMvAxCIPVMjJJLioRsmVgYRJbp8IAFAKJMjDwMwGNYWQAQQBjLA23') 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') ('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') 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') ('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') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', '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_chain0-method_chain0] ____________ [gw1] linux -- Python 3.12.3 /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 245 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('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') 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') ---------------------------------- 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_chain33-method_chain33] ___________ [gw3] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65550 | 65556 | a | 0 | - | E | chr12 | 65550 | 65556 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 257 | 5031 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AXicY4ytCNjDWMUABIwMjIyMDNxgFi8Qs4JEwBAowsjJAWYwQAS0hJYyMAAAkF0DfA==') 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') ('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') 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') ('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') 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') 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') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('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[upstream-True-opposite] _____________________ [gw0] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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 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 1209, in assert_frame_equal | assert_series_equal( | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 918, 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 414, in assert_attr_equal | raise_assert_detail(obj, msg, left_attr, right_attr) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 598, 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 | + | | | 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., | ) | 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 462 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY7TVOOzMyDBjWh0DIwMDAyMjiIQDRhQKzAQAh3YDIQ==') 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='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | 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., | 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('6.100.4', b'AXicY2QAAkaGGdPqgCSQxQgiGRggJBoFZgIARfcBtw==') 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 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 | 65794 | 65795 | 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., | ) | 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('6.100.4', b'AXicY7TVOOzMwMfAyMDAwMgIIkE0hGJAphgYADw2AYM=') 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/tmpybiux3py/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpybiux3py/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmpn20arf7a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn20arf7a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmpjhq3dm0s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjhq3dm0s/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 286594 293510 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 286594 | 293510 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on 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 286594 293510 + 0 df2 Chromosome Start End Strand Distance 0 chr1 286594 293510 + 0 Actual Chromosome Start End Strand Distance 0 chr1 286594 293510 + 0 Expected Chromosome Start End Strand Distance 0 chr1 286594 293510 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object 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/tmp0vu9fiyl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0vu9fiyl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3mt9emx4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3mt9emx4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwhf5gdk3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwhf5gdk3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp39u_fuky/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp39u_fuky/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4i6e67yz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4i6e67yz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfti6b1qu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfti6b1qu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvtiu7160/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvtiu7160/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm6dr4jpn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm6dr4jpn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo9aqgxou/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo9aqgxou/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfv5ka0ed/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfv5ka0ed/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmpx8zf4m4f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx8zf4m4f/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmpp6a7_p99/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp6a7_p99/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqx89wyx9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqx89wyx9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpomwewx0d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpomwewx0d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4f48kb2l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4f48kb2l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnf6qa_p2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnf6qa_p2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 286594 293510 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 286594 | 293510 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on 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 286594 293510 + 0 df2 Chromosome Start End Strand Distance 0 chr1 286594 293510 + 0 Actual Chromosome Start End Strand Distance 0 chr1 286594 293510 + 0 Expected Chromosome Start End Strand Distance 0 chr1 286594 293510 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object 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/tmp805x5vt2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp805x5vt2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmpm3p7zppd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm3p7zppd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi4fd5wl4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi4fd5wl4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmp2xczl6bo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2xczl6bo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3emrumff/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3emrumff/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmp4mjasknr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4mjasknr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmpxdoi6ejs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxdoi6ejs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp04pvss19/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp04pvss19/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2561 3331 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2561 | 3331 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on 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 2561 3331 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2561 3331 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2561 3331 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2561 3331 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object 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/tmpr6h_yg_w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr6h_yg_w/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2561 2570 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2561 | 2570 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on 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 2561 2570 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2561 2570 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2561 2570 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2561 2570 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object 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/tmpbl7dyxjf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbl7dyxjf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3n1w5f61/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3n1w5f61/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_g66p46w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_g66p46w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp62f_c1f1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp62f_c1f1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt8r7nxc5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt8r7nxc5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmdnmiudd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmdnmiudd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpivrewhk9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpivrewhk9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcdvhbd1p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcdvhbd1p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqlju_p6g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqlju_p6g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnoekyflo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnoekyflo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9e_s5_pj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9e_s5_pj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo8j073rc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo8j073rc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi1cate5m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi1cate5m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpakz_ny6g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpakz_ny6g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcjnb31em/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcjnb31em/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmy1y4a5q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmy1y4a5q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkjga_0_g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkjga_0_g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps9jbb05q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps9jbb05q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpupsizzr2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpupsizzr2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpabbh8nee/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpabbh8nee/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqfq2gma_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqfq2gma_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmp5exs5htx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5exs5htx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmpwa0xybwb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwa0xybwb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx7_ti4n5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx7_ti4n5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1r7070bj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1r7070bj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4ejb_ijo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ejb_ijo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmvrssoh0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmvrssoh0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxmbjcivh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxmbjcivh/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/tmpqxzmok7y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqxzmok7y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8icpj8nd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8icpj8nd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphhz8kgt3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphhz8kgt3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp20i8bpvx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp20i8bpvx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn_4fot18/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn_4fot18/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmpz62jtj03/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz62jtj03/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg6d_bnnx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg6d_bnnx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr2zxhcv6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr2zxhcv6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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_nvl_6d3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_nvl_6d3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmpk_2xw42v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk_2xw42v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmpswrd2n2w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpswrd2n2w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmp58day2te/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp58day2te/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmp48bf0d7r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp48bf0d7r/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmp4enl1vqb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4enl1vqb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmpchcxureo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpchcxureo/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/tmp7bch4g9k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7bch4g9k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn4k2vvfu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn4k2vvfu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjsplyrzz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjsplyrzz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmpvdk1d6ad/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvdk1d6ad/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/tmp19m55u5n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp19m55u5n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa12slavl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa12slavl/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[upstream-False-False] ______________________ [gw0] linux -- Python 3.12.3 /usr/bin/python3.12 nearest_how = 'upstream', 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:118: in _nearest r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, 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='upstream', 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:118 E (and 39 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') 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 -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmputc08fg2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmputc08fg2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps6wi48ra/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps6wi48ra/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmvbxwg8h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmvbxwg8h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1o04v0n2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1o04v0n2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7agwl91w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7agwl91w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl_gwi0mj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl_gwi0mj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmof6v_4c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmof6v_4c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9h_93csn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9h_93csn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz94p2aga/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz94p2aga/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpafz2eq8p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpafz2eq8p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjt86xmkb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjt86xmkb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoydtu67s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoydtu67s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv1lfpj2r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv1lfpj2r/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpebqmosc2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpebqmosc2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6n15j_e6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6n15j_e6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuh83d0vt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuh83d0vt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb_mzlxc1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb_mzlxc1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmjx3nnj7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmjx3nnj7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk15q3_21/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk15q3_21/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn2zop8gz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn2zop8gz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpas2xzvex/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpas2xzvex/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7y8ccesu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7y8ccesu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3859oz6a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3859oz6a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppul9mx0c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppul9mx0c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2niyyt13/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2niyyt13/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4v95z504/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4v95z504/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptm1w0gai/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptm1w0gai/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcnujt4nw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcnujt4nw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxdlm2ujd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxdlm2ujd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw09esqht/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw09esqht/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvkp4mfo8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvkp4mfo8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsm0dmajs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsm0dmajs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptv4yydi5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptv4yydi5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiubynjhy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiubynjhy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6f9za8qs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6f9za8qs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2jkx21vb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2jkx21vb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_txz1936/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_txz1936/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprdnh1823/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprdnh1823/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame 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/tmpt710ktcj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt710ktcj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame 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/tmp7z12g06i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7z12g06i/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame 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/tmpk5sedfbr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk5sedfbr/f2.bed) ___________ test_three_in_a_row[strandedness_chain64-method_chain64] ___________ [gw2] linux -- Python 3.12.3 /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, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1281 | 1371 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AAABAAEDAHgEgAEAAXoAAAAAAAEABgAFAABEAFkAAQ==') 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') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('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') 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') ('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') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', '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_chain1-method_chain1] ____________ [gw1] linux -- Python 3.12.3 /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 184 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('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') 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') 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') 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') ---------------------------------- 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-False-same] _______________________ [gw0] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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='upstream', | overlap=False, | strandedness='same', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 327685 | 327731 | 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 | 327685 | 327731 | 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 105 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY8ysyz/NwMrAyMDBoMHKwAJkMDHoMjAwMuKSAACnlgUl') 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=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 104 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') 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/tmpegdbap3f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpegdbap3f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprgftaz8j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprgftaz8j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp51bxuavj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp51bxuavj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp87ct4lh0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp87ct4lh0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo95279s5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo95279s5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzvk3jyak/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzvk3jyak/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk1s50yi7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk1s50yi7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphcxgpv0e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphcxgpv0e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2zoii6jp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2zoii6jp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsqs21pm0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsqs21pm0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoxhv24by/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoxhv24by/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_rs4hxjy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_rs4hxjy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxqv26djz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxqv26djz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpap4rx8si/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpap4rx8si/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppxeu31qr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppxeu31qr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwsu1c76m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwsu1c76m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_1kpk77i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_1kpk77i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqm0cgt_c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqm0cgt_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/tmpnu6cxpxq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnu6cxpxq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdnzdqsgi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdnzdqsgi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiwmfikj7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiwmfikj7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpshxt990t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpshxt990t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdti9e95c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdti9e95c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsgpdidqd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsgpdidqd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6owlkp34/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6owlkp34/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu82m3ntt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu82m3ntt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjc8i69_g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjc8i69_g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpybhg0rni/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpybhg0rni/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbxd74ns_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbxd74ns_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqio27b03/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqio27b03/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1odhwhga/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1odhwhga/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoo7b298n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoo7b298n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpac30opxd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpac30opxd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeltffckh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeltffckh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj_9s0qzl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj_9s0qzl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3k9hpyaf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3k9hpyaf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3cxntvvz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3cxntvvz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpje1v8c9w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpje1v8c9w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq3j19nzg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq3j19nzg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmpt6a6c2x2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt6a6c2x2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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__04ovrw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp__04ovrw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph3o_9sxk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph3o_9sxk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0qwtb5mr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0qwtb5mr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmpfcwiut2o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfcwiut2o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmpzhu7ag0e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzhu7ag0e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiizdid74/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiizdid74/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb16mj9x7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb16mj9x7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqsu4z800/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqsu4z800/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_chain117-method_chain117] __________ [gw3] linux -- Python 3.12.3 /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, 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('6.100.4', b'AXicY2BkgAEECwEAAFEAAw==') 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') ('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') 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') ('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') 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') ---------------------------------- 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] ___________ [gw1] linux -- Python 3.12.3 /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, 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('6.100.4', b'AXicY2BkgAEECwEAAFEAAw==') 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') ('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') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7160562 | 7162998 | a | 0 | - | | chr22 | 3718592 | 3726665 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('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') 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') 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') ---------------------------------- 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_chain158-method_chain158] __________ [gw2] linux -- Python 3.12.3 /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 64 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('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') 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') 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') 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') 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') ---------------------------------- 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-False-opposite] _____________________ [gw0] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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 | 2162690 | 2162703 | 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 | 1638401 | 1638403 | 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 104 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2RgZAACRoYyRSDByMADZIeCGCAkyQAWA3EAHCYBHw==') 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 104 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2QAA0YGOGBkxBBiAAAAngAG') 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/tmpfvhe_slk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfvhe_slk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmp70jqd421/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp70jqd421/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmpxaipd551/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxaipd551/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmpf104lglq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf104lglq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmpcltitr1b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcltitr1b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmp8cpvroqo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8cpvroqo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmpbkvrg1fe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbkvrg1fe/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpspz9j80b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpspz9j80b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnauy_kt6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnauy_kt6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvu2bb47c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvu2bb47c/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmp9qcw_m6t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9qcw_m6t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx7gdlvh5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx7gdlvh5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_c82xbud/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_c82xbud/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp8ymu662/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp8ymu662/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd0168rdi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd0168rdi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3oysbpmg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3oysbpmg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpebs4n0hj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpebs4n0hj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbkyxl1y6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbkyxl1y6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps68rdo2t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps68rdo2t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaa5crtr0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaa5crtr0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgitz2tg9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgitz2tg9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6yqwelh6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6yqwelh6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmpwmrqrugh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwmrqrugh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmpdr50kup_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdr50kup_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmpsy3y95if/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsy3y95if/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmps5u_e_7r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps5u_e_7r/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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_o17iaz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo_o17iaz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmpvx2n64c9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvx2n64c9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmpqsuoo0t0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqsuoo0t0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe8lzagky/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe8lzagky/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp12fmz4m9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp12fmz4m9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0xry8vfi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0xry8vfi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmpgia0rfdn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgia0rfdn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptlwx43oq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptlwx43oq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5a2tudod/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5a2tudod/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphudj5lcy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphudj5lcy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmpk8zccm8o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk8zccm8o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmpza87h1xs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpza87h1xs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy3uquz2v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy3uquz2v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmpbzpw2v1k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbzpw2v1k/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmpnn6wv5lk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnn6wv5lk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdr94v8pw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdr94v8pw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmpwl81vxa_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwl81vxa_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmpsvuvmlfm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsvuvmlfm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy2836i0x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy2836i0x/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp361kfpq7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp361kfpq7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpui4svf02/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpui4svf02/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7523oyeh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7523oyeh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3arsphtu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3arsphtu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_qht6z8k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_qht6z8k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptbs1uupr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptbs1uupr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl6345dea/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl6345dea/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp02o821bj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp02o821bj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5l_q3ht0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5l_q3ht0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfh346a5c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfh346a5c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzf78d4ue/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzf78d4ue/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl8bh8lqz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl8bh8lqz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmp5c8hbrmo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5c8hbrmo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuadvwdh9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuadvwdh9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3j7i1yat/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3j7i1yat/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp354epamu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp354epamu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxtgz0leh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxtgz0leh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsmpkshhy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsmpkshhy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpii_ibzq3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpii_ibzq3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmp7n4rfsv7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7n4rfsv7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcxltdfog/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcxltdfog/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj02cf2qo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj02cf2qo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyo94tndv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyo94tndv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkpya7ny0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkpya7ny0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [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/tmp3n6arjpk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3n6arjpk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvd1han0a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvd1han0a/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_chain119-method_chain119] __________ [gw3] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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 | 334604 | 335442 | a | 0 | + | | | chr1 | 334604 | 335442 | a | 0 | + | | | chr1 | 334604 | 335442 | a | 0 | + | | | chr3 | 334604 | 335442 | a | 0 | - | | | chr17 | 334604 | 335442 | 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 | 1901886 | 1906015 | a | 0 | + | | | chr1 | 77061 | 77318 | a | 0 | + | | | chr5 | 2656536 | 2657053 | a | 0 | - | | | chr17 | 9990 | 14119 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 4 rows and 6 columns from 3 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 | 1901886 | 1906015 | a | 0 | + | | | chr1 | 77061 | 77318 | a | 0 | + | | | chr5 | 2656536 | 2657053 | a | 0 | - | | | chr17 | 9990 | 14119 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 4 rows and 6 columns from 3 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 169 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicvU29SkJxHD3n93F/6r2ZipjZhxcaCqRWB3EQCRraRNoiopYGt6amlqAnaGjoSe5D9A5Nbe0N/oWeoTMdzqfMfx6f7qpV4I/Y9e/i6+F5Fdn95dUg/OK7GH++lfpe6fLjptr2ArVwJgxCIQ1XAZvQiMzQyjKrs6dbAJH7Xo7bSei5KwnkhAgaLJJJjFjabHz0oqjzzEQ6jl3A2squpJ2UEMxPXnf6qXPslKQc+NQZ0lTlqcGgYtR0BLbKYUdhwh7oErqvh9rfGP9zswY/lR/E') 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=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 769 | 1026 | 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 | 1 | 3331 | 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:11 | (and 344 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2C0YGBgYmRjZmSVYwACNhDBwMjADCYZGFgNGXkYgDwgmxssxQtkAQAbHgDV') 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') ('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') ('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') 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') 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') 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') 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') ('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_chain70-method_chain70] ___________ [gw1] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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 | 459788 | 469005 | a | 0 | + | | | chr1 | 69892 | 72714 | a | 0 | - | | | chr1 | 2164229 | 2166436 | a | 0 | - | | | chr1 | 460548 | 462135 | a | 0 | - | | | chr12 | 67589 | 69133 | 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 | 2883841 | 2883842 | a | 0 | + | | | chr5 | 2688258 | 2688259 | a | 0 | - | | | chr7 | 3473693 | 3473694 | a | 0 | + | | | chrY | 7176 | 7177 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 4 rows and 6 columns from 4 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 | 525384 | 534601 | a | 0 | + | | | chr1 | 394043 | 399346 | a | 0 | + | | | chr1 | 71685 | 81069 | a | 0 | + | | | chr1 | 525384 | 531534 | a | 0 | + | | | chr4 | 525384 | 534612 | a | 0 | - | | | chr12 | 525384 | 526758 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 6 rows and 6 columns from 3 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 166 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXichdA9SgNREAfw+c+8mbdhjZgYY1xi/CAoQVdwQSQp7DSgYBkQtdHCztJGxAsIdmKjlvEAksoT6CG8hAfw7SqClW/gTTNf/DC4ednB1f3dtbej/NfF96fN19vdj/SNt0tSOhm2uLM/GlheQ1VHsRc0FACFqKGHirBnLJgro8axSc97KaPhCJHzImougfPG45h1pN7FqnwYPSZcQTvWlnFJ84Em2XLfMiG0qQmoOKYl847IKJawy2vkVryZx5lcTF6mejr/mVCZyepCTgmOjEXGiGjaBB1Fi2gVlITcDEcb0waalL+5KaYS8lQHBBMA523aKBjSved/GLJfhi5I5v8wBBbH8s2Q/jD0Y9E110N7uMXn6w+1UcFwnElkXMVBYDDjjs4UDOwDVsFA3XBdAKAvKgkxcg==') 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 177 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', 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') ('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') 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') 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') ('nearest', 'set_union') ('nearest', 'set_union') ('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') 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') 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') ---------------------------------- 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_chain159-method_chain159] __________ [gw2] linux -- Python 3.12.3 /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/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/python3.12/typing.py:1195 E (and 105 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('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') 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') ---------------------------------- 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-False] ______________________ [gw0] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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 | 65816 | 65820 | 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('6.100.4', b'AXicY2QAA0YGOGBkZObI+QekmRjYGRnFGRg4GJgZGAEbWAGp') 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 | 71425 | 71429 | 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('6.100.4', b'AXicY2QAA0YGBGBk4Mj5B6IYGcUZGDgYmBkYARexAZw=') 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 1209, in assert_frame_equal | assert_series_equal( | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 918, 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 414, in assert_attr_equal | raise_assert_detail(obj, msg, left_attr, right_attr) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 598, 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 463 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') 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/tmp0r9jjete/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0r9jjete/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/tmp6mfrra4s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6mfrra4s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmproge042x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmproge042x/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4kxx6zww/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4kxx6zww/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsyitsyf_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsyitsyf_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 215622 220497 + 0 1 chr1 928226 938044 + 0 2 chr1 5646265 5656083 - 0 3 chr1 8573691 8575955 + 0 4 chr14 3379466 3379467 - 0 5 chr16 4738062 4739549 + 0 6 chr2 7343295 7352542 + 0 7 chr3 1927933 1931690 - 0 8 chr3 4382436 4392254 + 0 9 chr3 4979736 4980942 - 0 10 chr7 5790803 5793041 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 928226 | 938044 | a | 0 | ... | | chr1 | 215622 | 220497 | a | 0 | ... | | chr1 | 8573691 | 8575955 | a | 0 | ... | | chr1 | 5646265 | 5656083 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr3 | 4382436 | 4392254 | a | 0 | ... | | chr3 | 4979736 | 4980942 | a | 0 | ... | | chr3 | 1927933 | 1931690 | a | 0 | ... | | chr7 | 5790803 | 5793041 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 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 ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 215622 220497 + 0 0 chr1 928226 938044 + 0 7 chr3 1927933 1931690 - 0 9 chr14 3379466 3379467 - 0 5 chr3 4382436 4392254 + 0 10 chr16 4738062 4739549 + 0 6 chr3 4979736 4980942 - 0 3 chr1 5646265 5656083 - 0 8 chr7 5790803 5793041 - 0 4 chr2 7343295 7352542 + 0 2 chr1 8573691 8575955 + 0 df2 Chromosome Start End Strand Distance 0 chr1 215622 220497 + 0 1 chr1 928226 938044 + 0 7 chr3 1927933 1931690 - 0 4 chr14 3379466 3379467 - 0 8 chr3 4382436 4392254 + 0 5 chr16 4738062 4739549 + 0 9 chr3 4979736 4980942 - 0 2 chr1 5646265 5656083 - 0 10 chr7 5790803 5793041 - 0 6 chr2 7343295 7352542 + 0 3 chr1 8573691 8575955 + 0 Actual Chromosome Start End Strand Distance 0 chr1 215622 220497 + 0 1 chr1 928226 938044 + 0 2 chr1 5646265 5656083 - 0 3 chr1 8573691 8575955 + 0 4 chr14 3379466 3379467 - 0 5 chr16 4738062 4739549 + 0 6 chr2 7343295 7352542 + 0 7 chr3 1927933 1931690 - 0 8 chr3 4382436 4392254 + 0 9 chr3 4979736 4980942 - 0 10 chr7 5790803 5793041 - 0 Expected Chromosome Start End Strand Distance 0 chr1 215622 220497 + 0 1 chr1 928226 938044 + 0 2 chr1 5646265 5656083 - 0 3 chr1 8573691 8575955 + 0 4 chr14 3379466 3379467 - 0 5 chr16 4738062 4739549 + 0 6 chr2 7343295 7352542 + 0 7 chr3 1927933 1931690 - 0 8 chr3 4382436 4392254 + 0 9 chr3 4979736 4980942 - 0 10 chr7 5790803 5793041 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object 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 -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjy60gu4p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjy60gu4p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsw70wh6t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsw70wh6t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyms9txt1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyms9txt1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpco0vl4ch/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpco0vl4ch/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc50xeuro/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc50xeuro/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmc406pkf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmc406pkf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4356 8647 + 0 1 chr1 4612 8918 - 0 2 chr1 12292 12325 - 0 3 chr1 327694 328525 + 0 4 chr1 461057 469003 + 0 5 chr1 538119 541204 - 0 6 chr1 538119 545189 + 0 7 chr1 722689 726224 - 0 8 chr1 1901333 1901590 - 0 9 chr1 3084040 3084307 - 0 10 chrX 1123077 1128966 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 327694 | 328525 | a | 0 | ... | | chr1 | 461057 | 469003 | a | 0 | ... | | chr1 | 4356 | 8647 | a | 0 | ... | | chr1 | 538119 | 545189 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 722689 | 726224 | a | 0 | ... | | chr1 | 12292 | 12325 | a | 0 | ... | | chr1 | 1901333 | 1901590 | a | 0 | ... | | chr1 | 538119 | 541204 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 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 2 chr1 4356 8647 + 0 5 chr1 4612 8918 - 0 7 chr1 12292 12325 - 0 0 chr1 327694 328525 + 0 1 chr1 461057 469003 + 0 9 chr1 538119 541204 - 0 3 chr1 538119 545189 + 0 6 chr1 722689 726224 - 0 10 chrX 1123077 1128966 + 0 8 chr1 1901333 1901590 - 0 4 chr1 3084040 3084307 - 0 df2 Chromosome Start End Strand Distance 0 chr1 4356 8647 + 0 1 chr1 4612 8918 - 0 2 chr1 12292 12325 - 0 3 chr1 327694 328525 + 0 4 chr1 461057 469003 + 0 5 chr1 538119 541204 - 0 6 chr1 538119 545189 + 0 7 chr1 722689 726224 - 0 10 chrX 1123077 1128966 + 0 8 chr1 1901333 1901590 - 0 9 chr1 3084040 3084307 - 0 Actual Chromosome Start End Strand Distance 0 chr1 4356 8647 + 0 1 chr1 4612 8918 - 0 2 chr1 12292 12325 - 0 3 chr1 327694 328525 + 0 4 chr1 461057 469003 + 0 5 chr1 538119 541204 - 0 6 chr1 538119 545189 + 0 7 chr1 722689 726224 - 0 8 chr1 1901333 1901590 - 0 9 chr1 3084040 3084307 - 0 10 chrX 1123077 1128966 + 0 Expected Chromosome Start End Strand Distance 0 chr1 4356 8647 + 0 1 chr1 4612 8918 - 0 2 chr1 12292 12325 - 0 3 chr1 327694 328525 + 0 4 chr1 461057 469003 + 0 5 chr1 538119 541204 - 0 6 chr1 538119 545189 + 0 7 chr1 722689 726224 - 0 8 chr1 1901333 1901590 - 0 9 chr1 3084040 3084307 - 0 10 chrX 1123077 1128966 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object 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 -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8dv_xmey/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8dv_xmey/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_n4ep3p9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_n4ep3p9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe7r1wuiu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe7r1wuiu/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4356 8647 + 0 1 chr1 4612 8918 - 0 2 chr1 12292 12325 - 0 3 chr1 327694 328525 + 0 4 chr1 461057 469003 + 0 5 chr1 538119 541204 - 0 6 chr1 538119 545189 + 0 7 chr1 722689 726224 - 0 8 chr1 1901333 1901590 - 0 9 chr1 3084040 3084307 - 0 10 chrX 1123077 1128966 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 327694 | 328525 | a | 0 | ... | | chr1 | 461057 | 469003 | a | 0 | ... | | chr1 | 4356 | 8647 | a | 0 | ... | | chr1 | 538119 | 545189 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 722689 | 726224 | a | 0 | ... | | chr1 | 12292 | 12325 | a | 0 | ... | | chr1 | 1901333 | 1901590 | a | 0 | ... | | chr1 | 538119 | 541204 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 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 2 chr1 4356 8647 + 0 5 chr1 4612 8918 - 0 7 chr1 12292 12325 - 0 0 chr1 327694 328525 + 0 1 chr1 461057 469003 + 0 9 chr1 538119 541204 - 0 3 chr1 538119 545189 + 0 6 chr1 722689 726224 - 0 10 chrX 1123077 1128966 + 0 8 chr1 1901333 1901590 - 0 4 chr1 3084040 3084307 - 0 df2 Chromosome Start End Strand Distance 0 chr1 4356 8647 + 0 1 chr1 4612 8918 - 0 2 chr1 12292 12325 - 0 3 chr1 327694 328525 + 0 4 chr1 461057 469003 + 0 5 chr1 538119 541204 - 0 6 chr1 538119 545189 + 0 7 chr1 722689 726224 - 0 10 chrX 1123077 1128966 + 0 8 chr1 1901333 1901590 - 0 9 chr1 3084040 3084307 - 0 Actual Chromosome Start End Strand Distance 0 chr1 4356 8647 + 0 1 chr1 4612 8918 - 0 2 chr1 12292 12325 - 0 3 chr1 327694 328525 + 0 4 chr1 461057 469003 + 0 5 chr1 538119 541204 - 0 6 chr1 538119 545189 + 0 7 chr1 722689 726224 - 0 8 chr1 1901333 1901590 - 0 9 chr1 3084040 3084307 - 0 10 chrX 1123077 1128966 + 0 Expected Chromosome Start End Strand Distance 0 chr1 4356 8647 + 0 1 chr1 4612 8918 - 0 2 chr1 12292 12325 - 0 3 chr1 327694 328525 + 0 4 chr1 461057 469003 + 0 5 chr1 538119 541204 - 0 6 chr1 538119 545189 + 0 7 chr1 722689 726224 - 0 8 chr1 1901333 1901590 - 0 9 chr1 3084040 3084307 - 0 10 chrX 1123077 1128966 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object 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 -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe1nvcevx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe1nvcevx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4356 8647 + 0 1 chr1 4612 8918 - 0 2 chr1 12292 12325 - 0 3 chr1 327694 328525 + 0 4 chr1 461057 469003 + 0 5 chr1 538119 541204 - 0 6 chr1 538119 545189 + 0 7 chr1 722689 726224 - 0 8 chr1 1901333 1901590 - 0 9 chr1 3084040 3084307 - 0 10 chrX 1123077 1128966 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 327694 | 328525 | a | 0 | ... | | chr1 | 461057 | 469003 | a | 0 | ... | | chr1 | 4356 | 8647 | a | 0 | ... | | chr1 | 538119 | 545189 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 722689 | 726224 | a | 0 | ... | | chr1 | 12292 | 12325 | a | 0 | ... | | chr1 | 1901333 | 1901590 | a | 0 | ... | | chr1 | 538119 | 541204 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 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 2 chr1 4356 8647 + 0 5 chr1 4612 8918 - 0 7 chr1 12292 12325 - 0 0 chr1 327694 328525 + 0 1 chr1 461057 469003 + 0 9 chr1 538119 541204 - 0 3 chr1 538119 545189 + 0 6 chr1 722689 726224 - 0 10 chrX 1123077 1128966 + 0 8 chr1 1901333 1901590 - 0 4 chr1 3084040 3084307 - 0 df2 Chromosome Start End Strand Distance 0 chr1 4356 8647 + 0 1 chr1 4612 8918 - 0 2 chr1 12292 12325 - 0 3 chr1 327694 328525 + 0 4 chr1 461057 469003 + 0 5 chr1 538119 541204 - 0 6 chr1 538119 545189 + 0 7 chr1 722689 726224 - 0 10 chrX 1123077 1128966 + 0 8 chr1 1901333 1901590 - 0 9 chr1 3084040 3084307 - 0 Actual Chromosome Start End Strand Distance 0 chr1 4356 8647 + 0 1 chr1 4612 8918 - 0 2 chr1 12292 12325 - 0 3 chr1 327694 328525 + 0 4 chr1 461057 469003 + 0 5 chr1 538119 541204 - 0 6 chr1 538119 545189 + 0 7 chr1 722689 726224 - 0 8 chr1 1901333 1901590 - 0 9 chr1 3084040 3084307 - 0 10 chrX 1123077 1128966 + 0 Expected Chromosome Start End Strand Distance 0 chr1 4356 8647 + 0 1 chr1 4612 8918 - 0 2 chr1 12292 12325 - 0 3 chr1 327694 328525 + 0 4 chr1 461057 469003 + 0 5 chr1 538119 541204 - 0 6 chr1 538119 545189 + 0 7 chr1 722689 726224 - 0 8 chr1 1901333 1901590 - 0 9 chr1 3084040 3084307 - 0 10 chrX 1123077 1128966 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object 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 -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4iat4l6a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4iat4l6a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc4znmhzb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc4znmhzb/f2.bed) bedtools bedtools bedtools bedtools 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/tmpzkmhdjdq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzkmhdjdq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp72llz29r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp72llz29r/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/tmphefhslhi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphefhslhi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2hfd2syn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2hfd2syn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppmkzyap5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppmkzyap5/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/tmp7lywg1cf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7lywg1cf/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/tmpl7536yoa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl7536yoa/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/tmp9zzp2isn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9zzp2isn/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/tmpsbj16e1e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsbj16e1e/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/tmptraiu2qu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptraiu2qu/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/tmpa9143cdj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa9143cdj/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/tmp3dsixiaj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3dsixiaj/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/tmpa9l4slqd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa9l4slqd/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/tmpjo8mr3ig/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjo8mr3ig/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/tmp430c3lz4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp430c3lz4/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/tmpdkp7xy01/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdkp7xy01/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/tmpjv74t_x8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjv74t_x8/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/tmpu3xt3w0p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu3xt3w0p/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/tmpatbbudov/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpatbbudov/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/tmpyegxxhpm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyegxxhpm/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/tmpco90ywfx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpco90ywfx/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/tmpowtjlivr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpowtjlivr/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/tmp5oifqaxk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5oifqaxk/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/tmplmwuv4uy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplmwuv4uy/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/tmpsdo8ai08/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsdo8ai08/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/tmpns40sr7z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpns40sr7z/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/tmpqwd7mdzx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqwd7mdzx/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_m030gxi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_m030gxi/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/tmpz03ugcz1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz03ugcz1/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/tmp0zf9fln4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0zf9fln4/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/tmpso1la3d8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpso1la3d8/f2.bed) bedtools bedtools bedtools bedtools 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/tmpp73i9a66/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp73i9a66/f2.bed) bedtools bedtools bedtools bedtools 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/tmp8tr_6qgb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8tr_6qgb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfo2le0ak/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfo2le0ak/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyzu9amrc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyzu9amrc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfg817qr4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfg817qr4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjs5ypfrf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjs5ypfrf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1sx2pkm2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1sx2pkm2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_tj3i2kr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_tj3i2kr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpal53l_0j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpal53l_0j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyi30a2t0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyi30a2t0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp17m5oy2c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp17m5oy2c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpevxy9rzj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpevxy9rzj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsyev1c2b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsyev1c2b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmp74hy08/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmp74hy08/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz7r22u47/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz7r22u47/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpanb7rl_5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpanb7rl_5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph2i8qecm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph2i8qecm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfxjoukc4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfxjoukc4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo76fgh6l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo76fgh6l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppy0_n4q2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppy0_n4q2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0xnm5ajg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0xnm5ajg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6s4nlw39/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6s4nlw39/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgnviwe_i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgnviwe_i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwh87ynvc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwh87ynvc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpidg9aekb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpidg9aekb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_x2tkee6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_x2tkee6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzz0n0ka8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzz0n0ka8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwyshv0gm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwyshv0gm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyseph_1y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyseph_1y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpazjlqnjc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpazjlqnjc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz9pbz3qi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz9pbz3qi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmslh8hxe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmslh8hxe/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptl03ogwy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptl03ogwy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplggvlpjm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplggvlpjm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6wtvhama/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6wtvhama/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe5ce5yrg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe5ce5yrg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2x9cgmjp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2x9cgmjp/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_chain120-method_chain120] __________ [gw3] linux -- Python 3.12.3 /usr/bin/python3.12 strandedness_chain = ('same', 'opposite') method_chain = ('nearest', '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=('nearest', 'set_intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 7684 | 9036 | a | 0 | - | E | chr1 | 10510 | 11862 | a | 0 | - | E | chr2 | 5565459 | 5566811 | 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 | 3997704 | 4002252 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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:575 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2D01bDnzVMqZmSUi61eychQI83OqGe9wpOBkQGIGIFkyBshRkZRBjlmRiZWBk1eBoY0VneQDBAwAemsGC4uBgaQYgZbBnYGBh/BwwwMABSzCig=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- 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') 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') ('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') ('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') ---------------------------------- 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] __________ [gw2] linux -- Python 3.12.3 /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, # 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:575 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') 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') 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') 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') 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') 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') ___________ test_three_in_a_row[strandedness_chain71-method_chain71] ___________ [gw1] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr2 | 4903 | 6495 | a | 0 | + | | | chr14 | 2033187 | 2034779 | 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) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr2 | 4903 | 6495 | a | 0 | + | | | chr14 | 4903 | 6495 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 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) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr2 | 983043 | 986373 | a | 0 | + | | | chr10 | 983043 | 986373 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 2 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 186 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicYyqU0+pn8bKr/8PAyMDAy84IpNgYGOXZlNiAfGE1BgZJNnMWBkZGBlYGFgYGBibs6oEqsatnZOBkYGBnYUpi4GJgYgBxgDL8QCYjL1A9AB85CV0=') 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=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr2 | 4063234 | 4064772 | 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 | 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., | ) | 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:575 | (and 77 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2CU0+pn8WJkYACi//8ZgDQfg5cdkAfks4GE2YBibOwsID4DhIBSALPIA+I=') 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') 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') 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') ('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') ('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') 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') ('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') 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') ---------------------------------- 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] ______________________ [gw0] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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='downstream', | overlap=True, | strandedness='same', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 7686154 | 7688737 | a | 0 | - | | | chr1 | 9227103 | 9229686 | a | 0 | - | | | chr1 | 1363816 | 1366399 | a | 0 | - | | | chr7 | 9110773 | 9113356 | a | 0 | - | | | chr9 | 4179778 | 4182361 | 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 | 1246728 | 1248801 | a | 0 | + | | | chr1 | 329476 | 329782 | a | 0 | + | | | chr1 | 329476 | 338498 | a | 0 | + | | | chr2 | 329476 | 338193 | a | 0 | + | | | chr2 | 329476 | 329782 | a | 0 | + | | | chr4 | 329476 | 331299 | a | 0 | - | | | chr7 | 329476 | 329782 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 7 rows and 6 columns from 4 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('6.100.4', b'AXicDc7PKwNwFADw9973+31vszHNZhPbMu2waNkOoplfrVgtcdxhWnPYBRdNrZyUE7U7R7kslKI5yYUlilzcuCspVkxZVp8/4IO5mfEDXvQeN2nl7fGXqqOYracnquv8ufWXTTlVptefBLtGO4EFNSF2spDNGM3aqYCJ3NQHCC6BYnHO6lChRiW+o+vIemMvcu56KLSLtlHq8vZlsjYNiafn+5+b8u7dEkTbugExv3/Y7Nge5OWMkODshUkfvXqucmvX3x+l8IaaP619bVrPsNTAwslUpYX6y5inwVVKgo/Aw4BhAoWsDOCwAAZaKZsggJsIWGPrZrpYIGhEdVBA/AJg8Wq9MJAQgR4Tir4H7ZpAY5QNjGkghghr4TiHTUwIY9onRMwAwkM8IoYU+tihRQzAPysYQTI=') 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=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('6.100.4', b'AXicY2QAA0YGBGBEoqBsAACRAAY=') 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 1209, in assert_frame_equal | assert_series_equal( | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 918, 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 414, in assert_attr_equal | raise_assert_detail(obj, msg, left_attr, right_attr) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 598, 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 467 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') 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/tmpff05277h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpff05277h/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/tmpa_vg9ine/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa_vg9ine/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps8v1yika/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps8v1yika/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfewhg1o0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfewhg1o0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_7tvoku3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_7tvoku3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 65538 65838 + 0 1 chr1 274949 277294 + 0 2 chr1 3344905 3347250 + 0 3 chr1 3344905 3351317 + 0 4 chr11 2100236 2106382 + 0 5 chr22 4880 8983 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3344905 | 3351317 | a | 0 | ... | | chr1 | 65538 | 65838 | a | 0 | ... | | chr1 | 274949 | 277294 | a | 0 | ... | | chr1 | 3344905 | 3347250 | a | 0 | ... | | chr11 | 2100236 | 2106382 | a | 0 | ... | | chr22 | 4880 | 8983 | 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 chr22 4880 8983 + 0 1 chr1 65538 65838 + 0 2 chr1 274949 277294 + 0 4 chr11 2100236 2106382 + 0 3 chr1 3344905 3347250 + 0 0 chr1 3344905 3351317 + 0 df2 Chromosome Start End Strand Distance 5 chr22 4880 8983 + 0 0 chr1 65538 65838 + 0 1 chr1 274949 277294 + 0 4 chr11 2100236 2106382 + 0 2 chr1 3344905 3347250 + 0 3 chr1 3344905 3351317 + 0 Actual Chromosome Start End Strand Distance 0 chr1 65538 65838 + 0 1 chr1 274949 277294 + 0 2 chr1 3344905 3347250 + 0 3 chr1 3344905 3351317 + 0 4 chr11 2100236 2106382 + 0 5 chr22 4880 8983 + 0 Expected Chromosome Start End Strand Distance 0 chr1 65538 65838 + 0 1 chr1 274949 277294 + 0 2 chr1 3344905 3347250 + 0 3 chr1 3344905 3351317 + 0 4 chr11 2100236 2106382 + 0 5 chr22 4880 8983 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object 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/tmpw1e9b61h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw1e9b61h/f2.bed) bedtools bedtools bedtools bedtools 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/tmpkw_qukyd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkw_qukyd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp860ftioa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp860ftioa/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwz1mb5jp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwz1mb5jp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv1v76xyx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv1v76xyx/f2.bed) bedtools bedtools bedtools bedtools 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/tmp02fko6gw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp02fko6gw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa_xgtm74/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa_xgtm74/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4zygrqq4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4zygrqq4/f2.bed) bedtools bedtools bedtools bedtools 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/tmpaq1ieft9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaq1ieft9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1cvz0v5h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1cvz0v5h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpslyrma1j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpslyrma1j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgbkdl7c_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgbkdl7c_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_14w7re4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_14w7re4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp23uul1dz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp23uul1dz/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/tmpa6iz98am/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa6iz98am/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsbnmrq1a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsbnmrq1a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpozsa6tzg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpozsa6tzg/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/tmp06vqd8rh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp06vqd8rh/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/tmpe_rpn05n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe_rpn05n/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/tmpz8shk7cn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz8shk7cn/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/tmp_rbplhn6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_rbplhn6/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/tmp_mk1ie1l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_mk1ie1l/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/tmpck9_x7rb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpck9_x7rb/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/tmpk1p3wyog/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk1p3wyog/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/tmplzqpx5s6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplzqpx5s6/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/tmpevrrrp4n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpevrrrp4n/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/tmpj7x35pvq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj7x35pvq/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/tmptwao4hky/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptwao4hky/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/tmpcdmnc3dm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcdmnc3dm/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/tmp0cpue9rf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0cpue9rf/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/tmptq1212uj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptq1212uj/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/tmpzktxocy_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzktxocy_/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/tmp_993ut7k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_993ut7k/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/tmpa1zoulzs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa1zoulzs/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/tmpdqheywxj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdqheywxj/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/tmp6no1zcrn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6no1zcrn/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/tmpui6id_a2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpui6id_a2/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/tmp7adai7uv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7adai7uv/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/tmp2fut7aj_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2fut7aj_/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/tmp97qnlw8o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp97qnlw8o/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/tmp_y7zs9x7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_y7zs9x7/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/tmp9_8jqpbd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9_8jqpbd/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/tmpg7pyknfe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg7pyknfe/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6baxi0yg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6baxi0yg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgugnjx3n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgugnjx3n/f2.bed) bedtools bedtools bedtools bedtools 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/tmpzqvnj8pe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzqvnj8pe/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 -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpueico5xq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpueico5xq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpth6_3fir/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpth6_3fir/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 4412 + 0 1 chr1 1 4412 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4412 | a | 0 | ... | | chr1 | 1 | 4412 | 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 4412 + 0 1 chr1 1 4412 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 4412 + 0 1 chr1 1 4412 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 4412 + 0 1 chr1 1 4412 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 4412 + 0 1 chr1 1 4412 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object 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 -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6it23k2m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6it23k2m/f2.bed) bedtools bedtools bedtools bedtools 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/tmpo4_30cac/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo4_30cac/f2.bed) bedtools bedtools bedtools bedtools 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/tmpeeqto6_q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeeqto6_q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe7n94ypv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe7n94ypv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwb6476a_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwb6476a_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6czq45x2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6czq45x2/f2.bed) bedtools bedtools bedtools bedtools 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/tmp5_ljp97k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5_ljp97k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9en04qh0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9en04qh0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpexf6ai3p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpexf6ai3p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1i87p5wc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1i87p5wc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl4qjbpwg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl4qjbpwg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9hgqqsfu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9hgqqsfu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq2ta8j6b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq2ta8j6b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfn3s3lh9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfn3s3lh9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4jr0e3ph/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4jr0e3ph/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0_mflt8j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0_mflt8j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz12o6hhp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz12o6hhp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpplq_y5q8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpplq_y5q8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpomlxan5z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpomlxan5z/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/tmpyblvnj9u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyblvnj9u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0eps3gkc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0eps3gkc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiuo0d602/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiuo0d602/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5j82rsrl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5j82rsrl/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/tmpbbua_6ah/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbbua_6ah/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/tmpgn7gwq4l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgn7gwq4l/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/tmpcqanj747/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcqanj747/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/tmp15antr9i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp15antr9i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaslif1hz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaslif1hz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgn7iufqj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgn7iufqj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpttt_gzvm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpttt_gzvm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5mve_1ll/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5mve_1ll/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/tmp7dlidawa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7dlidawa/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/tmpj3hfowxt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj3hfowxt/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/tmp3rjc2_qw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3rjc2_qw/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/tmpwjsnubye/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwjsnubye/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt3imj2_e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt3imj2_e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9t7i730v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9t7i730v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpji7mr998/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpji7mr998/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1vr1m40g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1vr1m40g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz76xtp8k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz76xtp8k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprszbdwex/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprszbdwex/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_chain121-method_chain121] __________ [gw3] linux -- Python 3.12.3 /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 | 5617916 | 5621293 | a | 0 | + | E | chr1 | 7882955 | 7886543 | a | 0 | + | E | chr1 | 6002380 | 6002763 | 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 | 204289 | 204546 | a | 0 | + | E | chr1 | 204289 | 204546 | a | 0 | + | E | chr1 | 204289 | 204546 | a | 0 | + | E | chr1 | 204289 | 204546 | 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=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 170 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY+LvzN3EyDrpJx+jmlhMP4MQEyMjAyMDAwMLU3L0tNNCDJWhO34LMXEw5ld4nGJgZpDkNWBkVOZjZmJmEmGsA6pjZuJkZmQFamFiFmNiZGBmZBRjYmBmBhnCxyzHwMAIMowBTjMCAEkeDR4=') 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') 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') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('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') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') 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') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') 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') ('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') 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') 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') ('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') ('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') ---------------------------------- 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_chain161-method_chain161] __________ [gw2] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 3844 | 4101 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | 1770251 | 1770254 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AXicY2BkAANZRgiDkQFM8zMzgAUYGdihotLMXAysDEwMDAAJ2gBw') 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') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('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') ('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') 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') 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') ('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') 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') 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') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', '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_chain72-method_chain72] ___________ [gw1] linux -- Python 3.12.3 /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 | 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 30 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2RAAozYKDQOAADCAAY=') 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') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') 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') 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') 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') ('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') ('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') 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') ('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') 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') ('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_nearest[downstream-True-opposite] ____________________ [gw0] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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='downstream', | overlap=True, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 94 | 631 | a | 0 | + | | | chr1 | 94 | 7775 | 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 | 214802 | 214803 | 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('6.100.4', b'AXicY8wIu6HFmMl6SYCBiYERCBgYgCiWiTFGjoGdkY+RiZGdQZBJgoGLEcgAyjGyMjMysAPVACGzuyBYNQMDAAN8BMQ=') 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=True, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | | chr1 | 2 | 3 | a | 0 | + | | | chr1 | 2 | 3 | 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., | ) | 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 129 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2QQe3KMkQEIGDNZLwkAKTCbgQFOQdnIgBEAkGMDGQ==') 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 1209, in assert_frame_equal | assert_series_equal( | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 918, 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 414, in assert_attr_equal | raise_assert_detail(obj, msg, left_attr, right_attr) | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 598, 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 467 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY3QUe3KMgYGRAQEY4QQqYAQAUqYCBw==') 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/tmpol6mc2pf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpol6mc2pf/f2.bed) bedtools bedtools bedtools bedtools 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/tmp53v6im6i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp53v6im6i/f2.bed) bedtools bedtools bedtools bedtools 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/tmpk912rfmz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk912rfmz/f2.bed) bedtools bedtools bedtools bedtools 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/tmp6p1rn5cj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6p1rn5cj/f2.bed) bedtools bedtools bedtools bedtools 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/tmp85cmb_rd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp85cmb_rd/f2.bed) bedtools bedtools bedtools bedtools 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/tmpwdoc5qiq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwdoc5qiq/f2.bed) bedtools bedtools bedtools bedtools 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/tmp6362av9l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6362av9l/f2.bed) bedtools bedtools bedtools bedtools 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/tmpgyfgtnsr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgyfgtnsr/f2.bed) bedtools bedtools bedtools bedtools 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/tmpmmaf54de/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmmaf54de/f2.bed) bedtools bedtools bedtools bedtools 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/tmprey8x5c4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprey8x5c4/f2.bed) bedtools bedtools bedtools bedtools 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/tmpsov5g223/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsov5g223/f2.bed) bedtools bedtools bedtools bedtools 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/tmpkjot6iyk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkjot6iyk/f2.bed) bedtools bedtools bedtools bedtools 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/tmpgiwx_2xr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgiwx_2xr/f2.bed) bedtools bedtools bedtools bedtools 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_9_cz2d4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_9_cz2d4/f2.bed) bedtools bedtools bedtools bedtools 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/tmpxfdiaw4v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxfdiaw4v/f2.bed) bedtools bedtools bedtools bedtools 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/tmp6zgnhuon/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6zgnhuon/f2.bed) bedtools bedtools bedtools bedtools 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/tmps_2fix6m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps_2fix6m/f2.bed) bedtools bedtools bedtools bedtools 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/tmpj4qgnfzw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj4qgnfzw/f2.bed) bedtools bedtools bedtools bedtools 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/tmp7t45io_1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7t45io_1/f2.bed) bedtools bedtools bedtools bedtools 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/tmpv08hjhai/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv08hjhai/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_oc6hlwz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_oc6hlwz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4rkosuaz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4rkosuaz/f2.bed) bedtools bedtools bedtools bedtools 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/tmpo07yg5wx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo07yg5wx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp08ctuzdm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp08ctuzdm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2w7iksud/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2w7iksud/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpneb23qhi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpneb23qhi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiot02o2r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiot02o2r/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv3dglcc_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv3dglcc_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppys6f5at/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppys6f5at/f2.bed) bedtools bedtools bedtools bedtools 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/tmpwl6yngih/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwl6yngih/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpveyirjqc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpveyirjqc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbfs9y8jw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbfs9y8jw/f2.bed) bedtools bedtools bedtools bedtools 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/tmpg2arvesz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg2arvesz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7z5suvgt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7z5suvgt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpolg56yvt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpolg56yvt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj2if36t7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj2if36t7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1ji4oibh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1ji4oibh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_p6w4ora/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_p6w4ora/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxc5j1t46/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxc5j1t46/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpae5h5t9c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpae5h5t9c/f2.bed) bedtools bedtools bedtools bedtools 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/tmpyn781fmu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyn781fmu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk93wo552/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk93wo552/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg3jev6bc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg3jev6bc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 5297059 5301416 + 0 2 chr1 5297059 5305696 + 0 6 chr22 7533689 7535108 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5297059 | 5305696 | a | 0 | ... | | chr1 | 5297059 | 5301416 | a | 0 | ... | | chr22 | 7533689 | 7535108 | 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 1 chr1 5297059 5301416 + 0 0 chr1 5297059 5305696 + 0 2 chr22 7533689 7535108 + 0 df2 Chromosome Start End Strand Distance 1 chr1 5297059 5301416 + 0 2 chr1 5297059 5305696 + 0 6 chr22 7533689 7535108 + 0 Actual Chromosome Start End Strand Distance 0 chr1 5297059 5301416 + 0 1 chr1 5297059 5305696 + 0 2 chr22 7533689 7535108 + 0 Expected Chromosome Start End Strand Distance 0 chr1 5297059 5301416 + 0 1 chr1 5297059 5305696 + 0 2 chr22 7533689 7535108 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object 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/tmpb0w3rfks/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb0w3rfks/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi5cjzus2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi5cjzus2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxv_ae5l_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxv_ae5l_/f2.bed) bedtools bedtools bedtools bedtools 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/tmp7tfajo4p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7tfajo4p/f2.bed) bedtools bedtools bedtools bedtools 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/tmpvzcckh6r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvzcckh6r/f2.bed) bedtools bedtools bedtools bedtools 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/tmpp80wbtrg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp80wbtrg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp79qyxq4q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp79qyxq4q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp93amsrxt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp93amsrxt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpstys2f5y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpstys2f5y/f2.bed) bedtools bedtools bedtools bedtools 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/tmpdydgg69s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdydgg69s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp89uadav7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp89uadav7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5m3752nk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5m3752nk/f2.bed) bedtools bedtools bedtools bedtools 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/tmpmihzdpg5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmihzdpg5/f2.bed) bedtools bedtools bedtools bedtools 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/tmpo945yj_l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo945yj_l/f2.bed) bedtools bedtools bedtools bedtools 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/tmp4x_3t8w3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4x_3t8w3/f2.bed) bedtools bedtools bedtools bedtools 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/tmp5owmiedf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5owmiedf/f2.bed) bedtools bedtools bedtools bedtools 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/tmpwxxn6s57/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwxxn6s57/f2.bed) bedtools bedtools bedtools bedtools 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/tmpbitbjaty/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbitbjaty/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpufu30jf3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpufu30jf3/f2.bed) bedtools bedtools bedtools bedtools 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/tmphg4iiznr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphg4iiznr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr95o0jic/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr95o0jic/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmqb9hg9b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmqb9hg9b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2w_zrukz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2w_zrukz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1219933 1220773 - 0 1 chr1 1219933 1221888 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1219933 | 1221888 | a | 0 | ... | | chr1 | 1219933 | 1220773 | 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 1219933 1220773 - 0 0 chr1 1219933 1221888 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1219933 1220773 - 0 1 chr1 1219933 1221888 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1219933 1220773 - 0 1 chr1 1219933 1221888 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1219933 1220773 - 0 1 chr1 1219933 1221888 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object 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 -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6ip4mp98/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6ip4mp98/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp82pgc9v5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp82pgc9v5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj2h0n8oh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj2h0n8oh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcb42vccd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcb42vccd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdo7z1cmg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdo7z1cmg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk1on410h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk1on410h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpecsvzlwv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpecsvzlwv/f2.bed) bedtools bedtools bedtools bedtools 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/tmpw0b074tn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw0b074tn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzw1tt1rp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzw1tt1rp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi2dncyw3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi2dncyw3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu76y9y_z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu76y9y_z/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkuh6_nsc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkuh6_nsc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2uee0k5v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2uee0k5v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_g5ponma/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_g5ponma/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdsdt83j6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdsdt83j6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeg7d9m_p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeg7d9m_p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpra30bvgb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpra30bvgb/f2.bed) bedtools bedtools bedtools bedtools 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/tmpvu1vz6ba/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvu1vz6ba/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe7f2satt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe7f2satt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpji4f8w2z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpji4f8w2z/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxe_nhkee/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxe_nhkee/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 791553 793602 + 0 1 chr1 791553 794922 - 0 2 chr12 791553 792066 + 0 3 chr12 791553 795143 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 791553 | 793602 | a | 0 | ... | | chr1 | 791553 | 794922 | a | 0 | ... | | chr12 | 791553 | 792066 | a | 0 | ... | | chr12 | 791553 | 795143 | 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 ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr12 791553 792066 + 0 0 chr1 791553 793602 + 0 1 chr1 791553 794922 - 0 3 chr12 791553 795143 - 0 df2 Chromosome Start End Strand Distance 2 chr12 791553 792066 + 0 0 chr1 791553 793602 + 0 1 chr1 791553 794922 - 0 3 chr12 791553 795143 - 0 Actual Chromosome Start End Strand Distance 0 chr1 791553 793602 + 0 1 chr1 791553 794922 - 0 2 chr12 791553 792066 + 0 3 chr12 791553 795143 - 0 Expected Chromosome Start End Strand Distance 0 chr1 791553 793602 + 0 1 chr1 791553 794922 - 0 2 chr12 791553 792066 + 0 3 chr12 791553 795143 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object 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 -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpymh_hmz7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpymh_hmz7/f2.bed) bedtools bedtools bedtools bedtools 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/tmpg2ftr0z8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg2ftr0z8/f2.bed) bedtools bedtools bedtools bedtools 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/tmpk2vry5oo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk2vry5oo/f2.bed) bedtools bedtools bedtools bedtools 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/tmp58__vkt_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp58__vkt_/f2.bed) bedtools bedtools bedtools bedtools 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/tmppc6ksphy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppc6ksphy/f2.bed) bedtools bedtools bedtools bedtools 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/tmpl0n49nj_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl0n49nj_/f2.bed) bedtools bedtools bedtools bedtools 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/tmpp7b06lrs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp7b06lrs/f2.bed) bedtools bedtools bedtools bedtools 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/tmpx1geidvg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx1geidvg/f2.bed) bedtools bedtools bedtools bedtools 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/tmpdi41f8ef/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdi41f8ef/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_pwl_s4b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_pwl_s4b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbaqw9och/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbaqw9och/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1219933 1220773 - 0 1 chr1 1219933 1221888 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1219933 | 1221888 | a | 0 | ... | | chr1 | 1219933 | 1220773 | 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 1219933 1220773 - 0 0 chr1 1219933 1221888 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1219933 1220773 - 0 1 chr1 1219933 1221888 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1219933 1220773 - 0 1 chr1 1219933 1221888 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1219933 1220773 - 0 1 chr1 1219933 1221888 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object 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 -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz7yw2ma7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz7yw2ma7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdn3y7bbo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdn3y7bbo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp24m0t8vb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp24m0t8vb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4g7x7pbd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4g7x7pbd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_uet47e5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_uet47e5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbrzdvu1w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbrzdvu1w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf02jk00x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf02jk00x/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7vny4_53/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7vny4_53/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvjkprn9f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvjkprn9f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp77nzmfdw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp77nzmfdw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuw4ro58_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuw4ro58_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprzde2345/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprzde2345/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphoohhsyn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphoohhsyn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdbubimqz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdbubimqz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpem2iwrl3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpem2iwrl3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5uktpxwy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5uktpxwy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8y8ud7m8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8y8ud7m8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgmuhwxyp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgmuhwxyp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo3pdg5ot/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo3pdg5ot/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe_yhl4c3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe_yhl4c3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptailha1f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptailha1f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmput074ez_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmput074ez_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb6p39xy2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb6p39xy2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqa0w6g_b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqa0w6g_b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuu7w0f6t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuu7w0f6t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkt1hasdo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkt1hasdo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbb62jikw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbb62jikw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp74r8zf13/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp74r8zf13/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpalmkp9ff/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpalmkp9ff/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdmyibql8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdmyibql8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkj5rhyt7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkj5rhyt7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2d2_x4tu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2d2_x4tu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuo5rk_el/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuo5rk_el/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjtxo33m_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjtxo33m_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5awu7gsr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5awu7gsr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyvtkhzp2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyvtkhzp2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjlp7uxcj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjlp7uxcj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsvkyaqjo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsvkyaqjo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwirki9x4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwirki9x4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxdh685sd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxdh685sd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg4hmn0ip/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg4hmn0ip/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuokwvv28/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuokwvv28/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvhfpsvt8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvhfpsvt8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc3tsg3ze/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc3tsg3ze/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp25c66r91/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp25c66r91/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpngl2nklu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpngl2nklu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6jnyh1vw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6jnyh1vw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprl6lut01/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprl6lut01/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxs880a72/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxs880a72/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6oyamfi0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6oyamfi0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp34vjx9uq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp34vjx9uq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcerbxpvs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcerbxpvs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8doa1ep5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8doa1ep5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0n4uip70/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0n4uip70/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5chqqxn6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5chqqxn6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph7xpqdz3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph7xpqdz3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp729olpoe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp729olpoe/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxmisgiip/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxmisgiip/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9_huautp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9_huautp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxheedtw1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxheedtw1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4p9pimc8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4p9pimc8/f2.bed) bedtools bedtools bedtools bedtools 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/tmpw35ts1sj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw35ts1sj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb14uigad/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb14uigad/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx24syujh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx24syujh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsiut0ga0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsiut0ga0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo3sv8lun/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo3sv8lun/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp51o6uvcs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp51o6uvcs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxklbwveq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxklbwveq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq1q1bfrg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq1q1bfrg/f2.bed) bedtools bedtools bedtools bedtools 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/tmpvcudsmo7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvcudsmo7/f2.bed) bedtools bedtools bedtools bedtools 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/tmpy7ajskmq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy7ajskmq/f2.bed) bedtools bedtools bedtools bedtools 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/tmps4o_5e5_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps4o_5e5_/f2.bed) bedtools bedtools bedtools bedtools 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/tmpm5f5fj5a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm5f5fj5a/f2.bed) bedtools bedtools bedtools bedtools 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_zb9r6pr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_zb9r6pr/f2.bed) bedtools bedtools bedtools bedtools 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/tmp00lyyfiy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp00lyyfiy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp1kju9e3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp1kju9e3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnw99dk_u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnw99dk_u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2qq2hodc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2qq2hodc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxvkmc6sk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxvkmc6sk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp91wf8wv0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp91wf8wv0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfkmmp40f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfkmmp40f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe7ehagbc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe7ehagbc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxagbyr3k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxagbyr3k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp05s3xr81/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp05s3xr81/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp86f9ol1g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp86f9ol1g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn9bv3392/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn9bv3392/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnmb76aaa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnmb76aaa/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 -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx_r6uoye/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx_r6uoye/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5x9lwmcn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5x9lwmcn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptuqfazo4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptuqfazo4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwyvruldz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwyvruldz/f2.bed) bedtools bedtools bedtools bedtools 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/tmpmt39d0cc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmt39d0cc/f2.bed) bedtools bedtools bedtools bedtools 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/tmpcnpdzmlw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcnpdzmlw/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 -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1n62959q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1n62959q/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 -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj7_hdljh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj7_hdljh/f2.bed) bedtools bedtools bedtools bedtools 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/tmpzupel0r2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzupel0r2/f2.bed) bedtools bedtools bedtools bedtools 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/tmpwa4e408o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwa4e408o/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 -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4jzldqwq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4jzldqwq/f2.bed) bedtools bedtools bedtools bedtools 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/tmp7_jb12dp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7_jb12dp/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 -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpysmslj_a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpysmslj_a/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 -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpveb4rs_6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpveb4rs_6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4w11gxmi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4w11gxmi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz9c2u1nt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz9c2u1nt/f2.bed) bedtools bedtools bedtools bedtools 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/tmp3dm7rrx6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3dm7rrx6/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/tmp2fa7nzpb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2fa7nzpb/f2.bed) bedtools bedtools bedtools bedtools 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/tmpl7hf6uhk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl7hf6uhk/f2.bed) bedtools bedtools bedtools bedtools 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/tmp1x1qo9fd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1x1qo9fd/f2.bed) bedtools bedtools bedtools bedtools 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/tmpvhmx4xll/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvhmx4xll/f2.bed) bedtools bedtools bedtools bedtools 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/tmpgynvo229/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgynvo229/f2.bed) bedtools bedtools bedtools bedtools 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/tmps2qc_dvh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps2qc_dvh/f2.bed) bedtools bedtools bedtools bedtools 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/tmpdble7xym/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdble7xym/f2.bed) bedtools bedtools bedtools bedtools 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/tmpg1auar5o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg1auar5o/f2.bed) bedtools bedtools bedtools bedtools 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/tmploeva6g8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmploeva6g8/f2.bed) bedtools bedtools bedtools bedtools 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/tmpvtcivhra/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvtcivhra/f2.bed) bedtools bedtools bedtools bedtools 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/tmpspg5y2bl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpspg5y2bl/f2.bed) bedtools bedtools bedtools bedtools 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/tmpwv_dmdgk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwv_dmdgk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4x5_i7l6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4x5_i7l6/f2.bed) bedtools bedtools bedtools bedtools 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/tmp0cr_ucgb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0cr_ucgb/f2.bed) bedtools bedtools bedtools bedtools 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/tmpszf8jhwj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpszf8jhwj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm3phfs3t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm3phfs3t/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 -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3i7dv4mm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3i7dv4mm/f2.bed) bedtools bedtools bedtools bedtools 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/tmpgbkw4uwb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgbkw4uwb/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 -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpahw1kzhu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpahw1kzhu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphgtu5yl7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphgtu5yl7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzqzye_9s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzqzye_9s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcpfhrc73/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcpfhrc73/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_chain122-method_chain122] __________ [gw3] linux -- Python 3.12.3 /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 | 2 | 13 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | 65538 | 66819 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AXicY2LxaH/LwMAIhGCCC0gBmawMMAEQE8ICCwAAUdYB5A==') 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') ('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') 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') 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') ('nearest', 'nearest') ('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') ('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') ('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') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') 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') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') 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') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') 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') 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') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('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] __________ [gw2] linux -- Python 3.12.3 /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, 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('6.100.4', 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') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('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') ('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') 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') ('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') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('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') ('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') ('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') ---------------------------------- 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] ___________ [gw1] linux -- Python 3.12.3 /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 | 196715 | 196716 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AXicY7T19tzBAAbMDFkMjCAGmACSEBoG4DwAWtMB/Q==') 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') Empty PyRanges ('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') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') 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') ('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') ('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') ('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') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') 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-False-False] _____________________ [gw0] linux -- Python 3.12.3 /usr/bin/python3.12 nearest_how = 'downstream', 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:115: in _nearest r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, pyranges/methods/nearest.py:62: in _next_nonoverlapping r_idx, dist = nearest_next_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_nearest( E nearest_how='downstream', 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:115 E (and 39 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:34: ValueError ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7qp3ruan/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7qp3ruan/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprqly40jk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprqly40jk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwrnu_j3q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwrnu_j3q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphxyrf93n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphxyrf93n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn6_87rgm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn6_87rgm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3sf2792o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3sf2792o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk79_wlxi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk79_wlxi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyoq_vmee/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyoq_vmee/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy50gcmxb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy50gcmxb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp449d0_nj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp449d0_nj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppvuw6p05/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppvuw6p05/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps_zo61eb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps_zo61eb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcam8az19/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcam8az19/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpspz26lvm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpspz26lvm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpip40a_sn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpip40a_sn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphy51hbpl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphy51hbpl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw6kjpaln/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw6kjpaln/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbplu0zrv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbplu0zrv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8rtfcmo9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8rtfcmo9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4a660b3v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4a660b3v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkj2yy7ta/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkj2yy7ta/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz1b72_k9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz1b72_k9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwyc8wrmt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwyc8wrmt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp87t2noub/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp87t2noub/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyrydma13/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyrydma13/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp433ajbi_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp433ajbi_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphvc2id35/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphvc2id35/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnoygzn64/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnoygzn64/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpotqj72i5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpotqj72i5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphroug759/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphroug759/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppk7bplcl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppk7bplcl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplqlp1vbh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplqlp1vbh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmzy0qykr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmzy0qykr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5kncrh9s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5kncrh9s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmitxjatf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmitxjatf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpatmt24t1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpatmt24t1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqs6bqn28/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqs6bqn28/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0o4gn44g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0o4gn44g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp32d1v3ve/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp32d1v3ve/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7no_xt9t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7no_xt9t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp40rah4ui/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp40rah4ui/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9kxbanh_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9kxbanh_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa2fgd9rk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa2fgd9rk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjpq_saak/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjpq_saak/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpme4t654g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpme4t654g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpygwr8q97/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpygwr8q97/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps_d84b68/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps_d84b68/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphwcz149e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphwcz149e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp58jgmr_o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp58jgmr_o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3pn74ixb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3pn74ixb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphqsgr9bo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphqsgr9bo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppfemteah/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppfemteah/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5t2b_x3h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5t2b_x3h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7in9ru3w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7in9ru3w/f2.bed) bedtools bedtools bedtools bedtools 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/tmp8743q_o6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8743q_o6/f2.bed) bedtools bedtools bedtools bedtools 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/tmpjsy98afb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjsy98afb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn89temon/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn89temon/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpke2_r5qe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpke2_r5qe/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb29mdzfe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb29mdzfe/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz5vj4b40/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz5vj4b40/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo0528uly/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo0528uly/f2.bed) bedtools bedtools bedtools bedtools 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/tmpi0yykx0m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi0yykx0m/f2.bed) _____________________ test_nearest[downstream-False-same] ______________________ [gw0] linux -- Python 3.12.3 /usr/bin/python3.12 nearest_how = 'downstream', 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:115: in _nearest r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, pyranges/methods/nearest.py:62: in _next_nonoverlapping r_idx, dist = nearest_next_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_nearest( E nearest_how='downstream', 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 104 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:34: ValueError ----------------------------- 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/tmpx7di2bes/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx7di2bes/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfjzsp7_v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfjzsp7_v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6ct0f1v3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6ct0f1v3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph7lppyic/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph7lppyic/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_2skje5i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_2skje5i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp12n8cmw1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp12n8cmw1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpelb0vuzy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpelb0vuzy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphkc8ghnk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphkc8ghnk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe83juckp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe83juckp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpntht5rsv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpntht5rsv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprdfd8s2l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprdfd8s2l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpymbqgdki/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpymbqgdki/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnh1wayba/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnh1wayba/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt6p939wq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt6p939wq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4etqluxv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4etqluxv/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_utfwtmv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_utfwtmv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp81zqne0i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp81zqne0i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppc09aes5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppc09aes5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbubp0s12/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbubp0s12/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmepso5f8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmepso5f8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptp0g8fdf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptp0g8fdf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprwo0xlr6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprwo0xlr6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp19c4mzs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp19c4mzs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgwhohfsi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgwhohfsi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpenzl9qwr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpenzl9qwr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiqzqzb8p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiqzqzb8p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplf97f800/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplf97f800/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiak69bpk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiak69bpk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmdwjd21b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmdwjd21b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjp2d_xkd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjp2d_xkd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqbhf5vnb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqbhf5vnb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph23vw2nf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph23vw2nf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3to9zpje/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3to9zpje/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz4f7gndy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz4f7gndy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb65myh1p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb65myh1p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp24mlgsw6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp24mlgsw6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7g106a27/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7g106a27/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyu6h71wg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyu6h71wg/f2.bed) bedtools bedtools bedtools bedtools 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/tmpf8hlr_uv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf8hlr_uv/f2.bed) bedtools bedtools bedtools bedtools 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/tmpodddkqu9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpodddkqu9/f2.bed) bedtools bedtools bedtools bedtools 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/tmp5vk8na8w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5vk8na8w/f2.bed) __________ test_three_in_a_row[strandedness_chain123-method_chain123] __________ [gw3] linux -- Python 3.12.3 /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 | 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('6.100.4', b'AXicY5RiZmZkYAAiKIFOoQMABwoAJw==') 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') ('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') ('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') 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') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('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') ('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') ('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') 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') ('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') ('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') ('nearest', 'intersect') Empty PyRanges ('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_chain74-method_chain74] ___________ [gw1] linux -- Python 3.12.3 /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 | 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 30 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2QAA0Y4gU6hAwAA5gAG') 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') ('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') ('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') ('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') ('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') ('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') ('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') Empty PyRanges ('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') ('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') Empty PyRanges ('nearest', 'intersect') 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_chain164-method_chain164] __________ [gw2] linux -- Python 3.12.3 /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 | 2058 | 4366 | a | 0 | - | E | chr1 | 2058 | 5806 | a | 0 | - | E | chr1 | 2058 | 12058 | a | 0 | - | E | chr1 | 2058 | 3528 | a | 0 | - | E | ... | ... | ... | ... | ... | ... | E | chr1 | 1179964 | 1182781 | a | 0 | - | E | chr1 | 2058 | 3095 | a | 0 | - | E | chr1 | 2058 | 5900 | a | 0 | - | E | chr1 | 655361 | 664836 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 9 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 | 655882 | 659630 | a | 0 | + | E | chr1 | 2058 | 12058 | a | 0 | + | E | chr1 | 2058 | 3528 | a | 0 | + | E | chr1 | 2058 | 4897 | a | 0 | + | E | ... | ... | ... | ... | ... | ... | E | chr11 | 2058 | 11533 | a | 0 | + | E | chr14 | 2058 | 4398 | a | 0 | + | E | chr22 | 2058 | 9211 | a | 0 | + | E | chr22 | 2058 | 2071 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 9 rows and 6 columns from 4 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 | 2407440 | 2407726 | a | 0 | + | E | chr1 | 2407440 | 2407474 | 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: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 30 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicjc8rT8NQHIbx939OT9tzac9GsgmWQrZ2LOGSkTFYk4Zw+QAgECQDh8HgsFwCii+wICE49CQQDJKPgcKgUITQbQhws4/6PaLaXe977PAmjvYuvzxeePu+f3p57e1Piuh2OzqiC2d34apPG8/H7+fNGjuorXyKHW0lP7vunSILPAKl2ocClBZigjIAvtQUh3cdkWi0Rd2FY+aN6yh/s7NVZ4aviscZ47R0edn4FT9DJrkbSk9ZKoTspGEBov+uMTB/7AMXpqZLi0AQWywh5dRgVAxZ2aGiSwnRLGsb3tTQAqWR31WSoJgc+ud+/ZWP8fzx0A+jRnx4QO5i1ieVv9AgIUgebIguRYpaaymqefoB/H5Bug==') 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') ('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') ('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') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') 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') ('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') 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') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') 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') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2058 | 12058 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For 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') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') 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') ('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') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') 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_chain196-method_chain196] __________ [gw0] linux -- Python 3.12.3 /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, # 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 250 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('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') ('set_union', 'set_union') ('set_union', 'set_union') ('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') 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') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('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_chain124-method_chain124] __________ [gw3] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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 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=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 65795 | 66052 | 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 | 67335 | 67337 | 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('6.100.4', b'AXicY2BkYWJkYGBgZGAEssAMIIsJiEFsNkYmFgawoBwjOxuQSgXJMwAACeIAuw==') 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 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 | 65795 | 65796 | 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/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('6.100.4', b'AXicY2RkYWJgYGAEIkYQA8LGBHBBAAKSABA=') 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', '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 | 336386 | 339975 | a | 0 | ... | | chr1 | 2359582 | 2360361 | a | 0 | ... | | chr1 | 656954 | 660550 | a | 0 | ... | | chr9 | 921104 | 922641 | a | 0 | ... | | chr9 | 852230 | 852999 | 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 ('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') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 67335 | 77293 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For 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 | 67335 | 77293 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For 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 | 67335 | 77293 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For 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 | 67335 | 77293 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For 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 | 67335 | 77293 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For 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') ('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') 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') ('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') ('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') Empty PyRanges ('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') 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 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For 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') ---------------------------------- 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_chain75-method_chain75] ___________ [gw1] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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 | 287 | 1062 | a | 0 | + | | | chr18 | 287 | 1062 | a | 0 | + | | | chr18 | 287 | 1062 | a | 0 | - | | | chr18 | 287 | 1062 | a | 0 | - | | | chr18 | 287 | 1062 | a | 0 | - | | | chr18 | 287 | 1062 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 6 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 | 394252 | 395540 | a | 0 | + | | | chr1 | 394252 | 395540 | a | 0 | - | | | chr1 | 394252 | 398280 | a | 0 | - | | | chr5 | 394252 | 395903 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 4 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 177 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicFY0xDgFRFEXv/e/9/8dMDDMZZhJGwgJ0otMrJBOVXUhUNqFRK61AVGxAZwFEaQFiAUZ1mpNzbPBc34vbwUt3eHQ6fJ3d6PNmNf5SprtH7ubsXJAZJKEFcgMkIDhAJS4Ac5LCFJGU0rSYMFR4zbydCei9xvqnYqmN7emlan2BEoyFPQONjUVK1l2nUS6mdXWSmZXboG29q9O0HNAIC6Alin69B2W/KGqVP7HuFjs=') 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 | 2 | 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:575 | (and 63 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', 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', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('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') 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') ('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') 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') ('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') 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') 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') ('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') 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') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('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_chain166-method_chain166] __________ [gw2] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ 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 gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr11 | 6493698 | 6503683 | a | 0 | + | E | chr13 | 6493698 | 6503683 | a | 0 | + | E | chr13 | 6493698 | 6503683 | 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 ) E Explanation: E These lines 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 103 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkY2dkZGBiZGBkYGABYiBigFIMjJEGN/8zJrKtd2OsnzGtjgGokIuBgYchLlmMkUFCnYETpAgAwtcHQA==') 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') ('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') ('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') 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') 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') 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') 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') Empty PyRanges ('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') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('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') 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') ---------------------------------- 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_chain197-method_chain197] __________ [gw0] linux -- Python 3.12.3 /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, # 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 /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('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('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') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('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') 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') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('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_chain125-method_chain125] __________ [gw3] linux -- Python 3.12.3 /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 | 257 | 4310 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | 1542 | 1800 | a | 0 | + | E | chr1 | 80144 | 80402 | 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 30 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2SauPwVAyMQMmSDKTX+K2CaMZolIZRRmAEkw8jIyMZoyc/Ay8DGCuYxAgWBEswM7AzSrAwAEZgFZA==') 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') ('nearest', 'join') ('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') ('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') 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') ('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') ('nearest', 'join') ('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') ('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') ('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') ('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') ---------------------------------- 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_chain76-method_chain76] ___________ [gw1] linux -- Python 3.12.3 /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 | 3279618 | 3279876 | a | 0 | + | E | chr1 | 3279618 | 3279876 | 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 | 769 | 1026 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AXicFcrRCQAgDEPBF2utIjiCQ7j/cLb5CBeIY4RHZ1HR20KSKe2JRm44eaNQNXVtwAcX+gC/') 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') 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') ('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') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('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') 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') 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') 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') ('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') ---------------------------------- 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 3.12.3 /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, # 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('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('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') 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') 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') 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') 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') __________ test_three_in_a_row[strandedness_chain168-method_chain168] __________ [gw2] linux -- Python 3.12.3 /usr/bin/python3.12 strandedness_chain = ('opposite', False) method_chain = ('nearest', '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=('nearest', 'set_union'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr2 | 95003 | 95004 | a | 0 | + | E | chr2 | 95003 | 95004 | 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 | 6937952 | 6942046 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 247 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AAABRi0p5R4cAQABPlneEAF2X4YHAAAAAQAMAXMaAAAAAAAAAVNhAAYAAAAAAQA6ad1fAAAiD/0AAA==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- 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') 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') 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') ('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') 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') 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') 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') ('nearest', 'set_union') ('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') ('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') ---------------------------------- 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_chain126-method_chain126] __________ [gw3] linux -- Python 3.12.3 /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: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 240 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', 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') 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') 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') ('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') 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') 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') 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') 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') 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') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('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_chain77-method_chain77] ___________ [gw1] linux -- Python 3.12.3 /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, 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 145 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', 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') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('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') ('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') 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') 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') ('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') 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') 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') 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') ---------------------------------- 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_chain199-method_chain199] __________ [gw0] linux -- Python 3.12.3 /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('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('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') Empty PyRanges ('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') ('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') 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') 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') __________ test_three_in_a_row[strandedness_chain169-method_chain169] __________ [gw2] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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 | 1558 | 4375 | a | 0 | + | | | chr1 | 1558 | 4375 | 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 | 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 170 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2RgBIIYJ0c/BghgE2Vg5GZgBEIGRiEmhmqwIBOQxwDBIJKBGUgBAFJNAfY=') 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=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 5761 | 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) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr5 | 131329 | 131586 | 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 154 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2ZhZGRkAAEQycTAIFYPYbKJMkGEmBiqQdIsDCpMjGBlLEAMACeOAXI=') 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') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('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') ('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') ('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') ('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') 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') ('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') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('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') ---------------------------------- 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_chain127-method_chain127] __________ [gw3] linux -- Python 3.12.3 /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: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('6.100.4', 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') ('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') 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') ('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') 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') 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') ('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') 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') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', '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_chain200-method_chain200] __________ [gw0] linux -- Python 3.12.3 /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, # 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 194 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('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') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('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') 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') 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') ___________ test_three_in_a_row[strandedness_chain78-method_chain78] ___________ [gw1] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr3 | 65794 | 65801 | a | 0 | + | E | chr3 | 66306 | 66337 | 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=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 514 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AXicHYlBCoAwEMSSquulXgURfJXfKf6i+Fy3BgITxtukvf0BiuwjnZ1E4eIk8sl5LMGGwfp3ZVDSD65jAzs=') 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') ('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') ('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') ('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') ('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') ('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') ('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') 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') ('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') 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') ---------------------------------- 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 3.12.3 /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 | 131333 | 132106 | a | 0 | - | E | chr5 | 131333 | 132106 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 2 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/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 182 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2RmrmRlZGPSZGdgZGBgYQACcSZGFgZGZhZGRqAIIwMYQCk0DgAxwwDw') 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') 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') ('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') ('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') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('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') ('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') 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') ('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') ('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') ('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') ---------------------------------- 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_chain201-method_chain201] __________ [gw0] linux -- Python 3.12.3 /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/python3.12/typing.py:1195 E (and 131 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('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') ('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') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('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_chain129-method_chain129] __________ [gw3] linux -- Python 3.12.3 /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 | 2368667 | 2371238 | a | 0 | + | E | chr6 | 2003414 | 2003927 | a | 0 | - | E | chr9 | 6214451 | 6223873 | a | 0 | + | E | chr9 | 1124742 | 1125255 | a | 0 | - | E | chr11 | 2511759 | 2512272 | a | 0 | + | E | chr18 | 6514630 | 6521543 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 6 rows and 6 columns from 5 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 | 2368667 | 2369180 | a | 0 | + | E | chr6 | 209156 | 209669 | a | 0 | + | E | chr9 | 331273 | 340695 | a | 0 | + | E | chr9 | 331273 | 331786 | a | 0 | - | E | chr11 | 2511759 | 2514375 | a | 0 | + | E | chr20 | 395013 | 401926 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 6 rows and 6 columns from 5 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 | 262658 | 266513 | a | 0 | + | E | chr1 | 5235260 | 5237057 | a | 0 | - | E | chr1 | 2307881 | 2311736 | a | 0 | - | E | chr4 | 2307881 | 2311736 | a | 0 | + | E | chr17 | 2307881 | 2311736 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 5 rows and 6 columns from 3 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/join.py:104 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:106 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:12 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:14 E (and 40 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicrc49S4JRGMbx6z7nPvd5MtCeNMUUQXxBCcS3UguSotpMoqUoImiQxqiICGpqLIggosk1Imhua2hsioimwDXa+gA94N7UB7j+1483J/YrVrcuF3qW/e+t4kHmQfae1ruPobvSYlQv3R9FzrI7fHJ9dYwcwRdQMFVr4LikRSPuJCkDKiPLiLkImPzGaznG+Lz92uo8l0RJ4uItKHrtI/zt5k9HLe1ml88ZyXT6BlWLgs9Xs6Y5FmmMpF9SXgOIKDQ05XVRTytSoqKEAIO8Sw5THQD/pzkRhMcVy5W+jOLK0SVd7Atd43cMca7arP8lVZ6KTOFnVcZXiFWoK3TY7rBM8pylWdmex4CIwtAwAyFDJJqCIgaIaQjNtHtTUfZ2hHKqlhMqWYYN+Fms1SREg0LAL7zPRHo=') 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') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') 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') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') 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') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') 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') ('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') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') 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') 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') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') 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') ('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') ---------------------------------- 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_chain171-method_chain171] __________ [gw2] linux -- Python 3.12.3 /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 | 2648943 | 2652641 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | 201218 | 201224 | a | 0 | + | E | chr1 | 201218 | 201224 | a | 0 | + | E | chr1 | 201218 | 201224 | 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=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 170 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY8yw4eViYARDFo3sPAYGO75CMLeagYGBUbC8YgVjhFxqGUgEBJiAogyczEKMDHwMrCAVDJKMjMKMcgwAJrUGgw==') 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') ('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') ('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') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') 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') ('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_chain80-method_chain80] ___________ [gw1] linux -- Python 3.12.3 /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 | 215557 | 215563 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | 215557 | 217891 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | 327682 | 327690 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AXicY1TmZ2RiYARDEWYvFiDFzcDKwMDAiEWCUxZIAqVUOPi5wRIMQKUgkp2BAQBOLAHX') 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') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') 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') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9999999 | 10001207 | a | 0 | ... | | chr1 | 9593188 | 9595655 | a | 0 | ... | | chr1 | 5308859 | 5317868 | a | 0 | ... | | chr3 | 9996692 | 10001277 | a | 0 | ... | | chr13 | 927947 | 937909 | a | 0 | ... | | chrX | 9836961 | 9844140 | a | 0 | ... | | chrX | 5922255 | 5925659 | a | 0 | ... | | chrX | 6521797 | 6526526 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 4 chromosomes. For 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') ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 215557 | 217891 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For 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') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') 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') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8498668 | 8501710 | a | 0 | ... | | chr1 | 10000000 | 10006727 | a | 0 | ... | | chr1 | 1171418 | 1179347 | a | 0 | ... | | chr1 | 8007047 | 8010099 | a | 0 | ... | | chr21 | 3926315 | 3927218 | 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') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') 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') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('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') 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') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') 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') ('intersect', 'nearest') ('intersect', 'nearest') ('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_chain202-method_chain202] __________ [gw0] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('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') 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') 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') 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') 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') ---------------------------------- 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_chain131-method_chain131] __________ [gw3] linux -- Python 3.12.3 /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: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('6.100.4', 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') 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') 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') 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') Empty PyRanges ('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') ('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') Empty PyRanges ('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') ('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_three_in_a_row[strandedness_chain172-method_chain172] __________ [gw2] linux -- Python 3.12.3 /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 | 4741891 | 4746275 | a | 0 | + | E | chr1 | 9998105 | 10002489 | a | 0 | - | E | chr1 | 140036 | 144420 | a | 0 | - | E | chr1 | 140036 | 144420 | 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 gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 9191 | 9316 | a | 0 | + | E | chr1 | 9191 | 9316 | 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/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 170 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicYzRKFdNkTA3b/pvRhIGLiVGOkZGdAQgYGR1m9EswMgh5RDMxpDApMzPIC8ozgiWYQCQ3OzOIYmBmUH4GJGoYwICRk5FBlokBAN8VCJQ=') 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') 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') ('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') ('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') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') 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') ('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') ('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') ('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_chain82-method_chain82] ___________ [gw1] linux -- Python 3.12.3 /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('6.100.4', 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') ('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') 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') ('intersect', 'subtract') ('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') ('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') ('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') 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') ---------------------------------- 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 3.12.3 /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/python3.12/typing.py:1195 E (and 113 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('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') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('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') 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') ---------------------------------- 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_chain133-method_chain133] __________ [gw3] linux -- Python 3.12.3 /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/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/pyranges.py:4162 E (and 134 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('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') ('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') 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') 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') ---------------------------------- 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_chain173-method_chain173] __________ [gw2] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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 | 6012404 | 6012418 | a | 0 | + | | | chr1 | 6401 | 6415 | a | 0 | - | | | chr7 | 197378 | 207059 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 3 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 | 6506846 | 6513638 | a | 0 | + | | | chr1 | 66308 | 67101 | a | 0 | + | | | chr1 | 6506846 | 6507639 | a | 0 | + | | | chr1 | 2039564 | 2046478 | 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 170 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY/JhysxgMpjQmszm8mJG/bfuuU4cMQz8DAxsDIyMDIzMzIzSDPLy3EyMDJIMzIwp0Xs/AxlMqhfEGRh4GXiBwmKMTIzyvIzMDCLMDIzsG/mZmZl0mNQlmBlZGPRB5jAwyELMYYaaw5LsGcvLkGoepc0i1c7OzKq/2eqT1SdpRk4GZgYOBgZWZgmgHqBqPUYGOSZGAPRGFVU=') 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/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 135 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BAAEYGTAAAADQAAg==') 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', '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') 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') 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') 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') ('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') ('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') 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_chain204-method_chain204] __________ [gw0] linux -- Python 3.12.3 /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/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/python3.12/typing.py:1195 E (and 102 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('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') ('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') 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') 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') ---------------------------------- 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] ___________ [gw1] linux -- Python 3.12.3 /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('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('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') ('subtract', 'set_union') ('subtract', 'set_union') ('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') 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') ---------------------------------- 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_chain134-method_chain134] __________ [gw3] linux -- Python 3.12.3 /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('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('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') ('subtract', 'set_intersect') ('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_three_in_a_row[strandedness_chain205-method_chain205] __________ [gw0] linux -- Python 3.12.3 /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 63 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('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') 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') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('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') 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') Empty PyRanges ('set_intersect', '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_chain85-method_chain85] ___________ [gw1] linux -- Python 3.12.3 /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/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/pyranges.py:4162 E (and 118 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('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') ('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') ---------------------------------- 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 3.12.3 /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 | 131097 | 131105 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | 1769985 | 1769986 | a | 0 | - | E | chr1 | 1769985 | 1769986 | a | 0 | - | E | chr1 | 1769985 | 1769986 | a | 0 | - | E | chr1 | 1769985 | 1769986 | 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=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('6.100.4', b'AXicY1N4LPHj2tVnPg2lDGwMjAxMDOxMDBJABgMDOxCzMgK5LEwMDJJMAsyMvIwMzCApIJJmAqthAGpggLJANAsDANukBps=') 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') ('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') ('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') 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') ('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') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') 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') ('nearest', 'join') 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') ---------------------------------- 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_chain135-method_chain135] __________ [gw3] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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('6.100.4', b'AXicY2BkAAJGMATRUAYUAAAApQAI') 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') ('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') ('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') 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') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('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') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', '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_chain206-method_chain206] __________ [gw0] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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:575 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('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') 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') 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') 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') 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') ---------------------------------- 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] __________ [gw2] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr17 | 769 | 1027 | a | 0 | + | E | chr17 | 196874 | 197132 | 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 | chr2 | 3456996 | 3457542 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | 196893 | 197150 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 145 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicFcuxDYAwAAPBd1yBRIKQoKJhBzYhSzAB49GxCBINJQuQdNbZdv6uIyj52N4H6KXRaoIQhkHqispT2dRQdD1vWvawEIs4qzaK2Joh1Sf8KEsI6g==') 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') 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') 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') ('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') 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') ('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') ---------------------------------- 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] ___________ [gw1] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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('6.100.4', 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') 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') ('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') ('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') ('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') ('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') ('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') 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') ---------------------------------- 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_chain207-method_chain207] __________ [gw0] linux -- Python 3.12.3 /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 64 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('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') 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') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('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') 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') ---------------------------------- 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_chain136-method_chain136] __________ [gw3] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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 | 513 | 2306 | 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 | 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/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('6.100.4', b'AXicY+Pcw57x5qEsA084AzsDIwMPAwMDExADORwMMMAIEgPJMkI4QIIVKAJkMQIA2BUDxA==') 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=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 3330 | 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) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr8 | 257 | 514 | 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/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('6.100.4', b'AXicY+Rk4AlnYARDJgYQYOQFERkx3w4AaXawBAMYMzCyMjOBWIwAXIADEw==') 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') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('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 | 9 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For 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 | 2 | 10 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For 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 | 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 ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('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 | 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 ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('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_three_in_a_row[strandedness_chain176-method_chain176] __________ [gw2] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 366564 | 366565 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 322386 | 325470 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AAMlAAoGAAAAAAANBZfjAB4AAAAAAAEZIAAJAAE6AAEAATqsAAwAAQAAOgTrUQAADAsAAA==') 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') 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') ('intersect', 'set_intersect') ('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') 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') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', '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_chain87-method_chain87] ___________ [gw1] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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 | 5635 | 5637 | a | 0 | + | | | chr20 | 65537 | 65539 | 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=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 131074 | 131076 | a | 0 | + | | | chr1 | 131074 | 131076 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 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/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 | (and 58 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY7Q5wLCFj4GBmYFBmJGBkZGRCchgYGQAIQZeBjEmIAPExK6AEaYAyAEAlHkCZQ==') 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=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 5635 | 5637 | a | 0 | + | | | chr20 | 5635 | 5637 | 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) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 65795 | 70660 | 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/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('6.100.4', b'AXicY7ThY2BgZmAQZmRgZGRkAjIYGHgZxJgYgHwGBhaIJJIcmAOSYmUEACNjANk=') 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') 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') ('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') 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_chain208-method_chain208] __________ [gw0] linux -- Python 3.12.3 /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/python3.12/typing.py:1195 E (and 101 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('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') ('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') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('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_chain137-method_chain137] __________ [gw3] linux -- Python 3.12.3 /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 | chr3 | 4014144 | 4014152 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | 24853 | 24854 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AAABAAMuAEsZBgEBNRYc9wABAAACAABtPUA/AQBtAAcAAAABXHxzRgABAAEAAAwAYRQACwAAAAA=') 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') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('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') 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') ('subtract', 'intersect') Empty PyRanges ('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') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', '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_chain88-method_chain88] ___________ [gw1] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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('6.100.4', 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') 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') ('subtract', 'intersect') ('subtract', 'intersect') ('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') ('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') ('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') Empty PyRanges ('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') 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') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', '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_chain209-method_chain209] __________ [gw0] linux -- Python 3.12.3 /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/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:575 E /usr/lib/python3/dist-packages/pandas/core/common.py:140 E (and 62 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('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') Empty PyRanges ('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') 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') 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') ---------------------------------- 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_chain180-method_chain180] __________ [gw2] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 197377 | 198146 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 4656385 | 4656386 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 103 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2FgYORgYGJgZGDQ+b1DjpkZyAdiIJCXZgxYrDE75uENBg4GRnZGoCKQJEO2Oy8DAzsYMQAA6s8HAg==') 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') ('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') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('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') 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') 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') ---------------------------------- 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_chain138-method_chain138] __________ [gw3] linux -- Python 3.12.3 /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: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=('subtract', 'subtract'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 6750222 | 6753969 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 5310465 | 5314548 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AAMUG7tfAAkAAQAKAAVnAA0ABAAdDqIAAAEAAAgBGFcABgxWAQMABAABAA8CAQBwUQgAACQP8gAA') 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') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 327795 | 327797 | a | 0 | + | | chr1 | 1835522 | 1843975 | a | 0 | + | | chr1 | 65635 | 65892 | a | 0 | + | | chr1 | 1602564 | 1609736 | a | 0 | - | | chr1 | 71312 | 73620 | 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') ('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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr10 | 7439720 | 7443467 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 852005 | 852006 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr10 | 852005 | 852006 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr10 | 9274 | 9275 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 852005 | 852006 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr10 | 7439720 | 7443467 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr10 | 7439720 | 7443467 | 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 | 1025 | 1026 | 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 | 1025 | 1026 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr10 | 6750222 | 6753969 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr10 | 6750222 | 6753969 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr10 | 851973 | 851974 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr11 | 851973 | 851974 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr10 | 6750222 | 6753969 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr10 | 6750222 | 6750223 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr10 | 6750222 | 6753969 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr10 | 6750222 | 6753969 | 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 | 1025 | 1026 | 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 | 1025 | 1026 | 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') ---------------------------------- 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_chain89-method_chain89] ___________ [gw1] linux -- Python 3.12.3 /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, 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 20 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFWBkwAAAChAAc=') 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') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | 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') ('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 | 1794 | 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') 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') 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') ('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') ('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_chain210-method_chain210] __________ [gw0] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1538 | 1540 | a | 0 | + | E | chr1 | 1538 | 1540 | a | 0 | + | E | chr1 | 1538 | 1540 | a | 0 | + | E | chr1 | 1538 | 1540 | a | 0 | + | E | chr1 | 1538 | 1540 | a | 0 | + | E | chr1 | 1538 | 1540 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 6 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 | chr17 | 7095543 | 7100963 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | chr17 | 11068 | 11079 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 145 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AAQbQVYTBRGeILjyIxlE7TcBSc93EydCWAVVqXdZHt/qBwUxP/J2BhqDHwEACAQBAgUBAAEAAQAGAQB+AAEAAAcAJV2TSwAPAwAQDQBibET2AAsAaBUrAAIAAAAFfgAAAQAFAAAQAAABACs7CwBnAAoAAAA=') 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') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('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') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('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') ('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') 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') ---------------------------------- 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 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 69633 | 72962 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | 65537 | 65539 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AXicY3ViYmQAAx5GASDJy8DNwMjAyAgWZWSASgJFIJSiFJACABkPAMg=') 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') 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') ('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') ('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') ('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_three_in_a_row[strandedness_chain182-method_chain182] __________ [gw2] linux -- Python 3.12.3 /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=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/pyranges.py:4162 E (and 127 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('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') ('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_chain90-method_chain90] ___________ [gw1] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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('6.100.4', 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') ('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') 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') 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') 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_three_in_a_row[strandedness_chain211-method_chain211] __________ [gw0] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 28191 | 31776 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2884354 | 2889735 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AXicYxRmezePgZmBkQGI8uQYGPgYQIDJgVVejpmFiYGZCcgByTHqMAMJURYGRgB2/gMn') 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') ('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') 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') 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') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', '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_chain140-method_chain140] __________ [gw3] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 9176323 | 9177676 | a | 0 | + | E | chr1 | 1508097 | 1509450 | a | 0 | + | E | chr1 | 3305865 | 3307218 | 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=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 513 | 1284 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 195 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY45nis5gqWNgYGRhnzxrP4O8MCMng2wPKxMPY7k4M4McU+TLI3FGhR0M8nyKrB4MECDBxMgI1MHEAKKAgJGBiYFBmhlIAAAOoAm6') 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') ('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') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('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') ('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') 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') 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') 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') 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') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('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_three_in_a_row[strandedness_chain183-method_chain183] __________ [gw2] linux -- Python 3.12.3 /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 115 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('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') ('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') 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') ---------------------------------- 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_chain91-method_chain91] ___________ [gw1] linux -- Python 3.12.3 /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, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1283 | 9227 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 205 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AAABEZJS/gEBEQEAAQIFLmIAAAEAAQAFAgAHHwcAAA==') 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') ('join', 'set_union') ('join', 'set_union') ('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') ('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') 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') 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') ('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') Empty PyRanges ('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_three_in_a_row[strandedness_chain141-method_chain141] __________ [gw3] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 27167 | 27169 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 4 | 5 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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:575 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AARoCkuCAAABDgAFAGoeAAAKAAEAAAABVlbWBCcmCAEGABsCAAAAAQALAAADAAQAAAAA') 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') 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') 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') Empty PyRanges ('join', 'set_intersect') ('join', '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_chain215-method_chain215] __________ [gw0] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 66305 | 66306 | a | 0 | - | E | chr2 | 66305 | 66306 | a | 0 | - | E | chr9 | 66305 | 66306 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 275110 | 281717 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AXicY2RgZjjCyJptJ8TIYrT0EwMjIxAxMXAAKQYGBkZmBgZJIAUSZWBkT0ueYsSkxcCoyM7KzAAWYlAE6mJgsJQ8x8AAACUlB5w=') 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') ('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') 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') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', '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_chain184-method_chain184] __________ [gw2] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr19 | 3806701 | 3806709 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | 132609 | 134440 | a | 0 | - | E | chr1 | 132609 | 134440 | a | 0 | - | E | chr1 | 132609 | 137730 | a | 0 | - | E | chr17 | 132609 | 134440 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 4 rows and 6 columns from 2 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: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('6.100.4', b'AXicY7Sraf3OwMjAIAQkRKxE3wApfwZ2BgZGxjAW/T7GPKbieYyZiY9PMoYUeuQxMDIzMjIxCDACAUiTJBMbUIhBhIFBjl0NKMLIBJIBKmIAyQoyMDGkMwAABcwLqg==') 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') 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') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('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') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', '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_chain92-method_chain92] ___________ [gw1] linux -- Python 3.12.3 /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, 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('6.100.4', 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') ('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') Empty PyRanges ('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') ('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') 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') 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') ('join', 'set_intersect') ('join', 'set_intersect') ('join', '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_chain185-method_chain185] __________ [gw2] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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 | 7071157 | 7071238 | 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 | 7798785 | 7798787 | 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/join.py:14 | /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 | (and 60 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicYyvP4HFhAAJ2Bobsp1sYWBkSGQIYmEAiDOIgKQ4gg4mREUhyMABJtnIgi5GBkRNIAQDjiAVl') 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, | ) | 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('6.100.4', 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') 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') ('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') ('subtract', 'nearest') ('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') ('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') 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_chain143-method_chain143] __________ [gw3] linux -- Python 3.12.3 /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 | 9296900 | 9297988 | a | 0 | + | E | chr1 | 4033283 | 4038149 | a | 0 | + | E | chr1 | 429760 | 430208 | 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 | 9296900 | 9297672 | a | 0 | + | E | chr1 | 2564 | 3336 | 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 | 197121 | 197404 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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/join.py:19 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 (and 37 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicYzRgKTdmi2XJf8GUlxjKwMDAyMTA0HuHmZep8OuvGra+/bKMPrbdTAxcTNqM+3kY44QZBRkyWOwZ5AUYGA20Tp8A6haLBevyAepiYGTgYmZgYWZmYgQaxZTHCKQYgZCbgZGZCcRkYpQCUgCa1BKP') 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', 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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_chain217-method_chain217] __________ [gw0] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr10 | 4128860 | 4136458 | a | 0 | - | | | chr18 | 4128860 | 4130613 | 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 | 2305 | 6209 | 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 167 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicYwt96Linca84O6NT/pIdDEyMDIKcjBwMDJwMDDEb3/HbM0RzMkTKrmVktGK7wcDBwMjDwM3IyMAWClbMwCDIwMgAVszDkAdUzM0AAiAFjCAJAHvbDf8=') 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=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr2 | 6074863 | 6077168 | 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 | 589825 | 593729 | 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 207 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AAZVQm+kAAAAAQAAXLHuDw8AWwkAAAAAAQwACwEXBwEABDgAAgEAAQABAAAACQAAAG4PPwAA') 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') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('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') ('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') ('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') 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') ('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_chain94-method_chain94] ___________ [gw1] linux -- Python 3.12.3 /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 | 9570569 | 9575084 | a | 0 | + | E | chr1 | 2006284 | 2011613 | a | 0 | - | E | chr4 | 196623 | 204494 | 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 gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 525315 | 525379 | a | 0 | + | E | chr1 | 2006284 | 2014247 | a | 0 | - | E | chr4 | 720553 | 721322 | 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 | 526596 | 527113 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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/join.py:19 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 (and 35 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY3ZJ7VVnCfu36QDbjRR2BtfiM5MYBBkZRZiZGJmZGRiYGfgZgDQfM6OF3FxuNmYQm5GFQZyRwWj+It07V7j+rTCaxMnBwsRvaGdywN5DcJG8FJMgkwxDptw+YWYGEUYNkQsMEoyMQsxAXYwSzExAIwnaCLWLIQRouhATyHQGQSYTBnsORiWg6YxAMzTl7ICmMzAyMAjATQdqZQNKMbAxgAEHJzODMBPQUgDPsiHx') 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') ('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') ('join', 'nearest') ('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') ('join', 'nearest') ('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') ('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') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') 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') ('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_chain186-method_chain186] __________ [gw2] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr4 | 25870 | 28943 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | 3330 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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: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('6.100.4', b'AXicYywxfv+cgZGBgZmBgYMhlZeBgQfIA0EOBhYGMAMIGHnBJAMUAACUiQMp') 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') ('subtract', 'intersect') ('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') 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') ('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') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', '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_chain145-method_chain145] __________ [gw3] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 131074 | 131844 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1836906 | 1836907 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AXicY2FkYGRgAGJRJiDBaM/BDOYyM4swMViyMQmCmAwiDGBVTDLsmQzsQGkGACMKAY0=') 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') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('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') 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') Empty PyRanges ('join', 'subtract') ('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') ---------------------------------- 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] ___________ [gw1] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65808 | 66066 | a | 0 | + | E | chr1 | 655905 | 656163 | 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 | 6668209 | 6668979 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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:575 E (and 77 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AAABBSRzDQgAAQEBd15/BwEMAQEMAAAAAAEABQEBDwEBAAoCIAAAAgEBAAABZ2mQYgABAAEAAGRlv7AADQMBAAA=') 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') ('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') 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') ('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') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', '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_chain218-method_chain218] __________ [gw0] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2859535 | 2859537 | 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 | 5 | 263 | a | 0 | + | | | chr1 | 6829388 | 6829907 | a | 0 | + | | | chr1 | 67330 | 67849 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 3 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('6.100.4', b'AXicY66ZMa2egZ2BkYGNgVt7ER8DAxOQzcjOaKfDDhRmYWTgYGRkYQSKMzIzAAELUCTD1FuEQYQZqAyojpGBlZGRFSjDxAaUAgEhoFG6LMzyDABokwV3') 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=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr5 | 196865 | 197384 | 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 | 1537 | 8962 | 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:575 | (and 86 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AAABD3m+LAcAHwABAQkBAAAAAAQAFAMBAAAAAgYAAAF8mJZ/AAABAQAFAAYAAAEADh0AAAAB') 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') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('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') ('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') 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') ('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') Empty PyRanges ('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_chain187-method_chain187] __________ [gw2] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2295297 | 2295302 | a | 0 | + | E | chr1 | 2295297 | 2295309 | 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 | chr7 | 402179 | 402952 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AXicY0xh3TCJsYgllomBkZGRAQiV2YAkHwMLiMvNwADk8AMxAwMbECkzMTAws4AFQYCFgREAqU8DIQ==') 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') 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') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | 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') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2295297 | 2298137 | a | 0 | + | | chr6 | 2295297 | 2295299 | a | 0 | + | | chr6 | 2295297 | 2295612 | a | 0 | + | | chr6 | 2295297 | 2296066 | a | 0 | + | | chr6 | 2295297 | 2296329 | a | 0 | + | | chr6 | 2295297 | 2295304 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 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 | 6406 | 6920 | a | 0 | + | | chr1 | 2295297 | 2296077 | a | 0 | + | | chr1 | 2295297 | 2295309 | a | 0 | + | | chr1 | 2295297 | 2296325 | 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') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2824 | 2829 | a | 0 | + | | chr1 | 262 | 267 | 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') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 3 | a | 0 | + | | chr1 | 722689 | 722691 | 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 | 3 | a | 0 | + | | chr1 | 722689 | 722691 | 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 | 2295297 | 2298121 | 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 | 2295297 | 2298121 | 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 | 2295297 | 2297090 | a | 0 | + | | chr1 | 2295297 | 2297090 | 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 | 1025 | 1026 | a | 0 | + | | chr1 | 65552 | 65553 | a | 0 | + | | chr1 | 65552 | 65553 | 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 | 3 | a | 0 | + | | chr1 | 722689 | 722691 | 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 | 3 | a | 0 | + | | chr1 | 722689 | 722691 | 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') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 393220 | 393225 | a | 0 | + | | chr1 | 393220 | 396044 | 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 | 458767 | 458769 | a | 0 | + | | chr1 | 770 | 772 | 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') ---------------------------------- 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] __________ [gw0] linux -- Python 3.12.3 /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 | 1049090 | 1050115 | a | 0 | - | E | chr1 | 1049090 | 1050115 | a | 0 | - | E | chr1 | 1049090 | 1050115 | a | 0 | - | E | chr1 | 1049090 | 1050115 | 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 gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 12045 | 12057 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 170 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY7RsXbuamSnz6zsWPqZuNlZGBmZWBkYwZBBgYmRgZWFgA/GYHBrlfBk4QcJMDPo8DFYM3AxAwAjWzjaREQCO6gmv') 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') ('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') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('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') ('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') 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') ('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') ('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') ('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') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') 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') 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') ---------------------------------- 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_chain147-method_chain147] __________ [gw3] linux -- Python 3.12.3 /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, 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 258 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('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') ('set_union', 'set_union') ('set_union', 'set_union') ('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') 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') ('set_union', 'set_union') ('set_union', 'set_union') ('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_chain98-method_chain98] ___________ [gw1] linux -- Python 3.12.3 /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 248 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('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') ('set_union', 'set_union') ('set_union', 'set_union') ('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') 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') ('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_chain188-method_chain188] __________ [gw2] linux -- Python 3.12.3 /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 | chr15 | 30341 | 30382 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AAAAAAEAdgQFAAAAAyF80gAAAAAOAAAAdoQFAAAAKAAAAAA=') 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') ('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') 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') ---------------------------------- 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 3.12.3 /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 199 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('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') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('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') 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') ---------------------------------- 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] ___________ [gw1] linux -- Python 3.12.3 /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/python3.12/typing.py:1195 E (and 119 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('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') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('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') 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') ---------------------------------- 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] __________ [gw0] linux -- Python 3.12.3 /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 | 408128 | 409672 | a | 0 | + | E | chr1 | 408128 | 411979 | a | 0 | + | E | chr1 | 3344904 | 3347729 | a | 0 | + | E | chr1 | 408128 | 410953 | a | 0 | + | E | ... | ... | ... | ... | ... | ... | E | chr1 | 408128 | 410953 | a | 0 | + | E | chr1 | 408128 | 410953 | a | 0 | + | E | chr1 | 408128 | 410953 | a | 0 | + | E | chr1 | 408128 | 410953 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 9 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 | 66563 | 66564 | a | 0 | + | E | chr1 | 66563 | 66564 | a | 0 | + | E | chr1 | 66563 | 66564 | a | 0 | + | E | chr1 | 66563 | 66564 | 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=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 170 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicYzHqMBFjFbIJf8no0C79m7VmxrR6Zh+B5S6seT+1cmYZmEq9msNckqq2hsm4tOciK5vn6p1ggoGfm4ORgZGZh5OJxZiLnUGLzcremEGZjZ2XkZWfi4ERKMvFxsjAwMhgycPNwsjDx8fGyM7CxcrFwMoCEmVgZGFi4GMAASBHgoGBl5EBAB3wFos=') 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') ('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') ('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') ('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') ('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') ('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') ('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_chain189-method_chain189] __________ [gw2] linux -- Python 3.12.3 /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, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 258 | 259 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 97 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkYGVgYWBkYGBgZwADRiBkZuBlYGQEEuZgIQAFCABr') 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') 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') Empty PyRanges ('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') ('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') 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') ('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') 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') 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') 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') ---------------------------------- 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 3.12.3 /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, E ) E Explanation: E These lines 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('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('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') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('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') ('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') 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') 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') ---------------------------------- 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_chain100-method_chain100] __________ [gw1] linux -- Python 3.12.3 /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 179 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('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') 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') 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') 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') 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') ---------------------------------- 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_chain221-method_chain221] __________ [gw0] linux -- Python 3.12.3 /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 | 8771168 | 8771170 | a | 0 | + | E | chr1 | 8771168 | 8776803 | a | 0 | + | E | chr1 | 8771168 | 8771170 | a | 0 | + | E | chr1 | 722180 | 722182 | 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 gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 3585 | 3842 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 170 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicYxbUyDjPGOIovJ2lXHvSLRYmBiFBBgZGJmYpblZmBu/Wa/ESjMViTAyaDIx8zIwMDOxASUYgDQZ8IA6YBRQTArEYAfx7CFg=') 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') ('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') ('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') ('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') ('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') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') 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') ('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') 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_chain190-method_chain190] __________ [gw2] linux -- Python 3.12.3 /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, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 257 | 262 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AXicY2BkYGAA4iwgycgIYjEyQCkWBkYACeUAeg==') 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') ('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') 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') ('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') 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') 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') 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') 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') ('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') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', '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_chain150-method_chain150] __________ [gw3] linux -- Python 3.12.3 /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('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('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') Empty PyRanges ('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') ('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') 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') 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') ---------------------------------- 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_chain101-method_chain101] __________ [gw1] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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 181 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('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') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('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') ('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') 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') 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') ---------------------------------- 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_chain222-method_chain222] __________ [gw0] linux -- Python 3.12.3 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('nearest', '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=('nearest', '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/pandas/core/array_algos/take.py:575 E (and 62 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('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') 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') 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') 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') 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') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('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_chain151-method_chain151] __________ [gw3] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('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') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('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') 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') 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') ---------------------------------- 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_chain102-method_chain102] __________ [gw1] linux -- Python 3.12.3 /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 180 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('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') 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') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('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') ('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') 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') ---------------------------------- 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_chain192-method_chain192] __________ [gw2] linux -- Python 3.12.3 /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 | 6077552 | 6087552 | a | 0 | + | E | chr1 | 9381071 | 9382447 | a | 0 | - | E | chr8 | 2158854 | 2165797 | 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 gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 6077552 | 6079858 | a | 0 | - | E | chr1 | 4354 | 6660 | a | 0 | - | E | chr8 | 1966850 | 1969156 | 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 | 4831506 | 4834324 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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/join.py:19 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 (and 36 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2bkspnClHd9/Vk/y262xIcNmltm701ZqMMgxcQowsAoysjAzsDD4BOzJ1+O0UXhI6s0Iycjg+Nd47J+lXOczAy16vyiTHqs8WyMOdJyDPzMzAwMjAzMjAwyDExMjAysIDMZE4FmMtviMJNBjhlmIoMgIwODISuQx8hqzMDICDKK1XOnIAMDN5ANACebHYU=') 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') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') 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') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') 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') ('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') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') 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') ('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') 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') 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') ('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') ---------------------------------- 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_chain223-method_chain223] __________ [gw0] linux -- Python 3.12.3 /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 | 3740428 | 3740690 | a | 0 | - | E | chr1 | 3740428 | 3740690 | 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 | 770 | 773 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 182 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY3J6yOjHwMrMyMvIyMrAwMjAaSnMDaRZgXw+IJeRFyTIAsTcDEwMzEABBgYgAwQYGdgYAjgZqhgAho4DGQ==') 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') ('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') ('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') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('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') ('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') ('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') ('nearest', 'join') 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') ---------------------------------- 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] __________ [gw3] linux -- Python 3.12.3 /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, 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 193 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('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') ('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') 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') 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') 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') ---------------------------------- 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_chain103-method_chain103] __________ [gw1] linux -- Python 3.12.3 /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/python3.12/typing.py:1195 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 117 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('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') ('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') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('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_chain224-method_chain224] __________ [gw0] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1026 | 1027 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | 63 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 68 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BgBEI+IARSYAziszAyMIN4jJ58UFEQwcRgw8AAAA2PAMU=') 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') ('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') 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') 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') ('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') 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') ('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') ('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') 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') ---------------------------------- 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_chain194-method_chain194] __________ [gw2] linux -- Python 3.12.3 /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, 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('6.100.4', b'AXicY2BkgAEECwEAAFEAAw==') 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') ('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') 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') ('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') 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') 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') 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') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', '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_chain153-method_chain153] __________ [gw3] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('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') Empty PyRanges ('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') ('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') 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') 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') ---------------------------------- 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_chain104-method_chain104] __________ [gw1] linux -- Python 3.12.3 /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('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('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') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('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') 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') 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') ---------------------------------- 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_chain225-method_chain225] __________ [gw0] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ 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 gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1638401 | 1638660 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AAFfSSCbAAABAAoBAAAAAwAAAAAAARsDAwADAwEAAQERAwIAAAEAaBkAAAABAQIAAA==') 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') 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') ('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') ('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') 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') 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') ('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') 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') ---------------------------------- 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_chain229-method_chain229] __________ [gw2] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 260 | 1031 | a | 0 | + | E | chr1 | 260 | 1031 | a | 0 | + | E | chr1 | 9151647 | 9152418 | 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=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 257 | 9474 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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: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 28 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AAUDAgY1BB8BBtAEN2amsgAAAQECXIuknh8MMJ0i+LKPIAABAwAWAwIAAAABbTLcJQAFAAADDAADAAAAAQABAAEABwByJAAAAAE=') 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') ('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') 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') ('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') 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') ('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') 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') ---------------------------------- 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] __________ [gw3] linux -- Python 3.12.3 /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/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/python3.12/typing.py:1195 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 123 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('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') 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') 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') Empty PyRanges ('set_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_chain105-method_chain105] __________ [gw1] linux -- Python 3.12.3 /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/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 /usr/lib/python3.12/typing.py:1195 E (and 132 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('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') 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') ---------------------------------- 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_chain231-method_chain231] __________ [gw2] linux -- Python 3.12.3 /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 124 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('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') ('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') ---------------------------------- 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] __________ [gw3] linux -- Python 3.12.3 /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 104 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('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') ('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') ---------------------------------- 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_chain106-method_chain106] __________ [gw1] linux -- Python 3.12.3 /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/python3.12/typing.py:1195 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 102 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('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') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('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') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', '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] __________ [gw0] linux -- Python 3.12.3 /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 | 2619086 | 2621841 | a | 0 | + | E | chr1 | 8315114 | 8321679 | a | 0 | + | E | chr1 | 4492954 | 4495709 | a | 0 | - | E | chr9 | 10000000 | 10008633 | a | 0 | + | E | chr18 | 7846965 | 7849720 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 5 rows and 6 columns from 3 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 | 524585 | 532925 | a | 0 | + | E | chr1 | 61189 | 69529 | a | 0 | + | E | chr1 | 6701819 | 6710159 | a | 0 | + | E | chr1 | 8320177 | 8328517 | a | 0 | - | E | chr2 | 6112567 | 6120907 | a | 0 | - | E | chr3 | 2949139 | 2950676 | a | 0 | + | E | chr4 | 1578503 | 1579575 | a | 0 | + | E | chr15 | 2950940 | 2952272 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 8 rows and 6 columns from 5 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 | 4389429 | 4389435 | a | 0 | + | E | chr1 | 1543 | 1549 | a | 0 | - | E | chr1 | 65537 | 65543 | a | 0 | - | E | chr1 | 8320177 | 8320183 | a | 0 | - | E | chr2 | 5892223 | 5892229 | a | 0 | - | E | chr3 | 1315680 | 1315689 | a | 0 | - | E | chr4 | 8388848 | 8388854 | a | 0 | - | E | chr15 | 417094 | 417100 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 8 rows and 6 columns from 5 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('6.100.4', b'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') 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') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') 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 | 8320177 | 8321679 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For 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 | 8320177 | 8321679 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For 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 | 8320177 | 8321679 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For 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 | 8320177 | 8321679 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For 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 | 8320177 | 8321679 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For 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') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8320177 | 8321679 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For 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 | 8320177 | 8321679 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For 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') ('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') 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') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') 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_chain232-method_chain232] __________ [gw2] linux -- Python 3.12.3 /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/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/pyranges.py:4162 E (and 117 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('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') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('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') ('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_three_in_a_row[strandedness_chain107-method_chain107] __________ [gw1] linux -- Python 3.12.3 /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 64 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('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') ('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') 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') 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') 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') ---------------------------------- 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_chain156-method_chain156] __________ [gw3] linux -- Python 3.12.3 /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 64 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('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') 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') 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') 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') 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') ---------------------------------- 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_chain256-method_chain256] __________ [gw0] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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 64 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('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') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('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') ('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') 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') 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') ---------------------------------- 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_chain233-method_chain233] __________ [gw2] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 393219 | 393221 | a | 0 | + | E | chr1 | 393219 | 393221 | 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 | 20226 | 20228 | a | 0 | - | E | chr1 | 20226 | 20228 | 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/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('6.100.4', b'AXicYxJlZHRhjmRjYGJgYGRgANGMDIy8DEDAws9m+YVZkG+KFQM/G1COF6SAhcEfSILUgJRIgJkMAJFCA6M=') 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') 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') ('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') 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') ---------------------------------- 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] __________ [gw1] linux -- Python 3.12.3 /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:575 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('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') 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') 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') 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') 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') ---------------------------------- 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] __________ [gw3] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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:575 E /usr/lib/python3/dist-packages/pandas/core/common.py:140 E (and 62 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('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') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('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') ('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') 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') 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') ---------------------------------- 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_chain257-method_chain257] __________ [gw0] linux -- Python 3.12.3 /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/python3.12/typing.py:1195 E (and 101 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') 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') 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') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('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_chain234-method_chain234] __________ [gw2] linux -- Python 3.12.3 /usr/bin/python3.12 strandedness_chain = ('opposite', 'same') method_chain = ('subtract', '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: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', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 257 | 514 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | 1335 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AXicY8pkYUli4GZgZOBiYACSUIKRgQPC5ANRDKymbBA5BlYgZmFgBAA29QFR') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- 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') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('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') ('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') 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') ('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') ---------------------------------- 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_chain281-method_chain281] __________ [gw3] linux -- Python 3.12.3 /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/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/pyranges.py:4162 E (and 118 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('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') ('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') ---------------------------------- 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] __________ [gw1] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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 64 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('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') 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') 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') 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') Empty PyRanges ('set_intersect', '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_chain258-method_chain258] __________ [gw0] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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:575 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('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') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('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') ('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') 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') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', '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_chain235-method_chain235] __________ [gw2] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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('6.100.4', 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') ('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') ('subtract', 'intersect') ('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') ('subtract', 'intersect') ('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') 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') ---------------------------------- 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_chain110-method_chain110] __________ [gw1] linux -- Python 3.12.3 /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/python3.12/typing.py:1195 E (and 101 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('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') ('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') 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') ---------------------------------- 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_chain259-method_chain259] __________ [gw0] linux -- Python 3.12.3 /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, 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 312 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BAAEYGTAAAADQAAg==') 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') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('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') ('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') 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') ('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') 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') ---------------------------------- 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_chain282-method_chain282] __________ [gw3] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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 /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E /usr/lib/python3/dist-packages/natsort/utils.py:500 E (and 64 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2CAA0YGLAAAADUAAg==') 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') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('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') 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') 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') Empty PyRanges ('subtract', '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_chain111-method_chain111] __________ [gw1] linux -- Python 3.12.3 /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:575 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('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') 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') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('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') 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') ---------------------------------- 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_chain236-method_chain236] __________ [gw2] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 3160498 | 3160499 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | 197121 | 198658 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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: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('6.100.4', b'AXicY0ziSljHwAiEDMIGlhsZ2BgYGBgZORhAgJGBi5kJSLOBOWkijGoeYkIMAHrrA+M=') 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') ('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 | 3160498 | 3170420 | 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 | 3160498 | 3170420 | 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 | 3160498 | 3170420 | 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 | 3160498 | 3170420 | 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 | 3160498 | 3170420 | 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 | 3160498 | 3160506 | 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 | 3160498 | 3160506 | 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 | 3160498 | 3160506 | 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 | 1537 | 3332 | 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 | 2539777 | 2539785 | 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 | 2539777 | 2539785 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr18 | 2539777 | 2539785 | 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 | 3160498 | 3170420 | 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 | 3780865 | 3780867 | 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 | 3160498 | 3160500 | 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 | 3160498 | 3162547 | 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 | 3160498 | 3160499 | 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 | 3160498 | 3161019 | 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 | 3780865 | 3780867 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr20 | 3160498 | 3160500 | 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 | 3160498 | 3160499 | 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 | 393217 | 393738 | 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 | 3160498 | 3160499 | 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 | 3160498 | 3160499 | 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 | 3160498 | 3160757 | 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 | 3160498 | 3160500 | 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 | 3160498 | 3160500 | 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 | 1537 | 1796 | 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 | 3160498 | 3160757 | 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 | 3160498 | 3160500 | 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 | 3160498 | 3160500 | 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 | 3160498 | 3160500 | 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 | 3780865 | 3780867 | 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 | 1257530 | 1257531 | 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 | 3160498 | 3160499 | 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 | 3160498 | 3160499 | 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 | 3160498 | 3160499 | 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') ---------------------------------- 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] __________ [gw3] linux -- Python 3.12.3 /usr/bin/python3.12 strandedness_chain = ('opposite', 'opposite') method_chain = ('subtract', '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: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', '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/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:575 E /usr/lib/python3/dist-packages/pandas/core/common.py:140 E (and 62 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAI4AxkAAABSAAM=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('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') 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') 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') 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') ---------------------------------- 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_chain260-method_chain260] __________ [gw0] linux -- Python 3.12.3 /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, 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: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 /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('6.100.4', 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') 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') ('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') 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') ('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') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', '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_chain112-method_chain112] __________ [gw1] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 3021831 | 3031311 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 10 | 2827 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 313 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2ZNk1nDAAIiejJsDIyq7GAOGzsTAyMDIyOjNBsjB1iEm4GBE0wyAABVlAIk') 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') ('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') ('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') 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') Empty PyRanges ('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') ('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') 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') ('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') ---------------------------------- 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_chain237-method_chain237] __________ [gw2] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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('6.100.4', 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') Empty PyRanges ('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') ('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') ('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') 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') 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') ---------------------------------- 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_chain284-method_chain284] __________ [gw3] linux -- Python 3.12.3 /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 | 866817 | 866823 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AXicY2AAAsakBBYgyWmzNgPMZSjktQLTrEASADjLAuI=') 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') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('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') 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') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', '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_chain113-method_chain113] __________ [gw1] linux -- Python 3.12.3 /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, 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/python3.12/typing.py:1195 E (and 99 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', 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') ('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') 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') ('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') 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') ('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') ---------------------------------- 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_chain238-method_chain238] __________ [gw2] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 589826 | 589827 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | chr5 | 5053115 | 5054997 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 176 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2Bg4OViYGBnYGBgZOAFk4xAghNIgsQYGIWdD20E0iyMDFq+UrtAkuyRQD4AQHADvA==') 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') 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') ('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') 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') 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') ('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') 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') 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') ---------------------------------- 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_chain285-method_chain285] __________ [gw3] linux -- Python 3.12.3 /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, 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('6.100.4', 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 | 1 | 2 | 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') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8979969 | 8980164 | 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') ('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') 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') ('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') ('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') ('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_chain264-method_chain264] __________ [gw0] linux -- Python 3.12.3 /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, 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('6.100.4', 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') ('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') 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') ('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') ('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') 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') ('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') ---------------------------------- 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] __________ [gw3] linux -- Python 3.12.3 /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 | 393224 | 393492 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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: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('6.100.4', b'AAAAAAAAMyE9AAAAAQN6AAoAAAAAAAAGAAcAbAELAAEA') 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') ('subtract', 'join') ('subtract', 'join') ('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') ('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') 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') ('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') ---------------------------------- 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_chain239-method_chain239] __________ [gw2] linux -- Python 3.12.3 /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, 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:575 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', 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') ('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') 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') 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') 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') ('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') ---------------------------------- 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] __________ [gw1] linux -- Python 3.12.3 /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 | 2752574 | 2762346 | a | 0 | + | E | chr1 | 2134746 | 2138185 | a | 0 | + | E | chr1 | 8988718 | 8992157 | a | 0 | + | E | chr1 | 1537 | 4976 | a | 0 | - | E | chr1 | 8792442 | 8795881 | a | 0 | - | E | chr1 | 5372159 | 5375598 | a | 0 | - | E | chr1 | 4048023 | 4051462 | a | 0 | - | E | chr1 | 7897770 | 7907451 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 8 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 | 7943427 | 7946866 | a | 0 | - | E | chr1 | 2134746 | 2134788 | a | 0 | - | E | chr1 | 7943427 | 7946866 | a | 0 | - | E | chr1 | 7943427 | 7943491 | a | 0 | - | E | chr1 | 7943427 | 7946866 | a | 0 | - | E | chr1 | 7897770 | 7898544 | a | 0 | - | E | chr1 | 7943427 | 7946866 | a | 0 | - | E | chr2 | 7943427 | 7950752 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 8 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 | 7013921 | 7013922 | a | 0 | + | E | chr1 | 8418741 | 8419510 | a | 0 | + | E | chr1 | 6513332 | 6513534 | 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 ) E Explanation: E These lines 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 30 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicnc85S8NwGMfx5/gfNVRtEwrWakghkR7UEwtSQxZHFRwdRFCkQ6EoKBgncRAEJ4VOXRwrOIi+AIcuXcTVQV+DdBIHMR54rD781gc+X7aPL2vKbVQWyFpfu9Jyo7v4sL9zLTKPhfL5TediuFndnCfrbMZytm6lM9fuUqy+GoeCRBfQUCgYXcRxjmkETFDonNwnVei3G74ce9l7OsqVUjreWjndPWhlSQMVwCeuHubDadLUB3m2YQJyaICCAWlLJYyl51cwoGekmNLb3l1gLvfWiXGQoILoaZxVmBVY4klVlJDmhOoXPqVEmfM0BQD83yKO/NH+dkTqQP1YlWKphQfBKJpDzW+aRBTR14dF/rJg1FZTjgDz04JfFshQZIGOhWmGJEkQ8H5v68FSyA==') 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') ('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') ('overlap', 'nearest') ('overlap', 'nearest') ('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') Empty PyRanges ('overlap', 'nearest') 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') ('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') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4048023 | 4051462 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For 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') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4048023 | 4051462 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For 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 | 4048023 | 4051462 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For 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 | 4048023 | 4051462 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For 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') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4048023 | 4051462 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For 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') ('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') ('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') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') 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') ---------------------------------- 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_chain266-method_chain266] __________ [gw0] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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 | 258 | 2052 | a | 0 | - | | | chr3 | 258 | 2052 | 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) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 13825 | 17155 | a | 0 | + | | | chr1 | 5946209 | 5949539 | 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 179 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2RgYWZkNJqeLsLAyMjABMSMDFwgJj87kMkoqb95D2N640IxBpAYD4MZkHKI2p0A5PIyMgBJeXYGEGAEAAJaBwQ=') 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=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 5946209 | 5947746 | 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 | 132354 | 132356 | 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:11 | (and 336 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY0t/Oc/1iNz5xoViDAyMLAwOUbsTGBgZGNkYIICRl5GBgcWIgZ1NPF2EkYEFJMfAwMQKorhATEYApV4H5Q==') 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') 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') 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') ('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') ---------------------------------- 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_chain287-method_chain287] __________ [gw3] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 190015 | 197622 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | 190015 | 190026 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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/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('6.100.4', b'AXicY8zLZWBlYGBkZIhhembHAKRktzEA+ajCDGwMXEA5RgZ+dgYhoDgA0fQGOg==') 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') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('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') ('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') 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') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('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_three_in_a_row[strandedness_chain303-method_chain303] __________ [gw1] linux -- Python 3.12.3 /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 134 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('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') 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') 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') 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') 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') ---------------------------------- 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_chain267-method_chain267] __________ [gw0] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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 | 5306140 | 5306618 | 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 | 3940 | a | 0 | + | | | chr1 | 3339262 | 3340458 | a | 0 | - | | | chr11 | 284833 | 286587 | 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) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 136196 | 136967 | 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('6.100.4', b'AXicY5F85Nf8/TbHHrmXF8XjAtkOMrAwMDLwMegGfJdmYGYwZ7zLwMrAwMCqsZGpOengVpaY9bKPy5YoMIWtV+C41X65dEsQgywjIzcTIyeTCDOTHBMXM5MEAwMXgxSTvtHnv4KM1UDNDH4sEQtkmBkC2G4yMXAyMzMwM8Zbipl08ycJM8oyyjEwlJmJsqwWYmDkBNnMySjJKMXEyMCC4TJeoMuABgAtAioDWgQ0GQCg4iha') 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=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | 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 | 1 | 2 | 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:575 | (and 61 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2Bkak46aMoSw8AoyQACjAzMDAxQFhBmYhEEAHcZAs8=') 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') 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') 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') ('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') 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') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('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_chain243-method_chain243] __________ [gw2] linux -- Python 3.12.3 /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, 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:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:575 E /usr/lib/python3/dist-packages/pandas/core/common.py:140 E (and 62 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2Bg42WAAkYGTAAAAmEAFQ==') 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') ('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') 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') ('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') ('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') ('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') 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') ---------------------------------- 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] __________ [gw1] linux -- Python 3.12.3 /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, # 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 135 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('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') ('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') ('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') 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') __________ test_three_in_a_row[strandedness_chain288-method_chain288] __________ [gw3] linux -- Python 3.12.3 /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, 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:575 E (and 79 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', 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') 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') ('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') 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') ('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') 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') 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') ('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') 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') ('join', 'set_intersect') ('join', '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_chain268-method_chain268] __________ [gw0] linux -- Python 3.12.3 /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 | 721409 | 721666 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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=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 170 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY6xmAAJGIGQQ4mYCshhBmIWZkRUkysQAkWUAS7CBWQAfSgC8') 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') ('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') ('nearest', 'overlap') 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') 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') ('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') 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') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('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') 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') 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') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') 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') ('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_chain245-method_chain245] __________ [gw2] linux -- Python 3.12.3 /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 250 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('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') 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') 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') 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') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('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_chain305-method_chain305] __________ [gw1] linux -- Python 3.12.3 /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 134 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('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') 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') 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') 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') 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') ---------------------------------- 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_chain290-method_chain290] __________ [gw3] linux -- Python 3.12.3 /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 | 10000000 | 10000831 | a | 0 | + | E | chr1 | 3473322 | 3474860 | a | 0 | + | E | chr1 | 3473322 | 3473378 | a | 0 | + | E | chr1 | 3425140 | 3426193 | a | 0 | + | E | chr1 | 9095177 | 9096715 | a | 0 | + | E | chr2 | 1573657 | 1575195 | a | 0 | + | E | chr6 | 3473322 | 3474863 | a | 0 | + | E | chr7 | 2843460 | 2844998 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 8 rows and 6 columns from 4 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 | 5186142 | 5187035 | a | 0 | + | E | chr1 | 9541924 | 9542205 | a | 0 | + | E | chr1 | 10000000 | 10000893 | 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 | 261 | 275 | a | 0 | - | E | chr1 | 196622 | 196636 | a | 0 | - | E | chr1 | 131330 | 131344 | a | 0 | - | E | chr1 | 131330 | 131587 | 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 ) E Explanation: E These lines 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/join.py:19 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 (and 37 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY06dubBjw3/rBcWt9zVEZmnKG+ufYsvdWpgW3bGPnVFBRoSRWcpk2kkmh7LzO1jtL3rU78w8u6W1zLvpCWu2umUpm+P9vknLVyW8Ua3p/J3BYMzGyM3OwCjECAQWjBZshoxG7MwsDGyCjCIMDKwMDPIMpiyR2snOamwKXSc4bFjZTJyLmRkltvxcP2NavQQbCzuTBLMEEyuDksn/lUasOiwybMxMDOaMDOpsLKYMjMzszGKMlsx24gy6jCyMhswMjGyM7IwMDAxMrNx7vVj1H9xlZzJ5xBb38Vfi7pB4ke9HGDgZGaWZGYEWM8gAMQMHg9T/+8L+SrEsTDVACzkZKybOVAaayyjAKMHEyMDNXAOiGJjzJSdKM5aLRbIycjK4qbPIegJFGZkYxZkkGcAMRmYGXiYGoP0sDHJAHhMzM8gVDLwMjABhv0UB') 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') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') 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') ('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') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('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') ('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') ('join', 'nearest') Empty PyRanges ('join', 'nearest') 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') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') 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') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') 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') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') 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') ('join', 'nearest') ('join', 'nearest') ('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_chain269-method_chain269] __________ [gw0] linux -- Python 3.12.3 /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 | 65541 | 65543 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | 259 | 1029 | a | 0 | + | E | chr1 | 259 | 1029 | 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/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 170 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicYwxiZWdkYAAjFiAGQhZpJmZGJnZGIyCbkZEZIsfIxMDADGQBmXwMAuyMjAwAJhoBAw==') 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 PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') 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') 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') ('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') ('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') ('nearest', 'nearest') ('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') ('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') ('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') ('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') 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') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('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_chain306-method_chain306] __________ [gw1] linux -- Python 3.12.3 /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 176 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('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') ('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') 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') ---------------------------------- 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_chain246-method_chain246] __________ [gw2] linux -- Python 3.12.3 /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 134 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('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') ('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') 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') ---------------------------------- 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] __________ [gw0] linux -- Python 3.12.3 /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 | 276225 | 276482 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | 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 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('6.100.4', b'AXicY2RgZ+RgYARCBnYWcwYGRkYIhgNkNpQDAA6QAFw=') 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') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('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') ('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') ('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') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('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') ('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') 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') 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') 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_chain292-method_chain292] __________ [gw3] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65541 | 68359 | a | 0 | + | E | chr1 | 65541 | 65659 | 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=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 6 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AXicY8yX+n+TOX6pmKzMbFYGNkZGBkYGIGJhZ2DjZmRn4APyShlAgBEkyQSk2IEcdrAQAxtEgoWBEQA7GwUx') 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') 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') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9731760 | 9741317 | a | 0 | ... | | chr17 | 4664455 | 4666451 | 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 ('join', 'subtract') Empty PyRanges ('join', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9731760 | 9741317 | a | 0 | ... | | chr17 | 4664455 | 4666451 | 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 ('join', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9731760 | 9741317 | a | 0 | ... | | chr17 | 4664455 | 4666451 | 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 ('join', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9731760 | 9741317 | a | 0 | ... | | chr17 | 4664455 | 4666451 | 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 ('join', 'subtract') ('join', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr17 | 4664455 | 4666451 | 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 | 9731760 | 9741317 | a | 0 | ... | | chr17 | 4664455 | 4666451 | 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 ('join', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr17 | 4664455 | 4666451 | 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) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr17 | 4664455 | 4666451 | 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) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr17 | 4664455 | 4666451 | 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') ('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') Empty PyRanges ('join', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9731760 | 9733756 | 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') ('join', 'subtract') Empty PyRanges ('join', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9731760 | 9733756 | 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') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65541 | 65799 | a | 0 | ... | | chr1 | 65541 | 71578 | 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 ('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') 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') 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') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', '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_chain307-method_chain307] __________ [gw1] linux -- Python 3.12.3 /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 136 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') 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') 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') 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') Empty PyRanges ('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') ('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') 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') __________ test_three_in_a_row[strandedness_chain247-method_chain247] __________ [gw2] linux -- Python 3.12.3 /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 195 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('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') 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') 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') 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') 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') ---------------------------------- 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_chain308-method_chain308] __________ [gw1] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 119055 | 119057 | a | 0 | - | E | chr1 | 119055 | 119056 | 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=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 136462 | 136725 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 209 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AAI4ATesBQ8AAxMAAAEAdQHRDgEAEQABAAEAAAABAAEeAwAJAAYDAQYDAAQAAAAAAAAGAhUNAAABBgAA') 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') 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') ('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') ('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') ('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') 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') 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') ('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') ---------------------------------- 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] __________ [gw0] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 3996767 | 4006571 | a | 0 | - | | | chr1 | 5386659 | 5393058 | a | 0 | - | | | chrM | 5020882 | 5022743 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 3 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 | 736509 | 743029 | a | 0 | + | | | chrM | 4476061 | 4484766 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 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) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 68098 | 68106 | a | 0 | - | | | chr1 | 66050 | 66058 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 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 184 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY6yZMa2eTaw1I54pZ2rPaQYOJgYJVkZGBkZhBm6bP3FyTC4+cy7KMrLMLG8LMlzEIM3AZcmt5s3BzORsIsbuIsIkxCDNzCTNJMHIKvGPQYCZkZGNmYmRhZmZiYWRi1GGAWgQwgIQwcDBALWAEWQBHwPIAgZeRhbJcjYGQyUGIEDXAVQpBxRlZGQCQhZGZgaQ0UABBnYGRgB8Px5Q') 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, | 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:575 | (and 61 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', 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', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('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') ('nearest', 'subtract') ('nearest', 'subtract') ('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') 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') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('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') ('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') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('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') Empty PyRanges ('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') ('nearest', 'subtract') Empty PyRanges ('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_chain248-method_chain248] __________ [gw2] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('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') ('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') 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') 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') 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') ---------------------------------- 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_chain294-method_chain294] __________ [gw3] linux -- Python 3.12.3 /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 280 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('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') ('set_union', 'set_union') ('set_union', 'set_union') ('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') 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') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('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_chain309-method_chain309] __________ [gw1] linux -- Python 3.12.3 /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, 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 95 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', 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') ('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') ('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') ('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') ('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') 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') ('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') ('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') ---------------------------------- 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_chain249-method_chain249] __________ [gw2] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('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') Empty PyRanges ('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') ('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') 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') 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') ---------------------------------- 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] __________ [gw0] linux -- Python 3.12.3 /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 | 4870 | 5129 | a | 0 | + | E | chr1 | 4870 | 6153 | 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 | 262145 | 263427 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AXicHYhJAQAgDMOaHSAADWjAvzO29dG04d0MHLY66GTtNLSwESKqixZ9SQbeSs4HJ3QAxw==') 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') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') 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') ('nearest', 'join') Empty PyRanges ('nearest', 'join') 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') ('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') 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') ('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') ('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') ('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') ('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_chain295-method_chain295] __________ [gw3] linux -- Python 3.12.3 /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 196 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('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') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('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') 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') ---------------------------------- 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] __________ [gw2] linux -- Python 3.12.3 /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: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_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/python3.12/typing.py:1195 E (and 131 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('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') 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') 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') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('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_chain273-method_chain273] __________ [gw0] linux -- Python 3.12.3 /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, 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 312 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkYBBgAANGBkwAAAIBABM=') 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') 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') 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') ('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') 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') 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') 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') 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') ---------------------------------- 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_chain311-method_chain311] __________ [gw1] linux -- Python 3.12.3 /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 | 9825548 | 9828892 | a | 0 | + | E | chr1 | 2624516 | 2627860 | a | 0 | - | E | chr7 | 6103528 | 6106872 | a | 0 | + | E | chr18 | 475282 | 478626 | a | 0 | + | E | ... | ... | ... | ... | ... | ... | E | chr18 | 786454 | 789798 | a | 0 | - | E | chr18 | 1705348 | 1708692 | a | 0 | - | E | chr18 | 2624516 | 2625030 | a | 0 | - | E | chr18 | 7057356 | 7060700 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 10 rows and 6 columns from 3 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 | 9825548 | 9826646 | a | 0 | + | E | chr1 | 333066 | 334164 | a | 0 | + | E | chr1 | 333066 | 334164 | a | 0 | - | E | chr9 | 132448 | 133546 | a | 0 | + | E | ... | ... | ... | ... | ... | ... | E | chr18 | 4100720 | 4109176 | a | 0 | + | E | chr18 | 333066 | 335897 | a | 0 | + | E | chr18 | 2 | 1100 | a | 0 | + | E | chr18 | 6103528 | 6104626 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 9 rows and 6 columns from 3 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 | 2276380 | 2279771 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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/join.py:104 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:106 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:12 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:14 E (and 39 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXichdA/SAJRHMDx3+/9uXd3vrvnSQfVQeg1GEgQDgkVFtiQ2RYNBSFE1pAgtKtDQ40WGEIIQYubQRQETdEQtQWNFQTRUltzdJdLW8vjB7/h9/08Nleef9by9YzH663DGl+5fCpOyjGy9FJOVs8KrP/mSLWPq4/dB+KeCpa5rpx/XHzlOm26vdfaJbONO8Dk99tmdNmGrBIYB4xJSwcNwHNQL60m3icUFG7XN5qfEdcm6UG+k5amsfiaPagseOOEKBbf6t7bPCFm9pmRQibB5boumSE5+COSjtI+gr6MaMJEAEspZSsNpAHhnahpa6hRxGCFoCPlwINJ0JCjhRxBQ45gPY5qnDDBch0+HPSLXn/4BX/iEYcMIGiiMNDUQI/9Z6FrgSXoI4QXHV4LzpumPu0q7hpSBrxUN2Iry5K0lBDgsHzqN3aqOeCDDKIZOP6VBwLQyoYv/ADxdE0B') 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') ('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') ('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') ('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') ('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') ('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') 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') ('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') 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') 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') 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') ('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_chain296-method_chain296] __________ [gw3] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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 236 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('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') 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') 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') 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') 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') ---------------------------------- 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_chain251-method_chain251] __________ [gw2] linux -- Python 3.12.3 /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('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('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') Empty PyRanges ('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') ('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') 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') 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') ---------------------------------- 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] __________ [gw0] linux -- Python 3.12.3 /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, 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('6.100.4', 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') ('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') ('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') 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') 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') 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') 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') 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') 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') ('intersect', '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_chain313-method_chain313] __________ [gw1] linux -- Python 3.12.3 /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, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 10000000 | 10000033 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 93 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgEAGMAZTNTOm1TOwMygwMAIAE4ICWA==') 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') 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') 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') 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') 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') 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') ('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') 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') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', '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_chain297-method_chain297] __________ [gw3] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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 245 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('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') Empty PyRanges ('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') ('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') 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') 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') ---------------------------------- 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_chain252-method_chain252] __________ [gw2] linux -- Python 3.12.3 /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/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/python3.12/typing.py:1195 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('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('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') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('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') ('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') 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') ---------------------------------- 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] __________ [gw0] linux -- Python 3.12.3 /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, 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('6.100.4', 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') ('intersect', 'subtract') ('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') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('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') 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') 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') ('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') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('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_three_in_a_row[strandedness_chain315-method_chain315] __________ [gw1] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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 | 271 | 274 | 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 | 78451 | 78452 | 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 69 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2RwZ2BgYARCEMUHJJiAtHKwfwlIlIHRqIiXAQxASthAFD8DAEF0AmE=') 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=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 69121 | 69634 | 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 | 1537 | 1553 | 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 281 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2RwZ4ACRj4gwQRmMTAIAkkjBlaoDFARG4jiZ2AAABlhAQI=') 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') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('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') ('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') 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') 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') 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') ('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') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('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') ('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') ('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_chain298-method_chain298] __________ [gw3] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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 236 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('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') Empty PyRanges ('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') 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') 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') ---------------------------------- 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_chain253-method_chain253] __________ [gw2] linux -- Python 3.12.3 /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/python3.12/typing.py:1195 E (and 101 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('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') ('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') 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') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', '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_chain299-method_chain299] __________ [gw3] linux -- Python 3.12.3 /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 196 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('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') ('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') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('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_chain280-method_chain280] __________ [gw0] linux -- Python 3.12.3 /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 135 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('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') 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') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('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_chain316-method_chain316] __________ [gw1] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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 | 197122 | 197137 | 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 | 6243 | 6245 | a | 0 | - | | | chr1 | 6243 | 7524 | a | 0 | - | | | chr1 | 6243 | 14715 | a | 0 | - | | | chr1 | 6243 | 6245 | a | 0 | - | | | chr1 | 6243 | 6245 | a | 0 | - | | | chr1 | 6243 | 6245 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 6 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) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr3 | 1755179 | 1755698 | 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 71 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY0tQPNXDwMfAyMDMwMTMBKIYgVx2BgYGRmZ2NgYmBm4GLkYBoCgTQ/L1WEYefimggjTRUAYWoBImVgZZaSAfrF0iSZWRgZVBj1GEKVlRHGgEIwMjo+KMIkaQAiYGNgZuqRNaDPxsZkxs/GwMADzOCXk=') 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, | 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 134 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', 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') ('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') 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') ('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') 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') 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') 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') ('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') ---------------------------------- 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_chain254-method_chain254] __________ [gw2] linux -- Python 3.12.3 /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 64 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('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') 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') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('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') 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') 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') __________ test_three_in_a_row[strandedness_chain255-method_chain255] __________ [gw2] linux -- Python 3.12.3 /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, # 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:575 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('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') 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') 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') 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') 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') __________ test_three_in_a_row[strandedness_chain300-method_chain300] __________ [gw3] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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 245 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('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') 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') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('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') 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') ---------------------------------- 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_chain317-method_chain317] __________ [gw1] linux -- Python 3.12.3 /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 | 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('6.100.4', b'AXicY2RgZGNkYAAiKAGjGGFcBmRRIAAAAoUAEA==') 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') 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') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('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') ('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') ('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') ('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') 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') ('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') Empty PyRanges ('nearest', 'overlap') 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') 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_chain322-method_chain322] __________ [gw0] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 5301416 | 5301418 | a | 0 | + | E | chr1 | 2 | 4 | 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 | 7046935 | 7054618 | a | 0 | - | E | chr19 | 196636 | 197918 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 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 | 65549 | 66063 | a | 0 | + | E | chr4 | 68866 | 69380 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 2 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 169 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY9Rn71jHWsfAwMjOzszAyM0IYnIwJAQ8Wc7A4MnAyMDAVDtjWj1TUIs5EwM/kCvEy8DMyMjAz8dokN0uxsDGzCDNxcDIChRiZ2SQYwLqYATJgxArq54FFzsDC1CEgYeBh5GBGaiGhZGXkRVoB1AEqBxoIAAOMgs+') 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') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('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') 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') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('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_chain301-method_chain301] __________ [gw3] linux -- Python 3.12.3 /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 194 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('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') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('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') 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') ---------------------------------- 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_chain318-method_chain318] __________ [gw1] linux -- Python 3.12.3 /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 | 3997953 | 3997954 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | 6291467 | 6291468 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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/join.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:12 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 (and 76 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY1RiYORgYGBkYLAFYmYQCwR5QSJAlMDAxQABjKy5tgdMWKIYACZqAu0=') 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') ('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') 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') Empty PyRanges ('nearest', 'nearest') 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') 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') Empty PyRanges ('nearest', 'nearest') 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') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('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_chain323-method_chain323] __________ [gw0] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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/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 104 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2AsZgADRkYGBg4GNMCILgAEABeAAIA=') 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') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('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') 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') 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') ('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') ('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') 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') 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') ---------------------------------- 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_chain339-method_chain339] __________ [gw2] linux -- Python 3.12.3 /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 | 405511 | 407817 | a | 0 | + | E | chr1 | 526612 | 530459 | a | 0 | + | E | chr1 | 526612 | 526650 | a | 0 | + | E | chr1 | 526612 | 528918 | a | 0 | + | E | ... | ... | ... | ... | ... | ... | E | chr3 | 526612 | 526876 | a | 0 | + | E | chr4 | 526612 | 528918 | a | 0 | + | E | chr17 | 526612 | 535578 | a | 0 | + | E | chr22 | 526612 | 528918 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 10 rows and 6 columns from 5 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 | 337665 | 341001 | a | 0 | + | E | chr1 | 524290 | 527626 | a | 0 | - | E | chr1 | 342792 | 346128 | a | 0 | - | E | chr1 | 337665 | 341001 | a | 0 | - | E | chr1 | 337665 | 341001 | a | 0 | - | E | chr1 | 337665 | 341001 | a | 0 | - | E | chr1 | 337665 | 341001 | a | 0 | - | E | chr1 | 337665 | 341001 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 8 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 | 984077 | 985364 | a | 0 | + | E | chr1 | 131356 | 132643 | 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/join.py:19 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 (and 36 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicfY6/LkNhGMaf9/2+930dOV+LEpH2VA4VTSonDF0YLQZ7YxOdxCpiJJLegBsQkkaIwQUYLFY53EBXvQAkFp8b8Dzr7/lDne/y5qwIvj247/vZ7a9r35t8ODTXSPuOlsqZg8+B5hcZz9/+7O48l7T/evW+cfdmujmufQy75y+jy6PxiR4/nvZGe0+Bc3QcFQpXAIvcEMq0xcimFqSOtmGOFeRpTdfVCNMTSc2ByMQ1q0osy9LlrMKtxNg7571gBUgIYORGpIjw/4/jtwhprAYJqWwZRFaBECwY6M+aCpmDph5RgZpMdUKl6tOYlLjxC/3hMS8=') 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') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 82207 | 85447 | a | 0 | ... | | chr1 | 82207 | 85447 | a | 0 | ... | | chr1 | 82207 | 85447 | a | 0 | ... | | chr1 | 82207 | 86759 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 82207 | 84144 | a | 0 | ... | | chr1 | 82207 | 89921 | a | 0 | ... | | chr1 | 82207 | 89921 | a | 0 | ... | | chr1 | 82207 | 89921 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 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') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') 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') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') 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') ('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') 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') 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') ('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') ('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') 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') ('join', 'nearest') ('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_chain302-method_chain302] __________ [gw3] linux -- Python 3.12.3 /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 173 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('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') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('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') 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') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', '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_chain319-method_chain319] __________ [gw1] linux -- Python 3.12.3 /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 | 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('6.100.4', b'AXicY2Rg4GVgYGAEQhBiYECn0AEAA2QAFA==') 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') ('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') ('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') ('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') 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') ('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') ('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') ('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') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('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_chain341-method_chain341] __________ [gw2] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 88062 | 91136 | a | 0 | + | E | chr1 | 88062 | 91136 | 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=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr15 | 650135 | 650193 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 110 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AAFhC7wpASdwGWcAAAEARwFX/QAIDAEBAAEAAAABKlVsOG0D/QABNIfhRQAAAA4AHQnrlgAMADkAAQ==') 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') 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') ('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') ('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') ('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') ('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') ('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') ---------------------------------- 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_chain325-method_chain325] __________ [gw0] linux -- Python 3.12.3 /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 | 131329 | 131586 | a | 0 | + | E | chr1 | 6657 | 6914 | a | 0 | + | E | chr1 | 148093 | 148350 | a | 0 | + | E | chr2 | 6657 | 6914 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 4 rows and 6 columns from 2 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 | 131329 | 132099 | a | 0 | - | E | chr1 | 131329 | 132611 | 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 | 263 | 776 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AXicY2FM3/mdKWpGFztLKSOrKqvMRwYZZgYhBkZGBkZeZiAhwSDJxAgUkGKQYOZlcqqR52QEshmAJAMDIwtQNzsTQg9IFwNYAxODFDMjELIC+YxMjEwZTxn4IXrYmIACIAYAqPILZw==') 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') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 26 | 823 | a | 0 | ... | | chr1 | 26 | 823 | a | 0 | ... | | chr1 | 26 | 823 | a | 0 | ... | | chr1 | 8013570 | 8013576 | a | 0 | ... | | chr1 | 26 | 5925 | a | 0 | ... | | chr1 | 26 | 5925 | a | 0 | ... | | chr1 | 26 | 823 | 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 | 26 | 823 | a | 0 | ... | | chr1 | 26 | 823 | a | 0 | ... | | chr1 | 26 | 823 | a | 0 | ... | | chr1 | 8013570 | 8013576 | a | 0 | ... | | chr1 | 26 | 5925 | a | 0 | ... | | chr1 | 26 | 5925 | a | 0 | ... | | chr1 | 26 | 823 | 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') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 318 | 896 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For 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 | 318 | 896 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For 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 | 318 | 896 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For 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 | 318 | 896 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For 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') ('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') ('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') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 10000000 | 10001579 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For 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') ('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') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') 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') ('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') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') 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') 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') ('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_three_in_a_row[strandedness_chain354-method_chain354] __________ [gw3] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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 63 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('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') Empty PyRanges ('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') ('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') 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') 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') ---------------------------------- 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 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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 | 4918522 | 4918533 | 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 | 12036 | 15625 | a | 0 | + | | | chr1 | 12036 | 13070 | a | 0 | - | | | chr9 | 12036 | 13575 | a | 0 | + | | | chr10 | 12036 | 13068 | a | 0 | + | | | chr14 | 12036 | 13575 | a | 0 | - | | | chr21 | 12036 | 13574 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 6 rows and 6 columns from 5 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chrX | 8679696 | 8679698 | a | 0 | - | | | chrX | 1115906 | 1115907 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 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 114 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicLY69TgJBFIXPuXPnzg7CLibsYgaQ0FDYGBoKIBa0RktaQ2FlZQWJrZWPwEMZ43PwAnQMCcVJTnJ+8vF19f8HAeExe26f0Mr2IsDSYhNlZ/XR3wx0ay/Rv/t0WGx+rTl9Db8/K11XHz+oBTEEEzrcdwwYFYqOoudQeOanOzy6OUcaxaVL68E5MQ0uYP/UN9GgLWPDCaKsEDD0b6WiAFSxNEHj0RUqaOKkJsYDyXAppabElUPI28C8nYJkmWPwDHzqFcU=') 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, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 5464 | 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 197 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AAAAEitO1yE3E74AAAF9mJZ/AAEAAQAABAAAAAAYFVYAAA==') 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') ('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') ('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') 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_chain343-method_chain343] __________ [gw2] linux -- Python 3.12.3 /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 244 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') 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') 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') 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') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('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_chain327-method_chain327] __________ [gw0] linux -- Python 3.12.3 /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, 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 92 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', 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') ('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') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('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') 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') 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') Empty PyRanges ('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_chain355-method_chain355] __________ [gw3] linux -- Python 3.12.3 /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/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 105 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('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') 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') 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') 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') ---------------------------------- 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_chain321-method_chain321] __________ [gw1] linux -- Python 3.12.3 /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 | 27137 | 27142 | a | 0 | + | E | chr1 | 27137 | 28835 | 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 | 2563 | 3844 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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: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('6.100.4', b'AXicY7URuPKKkYGRAQgYGfgYshjYgCwWPgZ+XkYWtoUMTAwMrEAZoBQ7E0gFIwMXEz+7ESsDGDBJgEgJRgDTHwQZ') 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') Empty PyRanges ('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') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4245406 | 4246985 | a | 0 | ... | | chr1 | 4245406 | 4246985 | a | 0 | ... | | chr1 | 4239015 | 4248148 | a | 0 | ... | | chr1 | 4239015 | 4248148 | 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, Distance, ... (+ 5 more.) ('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') ('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') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('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_chain344-method_chain344] __________ [gw2] linux -- Python 3.12.3 /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 184 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('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') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('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') ('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') 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') ---------------------------------- 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_chain356-method_chain356] __________ [gw3] linux -- Python 3.12.3 /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/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:575 E /usr/lib/python3/dist-packages/pandas/core/common.py:140 E (and 62 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('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') 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') 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') 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') 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') ---------------------------------- 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_chain329-method_chain329] __________ [gw0] linux -- Python 3.12.3 /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 198 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('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') ('subtract', 'set_union') ('subtract', 'set_union') ('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') 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') ---------------------------------- 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_chain367-method_chain367] __________ [gw1] linux -- Python 3.12.3 /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 | 9237401 | 9237510 | a | 0 | - | E | chr1 | 9237401 | 9237403 | 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 | 327946 | 327947 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 194 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2RlZORhNKt6MJcBDHo+z2BkYGfIYWSsY2AEQSBgYORhkdjBAOKxMnKClTECMRcDJ6MmHyMjADHSBpQ=') 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') ('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') ('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') ('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') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('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') ('nearest', 'nearest') ('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') ---------------------------------- 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_chain345-method_chain345] __________ [gw2] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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 173 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('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') 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') 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') 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') 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') ---------------------------------- 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] __________ [gw3] linux -- Python 3.12.3 /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, 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 217 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', 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') 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') 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') 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') ('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') ('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') 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') 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') ---------------------------------- 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_chain330-method_chain330] __________ [gw0] linux -- Python 3.12.3 /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 186 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('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') 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') 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') 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') ---------------------------------- 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_chain368-method_chain368] __________ [gw1] linux -- Python 3.12.3 /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 | 6426580 | 6432914 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | 4 | 51 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AXicYzSw4a9nYARD5ST+y0CKS2IvAwMDoxUDAy+QYmBiYGBmZGBm0GMAiTLJAkkBHgYAmyMEAg==') 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') ('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') 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') ('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') ('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') 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_chain346-method_chain346] __________ [gw2] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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 176 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('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') 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') Empty PyRanges ('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') ('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') 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') ---------------------------------- 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_chain358-method_chain358] __________ [gw3] linux -- Python 3.12.3 /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, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr11 | 383 | 640 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 102 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AAABLRI6AAE0OQGZAAABACgABAAAAAoAAAABfgAAAQAAAA==') 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') 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') 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') ('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') ('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') ('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') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', '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_chain331-method_chain331] __________ [gw0] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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('6.100.4', 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') ('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') ('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') ('subtract', 'overlap') ('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') ('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') Empty PyRanges ('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') 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') ('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') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', '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_chain347-method_chain347] __________ [gw2] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('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') 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') 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') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('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') ('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') 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') ---------------------------------- 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_chain369-method_chain369] __________ [gw1] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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 | 459042 | 461360 | a | 0 | + | | | chr1 | 330756 | 333074 | a | 0 | + | | | chr1 | 13 | 7972 | a | 0 | + | | | chr3 | 658699 | 661017 | a | 0 | - | | | chr6 | 536591 | 538909 | a | 0 | - | | | chr10 | 203783 | 206101 | a | 0 | - | | | chr13 | 1902858 | 1905176 | a | 0 | + | | | chr21 | 67074 | 69392 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 8 rows and 6 columns from 6 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 | 131369 | 138000 | a | 0 | + | | | chr1 | 131369 | 132451 | a | 0 | - | | | chr1 | 131369 | 138000 | a | 0 | - | | | chr1 | 131369 | 138000 | a | 0 | - | | | ... | ... | ... | ... | ... | ... | | | chr1 | 131369 | 138000 | a | 0 | - | | | chr1 | 131369 | 138000 | a | 0 | - | | | chr1 | 131369 | 134704 | a | 0 | - | | | chr1 | 131369 | 132650 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 10 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 | 5677293 | 5681658 | 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 174 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicFU6xSgNBFHxv3+7t7d7uHYcxEkhIRI1BxATBaDSJYishnSCoWFn4A7FWEBERGxHBwsIupWCQ+AFioShibaMWamNhJeLdFFPMzHszkmafb353Di5F6/44N1V8YSV71MWYaOVwpsbKt0vd0/be8uO7hNZFo7z99Idh+7w4dtWh5NbCHUxKMApBDTIQfQLYAEDCAURAwiFKO8gCt+QL4WmrLbkS+12mkIRGT4TcE4bKNCFGWJKElBmlNPlimvsA6GCBVzFLEMGQ42aTMK+s5MAdUASS4ShiQgLHcYF14oxFQZ76bloTaFRofcZ7jGRWY0g1zCkOmxtfnFllMO/v97KG3A0k5dfyIq4Aj2FBwTCvKK1IgOMa62R9bqK3mHqrRgpgPd41t+q/xgcIme769UmFHqqdj5/04tknQDM0OjL+AXclNZk=') 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, | 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 137 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', 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', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('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') 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') 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') ('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') ('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') ('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') ('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') 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_chain332-method_chain332] __________ [gw0] linux -- Python 3.12.3 /usr/bin/python3.12 strandedness_chain = (False, None), method_chain = ('subtract', '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: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', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 131181 | 131182 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 171 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2AAA0ZmBgY21uhuBgZ2MJ+FiSGHiyEVIgkAHegB3g==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- 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') 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') ---------------------------------- 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_chain360-method_chain360] __________ [gw3] linux -- Python 3.12.3 /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 | 6888961 | 6890242 | a | 0 | + | E | chr1 | 6888961 | 6898002 | a | 0 | + | E | chr1 | 6888961 | 6889475 | a | 0 | + | E | chr1 | 7940666 | 7943995 | 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 gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 131336 | 134665 | a | 0 | - | E | chr1 | 131336 | 134665 | a | 0 | - | E | chr1 | 5628258 | 5631587 | a | 0 | - | E | chr1 | 7940666 | 7943995 | 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 | 96769 | 96771 | a | 0 | + | E | chr5 | 96769 | 96771 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 2 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('6.100.4', b'AXicY2cs1Nx2lVk6MfU8o+ohsevLZ25ZkqNhMV2LxdzD2o5BkJmRgVGKOaxSy5JBJlOOQZZBnZWBizFbOUCIiY+JkZmRnZmBl4FBkhmoiImJgYGBhet9bfh7wY8EDJVjlmUEmczE9PKAQejDRGmwFXJAExkEmBjZGUCGMsINZWZgZWRgYQBqYKwCcoEMBgAp6SLe') 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) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 260 | 1031 | a | 0 | ... | | chr4 | 1464402 | 1473879 | a | 0 | ... | | chr4 | 8323948 | 8324363 | 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 ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') 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') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8833483 | 8836469 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For 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') ('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') 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') ('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') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') 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') 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') Empty PyRanges ('overlap', 'nearest') 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') ---------------------------------- 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_chain348-method_chain348] __________ [gw2] linux -- Python 3.12.3 /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 185 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('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') ('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') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('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_chain370-method_chain370] __________ [gw1] linux -- Python 3.12.3 /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 | 7426 | 7428 | a | 0 | - | E | chr1 | 7426 | 7428 | 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 | 131073 | 131842 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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: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('6.100.4', b'AXicHcixFQAQEATRnRXIPHIaUpo+9OnORP8NeLqqn33VhKKhhRzG2EV5HZ9PkgIeYAYCDQ==') 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') ('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') ('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') ('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') ('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') 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_chain333-method_chain333] __________ [gw0] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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('6.100.4', 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') ('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') 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') 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') 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') 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') 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') ---------------------------------- 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_chain349-method_chain349] __________ [gw2] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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 180 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') 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') 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') 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') 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') 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') ---------------------------------- 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] __________ [gw3] linux -- Python 3.12.3 /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, 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 186 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', 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') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('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') ('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') 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') 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') 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') ---------------------------------- 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_chain371-method_chain371] __________ [gw1] linux -- Python 3.12.3 /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, 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 219 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2AAASkwyciACQAC2AAc') 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') 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') 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') ('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') 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') 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') 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') Empty PyRanges ('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_chain334-method_chain334] __________ [gw0] linux -- Python 3.12.3 /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, 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 188 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BAAEYGTAAAADQAAg==') 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') 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') 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 | 1918427 | 1926635 | 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') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('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') 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') Empty PyRanges ('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') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('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_chain350-method_chain350] __________ [gw2] linux -- Python 3.12.3 /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/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/python3.12/typing.py:1195 E (and 122 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('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') ('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') 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') ---------------------------------- 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_chain372-method_chain372] __________ [gw1] linux -- Python 3.12.3 /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, 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 104 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', 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') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('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') 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') 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') 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') 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') ('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') ---------------------------------- 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_chain364-method_chain364] __________ [gw3] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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 | 5535076 | 5537904 | 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 | 197121 | 197124 | 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 | 5 | 2313 | a | 0 | + | | | chr1 | 1966354 | 1966625 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 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 179 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicYyz6qndV/dZVdnYmPgZGBj4G7ZDSZAYuBiZubgZOoAAjQp6DgUFGRoqBgYGVmYmBGUgzAdUBVTDIMDNBCPYzz+rNGh8xcDIysjCCZJgZGeQYBZkYuYGqGVhAmjiZmRkZGfmAXADtxg9I') 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, | 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('6.100.4', 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') 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') 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') 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') ('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') 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') 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') 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') ---------------------------------- 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_chain335-method_chain335] __________ [gw0] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:369 E (and 25 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2CAA0YGLAAAADUAAg==') 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') ('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') ('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') ('subtract', 'join') ('subtract', 'join') ('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_three_in_a_row[strandedness_chain351-method_chain351] __________ [gw2] linux -- Python 3.12.3 /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/python3.12/typing.py:1195 E (and 104 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('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') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('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') ('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') ---------------------------------- 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_chain365-method_chain365] __________ [gw3] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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 | 720903 | 727053 | a | 0 | + | | | chr1 | 720903 | 728851 | a | 0 | - | | | chr14 | 720903 | 724749 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 3 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 | 786435 | 786713 | a | 0 | + | | | chr1 | 786435 | 787810 | a | 0 | - | | | chr1 | 459009 | 464760 | a | 0 | - | | | chr1 | 65802 | 66080 | 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=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 5065223 | 5070344 | 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('6.100.4', b'AXicHY69DcJQDITv7Lz3SEJEIIBIQNAj0TACJRIdJYIlED8DUFOyAzMwClPQ0eGHXJzP/nyyHF+3z/3wCHqePxeKbiNwqkoUworeuoawyuFr2S3fI0cFZrkgQYvacVBQ/hc1CpasjIYNG5lEUkPwlgUDorNdVJDsfbcIREaquRRoQ8jV8DRmCbi9I1IOOspMMI0vkJlJEvMvm7UvcO1bEn7dKg4v') 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, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | 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., | ) | 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 155 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2D013BmZeZmYGBgYWAEQhDgBVFAzAQkABlKAOc=') 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') ('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') ('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') 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') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('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_chain336-method_chain336] __________ [gw0] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 72193 | 72195 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2561 | 2562 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 176 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY+Kv0WJnYGBkYGSUAlMMQJKRjYmBUYiBkRksABFk4GKAAAAsLAEN') 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') 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') 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') 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') 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') Empty PyRanges ('join', 'set_union') Empty PyRanges ('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_three_in_a_row[strandedness_chain352-method_chain352] __________ [gw2] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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 63 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('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') 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') ('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') 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') 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') ---------------------------------- 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_chain374-method_chain374] __________ [gw1] linux -- Python 3.12.3 /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 | 8773956 | 8779628 | a | 0 | + | E | chr1 | 1832491 | 1837433 | a | 0 | - | E | chr5 | 2884657 | 2890329 | a | 0 | - | E | chr5 | 3408932 | 3417142 | a | 0 | - | E | chr5 | 1832491 | 1839476 | a | 0 | - | E | chr12 | 6881387 | 6883373 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 6 rows and 6 columns from 3 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 | 8773956 | 8779628 | a | 0 | - | E | chr1 | 4699776 | 4708345 | a | 0 | - | E | chr1 | 1832491 | 1841715 | a | 0 | - | E | chr4 | 8817666 | 8825876 | a | 0 | - | E | chr12 | 6881387 | 6883373 | a | 0 | - | E | chr17 | 1832491 | 1837433 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 6 rows and 6 columns from 4 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 | 65795 | a | 0 | + | E | chr1 | 65537 | 66306 | 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/join.py:104 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:106 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:12 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:14 E (and 41 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicpc89S0JxFAbw8/J/STOxUktvgd5MxUKuIpSlNDgUmE41+QmKCKIgp6LBltqtPciGVhuaWpyKCJoKAtuioYJojK4tbUEEh4fz8Ew/GmudL+jSPK70vdZltt7wKesNRjcOtXRduYMv6ycVj5S568L93QQZgCABBQKk0IIQQzeACCiBGTFCSitNYlxYSpjseB4KPpVrS7CcR3+tXXCyg5PkowRD8Ohy4PbgofHZbC2WjY/ENIvcu74wxWaod0pR0R9L8iBYFs2s9Zfc4NZKRDXE0R78HJNRYw7ySmIKgTEis4pBEzoF9miR5mGeJB+HKUyA9Bfb6Wr7+Cz8uHdjtipgaMSMIowDeCRmBXCXxLT0klcLh/rBJ0Vgd/8b755tbpv/x1fD1d/xEQ2AqrhDDt6yv86hnWwnStQM4Or0L+0YXps=') 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') ('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') ('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') ('intersect', 'nearest') 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') 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') 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') ---------------------------------- 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_chain366-method_chain366] __________ [gw3] linux -- Python 3.12.3 /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 | 71681 | 72452 | a | 0 | - | E | chr1 | 71681 | 72450 | a | 0 | - | E | chr20 | 71681 | 72840 | 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 gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1793 | 1794 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AXicYwp0M9Ni8mpfvIOdST58UTmDJDMDoxQzIyMbAysTgzADAxejBIM4M1MOSxsXAyszEycjMzMDAwMjIzuDGCMDBLBDKEYgZGaQAupnAADH5wa/') 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') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7022339 | 7028324 | a | 0 | ... | | chr7 | 6435476 | 6443736 | a | 0 | ... | | chr8 | 4490795 | 4497849 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 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 ('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') 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') ('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') ('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_chain353-method_chain353] __________ [gw2] linux -- Python 3.12.3 /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/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:575 E /usr/lib/python3/dist-packages/pandas/core/common.py:140 E (and 62 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('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') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('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') ('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') Empty PyRanges ('set_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_chain337-method_chain337] __________ [gw0] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr13 | 6 | 2055 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 6127 | 16126 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 155 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AAQ+iYPxAAAADABBAAAFAAwIAAAAAAEmuQAKAAAUAAkAAAMABgAAAAAAAAAEABfuAQB/Jw4AAAA=') 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') ('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') ('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') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', '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_chain378-method_chain378] __________ [gw3] linux -- Python 3.12.3 /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/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/pyranges.py:4162 E /usr/lib/python3.12/typing.py:1195 E (and 130 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('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') ---------------------------------- 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_chain376-method_chain376] __________ [gw1] linux -- Python 3.12.3 /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, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 275 | 283 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 103 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AAABFQQAAQABAAAAAgAAAAQAAAEAAQABEgAAAAcAAA==') 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') 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') Empty PyRanges ('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') ('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_chain388-method_chain388] __________ [gw2] linux -- Python 3.12.3 /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 | chr5 | 5074427 | 5080922 | a | 0 | - | E | chr9 | 4252936 | 4258977 | a | 0 | - | E | chr11 | 9542900 | 9545060 | a | 0 | + | E | chr15 | 7141546 | 7150324 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 4 rows and 6 columns from 4 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 | chr5 | 5074427 | 5080922 | a | 0 | - | E | chr9 | 4252936 | 4258977 | a | 0 | - | E | chr11 | 8553652 | 8555812 | a | 0 | + | E | chr15 | 7141546 | 7150324 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 4 rows and 6 columns from 4 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 | 9542900 | 9543675 | a | 0 | + | E | chr1 | 535900 | 536675 | a | 0 | + | E | chr1 | 535900 | 536675 | a | 0 | + | E | chr2 | 459745 | 460520 | a | 0 | + | E | ... | ... | ... | ... | ... | ... | E | chr15 | 535900 | 536675 | a | 0 | + | E | chr17 | 3746571 | 3747346 | a | 0 | + | E | chr18 | 4416532 | 4417307 | a | 0 | + | E | chr19 | 3804962 | 3805737 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 10 rows and 6 columns from 8 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('6.100.4', b'AXicY2eVW1ojxstXyxJ4fHe1t6UII8/En2tY6xgYGBlEmBn4xBkZWPiZGLhkmIUZ+ZkZGDgkmJlyfqwUYGZhDPPN/cXBpD5xzmdGJjkmWQYlh6fsDHwMouIzRBg4mXOUPMWY8jjyBRkYMiXjOJkZ2ZiAZrJTap3tnPXnmlo2E28jq0R22EFGO+nyC2wKvwXrrxmWhUpcYM7cMlXviXyPneoZFiVGETbG0n+rZHTm3WOMvFuftLl228+Z7a3TfFik131mEPlwkbnQJWIpi0bQl/kMyiyMSswMAuL8PAwMQiwcDLyCHLqsjAK8rMKcDHxsnHqMDILavLx8PEyM1rw8bAyMUvx8HCJs7OwMXAyGDCJW/IrqXDy8jGLOKcLM4JAzY2ax1OayZuNmZ35gzcjFps3O1sXCzaDIoRvNoMnMxsAAADf6VG0=') 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') ('join', 'nearest') ('join', 'nearest') ('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 | 3935962 | 3940395 | a | 0 | ... | | chr2 | 738381 | 742814 | a | 0 | ... | | chr3 | 2388050 | 2388551 | a | 0 | ... | | chr3 | 10000000 | 10004433 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr9 | 3874556 | 3878989 | a | 0 | ... | | chr14 | 6510073 | 6514506 | a | 0 | ... | | chr16 | 9243823 | 9248256 | a | 0 | ... | | chr17 | 738381 | 742814 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 17 columns from 7 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') ('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') ('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') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('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_chain379-method_chain379] __________ [gw3] linux -- Python 3.12.3 /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 115 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('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') ('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_three_in_a_row[strandedness_chain396-method_chain396] __________ [gw0] linux -- Python 3.12.3 /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 195 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('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') 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') 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') Empty PyRanges ('set_union', '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_chain403-method_chain403] __________ [gw1] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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 65 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('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') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('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') ('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') 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') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', '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_chain397-method_chain397] __________ [gw0] linux -- Python 3.12.3 /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 199 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('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') ('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_chain380-method_chain380] __________ [gw3] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 8 | 10 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | 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 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: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('6.100.4', b'AXicY2cAAkYQwQMi2MFcViDBxsAMFAdBMMHMIApTyGjIBhZkAAAL1wCD') 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') ('subtract', 'overlap') ('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') ('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') 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') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 131337 | 132109 | 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', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 131329 | 132101 | 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', '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') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', '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_chain390-method_chain390] __________ [gw2] linux -- Python 3.12.3 /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, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65793 | 65794 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AXicY2BkYGHgYgABRgYYxQjETCA2AAHbABY=') 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') ('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') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('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') 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') ('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') Empty PyRanges ('join', 'subtract') ('join', '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_chain404-method_chain404] __________ [gw1] linux -- Python 3.12.3 /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, 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 104 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('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') ('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') Empty PyRanges ('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_chain381-method_chain381] __________ [gw3] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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 | 6784147 | 6791317 | a | 0 | + | | | chr3 | 2696700 | 2701773 | a | 0 | + | | | chr6 | 217083 | 224253 | a | 0 | - | | | chr15 | 217083 | 222417 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 4 rows and 6 columns from 4 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 | 9659587 | 9667095 | a | 0 | + | | | chr1 | 9659587 | 9667095 | a | 0 | + | | | chr1 | 9659587 | 9659593 | a | 0 | + | | | chr1 | 9659587 | 9667095 | a | 0 | + | | | chr1 | 9659587 | 9667095 | a | 0 | + | | | chr18 | 9659587 | 9660101 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 6 rows and 6 columns from 2 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 62 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AAcCTJbK0wcFHaJFubsQJW3rsgZaueJ92gYWmUvISVk8BwFe5h2DvLxy1CpCZNdPABoDAAUeAxIBAAIDAAEDAR0DEAMbAAMBCQMAAA4KAFNnhJIVAVwpJfsJAQAWA0/6GAEAE9AKAm4U1QAAHAESAwEVAAAFAgECAQAAAAEK4wgAEANCOSQ9AAE5H1cAAwIBEwABDwEBCQIQAwAAAianvSdeiuMBK1qa3AADAQEEAAARAAEAR/PpxZuBx5NkwgIADwIBKwcGAxY1vwAFADYdUwYAAAEEAB0AAgEAAAA=') 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=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 196894 | 199455 | a | 0 | + | | | chr1 | 196894 | 199455 | 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) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr6 | 66049 | 69634 | 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/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:143 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:30 | /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 | (and 19 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2eyfFR7i01sJqMcMxMjAwMjAyMzoywDHxcDM4jHyMAJFAWyWBmAPCYGZgYGPrAiBhAA0YyMjADiHQPE') 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') 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') 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') ('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_chain398-method_chain398] __________ [gw0] linux -- Python 3.12.3 /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('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('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') Empty PyRanges ('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') ('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') 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') 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') ---------------------------------- 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_chain405-method_chain405] __________ [gw1] linux -- Python 3.12.3 /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:575 E /usr/lib/python3/dist-packages/pandas/core/common.py:140 E (and 62 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('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') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('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') ('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') 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') 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') ---------------------------------- 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_chain392-method_chain392] __________ [gw2] linux -- Python 3.12.3 /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 258 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('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') ('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_chain399-method_chain399] __________ [gw0] linux -- Python 3.12.3 /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/python3.12/typing.py:1195 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 123 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('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') ('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') 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') ---------------------------------- 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_chain382-method_chain382] __________ [gw3] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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('6.100.4', 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') 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') ('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') 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') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('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') 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') Empty PyRanges ('subtract', '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_chain393-method_chain393] __________ [gw2] linux -- Python 3.12.3 /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 197 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') 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') 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') ---------------------------------- 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_chain406-method_chain406] __________ [gw1] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr5 | 3329 | 3336 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 14655 | 15387 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AAF2IeyrAAkAAAQAAEsADQABAAEABgAJAAEAAAAADw0AABIACwACAGQFAAAAAQAHADk+DwkzAtsAAA==') 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') ('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') 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') 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') ('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') ('overlap', '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_chain400-method_chain400] __________ [gw0] linux -- Python 3.12.3 /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/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/python3.12/typing.py:1195 E (and 107 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('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') ('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') ---------------------------------- 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] __________ [gw3] linux -- Python 3.12.3 /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: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=('subtract', '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 | 723202 | 727009 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AAABAHXZBwQWsAAAAQCwAAQBVnsAAAEABwsJAQAUM6cO3gAB') 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') 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') 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') Empty PyRanges ('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 | 196620 | 197142 | 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') ('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') ---------------------------------- 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_chain394-method_chain394] __________ [gw2] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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 194 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('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') 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') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('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') ('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') ---------------------------------- 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_chain407-method_chain407] __________ [gw1] linux -- Python 3.12.3 /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: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_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('overlap', 'set_intersect'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 5240678 | 5250677 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | 5240678 | 5250677 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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/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('6.100.4', b'AXicY079s57n48P3H42vuZ6YwsDAyMUg7f89lYGdoV6djwHIz4fKcDEwMqDI8fMDRRh4GPiBpCA7IwCE3BH9') 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') 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') 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') 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') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', '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_chain401-method_chain401] __________ [gw0] linux -- Python 3.12.3 /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 64 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('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') 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') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('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') 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') ---------------------------------- 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] __________ [gw3] linux -- Python 3.12.3 /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 | 513 | 1538 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AAABAAIAAwEBBwAEAAUBAQAAAAAAAAACAAANBAAAAAA=') 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') ('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') ('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') ('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') ---------------------------------- 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_chain395-method_chain395] __________ [gw2] linux -- Python 3.12.3 /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 196 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('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') ('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') 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') Empty PyRanges ('set_union', '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_chain402-method_chain402] __________ [gw0] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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:575 E /usr/lib/python3/dist-packages/pandas/core/common.py:140 E (and 62 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAJGFAoCAABcAAQ=') 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') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('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') Empty PyRanges ('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') ---------------------------------- 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] __________ [gw3] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 97793 | 97794 | a | 0 | - | E | chr1 | 196726 | 196727 | 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 | 3541070 | 3545189 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | 3541070 | 3541083 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 98 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicYwzrlo1iCf9wOsV8x0sGBkYWRj1mhlJWBlbGOgYGBm4GBj4GRk4GTkZGBrgibgZGBlYGETMOXwYeBhMBMSDJyMAclmO3B6gfKsEAFgUAWe0PCw==') 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') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('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') 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') 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') Empty PyRanges ('join', 'set_union') Empty PyRanges ('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_three_in_a_row[strandedness_chain409-method_chain409] __________ [gw1] linux -- Python 3.12.3 /usr/bin/python3.12 strandedness_chain = ('opposite', 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=('opposite', 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 | 459537 | 461074 | a | 0 | + | E | chr1 | 342058 | 343595 | a | 0 | + | E | chr1 | 1377301 | 1378838 | a | 0 | + | E | chr1 | 3806469 | 3808006 | a | 0 | + | E | chr1 | 1902429 | 1912415 | a | 0 | - | E | chr1 | 3740455 | 3746943 | a | 0 | - | E | chr1 | 329217 | 330754 | a | 0 | - | E | chr1 | 3740455 | 3741992 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 8 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 | 1376770 | 1377555 | a | 0 | + | E | chr1 | 1376770 | 1377555 | a | 0 | + | E | chr1 | 66823 | 67608 | a | 0 | + | E | chr1 | 312 | 1097 | a | 0 | - | E | ... | ... | ... | ... | ... | ... | E | chr1 | 1376770 | 1377555 | a | 0 | - | E | chr1 | 1376770 | 1377555 | a | 0 | - | E | chr1 | 1376770 | 1377555 | a | 0 | - | E | chr1 | 1376770 | 1377555 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 10 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 | 327682 | 328196 | a | 0 | + | E | chr1 | 327682 | 328196 | a | 0 | + | E | chr1 | 327682 | 327943 | a | 0 | - | E | chr5 | 327682 | 328196 | a | 0 | + | E | ... | ... | ... | ... | ... | ... | E | chr5 | 327682 | 328196 | a | 0 | + | E | chr5 | 327682 | 328196 | a | 0 | + | E | chr5 | 327682 | 328196 | a | 0 | + | E | chr5 | 327682 | 327705 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 10 rows and 6 columns from 4 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 32 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicldA7SoNREAXgc+beuZOXSdS8FIKgYgyKjQHzIIKPxjqgoLHR2lLJFqzcgU1WYC2IG7BwCzZWFnY2gvc3qLXdnGIO34y2RpcDbjwO9o7Px1L4fH17frqZyuybFk9Or9xho/ag4f5laTi4lem76/HH++6FnJnMr3fSWANBU2rAjAphrhigdRu2fbfsS8rgvVkc8y6l7aaa80oSO53ZFQfruQYrcjB3hGpA0ydlJbS8IwqBwlVmhVQCjtuuERZYiUFbI03A7l9gSCaXjv2efeWyAeAWuYg+nNW//eUfP+uGtsfEn/NV62r0Q1OM/pymo5+M/pq5X7/9+X3it7A58bu4hPzED4a4C806hqzEm5PHGaoZmZOeBAE8FjQaTVAJFoMTTTKqQlFKXr1DsNjxBcAfNns=') 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') 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') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5958531 | 5964960 | a | 0 | ... | | chr1 | 5958531 | 5963667 | a | 0 | ... | | chr1 | 5958531 | 5966411 | a | 0 | ... | | chr8 | 5958531 | 5965178 | a | 0 | ... | | chr8 | 5958531 | 5966248 | a | 0 | ... | | chr8 | 5958531 | 5960198 | a | 0 | ... | | chr8 | 5958531 | 5961855 | a | 0 | ... | | chr8 | 5958531 | 5959401 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 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 ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5958531 | 5964960 | a | 0 | ... | | chr1 | 5958531 | 5963667 | a | 0 | ... | | chr1 | 5958531 | 5966411 | a | 0 | ... | | chr8 | 5958531 | 5965178 | a | 0 | ... | | chr8 | 5958531 | 5966248 | a | 0 | ... | | chr8 | 5958531 | 5960198 | a | 0 | ... | | chr8 | 5958531 | 5961855 | a | 0 | ... | | chr8 | 5958531 | 5959401 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 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 ('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') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 205518 | 213543 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For 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 | 205518 | 213543 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For 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') ('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') ('overlap', 'nearest') Empty PyRanges ('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_chain416-method_chain416] __________ [gw0] linux -- Python 3.12.3 /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 | 3883179 | 3888558 | a | 0 | + | E | chr1 | 3883179 | 3883948 | a | 0 | - | E | chr1 | 3883179 | 3883948 | a | 0 | - | E | chr1 | 3883179 | 3883948 | a | 0 | - | E | chr2 | 3883179 | 3893164 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 5 rows and 6 columns from 2 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 | 1537 | 1547 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 170 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY1WdNEmVsSRa7BibaLy3OYt3OasSCy8DEwMDJyMDCAo+eHfb2mEVBysbY4o6AzsLoygTgxgzgzArCwMDIyMrCxcjkGZhEGNgY2BgYGfgZADxwZCBlREAyfsKTw==') 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') 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') 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') ('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_chain386-method_chain386] __________ [gw3] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr3 | 5232220 | 5232477 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | 88912 | 98664 | a | 0 | + | E | chr1 | 88912 | 89174 | 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 | 88912 | 88927 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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/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:369 E (and 25 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2RumXqWgZeBgQkIo/2vRYPYjAwMbECCKUGRgZORkY2RGSTExhjtz8bArCbOwMXIysQAFEKRAlJ8DAwAWEEGXA==') 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') ('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') ('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') ---------------------------------- 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_chain411-method_chain411] __________ [gw2] linux -- Python 3.12.3 /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, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr3 | 2 | 262 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AXicY2AAA24hKQYGJgibQY6JhwHIZQQyGZkZGAEJvQCG') 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') ('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') 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') ('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') ---------------------------------- 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_chain421-method_chain421] __________ [gw1] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1708289 | 1708290 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 6946822 | 6950673 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 102 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY+FTLV7BAAL2UoIMUMBow2y5QJiZgZHJqLKJhYERCBnEsxhYGRj4uRgYAIteBME=') 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') ('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') 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') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', '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_chain417-method_chain417] __________ [gw0] linux -- Python 3.12.3 /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 | 5445892 | 5447174 | a | 0 | + | E | chr1 | 5445892 | 5447174 | a | 0 | + | E | chr1 | 5445892 | 5447174 | a | 0 | + | E | chr1 | 5445892 | 5447174 | a | 0 | - | E | chr10 | 131172 | 132454 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 5 rows and 6 columns from 2 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 | 3606275 | 3607557 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 170 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AAFCqFqbiwgoA2AZbMwFJJA1bQJ5gFxPAQYFrwAAAgcAAAkFAAABFQA4AgBjDgAATlMZAwAEBQEDAwEAAAYBLhirAAMAAB8AAAEAATcHAgABAAI7BwUBAAYAAQAAAQMAAAFLH7oA') 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') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') 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') 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') 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') ('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') ('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') ---------------------------------- 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] __________ [gw2] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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 | 257 | 4785 | a | 0 | + | | | chr1 | 1908240 | 1912768 | a | 0 | + | | | chr1 | 1908240 | 1912768 | a | 0 | - | | | chr1 | 1908240 | 1912768 | 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 | 9196918 | 9202849 | a | 0 | - | | | chr19 | 1362137 | 1368068 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 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) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 257 | 4785 | a | 0 | + | | | chr1 | 1908240 | 1912768 | a | 0 | + | | | chr1 | 1908240 | 1912768 | a | 0 | - | | | chr1 | 1908240 | 1912768 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 4 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 179 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2FrVnZkZL/dnfeWP1lNT5qNgY1BkImRn4GRgYFRgoEDRDPIyvHLM3npLxdcL87IyMTMKMTEwMUozszMKMLEBiQZGJj57zN6WrstQjKIgZGRQYgLqJ2dIeHv/fM9oaXcDOyMmjdebVhonyly4gYDQ4C4FisDIzNQHQtVHAEAtSEgRQ==') 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=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 8 | 9 | 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 | 786806 | 795318 | 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 247 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AAMjQQAAAAABAAUAAAcACAAAAAAAAR4COx0zAwEBAUk7RqIAAAEADwwBdQAAIT8AAA==') 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') 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') 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') ---------------------------------- 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] __________ [gw3] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 9693107 | 9693876 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65818 | 70173 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 104 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicYxbiYWQAA63JzzfxM8gxQ3iMDIx8aaxAmo2Vh52BFchnYGRklGRgFGRiYAQAfdcDeg==') 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') ('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') 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') 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') 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') ---------------------------------- 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_chain423-method_chain423] __________ [gw1] linux -- Python 3.12.3 /usr/bin/python3.12 strandedness_chain = ('opposite', 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=('opposite', 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 | 193509 | 199399 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | 193509 | 193524 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | 65544 | 65810 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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/join.py:104 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:106 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:12 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/join.py:14 E (and 43 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2RlNO9hYATDOKbPT0AMcQiX0RNTioGPgYGBkZGRAUSBEDuQ4GRgAAAp9gaP') 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') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') 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') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') 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') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') 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') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('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_chain414-method_chain414] __________ [gw2] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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 | 32021 | 40692 | a | 0 | + | | | chr1 | 32021 | 40692 | a | 0 | + | | | chr1 | 32021 | 40692 | a | 0 | + | | | chr1 | 32021 | 36873 | a | 0 | - | | | chr15 | 32021 | 40692 | 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 | 9379914 | 9387418 | 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 | 3073 | 3083 | 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 169 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY+M8Xv8y1/U2q2XyPiFWRjad4yzmp/xSSq4vZjGOOtHMwMzOzsQgy8fAyMDDUCvCxs7GWK7XYPta6DMDt+I9ThYGLgYGUUZGHgYmRgYGJnOTNDUGVqBafh4GvX4FT6CeZFl/Bk4GZDkGkDAzA0QYAEdTFhk=') 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=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 96047 | 98897 | a | 0 | + | | | chr1 | 96047 | 98897 | a | 0 | + | | | chr1 | 96047 | 98897 | a | 0 | + | | | chr10 | 96047 | 98897 | a | 0 | + | | | chr15 | 96047 | 98897 | 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=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 3073 | 3083 | 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 136 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AAYJx3/pbUXbBTljvhIFAQYsxwQ3yk5kdNejBDNayIMAEAEACQMHBwIAHQ4AAQAGAXcuAD0rEjMACyEeAQAAAAAAFQEBDAACAQAAAjc0ZiYAAAEPAEkADAADAE8ACQAAAA==') 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') 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') ('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') 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') ('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') ('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') ('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') ---------------------------------- 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_chain418-method_chain418] __________ [gw0] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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 | 5583545 | 5583802 | a | 0 | - | | | chr6 | 416463 | 418077 | 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) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 4065031 | 4065051 | a | 0 | + | | | chr1 | 4065031 | 4065051 | a | 0 | + | | | chr1 | 4065031 | 4065051 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 3 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) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr2 | 17182 | 18975 | 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 174 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicHYshDsJQEAXndbu7hAIJUItD1kACsgaNxHAPJJbDcAIOgO4x0ByBT/PUTOZ5v7zv7DA8v6v3J9MW4MYc1Oh42b8kZxvXgYpb13aPODs1DVKKUmWEJmhToJrOwopCfQYtaxeJjFqj9fFQdvrXCSXmB26PC6Q=') 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 | 394497 | 394502 | 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 137 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AAABBwABAgoBBwAAAQICAhsAAAEAAAYFAAAAAAQAAA==') 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', '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') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('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') 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_chain427-method_chain427] __________ [gw3] linux -- Python 3.12.3 /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/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/pyranges.py:4162 E /usr/lib/python3.12/typing.py:1195 E (and 130 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('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') 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') 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') 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') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('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_chain429-method_chain429] __________ [gw1] linux -- Python 3.12.3 /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, E ) E Explanation: E These lines 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('6.100.4', 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') 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') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('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') ('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') 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') 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') Empty PyRanges ('subtract', '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_chain415-method_chain415] __________ [gw2] linux -- Python 3.12.3 /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 | 1836033 | 1841157 | a | 0 | + | E | chr1 | 1836033 | 1841157 | a | 0 | + | E | chr1 | 1836033 | 1841157 | 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 | 262147 | 263196 | a | 0 | - | E | chr1 | 257 | 1306 | a | 0 | - | E | chr1 | 257 | 1306 | 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=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('6.100.4', b'AXicHYqhEYBAEMSyd/cnGCQCgaMEPPoboBsYumAoFcnDREQkUbfHc7+vM+thKx1q+BQwLxocikJmymKZRYAKBPaPKMZPBn1LzguN8QXg') 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') 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') 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') ('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') ('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') ('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') ('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') 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_chain428-method_chain428] __________ [gw3] linux -- Python 3.12.3 /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 117 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY2BkgAFGFAoMAABaAAQ=') 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') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('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') ('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') ---------------------------------- 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] __________ [gw0] linux -- Python 3.12.3 /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 | 257 | 516 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | 393474 | 393475 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AXicYxFN3sPEwMDIAMVMDIyMRqzR4gwQATZGIMHMAOZJMPAwMDCxMQIAUiUCJQ==') 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') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 656646 | 657970 | a | 0 | ... | | chr1 | 656646 | 657970 | a | 0 | ... | | chr1 | 656646 | 657970 | 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, Distance, ... (+ 5 more.) ('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') ('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') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') 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') 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') ('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_chain430-method_chain430] __________ [gw1] linux -- Python 3.12.3 /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: Optional[TResult] = func() | ^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262, in | lambda: ihook(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 103, in _multicall | res = hook_impl.function(*args) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 177, in pytest_runtest_call | raise e | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169, in pytest_runtest_call | item.runtest() | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792, 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 194, 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 1638, 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 | 928519 | 929032 | a | 0 | + | | | chr7 | 928519 | 929032 | a | 0 | - | | | chrY | 928519 | 930317 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 3 rows and 6 columns from 3 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 | 6145 | 6172 | a | 0 | - | | | chr2 | 1114370 | 1114397 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 2 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 58 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AAYhnQcFf5iWBgkFNQcGNAYFBQAeAwABFAMDAQAGAAAfFwAaDisGBgIdBwUAGAIACQEBBwIAAgEBAAAAAAEEeKmSAQR4AQIFZ4FqBwIN4qyHusMQVJ5CAAsBAQAAAQMBAAAYAAAIEQEBAB0AGgMAAA0ABAEBAA==') 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=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 66308 | 68357 | 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 | 28 | 285 | 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/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('6.100.4', b'AXicY1Ocy85aP2MaAwMjgwgjMzMDAwcDiC3LwMUAAjkMDNIgPkiQlUGCkVmMgQEAivwDig==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('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') 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') 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') 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') ('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_chain432-method_chain432] __________ [gw2] linux -- Python 3.12.3 /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: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', 'subtract'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 7473675 | 7479850 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | chr7 | 9999999 | 10000004 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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: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('6.100.4', b'AXicY6pmAAFGfoaMIi4udgYGCTkQl5GLgRFIszEy1M+YVgdkMLBA1DHwAKE4IwB/vAQz') 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') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7803835 | 7811736 | a | 0 | - | | chr1 | 5711290 | 5713890 | 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') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7803835 | 7811736 | a | 0 | - | | chr1 | 5711290 | 5713890 | 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 | 5711290 | 5711548 | a | 0 | + | | chr1 | 7803835 | 7811736 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 7473784 | 7473809 | a | 0 | + | | chr16 | 89906 | 91444 | 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 | 7803835 | 7811736 | a | 0 | + | | chr1 | 7803835 | 7804093 | 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 | 7803835 | 7811736 | a | 0 | - | | chr1 | 7803835 | 7806435 | 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 | 7473784 | 7473809 | a | 0 | + | | chr16 | 89906 | 91444 | 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 | 2022401 | 2022408 | a | 0 | + | | chr1 | 917856 | 917858 | 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 | 7803835 | 7804093 | a | 0 | + | | chr1 | 7803835 | 7811736 | 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 | 3245323 | 3245581 | a | 0 | - | | chr1 | 3245323 | 3251498 | 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 | 7473784 | 7473809 | a | 0 | + | | chr16 | 89906 | 91444 | 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 | 7803835 | 7806435 | a | 0 | + | | chr1 | 7803835 | 7804093 | 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 | 3245323 | 3245581 | a | 0 | + | | chr1 | 7803835 | 7811736 | 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') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr17 | 6175 | 6433 | a | 0 | + | | chrY | 6238598 | 6238856 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr17 | 7473784 | 7481770 | 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 | 7803835 | 7806435 | a | 0 | + | | chr1 | 7803835 | 7804093 | 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 | 7803835 | 7811736 | a | 0 | - | | chr1 | 7803835 | 7806435 | 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 | 7803835 | 7811736 | a | 0 | - | | chr1 | 7803835 | 7806435 | 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 | 2022401 | 2022408 | a | 0 | + | | chr1 | 917856 | 917858 | 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 | 7803835 | 7804093 | a | 0 | - | | chr1 | 7803835 | 7806435 | 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') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 65803 | 66061 | a | 0 | - | | chr1 | 65803 | 71978 | 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 | 7803835 | 7804093 | a | 0 | - | | chr1 | 7803835 | 7810010 | 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') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2022401 | 2022668 | a | 0 | - | | chr1 | 2022401 | 2022668 | 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 | 6175 | 6433 | a | 0 | - | | chr1 | 6175 | 7713 | 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 | 665348 | 665615 | a | 0 | - | | chr1 | 2022401 | 2022668 | 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 | 2022401 | 2022668 | a | 0 | - | | chr1 | 7473675 | 7473942 | 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 | 7473675 | 7473942 | a | 0 | - | | chr16 | 2022401 | 2022668 | 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 | 2022401 | 2022668 | a | 0 | - | | chr19 | 2022401 | 2022668 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr16 | 2022401 | 2022668 | a | 0 | - | | chr16 | 7473675 | 7473942 | 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 | 2022401 | 2022668 | a | 0 | - | | chr19 | 2022401 | 2022668 | 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') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 665348 | 665349 | 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 | 665348 | 665349 | 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 | 665348 | 673249 | 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 | 665348 | 665350 | 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 | 665348 | 665350 | 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 | 657153 | 657154 | 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') ---------------------------------- 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_chain435-method_chain435] __________ [gw3] linux -- Python 3.12.3 /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, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 257 | 262 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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/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:369 E (and 25 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AAABMw4BAQEAAAAAAQAAFUkAAQABAAcAAgABAAAFAA4ABAAMAAEA') 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') ('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') 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') ('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') ('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') 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') ('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') ('join', '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_chain420-method_chain420] __________ [gw0] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 9999999 | 10000256 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 259 | 287 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 145 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY0xNkt7OwMDIUD9jWh0DKyMDA4gDpkAMMAuMmRhYGKQZGACb3QP0') 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') 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') ('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') 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') ('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') 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') 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') 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') ('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') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('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_chain431-method_chain431] __________ [gw1] linux -- Python 3.12.3 /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 | 1793 | 1794 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AAABAAAABUMWCQEBQ1YJ2wAAAQACAAcAAAcAAAABAA==') 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') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('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') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', '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_chain433-method_chain433] __________ [gw2] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 525313 | 525570 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | chr15 | 1010433 | 1010704 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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('6.100.4', b'AXicY2NiVGdjAAMOFgYGTkYggzmYgZWBgZ+LgY+BkT+bgYGdkQ+sQIgBKMvMwAAAJ8gBdg==') 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') ('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') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('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_introns_single ______________________________ [gw1] linux -- Python 3.12.3 /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_chain439-method_chain439] __________ [gw0] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 7494559 | 7503969 | a | 0 | - | E | chr1 | 76293 | 85703 | 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=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 5 | 6 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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:369 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:373 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/multithreaded.py:380 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicY7KYFpjEmNw6uYaBkYGRnZGRgYlBpyh6HgsDL6PcIQYmRi0WBoYClYPsIGkGBgZ2BhYQxcCYLAZUCRZiYGFgBlEAujMIMQ==') 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') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6889155 | 6890383 | 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') 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') ('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') ('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') 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') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', '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_chain437-method_chain437] __________ [gw3] linux -- Python 3.12.3 /usr/bin/python3.12 strandedness_chain = ('opposite', 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=('opposite', 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 | 8549 | a | 0 | + | E | chr1 | 9583187 | 9584055 | a | 0 | + | E | chr1 | 4784191 | 4786861 | 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 | 2531585 | 2531857 | a | 0 | + | E | chr1 | 459878 | 460150 | a | 0 | - | E | chr1 | 259 | 531 | a | 0 | - | E | chr1 | 3019795 | 3026945 | a | 0 | - | E | chr2 | 918274 | 923868 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 5 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 | 3015195 | 3016995 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 31 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicFY6xagJhEIRndv+7X0UunnhC/DHhEOxymCKNor1eF04sLEQOy0BShkAeItiliqTIy+QB8ggp8g5Zt1mW2Zn59LJanTgvZ5XeyvSIvipI2ARslljQ9oAvdmdSv03vkYrc5MWV1qkESdGc5K2HDsu8RhvmE5o7ar/qV7SOTmv3FD//aiKf3+jQdF5nTopeN8bd+APBe44TJVVAIYYKeHdI+Jj9qGfsQviD50USOTa80sVib+waDffb3fs5EIK0kIG1j7w/E+AfMxsX4Q==') 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') ('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 | 8549 | 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') 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') ('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') 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') 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') ---------------------------------- 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[True] _______________________________ [gw1] linux -- Python 3.12.3 /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., 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/tmppv6xf7z7/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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr10 | 8894160 | 8894161 | 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/tmp4kpyyc1j/f1.bed) resultresultresultresultresultresultresultresultresultresult chr10 8894160 8894161 + 1 bedtools_df Chromosome Start End Strand Count 0 chr10 8894160 8894161 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr10 | 589831 | 589835 | 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/tmpu5xt04tk/f1.bed) resultresultresultresultresultresultresultresultresultresult chr10 589831 589835 + 1 bedtools_df Chromosome Start End Strand Count 0 chr10 589831 589835 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr10 | 589831 | 592136 | 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/tmp8dr5x_0y/f1.bed) resultresultresultresultresultresultresultresultresultresult chr10 589831 592136 - 1 bedtools_df Chromosome Start End Strand Count 0 chr10 589831 592136 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3073 | 3074 | a | 0 | - | | chr1 | 3073 | 3074 | 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/tmpb5anscpc/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3073 3074 - 2 bedtools_df Chromosome Start End Strand Count 0 chr1 3073 3074 - 2 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3073 | 3074 | a | 0 | + | | chr1 | 3073 | 3074 | 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/tmp5kqjwezk/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3073 3074 + 2 bedtools_df Chromosome Start End Strand Count 0 chr1 3073 3074 + 2 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 5287 | a | 0 | + | | chr1 | 1 | 5287 | 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/tmpblvzbbj2/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 5287 + 2 bedtools_df Chromosome Start End Strand Count 0 chr1 1 5287 + 2 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 5287 | a | 0 | + | | chr1 | 1 | 5287 | 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/tmpu7nrnn1a/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 5287 + 1 chr1 1 5287 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 5287 + 1 1 chr1 1 5287 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1227502 | 1231504 | a | 0 | + | | chr1 | 3839161 | 3849029 | a | 0 | + | | chr1 | 1 | 3964 | a | 0 | - | | chr1 | 2482028 | 2486445 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 8818824 | 8819391 | a | 0 | - | | chr1 | 6279640 | 6289065 | a | 0 | - | | chr1 | 1 | 8579 | a | 0 | - | | chr1 | 1767588 | 1775921 | 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/tmp3dsuhryy/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 8579 - 2 chr1 1227502 1231504 + 1 chr1 1767588 1775921 - 1 chr1 2482028 2486445 - 1 chr1 3839161 3849029 + 1 chr1 6279640 6289065 - 1 chr1 8818824 8819391 - 1 chr17 3680271 3689889 + 1 chr2 9673681 9675968 + 1 chr4 8257420 8263041 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 8579 - 2 1 chr1 1227502 1231504 + 1 2 chr1 1767588 1775921 - 1 3 chr1 2482028 2486445 - 1 4 chr1 3839161 3849029 + 1 5 chr1 6279640 6289065 - 1 6 chr1 8818824 8819391 - 1 7 chr17 3680271 3689889 + 1 8 chr2 9673681 9675968 + 1 9 chr4 8257420 8263041 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4136710 | 4136725 | a | 0 | - | | chr1 | 4136710 | 4138516 | a | 0 | - | | chr4 | 316 | 331 | a | 0 | - | | chr15 | 4066059 | 4066074 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr15 | 4136710 | 4136725 | a | 0 | - | | chr15 | 984626 | 984641 | a | 0 | - | | chr15 | 4136710 | 4136725 | a | 0 | - | | chr15 | 4136710 | 4136725 | 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 merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpu7lv81ae/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4136710 4138516 - 2 chr15 984626 984641 - 1 chr15 4066059 4066074 - 1 chr15 4136710 4136833 - 5 chr4 316 331 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4136710 4138516 - 2 1 chr15 984626 984641 - 1 2 chr15 4066059 4066074 - 1 3 chr15 4136710 4136833 - 5 4 chr4 316 331 - 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/tmpk0z34gat/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/tmpm0jjqa6z/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/tmptkeeci93/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/tmp7x5gx0s2/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/tmpeudc1bj_/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/tmpaeqfaljf/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/tmp6skfai62/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/tmp1aonyo4u/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/tmpydy6zmh7/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/tmp0yom6d1c/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/tmpr4jt8xzj/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/tmpqxo_7n3e/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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr9 | 7343837 | 7348946 | a | 0 | + | | chr9 | 3048670 | 3050996 | 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/tmp3l1ccw2v/f1.bed) resultresultresultresultresultresultresultresultresultresult chr9 3048670 3050996 - 1 chr9 7343837 7348946 + 1 bedtools_df Chromosome Start End Strand Count 0 chr9 3048670 3050996 - 1 1 chr9 7343837 7348946 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4459030 | 4464888 | a | 0 | - | | chr1 | 6058653 | 6063900 | a | 0 | - | | chr7 | 3727754 | 3733612 | a | 0 | - | | chr19 | 8445704 | 8453235 | 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/tmpy57l6d15/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4459030 4464888 - 1 chr1 6058653 6063900 - 1 chr19 8445704 8453235 - 1 chr7 3727754 3733612 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4459030 4464888 - 1 1 chr1 6058653 6063900 - 1 2 chr19 8445704 8453235 - 1 3 chr7 3727754 3733612 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6330832 | 6336977 | a | 0 | + | | chr1 | 4313479 | 4322542 | a | 0 | + | | chr1 | 4313479 | 4316864 | a | 0 | - | | chr1 | 4313479 | 4323160 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr15 | 4313479 | 4314061 | a | 0 | - | | chr15 | 4313479 | 4318575 | a | 0 | - | | chr18 | 4313479 | 4313480 | a | 0 | + | | chr18 | 4313479 | 4315410 | 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/tmpt90_8udz/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4267427 4277264 - 1 chr1 4313479 4323160 - 3 chr1 4313479 4322542 + 1 chr1 5419097 5420600 - 1 chr1 6330832 6336977 + 1 chr15 4313479 4318575 - 2 chr18 4313479 4313480 + 1 chr18 4313479 4315410 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4267427 4277264 - 1 1 chr1 4313479 4323160 - 3 2 chr1 4313479 4322542 + 1 3 chr1 5419097 5420600 - 1 4 chr1 6330832 6336977 + 1 5 chr15 4313479 4318575 - 2 6 chr18 4313479 4313480 + 1 7 chr18 4313479 4315410 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 10000000 | 10006404 | a | 0 | + | | chr1 | 7191983 | 7193093 | a | 0 | + | | chr1 | 10000000 | 10004543 | a | 0 | - | | chr1 | 7739877 | 7748997 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr5 | 812313 | 813017 | a | 0 | + | | chr6 | 10000000 | 10001613 | a | 0 | - | | chr12 | 10000000 | 10003090 | a | 0 | - | | chr16 | 10000000 | 10000001 | 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 -s -i <(sort -k1,1 -k2,2n /tmp/tmp0tcqtlzd/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7191983 7193093 + 1 chr1 7739877 7748997 - 1 chr1 10000000 10009213 - 2 chr1 10000000 10006404 + 1 chr12 10000000 10003090 - 1 chr16 10000000 10000001 - 1 chr5 812313 813017 + 1 chr6 10000000 10001613 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 7191983 7193093 + 1 1 chr1 7739877 7748997 - 1 2 chr1 10000000 10009213 - 2 3 chr1 10000000 10006404 + 1 4 chr12 10000000 10003090 - 1 5 chr16 10000000 10000001 - 1 6 chr5 812313 813017 + 1 7 chr6 10000000 10001613 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr12 | 3755421 | 3762975 | a | 0 | + | | chr12 | 9950637 | 9958191 | 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/tmp3zfuhxx9/f1.bed) resultresultresultresultresultresultresultresultresultresult chr12 3755421 3762975 + 1 chr12 9950637 9958191 - 1 bedtools_df Chromosome Start End Strand Count 0 chr12 3755421 3762975 + 1 1 chr12 9950637 9958191 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4503105 | 4504721 | 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/tmp19csqrub/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4503105 4504721 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4503105 4504721 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6875086 | 6879027 | a | 0 | + | | chr14 | 3875785 | 3883249 | 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/tmp8i5ipyx0/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6875086 6879027 + 1 chr14 3875785 3883249 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 6875086 6879027 + 1 1 chr14 3875785 3883249 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2542974 | 2550689 | a | 0 | + | | chr1 | 3954344 | 3960878 | a | 0 | + | | chr1 | 7367698 | 7371540 | a | 0 | + | | chr1 | 2934486 | 2940009 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr13 | 7230376 | 7240375 | a | 0 | - | | chr14 | 29262 | 35161 | a | 0 | + | | chr15 | 8297220 | 8304477 | a | 0 | - | | chr20 | 6834848 | 6844370 | 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/tmpxkp8q_bh/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2542974 2550689 + 1 chr1 2934486 2940009 - 1 chr1 3954344 3960878 + 1 chr1 7367698 7371540 + 1 chr1 7367698 7377698 - 1 chr11 5476003 5483260 - 1 chr13 7230376 7240375 - 1 chr14 29262 35161 + 1 chr15 8297220 8304477 - 1 chr20 6834848 6844370 + 1 chr3 8553486 8560170 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2542974 2550689 + 1 1 chr1 2934486 2940009 - 1 2 chr1 3954344 3960878 + 1 3 chr1 7367698 7371540 + 1 4 chr1 7367698 7377698 - 1 5 chr11 5476003 5483260 - 1 6 chr13 7230376 7240375 - 1 7 chr14 29262 35161 + 1 8 chr15 8297220 8304477 - 1 9 chr20 6834848 6844370 + 1 10 chr3 8553486 8560170 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6498854 | 6499217 | a | 0 | - | | chr1 | 5782559 | 5791625 | a | 0 | - | | chr1 | 455876 | 460116 | a | 0 | - | | chr1 | 601633 | 608473 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr19 | 1461181 | 1462038 | a | 0 | - | | chr19 | 601633 | 603718 | a | 0 | - | | chrM | 3566664 | 3566733 | a | 0 | - | | chrX | 10000000 | 10004819 | 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/tmph2pb43dr/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 176491 183550 - 1 chr1 455876 460116 - 1 chr1 601633 608473 - 1 chr1 5782559 5791625 - 1 chr1 6498854 6499217 - 1 chr12 3038703 3040218 + 1 chr19 601633 603718 - 1 chr19 1461181 1462038 - 1 chr2 601633 602286 + 1 chrM 3566664 3566733 - 1 chrX 10000000 10004819 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 176491 183550 - 1 1 chr1 455876 460116 - 1 2 chr1 601633 608473 - 1 3 chr1 5782559 5791625 - 1 4 chr1 6498854 6499217 - 1 5 chr12 3038703 3040218 + 1 6 chr19 601633 603718 - 1 7 chr19 1461181 1462038 - 1 8 chr2 601633 602286 + 1 9 chrM 3566664 3566733 - 1 10 chrX 10000000 10004819 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5622830 | 5626152 | a | 0 | + | | chr1 | 8392146 | 8395468 | a | 0 | - | | chr8 | 10000000 | 10003322 | a | 0 | - | | chr11 | 1 | 3323 | 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/tmpyipzvy6h/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5622830 5626152 + 1 chr1 8392146 8395468 - 1 chr11 1 3323 + 1 chr8 10000000 10003322 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 5622830 5626152 + 1 1 chr1 8392146 8395468 - 1 2 chr11 1 3323 + 1 3 chr8 10000000 10003322 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8735840 | 8745839 | a | 0 | + | | chr1 | 2418727 | 2427297 | a | 0 | - | | chr1 | 5015318 | 5018367 | a | 0 | - | | chr17 | 497055 | 501049 | 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/tmpwjemglrz/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2418727 2427297 - 1 chr1 5015318 5018367 - 1 chr1 8735840 8745839 + 1 chr17 497055 501049 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2418727 2427297 - 1 1 chr1 5015318 5018367 - 1 2 chr1 8735840 8745839 + 1 3 chr17 497055 501049 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8591616 | 8595297 | a | 0 | - | | chr12 | 8987568 | 8991249 | a | 0 | - | | chrM | 8615903 | 8623316 | 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/tmpbg_fmpkh/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 8591616 8595297 - 1 chr12 8987568 8991249 - 1 chrM 8615903 8623316 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 8591616 8595297 - 1 1 chr12 8987568 8991249 - 1 2 chrM 8615903 8623316 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7064038 | 7069386 | a | 0 | + | | chr1 | 7064038 | 7064559 | 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/tmp_sjh5hbw/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7064038 7069386 + 2 bedtools_df Chromosome Start End Strand Count 0 chr1 7064038 7069386 + 2 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3359853 | 3362515 | a | 0 | + | | chr1 | 5778866 | 5778867 | a | 0 | + | | chr1 | 2242307 | 2243684 | a | 0 | + | | chr1 | 6285912 | 6287474 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr7 | 4454081 | 4456338 | a | 0 | + | | chr19 | 4263308 | 4266945 | a | 0 | - | | chrM | 4124452 | 4128089 | a | 0 | + | | chrX | 7681328 | 7684965 | 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/tmpcixvjywj/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2242307 2243684 + 1 chr1 2711935 2716685 - 1 chr1 3359853 3362515 + 1 chr1 5529467 5537360 - 1 chr1 5778866 5778867 + 1 chr1 6285912 6287474 + 1 chr1 9584865 9590075 + 1 chr19 4263308 4266945 - 1 chr7 4454081 4456338 + 1 chrM 4124452 4128089 + 1 chrX 7681328 7684965 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2242307 2243684 + 1 1 chr1 2711935 2716685 - 1 2 chr1 3359853 3362515 + 1 3 chr1 5529467 5537360 - 1 4 chr1 5778866 5778867 + 1 5 chr1 6285912 6287474 + 1 6 chr1 9584865 9590075 + 1 7 chr19 4263308 4266945 - 1 8 chr7 4454081 4456338 + 1 9 chrM 4124452 4128089 + 1 10 chrX 7681328 7684965 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr7 | 4732085 | 4740151 | a | 0 | + | | chr7 | 5274403 | 5280903 | a | 0 | + | | chr7 | 5092552 | 5097078 | a | 0 | - | | chr19 | 5330939 | 5338924 | a | 0 | + | | chrM | 5330939 | 5333309 | 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 -s -i <(sort -k1,1 -k2,2n /tmp/tmpdhm7898k/f1.bed) resultresultresultresultresultresultresultresultresultresult chr19 5330939 5338924 + 1 chr7 4732085 4740151 + 1 chr7 5092552 5097078 - 1 chr7 5274403 5280903 + 1 chrM 5330939 5333309 - 1 bedtools_df Chromosome Start End Strand Count 0 chr19 5330939 5338924 + 1 1 chr7 4732085 4740151 + 1 2 chr7 5092552 5097078 - 1 3 chr7 5274403 5280903 + 1 4 chrM 5330939 5333309 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8768377 | 8772556 | a | 0 | + | | chr1 | 2225802 | 2229261 | a | 0 | + | | chr1 | 1224961 | 1227259 | a | 0 | - | | chr8 | 7505408 | 7510866 | a | 0 | + | | chr10 | 4377131 | 4385901 | a | 0 | - | | chr11 | 8251209 | 8256339 | a | 0 | - | | chrM | 4377131 | 4383160 | a | 0 | - | | chrY | 4813625 | 4818581 | 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 -s -i <(sort -k1,1 -k2,2n /tmp/tmpvl280imv/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1224961 1227259 - 1 chr1 2225802 2229261 + 1 chr1 8768377 8772556 + 1 chr10 4377131 4385901 - 1 chr11 8251209 8256339 - 1 chr8 7505408 7510866 + 1 chrM 4377131 4383160 - 1 chrY 4813625 4818581 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1224961 1227259 - 1 1 chr1 2225802 2229261 + 1 2 chr1 8768377 8772556 + 1 3 chr10 4377131 4385901 - 1 4 chr11 8251209 8256339 - 1 5 chr8 7505408 7510866 + 1 6 chrM 4377131 4383160 - 1 7 chrY 4813625 4818581 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4046036 | 4051421 | a | 0 | + | | chr1 | 16637 | 22022 | a | 0 | + | | chr1 | 2068965 | 2074350 | a | 0 | - | | chr1 | 2489999 | 2495026 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr15 | 9999999 | 10005384 | a | 0 | + | | chr15 | 2642434 | 2647819 | a | 0 | + | | chr15 | 9977987 | 9983372 | a | 0 | + | | chr15 | 1728488 | 1733873 | 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/tmp0fb_t3a7/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 16637 22022 + 1 chr1 2068965 2074350 - 1 chr1 2489999 2495026 - 1 chr1 4046036 4051421 + 1 chr15 1728488 1733873 - 1 chr15 2642434 2647819 + 1 chr15 9977987 9983372 + 1 chr15 9999999 10005384 + 1 chr17 8255042 8260427 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 16637 22022 + 1 1 chr1 2068965 2074350 - 1 2 chr1 2489999 2495026 - 1 3 chr1 4046036 4051421 + 1 4 chr15 1728488 1733873 - 1 5 chr15 2642434 2647819 + 1 6 chr15 9977987 9983372 + 1 7 chr15 9999999 10005384 + 1 8 chr17 8255042 8260427 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3678781 | 3680298 | a | 0 | + | | chr1 | 3005000 | 3010633 | a | 0 | + | | chr1 | 10000000 | 10004938 | a | 0 | + | | chr1 | 7482085 | 7491718 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr17 | 224598 | 228837 | a | 0 | - | | chr19 | 6820748 | 6824453 | a | 0 | + | | chr20 | 7498842 | 7503613 | a | 0 | - | | chr22 | 3445685 | 3451984 | 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/tmpwys35g09/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3005000 3010633 + 1 chr1 3678781 3680298 + 1 chr1 7482085 7491718 - 1 chr1 9684804 9690582 - 1 chr1 10000000 10004938 + 1 chr12 477778 486620 - 1 chr17 224598 228837 - 1 chr19 6820748 6824453 + 1 chr20 7498842 7503613 - 1 chr22 3445685 3451984 + 1 chr4 7177350 7184777 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 3005000 3010633 + 1 1 chr1 3678781 3680298 + 1 2 chr1 7482085 7491718 - 1 3 chr1 9684804 9690582 - 1 4 chr1 10000000 10004938 + 1 5 chr12 477778 486620 - 1 6 chr17 224598 228837 - 1 7 chr19 6820748 6824453 + 1 8 chr20 7498842 7503613 - 1 9 chr22 3445685 3451984 + 1 10 chr4 7177350 7184777 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9871632 | 9876269 | a | 0 | + | | chr1 | 8991474 | 8999244 | a | 0 | + | | chr1 | 6580585 | 6584484 | a | 0 | + | | chr1 | 5518160 | 5524631 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr10 | 5711458 | 5713879 | a | 0 | - | | chr15 | 6115694 | 6123924 | a | 0 | - | | chr16 | 7792415 | 7792540 | a | 0 | - | | chr20 | 9763407 | 9763431 | 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/tmpdl5cd1i8/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5518160 5524631 + 1 chr1 6580585 6584484 + 1 chr1 6948907 6958638 - 1 chr1 8991474 8999244 + 1 chr1 9454444 9458725 - 1 chr1 9871632 9876269 + 1 chr10 5711458 5713879 - 1 chr15 6115694 6123924 - 1 chr16 7792415 7792540 - 1 chr20 9763407 9763431 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 5518160 5524631 + 1 1 chr1 6580585 6584484 + 1 2 chr1 6948907 6958638 - 1 3 chr1 8991474 8999244 + 1 4 chr1 9454444 9458725 - 1 5 chr1 9871632 9876269 + 1 6 chr10 5711458 5713879 - 1 7 chr15 6115694 6123924 - 1 8 chr16 7792415 7792540 - 1 9 chr20 9763407 9763431 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3159003 | 3163201 | a | 0 | + | | chr1 | 4708408 | 4717601 | a | 0 | + | | chr1 | 7305986 | 7308189 | a | 0 | + | | chr1 | 4784584 | 4792047 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr13 | 1597497 | 1605615 | a | 0 | - | | chr19 | 8885154 | 8892209 | a | 0 | + | | chr22 | 9380771 | 9388640 | a | 0 | - | | chrM | 8555127 | 8556190 | 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/tmpn2vemrl5/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 83888 89539 - 1 chr1 218694 219499 - 1 chr1 3159003 3163201 + 1 chr1 4708408 4717601 + 1 chr1 4784584 4792047 + 1 chr1 7305986 7308189 + 1 chr1 9171177 9175540 + 1 chr13 1597497 1605615 - 1 chr19 8885154 8892209 + 1 chr22 9380771 9388640 - 1 chrM 8555127 8556190 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 83888 89539 - 1 1 chr1 218694 219499 - 1 2 chr1 3159003 3163201 + 1 3 chr1 4708408 4717601 + 1 4 chr1 4784584 4792047 + 1 5 chr1 7305986 7308189 + 1 6 chr1 9171177 9175540 + 1 7 chr13 1597497 1605615 - 1 8 chr19 8885154 8892209 + 1 9 chr22 9380771 9388640 - 1 10 chrM 8555127 8556190 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3902965 | 3906372 | a | 0 | + | | chr1 | 8527104 | 8535817 | a | 0 | + | | chr1 | 1408656 | 1416458 | a | 0 | + | | chr6 | 2560759 | 2565873 | a | 0 | + | | chr10 | 7959249 | 7963887 | a | 0 | + | | chr17 | 8594066 | 8596207 | 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/tmpwc1nm080/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1408656 1416458 + 1 chr1 3902965 3906372 + 1 chr1 8527104 8535817 + 1 chr10 7959249 7963887 + 1 chr17 8594066 8596207 + 1 chr6 2560759 2565873 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1408656 1416458 + 1 1 chr1 3902965 3906372 + 1 2 chr1 8527104 8535817 + 1 3 chr10 7959249 7963887 + 1 4 chr17 8594066 8596207 + 1 5 chr6 2560759 2565873 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9134729 | 9138653 | a | 0 | + | | chr2 | 5350221 | 5358029 | 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/tmpwh26ot3j/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 9134729 9138653 + 1 chr2 5350221 5358029 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 9134729 9138653 + 1 1 chr2 5350221 5358029 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7428668 | 7429648 | a | 0 | + | | chr1 | 4109492 | 4112805 | a | 0 | + | | chr1 | 1450148 | 1457018 | a | 0 | + | | chr1 | 9062653 | 9068312 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 1450148 | 1457018 | a | 0 | + | | chr1 | 9062653 | 9068312 | a | 0 | - | | chr1 | 2 | 7648 | a | 0 | - | | chr1 | 8768758 | 8769456 | 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/tmpbdbpmeuv/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2 7648 - 1 chr1 1450148 1457018 + 1 chr1 4109492 4112805 + 1 chr1 7428668 7429648 + 1 chr1 8768758 8769456 - 1 chr1 9062653 9068312 - 1 chr3 3176515 3178799 - 1 chr9 9711387 9714930 - 1 chrX 4311091 4315053 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2 7648 - 1 1 chr1 1450148 1457018 + 1 2 chr1 4109492 4112805 + 1 3 chr1 7428668 7429648 + 1 4 chr1 8768758 8769456 - 1 5 chr1 9062653 9068312 - 1 6 chr3 3176515 3178799 - 1 7 chr9 9711387 9714930 - 1 8 chrX 4311091 4315053 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7531733 | 7534949 | a | 0 | + | | chr1 | 9820449 | 9828979 | a | 0 | + | | chr1 | 7270101 | 7274228 | a | 0 | + | | chr1 | 609425 | 618796 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr2 | 8704747 | 8710921 | a | 0 | + | | chr11 | 3230505 | 3239587 | a | 0 | + | | chr14 | 9673175 | 9673934 | a | 0 | - | | chr15 | 9999999 | 10008267 | 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 -s -i <(sort -k1,1 -k2,2n /tmp/tmpzljmekc0/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 609425 618796 + 1 chr1 6187619 6195034 - 1 chr1 7270101 7274228 + 1 chr1 7531733 7534949 + 1 chr1 9820449 9828979 + 1 chr11 3230505 3239587 + 1 chr14 9673175 9673934 - 1 chr15 9999999 10008267 + 1 chr2 8704747 8710921 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 609425 618796 + 1 1 chr1 6187619 6195034 - 1 2 chr1 7270101 7274228 + 1 3 chr1 7531733 7534949 + 1 4 chr1 9820449 9828979 + 1 5 chr11 3230505 3239587 + 1 6 chr14 9673175 9673934 - 1 7 chr15 9999999 10008267 + 1 8 chr2 8704747 8710921 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2041915 | 2047691 | a | 0 | + | | chr19 | 9999999 | 10007520 | a | 0 | + | | chr19 | 5079939 | 5084237 | a | 0 | + | | chr19 | 9296145 | 9305992 | a | 0 | + | | chr19 | 4513984 | 4519711 | a | 0 | + | | chr19 | 2681162 | 2687922 | a | 0 | - | | chr19 | 1571321 | 1577931 | 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/tmplujb4nmg/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2041915 2047691 + 1 chr19 1571321 1577931 - 1 chr19 2681162 2687922 - 1 chr19 4513984 4519711 + 1 chr19 5079939 5084237 + 1 chr19 9296145 9305992 + 1 chr19 9999999 10007520 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2041915 2047691 + 1 1 chr19 1571321 1577931 - 1 2 chr19 2681162 2687922 - 1 3 chr19 4513984 4519711 + 1 4 chr19 5079939 5084237 + 1 5 chr19 9296145 9305992 + 1 6 chr19 9999999 10007520 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr6 | 2924839 | 2931749 | 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/tmpp2m4ynoc/f1.bed) resultresultresultresultresultresultresultresultresultresult chr6 2924839 2931749 - 1 bedtools_df Chromosome Start End Strand Count 0 chr6 2924839 2931749 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7866720 | 7874546 | a | 0 | + | | chr1 | 5305160 | 5312661 | a | 0 | - | | chr6 | 921163 | 923253 | a | 0 | + | | chr6 | 1234914 | 1243529 | a | 0 | - | | chr13 | 3730455 | 3734017 | 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 -s -i <(sort -k1,1 -k2,2n /tmp/tmp7m70a5d7/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5305160 5312661 - 1 chr1 7866720 7874546 + 1 chr13 3730455 3734017 + 1 chr6 921163 923253 + 1 chr6 1234914 1243529 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 5305160 5312661 - 1 1 chr1 7866720 7874546 + 1 2 chr13 3730455 3734017 + 1 3 chr6 921163 923253 + 1 4 chr6 1234914 1243529 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5715755 | 5724403 | a | 0 | + | | chr1 | 9339998 | 9344668 | 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/tmpd0u76ybk/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5715755 5724403 + 1 chr1 9339998 9344668 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 5715755 5724403 + 1 1 chr1 9339998 9344668 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5619160 | 5625330 | a | 0 | + | | chr1 | 3226070 | 3226071 | a | 0 | + | | chr1 | 1 | 5347 | a | 0 | + | | chr1 | 4166021 | 4173114 | a | 0 | + | | chr1 | 7513866 | 7520520 | a | 0 | + | | chr1 | 2798066 | 2802055 | a | 0 | + | | chr1 | 212822 | 214284 | 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/tmps4o1zdgr/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 5347 + 1 chr1 212822 214284 + 1 chr1 2798066 2802055 + 1 chr1 3226070 3226071 + 1 chr1 4166021 4173114 + 1 chr1 5619160 5625330 + 1 chr1 7513866 7520520 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 5347 + 1 1 chr1 212822 214284 + 1 2 chr1 2798066 2802055 + 1 3 chr1 3226070 3226071 + 1 4 chr1 4166021 4173114 + 1 5 chr1 5619160 5625330 + 1 6 chr1 7513866 7520520 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1967017 | 1972952 | a | 0 | - | | chrX | 7022219 | 7031012 | 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/tmpm_flcwp4/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1967017 1972952 - 1 chrX 7022219 7031012 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1967017 1972952 - 1 1 chrX 7022219 7031012 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6006861 | 6015358 | a | 0 | + | | chr1 | 2233660 | 2238147 | a | 0 | - | | chr1 | 9996610 | 10000565 | a | 0 | - | | chr1 | 7049713 | 7051352 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr12 | 3695141 | 3699054 | a | 0 | + | | chr14 | 1068054 | 1071580 | a | 0 | - | | chr15 | 7177155 | 7185415 | a | 0 | - | | chrM | 8565518 | 8574773 | 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/tmppaeg9vvx/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2233660 2238147 - 1 chr1 5889816 5895545 - 1 chr1 6006861 6015358 + 1 chr1 7049713 7051352 - 1 chr1 9996610 10000565 - 1 chr12 3695141 3699054 + 1 chr14 1068054 1071580 - 1 chr15 7177155 7185415 - 1 chr9 2983299 2988642 + 1 chr9 5006614 5008894 + 1 chrM 8565518 8574773 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2233660 2238147 - 1 1 chr1 5889816 5895545 - 1 2 chr1 6006861 6015358 + 1 3 chr1 7049713 7051352 - 1 4 chr1 9996610 10000565 - 1 5 chr12 3695141 3699054 + 1 6 chr14 1068054 1071580 - 1 7 chr15 7177155 7185415 - 1 8 chr9 2983299 2988642 + 1 9 chr9 5006614 5008894 + 1 10 chrM 8565518 8574773 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9135317 | 9138363 | a | 0 | + | | chr1 | 7796062 | 7796678 | a | 0 | + | | chr1 | 9999999 | 10003137 | a | 0 | + | | chr1 | 2140000 | 2142571 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr9 | 1721313 | 1721486 | a | 0 | - | | chr15 | 1 | 5325 | a | 0 | - | | chr21 | 6728450 | 6737086 | a | 0 | + | | chrX | 3684269 | 3690128 | 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/tmpcwx3sk4t/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 314750 321715 - 1 chr1 2140000 2142571 + 1 chr1 6754727 6758569 - 1 chr1 7796062 7796678 + 1 chr1 9135317 9138363 + 1 chr1 9999999 10003137 + 1 chr15 1 5325 - 1 chr21 6728450 6737086 + 1 chr6 7401215 7405977 - 1 chr9 1721313 1721486 - 1 chrX 3684269 3690128 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 314750 321715 - 1 1 chr1 2140000 2142571 + 1 2 chr1 6754727 6758569 - 1 3 chr1 7796062 7796678 + 1 4 chr1 9135317 9138363 + 1 5 chr1 9999999 10003137 + 1 6 chr15 1 5325 - 1 7 chr21 6728450 6737086 + 1 8 chr6 7401215 7405977 - 1 9 chr9 1721313 1721486 - 1 10 chrX 3684269 3690128 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2618512 | 2626209 | a | 0 | - | | chr1 | 6861764 | 6861902 | a | 0 | - | | chr1 | 940374 | 947139 | a | 0 | - | | chr1 | 5084778 | 5089038 | a | 0 | - | | chr1 | 5589388 | 5589413 | a | 0 | - | | chr18 | 1929973 | 1933472 | 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/tmpfpb5col4/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 940374 947139 - 1 chr1 2618512 2626209 - 1 chr1 5084778 5089038 - 1 chr1 5589388 5589413 - 1 chr1 6861764 6861902 - 1 chr18 1929973 1933472 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 940374 947139 - 1 1 chr1 2618512 2626209 - 1 2 chr1 5084778 5089038 - 1 3 chr1 5589388 5589413 - 1 4 chr1 6861764 6861902 - 1 5 chr18 1929973 1933472 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7115428 | 7119010 | a | 0 | + | | chr1 | 2267168 | 2269170 | a | 0 | + | | chr1 | 8852367 | 8853463 | a | 0 | - | | chr1 | 3160681 | 3170655 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chrX | 1920090 | 1926596 | a | 0 | + | | chrX | 2915992 | 2922553 | a | 0 | - | | chrX | 7143049 | 7152671 | a | 0 | - | | chrX | 1074702 | 1084499 | 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/tmptx6qlfl2/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2267168 2269170 + 1 chr1 3160681 3170655 - 1 chr1 7115428 7119010 + 1 chr1 8852367 8853463 - 1 chr12 4081765 4083469 + 1 chr7 5508126 5517079 + 1 chrX 758802 767551 + 1 chrX 1074702 1084499 - 1 chrX 1920090 1926596 + 1 chrX 2915992 2922553 - 1 chrX 7143049 7152671 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2267168 2269170 + 1 1 chr1 3160681 3170655 - 1 2 chr1 7115428 7119010 + 1 3 chr1 8852367 8853463 - 1 4 chr12 4081765 4083469 + 1 5 chr7 5508126 5517079 + 1 6 chrX 758802 767551 + 1 7 chrX 1074702 1084499 - 1 8 chrX 1920090 1926596 + 1 9 chrX 2915992 2922553 - 1 10 chrX 7143049 7152671 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 4415 | a | 0 | + | | chr1 | 1 | 4978 | a | 0 | + | | chr1 | 2 | 5297 | a | 0 | + | | chr10 | 10000000 | 10007886 | a | 0 | + | | chrM | 1 | 3945 | 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 -s -i <(sort -k1,1 -k2,2n /tmp/tmpijb38men/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 5297 + 3 chr10 10000000 10007886 + 1 chrM 1 3945 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 5297 + 3 1 chr10 10000000 10007886 + 1 2 chrM 1 3945 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6242144 | 6249695 | a | 0 | + | | chr1 | 3497735 | 3500871 | a | 0 | + | | chr1 | 7926983 | 7936957 | a | 0 | + | | chr1 | 4664956 | 4668084 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 8422540 | 8428874 | a | 0 | - | | chr1 | 7280505 | 7282033 | a | 0 | - | | chr1 | 4949544 | 4957621 | a | 0 | - | | chr1 | 9447260 | 9448488 | 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/tmp_hax7e44/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3497735 3500871 + 1 chr1 4664956 4668084 + 1 chr1 4949544 4957621 - 1 chr1 6242144 6249695 + 1 chr1 7280505 7282033 - 1 chr1 7926983 7936957 + 1 chr1 8422540 8428874 - 1 chr1 9447260 9448488 - 1 chr1 9649355 9652755 + 1 chr14 9802217 9803260 - 1 chr19 7669782 7678362 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 3497735 3500871 + 1 1 chr1 4664956 4668084 + 1 2 chr1 4949544 4957621 - 1 3 chr1 6242144 6249695 + 1 4 chr1 7280505 7282033 - 1 5 chr1 7926983 7936957 + 1 6 chr1 8422540 8428874 - 1 7 chr1 9447260 9448488 - 1 8 chr1 9649355 9652755 + 1 9 chr14 9802217 9803260 - 1 10 chr19 7669782 7678362 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4879070 | 4887437 | a | 0 | + | | chr1 | 1051839 | 1060206 | a | 0 | + | | chr1 | 349777 | 358144 | a | 0 | - | | chr1 | 1299639 | 1307837 | a | 0 | - | | chr1 | 9152126 | 9156569 | a | 0 | - | | chr1 | 527533 | 535900 | a | 0 | - | | chr1 | 7695393 | 7700033 | a | 0 | - | | chr1 | 631675 | 640042 | 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 merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpcbgrmknz/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 349777 358144 - 1 chr1 527533 535900 - 1 chr1 631675 640042 - 1 chr1 1051839 1060206 + 1 chr1 1299639 1307837 - 1 chr1 4879070 4887437 + 1 chr1 7695393 7700033 - 1 chr1 9152126 9156569 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 349777 358144 - 1 1 chr1 527533 535900 - 1 2 chr1 631675 640042 - 1 3 chr1 1051839 1060206 + 1 4 chr1 1299639 1307837 - 1 5 chr1 4879070 4887437 + 1 6 chr1 7695393 7700033 - 1 7 chr1 9152126 9156569 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7528601 | 7536803 | a | 0 | + | | chr1 | 5183803 | 5186270 | a | 0 | + | | chr1 | 7005143 | 7008762 | a | 0 | + | | chr1 | 7910494 | 7920494 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr15 | 1809284 | 1816149 | a | 0 | - | | chr17 | 1758736 | 1762452 | a | 0 | + | | chrM | 7528601 | 7532082 | a | 0 | + | | chrY | 4928417 | 4934771 | 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/tmpn5utkkp0/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5183803 5186270 + 1 chr1 5498480 5506015 - 1 chr1 7005143 7008762 + 1 chr1 7528601 7536803 + 1 chr1 7910494 7920494 - 1 chr12 8634708 8642624 + 1 chr15 1809284 1816149 - 1 chr17 1758736 1762452 + 1 chr7 988849 988851 + 1 chrM 7528601 7532082 + 1 chrY 4928417 4934771 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 5183803 5186270 + 1 1 chr1 5498480 5506015 - 1 2 chr1 7005143 7008762 + 1 3 chr1 7528601 7536803 + 1 4 chr1 7910494 7920494 - 1 5 chr12 8634708 8642624 + 1 6 chr15 1809284 1816149 - 1 7 chr17 1758736 1762452 + 1 8 chr7 988849 988851 + 1 9 chrM 7528601 7532082 + 1 10 chrY 4928417 4934771 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8849770 | 8854855 | a | 0 | + | | chr1 | 1809936 | 1815482 | a | 0 | + | | chr1 | 3145562 | 3153898 | a | 0 | + | | chr1 | 9871390 | 9871467 | a | 0 | + | | chr1 | 1 | 5973 | a | 0 | + | | chr4 | 2068362 | 2075855 | a | 0 | + | | chr22 | 4825785 | 4834486 | a | 0 | + | | chrM | 9246246 | 9248462 | 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/tmp86nnfl_b/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 5973 + 1 chr1 1809936 1815482 + 1 chr1 3145562 3153898 + 1 chr1 8849770 8854855 + 1 chr1 9871390 9871467 + 1 chr22 4825785 4834486 + 1 chr4 2068362 2075855 + 1 chrM 9246246 9248462 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 5973 + 1 1 chr1 1809936 1815482 + 1 2 chr1 3145562 3153898 + 1 3 chr1 8849770 8854855 + 1 4 chr1 9871390 9871467 + 1 5 chr22 4825785 4834486 + 1 6 chr4 2068362 2075855 + 1 7 chrM 9246246 9248462 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6544376 | 6546546 | a | 0 | + | | chr17 | 7228934 | 7238183 | 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/tmpi6ug6256/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6544376 6546546 + 1 chr17 7228934 7238183 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 6544376 6546546 + 1 1 chr17 7228934 7238183 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9539658 | 9549372 | a | 0 | + | | chr1 | 5970592 | 5979722 | a | 0 | + | | chr1 | 2656930 | 2666929 | a | 0 | + | | chr1 | 3402177 | 3408588 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr3 | 3402177 | 3404595 | a | 0 | - | | chr5 | 3530727 | 3535565 | a | 0 | - | | chr17 | 37677 | 44410 | a | 0 | - | | chr17 | 3402177 | 3408078 | 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/tmp027fl7sx/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1932161 1935385 + 1 chr1 2656930 2666929 + 1 chr1 3402177 3407103 - 1 chr1 3402177 3412025 + 2 chr1 5970592 5979722 + 1 chr1 9539658 9549372 + 1 chr17 37677 44410 - 1 chr17 3402177 3408078 - 1 chr3 3402177 3404595 - 1 chr5 3530727 3535565 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1932161 1935385 + 1 1 chr1 2656930 2666929 + 1 2 chr1 3402177 3407103 - 1 3 chr1 3402177 3412025 + 2 4 chr1 5970592 5979722 + 1 5 chr1 9539658 9549372 + 1 6 chr17 37677 44410 - 1 7 chr17 3402177 3408078 - 1 8 chr3 3402177 3404595 - 1 9 chr5 3530727 3535565 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5114036 | 5119010 | 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/tmp0b_0eij3/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5114036 5119010 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 5114036 5119010 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7573265 | 7582766 | a | 0 | + | | chr1 | 7573265 | 7578397 | a | 0 | - | | chr1 | 7573265 | 7577159 | a | 0 | - | | chr1 | 7573265 | 7574064 | a | 0 | - | | chr1 | 2056313 | 2064617 | a | 0 | - | | chr19 | 7573265 | 7577667 | a | 0 | + | | chrY | 7573265 | 7575823 | 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 merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpiz19h7mm/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2056313 2064617 - 1 chr1 7573265 7578397 - 3 chr1 7573265 7582766 + 1 chr19 7573265 7577667 + 1 chrY 7573265 7575823 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2056313 2064617 - 1 1 chr1 7573265 7578397 - 3 2 chr1 7573265 7582766 + 1 3 chr19 7573265 7577667 + 1 4 chrY 7573265 7575823 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr21 | 1272887 | 1273754 | 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/tmplsrc7gnk/f1.bed) resultresultresultresultresultresultresultresultresultresult chr21 1272887 1273754 + 1 bedtools_df Chromosome Start End Strand Count 0 chr21 1272887 1273754 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7181659 | 7183071 | a | 0 | + | | chr1 | 9200164 | 9209836 | a | 0 | - | | chr3 | 5656998 | 5666388 | a | 0 | + | | chr5 | 2032993 | 2038022 | a | 0 | + | | chr11 | 8402064 | 8410692 | a | 0 | - | | chr13 | 6069577 | 6076667 | a | 0 | + | | chrX | 3023474 | 3027620 | 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/tmpuq5k_onj/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7181659 7183071 + 1 chr1 9200164 9209836 - 1 chr11 8402064 8410692 - 1 chr13 6069577 6076667 + 1 chr3 5656998 5666388 + 1 chr5 2032993 2038022 + 1 chrX 3023474 3027620 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 7181659 7183071 + 1 1 chr1 9200164 9209836 - 1 2 chr11 8402064 8410692 - 1 3 chr13 6069577 6076667 + 1 4 chr3 5656998 5666388 + 1 5 chr5 2032993 2038022 + 1 6 chrX 3023474 3027620 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2598763 | 2606181 | a | 0 | + | | chr1 | 9611516 | 9620474 | a | 0 | - | | chr1 | 8275041 | 8279705 | a | 0 | - | | chr1 | 9491982 | 9501570 | a | 0 | - | | chr1 | 3743518 | 3747401 | a | 0 | - | | chr7 | 9037084 | 9043607 | a | 0 | - | | chr11 | 8175509 | 8183042 | a | 0 | + | | chr12 | 4505937 | 4506846 | 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/tmpxc7db4yn/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2598763 2606181 + 1 chr1 3743518 3747401 - 1 chr1 8275041 8279705 - 1 chr1 9491982 9501570 - 1 chr1 9611516 9620474 - 1 chr11 8175509 8183042 + 1 chr12 4505937 4506846 - 1 chr7 9037084 9043607 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2598763 2606181 + 1 1 chr1 3743518 3747401 - 1 2 chr1 8275041 8279705 - 1 3 chr1 9491982 9501570 - 1 4 chr1 9611516 9620474 - 1 5 chr11 8175509 8183042 + 1 6 chr12 4505937 4506846 - 1 7 chr7 9037084 9043607 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7661748 | 7667858 | a | 0 | + | | chr1 | 5550338 | 5550339 | a | 0 | + | | chr1 | 10000000 | 10010000 | a | 0 | + | | chr1 | 7648462 | 7655256 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr10 | 3351972 | 3361126 | a | 0 | + | | chr12 | 6739941 | 6741393 | a | 0 | - | | chr15 | 1924148 | 1932089 | a | 0 | + | | chr22 | 1616613 | 1617054 | 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/tmpgx8yq8k1/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5550338 5550339 + 1 chr1 5970275 5970276 - 1 chr1 7648462 7655256 + 1 chr1 7661748 7667858 + 1 chr1 10000000 10010000 + 1 chr10 3351972 3361126 + 1 chr12 6739941 6741393 - 1 chr15 1924148 1932089 + 1 chr22 1616613 1617054 - 1 chr7 7722510 7723126 + 1 chr8 9299347 9303341 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 5550338 5550339 + 1 1 chr1 5970275 5970276 - 1 2 chr1 7648462 7655256 + 1 3 chr1 7661748 7667858 + 1 4 chr1 10000000 10010000 + 1 5 chr10 3351972 3361126 + 1 6 chr12 6739941 6741393 - 1 7 chr15 1924148 1932089 + 1 8 chr22 1616613 1617054 - 1 9 chr7 7722510 7723126 + 1 10 chr8 9299347 9303341 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3935281 | 3936393 | a | 0 | + | | chr1 | 3143571 | 3144057 | a | 0 | + | | chr1 | 1471884 | 1473762 | a | 0 | - | | chr1 | 1 | 3264 | a | 0 | - | | chr22 | 3143571 | 3146716 | a | 0 | + | | chr22 | 7282817 | 7286248 | a | 0 | - | | chrM | 3143571 | 3153258 | 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 merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpqtc0bhmf/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 3264 - 1 chr1 1471884 1473762 - 1 chr1 3143571 3144057 + 1 chr1 3935281 3936393 + 1 chr22 3143571 3146716 + 1 chr22 7282817 7286248 - 1 chrM 3143571 3153258 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 3264 - 1 1 chr1 1471884 1473762 - 1 2 chr1 3143571 3144057 + 1 3 chr1 3935281 3936393 + 1 4 chr22 3143571 3146716 + 1 5 chr22 7282817 7286248 - 1 6 chrM 3143571 3153258 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9877318 | 9883966 | a | 0 | + | | chr1 | 9877318 | 9881321 | 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/tmpiq_q6qwj/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 9877318 9883966 + 2 bedtools_df Chromosome Start End Strand Count 0 chr1 9877318 9883966 + 2 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3560055 | 3561585 | a | 0 | - | | chr12 | 3560055 | 3560392 | a | 0 | - | | chr17 | 3560055 | 3565738 | 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/tmpl7c9ap84/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3560055 3561585 - 1 chr12 3560055 3560392 - 1 chr17 3560055 3565738 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 3560055 3561585 - 1 1 chr12 3560055 3560392 - 1 2 chr17 3560055 3565738 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6698547 | 6698548 | a | 0 | - | | chr1 | 6041949 | 6046091 | a | 0 | - | | chr1 | 8203131 | 8209484 | a | 0 | - | | chr1 | 3500319 | 3505908 | a | 0 | - | | chr15 | 5301327 | 5304191 | a | 0 | - | | chr15 | 6698547 | 6706221 | 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/tmpf062l320/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3500319 3505908 - 1 chr1 6041949 6046091 - 1 chr1 6698547 6698548 - 1 chr1 8203131 8209484 - 1 chr15 5301327 5304191 - 1 chr15 6698547 6706221 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 3500319 3505908 - 1 1 chr1 6041949 6046091 - 1 2 chr1 6698547 6698548 - 1 3 chr1 8203131 8209484 - 1 4 chr15 5301327 5304191 - 1 5 chr15 6698547 6706221 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9937690 | 9938304 | a | 0 | + | | chr1 | 6691106 | 6694932 | a | 0 | + | | chr1 | 2839630 | 2846150 | a | 0 | - | | chr1 | 1260504 | 1269361 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 1260504 | 1269361 | a | 0 | - | | chr1 | 41303 | 42402 | a | 0 | - | | chr1 | 1237683 | 1239759 | a | 0 | - | | chr1 | 1260504 | 1260853 | 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/tmp8iz2109j/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 41303 42402 - 1 chr1 1237683 1239759 - 1 chr1 1260504 1269361 - 2 chr1 2839630 2846150 - 1 chr1 6691106 6694932 + 1 chr1 9937690 9938304 + 1 chr11 8452794 8454803 + 1 chr7 2007800 2017800 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 41303 42402 - 1 1 chr1 1237683 1239759 - 1 2 chr1 1260504 1269361 - 2 3 chr1 2839630 2846150 - 1 4 chr1 6691106 6694932 + 1 5 chr1 9937690 9938304 + 1 6 chr11 8452794 8454803 + 1 7 chr7 2007800 2017800 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 543129 | 546807 | a | 0 | + | | chr1 | 9265358 | 9271553 | a | 0 | + | | chr1 | 6862858 | 6872772 | a | 0 | + | | chr1 | 806912 | 807314 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr11 | 9623738 | 9628210 | a | 0 | + | | chr16 | 4468702 | 4470101 | a | 0 | + | | chr20 | 1337790 | 1347754 | a | 0 | - | | chrY | 6399423 | 6409073 | 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/tmp21v5bd1d/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 344659 346972 - 1 chr1 543129 546807 + 1 chr1 565911 568038 - 1 chr1 806912 807314 - 1 chr1 5185175 5188803 - 1 chr1 6862858 6872772 + 1 chr1 9265358 9271553 + 1 chr11 9623738 9628210 + 1 chr16 4468702 4470101 + 1 chr20 1337790 1347754 - 1 chrY 6399423 6409073 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 344659 346972 - 1 1 chr1 543129 546807 + 1 2 chr1 565911 568038 - 1 3 chr1 806912 807314 - 1 4 chr1 5185175 5188803 - 1 5 chr1 6862858 6872772 + 1 6 chr1 9265358 9271553 + 1 7 chr11 9623738 9628210 + 1 8 chr16 4468702 4470101 + 1 9 chr20 1337790 1347754 - 1 10 chrY 6399423 6409073 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 321333 | 323622 | a | 0 | + | | chr1 | 1 | 2290 | a | 0 | - | | chr1 | 2220568 | 2222857 | a | 0 | - | | chr1 | 1 | 2290 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr14 | 4325321 | 4327610 | a | 0 | - | | chr17 | 8840466 | 8842755 | a | 0 | - | | chr20 | 8377914 | 8380203 | a | 0 | - | | chrX | 1 | 2290 | 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/tmpvm3mffcu/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2290 - 2 chr1 321333 323622 + 1 chr1 2220568 2222857 - 1 chr14 4325321 4327610 - 1 chr17 8840466 8842755 - 1 chr20 8377914 8380203 - 1 chr4 2759734 2762023 - 1 chr5 8146316 8148605 - 1 chr7 9430307 9434315 + 1 chrX 1 2290 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2290 - 2 1 chr1 321333 323622 + 1 2 chr1 2220568 2222857 - 1 3 chr14 4325321 4327610 - 1 4 chr17 8840466 8842755 - 1 5 chr20 8377914 8380203 - 1 6 chr4 2759734 2762023 - 1 7 chr5 8146316 8148605 - 1 8 chr7 9430307 9434315 + 1 9 chrX 1 2290 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr9 | 9165327 | 9165594 | a | 0 | - | | chr21 | 2516924 | 2523246 | 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/tmpfmvx5577/f1.bed) resultresultresultresultresultresultresultresultresultresult chr21 2516924 2523246 - 1 chr9 9165327 9165594 - 1 bedtools_df Chromosome Start End Strand Count 0 chr21 2516924 2523246 - 1 1 chr9 9165327 9165594 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 111134 | 114993 | a | 0 | + | | chr1 | 111134 | 115666 | a | 0 | + | | chr1 | 111134 | 116351 | 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/tmpscie1vp6/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 111134 115666 + 2 chr1 111134 116351 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 111134 115666 + 2 1 chr1 111134 116351 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7047656 | 7047760 | a | 0 | + | | chr1 | 7763485 | 7768863 | a | 0 | + | | chr1 | 7047656 | 7057656 | a | 0 | + | | chr1 | 7047656 | 7050268 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 7047656 | 7056194 | a | 0 | - | | chr1 | 7047656 | 7054674 | a | 0 | - | | chr1 | 7047656 | 7049566 | a | 0 | - | | chr1 | 7047656 | 7055779 | 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 merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpiwksiuaf/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7047656 7057656 + 2 chr1 7047656 7056194 - 5 chr1 7763485 7768863 + 1 chr22 7047656 7051788 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 7047656 7057656 + 2 1 chr1 7047656 7056194 - 5 2 chr1 7763485 7768863 + 1 3 chr22 7047656 7051788 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7325894 | 7331009 | a | 0 | + | | chr1 | 560654 | 568741 | a | 0 | + | | chr1 | 7248217 | 7254710 | a | 0 | + | | chr1 | 7989552 | 7994473 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr10 | 10000000 | 10002395 | a | 0 | - | | chr19 | 3979008 | 3979009 | a | 0 | - | | chr19 | 5740536 | 5745568 | a | 0 | - | | chr22 | 5254123 | 5259675 | 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/tmpkk8gj4m6/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 33496 38632 - 1 chr1 560654 568741 + 1 chr1 7248217 7254710 + 1 chr1 7325894 7331009 + 1 chr1 7989552 7994473 + 1 chr10 10000000 10002395 - 1 chr19 3979008 3979009 - 1 chr19 5740536 5745568 - 1 chr22 5254123 5259675 - 1 chr4 6839869 6842374 - 1 chr8 8069724 8074845 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 33496 38632 - 1 1 chr1 560654 568741 + 1 2 chr1 7248217 7254710 + 1 3 chr1 7325894 7331009 + 1 4 chr1 7989552 7994473 + 1 5 chr10 10000000 10002395 - 1 6 chr19 3979008 3979009 - 1 7 chr19 5740536 5745568 - 1 8 chr22 5254123 5259675 - 1 9 chr4 6839869 6842374 - 1 10 chr8 8069724 8074845 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5859261 | 5863845 | a | 0 | + | | chr1 | 7657732 | 7659370 | a | 0 | - | | chr1 | 2564188 | 2567999 | a | 0 | - | | chr1 | 7786027 | 7789630 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr5 | 169701 | 173229 | a | 0 | + | | chr5 | 5133704 | 5140696 | a | 0 | - | | chr8 | 5639826 | 5639827 | a | 0 | + | | chr18 | 7758944 | 7762112 | 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/tmprcc3g7g5/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2564188 2567999 - 1 chr1 3934501 3942583 - 1 chr1 5859261 5863845 + 1 chr1 6223398 6233324 - 1 chr1 7657732 7659370 - 1 chr1 7786027 7789630 - 1 chr18 7758944 7762112 - 1 chr2 9056732 9060507 + 1 chr5 169701 173229 + 1 chr5 5133704 5140696 - 1 chr8 5639826 5639827 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2564188 2567999 - 1 1 chr1 3934501 3942583 - 1 2 chr1 5859261 5863845 + 1 3 chr1 6223398 6233324 - 1 4 chr1 7657732 7659370 - 1 5 chr1 7786027 7789630 - 1 6 chr18 7758944 7762112 - 1 7 chr2 9056732 9060507 + 1 8 chr5 169701 173229 + 1 9 chr5 5133704 5140696 - 1 10 chr8 5639826 5639827 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4506944 | 4507406 | a | 0 | + | | chr1 | 2 | 8061 | a | 0 | - | | chr1 | 1212013 | 1219622 | a | 0 | - | | chr1 | 5952296 | 5952662 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr18 | 4396400 | 4406248 | a | 0 | - | | chr22 | 8348226 | 8349076 | a | 0 | - | | chrX | 9579926 | 9588229 | a | 0 | + | | chrX | 325343 | 329223 | 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/tmpp7td72mi/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2 8061 - 1 chr1 1212013 1219622 - 1 chr1 4506944 4507406 + 1 chr1 5952296 5952662 - 1 chr1 8663268 8665826 - 1 chr10 7080219 7087679 - 1 chr18 4396400 4406248 - 1 chr22 8348226 8349076 - 1 chrX 325343 329223 + 1 chrX 9579926 9588229 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2 8061 - 1 1 chr1 1212013 1219622 - 1 2 chr1 4506944 4507406 + 1 3 chr1 5952296 5952662 - 1 4 chr1 8663268 8665826 - 1 5 chr10 7080219 7087679 - 1 6 chr18 4396400 4406248 - 1 7 chr22 8348226 8349076 - 1 8 chrX 325343 329223 + 1 9 chrX 9579926 9588229 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4723522 | 4726640 | 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/tmplf4bq76_/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4723522 4726640 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4723522 4726640 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 104143 | 113801 | a | 0 | + | | chr1 | 4082624 | 4084323 | a | 0 | - | | chr1 | 6262555 | 6266972 | a | 0 | - | | chr4 | 4082624 | 4083353 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr12 | 4082624 | 4083330 | a | 0 | + | | chr15 | 4082624 | 4090730 | a | 0 | + | | chr20 | 3118983 | 3121093 | a | 0 | - | | chr21 | 2216887 | 2222246 | 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/tmp6035ix82/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 104143 113801 + 1 chr1 4082624 4084323 - 1 chr1 6262555 6266972 - 1 chr12 4082624 4083330 + 1 chr15 4082624 4090730 + 1 chr20 3118983 3121093 - 1 chr21 2216887 2222246 - 1 chr4 3762530 3772490 - 1 chr4 4082624 4083353 - 1 chr5 4082624 4092455 + 1 chr6 4082624 4089675 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 104143 113801 + 1 1 chr1 4082624 4084323 - 1 2 chr1 6262555 6266972 - 1 3 chr12 4082624 4083330 + 1 4 chr15 4082624 4090730 + 1 5 chr20 3118983 3121093 - 1 6 chr21 2216887 2222246 - 1 7 chr4 3762530 3772490 - 1 8 chr4 4082624 4083353 - 1 9 chr5 4082624 4092455 + 1 10 chr6 4082624 4089675 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4299549 | 4305386 | a | 0 | + | | chr6 | 9194230 | 9198395 | 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/tmp_fsn4hj0/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4299549 4305386 + 1 chr6 9194230 9198395 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4299549 4305386 + 1 1 chr6 9194230 9198395 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9999999 | 10002764 | a | 0 | + | | chr1 | 9999999 | 10005998 | a | 0 | + | | chr1 | 9999999 | 10009436 | a | 0 | + | | chr1 | 4768188 | 4775986 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 251498 | 252494 | a | 0 | + | | chr1 | 9999999 | 10004150 | a | 0 | - | | chr1 | 9999999 | 10006071 | a | 0 | - | | chr1 | 997644 | 1000090 | 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 merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpt18ft985/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 251498 252494 + 1 chr1 997644 1000090 - 1 chr1 4768188 4775986 + 1 chr1 9999999 10009436 + 3 chr1 9999999 10006071 - 2 chr11 5395267 5405148 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 251498 252494 + 1 1 chr1 997644 1000090 - 1 2 chr1 4768188 4775986 + 1 3 chr1 9999999 10009436 + 3 4 chr1 9999999 10006071 - 2 5 chr11 5395267 5405148 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7091619 | 7096389 | a | 0 | + | | chr1 | 277487 | 280436 | a | 0 | + | | chr1 | 4377337 | 4386413 | a | 0 | + | | chr1 | 2877130 | 2877132 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr7 | 260019 | 261121 | a | 0 | - | | chr10 | 5087066 | 5094427 | a | 0 | + | | chr13 | 2485786 | 2490419 | a | 0 | + | | chr13 | 2285090 | 2288094 | 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/tmpo5okh1wk/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 3103 - 1 chr1 277487 280436 + 1 chr1 975030 985030 - 1 chr1 2054228 2057080 - 1 chr1 2877130 2877132 + 1 chr1 4377337 4386413 + 1 chr1 7091619 7096389 + 1 chr10 5087066 5094427 + 1 chr13 2285090 2288094 - 1 chr13 2485786 2490419 + 1 chr7 260019 261121 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 3103 - 1 1 chr1 277487 280436 + 1 2 chr1 975030 985030 - 1 3 chr1 2054228 2057080 - 1 4 chr1 2877130 2877132 + 1 5 chr1 4377337 4386413 + 1 6 chr1 7091619 7096389 + 1 7 chr10 5087066 5094427 + 1 8 chr13 2285090 2288094 - 1 9 chr13 2485786 2490419 + 1 10 chr7 260019 261121 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr7 | 6412350 | 6415248 | 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/tmpe7afblsd/f1.bed) resultresultresultresultresultresultresultresultresultresult chr7 6412350 6415248 - 1 bedtools_df Chromosome Start End Strand Count 0 chr7 6412350 6415248 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8851456 | 8854751 | a | 0 | + | | chr1 | 3610496 | 3618241 | a | 0 | + | | chr1 | 9276911 | 9284656 | a | 0 | + | | chr1 | 9312919 | 9320664 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr3 | 8851456 | 8859201 | a | 0 | + | | chr3 | 4574859 | 4582604 | a | 0 | - | | chr10 | 4147723 | 4155468 | a | 0 | + | | chr12 | 3703276 | 3711021 | 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/tmpy1lz3n7u/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 943785 951530 + 1 chr1 3563523 3567570 + 1 chr1 3610496 3618241 + 1 chr1 8851456 8854751 + 1 chr1 9276911 9284656 + 1 chr1 9312919 9320664 + 1 chr10 4147723 4155468 + 1 chr12 3703276 3711021 + 1 chr3 4574859 4582604 - 1 chr3 8851456 8859201 + 1 chrM 8054013 8061758 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 943785 951530 + 1 1 chr1 3563523 3567570 + 1 2 chr1 3610496 3618241 + 1 3 chr1 8851456 8854751 + 1 4 chr1 9276911 9284656 + 1 5 chr1 9312919 9320664 + 1 6 chr10 4147723 4155468 + 1 7 chr12 3703276 3711021 + 1 8 chr3 4574859 4582604 - 1 9 chr3 8851456 8859201 + 1 10 chrM 8054013 8061758 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 77013 | 80603 | a | 0 | + | | chr1 | 251437 | 258225 | a | 0 | + | | chr1 | 5195822 | 5200315 | a | 0 | + | | chr1 | 6797876 | 6805292 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 9567644 | 9571043 | a | 0 | + | | chr1 | 77013 | 78920 | a | 0 | + | | chr1 | 5481256 | 5483452 | a | 0 | - | | chr1 | 6372390 | 6373069 | 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/tmp1_6v2rtw/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 77013 80603 + 2 chr1 251437 258225 + 1 chr1 5195822 5200315 + 1 chr1 5481256 5483452 - 1 chr1 6372390 6373069 - 1 chr1 6797876 6805292 + 1 chr1 9567644 9571043 + 1 chr15 5166724 5167943 - 1 chr4 77013 81875 + 1 chrY 77013 82926 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 77013 80603 + 2 1 chr1 251437 258225 + 1 2 chr1 5195822 5200315 + 1 3 chr1 5481256 5483452 - 1 4 chr1 6372390 6373069 - 1 5 chr1 6797876 6805292 + 1 6 chr1 9567644 9571043 + 1 7 chr15 5166724 5167943 - 1 8 chr4 77013 81875 + 1 9 chrY 77013 82926 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4264930 | 4271372 | a | 0 | + | | chr1 | 4865495 | 4867059 | a | 0 | + | | chr1 | 9138840 | 9144377 | a | 0 | + | | chr1 | 1587193 | 1592730 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr6 | 9138840 | 9144556 | a | 0 | - | | chr9 | 9138840 | 9139631 | a | 0 | + | | chr10 | 696292 | 701844 | a | 0 | + | | chr17 | 4364044 | 4364102 | 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/tmpkgq5wz6z/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 155139 162403 + 1 chr1 1587193 1592730 + 1 chr1 4062991 4072425 - 1 chr1 4264930 4271372 + 1 chr1 4865495 4867059 + 1 chr1 9138840 9144377 + 1 chr1 9138840 9147329 - 1 chr10 696292 701844 + 1 chr17 4364044 4364102 + 1 chr6 9138840 9144556 - 1 chr9 9138840 9139631 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 155139 162403 + 1 1 chr1 1587193 1592730 + 1 2 chr1 4062991 4072425 - 1 3 chr1 4264930 4271372 + 1 4 chr1 4865495 4867059 + 1 5 chr1 9138840 9144377 + 1 6 chr1 9138840 9147329 - 1 7 chr10 696292 701844 + 1 8 chr17 4364044 4364102 + 1 9 chr6 9138840 9144556 - 1 10 chr9 9138840 9139631 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 171496 | 174017 | 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/tmp7c5450hr/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 171496 174017 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 171496 174017 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 7183 | 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/tmp2zst_ig2/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 7183 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 7183 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4021124 | 4029967 | a | 0 | + | | chr1 | 4021124 | 4022182 | a | 0 | + | | chr1 | 8326386 | 8326674 | a | 0 | + | | chr1 | 8161684 | 8162171 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr14 | 5202586 | 5207666 | a | 0 | - | | chr19 | 2632336 | 2634760 | a | 0 | + | | chr19 | 2191207 | 2198456 | a | 0 | + | | chr20 | 8797157 | 8804257 | 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/tmpexlnj96n/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1159923 1160905 - 1 chr1 4021124 4029967 + 2 chr1 4188740 4192569 + 1 chr1 8161684 8162171 + 1 chr1 8326386 8326674 + 1 chr14 5202586 5207666 - 1 chr19 2191207 2198456 + 1 chr19 2632336 2634760 + 1 chr20 8797157 8804257 + 1 chr4 1166463 1169723 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1159923 1160905 - 1 1 chr1 4021124 4029967 + 2 2 chr1 4188740 4192569 + 1 3 chr1 8161684 8162171 + 1 4 chr1 8326386 8326674 + 1 5 chr14 5202586 5207666 - 1 6 chr19 2191207 2198456 + 1 7 chr19 2632336 2634760 + 1 8 chr20 8797157 8804257 + 1 9 chr4 1166463 1169723 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8239682 | 8247670 | a | 0 | + | | chr1 | 6347586 | 6349564 | a | 0 | + | | chr1 | 5464670 | 5473973 | a | 0 | + | | chr1 | 2400681 | 2410681 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 5464670 | 5471453 | a | 0 | - | | chr1 | 4855169 | 4859829 | a | 0 | - | | chr1 | 5464670 | 5468031 | a | 0 | - | | chr1 | 4085428 | 4089879 | 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/tmppepul1r4/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2400681 2410681 + 1 chr1 4085428 4089879 - 1 chr1 4855169 4859829 - 1 chr1 5464670 5471453 - 3 chr1 5464670 5473973 + 1 chr1 6347586 6349564 + 1 chr1 8239682 8247670 + 1 chr20 5464670 5464671 - 1 chr5 614343 617655 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2400681 2410681 + 1 1 chr1 4085428 4089879 - 1 2 chr1 4855169 4859829 - 1 3 chr1 5464670 5471453 - 3 4 chr1 5464670 5473973 + 1 5 chr1 6347586 6349564 + 1 6 chr1 8239682 8247670 + 1 7 chr20 5464670 5464671 - 1 8 chr5 614343 617655 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8136788 | 8140241 | 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/tmpr7pld4j8/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 8136788 8140241 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 8136788 8140241 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4437595 | 4437960 | a | 0 | + | | chr1 | 2124944 | 2134943 | a | 0 | + | | chr1 | 265085 | 266991 | a | 0 | + | | chr1 | 9079535 | 9088658 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr10 | 9728849 | 9729657 | a | 0 | + | | chr11 | 6525579 | 6526179 | a | 0 | - | | chr16 | 8328086 | 8328363 | a | 0 | - | | chrM | 2714907 | 2723772 | 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/tmpwvnly2ck/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 265085 266991 + 1 chr1 2124944 2134943 + 1 chr1 4437595 4437960 + 1 chr1 8303097 8312784 + 1 chr1 9079535 9088658 + 1 chr1 9181090 9184424 - 1 chr10 9728849 9729657 + 1 chr11 6525579 6526179 - 1 chr16 8328086 8328363 - 1 chr4 6182890 6183121 + 1 chrM 2714907 2723772 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 265085 266991 + 1 1 chr1 2124944 2134943 + 1 2 chr1 4437595 4437960 + 1 3 chr1 8303097 8312784 + 1 4 chr1 9079535 9088658 + 1 5 chr1 9181090 9184424 - 1 6 chr10 9728849 9729657 + 1 7 chr11 6525579 6526179 - 1 8 chr16 8328086 8328363 - 1 9 chr4 6182890 6183121 + 1 10 chrM 2714907 2723772 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3060467 | 3062610 | a | 0 | + | | chr2 | 3987111 | 3988647 | a | 0 | - | | chr6 | 1797492 | 1803849 | a | 0 | + | | chr9 | 9266042 | 9270890 | a | 0 | - | | chr13 | 9372104 | 9376773 | a | 0 | - | | chr14 | 9792956 | 9798315 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 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/tmp_3_qq034/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3060467 3062610 + 1 chr13 9372104 9376773 - 1 chr14 9792956 9798315 - 1 chr2 3987111 3988647 - 1 chr6 1797492 1803849 + 1 chr9 9266042 9270890 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 3060467 3062610 + 1 1 chr13 9372104 9376773 - 1 2 chr14 9792956 9798315 - 1 3 chr2 3987111 3988647 - 1 4 chr6 1797492 1803849 + 1 5 chr9 9266042 9270890 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3200452 | 3203586 | a | 0 | + | | chr1 | 3801990 | 3808651 | a | 0 | - | | chr1 | 1067283 | 1067677 | a | 0 | - | | chr1 | 5082132 | 5091245 | a | 0 | - | | chr1 | 6398670 | 6400050 | a | 0 | - | | chr16 | 8554278 | 8559756 | 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/tmp4l1ouc4j/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1067283 1067677 - 1 chr1 3200452 3203586 + 1 chr1 3801990 3808651 - 1 chr1 5082132 5091245 - 1 chr1 6398670 6400050 - 1 chr16 8554278 8559756 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1067283 1067677 - 1 1 chr1 3200452 3203586 + 1 2 chr1 3801990 3808651 - 1 3 chr1 5082132 5091245 - 1 4 chr1 6398670 6400050 - 1 5 chr16 8554278 8559756 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4400513 | 4400981 | a | 0 | + | | chr1 | 1601743 | 1606206 | a | 0 | + | | chr1 | 8314076 | 8314394 | a | 0 | + | | chr1 | 5198823 | 5206302 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr2 | 4461347 | 4467373 | a | 0 | - | | chr4 | 3089358 | 3096413 | a | 0 | - | | chr7 | 5571416 | 5573911 | a | 0 | + | | chr22 | 5198823 | 5203808 | 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/tmppje_lrrt/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1601743 1606206 + 1 chr1 3809323 3812895 - 1 chr1 4203082 4210817 - 1 chr1 4400513 4400981 + 1 chr1 5198823 5206302 + 1 chr1 8314076 8314394 + 1 chr1 10000000 10003993 - 1 chr2 4461347 4467373 - 1 chr22 5198823 5203808 + 1 chr4 3089358 3096413 - 1 chr7 5571416 5573911 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1601743 1606206 + 1 1 chr1 3809323 3812895 - 1 2 chr1 4203082 4210817 - 1 3 chr1 4400513 4400981 + 1 4 chr1 5198823 5206302 + 1 5 chr1 8314076 8314394 + 1 6 chr1 10000000 10003993 - 1 7 chr2 4461347 4467373 - 1 8 chr22 5198823 5203808 + 1 9 chr4 3089358 3096413 - 1 10 chr7 5571416 5573911 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8576814 | 8586748 | a | 0 | + | | chr1 | 9946246 | 9955472 | a | 0 | + | | chr1 | 913561 | 923560 | a | 0 | + | | chr1 | 1788187 | 1791232 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 9237188 | 9239545 | a | 0 | - | | chr1 | 8787886 | 8790411 | a | 0 | - | | chr1 | 8298485 | 8306891 | a | 0 | - | | chr1 | 8452680 | 8454659 | 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 -s -i <(sort -k1,1 -k2,2n /tmp/tmpr7ioeztk/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 913561 923560 + 1 chr1 1788187 1791232 + 1 chr1 5382121 5390828 + 1 chr1 7438260 7446989 - 1 chr1 8298485 8306891 - 1 chr1 8452680 8454659 - 1 chr1 8576814 8586748 + 1 chr1 8787886 8790411 - 1 chr1 9237188 9239545 - 1 chr1 9946246 9955472 + 1 chr22 2675365 2675951 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 913561 923560 + 1 1 chr1 1788187 1791232 + 1 2 chr1 5382121 5390828 + 1 3 chr1 7438260 7446989 - 1 4 chr1 8298485 8306891 - 1 5 chr1 8452680 8454659 - 1 6 chr1 8576814 8586748 + 1 7 chr1 8787886 8790411 - 1 8 chr1 9237188 9239545 - 1 9 chr1 9946246 9955472 + 1 10 chr22 2675365 2675951 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr16 | 3631673 | 3637742 | 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/tmptp3u89l5/f1.bed) resultresultresultresultresultresultresultresultresultresult chr16 3631673 3637742 - 1 bedtools_df Chromosome Start End Strand Count 0 chr16 3631673 3637742 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6958664 | 6961338 | a | 0 | + | | chr1 | 5939951 | 5939952 | a | 0 | + | | chr1 | 8795348 | 8802618 | a | 0 | + | | chr1 | 705946 | 713962 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr5 | 9002877 | 9006632 | a | 0 | + | | chr20 | 8156252 | 8164268 | a | 0 | + | | chrM | 7018772 | 7026788 | a | 0 | - | | chrM | 1909891 | 1917907 | 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/tmps06vk12a/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 705946 713962 + 1 chr1 705946 713962 - 1 chr1 5939951 5939952 + 1 chr1 6654075 6656013 - 1 chr1 6958664 6961338 + 1 chr1 8795348 8802618 + 1 chr20 8156252 8164268 + 1 chr4 7937680 7940483 + 1 chr5 9002877 9006632 + 1 chrM 1909891 1917907 - 1 chrM 7018772 7026788 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 705946 713962 + 1 1 chr1 705946 713962 - 1 2 chr1 5939951 5939952 + 1 3 chr1 6654075 6656013 - 1 4 chr1 6958664 6961338 + 1 5 chr1 8795348 8802618 + 1 6 chr20 8156252 8164268 + 1 7 chr4 7937680 7940483 + 1 8 chr5 9002877 9006632 + 1 9 chrM 1909891 1917907 - 1 10 chrM 7018772 7026788 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 10817 | 19791 | 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/tmpdkxjfs0d/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 10817 19791 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 10817 19791 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6805476 | 6807317 | a | 0 | + | | chr1 | 1427779 | 1431951 | a | 0 | + | | chr4 | 6807046 | 6815864 | a | 0 | + | | chr17 | 6684114 | 6689929 | a | 0 | + | | chr17 | 5049161 | 5054499 | a | 0 | - | | chrM | 6822177 | 6823813 | 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/tmpzl9cjzsg/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1427779 1431951 + 1 chr1 6805476 6807317 + 1 chr17 5049161 5054499 - 1 chr17 6684114 6689929 + 1 chr4 6807046 6815864 + 1 chrM 6822177 6823813 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1427779 1431951 + 1 1 chr1 6805476 6807317 + 1 2 chr17 5049161 5054499 - 1 3 chr17 6684114 6689929 + 1 4 chr4 6807046 6815864 + 1 5 chrM 6822177 6823813 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4012402 | 4017408 | a | 0 | + | | chr2 | 3411096 | 3411240 | a | 0 | + | | chrX | 416800 | 417363 | 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/tmpp7xrpx_2/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4012402 4017408 + 1 chr2 3411096 3411240 + 1 chrX 416800 417363 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4012402 4017408 + 1 1 chr2 3411096 3411240 + 1 2 chrX 416800 417363 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr9 | 5684034 | 5685136 | a | 0 | + | | chr9 | 1447310 | 1447640 | a | 0 | - | | chr9 | 6424136 | 6430432 | 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/tmpsk9i3hti/f1.bed) resultresultresultresultresultresultresultresultresultresult chr9 1447310 1447640 - 1 chr9 5684034 5685136 + 1 chr9 6424136 6430432 - 1 bedtools_df Chromosome Start End Strand Count 0 chr9 1447310 1447640 - 1 1 chr9 5684034 5685136 + 1 2 chr9 6424136 6430432 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5357029 | 5359624 | a | 0 | + | | chr1 | 9235002 | 9235538 | a | 0 | - | | chr1 | 4564059 | 4568816 | a | 0 | - | | chr6 | 9235002 | 9239115 | 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/tmp396rlpla/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4564059 4568816 - 1 chr1 5357029 5359624 + 1 chr1 9235002 9235538 - 1 chr6 9235002 9239115 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4564059 4568816 - 1 1 chr1 5357029 5359624 + 1 2 chr1 9235002 9235538 - 1 3 chr6 9235002 9239115 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5978432 | 5978524 | a | 0 | + | | chr1 | 4861767 | 4871300 | a | 0 | - | | chr1 | 5008583 | 5012858 | a | 0 | - | | chr1 | 5202041 | 5210589 | a | 0 | - | | chr3 | 6161561 | 6168511 | a | 0 | - | | chr9 | 8655647 | 8657630 | a | 0 | - | | chr11 | 4861767 | 4870315 | a | 0 | - | | chr20 | 1841074 | 1843018 | 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 merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp0kmxrnu9/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4861767 4871300 - 1 chr1 5008583 5012858 - 1 chr1 5202041 5210589 - 1 chr1 5978432 5978524 + 1 chr11 4861767 4870315 - 1 chr20 1841074 1843018 - 1 chr3 6161561 6168511 - 1 chr9 8655647 8657630 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4861767 4871300 - 1 1 chr1 5008583 5012858 - 1 2 chr1 5202041 5210589 - 1 3 chr1 5978432 5978524 + 1 4 chr11 4861767 4870315 - 1 5 chr20 1841074 1843018 - 1 6 chr3 6161561 6168511 - 1 7 chr9 8655647 8657630 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 897271 | 903483 | a | 0 | + | | chr1 | 803819 | 812258 | a | 0 | + | | chr1 | 7422885 | 7423921 | 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/tmp8x6m_jse/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 803819 812258 + 1 chr1 897271 903483 + 1 chr1 7422885 7423921 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 803819 812258 + 1 1 chr1 897271 903483 + 1 2 chr1 7422885 7423921 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3473707 | 3475300 | a | 0 | - | | chr1 | 1083391 | 1087595 | 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/tmpc0fo_e34/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1083391 1087595 - 1 chr1 3473707 3475300 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1083391 1087595 - 1 1 chr1 3473707 3475300 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr8 | 7281583 | 7288014 | a | 0 | - | | chr16 | 6109789 | 6116341 | a | 0 | - | | chr20 | 6305370 | 6311801 | 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/tmpnixlb8ny/f1.bed) resultresultresultresultresultresultresultresultresultresult chr16 6109789 6116341 - 1 chr20 6305370 6311801 - 1 chr8 7281583 7288014 - 1 bedtools_df Chromosome Start End Strand Count 0 chr16 6109789 6116341 - 1 1 chr20 6305370 6311801 - 1 2 chr8 7281583 7288014 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8403114 | 8409923 | a | 0 | + | | chr1 | 8403114 | 8403293 | a | 0 | - | | chr1 | 8403114 | 8403591 | a | 0 | - | | chr13 | 8838348 | 8840977 | a | 0 | + | | chr17 | 3372597 | 3378636 | 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 -s -i <(sort -k1,1 -k2,2n /tmp/tmpd8fknlqc/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 8403114 8403591 - 2 chr1 8403114 8409923 + 1 chr13 8838348 8840977 + 1 chr17 3372597 3378636 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 8403114 8403591 - 2 1 chr1 8403114 8409923 + 1 2 chr13 8838348 8840977 + 1 3 chr17 3372597 3378636 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2055023 | 2064730 | a | 0 | + | | chr1 | 732421 | 740051 | a | 0 | - | | chr1 | 9731060 | 9734318 | a | 0 | - | | chr1 | 6024334 | 6029972 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr12 | 10000000 | 10005922 | a | 0 | - | | chr15 | 9632152 | 9636659 | a | 0 | - | | chrM | 5878755 | 5887283 | a | 0 | + | | chrY | 2208315 | 2213156 | 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/tmpmvjghbai/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 732421 740051 - 1 chr1 2012677 2016707 - 1 chr1 2055023 2064730 + 1 chr1 3745086 3746474 - 1 chr1 6024334 6029972 - 1 chr1 9731060 9734318 - 1 chr10 2044270 2051751 + 1 chr12 10000000 10005922 - 1 chr15 9632152 9636659 - 1 chrM 5878755 5887283 + 1 chrY 2208315 2213156 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 732421 740051 - 1 1 chr1 2012677 2016707 - 1 2 chr1 2055023 2064730 + 1 3 chr1 3745086 3746474 - 1 4 chr1 6024334 6029972 - 1 5 chr1 9731060 9734318 - 1 6 chr10 2044270 2051751 + 1 7 chr12 10000000 10005922 - 1 8 chr15 9632152 9636659 - 1 9 chrM 5878755 5887283 + 1 10 chrY 2208315 2213156 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3556727 | 3560643 | 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/tmpbxan3j0w/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3556727 3560643 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 3556727 3560643 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5528624 | 5536797 | a | 0 | + | | chr1 | 9763089 | 9768821 | a | 0 | + | | chr1 | 7549690 | 7551217 | a | 0 | - | | chr1 | 3247272 | 3248704 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr8 | 9803503 | 9813503 | a | 0 | + | | chr18 | 8326373 | 8329307 | a | 0 | - | | chr19 | 7360074 | 7367636 | a | 0 | - | | chr21 | 7210412 | 7210676 | 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 -s -i <(sort -k1,1 -k2,2n /tmp/tmpj87rbfct/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 456845 462233 - 1 chr1 3247272 3248704 - 1 chr1 5528624 5536797 + 1 chr1 7549690 7551217 - 1 chr1 9763089 9768821 + 1 chr18 8326373 8329307 - 1 chr19 7360074 7367636 - 1 chr21 7210412 7210676 - 1 chr8 9803503 9813503 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 456845 462233 - 1 1 chr1 3247272 3248704 - 1 2 chr1 5528624 5536797 + 1 3 chr1 7549690 7551217 - 1 4 chr1 9763089 9768821 + 1 5 chr18 8326373 8329307 - 1 6 chr19 7360074 7367636 - 1 7 chr21 7210412 7210676 - 1 8 chr8 9803503 9813503 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7126059 | 7134473 | a | 0 | + | | chr14 | 2681421 | 2689128 | a | 0 | + | | chr15 | 7639780 | 7641608 | 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/tmpi9kh6d0s/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7126059 7134473 + 1 chr14 2681421 2689128 + 1 chr15 7639780 7641608 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 7126059 7134473 + 1 1 chr14 2681421 2689128 + 1 2 chr15 7639780 7641608 - 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/tmp3z6oltqr/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 1 ---------------------------------- 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] __________ [gw2] linux -- Python 3.12.3 /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=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 66305 | 73219 | a | 0 | + | E | chr1 | 66305 | 73219 | 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 | 2817 | 2818 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 | 66305 | 73219 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E 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 97 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.100.4', b'AXicNcqxDQAgDAPBdxLRkIaaQdh/MwKC0vdWaDWzkQLhcrCpOEuJHbylQ6XCePCvsAEmkQDg') 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') ('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') ('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') 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') 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') ('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') ---------------------------------- 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 3.12.3 /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., 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/tmpe3oz_2n9/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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr17 | 1 | 6426 | 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/tmpa4veneke/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr17 1 6426 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr17 | 1 | 6426 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr17 | 3622170 | 3622251 | 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/tmpqxfjvehh/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr17 3622170 3622251 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr17 | 3622170 | 3622251 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr17 | 3622170 | 3626267 | 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/tmpkyrlvqo0/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr17 3622170 3626267 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr17 | 3622170 | 3626267 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr17 | 3622170 | 3626267 | 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/tmpu6sm3eqf/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr17 3622170 3626267 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr17 | 3622170 | 3626267 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr17 | 3622170 | 3628571 | 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/tmp6h0dlgwm/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr17 3622170 3628571 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr17 | 3622170 | 3628571 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr17 | 3622170 | 3628571 | 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/tmpkz5p2g85/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr17 3622170 3628571 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr17 | 3622170 | 3628571 | 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 | 8800628 | 8805946 | a | 0 | + | | chr1 | 8800628 | 8807015 | a | 0 | - | | chr3 | 8800628 | 8806275 | a | 0 | + | | chr7 | 8800628 | 8809871 | a | 0 | + | | chr8 | 8800628 | 8805024 | a | 0 | + | | chr8 | 8800628 | 8802263 | a | 0 | - | | chr14 | 8800628 | 8809286 | a | 0 | - | | chr17 | 8800628 | 8807567 | 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/tmpbfxwmqr5/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 8800628 8805946 a 0 + 1 1 chr1 8800628 8807015 a 0 - 2 2 chr14 8800628 8809286 a 0 - 3 3 chr17 8800628 8807567 a 0 - 4 4 chr3 8800628 8806275 a 0 + 5 5 chr7 8800628 8809871 a 0 + 6 6 chr8 8800628 8805024 a 0 + 7 7 chr8 8800628 8802263 a 0 - 8 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8800628 | 8805946 | a | 0 | + | | chr1 | 8800628 | 8807015 | a | 0 | - | | chr3 | 8800628 | 8806275 | a | 0 | + | | chr7 | 8800628 | 8809871 | a | 0 | + | | chr8 | 8800628 | 8805024 | a | 0 | + | | chr8 | 8800628 | 8802263 | a | 0 | - | | chr14 | 8800628 | 8809286 | a | 0 | - | | chr17 | 8800628 | 8807567 | 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 | 8884843 | 8889546 | a | 0 | + | | chr1 | 6438617 | 6443320 | a | 0 | + | | chr1 | 4046434 | 4046884 | a | 0 | + | | chr1 | 6458193 | 6465522 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr4 | 3869634 | 3874337 | a | 0 | - | | chr16 | 8884843 | 8886934 | a | 0 | - | | chr19 | 570966 | 575925 | a | 0 | + | | chrY | 1501868 | 1507454 | 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 cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp2u8y0pg9/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4046434 4046884 a 0 + 1 1 chr1 6438617 6443320 a 0 + 2 2 chr1 6458193 6465522 a 0 + 3 3 chr1 8884843 8889546 a 0 + 4 4 chr16 8884843 8886934 a 0 - 5 5 chr19 570966 575925 a 0 + 6 6 chr2 2785903 2794293 a 0 - 7 7 chr4 3869634 3874337 a 0 - 8 8 chrY 1501868 1507454 a 0 - 9 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8884843 | 8889546 | a | 0 | + | | chr1 | 6438617 | 6443320 | a | 0 | + | | chr1 | 4046434 | 4046884 | a | 0 | + | | chr1 | 6458193 | 6465522 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr4 | 3869634 | 3874337 | a | 0 | - | | chr16 | 8884843 | 8886934 | a | 0 | - | | chr19 | 570966 | 575925 | a | 0 | + | | chrY | 1501868 | 1507454 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 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 | 8884843 | 8889546 | a | 0 | - | | chr1 | 6438617 | 6443320 | a | 0 | - | | chr1 | 4046434 | 4046884 | a | 0 | - | | chr1 | 6458193 | 6465522 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr4 | 3869634 | 3874337 | a | 0 | - | | chr16 | 8884843 | 8886934 | a | 0 | - | | chr19 | 570966 | 575925 | a | 0 | - | | chrY | 1501868 | 1507454 | 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 cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpfrjnkalx/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4046434 4046884 a 0 - 1 1 chr1 6438617 6443320 a 0 - 2 2 chr1 6458193 6465522 a 0 - 3 3 chr1 8884843 8889546 a 0 - 4 4 chr16 8884843 8886934 a 0 - 5 5 chr19 570966 575925 a 0 - 6 6 chr2 2785903 2794293 a 0 - 7 7 chr4 3869634 3874337 a 0 - 8 8 chrY 1501868 1507454 a 0 + 9 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8884843 | 8889546 | a | 0 | - | | chr1 | 6438617 | 6443320 | a | 0 | - | | chr1 | 4046434 | 4046884 | a | 0 | - | | chr1 | 6458193 | 6465522 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr4 | 3869634 | 3874337 | a | 0 | - | | chr16 | 8884843 | 8886934 | a | 0 | - | | chr19 | 570966 | 575925 | a | 0 | - | | chrY | 1501868 | 1507454 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 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 | 2 | 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/tmpxwvqd1b5/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/tmpb9odopwm/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/tmpcszx2fjj/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/tmp57qi8yzl/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/tmpwrdsvo3j/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/tmpyel07zys/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/tmptx950ll7/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/tmpuf0c8zxi/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/tmpoqvbe4tt/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/tmpfloa36t0/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/tmpuaj9l9by/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/tmpws5pmcg0/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 | 7109017 | 7110937 | 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/tmpvpiz2fmj/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 7109017 7110937 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7109017 | 7110937 | 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 | 4646532 | 4646533 | 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/tmpguf2i7ca/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4646532 4646533 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4646532 | 4646533 | 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 | 5338929 | 5342179 | 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/tmpizrul00t/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5338929 5342179 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5338929 | 5342179 | 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 | 3333031 | 3333595 | a | 0 | + | | chr1 | 4580383 | 4586067 | a | 0 | + | | chr1 | 6254986 | 6260223 | a | 0 | - | | chr1 | 9377796 | 9385535 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr14 | 7948235 | 7953919 | a | 0 | + | | chr16 | 3829181 | 3834865 | a | 0 | + | | chr21 | 2981059 | 2990638 | a | 0 | + | | chrY | 8592912 | 8598596 | 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/tmpdmknympg/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3333031 3333595 a 0 + 1 1 chr1 4580383 4586067 a 0 + 2 2 chr1 6254986 6260223 a 0 - 3 3 chr1 8184981 8190665 a 0 - 4 4 chr1 9377796 9385535 a 0 - 5 5 chr11 3179962 3188037 a 0 + 6 6 chr11 1055749 1061433 a 0 - 7 7 chr14 7948235 7953919 a 0 + 8 8 chr16 3829181 3834865 a 0 + 9 9 chr21 2981059 2990638 a 0 + 10 10 chrY 8592912 8598596 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3333031 | 3333595 | a | 0 | + | | chr1 | 4580383 | 4586067 | a | 0 | + | | chr1 | 6254986 | 6260223 | a | 0 | - | | chr1 | 9377796 | 9385535 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr14 | 7948235 | 7953919 | a | 0 | + | | chr16 | 3829181 | 3834865 | a | 0 | + | | chr21 | 2981059 | 2990638 | a | 0 | + | | chrY | 8592912 | 8598596 | 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 | 3053209 | 3056712 | a | 0 | + | | chr1 | 3053209 | 3053840 | a | 0 | + | | chr1 | 9437938 | 9442780 | 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/tmpy9ifqiqt/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3053209 3053840 a 0 + 1 1 chr1 3053209 3056712 a 0 + 1 2 chr1 9437938 9442780 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3053209 | 3056712 | a | 0 | + | | chr1 | 3053209 | 3053840 | a | 0 | + | | chr1 | 9437938 | 9442780 | 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 | 7823584 | 7832014 | a | 0 | + | | chr1 | 9717298 | 9724514 | a | 0 | - | | chr1 | 9717298 | 9721436 | a | 0 | - | | chr12 | 9700289 | 9701357 | a | 0 | - | | chr19 | 9717298 | 9726892 | a | 0 | + | | chrY | 7678648 | 7688153 | 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 -s -i <(sort -k1,1 -k2,2n /tmp/tmp53zkt6xb/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 7823584 7832014 a 0 + 1 1 chr1 9717298 9721436 a 0 - 2 2 chr1 9717298 9724514 a 0 - 2 3 chr12 9700289 9701357 a 0 - 3 4 chr19 9717298 9726892 a 0 + 4 5 chrY 7678648 7688153 a 0 + 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7823584 | 7832014 | a | 0 | + | | chr1 | 9717298 | 9724514 | a | 0 | - | | chr1 | 9717298 | 9721436 | a | 0 | - | | chr12 | 9700289 | 9701357 | a | 0 | - | | chr19 | 9717298 | 9726892 | a | 0 | + | | chrY | 7678648 | 7688153 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr8 | 8078695 | 8084994 | a | 0 | + | | chr8 | 8078695 | 8088364 | a | 0 | + | | chr8 | 1150842 | 1151152 | a | 0 | + | | chr8 | 8078695 | 8085765 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr8 | 8078695 | 8082362 | a | 0 | - | | chr8 | 4616841 | 4623094 | a | 0 | - | | chr8 | 8078695 | 8084067 | a | 0 | - | | chr8 | 8041269 | 8044606 | 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/tmpqnwb56im/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr8 1150842 1151152 a 0 + 1 1 chr8 8078695 8081844 a 0 + 2 2 chr8 8078695 8083343 a 0 + 2 3 chr8 8078695 8084994 a 0 + 2 4 chr8 8078695 8085765 a 0 + 2 5 chr8 8078695 8086836 a 0 + 2 6 chr8 8078695 8088364 a 0 + 2 7 chr8 4616841 4623094 a 0 - 3 8 chr8 8041269 8044606 a 0 - 4 9 chr8 8078695 8082362 a 0 - 5 10 chr8 8078695 8084067 a 0 - 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr8 | 8078695 | 8084994 | a | 0 | + | | chr8 | 8078695 | 8088364 | a | 0 | + | | chr8 | 1150842 | 1151152 | a | 0 | + | | chr8 | 8078695 | 8085765 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr8 | 8078695 | 8082362 | a | 0 | - | | chr8 | 4616841 | 4623094 | a | 0 | - | | chr8 | 8078695 | 8084067 | a | 0 | - | | chr8 | 8041269 | 8044606 | 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 | 8223215 | 8228234 | 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/tmpibl9itdd/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 8223215 8228234 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8223215 | 8228234 | 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 | 8262729 | 8270220 | a | 0 | + | | chr1 | 9824116 | 9824370 | a | 0 | - | | chr4 | 7325572 | 7329520 | a | 0 | - | | chr5 | 7932167 | 7939630 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr20 | 81266 | 86913 | a | 0 | + | | chr22 | 2893272 | 2898376 | a | 0 | - | | chrX | 2267116 | 2267117 | a | 0 | + | | chrX | 6256240 | 6257754 | 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/tmpflf4ji_2/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 8262729 8270220 a 0 + 1 1 chr1 9824116 9824370 a 0 - 2 2 chr20 81266 86913 a 0 + 3 3 chr22 2893272 2898376 a 0 - 4 4 chr4 7325572 7329520 a 0 - 5 5 chr5 7932167 7939630 a 0 + 6 6 chr5 6520287 6526132 a 0 - 7 7 chr5 8548940 8549125 a 0 - 8 8 chr6 5350437 5356516 a 0 - 9 9 chrX 2267116 2267117 a 0 + 10 10 chrX 6256240 6257754 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8262729 | 8270220 | a | 0 | + | | chr1 | 9824116 | 9824370 | a | 0 | - | | chr4 | 7325572 | 7329520 | a | 0 | - | | chr5 | 7932167 | 7939630 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr20 | 81266 | 86913 | a | 0 | + | | chr22 | 2893272 | 2898376 | a | 0 | - | | chrX | 2267116 | 2267117 | a | 0 | + | | chrX | 6256240 | 6257754 | 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 | 5793545 | 5802215 | 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/tmpxovlat7x/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5793545 5802215 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5793545 | 5802215 | 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 | 3493060 | 3500367 | a | 0 | + | | chr1 | 1907233 | 1914540 | a | 0 | + | | chr1 | 2068177 | 2072834 | a | 0 | + | | chr1 | 3871547 | 3878854 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 4610114 | 4617765 | a | 0 | - | | chr1 | 1346075 | 1351562 | a | 0 | - | | chr1 | 3359942 | 3364511 | a | 0 | - | | chr1 | 5383587 | 5390894 | 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/tmpxtcaaskc/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1907233 1914540 a 0 + 1 1 chr1 2068177 2072834 a 0 + 2 2 chr1 3493060 3500367 a 0 + 3 3 chr1 1346075 1351562 a 0 - 4 4 chr1 3359942 3364511 a 0 - 5 5 chr1 3871547 3878854 a 0 - 6 6 chr1 4610114 4617765 a 0 - 7 7 chr1 5383587 5390894 a 0 - 8 8 chr5 944771 945865 a 0 + 9 9 chr5 556764 564071 a 0 - 10 10 chr9 6494239 6502684 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3493060 | 3500367 | a | 0 | + | | chr1 | 1907233 | 1914540 | a | 0 | + | | chr1 | 2068177 | 2072834 | a | 0 | + | | chr1 | 3871547 | 3878854 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 4610114 | 4617765 | a | 0 | - | | chr1 | 1346075 | 1351562 | a | 0 | - | | chr1 | 3359942 | 3364511 | a | 0 | - | | chr1 | 5383587 | 5390894 | 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 | 9206669 | 9210096 | a | 0 | + | | chr1 | 9206669 | 9214779 | a | 0 | + | | chr1 | 1 | 2637 | a | 0 | + | | chr1 | 9206669 | 9208824 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 9206669 | 9208824 | a | 0 | + | | chr1 | 7001336 | 7006517 | a | 0 | + | | chr1 | 2775249 | 2783687 | a | 0 | - | | chr1 | 613648 | 617039 | 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 -s -i <(sort -k1,1 -k2,2n /tmp/tmpctz1v01o/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2637 a 0 + 1 1 chr1 7001336 7006517 a 0 + 2 2 chr1 9206669 9208824 a 0 + 3 3 chr1 9206669 9210096 a 0 + 3 4 chr1 9206669 9214779 a 0 + 3 5 chr1 613648 617039 a 0 - 4 6 chr1 2775249 2783687 a 0 - 5 7 chr11 6306499 6314374 a 0 + 6 8 chr5 29492 37828 a 0 + 7 9 chr5 4842679 4852140 a 0 + 8 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9206669 | 9210096 | a | 0 | + | | chr1 | 9206669 | 9214779 | a | 0 | + | | chr1 | 1 | 2637 | a | 0 | + | | chr1 | 9206669 | 9208824 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 9206669 | 9208824 | a | 0 | + | | chr1 | 7001336 | 7006517 | a | 0 | + | | chr1 | 2775249 | 2783687 | a | 0 | - | | chr1 | 613648 | 617039 | 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 | 1835608 | 1838225 | a | 0 | + | | chr1 | 5512523 | 5512524 | a | 0 | + | | chr1 | 5579846 | 5583745 | a | 0 | + | | chr1 | 9294152 | 9302028 | a | 0 | + | | chr1 | 5068841 | 5073500 | a | 0 | - | | chr4 | 3445779 | 3452523 | a | 0 | + | | chrM | 2890921 | 2892946 | 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/tmp2prqiufq/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1835608 1838225 a 0 + 1 1 chr1 5512523 5512524 a 0 + 2 2 chr1 5579846 5583745 a 0 + 3 3 chr1 9294152 9302028 a 0 + 4 4 chr1 5068841 5073500 a 0 - 5 5 chr4 3445779 3452523 a 0 + 6 6 chrM 2890921 2892946 a 0 + 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1835608 | 1838225 | a | 0 | + | | chr1 | 5512523 | 5512524 | a | 0 | + | | chr1 | 5579846 | 5583745 | a | 0 | + | | chr1 | 9294152 | 9302028 | a | 0 | + | | chr1 | 5068841 | 5073500 | a | 0 | - | | chr4 | 3445779 | 3452523 | a | 0 | + | | chrM | 2890921 | 2892946 | 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 | 2956357 | 2958904 | a | 0 | + | | chr1 | 5211083 | 5213630 | a | 0 | + | | chr1 | 1014316 | 1016863 | a | 0 | + | | chr1 | 8820046 | 8822593 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr15 | 6941641 | 6944188 | a | 0 | + | | chr19 | 3161713 | 3164260 | a | 0 | + | | chr22 | 8495335 | 8499235 | a | 0 | - | | chrX | 1421942 | 1428421 | 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/tmp0hqpz1fh/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1014316 1016863 a 0 + 1 1 chr1 2956357 2958904 a 0 + 2 2 chr1 5211083 5213630 a 0 + 3 3 chr1 8820046 8822593 a 0 - 4 4 chr10 1147196 1149743 a 0 + 5 5 chr15 6941641 6944188 a 0 + 6 6 chr19 3161713 3164260 a 0 + 7 7 chr22 8495335 8499235 a 0 - 8 8 chr4 7264148 7266695 a 0 + 9 9 chr6 1014316 1016863 a 0 - 10 10 chrX 1421942 1428421 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2956357 | 2958904 | a | 0 | + | | chr1 | 5211083 | 5213630 | a | 0 | + | | chr1 | 1014316 | 1016863 | a | 0 | + | | chr1 | 8820046 | 8822593 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr15 | 6941641 | 6944188 | a | 0 | + | | chr19 | 3161713 | 3164260 | a | 0 | + | | chr22 | 8495335 | 8499235 | a | 0 | - | | chrX | 1421942 | 1428421 | 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 | 2631790 | 2633881 | a | 0 | + | | chr9 | 9793360 | 9795200 | a | 0 | - | | chr13 | 5753079 | 5756166 | a | 0 | + | | chr20 | 8391721 | 8395944 | 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/tmp6ngxhn68/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2631790 2633881 a 0 + 1 1 chr13 5753079 5756166 a 0 + 2 2 chr20 8391721 8395944 a 0 + 3 3 chr9 9793360 9795200 a 0 - 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2631790 | 2633881 | a | 0 | + | | chr9 | 9793360 | 9795200 | a | 0 | - | | chr13 | 5753079 | 5756166 | a | 0 | + | | chr20 | 8391721 | 8395944 | 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 | 1708953 | 1716068 | a | 0 | - | | chr7 | 8754710 | 8754711 | a | 0 | + | | chr7 | 4653836 | 4660090 | a | 0 | - | | chr15 | 2190043 | 2193733 | 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/tmpxpdu7x89/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1708953 1716068 a 0 - 1 1 chr15 2190043 2193733 a 0 - 2 2 chr7 8754710 8754711 a 0 + 3 3 chr7 4653836 4660090 a 0 - 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1708953 | 1716068 | a | 0 | - | | chr7 | 8754710 | 8754711 | a | 0 | + | | chr7 | 4653836 | 4660090 | a | 0 | - | | chr15 | 2190043 | 2193733 | 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 | 9202722 | 9208302 | a | 0 | - | | chr1 | 7383474 | 7391448 | a | 0 | - | | chr14 | 9995825 | 9995917 | 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/tmpwnymst0q/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 7383474 7391448 a 0 - 1 1 chr1 9202722 9208302 a 0 - 2 2 chr14 9995825 9995917 a 0 - 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9202722 | 9208302 | a | 0 | - | | chr1 | 7383474 | 7391448 | a | 0 | - | | chr14 | 9995825 | 9995917 | 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 | 9708942 | 9708944 | a | 0 | - | | chr18 | 9448215 | 9455162 | a | 0 | - | | chrY | 4452976 | 4462976 | 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/tmp0253_ymu/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 9708942 9708944 a 0 - 1 1 chr18 9448215 9455162 a 0 - 2 2 chrY 4452976 4462976 a 0 + 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9708942 | 9708944 | a | 0 | - | | chr18 | 9448215 | 9455162 | a | 0 | - | | chrY | 4452976 | 4462976 | 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 | 7303340 | 7309952 | a | 0 | + | | chr1 | 6703048 | 6712555 | a | 0 | + | | chr1 | 1831587 | 1835837 | a | 0 | + | | chr1 | 7279003 | 7280700 | a | 0 | - | | chr1 | 5398025 | 5401100 | a | 0 | - | | chr3 | 9108685 | 9109165 | a | 0 | - | | chr19 | 6904532 | 6905179 | a | 0 | + | | chr22 | 5895949 | 5903553 | 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/tmp9k9f3n3f/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1831587 1835837 a 0 + 1 1 chr1 6703048 6712555 a 0 + 2 2 chr1 7303340 7309952 a 0 + 3 3 chr1 5398025 5401100 a 0 - 4 4 chr1 7279003 7280700 a 0 - 5 5 chr19 6904532 6905179 a 0 + 6 6 chr22 5895949 5903553 a 0 + 7 7 chr3 9108685 9109165 a 0 - 8 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7303340 | 7309952 | a | 0 | + | | chr1 | 6703048 | 6712555 | a | 0 | + | | chr1 | 1831587 | 1835837 | a | 0 | + | | chr1 | 7279003 | 7280700 | a | 0 | - | | chr1 | 5398025 | 5401100 | a | 0 | - | | chr3 | 9108685 | 9109165 | a | 0 | - | | chr19 | 6904532 | 6905179 | a | 0 | + | | chr22 | 5895949 | 5903553 | 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 | 8169077 | 8174014 | a | 0 | - | | chr16 | 8625589 | 8628064 | 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/tmpyjwofp81/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 8169077 8174014 a 0 - 1 1 chr16 8625589 8628064 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8169077 | 8174014 | a | 0 | - | | chr16 | 8625589 | 8628064 | 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 | 4107269 | 4112539 | a | 0 | + | | chr1 | 992896 | 993705 | a | 0 | + | | chr1 | 2095050 | 2103225 | a | 0 | + | | chr1 | 8523165 | 8523184 | a | 0 | - | | chr1 | 2148241 | 2157454 | a | 0 | - | | chr1 | 8576623 | 8585248 | a | 0 | - | | chr1 | 8790916 | 8797664 | 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/tmpydl193ae/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 992896 993705 a 0 + 1 1 chr1 2095050 2103225 a 0 + 2 2 chr1 4107269 4112539 a 0 + 3 3 chr1 2148241 2157454 a 0 - 4 4 chr1 8523165 8523184 a 0 - 5 5 chr1 8576623 8585248 a 0 - 6 6 chr1 8790916 8797664 a 0 - 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4107269 | 4112539 | a | 0 | + | | chr1 | 992896 | 993705 | a | 0 | + | | chr1 | 2095050 | 2103225 | a | 0 | + | | chr1 | 8523165 | 8523184 | a | 0 | - | | chr1 | 2148241 | 2157454 | a | 0 | - | | chr1 | 8576623 | 8585248 | a | 0 | - | | chr1 | 8790916 | 8797664 | 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 | 9139766 | 9146937 | a | 0 | - | | chr1 | 5070684 | 5078437 | a | 0 | - | | chr16 | 3676311 | 3683828 | a | 0 | - | | chrM | 7428410 | 7436163 | 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/tmpjfsno3v2/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5070684 5078437 a 0 - 1 1 chr1 9139766 9146937 a 0 - 2 2 chr16 3676311 3683828 a 0 - 3 3 chrM 7428410 7436163 a 0 + 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9139766 | 9146937 | a | 0 | - | | chr1 | 5070684 | 5078437 | a | 0 | - | | chr16 | 3676311 | 3683828 | a | 0 | - | | chrM | 7428410 | 7436163 | 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 | 3913880 | 3914633 | a | 0 | + | | chr1 | 20654 | 28773 | a | 0 | + | | chr1 | 6159336 | 6161417 | a | 0 | - | | chr1 | 5281194 | 5291146 | 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/tmpn93vdfye/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 20654 28773 a 0 + 1 1 chr1 3913880 3914633 a 0 + 2 2 chr1 5281194 5291146 a 0 - 3 3 chr1 6159336 6161417 a 0 - 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3913880 | 3914633 | a | 0 | + | | chr1 | 20654 | 28773 | a | 0 | + | | chr1 | 6159336 | 6161417 | a | 0 | - | | chr1 | 5281194 | 5291146 | 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 | 9442710 | 9448341 | a | 0 | + | | chr1 | 9949925 | 9959924 | a | 0 | + | | chr1 | 3014074 | 3023852 | a | 0 | + | | chr1 | 6117556 | 6123236 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 1652438 | 1660061 | a | 0 | - | | chr1 | 9890695 | 9895302 | a | 0 | - | | chr1 | 4882224 | 4889008 | a | 0 | - | | chr1 | 3783840 | 3783842 | 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/tmpvjpyq5rn/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3014074 3023852 a 0 + 1 1 chr1 6117556 6123236 a 0 + 2 2 chr1 9442710 9448341 a 0 + 3 3 chr1 9949925 9959924 a 0 + 4 4 chr1 1652438 1660061 a 0 - 5 5 chr1 3618393 3626023 a 0 - 6 6 chr1 3783840 3783842 a 0 - 7 7 chr1 4882224 4889008 a 0 - 8 8 chr1 9890695 9895302 a 0 - 9 9 chr14 518086 528086 a 0 + 10 10 chrM 3112782 3113447 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9442710 | 9448341 | a | 0 | + | | chr1 | 9949925 | 9959924 | a | 0 | + | | chr1 | 3014074 | 3023852 | a | 0 | + | | chr1 | 6117556 | 6123236 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 1652438 | 1660061 | a | 0 | - | | chr1 | 9890695 | 9895302 | a | 0 | - | | chr1 | 4882224 | 4889008 | a | 0 | - | | chr1 | 3783840 | 3783842 | 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 | 5506716 | 5515813 | a | 0 | + | | chr1 | 3392037 | 3401239 | a | 0 | + | | chr1 | 8938015 | 8940348 | a | 0 | + | | chr19 | 5736890 | 5742062 | a | 0 | - | | chr20 | 8924477 | 8933523 | 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 -s -i <(sort -k1,1 -k2,2n /tmp/tmpqx4sooqt/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3392037 3401239 a 0 + 1 1 chr1 5506716 5515813 a 0 + 2 2 chr1 8938015 8940348 a 0 + 3 3 chr19 5736890 5742062 a 0 - 4 4 chr20 8924477 8933523 a 0 - 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5506716 | 5515813 | a | 0 | + | | chr1 | 3392037 | 3401239 | a | 0 | + | | chr1 | 8938015 | 8940348 | a | 0 | + | | chr19 | 5736890 | 5742062 | a | 0 | - | | chr20 | 8924477 | 8933523 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2679888 | 2684321 | a | 0 | + | | chr1 | 7380521 | 7388698 | a | 0 | + | | chr1 | 3551138 | 3554354 | a | 0 | + | | chr1 | 4325245 | 4329643 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr8 | 1607994 | 1615804 | a | 0 | - | | chr12 | 5009484 | 5014631 | a | 0 | - | | chr17 | 3374746 | 3378624 | a | 0 | - | | chr18 | 7464752 | 7474504 | 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/tmp5eplqi7h/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2679888 2684321 a 0 + 1 1 chr1 3551138 3554354 a 0 + 2 2 chr1 7380521 7388698 a 0 + 3 3 chr1 1224077 1231229 a 0 - 4 4 chr1 4325245 4329643 a 0 - 5 5 chr1 7413051 7418294 a 0 - 6 6 chr1 7611349 7621052 a 0 - 7 7 chr12 5009484 5014631 a 0 - 8 8 chr17 3374746 3378624 a 0 - 9 9 chr18 7464752 7474504 a 0 + 10 10 chr8 1607994 1615804 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2679888 | 2684321 | a | 0 | + | | chr1 | 7380521 | 7388698 | a | 0 | + | | chr1 | 3551138 | 3554354 | a | 0 | + | | chr1 | 4325245 | 4329643 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr8 | 1607994 | 1615804 | a | 0 | - | | chr12 | 5009484 | 5014631 | a | 0 | - | | chr17 | 3374746 | 3378624 | a | 0 | - | | chr18 | 7464752 | 7474504 | 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 | 2749319 | 2749684 | a | 0 | + | | chr1 | 8190758 | 8200679 | a | 0 | + | | chr1 | 1380708 | 1383218 | a | 0 | - | | chr6 | 9959332 | 9960703 | a | 0 | + | | chr8 | 3794299 | 3801661 | 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 -s -i <(sort -k1,1 -k2,2n /tmp/tmpqtkfmms8/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2749319 2749684 a 0 + 1 1 chr1 8190758 8200679 a 0 + 2 2 chr1 1380708 1383218 a 0 - 3 3 chr6 9959332 9960703 a 0 + 4 4 chr8 3794299 3801661 a 0 - 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2749319 | 2749684 | a | 0 | + | | chr1 | 8190758 | 8200679 | a | 0 | + | | chr1 | 1380708 | 1383218 | a | 0 | - | | chr6 | 9959332 | 9960703 | a | 0 | + | | chr8 | 3794299 | 3801661 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr12 | 6043022 | 6048399 | 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/tmp_939l8vv/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr12 6043022 6048399 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr12 | 6043022 | 6048399 | 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 | 6884201 | 6884285 | 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/tmphmb_ssoh/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6884201 6884285 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6884201 | 6884285 | 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 | 2822929 | 2828123 | a | 0 | + | | chr1 | 2822929 | 2832048 | a | 0 | + | | chr1 | 2822929 | 2824880 | a | 0 | - | | chr1 | 2822929 | 2826709 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 2822929 | 2830365 | a | 0 | - | | chr1 | 2822929 | 2824537 | a | 0 | - | | chr1 | 2822929 | 2827612 | a | 0 | - | | chr1 | 2822929 | 2825938 | 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/tmp_q9aakja/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2822929 2828123 a 0 + 1 1 chr1 2822929 2832048 a 0 + 1 2 chr1 2822929 2824537 a 0 - 2 3 chr1 2822929 2824880 a 0 - 2 4 chr1 2822929 2825938 a 0 - 2 5 chr1 2822929 2826709 a 0 - 2 6 chr1 2822929 2827612 a 0 - 2 7 chr1 2822929 2828184 a 0 - 2 8 chr1 2822929 2830314 a 0 - 2 9 chr1 2822929 2830365 a 0 - 2 10 chr1 2822929 2832929 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2822929 | 2828123 | a | 0 | + | | chr1 | 2822929 | 2832048 | a | 0 | + | | chr1 | 2822929 | 2824880 | a | 0 | - | | chr1 | 2822929 | 2826709 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 2822929 | 2830365 | a | 0 | - | | chr1 | 2822929 | 2824537 | a | 0 | - | | chr1 | 2822929 | 2827612 | a | 0 | - | | chr1 | 2822929 | 2825938 | 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 | 9742519 | 9751156 | a | 0 | + | | chr1 | 9009451 | 9012594 | a | 0 | + | | chr6 | 6405362 | 6414057 | a | 0 | - | | chr12 | 9249742 | 9256600 | a | 0 | - | | chr13 | 6317621 | 6323625 | a | 0 | + | | chr14 | 8803884 | 8811554 | 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/tmpoo7vkk84/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 9009451 9012594 a 0 + 1 1 chr1 9742519 9751156 a 0 + 2 2 chr12 9249742 9256600 a 0 - 3 3 chr13 6317621 6323625 a 0 + 4 4 chr14 8803884 8811554 a 0 + 5 5 chr6 6405362 6414057 a 0 - 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9742519 | 9751156 | a | 0 | + | | chr1 | 9009451 | 9012594 | a | 0 | + | | chr6 | 6405362 | 6414057 | a | 0 | - | | chr12 | 9249742 | 9256600 | a | 0 | - | | chr13 | 6317621 | 6323625 | a | 0 | + | | chr14 | 8803884 | 8811554 | 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 | 254341 | 256075 | a | 0 | - | | chr1 | 3336248 | 3343651 | a | 0 | - | | chr7 | 7188521 | 7190255 | 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/tmpkq9h3mse/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 254341 256075 a 0 - 1 1 chr1 3336248 3343651 a 0 - 2 2 chr7 7188521 7190255 a 0 - 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 254341 | 256075 | a | 0 | - | | chr1 | 3336248 | 3343651 | a | 0 | - | | chr7 | 7188521 | 7190255 | 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 | 8117547 | 8127547 | a | 0 | + | | chr1 | 7202783 | 7208934 | a | 0 | + | | chr1 | 9148569 | 9157443 | a | 0 | - | | chr1 | 2741632 | 2750506 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr19 | 1805179 | 1814053 | a | 0 | - | | chrX | 3969134 | 3970853 | a | 0 | + | | chrX | 324771 | 333645 | a | 0 | - | | chrY | 9999999 | 10004335 | 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/tmpvjk340ai/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 7202783 7208934 a 0 + 1 1 chr1 8117547 8127547 a 0 + 2 2 chr1 2741632 2750506 a 0 - 3 3 chr1 9148569 9157443 a 0 - 4 4 chr19 1805179 1814053 a 0 - 5 5 chr3 6744254 6747669 a 0 - 6 6 chr6 2598660 2602686 a 0 - 7 7 chr9 754314 763188 a 0 + 8 8 chrX 3969134 3970853 a 0 + 9 9 chrX 324771 333645 a 0 - 10 10 chrY 9999999 10004335 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8117547 | 8127547 | a | 0 | + | | chr1 | 7202783 | 7208934 | a | 0 | + | | chr1 | 9148569 | 9157443 | a | 0 | - | | chr1 | 2741632 | 2750506 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr19 | 1805179 | 1814053 | a | 0 | - | | chrX | 3969134 | 3970853 | a | 0 | + | | chrX | 324771 | 333645 | a | 0 | - | | chrY | 9999999 | 10004335 | 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 | 2140830 | 2148404 | a | 0 | + | | chr1 | 1 | 4783 | a | 0 | + | | chr1 | 9483705 | 9484689 | a | 0 | + | | chr1 | 1 | 4560 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr11 | 2 | 5295 | a | 0 | + | | chr11 | 418040 | 427280 | a | 0 | - | | chr12 | 5954333 | 5956175 | a | 0 | + | | chr13 | 1 | 4555 | 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/tmpnhiv_gto/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 4560 a 0 + 1 1 chr1 1 4783 a 0 + 1 2 chr1 1 8091 a 0 + 1 3 chr1 2140830 2148404 a 0 + 2 4 chr1 7283859 7285515 a 0 + 3 5 chr1 9483705 9484689 a 0 + 4 6 chr11 2 5295 a 0 + 5 7 chr11 418040 427280 a 0 - 6 8 chr12 5954333 5956175 a 0 + 7 9 chr13 1 4555 a 0 + 8 10 chrX 1 1183 a 0 - 9 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2140830 | 2148404 | a | 0 | + | | chr1 | 1 | 4783 | a | 0 | + | | chr1 | 9483705 | 9484689 | a | 0 | + | | chr1 | 1 | 4560 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr11 | 2 | 5295 | a | 0 | + | | chr11 | 418040 | 427280 | a | 0 | - | | chr12 | 5954333 | 5956175 | a | 0 | + | | chr13 | 1 | 4555 | 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 | 4875380 | 4881937 | a | 0 | + | | chr12 | 5252576 | 5256470 | 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/tmpsgr4i0h8/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4875380 4881937 a 0 + 1 1 chr12 5252576 5256470 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4875380 | 4881937 | a | 0 | + | | chr12 | 5252576 | 5256470 | 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 | 3090466 | 3091907 | a | 0 | + | | chr13 | 7014517 | 7015958 | 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/tmpoom8klcb/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3090466 3091907 a 0 + 1 1 chr13 7014517 7015958 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3090466 | 3091907 | a | 0 | + | | chr13 | 7014517 | 7015958 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 4447854 | 4454948 | a | 0 | - | | chr10 | 3395410 | 3405222 | a | 0 | + | | chr10 | 2273623 | 2281492 | a | 0 | + | | chr10 | 9540122 | 9549227 | 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/tmpbxyoa47v/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr10 2273623 2281492 a 0 + 1 1 chr10 3395410 3405222 a 0 + 2 2 chr10 9540122 9549227 a 0 - 3 3 chr2 4447854 4454948 a 0 - 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 4447854 | 4454948 | a | 0 | - | | chr10 | 3395410 | 3405222 | a | 0 | + | | chr10 | 2273623 | 2281492 | a | 0 | + | | chr10 | 9540122 | 9549227 | 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 | 9999999 | 10008412 | a | 0 | - | | chr1 | 101649 | 104078 | a | 0 | - | | chr8 | 1947512 | 1955492 | a | 0 | - | | chr8 | 9457527 | 9463388 | a | 0 | - | | chr10 | 3789690 | 3798100 | a | 0 | - | | chr15 | 637641 | 645832 | a | 0 | - | | chr15 | 3549170 | 3552230 | 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/tmpnl497cx_/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 101649 104078 a 0 - 1 1 chr1 9999999 10008412 a 0 - 2 2 chr10 3789690 3798100 a 0 - 3 3 chr15 637641 645832 a 0 - 4 4 chr15 3549170 3552230 a 0 - 5 5 chr8 1947512 1955492 a 0 - 6 6 chr8 9457527 9463388 a 0 - 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9999999 | 10008412 | a | 0 | - | | chr1 | 101649 | 104078 | a | 0 | - | | chr8 | 1947512 | 1955492 | a | 0 | - | | chr8 | 9457527 | 9463388 | a | 0 | - | | chr10 | 3789690 | 3798100 | a | 0 | - | | chr15 | 637641 | 645832 | a | 0 | - | | chr15 | 3549170 | 3552230 | 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 | 7261031 | 7267515 | a | 0 | + | | chr1 | 6400111 | 6401006 | a | 0 | + | | chr1 | 7261031 | 7261926 | a | 0 | + | | chr1 | 4472716 | 4481071 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr10 | 1973274 | 1974169 | a | 0 | - | | chr13 | 8312965 | 8315031 | a | 0 | + | | chr17 | 7261031 | 7261926 | a | 0 | + | | chrM | 4498026 | 4498921 | 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/tmp9trc8mmk/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2814119 2815014 a 0 + 1 1 chr1 4472716 4481071 a 0 + 2 2 chr1 6400111 6401006 a 0 + 3 3 chr1 7261031 7261926 a 0 + 4 4 chr1 7261031 7267515 a 0 + 4 5 chr1 4131126 4133740 a 0 - 5 6 chr10 1973274 1974169 a 0 - 6 7 chr13 8312965 8315031 a 0 + 7 8 chr17 7261031 7261926 a 0 + 8 9 chr6 8467381 8470334 a 0 - 9 10 chrM 4498026 4498921 a 0 - 10 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7261031 | 7267515 | a | 0 | + | | chr1 | 6400111 | 6401006 | a | 0 | + | | chr1 | 7261031 | 7261926 | a | 0 | + | | chr1 | 4472716 | 4481071 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr10 | 1973274 | 1974169 | a | 0 | - | | chr13 | 8312965 | 8315031 | a | 0 | + | | chr17 | 7261031 | 7261926 | a | 0 | + | | chrM | 4498026 | 4498921 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr10 | 8295303 | 8304376 | a | 0 | - | | chr11 | 5459216 | 5468402 | a | 0 | + | | chr12 | 1202480 | 1209477 | a | 0 | - | | chr21 | 4289763 | 4298568 | 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/tmprhctqnfs/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr10 8295303 8304376 a 0 - 1 1 chr11 5459216 5468402 a 0 + 2 2 chr12 1202480 1209477 a 0 - 3 3 chr21 4289763 4298568 a 0 - 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr10 | 8295303 | 8304376 | a | 0 | - | | chr11 | 5459216 | 5468402 | a | 0 | + | | chr12 | 1202480 | 1209477 | a | 0 | - | | chr21 | 4289763 | 4298568 | 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 | 6640961 | 6646292 | a | 0 | + | | chr1 | 1 | 5332 | a | 0 | - | | chr2 | 7260090 | 7265421 | a | 0 | + | | chr10 | 6149997 | 6155328 | 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/tmpzuifaw4s/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6640961 6646292 a 0 + 1 1 chr1 1 5332 a 0 - 2 2 chr10 6149997 6155328 a 0 - 3 3 chr2 7260090 7265421 a 0 + 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6640961 | 6646292 | a | 0 | + | | chr1 | 1 | 5332 | a | 0 | - | | chr2 | 7260090 | 7265421 | a | 0 | + | | chr10 | 6149997 | 6155328 | 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 | 9160443 | 9167201 | a | 0 | + | | chr14 | 5196411 | 5200922 | a | 0 | + | | chr14 | 7387956 | 7397866 | a | 0 | - | | chr20 | 1649345 | 1654842 | a | 0 | - | | chr22 | 10000000 | 10007547 | 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/tmpvq0vv03b/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 9160443 9167201 a 0 + 1 1 chr14 5196411 5200922 a 0 + 2 2 chr14 7387956 7397866 a 0 - 3 3 chr20 1649345 1654842 a 0 - 4 4 chr22 10000000 10007547 a 0 - 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9160443 | 9167201 | a | 0 | + | | chr14 | 5196411 | 5200922 | a | 0 | + | | chr14 | 7387956 | 7397866 | a | 0 | - | | chr20 | 1649345 | 1654842 | a | 0 | - | | chr22 | 10000000 | 10007547 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr4 | 5757925 | 5765288 | a | 0 | + | | chr4 | 6846825 | 6851542 | a | 0 | - | | chr4 | 4551938 | 4561464 | a | 0 | - | | chr4 | 8354431 | 8361650 | 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/tmpzipoenh8/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr4 5757925 5765288 a 0 + 1 1 chr4 4551938 4561464 a 0 - 2 2 chr4 6846825 6851542 a 0 - 3 3 chr4 8354431 8361650 a 0 - 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr4 | 5757925 | 5765288 | a | 0 | + | | chr4 | 6846825 | 6851542 | a | 0 | - | | chr4 | 4551938 | 4561464 | a | 0 | - | | chr4 | 8354431 | 8361650 | 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 | 8353154 | 8353155 | a | 0 | + | | chr1 | 8353154 | 8360903 | a | 0 | - | | chr1 | 8353154 | 8356131 | a | 0 | - | | chr1 | 9859609 | 9859910 | a | 0 | - | | chr8 | 7019423 | 7022667 | a | 0 | - | | chr13 | 8353154 | 8361345 | a | 0 | + | | chrY | 7049356 | 7050437 | 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/tmpmsupph08/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 8353154 8353155 a 0 + 1 1 chr1 8353154 8356131 a 0 - 2 2 chr1 8353154 8360903 a 0 - 2 3 chr1 9859609 9859910 a 0 - 3 4 chr13 8353154 8361345 a 0 + 4 5 chr8 7019423 7022667 a 0 - 5 6 chrY 7049356 7050437 a 0 + 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8353154 | 8353155 | a | 0 | + | | chr1 | 8353154 | 8360903 | a | 0 | - | | chr1 | 8353154 | 8356131 | a | 0 | - | | chr1 | 9859609 | 9859910 | a | 0 | - | | chr8 | 7019423 | 7022667 | a | 0 | - | | chr13 | 8353154 | 8361345 | a | 0 | + | | chrY | 7049356 | 7050437 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 4127819 | 4136759 | a | 0 | - | | chr20 | 8367169 | 8368856 | 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/tmpsavq128p/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr2 4127819 4136759 a 0 - 1 1 chr20 8367169 8368856 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 4127819 | 4136759 | a | 0 | - | | chr20 | 8367169 | 8368856 | 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 | 3809500 | 3818991 | a | 0 | + | | chr1 | 7358749 | 7363388 | a | 0 | - | | chr1 | 6706844 | 6711151 | a | 0 | - | | chr1 | 8058005 | 8061867 | a | 0 | - | | chr1 | 5023456 | 5032632 | a | 0 | - | | chr15 | 8305035 | 8312402 | a | 0 | + | | chr19 | 2609496 | 2616358 | a | 0 | - | | chr22 | 6722417 | 6722644 | 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/tmp7b1seyac/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3809500 3818991 a 0 + 1 1 chr1 5023456 5032632 a 0 - 2 2 chr1 6706844 6711151 a 0 - 3 3 chr1 7358749 7363388 a 0 - 4 4 chr1 8058005 8061867 a 0 - 5 5 chr15 8305035 8312402 a 0 + 6 6 chr19 2609496 2616358 a 0 - 7 7 chr22 6722417 6722644 a 0 - 8 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3809500 | 3818991 | a | 0 | + | | chr1 | 7358749 | 7363388 | a | 0 | - | | chr1 | 6706844 | 6711151 | a | 0 | - | | chr1 | 8058005 | 8061867 | a | 0 | - | | chr1 | 5023456 | 5032632 | a | 0 | - | | chr15 | 8305035 | 8312402 | a | 0 | + | | chr19 | 2609496 | 2616358 | a | 0 | - | | chr22 | 6722417 | 6722644 | 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 | 7541036 | 7545730 | a | 0 | - | | chr11 | 7541036 | 7541718 | a | 0 | + | | chr15 | 8279788 | 8281611 | a | 0 | + | | chr18 | 7541036 | 7549570 | a | 0 | - | | chrY | 7541036 | 7542789 | 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/tmpdmtus3_0/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 7541036 7545730 a 0 - 1 1 chr11 7541036 7541718 a 0 + 2 2 chr15 8279788 8281611 a 0 + 3 3 chr18 7541036 7549570 a 0 - 4 4 chrY 7541036 7542789 a 0 - 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7541036 | 7545730 | a | 0 | - | | chr11 | 7541036 | 7541718 | a | 0 | + | | chr15 | 8279788 | 8281611 | a | 0 | + | | chr18 | 7541036 | 7549570 | a | 0 | - | | chrY | 7541036 | 7542789 | 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 | 7785890 | 7793256 | a | 0 | + | | chr1 | 8548015 | 8557749 | a | 0 | + | | chr5 | 8548015 | 8557598 | a | 0 | + | | chr13 | 8138854 | 8141464 | 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/tmpiyymdwdw/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 7785890 7793256 a 0 + 1 1 chr1 8548015 8557749 a 0 + 2 2 chr13 8138854 8141464 a 0 + 3 3 chr5 8548015 8557598 a 0 + 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7785890 | 7793256 | a | 0 | + | | chr1 | 8548015 | 8557749 | a | 0 | + | | chr5 | 8548015 | 8557598 | a | 0 | + | | chr13 | 8138854 | 8141464 | 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 | 661696 | 671506 | a | 0 | - | | chr1 | 661696 | 666126 | a | 0 | - | | chr17 | 661696 | 665741 | a | 0 | + | | chr17 | 661696 | 669581 | 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/tmpvcouy9wt/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 661696 666126 a 0 - 1 1 chr1 661696 671506 a 0 - 1 2 chr17 661696 665741 a 0 + 2 3 chr17 661696 669581 a 0 - 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 661696 | 671506 | a | 0 | - | | chr1 | 661696 | 666126 | a | 0 | - | | chr17 | 661696 | 665741 | a | 0 | + | | chr17 | 661696 | 669581 | 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 | 6267864 | 6277721 | a | 0 | + | | chr1 | 1472133 | 1473362 | a | 0 | + | | chr1 | 6776981 | 6778210 | a | 0 | - | | chr1 | 2428484 | 2429713 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 6776981 | 6778210 | a | 0 | - | | chr1 | 2428484 | 2429713 | a | 0 | - | | chr1 | 2193190 | 2194419 | a | 0 | - | | chr1 | 1 | 1230 | 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/tmpgammngp4/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1472133 1473362 a 0 + 1 1 chr1 6267864 6277721 a 0 + 2 2 chr1 1 1230 a 0 - 3 3 chr1 2193190 2194419 a 0 - 4 4 chr1 2428484 2429713 a 0 - 5 5 chr1 6776981 6778210 a 0 - 6 6 chr12 129385 131357 a 0 - 7 7 chr2 7095477 7096706 a 0 - 8 8 chr22 6297584 6298813 a 0 - 9 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6267864 | 6277721 | a | 0 | + | | chr1 | 1472133 | 1473362 | a | 0 | + | | chr1 | 6776981 | 6778210 | a | 0 | - | | chr1 | 2428484 | 2429713 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 6776981 | 6778210 | a | 0 | - | | chr1 | 2428484 | 2429713 | a | 0 | - | | chr1 | 2193190 | 2194419 | a | 0 | - | | chr1 | 1 | 1230 | 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 | 4817744 | 4819403 | a | 0 | + | | chr1 | 9584706 | 9585158 | a | 0 | + | | chr1 | 8697007 | 8704145 | a | 0 | + | | chr1 | 4817744 | 4823457 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr10 | 2152042 | 2155615 | a | 0 | + | | chr10 | 6524068 | 6527989 | a | 0 | - | | chr19 | 956549 | 962956 | a | 0 | - | | chr21 | 2181609 | 2187874 | 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/tmp1ab_z5vc/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4817744 4819403 a 0 + 1 1 chr1 4817744 4823457 a 0 + 1 2 chr1 7326122 7334065 a 0 + 2 3 chr1 8697007 8704145 a 0 + 3 4 chr1 9584706 9585158 a 0 + 4 5 chr10 2152042 2155615 a 0 + 5 6 chr10 6524068 6527989 a 0 - 6 7 chr19 956549 962956 a 0 - 7 8 chr21 2181609 2187874 a 0 + 8 9 chr6 4817744 4827744 a 0 - 9 10 chrX 9375769 9375771 a 0 + 10 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4817744 | 4819403 | a | 0 | + | | chr1 | 9584706 | 9585158 | a | 0 | + | | chr1 | 8697007 | 8704145 | a | 0 | + | | chr1 | 4817744 | 4823457 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr10 | 2152042 | 2155615 | a | 0 | + | | chr10 | 6524068 | 6527989 | a | 0 | - | | chr19 | 956549 | 962956 | a | 0 | - | | chr21 | 2181609 | 2187874 | 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 | 688532 | 690360 | a | 0 | - | | chr1 | 2 | 4 | a | 0 | - | | chr1 | 3007976 | 3016622 | a | 0 | - | | chr1 | 9334419 | 9340735 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr5 | 952696 | 953623 | a | 0 | - | | chr9 | 2173003 | 2181649 | a | 0 | + | | chr10 | 8021587 | 8025368 | a | 0 | - | | chr22 | 2892424 | 2896979 | 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/tmpwunjw6tj/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2 4 a 0 - 1 1 chr1 688532 690360 a 0 - 2 2 chr1 3007976 3016622 a 0 - 3 3 chr1 8146634 8152490 a 0 - 4 4 chr1 9334419 9340735 a 0 - 5 5 chr10 8021587 8025368 a 0 - 6 6 chr22 2892424 2896979 a 0 - 7 7 chr5 952696 953623 a 0 - 8 8 chr9 2173003 2181649 a 0 + 9 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 688532 | 690360 | a | 0 | - | | chr1 | 2 | 4 | a | 0 | - | | chr1 | 3007976 | 3016622 | a | 0 | - | | chr1 | 9334419 | 9340735 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr5 | 952696 | 953623 | a | 0 | - | | chr9 | 2173003 | 2181649 | a | 0 | + | | chr10 | 8021587 | 8025368 | a | 0 | - | | chr22 | 2892424 | 2896979 | 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 | 5074279 | 5082164 | a | 0 | + | | chr1 | 1 | 223 | a | 0 | + | | chr1 | 9488594 | 9490521 | a | 0 | + | | chr1 | 3200145 | 3205641 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 9924896 | 9932031 | a | 0 | + | | chr1 | 8386905 | 8394979 | a | 0 | + | | chr1 | 9488594 | 9490914 | a | 0 | - | | chr1 | 1451448 | 1460122 | 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/tmpz65c61gd/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 223 a 0 + 1 1 chr1 3200145 3205641 a 0 + 2 2 chr1 5074279 5082164 a 0 + 3 3 chr1 8386905 8394979 a 0 + 4 4 chr1 9488594 9490521 a 0 + 5 5 chr1 9924896 9932031 a 0 + 6 6 chr1 1451448 1460122 a 0 - 7 7 chr1 9488594 9490914 a 0 - 8 8 chr10 2450257 2453155 a 0 - 9 9 chr14 7847281 7851915 a 0 + 10 10 chr19 1223143 1231965 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5074279 | 5082164 | a | 0 | + | | chr1 | 1 | 223 | a | 0 | + | | chr1 | 9488594 | 9490521 | a | 0 | + | | chr1 | 3200145 | 3205641 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 9924896 | 9932031 | a | 0 | + | | chr1 | 8386905 | 8394979 | a | 0 | + | | chr1 | 9488594 | 9490914 | a | 0 | - | | chr1 | 1451448 | 1460122 | 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 | 8487486 | 8492265 | a | 0 | + | | chr1 | 850252 | 852967 | a | 0 | + | | chr1 | 7100096 | 7100098 | a | 0 | + | | chr22 | 8272133 | 8273979 | 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/tmpasyq_xu6/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 850252 852967 a 0 + 1 1 chr1 7100096 7100098 a 0 + 2 2 chr1 8487486 8492265 a 0 + 3 3 chr22 8272133 8273979 a 0 - 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8487486 | 8492265 | a | 0 | + | | chr1 | 850252 | 852967 | a | 0 | + | | chr1 | 7100096 | 7100098 | a | 0 | + | | chr22 | 8272133 | 8273979 | 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 | 6255656 | 6261634 | a | 0 | + | | chr1 | 420136 | 421965 | 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/tmpmi8cr9jw/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 420136 421965 a 0 + 1 1 chr1 6255656 6261634 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6255656 | 6261634 | a | 0 | + | | chr1 | 420136 | 421965 | 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 | 3132971 | 3138840 | a | 0 | + | | chr1 | 3300739 | 3308054 | a | 0 | + | | chr1 | 8626823 | 8636108 | a | 0 | + | | chr1 | 1593523 | 1596773 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr5 | 4192617 | 4201509 | a | 0 | + | | chr7 | 2939608 | 2940963 | a | 0 | + | | chr9 | 9389753 | 9398446 | a | 0 | - | | chr12 | 3801438 | 3802022 | 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/tmpt9lgeqtm/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1593523 1596773 a 0 + 1 1 chr1 3132971 3138840 a 0 + 2 2 chr1 3300739 3308054 a 0 + 3 3 chr1 8626823 8636108 a 0 + 4 4 chr1 7337809 7345252 a 0 - 5 5 chr1 8216379 8226379 a 0 - 6 6 chr1 9999999 10000258 a 0 - 7 7 chr12 3801438 3802022 a 0 - 8 8 chr5 4192617 4201509 a 0 + 9 9 chr7 2939608 2940963 a 0 + 10 10 chr9 9389753 9398446 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3132971 | 3138840 | a | 0 | + | | chr1 | 3300739 | 3308054 | a | 0 | + | | chr1 | 8626823 | 8636108 | a | 0 | + | | chr1 | 1593523 | 1596773 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr5 | 4192617 | 4201509 | a | 0 | + | | chr7 | 2939608 | 2940963 | a | 0 | + | | chr9 | 9389753 | 9398446 | a | 0 | - | | chr12 | 3801438 | 3802022 | 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 | 6886823 | 6892618 | a | 0 | - | | chr1 | 3966682 | 3969854 | a | 0 | - | | chr1 | 3582696 | 3583401 | a | 0 | - | | chr1 | 9051535 | 9054707 | 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/tmpva4cza6n/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3582696 3583401 a 0 - 1 1 chr1 3966682 3969854 a 0 - 2 2 chr1 6886823 6892618 a 0 - 3 3 chr1 9051535 9054707 a 0 - 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6886823 | 6892618 | a | 0 | - | | chr1 | 3966682 | 3969854 | a | 0 | - | | chr1 | 3582696 | 3583401 | a | 0 | - | | chr1 | 9051535 | 9054707 | 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 | 8378359 | 8385723 | a | 0 | + | | chr12 | 3772595 | 3779959 | 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/tmp24hwkpj5/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 8378359 8385723 a 0 + 1 1 chr12 3772595 3779959 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8378359 | 8385723 | a | 0 | + | | chr12 | 3772595 | 3779959 | 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 | 3905578 | 3908290 | 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/tmpsxtdja12/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3905578 3908290 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3905578 | 3908290 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr5 | 9652043 | 9652044 | a | 0 | - | | chr14 | 5453875 | 5463875 | 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/tmp2_54hxqv/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr14 5453875 5463875 a 0 - 1 1 chr5 9652043 9652044 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr5 | 9652043 | 9652044 | a | 0 | - | | chr14 | 5453875 | 5463875 | 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 | 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. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp7bzpoz8c/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 3 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 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. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4178516 | 4181225 | a | 0 | + | | chr1 | 3484647 | 3491803 | a | 0 | + | | chr1 | 171879 | 178253 | a | 0 | - | | chr1 | 1118684 | 1120875 | a | 0 | - | | chr1 | 1610608 | 1612799 | a | 0 | - | | chr14 | 4398726 | 4406279 | a | 0 | - | | chr19 | 9432604 | 9442547 | 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/tmpddhrog83/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3484647 3491803 a 0 + 1 1 chr1 4178516 4181225 a 0 + 2 2 chr1 171879 178253 a 0 - 3 3 chr1 1118684 1120875 a 0 - 4 4 chr1 1610608 1612799 a 0 - 5 5 chr14 4398726 4406279 a 0 - 6 6 chr19 9432604 9442547 a 0 - 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4178516 | 4181225 | a | 0 | + | | chr1 | 3484647 | 3491803 | a | 0 | + | | chr1 | 171879 | 178253 | a | 0 | - | | chr1 | 1118684 | 1120875 | a | 0 | - | | chr1 | 1610608 | 1612799 | a | 0 | - | | chr14 | 4398726 | 4406279 | a | 0 | - | | chr19 | 9432604 | 9442547 | 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 | 1162694 | 1166821 | a | 0 | + | | chr1 | 4298797 | 4306786 | a | 0 | + | | chr1 | 1357796 | 1359412 | a | 0 | + | | chr1 | 6224666 | 6230541 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr13 | 9999999 | 10001891 | a | 0 | - | | chr17 | 349764 | 356153 | a | 0 | - | | chr18 | 8235705 | 8244006 | a | 0 | - | | chr22 | 3545331 | 3550209 | 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/tmpewj02com/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1162694 1166821 a 0 + 1 1 chr1 1357796 1359412 a 0 + 2 2 chr1 4298797 4306786 a 0 + 3 3 chr1 6224666 6230541 a 0 + 4 4 chr1 1887680 1891321 a 0 - 5 5 chr1 6792516 6798994 a 0 - 6 6 chr13 9999999 10001891 a 0 - 7 7 chr17 349764 356153 a 0 - 8 8 chr18 8235705 8244006 a 0 - 9 9 chr22 3545331 3550209 a 0 + 10 10 chr9 677026 687026 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1162694 | 1166821 | a | 0 | + | | chr1 | 4298797 | 4306786 | a | 0 | + | | chr1 | 1357796 | 1359412 | a | 0 | + | | chr1 | 6224666 | 6230541 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr13 | 9999999 | 10001891 | a | 0 | - | | chr17 | 349764 | 356153 | a | 0 | - | | chr18 | 8235705 | 8244006 | a | 0 | - | | chr22 | 3545331 | 3550209 | 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 | 5061266 | 5069073 | a | 0 | - | | chr1 | 8032717 | 8040524 | a | 0 | - | | chr6 | 9216708 | 9224515 | a | 0 | - | | chr6 | 4648332 | 4656139 | a | 0 | - | | chr15 | 5434976 | 5437935 | 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 -s -i <(sort -k1,1 -k2,2n /tmp/tmpp3k1r2u5/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5061266 5069073 a 0 - 1 1 chr1 8032717 8040524 a 0 - 2 2 chr15 5434976 5437935 a 0 - 3 3 chr6 4648332 4656139 a 0 - 4 4 chr6 9216708 9224515 a 0 - 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5061266 | 5069073 | a | 0 | - | | chr1 | 8032717 | 8040524 | a | 0 | - | | chr6 | 9216708 | 9224515 | a | 0 | - | | chr6 | 4648332 | 4656139 | a | 0 | - | | chr15 | 5434976 | 5437935 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3070610 | 3071483 | a | 0 | + | | chr2 | 2832445 | 2838644 | a | 0 | - | | chr16 | 7818629 | 7821873 | a | 0 | - | | chr20 | 10000000 | 10001731 | 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/tmp6eeripwt/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3070610 3071483 a 0 + 1 1 chr16 7818629 7821873 a 0 - 2 2 chr2 2832445 2838644 a 0 - 3 3 chr20 10000000 10001731 a 0 - 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3070610 | 3071483 | a | 0 | + | | chr2 | 2832445 | 2838644 | a | 0 | - | | chr16 | 7818629 | 7821873 | a | 0 | - | | chr20 | 10000000 | 10001731 | 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 | 3790456 | 3799572 | a | 0 | + | | chr1 | 7738930 | 7748046 | a | 0 | - | | chr5 | 5085332 | 5094448 | a | 0 | - | | chr6 | 9471469 | 9480585 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr11 | 2092178 | 2101294 | a | 0 | + | | chr22 | 1765993 | 1775109 | a | 0 | - | | chrY | 9116072 | 9125188 | a | 0 | - | | chrY | 5268578 | 5277694 | 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 cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpu9hy0sy3/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3790456 3799572 a 0 + 1 1 chr1 7738930 7748046 a 0 - 2 2 chr10 7436522 7445638 a 0 - 3 3 chr11 2092178 2101294 a 0 + 4 4 chr22 1765993 1775109 a 0 - 5 5 chr5 5085332 5094448 a 0 - 6 6 chr6 9471469 9480585 a 0 - 7 7 chrY 5268578 5277694 a 0 - 8 8 chrY 9116072 9125188 a 0 - 9 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3790456 | 3799572 | a | 0 | + | | chr1 | 7738930 | 7748046 | a | 0 | - | | chr5 | 5085332 | 5094448 | a | 0 | - | | chr6 | 9471469 | 9480585 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr11 | 2092178 | 2101294 | a | 0 | + | | chr22 | 1765993 | 1775109 | a | 0 | - | | chrY | 9116072 | 9125188 | a | 0 | - | | chrY | 5268578 | 5277694 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 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 | 4839463 | 4842422 | a | 0 | + | | chr1 | 3428452 | 3428882 | a | 0 | - | | chr1 | 1887615 | 1890564 | a | 0 | - | | chr2 | 2639471 | 2643668 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr11 | 5393918 | 5400006 | a | 0 | + | | chr18 | 8571072 | 8575191 | a | 0 | + | | chr18 | 9828475 | 9834261 | a | 0 | - | | chr22 | 1 | 7871 | 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 cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp9pha0ymv/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4839463 4842422 a 0 + 1 1 chr1 1887615 1890564 a 0 - 2 2 chr1 3428452 3428882 a 0 - 3 3 chr11 5393918 5400006 a 0 + 4 4 chr18 8571072 8575191 a 0 + 5 5 chr18 9828475 9834261 a 0 - 6 6 chr2 2639471 2643668 a 0 - 7 7 chr22 1 7871 a 0 - 8 8 chr4 3175539 3178988 a 0 - 9 9 chr5 1 3833 a 0 + 10 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4839463 | 4842422 | a | 0 | + | | chr1 | 3428452 | 3428882 | a | 0 | - | | chr1 | 1887615 | 1890564 | a | 0 | - | | chr2 | 2639471 | 2643668 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr11 | 5393918 | 5400006 | a | 0 | + | | chr18 | 8571072 | 8575191 | a | 0 | + | | chr18 | 9828475 | 9834261 | a | 0 | - | | chr22 | 1 | 7871 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 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 | 7557975 | 7567975 | a | 0 | + | | chr1 | 3767060 | 3771706 | a | 0 | - | | chr1 | 5386068 | 5391199 | a | 0 | - | | chr1 | 6467537 | 6475189 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr15 | 4667004 | 4668101 | a | 0 | + | | chr20 | 4937092 | 4942994 | a | 0 | + | | chr22 | 8583674 | 8588089 | a | 0 | - | | chrX | 3208712 | 3209809 | 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/tmpf6k8hafs/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 7557975 7567975 a 0 + 1 1 chr1 3767060 3771706 a 0 - 2 2 chr1 5386068 5391199 a 0 - 3 3 chr1 5386068 5395935 a 0 - 3 4 chr1 5527830 5531467 a 0 - 4 5 chr1 6467537 6475189 a 0 - 5 6 chr15 4667004 4668101 a 0 + 6 7 chr20 4937092 4942994 a 0 + 7 8 chr22 8583674 8588089 a 0 - 8 9 chr3 6133873 6135391 a 0 + 9 10 chrX 3208712 3209809 a 0 + 10 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7557975 | 7567975 | a | 0 | + | | chr1 | 3767060 | 3771706 | a | 0 | - | | chr1 | 5386068 | 5391199 | a | 0 | - | | chr1 | 6467537 | 6475189 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr15 | 4667004 | 4668101 | a | 0 | + | | chr20 | 4937092 | 4942994 | a | 0 | + | | chr22 | 8583674 | 8588089 | a | 0 | - | | chrX | 3208712 | 3209809 | 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 | 3267222 | 3275613 | 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/tmpm993a3rq/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3267222 3275613 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3267222 | 3275613 | 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 | 145818 | 155817 | 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/tmp76asqbk4/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 145818 155817 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 145818 | 155817 | 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 | 2654115 | 2659452 | a | 0 | - | | chr1 | 630907 | 633934 | a | 0 | - | | chr1 | 2 | 4552 | a | 0 | - | | chr8 | 6031094 | 6038487 | a | 0 | - | | chr14 | 8464750 | 8468286 | 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 -s -i <(sort -k1,1 -k2,2n /tmp/tmp5a8qttr6/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2 4552 a 0 - 1 1 chr1 630907 633934 a 0 - 2 2 chr1 2654115 2659452 a 0 - 3 3 chr14 8464750 8468286 a 0 - 4 4 chr8 6031094 6038487 a 0 - 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2654115 | 2659452 | a | 0 | - | | chr1 | 630907 | 633934 | a | 0 | - | | chr1 | 2 | 4552 | a | 0 | - | | chr8 | 6031094 | 6038487 | a | 0 | - | | chr14 | 8464750 | 8468286 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6251545 | 6253441 | a | 0 | - | | chr1 | 2392499 | 2399373 | a | 0 | - | | chr1 | 803413 | 807742 | a | 0 | - | | chrM | 9171791 | 9180987 | 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/tmpoy5xu8rf/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 803413 807742 a 0 - 1 1 chr1 2392499 2399373 a 0 - 2 2 chr1 6251545 6253441 a 0 - 3 3 chrM 9171791 9180987 a 0 + 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6251545 | 6253441 | a | 0 | - | | chr1 | 2392499 | 2399373 | a | 0 | - | | chr1 | 803413 | 807742 | a | 0 | - | | chrM | 9171791 | 9180987 | 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 | 3760991 | 3765568 | a | 0 | + | | chr20 | 3760991 | 3765568 | 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/tmpkcxsdqbe/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3760991 3765568 a 0 + 1 1 chr20 3760991 3765568 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3760991 | 3765568 | a | 0 | + | | chr20 | 3760991 | 3765568 | 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 | 9999999 | 10000241 | a | 0 | + | | chr1 | 10000000 | 10003266 | a | 0 | + | | chr3 | 5076431 | 5076433 | a | 0 | - | | chr3 | 8007839 | 8012389 | a | 0 | - | | chr14 | 442974 | 445822 | a | 0 | + | | chr18 | 4020448 | 4027431 | a | 0 | + | | chr19 | 8058253 | 8066023 | 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/tmp7zgjw_wh/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 9999999 10000241 a 0 + 1 1 chr1 10000000 10003266 a 0 + 1 2 chr14 442974 445822 a 0 + 2 3 chr18 4020448 4027431 a 0 + 3 4 chr19 8058253 8066023 a 0 - 4 5 chr3 5076431 5076433 a 0 - 5 6 chr3 8007839 8012389 a 0 - 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9999999 | 10000241 | a | 0 | + | | chr1 | 10000000 | 10003266 | a | 0 | + | | chr3 | 5076431 | 5076433 | a | 0 | - | | chr3 | 8007839 | 8012389 | a | 0 | - | | chr14 | 442974 | 445822 | a | 0 | + | | chr18 | 4020448 | 4027431 | a | 0 | + | | chr19 | 8058253 | 8066023 | 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 | 475788 | 483627 | a | 0 | + | | chr1 | 7365278 | 7365524 | a | 0 | - | | chr1 | 475788 | 475789 | a | 0 | - | | chrX | 8684030 | 8692128 | a | 0 | - | | chrY | 475788 | 475809 | 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 -s -i <(sort -k1,1 -k2,2n /tmp/tmpgmh9jstb/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 475788 483627 a 0 + 1 1 chr1 475788 475789 a 0 - 2 2 chr1 7365278 7365524 a 0 - 3 3 chrX 8684030 8692128 a 0 - 4 4 chrY 475788 475809 a 0 - 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 475788 | 483627 | a | 0 | + | | chr1 | 7365278 | 7365524 | a | 0 | - | | chr1 | 475788 | 475789 | a | 0 | - | | chrX | 8684030 | 8692128 | a | 0 | - | | chrY | 475788 | 475809 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr10 | 9654154 | 9661617 | 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/tmp7szs_xbk/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr10 9654154 9661617 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr10 | 9654154 | 9661617 | 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 | 9862635 | 9872431 | a | 0 | + | | chr1 | 8322672 | 8331133 | a | 0 | + | | chr1 | 9990786 | 10000266 | a | 0 | + | | chr1 | 4721384 | 4725021 | a | 0 | + | | chr1 | 4377029 | 4377173 | a | 0 | - | | chrM | 9056577 | 9066535 | 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/tmpjaegihfv/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4721384 4725021 a 0 + 1 1 chr1 8322672 8331133 a 0 + 2 2 chr1 9862635 9872431 a 0 + 3 3 chr1 9990786 10000266 a 0 + 4 4 chr1 4377029 4377173 a 0 - 5 5 chrM 9056577 9066535 a 0 - 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9862635 | 9872431 | a | 0 | + | | chr1 | 8322672 | 8331133 | a | 0 | + | | chr1 | 9990786 | 10000266 | a | 0 | + | | chr1 | 4721384 | 4725021 | a | 0 | + | | chr1 | 4377029 | 4377173 | a | 0 | - | | chrM | 9056577 | 9066535 | 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 | 3846273 | 3849319 | a | 0 | + | | chr1 | 5796272 | 5805665 | a | 0 | - | | chr1 | 4194301 | 4197647 | a | 0 | - | | chr1 | 5471783 | 5475129 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr16 | 6646250 | 6649596 | a | 0 | - | | chr16 | 391364 | 398587 | a | 0 | - | | chr16 | 6739136 | 6739779 | a | 0 | - | | chr16 | 2933851 | 2935489 | 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/tmpn9pcoe1_/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3846273 3849319 a 0 + 1 1 chr1 4194301 4197647 a 0 - 2 2 chr1 5471783 5475129 a 0 - 3 3 chr1 5796272 5805665 a 0 - 4 4 chr16 4256329 4266328 a 0 + 5 5 chr16 391364 398587 a 0 - 6 6 chr16 2933851 2935489 a 0 - 7 7 chr16 6646250 6649596 a 0 - 8 8 chr16 6739136 6739779 a 0 - 9 9 chr8 6181409 6182549 a 0 + 10 10 chr8 4194301 4197647 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3846273 | 3849319 | a | 0 | + | | chr1 | 5796272 | 5805665 | a | 0 | - | | chr1 | 4194301 | 4197647 | a | 0 | - | | chr1 | 5471783 | 5475129 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr16 | 6646250 | 6649596 | a | 0 | - | | chr16 | 391364 | 398587 | a | 0 | - | | chr16 | 6739136 | 6739779 | a | 0 | - | | chr16 | 2933851 | 2935489 | 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 | 587059 | 587060 | a | 0 | + | | chr1 | 5197060 | 5198071 | a | 0 | + | | chr1 | 5197060 | 5197351 | a | 0 | + | | chr1 | 5197060 | 5197061 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 1007937 | 1009892 | a | 0 | - | | chr1 | 5197060 | 5201275 | a | 0 | - | | chr1 | 6296108 | 6300490 | a | 0 | - | | chr1 | 5197060 | 5200826 | 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/tmpjbd_p1db/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 587059 587060 a 0 + 1 1 chr1 668721 672123 a 0 + 2 2 chr1 5197060 5197061 a 0 + 3 3 chr1 5197060 5197351 a 0 + 3 4 chr1 5197060 5198071 a 0 + 3 5 chr1 5197060 5200531 a 0 + 3 6 chr1 1007937 1009892 a 0 - 4 7 chr1 5197060 5198825 a 0 - 5 8 chr1 5197060 5200826 a 0 - 5 9 chr1 5197060 5201275 a 0 - 5 10 chr1 6296108 6300490 a 0 - 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 587059 | 587060 | a | 0 | + | | chr1 | 5197060 | 5198071 | a | 0 | + | | chr1 | 5197060 | 5197351 | a | 0 | + | | chr1 | 5197060 | 5197061 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 1007937 | 1009892 | a | 0 | - | | chr1 | 5197060 | 5201275 | a | 0 | - | | chr1 | 6296108 | 6300490 | a | 0 | - | | chr1 | 5197060 | 5200826 | 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 | 2473947 | 2483629 | a | 0 | + | | chr1 | 8080178 | 8082908 | a | 0 | + | | chr1 | 3291113 | 3300036 | a | 0 | + | | chr1 | 6686690 | 6695634 | a | 0 | - | | chr6 | 4791378 | 4797330 | a | 0 | + | | chr12 | 1611456 | 1611542 | 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/tmpm9yr02qi/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2473947 2483629 a 0 + 1 1 chr1 3291113 3300036 a 0 + 2 2 chr1 8080178 8082908 a 0 + 3 3 chr1 6686690 6695634 a 0 - 4 4 chr12 1611456 1611542 a 0 - 5 5 chr6 4791378 4797330 a 0 + 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2473947 | 2483629 | a | 0 | + | | chr1 | 8080178 | 8082908 | a | 0 | + | | chr1 | 3291113 | 3300036 | a | 0 | + | | chr1 | 6686690 | 6695634 | a | 0 | - | | chr6 | 4791378 | 4797330 | a | 0 | + | | chr12 | 1611456 | 1611542 | 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 | 1 | 2 | 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/tmpr_s8ch06/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. ---------------------------------- 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] _______________________________ [gw1] linux -- Python 3.12.3 /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., 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/tmpwtb8ya8t/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 | 49327 | 55622 | a | 0 | - | | chr4 | 7486093 | 7490110 | a | 0 | + | | chr6 | 2696224 | 2696951 | a | 0 | - | | chrY | 212196 | 213656 | 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/tmpnheowl7h/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 49327 55622 - 1 chr4 7486093 7490110 + 1 chr6 2696224 2696951 - 1 chrY 212196 213656 + 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 49327 55622 1 1 chr4 7486093 7490110 1 2 chr6 2696224 2696951 1 3 chrY 212196 213656 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7486093 | 7490110 | a | 0 | + | | chr1 | 212196 | 213656 | a | 0 | + | | chr1 | 49327 | 55622 | a | 0 | - | | chr1 | 655384 | 656111 | 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/tmprqvgc5np/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 49327 55622 - 1 chr1 212196 213656 + 1 chr1 655384 656111 - 1 chr1 7486093 7490110 + 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 49327 55622 1 1 chr1 212196 213656 1 2 chr1 655384 656111 1 3 chr1 7486093 7490110 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 49327 | 55622 | a | 0 | + | | chr1 | 212196 | 213656 | a | 0 | + | | chr1 | 655384 | 661027 | a | 0 | + | | chr1 | 202800 | 203570 | a | 0 | + | | chr1 | 7486093 | 7490110 | 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/tmpoa0g83ja/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 49327 55622 + 1 chr1 202800 203570 + 1 chr1 212196 213656 + 1 chr1 655384 661027 + 1 chr1 7486093 7490110 - 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 49327 55622 1 1 chr1 202800 203570 1 2 chr1 212196 213656 1 3 chr1 655384 661027 1 4 chr1 7486093 7490110 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7486093 | 7487553 | a | 0 | + | | chr1 | 49327 | 53939 | a | 0 | + | | chr1 | 655384 | 656668 | a | 0 | + | | chr1 | 212196 | 212972 | 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/tmpdcu645mx/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 49327 53939 + 1 chr1 212196 212972 - 1 chr1 655384 656668 + 1 chr1 7486093 7487553 + 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 49327 53939 1 1 chr1 212196 212972 1 2 chr1 655384 656668 1 3 chr1 7486093 7487553 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 212196 | 212972 | a | 0 | + | | chr1 | 7486093 | 7487553 | a | 0 | - | | chr1 | 49327 | 53939 | a | 0 | - | | chr1 | 655384 | 656668 | 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/tmpiu0c2iiw/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 49327 53939 - 1 chr1 212196 212972 + 1 chr1 655384 656668 - 1 chr1 7486093 7487553 - 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 49327 53939 1 1 chr1 212196 212972 1 2 chr1 655384 656668 1 3 chr1 7486093 7487553 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7486093 | 7486866 | a | 0 | + | | chr18 | 7486093 | 7486114 | a | 0 | - | | chrY | 7486093 | 7486268 | 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/tmp3kh688u3/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7486093 7486866 + 1 chr18 7486093 7486114 - 1 chrY 7486093 7486268 - 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 7486093 7486866 1 1 chr18 7486093 7486114 1 2 chrY 7486093 7486268 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7486093 | 7486866 | a | 0 | + | | chr18 | 7486093 | 7486114 | a | 0 | - | | chrY | 7486093 | 7486268 | 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/tmpn6c07rsi/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7486093 7486866 + 1 chr18 7486093 7486114 - 1 chrY 7486093 7486268 - 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 7486093 7486866 1 1 chr18 7486093 7486114 1 2 chrY 7486093 7486268 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3443104 | 3451565 | a | 0 | + | | chr1 | 1 | 7646 | a | 0 | + | | chr1 | 5575848 | 5585047 | a | 0 | + | | chr1 | 7425999 | 7433731 | a | 0 | - | | chr1 | 5575848 | 5578212 | a | 0 | - | | chr1 | 5575848 | 5579641 | a | 0 | - | | chr1 | 5575848 | 5576899 | a | 0 | - | | chr1 | 6320516 | 6325776 | 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 merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpprrl9d04/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 7646 + 1 chr1 3443104 3451565 + 1 chr1 5575848 5585047 - 4 chr1 6320516 6325776 - 1 chr1 7425999 7433731 - 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 7646 1 1 chr1 3443104 3451565 1 2 chr1 5575848 5585047 4 3 chr1 6320516 6325776 1 4 chr1 7425999 7433731 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 407137 | 415598 | a | 0 | + | | chr1 | 407137 | 414782 | a | 0 | + | | chr1 | 407137 | 416336 | a | 0 | + | | chr1 | 407137 | 414869 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 5230086 | 5235346 | a | 0 | - | | chr1 | 407137 | 410930 | a | 0 | - | | chr1 | 407137 | 410930 | a | 0 | - | | chr1 | 407137 | 410930 | 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/tmpxynogop9/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 407137 416336 - 10 chr1 5230086 5235346 - 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 407137 416336 10 1 chr1 5230086 5235346 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/tmp8j4_zgu3/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/tmpcqxquvt9/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/tmpsyo643sg/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/tmpsmypjq9k/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/tmpoqmn5m47/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/tmpuywprqip/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/tmpis310077/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/tmp9ccnbmhy/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/tmpk1jl0smg/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/tmp8cphtgyw/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/tmpwc5us_lq/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/tmpau_2qug2/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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr9 | 2592059 | 2601297 | a | 0 | - | | chr12 | 3038111 | 3042532 | a | 0 | - | | chrM | 7561821 | 7568499 | a | 0 | + | | chrM | 4506940 | 4510660 | a | 0 | + | | chrX | 7650 | 14731 | 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/tmp20tu0abr/f1.bed) resultresultresultresultresultresultresultresultresultresult chr12 3038111 3042532 - 1 chr9 2592059 2601297 - 1 chrM 4506940 4510660 + 1 chrM 7561821 7568499 + 1 chrX 7650 14731 + 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 chr12 3038111 3042532 1 1 chr9 2592059 2601297 1 2 chrM 4506940 4510660 1 3 chrM 7561821 7568499 1 4 chrX 7650 14731 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8860835 | 8862252 | a | 0 | + | | chr1 | 8540623 | 8542644 | a | 0 | + | | chr1 | 4143129 | 4151287 | a | 0 | - | | chr1 | 7361936 | 7369247 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 6507316 | 6512307 | a | 0 | - | | chr1 | 4093626 | 4100471 | a | 0 | - | | chr1 | 123261 | 128520 | a | 0 | - | | chr1 | 316454 | 324213 | 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/tmpcwu84dwx/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 123261 128520 - 1 chr1 316454 324213 - 1 chr1 4093626 4100471 - 1 chr1 4143129 4151287 - 1 chr1 6507316 6512307 - 1 chr1 7361936 7369247 - 1 chr1 8540623 8542644 + 1 chr1 8860835 8862252 + 1 chr1 8913331 8920990 - 1 chr19 2630871 2630872 - 1 chr21 1514446 1519947 + 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 123261 128520 1 1 chr1 316454 324213 1 2 chr1 4093626 4100471 1 3 chr1 4143129 4151287 1 4 chr1 6507316 6512307 1 5 chr1 7361936 7369247 1 6 chr1 8540623 8542644 1 7 chr1 8860835 8862252 1 8 chr1 8913331 8920990 1 9 chr19 2630871 2630872 1 10 chr21 1514446 1519947 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr12 | 9051695 | 9053255 | 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/tmp4w4tim33/f1.bed) resultresultresultresultresultresultresultresultresultresult chr12 9051695 9053255 - 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 chr12 9051695 9053255 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6339424 | 6347254 | a | 0 | + | | chr1 | 9285059 | 9285398 | a | 0 | + | | chr1 | 8469287 | 8477784 | a | 0 | + | | chr1 | 5671702 | 5675205 | a | 0 | - | | chr2 | 6339424 | 6347828 | a | 0 | - | | chr3 | 4429241 | 4431306 | a | 0 | - | | chr12 | 2960055 | 2969396 | 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/tmpp2e47fcy/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5671702 5675205 - 1 chr1 6339424 6347254 + 1 chr1 8469287 8477784 + 1 chr1 9285059 9285398 + 1 chr12 2960055 2969396 - 1 chr2 6339424 6347828 - 1 chr3 4429241 4431306 - 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 5671702 5675205 1 1 chr1 6339424 6347254 1 2 chr1 8469287 8477784 1 3 chr1 9285059 9285398 1 4 chr12 2960055 2969396 1 5 chr2 6339424 6347828 1 6 chr3 4429241 4431306 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4569387 | 4576618 | a | 0 | + | | chr1 | 7881193 | 7884628 | a | 0 | + | | chr3 | 12574 | 21584 | a | 0 | - | | chr5 | 1340756 | 1347783 | a | 0 | - | | chr7 | 6781459 | 6789280 | a | 0 | + | | chr8 | 4074423 | 4084013 | a | 0 | - | | chr11 | 468275 | 470572 | a | 0 | - | | chr15 | 2806242 | 2815290 | 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/tmpedhxv4j7/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4569387 4576618 + 1 chr1 7881193 7884628 + 1 chr11 468275 470572 - 1 chr15 2806242 2815290 - 1 chr3 12574 21584 - 1 chr5 1340756 1347783 - 1 chr7 6781459 6789280 + 1 chr8 4074423 4084013 - 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 4569387 4576618 1 1 chr1 7881193 7884628 1 2 chr11 468275 470572 1 3 chr15 2806242 2815290 1 4 chr3 12574 21584 1 5 chr5 1340756 1347783 1 6 chr7 6781459 6789280 1 7 chr8 4074423 4084013 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 719699 | 721835 | a | 0 | + | | chr1 | 9004854 | 9008794 | a | 0 | - | | chr1 | 5019479 | 5021698 | a | 0 | - | | chr1 | 7612186 | 7622186 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr18 | 9210955 | 9220030 | a | 0 | + | | chr18 | 9611146 | 9617560 | a | 0 | + | | chr18 | 3742230 | 3743176 | a | 0 | - | | chr18 | 7693254 | 7694429 | 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/tmpvoo4ibvs/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 719699 721835 + 1 chr1 5019479 5021698 - 1 chr1 7612186 7622186 - 1 chr1 9004854 9008794 - 1 chr16 4884125 4889042 + 1 chr18 3742230 3743176 - 1 chr18 7693254 7694429 - 1 chr18 9210955 9220030 + 1 chr18 9611146 9617560 + 1 chr2 4437811 4444385 - 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 719699 721835 1 1 chr1 5019479 5021698 1 2 chr1 7612186 7622186 1 3 chr1 9004854 9008794 1 4 chr16 4884125 4889042 1 5 chr18 3742230 3743176 1 6 chr18 7693254 7694429 1 7 chr18 9210955 9220030 1 8 chr18 9611146 9617560 1 9 chr2 4437811 4444385 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 970898 | 980898 | 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/tmpd3rgmz57/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 970898 980898 - 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 970898 980898 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2181225 | 2184404 | a | 0 | + | | chr1 | 9607392 | 9613043 | a | 0 | - | | chr12 | 1894013 | 1894014 | a | 0 | + | | chr19 | 2013874 | 2013875 | 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 -i <(sort -k1,1 -k2,2n /tmp/tmp8qjd776a/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2181225 2184404 + 1 chr1 9607392 9613043 - 1 chr12 1894013 1894014 + 1 chr19 2013874 2013875 + 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 2181225 2184404 1 1 chr1 9607392 9613043 1 2 chr12 1894013 1894014 1 3 chr19 2013874 2013875 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6163275 | 6170009 | a | 0 | + | | chr1 | 7605209 | 7608588 | a | 0 | + | | chr1 | 376669 | 381955 | a | 0 | + | | chr1 | 388127 | 396694 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 7146738 | 7155828 | a | 0 | + | | chr1 | 3647139 | 3651878 | a | 0 | - | | chr1 | 3403971 | 3412037 | a | 0 | - | | chr1 | 7146738 | 7150273 | 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/tmpb0756v2j/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 376669 381955 + 1 chr1 388127 396694 + 1 chr1 3403971 3412037 - 1 chr1 3647139 3651878 - 1 chr1 6163275 6170009 + 1 chr1 7146738 7155828 - 2 chr1 7605209 7608588 + 1 chr15 230425 231516 - 1 chr17 5195837 5199216 + 1 chr2 5202380 5209970 - 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 376669 381955 1 1 chr1 388127 396694 1 2 chr1 3403971 3412037 1 3 chr1 3647139 3651878 1 4 chr1 6163275 6170009 1 5 chr1 7146738 7155828 2 6 chr1 7605209 7608588 1 7 chr15 230425 231516 1 8 chr17 5195837 5199216 1 9 chr2 5202380 5209970 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7894797 | 7903038 | 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/tmpbo6la80r/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7894797 7903038 - 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 7894797 7903038 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2224179 | 2229463 | 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/tmpnk246egj/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2224179 2229463 + 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 2224179 2229463 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7916723 | 7925736 | a | 0 | + | | chr1 | 7916723 | 7920746 | a | 0 | + | | chr1 | 7916723 | 7925736 | a | 0 | - | | chr1 | 7916723 | 7923091 | a | 0 | - | | chr8 | 7262914 | 7271927 | a | 0 | - | | chr8 | 7916723 | 7922454 | a | 0 | - | | chr15 | 7916723 | 7921828 | 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 merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpipjnr4my/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7916723 7925736 + 4 chr15 7916723 7921828 - 1 chr8 7262914 7271927 - 1 chr8 7916723 7922454 - 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 7916723 7925736 4 1 chr15 7916723 7921828 1 2 chr8 7262914 7271927 1 3 chr8 7916723 7922454 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2105316 | 2112862 | 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/tmpzx7qu27n/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2105316 2112862 + 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 2105316 2112862 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2971577 | 2975848 | a | 0 | + | | chr1 | 2971577 | 2974994 | a | 0 | + | | chr1 | 7593191 | 7595810 | a | 0 | - | | chr1 | 8068244 | 8071194 | a | 0 | - | | chr2 | 281067 | 290946 | a | 0 | + | | chr21 | 9301707 | 9309283 | a | 0 | + | | chr21 | 2971577 | 2971647 | a | 0 | + | | chr21 | 1106945 | 1108402 | 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/tmp2f4x34b5/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2971577 2975848 + 2 chr1 7593191 7595810 - 1 chr1 8068244 8071194 - 1 chr2 281067 290946 + 1 chr21 1106945 1108402 - 1 chr21 2971577 2971647 + 1 chr21 9301707 9309283 + 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 2971577 2975848 2 1 chr1 7593191 7595810 1 2 chr1 8068244 8071194 1 3 chr2 281067 290946 1 4 chr21 1106945 1108402 1 5 chr21 2971577 2971647 1 6 chr21 9301707 9309283 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2234397 | 2243765 | a | 0 | - | | chr18 | 614296 | 617430 | 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/tmpf_to68gj/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2234397 2243765 - 1 chr18 614296 617430 - 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 2234397 2243765 1 1 chr18 614296 617430 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4020031 | 4022056 | a | 0 | + | | chr1 | 7209510 | 7213226 | a | 0 | - | | chr1 | 6733458 | 6734195 | a | 0 | - | | chr1 | 3211486 | 3215542 | a | 0 | - | | chr1 | 8221849 | 8227307 | a | 0 | - | | chr2 | 5901401 | 5908654 | a | 0 | - | | chr7 | 6733458 | 6739166 | a | 0 | - | | chr9 | 9870275 | 9873236 | 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 -i <(sort -k1,1 -k2,2n /tmp/tmpkkmr_o5a/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3211486 3215542 - 1 chr1 4020031 4022056 + 1 chr1 6733458 6734195 - 1 chr1 7209510 7213226 - 1 chr1 8221849 8227307 - 1 chr2 5901401 5908654 - 1 chr7 6733458 6739166 - 1 chr9 9870275 9873236 + 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 3211486 3215542 1 1 chr1 4020031 4022056 1 2 chr1 6733458 6734195 1 3 chr1 7209510 7213226 1 4 chr1 8221849 8227307 1 5 chr2 5901401 5908654 1 6 chr7 6733458 6739166 1 7 chr9 9870275 9873236 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7139519 | 7147037 | a | 0 | - | | chr1 | 9535503 | 9538109 | a | 0 | - | | chr7 | 1411589 | 1413848 | 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/tmpwk0o2m1r/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7139519 7147037 - 1 chr1 9535503 9538109 - 1 chr7 1411589 1413848 - 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 7139519 7147037 1 1 chr1 9535503 9538109 1 2 chr7 1411589 1413848 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6578467 | 6579551 | a | 0 | + | | chr1 | 3714727 | 3721982 | a | 0 | - | | chr1 | 9202548 | 9208439 | a | 0 | - | | chr5 | 819441 | 821110 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr5 | 7680678 | 7685809 | a | 0 | - | | chr5 | 9583773 | 9584384 | a | 0 | - | | chr5 | 710598 | 713227 | a | 0 | - | | chr5 | 710598 | 712387 | 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/tmpzywepfud/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3714727 3721982 - 1 chr1 6578467 6579551 + 1 chr1 9202548 9208439 - 1 chr10 710598 710676 + 1 chr5 710598 713227 - 2 chr5 819441 821110 + 1 chr5 3184653 3193010 - 1 chr5 4327443 4332762 + 1 chr5 7680678 7685809 - 1 chr5 9583773 9584384 - 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 3714727 3721982 1 1 chr1 6578467 6579551 1 2 chr1 9202548 9208439 1 3 chr10 710598 710676 1 4 chr5 710598 713227 2 5 chr5 819441 821110 1 6 chr5 3184653 3193010 1 7 chr5 4327443 4332762 1 8 chr5 7680678 7685809 1 9 chr5 9583773 9584384 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4895980 | 4903956 | a | 0 | + | | chr1 | 10000000 | 10009316 | a | 0 | - | | chr1 | 5513067 | 5521589 | a | 0 | - | | chr4 | 3257573 | 3264081 | a | 0 | - | | chr5 | 3257573 | 3259862 | 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/tmp5raljday/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4895980 4903956 + 1 chr1 5513067 5521589 - 1 chr1 10000000 10009316 - 1 chr4 3257573 3264081 - 1 chr5 3257573 3259862 + 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 4895980 4903956 1 1 chr1 5513067 5521589 1 2 chr1 10000000 10009316 1 3 chr4 3257573 3264081 1 4 chr5 3257573 3259862 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7425512 | 7434335 | 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/tmpr58nhx0c/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7425512 7434335 - 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 7425512 7434335 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr10 | 9856987 | 9864660 | a | 0 | - | | chr13 | 3568259 | 3578174 | 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/tmp0_9ob8ig/f1.bed) resultresultresultresultresultresultresultresultresultresult chr10 9856987 9864660 - 1 chr13 3568259 3578174 - 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 9856987 9864660 1 1 chr13 3568259 3578174 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4385636 | 4391708 | a | 0 | + | | chr1 | 6072640 | 6081331 | a | 0 | + | | chr1 | 1597245 | 1598479 | a | 0 | + | | chr1 | 845076 | 846979 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr3 | 3844328 | 3852226 | a | 0 | + | | chr10 | 766396 | 768299 | a | 0 | + | | chr11 | 8156300 | 8164019 | a | 0 | + | | chr18 | 3337428 | 3344329 | 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/tmpqe0nnqec/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 845076 846979 + 1 chr1 1329498 1331981 - 1 chr1 1597245 1598479 + 1 chr1 4385636 4391708 + 1 chr1 6072640 6081331 + 1 chr1 7729115 7734202 + 1 chr1 9358656 9366130 + 1 chr10 766396 768299 + 1 chr11 8156300 8164019 + 1 chr18 3337428 3344329 + 1 chr3 3844328 3852226 + 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 845076 846979 1 1 chr1 1329498 1331981 1 2 chr1 1597245 1598479 1 3 chr1 4385636 4391708 1 4 chr1 6072640 6081331 1 5 chr1 7729115 7734202 1 6 chr1 9358656 9366130 1 7 chr10 766396 768299 1 8 chr11 8156300 8164019 1 9 chr18 3337428 3344329 1 10 chr3 3844328 3852226 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2060649 | 2061803 | a | 0 | + | | chr1 | 2537928 | 2537930 | a | 0 | + | | chr1 | 2300073 | 2301227 | a | 0 | - | | chr14 | 3008793 | 3009947 | a | 0 | + | | chrY | 2490398 | 2491552 | 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/tmpuy4lmgz3/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2060649 2061803 + 1 chr1 2300073 2301227 - 1 chr1 2537928 2537930 + 1 chr14 3008793 3009947 + 1 chrY 2490398 2491552 + 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 2060649 2061803 1 1 chr1 2300073 2301227 1 2 chr1 2537928 2537930 1 3 chr14 3008793 3009947 1 4 chrY 2490398 2491552 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5856110 | 5857876 | a | 0 | - | | chr1 | 10000000 | 10007288 | a | 0 | - | | chr1 | 2618572 | 2618846 | a | 0 | - | | chr6 | 9506410 | 9506734 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr9 | 1775727 | 1778260 | a | 0 | - | | chr20 | 2339806 | 2343313 | a | 0 | + | | chr22 | 5044677 | 5044698 | a | 0 | + | | chrM | 9702300 | 9710857 | 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/tmp2adsm6ia/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2618572 2618846 - 1 chr1 5856110 5857876 - 1 chr1 10000000 10007288 - 1 chr20 2339806 2343313 + 1 chr22 5044677 5044698 + 1 chr6 9506410 9506734 + 1 chr7 1029850 1031089 + 1 chr7 1775727 1785707 - 1 chr7 4981886 4985915 - 1 chr9 1775727 1778260 - 1 chrM 9702300 9710857 - 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 2618572 2618846 1 1 chr1 5856110 5857876 1 2 chr1 10000000 10007288 1 3 chr20 2339806 2343313 1 4 chr22 5044677 5044698 1 5 chr6 9506410 9506734 1 6 chr7 1029850 1031089 1 7 chr7 1775727 1785707 1 8 chr7 4981886 4985915 1 9 chr9 1775727 1778260 1 10 chrM 9702300 9710857 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2663851 | 2667085 | a | 0 | - | | chr7 | 3440427 | 3442855 | 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/tmp13pr5aq7/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2663851 2667085 - 1 chr7 3440427 3442855 - 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 2663851 2667085 1 1 chr7 3440427 3442855 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8118053 | 8126244 | a | 0 | + | | chr1 | 8648401 | 8658401 | a | 0 | + | | chr1 | 2322293 | 2329600 | a | 0 | - | | chr1 | 8648401 | 8648587 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr7 | 2909882 | 2914433 | a | 0 | - | | chr19 | 555762 | 558329 | a | 0 | - | | chr21 | 8648401 | 8657071 | a | 0 | - | | chrM | 1205906 | 1211834 | 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/tmpccwghp7x/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1990278 1991049 - 1 chr1 2322293 2329600 - 1 chr1 5516290 5525056 - 1 chr1 8118053 8126244 + 1 chr1 8648401 8658401 - 2 chr19 555762 558329 - 1 chr2 8648401 8657373 - 1 chr21 8648401 8657071 - 1 chr7 2909882 2914433 - 1 chrM 1205906 1211834 + 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 1990278 1991049 1 1 chr1 2322293 2329600 1 2 chr1 5516290 5525056 1 3 chr1 8118053 8126244 1 4 chr1 8648401 8658401 2 5 chr19 555762 558329 1 6 chr2 8648401 8657373 1 7 chr21 8648401 8657071 1 8 chr7 2909882 2914433 1 9 chrM 1205906 1211834 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3580425 | 3583076 | a | 0 | + | | chr1 | 5658532 | 5660194 | a | 0 | + | | chr1 | 9886525 | 9889176 | a | 0 | + | | chr1 | 9044652 | 9046079 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr9 | 10000000 | 10002651 | a | 0 | + | | chr13 | 2943969 | 2946620 | a | 0 | + | | chrY | 1056296 | 1058947 | a | 0 | - | | chrY | 9391568 | 9400756 | 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/tmpccs_jx9u/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2423896 2426547 - 1 chr1 3580425 3583076 + 1 chr1 4745451 4751066 - 1 chr1 5658532 5660194 + 1 chr1 8739202 8744674 - 1 chr1 9044652 9046079 + 1 chr1 9886525 9889176 + 1 chr13 2943969 2946620 + 1 chr9 10000000 10002651 + 1 chrY 1056296 1058947 - 1 chrY 9391568 9400756 - 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 2423896 2426547 1 1 chr1 3580425 3583076 1 2 chr1 4745451 4751066 1 3 chr1 5658532 5660194 1 4 chr1 8739202 8744674 1 5 chr1 9044652 9046079 1 6 chr1 9886525 9889176 1 7 chr13 2943969 2946620 1 8 chr9 10000000 10002651 1 9 chrY 1056296 1058947 1 10 chrY 9391568 9400756 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9631625 | 9638925 | a | 0 | - | | chr1 | 4054284 | 4054495 | a | 0 | - | | chr1 | 3377243 | 3381589 | a | 0 | - | | chr5 | 547699 | 548448 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr13 | 1 | 1670 | a | 0 | - | | chr14 | 1590355 | 1591332 | a | 0 | + | | chr14 | 6863999 | 6872099 | a | 0 | + | | chrY | 8185629 | 8186606 | 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 -i <(sort -k1,1 -k2,2n /tmp/tmpfwipxs0k/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3377243 3381589 - 1 chr1 4054284 4054495 - 1 chr1 9631625 9638925 - 1 chr13 1 1670 - 1 chr14 1590355 1591332 + 1 chr14 6863999 6872099 + 1 chr5 547699 548448 + 1 chr6 3091015 3091992 + 1 chrY 8185629 8186606 + 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 3377243 3381589 1 1 chr1 4054284 4054495 1 2 chr1 9631625 9638925 1 3 chr13 1 1670 1 4 chr14 1590355 1591332 1 5 chr14 6863999 6872099 1 6 chr5 547699 548448 1 7 chr6 3091015 3091992 1 8 chrY 8185629 8186606 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4526347 | 4528461 | a | 0 | + | | chr1 | 5589612 | 5594189 | a | 0 | + | | chr1 | 7761267 | 7768085 | a | 0 | + | | chr1 | 238907 | 239667 | a | 0 | + | | chr1 | 9905945 | 9910792 | a | 0 | + | | chr10 | 9254217 | 9264216 | a | 0 | + | | chr10 | 7880404 | 7884240 | a | 0 | - | | chr10 | 4675577 | 4682838 | 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 merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp28sd_bl9/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 238907 239667 + 1 chr1 4526347 4528461 + 1 chr1 5589612 5594189 + 1 chr1 7761267 7768085 + 1 chr1 9905945 9910792 + 1 chr10 4675577 4682838 - 1 chr10 7880404 7884240 - 1 chr10 9254217 9264216 + 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 238907 239667 1 1 chr1 4526347 4528461 1 2 chr1 5589612 5594189 1 3 chr1 7761267 7768085 1 4 chr1 9905945 9910792 1 5 chr10 4675577 4682838 1 6 chr10 7880404 7884240 1 7 chr10 9254217 9264216 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr5 | 7906132 | 7916132 | a | 0 | - | | chr6 | 1086759 | 1087065 | a | 0 | + | | chr7 | 3633010 | 3639912 | 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/tmpfho7zujv/f1.bed) resultresultresultresultresultresultresultresultresultresult chr5 7906132 7916132 - 1 chr6 1086759 1087065 + 1 chr7 3633010 3639912 + 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 chr5 7906132 7916132 1 1 chr6 1086759 1087065 1 2 chr7 3633010 3639912 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9502867 | 9511795 | a | 0 | + | | chr1 | 3158545 | 3160873 | a | 0 | - | | chr1 | 1770222 | 1773828 | a | 0 | - | | chr1 | 8861330 | 8863296 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr11 | 1262164 | 1271784 | a | 0 | - | | chr11 | 7676190 | 7680807 | a | 0 | - | | chr14 | 2404675 | 2405489 | a | 0 | + | | chr18 | 7470295 | 7473195 | 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/tmpzwifspnn/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1770222 1773828 - 1 chr1 3158545 3160873 - 1 chr1 4122391 4128101 - 1 chr1 8861330 8863296 - 1 chr1 9502867 9511795 + 1 chr11 1262164 1271784 - 1 chr11 7676190 7680807 - 1 chr14 2404675 2405489 + 1 chr18 7470295 7473195 - 1 chr5 1770222 1772965 - 1 chr8 9309860 9311523 + 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 1770222 1773828 1 1 chr1 3158545 3160873 1 2 chr1 4122391 4128101 1 3 chr1 8861330 8863296 1 4 chr1 9502867 9511795 1 5 chr11 1262164 1271784 1 6 chr11 7676190 7680807 1 7 chr14 2404675 2405489 1 8 chr18 7470295 7473195 1 9 chr5 1770222 1772965 1 10 chr8 9309860 9311523 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7058057 | 7067088 | a | 0 | - | | chr1 | 30890 | 33662 | a | 0 | - | | chr8 | 2494007 | 2502771 | a | 0 | - | | chr9 | 3624649 | 3632519 | a | 0 | + | | chr9 | 6354825 | 6360655 | 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/tmpyxg64zvy/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 30890 33662 - 1 chr1 7058057 7067088 - 1 chr8 2494007 2502771 - 1 chr9 3624649 3632519 + 1 chr9 6354825 6360655 - 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 30890 33662 1 1 chr1 7058057 7067088 1 2 chr8 2494007 2502771 1 3 chr9 3624649 3632519 1 4 chr9 6354825 6360655 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2117223 | 2117941 | a | 0 | + | | chr15 | 1462928 | 1466793 | 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/tmpfidr_dlk/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2117223 2117941 + 1 chr15 1462928 1466793 + 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 2117223 2117941 1 1 chr15 1462928 1466793 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr14 | 5465806 | 5472863 | a | 0 | + | | chr22 | 3180137 | 3185342 | 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/tmp5z8rikla/f1.bed) resultresultresultresultresultresultresultresultresultresult chr14 5465806 5472863 + 1 chr22 3180137 3185342 - 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 5465806 5472863 1 1 chr22 3180137 3185342 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3151327 | 3157795 | a | 0 | + | | chr1 | 2956859 | 2959922 | a | 0 | + | | chr1 | 2433949 | 2437012 | a | 0 | - | | chr1 | 1154022 | 1157085 | a | 0 | - | | chr1 | 6806347 | 6809410 | 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/tmpbzswm2b2/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1154022 1157085 - 1 chr1 2433949 2437012 - 1 chr1 2956859 2959922 + 1 chr1 3151327 3157795 + 1 chr1 6806347 6809410 - 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 1154022 1157085 1 1 chr1 2433949 2437012 1 2 chr1 2956859 2959922 1 3 chr1 3151327 3157795 1 4 chr1 6806347 6809410 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7603825 | 7609106 | 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/tmppiwn5n97/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7603825 7609106 - 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 7603825 7609106 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7086194 | 7094854 | a | 0 | + | | chr1 | 7400523 | 7409489 | a | 0 | + | | chr1 | 737836 | 738906 | a | 0 | + | | chr1 | 9307121 | 9308394 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr12 | 1085786 | 1091815 | a | 0 | - | | chrX | 1706102 | 1712757 | a | 0 | + | | chrX | 2443051 | 2453005 | a | 0 | - | | chrY | 8465975 | 8466662 | 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/tmpxlap5k0c/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 737836 738906 + 1 chr1 752511 761060 - 1 chr1 3139565 3148783 - 1 chr1 7086194 7094854 + 1 chr1 7400523 7409489 + 1 chr1 9307121 9308394 - 1 chr12 1085786 1091815 - 1 chr6 3369907 3374529 - 1 chrX 1706102 1712757 + 1 chrX 2443051 2453005 - 1 chrY 8465975 8466662 - 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 737836 738906 1 1 chr1 752511 761060 1 2 chr1 3139565 3148783 1 3 chr1 7086194 7094854 1 4 chr1 7400523 7409489 1 5 chr1 9307121 9308394 1 6 chr12 1085786 1091815 1 7 chr6 3369907 3374529 1 8 chrX 1706102 1712757 1 9 chrX 2443051 2453005 1 10 chrY 8465975 8466662 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3005579 | 3011832 | a | 0 | + | | chr1 | 6697544 | 6698913 | a | 0 | + | | chr4 | 4823244 | 4830910 | a | 0 | - | | chr10 | 3005579 | 3014067 | a | 0 | + | | chr10 | 7765122 | 7774912 | 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/tmptxrb3tvu/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3005579 3011832 + 1 chr1 6697544 6698913 + 1 chr10 3005579 3014067 + 1 chr10 7765122 7774912 - 1 chr4 4823244 4830910 - 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 3005579 3011832 1 1 chr1 6697544 6698913 1 2 chr10 3005579 3014067 1 3 chr10 7765122 7774912 1 4 chr4 4823244 4830910 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4979979 | 4984392 | a | 0 | + | | chr1 | 1230151 | 1236112 | a | 0 | - | | chr14 | 8632841 | 8642841 | 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/tmp7p2h8h65/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1230151 1236112 - 1 chr1 4979979 4984392 + 1 chr14 8632841 8642841 + 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 1230151 1236112 1 1 chr1 4979979 4984392 1 2 chr14 8632841 8642841 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9788611 | 9791920 | a | 0 | - | | chr1 | 9105747 | 9108617 | a | 0 | - | | chr1 | 9105747 | 9115649 | a | 0 | - | | chr1 | 9105747 | 9109215 | a | 0 | - | | chr3 | 9105747 | 9107998 | a | 0 | + | | chr12 | 1501741 | 1508044 | 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 -i <(sort -k1,1 -k2,2n /tmp/tmp9b9tjntb/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 9105747 9115649 - 3 chr1 9788611 9791920 - 1 chr12 1501741 1508044 - 1 chr3 9105747 9107998 + 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 9105747 9115649 3 1 chr1 9788611 9791920 1 2 chr12 1501741 1508044 1 3 chr3 9105747 9107998 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7058646 | 7063024 | a | 0 | + | | chr1 | 8803222 | 8813222 | a | 0 | + | | chr1 | 8803222 | 8807127 | a | 0 | + | | chr1 | 8803222 | 8807127 | a | 0 | - | | chr1 | 562022 | 571643 | a | 0 | - | | chr1 | 8803222 | 8807127 | 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/tmpccza1fb7/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 562022 571643 - 1 chr1 7058646 7063024 + 1 chr1 8803222 8813222 + 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 562022 571643 1 1 chr1 7058646 7063024 1 2 chr1 8803222 8813222 4 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 3922 | a | 0 | + | | chr1 | 1 | 442 | a | 0 | - | | chr2 | 1 | 6426 | a | 0 | + | | chr5 | 1 | 1001 | a | 0 | - | | chr8 | 6029761 | 6039577 | a | 0 | - | | chr8 | 1 | 1449 | a | 0 | - | | chr13 | 1 | 7904 | a | 0 | + | | chr20 | 720023 | 729012 | 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/tmpqkarqznj/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 3922 + 2 chr13 1 7904 + 1 chr2 1 6426 + 1 chr20 720023 729012 + 1 chr5 1 1001 - 1 chr8 1 1449 - 1 chr8 6029761 6039577 - 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 3922 2 1 chr13 1 7904 1 2 chr2 1 6426 1 3 chr20 720023 729012 1 4 chr5 1 1001 1 5 chr8 1 1449 1 6 chr8 6029761 6039577 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9466271 | 9471008 | a | 0 | + | | chr1 | 3376240 | 3381264 | a | 0 | + | | chr1 | 1916080 | 1918546 | a | 0 | - | | chr1 | 5984472 | 5989804 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr13 | 415894 | 418068 | a | 0 | + | | chr17 | 8912816 | 8918282 | a | 0 | + | | chr21 | 8503014 | 8511230 | a | 0 | + | | chrY | 1817068 | 1819405 | 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/tmpo5h0874f/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1916080 1918546 - 1 chr1 3376240 3381264 + 1 chr1 5984472 5989804 - 1 chr1 9466271 9471008 + 1 chr13 415894 418068 + 1 chr17 8912816 8918282 + 1 chr21 8503014 8511230 + 1 chr3 6965665 6967652 + 1 chr3 8551982 8559540 - 1 chr8 703252 704451 + 1 chrY 1817068 1819405 - 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 1916080 1918546 1 1 chr1 3376240 3381264 1 2 chr1 5984472 5989804 1 3 chr1 9466271 9471008 1 4 chr13 415894 418068 1 5 chr17 8912816 8918282 1 6 chr21 8503014 8511230 1 7 chr3 6965665 6967652 1 8 chr3 8551982 8559540 1 9 chr8 703252 704451 1 10 chrY 1817068 1819405 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr7 | 6685431 | 6687828 | 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/tmp7oz5iyax/f1.bed) resultresultresultresultresultresultresultresultresultresult chr7 6685431 6687828 - 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 chr7 6685431 6687828 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9361752 | 9369876 | a | 0 | - | | chr2 | 9944016 | 9947672 | a | 0 | + | | chr11 | 384130 | 393151 | a | 0 | + | | chr12 | 2229826 | 2236633 | a | 0 | - | | chr17 | 9104518 | 9113038 | a | 0 | + | | chr19 | 3612469 | 3617098 | a | 0 | - | | chrM | 8613627 | 8619118 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 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/tmpsefyxv7r/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 9361752 9369876 - 1 chr11 384130 393151 + 1 chr12 2229826 2236633 - 1 chr17 9104518 9113038 + 1 chr19 3612469 3617098 - 1 chr2 9944016 9947672 + 1 chrM 8613627 8619118 - 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 9361752 9369876 1 1 chr11 384130 393151 1 2 chr12 2229826 2236633 1 3 chr17 9104518 9113038 1 4 chr19 3612469 3617098 1 5 chr2 9944016 9947672 1 6 chrM 8613627 8619118 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 858913 | 868340 | a | 0 | + | | chr1 | 4544460 | 4548125 | a | 0 | + | | chr1 | 9704198 | 9712281 | a | 0 | + | | chr1 | 7672148 | 7676682 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr2 | 4314423 | 4319858 | a | 0 | + | | chr3 | 6665847 | 6673732 | a | 0 | + | | chr11 | 1498148 | 1501005 | a | 0 | - | | chr22 | 9704198 | 9713543 | 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/tmp7lhk4tmh/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 858913 868340 + 1 chr1 4044707 4052955 - 1 chr1 4092821 4097522 + 1 chr1 4544460 4548125 + 1 chr1 7672148 7676682 + 1 chr1 9704198 9712281 - 2 chr11 1498148 1501005 - 1 chr2 4314423 4319858 + 1 chr22 9704198 9713543 - 1 chr3 6665847 6673732 + 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 858913 868340 1 1 chr1 4044707 4052955 1 2 chr1 4092821 4097522 1 3 chr1 4544460 4548125 1 4 chr1 7672148 7676682 1 5 chr1 9704198 9712281 2 6 chr11 1498148 1501005 1 7 chr2 4314423 4319858 1 8 chr22 9704198 9713543 1 9 chr3 6665847 6673732 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 6007 | a | 0 | + | | chr1 | 7699047 | 7702929 | a | 0 | + | | chr1 | 4974492 | 4983188 | a | 0 | + | | chr1 | 6791152 | 6798751 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr4 | 8842710 | 8842712 | a | 0 | - | | chr9 | 8481827 | 8491798 | a | 0 | - | | chr11 | 5640484 | 5648306 | a | 0 | - | | chrX | 7018662 | 7027306 | 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/tmp7oy5wrbt/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 6007 + 1 chr1 3169310 3172445 - 1 chr1 3993712 3995132 - 1 chr1 4974492 4983188 + 1 chr1 6791152 6798751 + 1 chr1 7699047 7702929 + 1 chr11 5640484 5648306 - 1 chr3 9714720 9718822 - 1 chr4 8842710 8842712 - 1 chr9 8481827 8491798 - 1 chrX 7018662 7027306 + 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 6007 1 1 chr1 3169310 3172445 1 2 chr1 3993712 3995132 1 3 chr1 4974492 4983188 1 4 chr1 6791152 6798751 1 5 chr1 7699047 7702929 1 6 chr11 5640484 5648306 1 7 chr3 9714720 9718822 1 8 chr4 8842710 8842712 1 9 chr9 8481827 8491798 1 10 chrX 7018662 7027306 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3335856 | 3344269 | a | 0 | + | | chr1 | 1709402 | 1716675 | a | 0 | + | | chr1 | 6781985 | 6785284 | a | 0 | - | | chr1 | 2683016 | 2688888 | 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/tmp_wbz_6cz/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1709402 1716675 + 1 chr1 2683016 2688888 - 1 chr1 3335856 3344269 + 1 chr1 6781985 6785284 - 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 1709402 1716675 1 1 chr1 2683016 2688888 1 2 chr1 3335856 3344269 1 3 chr1 6781985 6785284 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6452976 | 6461013 | a | 0 | - | | chr3 | 2054632 | 2062669 | a | 0 | + | | chr11 | 6452976 | 6459842 | a | 0 | + | | chr13 | 6452976 | 6461013 | a | 0 | - | | chr20 | 6452976 | 6461013 | a | 0 | + | | chr22 | 6452976 | 6461013 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 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/tmp3d7f_hge/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6452976 6461013 - 1 chr11 6452976 6459842 + 1 chr13 6452976 6461013 - 1 chr20 6452976 6461013 + 1 chr22 6452976 6461013 - 1 chr3 2054632 2062669 + 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 6452976 6461013 1 1 chr11 6452976 6459842 1 2 chr13 6452976 6461013 1 3 chr20 6452976 6461013 1 4 chr22 6452976 6461013 1 5 chr3 2054632 2062669 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chrM | 1025517 | 1026786 | 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/tmpckw09mor/f1.bed) resultresultresultresultresultresultresultresultresultresult chrM 1025517 1026786 + 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 chrM 1025517 1026786 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4746218 | 4749724 | a | 0 | + | | chr1 | 9539370 | 9543049 | 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/tmp6uvblu_w/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4746218 4749724 + 1 chr1 9539370 9543049 + 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 4746218 4749724 1 1 chr1 9539370 9543049 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1963756 | 1971106 | 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/tmpiea0ojsj/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1963756 1971106 - 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 1963756 1971106 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5644535 | 5645021 | a | 0 | + | | chr1 | 1 | 4240 | a | 0 | + | | chr1 | 3640935 | 3650935 | a | 0 | + | | chr1 | 5175715 | 5179954 | a | 0 | - | | chr7 | 6994793 | 6995012 | a | 0 | - | | chr17 | 5816884 | 5821123 | a | 0 | + | | chr17 | 5214895 | 5222592 | a | 0 | - | | chr17 | 2524979 | 2529218 | 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/tmpe9qgdl50/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 4240 + 1 chr1 3640935 3650935 + 1 chr1 5175715 5179954 - 1 chr1 5644535 5645021 + 1 chr17 2524979 2529218 - 1 chr17 5214895 5222592 - 1 chr17 5816884 5821123 + 1 chr7 6994793 6995012 - 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 4240 1 1 chr1 3640935 3650935 1 2 chr1 5175715 5179954 1 3 chr1 5644535 5645021 1 4 chr17 2524979 2529218 1 5 chr17 5214895 5222592 1 6 chr17 5816884 5821123 1 7 chr7 6994793 6995012 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4564430 | 4570741 | a | 0 | + | | chr1 | 3294706 | 3300446 | a | 0 | - | | chr1 | 4564430 | 4572916 | 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/tmp5_33ev5_/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3294706 3300446 - 1 chr1 4564430 4572916 + 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 3294706 3300446 1 1 chr1 4564430 4572916 2 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5300875 | 5305932 | a | 0 | - | | chr12 | 8016709 | 8019135 | a | 0 | - | | chr22 | 3392771 | 3395310 | a | 0 | + | | chr22 | 3472808 | 3473550 | a | 0 | + | | chr22 | 809277 | 811703 | a | 0 | + | | chr22 | 79392 | 88467 | a | 0 | - | | chr22 | 9872126 | 9873957 | a | 0 | - | | chr22 | 5700096 | 5708837 | 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/tmpl1pmygog/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5300875 5305932 - 1 chr12 8016709 8019135 - 1 chr22 79392 88467 - 1 chr22 809277 811703 + 1 chr22 3392771 3395310 + 1 chr22 3472808 3473550 + 1 chr22 5700096 5708837 - 1 chr22 9872126 9873957 - 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 5300875 5305932 1 1 chr12 8016709 8019135 1 2 chr22 79392 88467 1 3 chr22 809277 811703 1 4 chr22 3392771 3395310 1 5 chr22 3472808 3473550 1 6 chr22 5700096 5708837 1 7 chr22 9872126 9873957 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr21 | 1541729 | 1548160 | 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/tmp1a6a2wbt/f1.bed) resultresultresultresultresultresultresultresultresultresult chr21 1541729 1548160 - 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 1541729 1548160 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2 | 4156 | a | 0 | + | | chr1 | 1281029 | 1285183 | a | 0 | + | | chr1 | 3537798 | 3541952 | a | 0 | - | | chr1 | 2749732 | 2753886 | 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/tmpkpbujise/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2 4156 + 1 chr1 1281029 1285183 + 1 chr1 2749732 2753886 - 1 chr1 3537798 3541952 - 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 4156 1 1 chr1 1281029 1285183 1 2 chr1 2749732 2753886 1 3 chr1 3537798 3541952 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr4 | 764969 | 765327 | 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/tmpyf5_8qfk/f1.bed) resultresultresultresultresultresultresultresultresultresult chr4 764969 765327 + 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 764969 765327 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 876305 | 881657 | a | 0 | + | | chr1 | 2762254 | 2767606 | a | 0 | + | | chr1 | 6780969 | 6786321 | a | 0 | - | | chr7 | 4062630 | 4067982 | a | 0 | - | | chrX | 1231853 | 1237205 | 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/tmpl_6gmt7c/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 876305 881657 + 1 chr1 2762254 2767606 + 1 chr1 6780969 6786321 - 1 chr7 4062630 4067982 - 1 chrX 1231853 1237205 + 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 876305 881657 1 1 chr1 2762254 2767606 1 2 chr1 6780969 6786321 1 3 chr7 4062630 4067982 1 4 chrX 1231853 1237205 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2980 | a | 0 | + | | chr1 | 483829 | 487212 | a | 0 | - | | chr1 | 4076535 | 4083919 | a | 0 | - | | chr1 | 6032514 | 6040147 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr20 | 1514237 | 1522942 | a | 0 | + | | chr20 | 76516 | 81069 | a | 0 | - | | chrM | 8995366 | 8998474 | a | 0 | + | | chrX | 8995366 | 8999990 | 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/tmpp5a2myyn/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2980 + 1 chr1 483829 487212 - 1 chr1 1908205 1912355 - 1 chr1 4076535 4083919 - 1 chr1 6032514 6040147 - 1 chr2 7501763 7511136 + 1 chr20 76516 81069 - 1 chr20 1514237 1522942 + 1 chr7 9406263 9410921 - 1 chrM 8995366 8998474 + 1 chrX 8995366 8999990 + 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 2980 1 1 chr1 483829 487212 1 2 chr1 1908205 1912355 1 3 chr1 4076535 4083919 1 4 chr1 6032514 6040147 1 5 chr2 7501763 7511136 1 6 chr20 76516 81069 1 7 chr20 1514237 1522942 1 8 chr7 9406263 9410921 1 9 chrM 8995366 8998474 1 10 chrX 8995366 8999990 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4709369 | 4716431 | 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/tmpuve9zvdi/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4709369 4716431 + 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 4709369 4716431 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5631776 | 5639625 | a | 0 | - | | chr7 | 2338789 | 2341266 | a | 0 | + | | chr19 | 2001149 | 2001444 | 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/tmp3n_1o0ai/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5631776 5639625 - 1 chr19 2001149 2001444 - 1 chr7 2338789 2341266 + 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 5631776 5639625 1 1 chr19 2001149 2001444 1 2 chr7 2338789 2341266 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2155014 | 2164757 | a | 0 | + | | chr1 | 7876119 | 7885862 | a | 0 | - | | chr1 | 2935699 | 2938365 | a | 0 | - | | chr1 | 3687596 | 3687996 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr12 | 7967484 | 7974542 | a | 0 | + | | chr14 | 2935699 | 2945442 | a | 0 | - | | chr19 | 2935699 | 2945442 | a | 0 | + | | chrY | 1691007 | 1699970 | 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/tmphzkadolv/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2155014 2164757 + 1 chr1 2935699 2940586 - 2 chr1 3687596 3687996 - 1 chr1 4572272 4582015 - 1 chr1 7876119 7885862 - 1 chr10 8698278 8704453 + 1 chr12 7967484 7974542 + 1 chr14 2935699 2945442 - 1 chr19 2935699 2945442 + 1 chrY 1691007 1699970 - 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 2155014 2164757 1 1 chr1 2935699 2940586 2 2 chr1 3687596 3687996 1 3 chr1 4572272 4582015 1 4 chr1 7876119 7885862 1 5 chr10 8698278 8704453 1 6 chr12 7967484 7974542 1 7 chr14 2935699 2945442 1 8 chr19 2935699 2945442 1 9 chrY 1691007 1699970 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9979376 | 9988145 | a | 0 | + | | chr1 | 9493041 | 9500540 | a | 0 | + | | chr1 | 1078830 | 1087599 | a | 0 | - | | chr1 | 905560 | 914329 | a | 0 | - | | chr4 | 5718929 | 5724022 | a | 0 | - | | chr9 | 4286888 | 4293563 | 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 -i <(sort -k1,1 -k2,2n /tmp/tmpogs_2d8q/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 905560 914329 - 1 chr1 1078830 1087599 - 1 chr1 9493041 9500540 + 1 chr1 9979376 9988145 + 1 chr4 5718929 5724022 - 1 chr9 4286888 4293563 - 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 905560 914329 1 1 chr1 1078830 1087599 1 2 chr1 9493041 9500540 1 3 chr1 9979376 9988145 1 4 chr4 5718929 5724022 1 5 chr9 4286888 4293563 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 959945 | 969017 | a | 0 | + | | chr1 | 1176961 | 1183776 | a | 0 | + | | chr1 | 1696941 | 1703239 | a | 0 | + | | chr1 | 5784316 | 5785559 | a | 0 | + | | chr3 | 884546 | 885060 | a | 0 | + | | chr5 | 5707597 | 5708840 | 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 -i <(sort -k1,1 -k2,2n /tmp/tmpkkjpqcpk/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 959945 969017 + 1 chr1 1176961 1183776 + 1 chr1 1696941 1703239 + 1 chr1 5784316 5785559 + 1 chr3 884546 885060 + 1 chr5 5707597 5708840 - 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 959945 969017 1 1 chr1 1176961 1183776 1 2 chr1 1696941 1703239 1 3 chr1 5784316 5785559 1 4 chr3 884546 885060 1 5 chr5 5707597 5708840 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8036259 | 8045567 | 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/tmpb0y8tco1/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 8036259 8045567 - 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 8036259 8045567 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3528919 | 3530705 | a | 0 | + | | chr1 | 9148373 | 9156580 | a | 0 | - | | chr1 | 4121486 | 4123187 | a | 0 | - | | chr9 | 9148373 | 9151225 | a | 0 | - | | chr18 | 951213 | 961212 | a | 0 | - | | chr19 | 3751711 | 3761370 | 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/tmpolfu8_2s/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3528919 3530705 + 1 chr1 4121486 4123187 - 1 chr1 9148373 9156580 - 1 chr18 951213 961212 - 1 chr19 3751711 3761370 + 1 chr9 9148373 9151225 - 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 3528919 3530705 1 1 chr1 4121486 4123187 1 2 chr1 9148373 9156580 1 3 chr18 951213 961212 1 4 chr19 3751711 3761370 1 5 chr9 9148373 9151225 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1704071 | 1712843 | a | 0 | + | | chr1 | 3522018 | 3529452 | a | 0 | - | | chr9 | 2574188 | 2582764 | a | 0 | - | | chr17 | 1682357 | 1684120 | 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 -i <(sort -k1,1 -k2,2n /tmp/tmpei75qva3/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1704071 1712843 + 1 chr1 3522018 3529452 - 1 chr17 1682357 1684120 - 1 chr9 2574188 2582764 - 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 1704071 1712843 1 1 chr1 3522018 3529452 1 2 chr17 1682357 1684120 1 3 chr9 2574188 2582764 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 18515 | 23789 | a | 0 | + | | chr1 | 9668790 | 9676510 | a | 0 | + | | chr1 | 5399852 | 5407140 | a | 0 | + | | chr1 | 3609334 | 3615953 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr18 | 974603 | 981891 | a | 0 | + | | chr18 | 519951 | 521964 | a | 0 | - | | chr19 | 8702741 | 8710029 | a | 0 | - | | chr22 | 9960617 | 9967905 | 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/tmpmm_gtjnt/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 18515 23789 + 1 chr1 3609334 3615953 - 1 chr1 5399852 5407140 + 1 chr1 9668790 9676510 + 1 chr16 4221782 4229070 + 1 chr18 519951 521964 - 1 chr18 974603 981891 + 1 chr19 8702741 8710029 - 1 chr22 3224780 3229258 + 1 chr22 9960617 9967905 - 1 chr8 8919862 8927150 + 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 18515 23789 1 1 chr1 3609334 3615953 1 2 chr1 5399852 5407140 1 3 chr1 9668790 9676510 1 4 chr16 4221782 4229070 1 5 chr18 519951 521964 1 6 chr18 974603 981891 1 7 chr19 8702741 8710029 1 8 chr22 3224780 3229258 1 9 chr22 9960617 9967905 1 10 chr8 8919862 8927150 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7096122 | 7096697 | a | 0 | + | | chr1 | 2303579 | 2310639 | a | 0 | - | | chr10 | 9988706 | 9996821 | a | 0 | - | | chr21 | 9247509 | 9250226 | 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 -i <(sort -k1,1 -k2,2n /tmp/tmpxj9h_z2o/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2303579 2310639 - 1 chr1 7096122 7096697 + 1 chr10 9988706 9996821 - 1 chr21 9247509 9250226 + 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 2303579 2310639 1 1 chr1 7096122 7096697 1 2 chr10 9988706 9996821 1 3 chr21 9247509 9250226 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7457966 | 7460173 | a | 0 | + | | chr5 | 4328048 | 4336971 | a | 0 | + | | chr19 | 211262 | 213943 | a | 0 | - | | chr20 | 4234510 | 4237199 | 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/tmpnej_z134/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7457966 7460173 + 1 chr19 211262 213943 - 1 chr20 4234510 4237199 - 1 chr5 4328048 4336971 + 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 7457966 7460173 1 1 chr19 211262 213943 1 2 chr20 4234510 4237199 1 3 chr5 4328048 4336971 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3152985 | 3158911 | a | 0 | + | | chr1 | 6533792 | 6538945 | a | 0 | - | | chr14 | 1329304 | 1336329 | 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/tmp_i1hbc45/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3152985 3158911 + 1 chr1 6533792 6538945 - 1 chr14 1329304 1336329 + 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 3152985 3158911 1 1 chr1 6533792 6538945 1 2 chr14 1329304 1336329 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2558471 | 2559145 | a | 0 | + | | chr1 | 1408057 | 1410544 | a | 0 | + | | chr1 | 7491255 | 7495355 | a | 0 | + | | chr5 | 7491255 | 7498357 | a | 0 | + | | chr13 | 1015174 | 1019274 | a | 0 | - | | chr14 | 2003459 | 2007559 | a | 0 | - | | chr22 | 755393 | 761642 | a | 0 | - | | chrM | 5500148 | 5503390 | 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/tmp0wldlj5q/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1408057 1410544 + 1 chr1 2558471 2559145 + 1 chr1 7491255 7495355 + 1 chr13 1015174 1019274 - 1 chr14 2003459 2007559 - 1 chr22 755393 761642 - 1 chr5 7491255 7498357 + 1 chrM 5500148 5503390 + 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 1408057 1410544 1 1 chr1 2558471 2559145 1 2 chr1 7491255 7495355 1 3 chr13 1015174 1019274 1 4 chr14 2003459 2007559 1 5 chr22 755393 761642 1 6 chr5 7491255 7498357 1 7 chrM 5500148 5503390 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2953594 | 2955562 | 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/tmpf_v0ee6s/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2953594 2955562 - 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 2953594 2955562 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6611958 | 6618058 | a | 0 | + | | chr1 | 8941997 | 8943840 | a | 0 | + | | chr1 | 3941189 | 3941894 | a | 0 | + | | chr1 | 9733071 | 9740116 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 4264718 | 4270526 | a | 0 | - | | chr1 | 1786024 | 1789625 | a | 0 | - | | chr1 | 6177711 | 6183115 | a | 0 | - | | chr1 | 2203211 | 2211058 | 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/tmpssr820kf/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1786024 1789625 - 1 chr1 2203211 2211058 - 1 chr1 3634203 3636928 - 1 chr1 3941189 3941894 + 1 chr1 4264718 4270526 - 1 chr1 6177711 6183115 - 1 chr1 6611958 6618058 + 1 chr1 8941997 8943840 + 1 chr1 9733071 9740116 - 1 chr18 3901741 3903612 - 1 chr9 8941997 8944151 + 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 1786024 1789625 1 1 chr1 2203211 2211058 1 2 chr1 3634203 3636928 1 3 chr1 3941189 3941894 1 4 chr1 4264718 4270526 1 5 chr1 6177711 6183115 1 6 chr1 6611958 6618058 1 7 chr1 8941997 8943840 1 8 chr1 9733071 9740116 1 9 chr18 3901741 3903612 1 10 chr9 8941997 8944151 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 471002 | 472597 | a | 0 | + | | chr1 | 4081016 | 4090830 | a | 0 | + | | chr1 | 471002 | 475835 | a | 0 | - | | chr1 | 471002 | 475517 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr7 | 9582757 | 9587851 | a | 0 | + | | chr9 | 8666454 | 8666732 | a | 0 | - | | chr17 | 471002 | 478933 | a | 0 | - | | chr19 | 299008 | 307207 | 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/tmpfzqculo7/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 471002 475835 + 3 chr1 4081016 4090830 + 1 chr1 6165331 6169385 - 1 chr17 471002 478933 - 1 chr19 299008 307207 - 1 chr7 9582757 9587851 + 1 chr9 8666454 8666732 - 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 471002 475835 3 1 chr1 4081016 4090830 1 2 chr1 6165331 6169385 1 3 chr17 471002 478933 1 4 chr19 299008 307207 1 5 chr7 9582757 9587851 1 6 chr9 8666454 8666732 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr5 | 9411453 | 9420107 | 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/tmpvegme4kq/f1.bed) resultresultresultresultresultresultresultresultresultresult chr5 9411453 9420107 - 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 chr5 9411453 9420107 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7051913 | 7058582 | a | 0 | + | | chr1 | 2 | 6671 | a | 0 | + | | chr1 | 5470876 | 5477545 | a | 0 | - | | chr9 | 8311485 | 8318154 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr11 | 2493645 | 2500314 | a | 0 | - | | chr17 | 5333928 | 5340597 | a | 0 | - | | chrM | 7478905 | 7485574 | a | 0 | + | | chrY | 8866680 | 8873349 | 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 -i <(sort -k1,1 -k2,2n /tmp/tmp75lbdh4c/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2 6671 + 1 chr1 5470876 5477545 - 1 chr1 7051913 7058582 + 1 chr11 2493645 2500314 - 1 chr17 5333928 5340597 - 1 chr9 5643378 5650047 + 1 chr9 8311485 8318154 + 1 chrM 7478905 7485574 + 1 chrY 8866680 8873349 - 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 6671 1 1 chr1 5470876 5477545 1 2 chr1 7051913 7058582 1 3 chr11 2493645 2500314 1 4 chr17 5333928 5340597 1 5 chr9 5643378 5650047 1 6 chr9 8311485 8318154 1 7 chrM 7478905 7485574 1 8 chrY 8866680 8873349 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2 | 4671 | a | 0 | + | | chr1 | 10000000 | 10008029 | a | 0 | + | | chr1 | 4979330 | 4989330 | a | 0 | + | | chr1 | 8693410 | 8702377 | a | 0 | - | | chr11 | 2 | 4952 | a | 0 | - | | chr13 | 4728967 | 4735565 | 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 -i <(sort -k1,1 -k2,2n /tmp/tmp2tcffrb8/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2 4671 + 1 chr1 4979330 4989330 + 1 chr1 8693410 8702377 - 1 chr1 10000000 10008029 + 1 chr11 2 4952 - 1 chr13 4728967 4735565 - 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 4671 1 1 chr1 4979330 4989330 1 2 chr1 8693410 8702377 1 3 chr1 10000000 10008029 1 4 chr11 2 4952 1 5 chr13 4728967 4735565 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 32404 | 36458 | a | 0 | + | | chr1 | 603116 | 613116 | a | 0 | + | | chr18 | 1872946 | 1878158 | 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/tmpqp3_guy3/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 32404 36458 + 1 chr1 603116 613116 + 1 chr18 1872946 1878158 - 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 32404 36458 1 1 chr1 603116 613116 1 2 chr18 1872946 1878158 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr19 | 2821133 | 2824726 | 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/tmpj8cmwejk/f1.bed) resultresultresultresultresultresultresultresultresultresult chr19 2821133 2824726 + 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 chr19 2821133 2824726 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 70284 | 77514 | a | 0 | + | | chr8 | 9591214 | 9593333 | a | 0 | + | | chr8 | 4746367 | 4747213 | a | 0 | + | | chr11 | 7200870 | 7208434 | a | 0 | + | | chr11 | 1 | 9326 | a | 0 | - | | chr20 | 7387233 | 7392269 | a | 0 | - | | chr22 | 1 | 2502 | 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 merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp2vhd1ni6/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 70284 77514 + 1 chr11 1 9326 - 1 chr11 7200870 7208434 + 1 chr20 7387233 7392269 - 1 chr22 1 2502 - 1 chr8 4746367 4747213 + 1 chr8 9591214 9593333 + 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 70284 77514 1 1 chr11 1 9326 1 2 chr11 7200870 7208434 1 3 chr20 7387233 7392269 1 4 chr22 1 2502 1 5 chr8 4746367 4747213 1 6 chr8 9591214 9593333 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7263618 | 7264400 | a | 0 | - | | chr1 | 2340611 | 2347664 | a | 0 | - | | chr1 | 2735312 | 2736094 | a | 0 | - | | chr1 | 313072 | 313854 | a | 0 | - | | chr1 | 7824544 | 7825326 | a | 0 | - | | chr12 | 8951951 | 8952733 | 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/tmpjsfmz6ld/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 313072 313854 - 1 chr1 2340611 2347664 - 1 chr1 2735312 2736094 - 1 chr1 7263618 7264400 - 1 chr1 7824544 7825326 - 1 chr12 8951951 8952733 - 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 313072 313854 1 1 chr1 2340611 2347664 1 2 chr1 2735312 2736094 1 3 chr1 7263618 7264400 1 4 chr1 7824544 7825326 1 5 chr12 8951951 8952733 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6027123 | 6029191 | a | 0 | + | | chr1 | 7426695 | 7430664 | a | 0 | - | | chr1 | 4460776 | 4462465 | a | 0 | - | | chr7 | 2020307 | 2022746 | a | 0 | - | | chr9 | 5826713 | 5835260 | a | 0 | + | | chr10 | 4971341 | 4979384 | a | 0 | - | | chr16 | 9457598 | 9464286 | a | 0 | - | | chrX | 6182849 | 6187343 | 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/tmpwy6ujuco/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4460776 4462465 - 1 chr1 6027123 6029191 + 1 chr1 7426695 7430664 - 1 chr10 4971341 4979384 - 1 chr16 9457598 9464286 - 1 chr7 2020307 2022746 - 1 chr9 5826713 5835260 + 1 chrX 6182849 6187343 - 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 4460776 4462465 1 1 chr1 6027123 6029191 1 2 chr1 7426695 7430664 1 3 chr10 4971341 4979384 1 4 chr16 9457598 9464286 1 5 chr7 2020307 2022746 1 6 chr9 5826713 5835260 1 7 chrX 6182849 6187343 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 586784 | 592785 | a | 0 | - | | chr1 | 1632381 | 1636430 | a | 0 | - | | chr1 | 860298 | 860517 | a | 0 | - | | chr2 | 1273619 | 1282007 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr14 | 8108487 | 8114240 | a | 0 | - | | chr15 | 283502 | 289348 | a | 0 | - | | chr15 | 2451713 | 2459561 | a | 0 | - | | chr17 | 6033410 | 6040789 | 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/tmpggh6f0ha/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 586784 592785 - 1 chr1 860298 860517 - 1 chr1 1632381 1636430 - 1 chr14 8108487 8114240 - 1 chr15 283502 289348 - 1 chr15 2451713 2459561 - 1 chr17 6033410 6040789 - 1 chr2 1273619 1282007 - 1 chr3 2505637 2510032 - 1 chr5 5049171 5056363 - 1 chr9 4050209 4054931 - 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 586784 592785 1 1 chr1 860298 860517 1 2 chr1 1632381 1636430 1 3 chr14 8108487 8114240 1 4 chr15 283502 289348 1 5 chr15 2451713 2459561 1 6 chr17 6033410 6040789 1 7 chr2 1273619 1282007 1 8 chr3 2505637 2510032 1 9 chr5 5049171 5056363 1 10 chr9 4050209 4054931 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6431831 | 6435509 | a | 0 | + | | chr1 | 6176737 | 6183853 | a | 0 | + | | chr1 | 9859754 | 9869476 | a | 0 | - | | chr1 | 7982312 | 7990179 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr15 | 4500675 | 4506074 | a | 0 | + | | chr15 | 1 | 9748 | a | 0 | - | | chr19 | 2979077 | 2981252 | a | 0 | + | | chr21 | 6295998 | 6297070 | 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/tmpiaqb_tqa/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6176737 6183853 + 1 chr1 6431831 6435509 + 1 chr1 7982312 7990179 - 1 chr1 9859754 9869476 - 1 chr14 9681871 9682070 + 1 chr15 1 9748 - 1 chr15 4500675 4506074 + 1 chr19 2979077 2981252 + 1 chr21 6295998 6297070 - 1 chr4 5387903 5390400 - 1 chr9 201803 206219 - 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 6176737 6183853 1 1 chr1 6431831 6435509 1 2 chr1 7982312 7990179 1 3 chr1 9859754 9869476 1 4 chr14 9681871 9682070 1 5 chr15 1 9748 1 6 chr15 4500675 4506074 1 7 chr19 2979077 2981252 1 8 chr21 6295998 6297070 1 9 chr4 5387903 5390400 1 10 chr9 201803 206219 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1387769 | 1393302 | a | 0 | + | | chr1 | 6802455 | 6807988 | a | 0 | + | | chr1 | 4095451 | 4100984 | a | 0 | - | | chr1 | 6732814 | 6738347 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr9 | 6255352 | 6260354 | a | 0 | - | | chr10 | 2229580 | 2236356 | a | 0 | + | | chr22 | 6045992 | 6051525 | a | 0 | - | | chrM | 6255352 | 6260885 | 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/tmpopjwgtd3/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 359378 362826 - 1 chr1 1387769 1393302 + 1 chr1 4095451 4100984 - 1 chr1 6371291 6376824 - 1 chr1 6732814 6738347 - 1 chr1 6802455 6807988 + 1 chr10 2229580 2236356 + 1 chr22 6045992 6051525 - 1 chr3 8677588 8683121 - 1 chr9 6255352 6260354 - 1 chrM 6255352 6260885 - 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 359378 362826 1 1 chr1 1387769 1393302 1 2 chr1 4095451 4100984 1 3 chr1 6371291 6376824 1 4 chr1 6732814 6738347 1 5 chr1 6802455 6807988 1 6 chr10 2229580 2236356 1 7 chr22 6045992 6051525 1 8 chr3 8677588 8683121 1 9 chr9 6255352 6260354 1 10 chrM 6255352 6260885 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2 | 6795 | a | 0 | + | | chr1 | 1275369 | 1283586 | a | 0 | + | | chr1 | 6245042 | 6251608 | a | 0 | + | | chr1 | 7383100 | 7386013 | a | 0 | - | | chr14 | 2 | 5151 | 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 -i <(sort -k1,1 -k2,2n /tmp/tmpktzbjjfw/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2 6795 + 1 chr1 1275369 1283586 + 1 chr1 6245042 6251608 + 1 chr1 7383100 7386013 - 1 chr14 2 5151 + 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 6795 1 1 chr1 1275369 1283586 1 2 chr1 6245042 6251608 1 3 chr1 7383100 7386013 1 4 chr14 2 5151 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7911202 | 7920232 | a | 0 | - | | chr12 | 3433499 | 3434492 | a | 0 | - | | chr19 | 6456141 | 6461422 | a | 0 | - | | chrY | 251412 | 256232 | 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/tmpg6nnynwb/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7911202 7920232 - 1 chr12 3433499 3434492 - 1 chr19 6456141 6461422 - 1 chrY 251412 256232 + 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 7911202 7920232 1 1 chr12 3433499 3434492 1 2 chr19 6456141 6461422 1 3 chrY 251412 256232 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/tmpeezxgn2n/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 ---------------------------------- 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[False] ______________________________ [gw0] linux -- Python 3.12.3 /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., 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/tmptisn6mjp/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 | 564808 | 567173 | 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/tmpn9ne3r7a/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 564808 567173 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 564808 | 567173 | 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 | 564808 | 568658 | 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/tmpwa22deup/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 564808 568658 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 564808 | 568658 | 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 | 589825 | 593675 | 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/tmp9jxbcwxz/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 589825 593675 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 589825 | 593675 | 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 | 985345 | 989195 | 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/tmpiqghapox/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 985345 989195 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 985345 | 989195 | 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 | 589840 | 589841 | 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/tmp81k22n3f/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 589840 589841 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 589840 | 589841 | 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 | 589840 | 589856 | 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/tmplxyyc2ds/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 589840 589856 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 589840 | 589856 | 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 | 589840 | 592145 | 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/tmpao3wtvc8/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 589840 592145 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 589840 | 592145 | 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 | 485102 | 491080 | a | 0 | + | | chr1 | 5732029 | 5734175 | a | 0 | + | | chr20 | 2014584 | 2021213 | 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/tmpwda8jdok/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 485102 491080 a 0 + 1 1 chr1 5732029 5734175 a 0 + 2 2 chr20 2014584 2021213 a 0 + 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 485102 | 491080 | a | 0 | + | | chr1 | 5732029 | 5734175 | a | 0 | + | | chr20 | 2014584 | 2021213 | 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 | 485102 | 485103 | a | 0 | + | | chr1 | 5732029 | 5734175 | a | 0 | + | | chr20 | 2014584 | 2020562 | 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/tmpgrz_92m3/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 485102 485103 a 0 + 1 1 chr1 5732029 5734175 a 0 + 2 2 chr20 2014584 2020562 a 0 + 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 485102 | 485103 | a | 0 | + | | chr1 | 5732029 | 5734175 | a | 0 | + | | chr20 | 2014584 | 2020562 | 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 | 2 | 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/tmpdp8hsbe5/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/tmpcezbr768/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/tmp31ai9vku/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/tmp90mjeixw/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/tmpxzaecl9j/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/tmpfox5zou2/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/tmp4zb3j83j/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/tmp7u8n3ngu/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/tmpa359xbeg/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/tmpizyfggp2/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/tmp5pc75ojx/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/tmpao_j831x/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 | 6070683 | 6076877 | a | 0 | + | | chr1 | 6070683 | 6072472 | a | 0 | + | | chr1 | 9653136 | 9657048 | a | 0 | + | | chr1 | 9666667 | 9672427 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr9 | 1018041 | 1026079 | a | 0 | + | | chr13 | 5651282 | 5655642 | a | 0 | + | | chr14 | 7380500 | 7386915 | a | 0 | + | | chr21 | 3645727 | 3648826 | 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/tmpwtx6ktah/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6070683 6072472 a 0 + 1 1 chr1 6070683 6072484 a 0 + 1 2 chr1 6070683 6075710 a 0 - 1 3 chr1 6070683 6076877 a 0 + 1 4 chr1 9653136 9657048 a 0 + 2 5 chr1 9666667 9672427 a 0 + 3 6 chr13 5651282 5655642 a 0 + 4 7 chr14 7380500 7386915 a 0 + 5 8 chr21 3645727 3648826 a 0 + 6 9 chr8 6070683 6073863 a 0 + 7 10 chr9 1018041 1026079 a 0 + 8 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6070683 | 6076877 | a | 0 | + | | chr1 | 6070683 | 6072472 | a | 0 | + | | chr1 | 9653136 | 9657048 | a | 0 | + | | chr1 | 9666667 | 9672427 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr9 | 1018041 | 1026079 | a | 0 | + | | chr13 | 5651282 | 5655642 | a | 0 | + | | chr14 | 7380500 | 7386915 | a | 0 | + | | chr21 | 3645727 | 3648826 | 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 | 7999884 | 8003739 | a | 0 | + | | chr1 | 5789141 | 5797469 | a | 0 | + | | chr1 | 7511880 | 7520426 | a | 0 | - | | chr1 | 79534 | 86733 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr12 | 5537091 | 5547091 | a | 0 | - | | chr16 | 6746649 | 6746650 | a | 0 | + | | chr19 | 6898033 | 6898034 | a | 0 | - | | chr22 | 34062 | 41331 | 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/tmpn9otoj2s/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 79534 86733 a 0 - 1 1 chr1 2003791 2005208 a 0 - 2 2 chr1 4155905 4159143 a 0 - 3 3 chr1 5789141 5797469 a 0 + 4 4 chr1 6218223 6227006 a 0 - 5 5 chr1 7511880 7520426 a 0 - 6 6 chr1 7999884 8003739 a 0 + 7 7 chr12 5537091 5547091 a 0 - 8 8 chr16 6746649 6746650 a 0 + 9 9 chr19 6898033 6898034 a 0 - 10 10 chr22 34062 41331 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7999884 | 8003739 | a | 0 | + | | chr1 | 5789141 | 5797469 | a | 0 | + | | chr1 | 7511880 | 7520426 | a | 0 | - | | chr1 | 79534 | 86733 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr12 | 5537091 | 5547091 | a | 0 | - | | chr16 | 6746649 | 6746650 | a | 0 | + | | chr19 | 6898033 | 6898034 | a | 0 | - | | chr22 | 34062 | 41331 | 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 | 169901 | 176988 | a | 0 | + | | chr1 | 9746866 | 9750452 | a | 0 | - | | chr22 | 7219064 | 7226151 | a | 0 | + | | chrX | 7031880 | 7036618 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chrX | 8487334 | 8494421 | a | 0 | - | | chrX | 4398044 | 4399456 | a | 0 | - | | chrX | 3103128 | 3104036 | a | 0 | - | | chrX | 2413713 | 2419760 | 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/tmp7flq7e76/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 169901 176988 a 0 + 1 1 chr1 9746866 9750452 a 0 - 2 2 chr22 7219064 7226151 a 0 + 3 3 chrX 1772498 1774519 a 0 + 4 4 chrX 2413713 2419760 a 0 - 5 5 chrX 3103128 3104036 a 0 - 6 6 chrX 4398044 4399456 a 0 - 7 7 chrX 5591687 5597555 a 0 - 8 8 chrX 7031880 7036618 a 0 + 9 9 chrX 8487334 8494421 a 0 - 10 10 chrX 9402372 9409459 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 169901 | 176988 | a | 0 | + | | chr1 | 9746866 | 9750452 | a | 0 | - | | chr22 | 7219064 | 7226151 | a | 0 | + | | chrX | 7031880 | 7036618 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chrX | 8487334 | 8494421 | a | 0 | - | | chrX | 4398044 | 4399456 | a | 0 | - | | chrX | 3103128 | 3104036 | a | 0 | - | | chrX | 2413713 | 2419760 | 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 | 8171463 | 8178075 | a | 0 | + | | chr1 | 1575479 | 1580637 | a | 0 | + | | chr1 | 10000000 | 10009966 | a | 0 | + | | chr1 | 3389955 | 3392186 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr7 | 9213456 | 9215758 | a | 0 | - | | chr12 | 7302298 | 7306646 | a | 0 | - | | chr13 | 6351019 | 6351622 | a | 0 | + | | chrY | 9667319 | 9676303 | 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/tmpfwsy_cmc/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1575479 1580637 a 0 + 1 1 chr1 3389955 3392186 a 0 - 2 2 chr1 3442746 3449671 a 0 - 3 3 chr1 8171463 8178075 a 0 + 4 4 chr1 9775108 9775765 a 0 - 5 5 chr1 10000000 10009966 a 0 + 6 6 chr12 7302298 7306646 a 0 - 7 7 chr13 6351019 6351622 a 0 + 8 8 chr5 1 1461 a 0 + 9 9 chr7 9213456 9215758 a 0 - 10 10 chrY 9667319 9676303 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8171463 | 8178075 | a | 0 | + | | chr1 | 1575479 | 1580637 | a | 0 | + | | chr1 | 10000000 | 10009966 | a | 0 | + | | chr1 | 3389955 | 3392186 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr7 | 9213456 | 9215758 | a | 0 | - | | chr12 | 7302298 | 7306646 | a | 0 | - | | chr13 | 6351019 | 6351622 | a | 0 | + | | chrY | 9667319 | 9676303 | 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 | 1102062 | 1110525 | a | 0 | + | | chr1 | 9999999 | 10004364 | a | 0 | - | | chr11 | 6538996 | 6545732 | a | 0 | + | | chr11 | 1843737 | 1844959 | a | 0 | - | | chr11 | 8468885 | 8475577 | a | 0 | - | | chrM | 5573685 | 5574027 | 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 -i <(sort -k1,1 -k2,2n /tmp/tmplplp04r1/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1102062 1110525 a 0 + 1 1 chr1 9999999 10004364 a 0 - 2 2 chr11 1843737 1844959 a 0 - 3 3 chr11 6538996 6545732 a 0 + 4 4 chr11 8468885 8475577 a 0 - 5 5 chrM 5573685 5574027 a 0 + 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1102062 | 1110525 | a | 0 | + | | chr1 | 9999999 | 10004364 | a | 0 | - | | chr11 | 6538996 | 6545732 | a | 0 | + | | chr11 | 1843737 | 1844959 | a | 0 | - | | chr11 | 8468885 | 8475577 | a | 0 | - | | chrM | 5573685 | 5574027 | 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 | 6592733 | 6592897 | a | 0 | + | | chr1 | 6282329 | 6283226 | a | 0 | + | | chr1 | 565087 | 573656 | a | 0 | + | | chr1 | 3735387 | 3736714 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 1801073 | 1804297 | a | 0 | - | | chr1 | 6769869 | 6770766 | a | 0 | - | | chr1 | 944432 | 949371 | a | 0 | - | | chr1 | 2480660 | 2482459 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 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/tmpt25646te/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 565087 573656 a 0 + 1 1 chr1 944432 949371 a 0 - 2 2 chr1 1801073 1804297 a 0 - 3 3 chr1 2480660 2482459 a 0 - 4 4 chr1 3735387 3736714 a 0 + 5 5 chr1 6136496 6139064 a 0 + 6 6 chr1 6282329 6283226 a 0 + 7 7 chr1 6592733 6592897 a 0 + 8 8 chr1 6769869 6770766 a 0 - 9 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6592733 | 6592897 | a | 0 | + | | chr1 | 6282329 | 6283226 | a | 0 | + | | chr1 | 565087 | 573656 | a | 0 | + | | chr1 | 3735387 | 3736714 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 1801073 | 1804297 | a | 0 | - | | chr1 | 6769869 | 6770766 | a | 0 | - | | chr1 | 944432 | 949371 | a | 0 | - | | chr1 | 2480660 | 2482459 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 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 | 5200692 | 5204974 | a | 0 | + | | chr17 | 1106010 | 1113221 | a | 0 | + | | chrX | 3074786 | 3084786 | 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/tmp5l7h4hwl/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr13 5200692 5204974 a 0 + 1 1 chr17 1106010 1113221 a 0 + 2 2 chrX 3074786 3084786 a 0 - 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr13 | 5200692 | 5204974 | a | 0 | + | | chr17 | 1106010 | 1113221 | a | 0 | + | | chrX | 3074786 | 3084786 | 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 | 2774490 | 2784138 | a | 0 | - | | chr8 | 7821748 | 7828776 | a | 0 | - | | chr15 | 23730 | 25510 | a | 0 | - | | chr17 | 3776264 | 3780251 | a | 0 | - | | chr19 | 4572789 | 4573910 | a | 0 | + | | chrX | 7394733 | 7401761 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 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/tmpv8u06pdu/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2774490 2784138 a 0 - 1 1 chr15 23730 25510 a 0 - 2 2 chr17 3776264 3780251 a 0 - 3 3 chr19 4572789 4573910 a 0 + 4 4 chr8 7821748 7828776 a 0 - 5 5 chrX 7394733 7401761 a 0 + 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2774490 | 2784138 | a | 0 | - | | chr8 | 7821748 | 7828776 | a | 0 | - | | chr15 | 23730 | 25510 | a | 0 | - | | chr17 | 3776264 | 3780251 | a | 0 | - | | chr19 | 4572789 | 4573910 | a | 0 | + | | chrX | 7394733 | 7401761 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 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 | 7355159 | 7356295 | a | 0 | + | | chr1 | 7355159 | 7360941 | a | 0 | + | | chr1 | 7355159 | 7358176 | 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/tmp7pekd6ri/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 7355159 7356295 a 0 + 1 1 chr1 7355159 7358176 a 0 - 1 2 chr1 7355159 7360941 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7355159 | 7356295 | a | 0 | + | | chr1 | 7355159 | 7360941 | a | 0 | + | | chr1 | 7355159 | 7358176 | 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 | 8603781 | 8613781 | a | 0 | - | | chr1 | 3539303 | 3547557 | a | 0 | - | | chr1 | 1 | 1828 | a | 0 | - | | chr1 | 1784396 | 1787619 | a | 0 | - | | chrM | 7096906 | 7102271 | 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/tmpbke_86xm/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 1828 a 0 - 1 1 chr1 1784396 1787619 a 0 - 2 2 chr1 3539303 3547557 a 0 - 3 3 chr1 8603781 8613781 a 0 - 4 4 chrM 7096906 7102271 a 0 - 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8603781 | 8613781 | a | 0 | - | | chr1 | 3539303 | 3547557 | a | 0 | - | | chr1 | 1 | 1828 | a | 0 | - | | chr1 | 1784396 | 1787619 | a | 0 | - | | chrM | 7096906 | 7102271 | 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 | 4560567 | 4563423 | a | 0 | + | | chr1 | 1686240 | 1686250 | a | 0 | + | | chr1 | 3041537 | 3050694 | a | 0 | - | | chr1 | 7412387 | 7420491 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr6 | 3617047 | 3621402 | a | 0 | + | | chr11 | 4115461 | 4116271 | a | 0 | + | | chr15 | 309542 | 311330 | a | 0 | + | | chr17 | 7629287 | 7629887 | 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/tmpxk5gu4v2/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1686240 1686250 a 0 + 1 1 chr1 3041537 3050694 a 0 - 2 2 chr1 4403542 4406879 a 0 - 3 3 chr1 4560567 4563423 a 0 + 4 4 chr1 7412387 7420491 a 0 - 5 5 chr11 4115461 4116271 a 0 + 6 6 chr15 309542 311330 a 0 + 7 7 chr17 7629287 7629887 a 0 + 8 8 chr3 8031316 8033573 a 0 - 9 9 chr5 1283625 1288785 a 0 + 10 10 chr6 3617047 3621402 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4560567 | 4563423 | a | 0 | + | | chr1 | 1686240 | 1686250 | a | 0 | + | | chr1 | 3041537 | 3050694 | a | 0 | - | | chr1 | 7412387 | 7420491 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr6 | 3617047 | 3621402 | a | 0 | + | | chr11 | 4115461 | 4116271 | a | 0 | + | | chr15 | 309542 | 311330 | a | 0 | + | | chr17 | 7629287 | 7629887 | 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 | 5577737 | 5582890 | 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/tmpifggrhpv/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5577737 5582890 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5577737 | 5582890 | 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 | 7181103 | 7190611 | a | 0 | + | | chr1 | 9265887 | 9269096 | a | 0 | + | | chr1 | 792101 | 801502 | a | 0 | - | | chr3 | 9673697 | 9676323 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr10 | 5843392 | 5853117 | a | 0 | + | | chr10 | 5816608 | 5818935 | a | 0 | + | | chr10 | 7371108 | 7379741 | a | 0 | - | | chr10 | 1 | 1024 | 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/tmpyu7ik8kv/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 792101 801502 a 0 - 1 1 chr1 7181103 7190611 a 0 + 2 2 chr1 9265887 9269096 a 0 + 3 3 chr10 1 1024 a 0 - 4 4 chr10 5816608 5818935 a 0 + 5 5 chr10 5843392 5853117 a 0 + 6 6 chr10 7371108 7379741 a 0 - 7 7 chr17 5113163 5121381 a 0 + 8 8 chr20 1611134 1618687 a 0 + 9 9 chr3 9673697 9676323 a 0 + 10 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7181103 | 7190611 | a | 0 | + | | chr1 | 9265887 | 9269096 | a | 0 | + | | chr1 | 792101 | 801502 | a | 0 | - | | chr3 | 9673697 | 9676323 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr10 | 5843392 | 5853117 | a | 0 | + | | chr10 | 5816608 | 5818935 | a | 0 | + | | chr10 | 7371108 | 7379741 | a | 0 | - | | chr10 | 1 | 1024 | 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 | 7461524 | 7468471 | a | 0 | + | | chr1 | 9440171 | 9447118 | a | 0 | + | | chr1 | 5929731 | 5936678 | a | 0 | + | | chr1 | 7657273 | 7664220 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr13 | 9611831 | 9618778 | a | 0 | - | | chr22 | 3957205 | 3964152 | a | 0 | + | | chr22 | 28727 | 35674 | a | 0 | - | | chrY | 968812 | 975759 | 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/tmplc90fcgw/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1912996 1919246 a 0 - 1 1 chr1 5929731 5936678 a 0 + 2 2 chr1 7461524 7468471 a 0 + 3 3 chr1 7657273 7664220 a 0 - 4 4 chr1 9440171 9447118 a 0 + 5 5 chr1 9891614 9898561 a 0 - 6 6 chr13 9611831 9618778 a 0 - 7 7 chr22 28727 35674 a 0 - 8 8 chr22 3957205 3964152 a 0 + 9 9 chr5 8256454 8263401 a 0 + 10 10 chrY 968812 975759 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7461524 | 7468471 | a | 0 | + | | chr1 | 9440171 | 9447118 | a | 0 | + | | chr1 | 5929731 | 5936678 | a | 0 | + | | chr1 | 7657273 | 7664220 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr13 | 9611831 | 9618778 | a | 0 | - | | chr22 | 3957205 | 3964152 | a | 0 | + | | chr22 | 28727 | 35674 | a | 0 | - | | chrY | 968812 | 975759 | 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 | 4666908 | 4675212 | a | 0 | + | | chr1 | 1 | 5221 | 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/tmpnxsl0nzu/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 5221 a 0 - 1 1 chr1 4666908 4675212 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4666908 | 4675212 | a | 0 | + | | chr1 | 1 | 5221 | 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 | 2418841 | 2424970 | a | 0 | + | | chr1 | 2568628 | 2575605 | a | 0 | + | | chr1 | 5807462 | 5807794 | a | 0 | + | | chr1 | 2373040 | 2380275 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr5 | 5400359 | 5407004 | a | 0 | - | | chr6 | 2341305 | 2349477 | a | 0 | + | | chr10 | 6777977 | 6783506 | a | 0 | + | | chr20 | 5408378 | 5408405 | 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/tmp21y3ozuy/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2280808 2286911 a 0 - 1 1 chr1 2373040 2380275 a 0 - 2 2 chr1 2418841 2424970 a 0 + 3 3 chr1 2568628 2575605 a 0 + 4 4 chr1 3207040 3212162 a 0 - 5 5 chr1 5807462 5807794 a 0 + 6 6 chr10 6777977 6783506 a 0 + 7 7 chr20 5408378 5408405 a 0 - 8 8 chr4 8315139 8319058 a 0 - 9 9 chr5 5400359 5407004 a 0 - 10 10 chr6 2341305 2349477 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2418841 | 2424970 | a | 0 | + | | chr1 | 2568628 | 2575605 | a | 0 | + | | chr1 | 5807462 | 5807794 | a | 0 | + | | chr1 | 2373040 | 2380275 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr5 | 5400359 | 5407004 | a | 0 | - | | chr6 | 2341305 | 2349477 | a | 0 | + | | chr10 | 6777977 | 6783506 | a | 0 | + | | chr20 | 5408378 | 5408405 | 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 | 7623043 | 7627847 | a | 0 | + | | chr1 | 1682031 | 1684274 | a | 0 | + | | chr1 | 1008037 | 1016772 | a | 0 | + | | chr1 | 3477839 | 3477840 | a | 0 | - | | chr1 | 7885132 | 7889945 | 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 -i <(sort -k1,1 -k2,2n /tmp/tmppj9cxw7n/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1008037 1016772 a 0 + 1 1 chr1 1682031 1684274 a 0 + 2 2 chr1 3477839 3477840 a 0 - 3 3 chr1 7623043 7627847 a 0 + 4 4 chr1 7885132 7889945 a 0 - 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7623043 | 7627847 | a | 0 | + | | chr1 | 1682031 | 1684274 | a | 0 | + | | chr1 | 1008037 | 1016772 | a | 0 | + | | chr1 | 3477839 | 3477840 | a | 0 | - | | chr1 | 7885132 | 7889945 | 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 | 2 | 3647 | a | 0 | + | | chr1 | 9627155 | 9631825 | a | 0 | + | | chr1 | 2818461 | 2828460 | a | 0 | + | | chr1 | 1323460 | 1331185 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr9 | 1323460 | 1325751 | a | 0 | - | | chr15 | 715542 | 722402 | a | 0 | + | | chr16 | 1323460 | 1330953 | a | 0 | + | | chr21 | 9393930 | 9399922 | 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/tmpg97_dbd7/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2 3647 a 0 + 1 1 chr1 1323460 1331185 a 0 - 2 2 chr1 1323460 1332108 a 0 - 2 3 chr1 2818461 2828460 a 0 + 3 4 chr1 9627155 9631825 a 0 + 4 5 chr15 715542 722402 a 0 + 5 6 chr16 1323460 1330953 a 0 + 6 7 chr2 4262685 4271093 a 0 - 7 8 chr2 6374603 6382080 a 0 - 8 9 chr21 9393930 9399922 a 0 - 9 10 chr9 1323460 1325751 a 0 - 10 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2 | 3647 | a | 0 | + | | chr1 | 9627155 | 9631825 | a | 0 | + | | chr1 | 2818461 | 2828460 | a | 0 | + | | chr1 | 1323460 | 1331185 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr9 | 1323460 | 1325751 | a | 0 | - | | chr15 | 715542 | 722402 | a | 0 | + | | chr16 | 1323460 | 1330953 | a | 0 | + | | chr21 | 9393930 | 9399922 | 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 | 4542006 | 4551236 | 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/tmpoei7z918/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4542006 4551236 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4542006 | 4551236 | 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 | 5519341 | 5522126 | a | 0 | + | | chr1 | 9237029 | 9239245 | a | 0 | - | | chr1 | 3928640 | 3933905 | a | 0 | - | | chr7 | 4949435 | 4956363 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr9 | 6494962 | 6504962 | a | 0 | + | | chr9 | 7580229 | 7586688 | a | 0 | - | | chr9 | 3265186 | 3267410 | a | 0 | - | | chr9 | 2937374 | 2941772 | 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/tmpsswslgby/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3928640 3933905 a 0 - 1 1 chr1 5519341 5522126 a 0 + 2 2 chr1 9237029 9239245 a 0 - 3 3 chr21 6511413 6517186 a 0 + 4 4 chr7 4949435 4956363 a 0 - 5 5 chr9 2937374 2941772 a 0 - 6 6 chr9 3265186 3267410 a 0 - 7 7 chr9 6494962 6504962 a 0 + 8 8 chr9 7580229 7586688 a 0 - 9 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5519341 | 5522126 | a | 0 | + | | chr1 | 9237029 | 9239245 | a | 0 | - | | chr1 | 3928640 | 3933905 | a | 0 | - | | chr7 | 4949435 | 4956363 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr9 | 6494962 | 6504962 | a | 0 | + | | chr9 | 7580229 | 7586688 | a | 0 | - | | chr9 | 3265186 | 3267410 | a | 0 | - | | chr9 | 2937374 | 2941772 | 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 | 7364083 | 7369713 | a | 0 | + | | chr1 | 7364083 | 7367946 | a | 0 | + | | chr1 | 7364083 | 7370396 | a | 0 | - | | chr1 | 7364083 | 7374083 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr11 | 7364083 | 7370607 | a | 0 | - | | chr11 | 7364083 | 7374083 | a | 0 | - | | chr16 | 2810424 | 2818870 | a | 0 | - | | chrX | 7364083 | 7371199 | 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/tmpco282bow/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 7364083 7366797 a 0 - 1 1 chr1 7364083 7367946 a 0 + 1 2 chr1 7364083 7369713 a 0 + 1 3 chr1 7364083 7370396 a 0 - 1 4 chr1 7364083 7371934 a 0 - 1 5 chr1 7364083 7374083 a 0 - 1 6 chr11 7364083 7370607 a 0 - 2 7 chr11 7364083 7374083 a 0 - 2 8 chr16 2810424 2818870 a 0 - 3 9 chrX 7364083 7371199 a 0 - 4 10 chrY 7364083 7368629 a 0 - 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7364083 | 7369713 | a | 0 | + | | chr1 | 7364083 | 7367946 | a | 0 | + | | chr1 | 7364083 | 7370396 | a | 0 | - | | chr1 | 7364083 | 7374083 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr11 | 7364083 | 7370607 | a | 0 | - | | chr11 | 7364083 | 7374083 | a | 0 | - | | chr16 | 2810424 | 2818870 | a | 0 | - | | chrX | 7364083 | 7371199 | 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 | 5883721 | 5890596 | a | 0 | + | | chr1 | 9267211 | 9271053 | a | 0 | + | | chr1 | 6571080 | 6576704 | a | 0 | + | | chr1 | 6259231 | 6261266 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 1218261 | 1225872 | a | 0 | + | | chr1 | 6781099 | 6790033 | a | 0 | - | | chr1 | 7160457 | 7163468 | a | 0 | - | | chr1 | 7777304 | 7785276 | 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/tmptgyx02wo/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1218261 1225872 a 0 + 1 1 chr1 5883721 5890596 a 0 + 2 2 chr1 6259231 6261266 a 0 + 3 3 chr1 6571080 6576704 a 0 + 4 4 chr1 6781099 6790033 a 0 - 5 5 chr1 7160457 7163468 a 0 - 6 6 chr1 7777304 7785276 a 0 - 7 7 chr1 9267211 9271053 a 0 + 8 8 chr11 2231263 2234530 a 0 - 9 9 chr11 8300872 8310032 a 0 - 10 10 chr4 775563 776155 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5883721 | 5890596 | a | 0 | + | | chr1 | 9267211 | 9271053 | a | 0 | + | | chr1 | 6571080 | 6576704 | a | 0 | + | | chr1 | 6259231 | 6261266 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 1218261 | 1225872 | a | 0 | + | | chr1 | 6781099 | 6790033 | a | 0 | - | | chr1 | 7160457 | 7163468 | a | 0 | - | | chr1 | 7777304 | 7785276 | 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 | 5634812 | 5642055 | a | 0 | + | | chr1 | 9861619 | 9868576 | a | 0 | - | | chr4 | 8009761 | 8013124 | a | 0 | + | | chr4 | 691775 | 699018 | a | 0 | + | | chr4 | 8755594 | 8762837 | a | 0 | - | | chr21 | 10000000 | 10009167 | 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 -i <(sort -k1,1 -k2,2n /tmp/tmp5l25y3yc/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5634812 5642055 a 0 + 1 1 chr1 9861619 9868576 a 0 - 2 2 chr21 10000000 10009167 a 0 - 3 3 chr4 691775 699018 a 0 + 4 4 chr4 8009761 8013124 a 0 + 5 5 chr4 8755594 8762837 a 0 - 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5634812 | 5642055 | a | 0 | + | | chr1 | 9861619 | 9868576 | a | 0 | - | | chr4 | 8009761 | 8013124 | a | 0 | + | | chr4 | 691775 | 699018 | a | 0 | + | | chr4 | 8755594 | 8762837 | a | 0 | - | | chr21 | 10000000 | 10009167 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr6 | 6317197 | 6326989 | a | 0 | - | | chrM | 3750511 | 3759159 | 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/tmpc5xfj0dm/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr6 6317197 6326989 a 0 - 1 1 chrM 3750511 3759159 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr6 | 6317197 | 6326989 | a | 0 | - | | chrM | 3750511 | 3759159 | 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 | 3777685 | 3784149 | 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/tmptvrjhzmn/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3777685 3784149 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3777685 | 3784149 | 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 | 6805926 | 6811881 | a | 0 | - | | chr1 | 9551959 | 9553334 | a | 0 | - | | chr1 | 8092879 | 8096355 | a | 0 | - | | chr4 | 9165313 | 9174304 | a | 0 | + | | chr4 | 6164472 | 6170427 | a | 0 | + | | chr4 | 113610 | 114332 | a | 0 | - | | chr4 | 4221762 | 4227564 | a | 0 | - | | chr4 | 1 | 3658 | 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/tmp8sckgbk1/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6805926 6811881 a 0 - 1 1 chr1 8092879 8096355 a 0 - 2 2 chr1 9551959 9553334 a 0 - 3 3 chr4 1 3658 a 0 - 4 4 chr4 113610 114332 a 0 - 5 5 chr4 4221762 4227564 a 0 - 6 6 chr4 6164472 6170427 a 0 + 7 7 chr4 9165313 9174304 a 0 + 8 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6805926 | 6811881 | a | 0 | - | | chr1 | 9551959 | 9553334 | a | 0 | - | | chr1 | 8092879 | 8096355 | a | 0 | - | | chr4 | 9165313 | 9174304 | a | 0 | + | | chr4 | 6164472 | 6170427 | a | 0 | + | | chr4 | 113610 | 114332 | a | 0 | - | | chr4 | 4221762 | 4227564 | a | 0 | - | | chr4 | 1 | 3658 | 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 | 8046064 | 8046708 | a | 0 | + | | chr1 | 4551963 | 4561962 | a | 0 | - | | chr15 | 8347618 | 8350273 | a | 0 | + | | chr18 | 9397379 | 9399033 | a | 0 | - | | chrM | 3281906 | 3283150 | 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/tmpffs1x65y/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4551963 4561962 a 0 - 1 1 chr1 8046064 8046708 a 0 + 2 2 chr15 8347618 8350273 a 0 + 3 3 chr18 9397379 9399033 a 0 - 4 4 chrM 3281906 3283150 a 0 + 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8046064 | 8046708 | a | 0 | + | | chr1 | 4551963 | 4561962 | a | 0 | - | | chr15 | 8347618 | 8350273 | a | 0 | + | | chr18 | 9397379 | 9399033 | a | 0 | - | | chrM | 3281906 | 3283150 | 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 | 2594547 | 2601910 | a | 0 | + | | chr1 | 2757916 | 2758743 | a | 0 | + | | chr1 | 6940915 | 6942809 | a | 0 | + | | chr1 | 1383767 | 1385933 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 6940915 | 6942809 | a | 0 | + | | chr1 | 1383767 | 1385933 | a | 0 | - | | chr1 | 1493925 | 1494894 | a | 0 | - | | chr1 | 2705679 | 2705680 | 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/tmpcwahbmdf/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1383767 1385933 a 0 - 1 1 chr1 1493925 1494894 a 0 - 2 2 chr1 2594547 2601910 a 0 + 3 3 chr1 2705679 2705680 a 0 - 4 4 chr1 2757916 2758743 a 0 + 5 5 chr1 6940915 6942809 a 0 + 6 6 chr13 3693489 3698560 a 0 + 7 7 chr13 9162743 9164979 a 0 - 8 8 chr5 4926503 4928007 a 0 - 9 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2594547 | 2601910 | a | 0 | + | | chr1 | 2757916 | 2758743 | a | 0 | + | | chr1 | 6940915 | 6942809 | a | 0 | + | | chr1 | 1383767 | 1385933 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 6940915 | 6942809 | a | 0 | + | | chr1 | 1383767 | 1385933 | a | 0 | - | | chr1 | 1493925 | 1494894 | a | 0 | - | | chr1 | 2705679 | 2705680 | 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 | 2060096 | 2065880 | a | 0 | - | | chr19 | 2060096 | 2061267 | 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/tmpwvqrilcd/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2060096 2065880 a 0 - 1 1 chr19 2060096 2061267 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2060096 | 2065880 | a | 0 | - | | chr19 | 2060096 | 2061267 | 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 | 2756053 | 2760970 | a | 0 | + | | chr1 | 9013873 | 9018790 | a | 0 | + | | chr1 | 4725263 | 4730180 | a | 0 | - | | chr5 | 2025937 | 2034434 | a | 0 | - | | chr10 | 8960032 | 8965235 | a | 0 | + | | chr10 | 1532453 | 1537370 | 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 -i <(sort -k1,1 -k2,2n /tmp/tmpi8n2ymxz/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2756053 2760970 a 0 + 1 1 chr1 4725263 4730180 a 0 - 2 2 chr1 9013873 9018790 a 0 + 3 3 chr10 1532453 1537370 a 0 - 4 4 chr10 8960032 8965235 a 0 + 5 5 chr5 2025937 2034434 a 0 - 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2756053 | 2760970 | a | 0 | + | | chr1 | 9013873 | 9018790 | a | 0 | + | | chr1 | 4725263 | 4730180 | a | 0 | - | | chr5 | 2025937 | 2034434 | a | 0 | - | | chr10 | 8960032 | 8965235 | a | 0 | + | | chr10 | 1532453 | 1537370 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr8 | 673838 | 680699 | a | 0 | + | | chr20 | 9559998 | 9561519 | 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/tmpf2q28uor/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr20 9559998 9561519 a 0 - 1 1 chr8 673838 680699 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr8 | 673838 | 680699 | a | 0 | + | | chr20 | 9559998 | 9561519 | 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 | 8190035 | 8193113 | a | 0 | + | | chr1 | 2404477 | 2405625 | a | 0 | + | | chr3 | 3967982 | 3972554 | a | 0 | + | | chr11 | 3967982 | 3969332 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr18 | 8346692 | 8351621 | a | 0 | + | | chr18 | 5245405 | 5255404 | a | 0 | + | | chr18 | 3028134 | 3030997 | a | 0 | + | | chr18 | 5722032 | 5726111 | 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/tmpbjl12w4d/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2404477 2405625 a 0 + 1 1 chr1 8190035 8193113 a 0 + 2 2 chr11 3967982 3969332 a 0 + 3 3 chr18 3028134 3030997 a 0 + 4 4 chr18 5245405 5255404 a 0 + 5 5 chr18 5722032 5726111 a 0 + 6 6 chr18 8346692 8351621 a 0 + 7 7 chr20 6419216 6428024 a 0 + 8 8 chr3 3967982 3972554 a 0 + 9 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8190035 | 8193113 | a | 0 | + | | chr1 | 2404477 | 2405625 | a | 0 | + | | chr3 | 3967982 | 3972554 | a | 0 | + | | chr11 | 3967982 | 3969332 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr18 | 8346692 | 8351621 | a | 0 | + | | chr18 | 5245405 | 5255404 | a | 0 | + | | chr18 | 3028134 | 3030997 | a | 0 | + | | chr18 | 5722032 | 5726111 | 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 | 8293228 | 8298776 | a | 0 | + | | chr1 | 2093621 | 2102115 | a | 0 | - | | chr1 | 3502994 | 3507348 | a | 0 | - | | chr1 | 6109312 | 6111724 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr14 | 4917295 | 4926336 | a | 0 | - | | chr18 | 6420728 | 6429249 | a | 0 | - | | chr18 | 2256368 | 2256807 | a | 0 | - | | chr22 | 7217327 | 7220124 | 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_qnrackx/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2093621 2102115 a 0 - 1 1 chr1 3502994 3507348 a 0 - 2 2 chr1 6109312 6111724 a 0 - 3 3 chr1 7751428 7757849 a 0 - 4 4 chr1 8293228 8298776 a 0 + 5 5 chr1 8569431 8575567 a 0 - 6 6 chr14 4917295 4926336 a 0 - 7 7 chr18 2256368 2256807 a 0 - 8 8 chr18 6420728 6429249 a 0 - 9 9 chr22 7217327 7220124 a 0 - 10 10 chr3 1649261 1657923 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8293228 | 8298776 | a | 0 | + | | chr1 | 2093621 | 2102115 | a | 0 | - | | chr1 | 3502994 | 3507348 | a | 0 | - | | chr1 | 6109312 | 6111724 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr14 | 4917295 | 4926336 | a | 0 | - | | chr18 | 6420728 | 6429249 | a | 0 | - | | chr18 | 2256368 | 2256807 | a | 0 | - | | chr22 | 7217327 | 7220124 | 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 | 2890853 | 2891644 | a | 0 | + | | chr1 | 2890853 | 2900852 | a | 0 | + | | chr1 | 2890853 | 2900702 | a | 0 | + | | chr1 | 2890853 | 2899292 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 2890853 | 2900702 | a | 0 | + | | chr1 | 2890853 | 2899292 | a | 0 | + | | chr1 | 1837369 | 1838160 | a | 0 | - | | chr1 | 2890853 | 2897498 | 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/tmpv_w2kdho/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1837369 1838160 a 0 - 1 1 chr1 2890853 2891644 a 0 + 2 2 chr1 2890853 2897498 a 0 - 2 3 chr1 2890853 2899292 a 0 + 2 4 chr1 2890853 2900702 a 0 + 2 5 chr1 2890853 2900852 a 0 + 2 6 chr11 2890853 2895611 a 0 + 3 7 chr4 4389847 4397094 a 0 + 4 8 chrX 2890853 2898368 a 0 - 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2890853 | 2891644 | a | 0 | + | | chr1 | 2890853 | 2900852 | a | 0 | + | | chr1 | 2890853 | 2900702 | a | 0 | + | | chr1 | 2890853 | 2899292 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 2890853 | 2900702 | a | 0 | + | | chr1 | 2890853 | 2899292 | a | 0 | + | | chr1 | 1837369 | 1838160 | a | 0 | - | | chr1 | 2890853 | 2897498 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr13 | 9411543 | 9412991 | 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/tmpif4ngc23/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr13 9411543 9412991 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr13 | 9411543 | 9412991 | 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 | 3826037 | 3829811 | a | 0 | + | | chr1 | 3831516 | 3836729 | a | 0 | + | | chr1 | 3831516 | 3832749 | a | 0 | + | | chr1 | 3831516 | 3836055 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 3831516 | 3832749 | a | 0 | + | | chr1 | 3831516 | 3836055 | a | 0 | + | | chr1 | 3831516 | 3841516 | a | 0 | - | | chr1 | 451400 | 451401 | 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/tmpmt6rnp9o/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 451400 451401 a 0 - 1 1 chr1 3826037 3829811 a 0 + 2 2 chr1 3831516 3832749 a 0 + 3 3 chr1 3831516 3836055 a 0 + 3 4 chr1 3831516 3836729 a 0 + 3 5 chr1 3831516 3841516 a 0 - 3 6 chr16 8874177 8874553 a 0 + 4 7 chr21 3831516 3839892 a 0 + 5 8 chr8 3831516 3832107 a 0 + 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3826037 | 3829811 | a | 0 | + | | chr1 | 3831516 | 3836729 | a | 0 | + | | chr1 | 3831516 | 3832749 | a | 0 | + | | chr1 | 3831516 | 3836055 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 3831516 | 3832749 | a | 0 | + | | chr1 | 3831516 | 3836055 | a | 0 | + | | chr1 | 3831516 | 3841516 | a | 0 | - | | chr1 | 451400 | 451401 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr15 | 8557387 | 8567028 | a | 0 | + | | chrY | 673045 | 681749 | 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/tmp05y4iw05/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr15 8557387 8567028 a 0 + 1 1 chrY 673045 681749 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr15 | 8557387 | 8567028 | a | 0 | + | | chrY | 673045 | 681749 | 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 | 9644764 | 9652054 | a | 0 | + | | chr1 | 3931259 | 3938549 | a | 0 | + | | chr1 | 2 | 7292 | 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/tmpauyqxe9k/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2 7292 a 0 + 1 1 chr1 3931259 3938549 a 0 + 2 2 chr1 9644764 9652054 a 0 + 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9644764 | 9652054 | a | 0 | + | | chr1 | 3931259 | 3938549 | a | 0 | + | | chr1 | 2 | 7292 | 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 | 9017670 | 9023620 | a | 0 | - | | chrY | 6016444 | 6024657 | 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/tmp5aw8369m/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 9017670 9023620 a 0 - 1 1 chrY 6016444 6024657 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9017670 | 9023620 | a | 0 | - | | chrY | 6016444 | 6024657 | 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 | 5109650 | 5116432 | a | 0 | + | | chr1 | 9752711 | 9759493 | a | 0 | + | | chr1 | 416025 | 422078 | a | 0 | + | | chr1 | 1588391 | 1595173 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 7084085 | 7090867 | a | 0 | - | | chr1 | 6384630 | 6391412 | a | 0 | - | | chr1 | 2546530 | 2553312 | a | 0 | - | | chr1 | 4803378 | 4810160 | 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/tmpxgdjkm9v/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 416025 422078 a 0 + 1 1 chr1 1588391 1595173 a 0 + 2 2 chr1 2546530 2553312 a 0 - 3 3 chr1 4803378 4810160 a 0 - 4 4 chr1 5109650 5116432 a 0 + 5 5 chr1 6384630 6391412 a 0 - 6 6 chr1 7084085 7090867 a 0 - 7 7 chr1 8438639 8445421 a 0 + 8 8 chr1 8662039 8668821 a 0 + 9 9 chr1 9752711 9759493 a 0 + 10 10 chr17 603753 610535 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5109650 | 5116432 | a | 0 | + | | chr1 | 9752711 | 9759493 | a | 0 | + | | chr1 | 416025 | 422078 | a | 0 | + | | chr1 | 1588391 | 1595173 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 7084085 | 7090867 | a | 0 | - | | chr1 | 6384630 | 6391412 | a | 0 | - | | chr1 | 2546530 | 2553312 | a | 0 | - | | chr1 | 4803378 | 4810160 | 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 | 3300563 | 3306822 | a | 0 | + | | chr1 | 7582231 | 7582232 | a | 0 | + | | chr1 | 5876038 | 5876631 | a | 0 | + | | chr1 | 8585875 | 8594712 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr6 | 8202374 | 8211374 | a | 0 | - | | chr15 | 1216647 | 1226369 | a | 0 | + | | chr17 | 879098 | 882448 | a | 0 | + | | chr19 | 1909513 | 1913638 | 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/tmpgxhgicuc/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3300563 3306822 a 0 + 1 1 chr1 5876038 5876631 a 0 + 2 2 chr1 7582231 7582232 a 0 + 3 3 chr1 8585875 8594712 a 0 + 4 4 chr1 9469603 9471010 a 0 - 5 5 chr15 1216647 1226369 a 0 + 6 6 chr17 879098 882448 a 0 + 7 7 chr19 1909513 1913638 a 0 - 8 8 chr2 5277982 5284027 a 0 - 9 9 chr3 6616013 6621084 a 0 + 10 10 chr6 8202374 8211374 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3300563 | 3306822 | a | 0 | + | | chr1 | 7582231 | 7582232 | a | 0 | + | | chr1 | 5876038 | 5876631 | a | 0 | + | | chr1 | 8585875 | 8594712 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr6 | 8202374 | 8211374 | a | 0 | - | | chr15 | 1216647 | 1226369 | a | 0 | + | | chr17 | 879098 | 882448 | a | 0 | + | | chr19 | 1909513 | 1913638 | 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 | 8832 | 13993 | a | 0 | + | | chr1 | 420979 | 429077 | a | 0 | + | | chr1 | 6409387 | 6411596 | a | 0 | - | | chr1 | 3414762 | 3416685 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 9834977 | 9836859 | a | 0 | - | | chr1 | 7070471 | 7079248 | a | 0 | - | | chr1 | 3829950 | 3833669 | a | 0 | - | | chr1 | 5160956 | 5169817 | 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/tmpzwgycrmo/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 8832 13993 a 0 + 1 1 chr1 420979 429077 a 0 + 2 2 chr1 3281590 3290367 a 0 - 3 3 chr1 3414762 3416685 a 0 - 4 4 chr1 3829950 3833669 a 0 - 5 5 chr1 5160956 5169817 a 0 - 6 6 chr1 6409387 6411596 a 0 - 7 7 chr1 7070471 7079248 a 0 - 8 8 chr1 9834977 9836859 a 0 - 9 9 chr17 6035494 6044271 a 0 - 10 10 chr3 8957387 8964088 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8832 | 13993 | a | 0 | + | | chr1 | 420979 | 429077 | a | 0 | + | | chr1 | 6409387 | 6411596 | a | 0 | - | | chr1 | 3414762 | 3416685 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 9834977 | 9836859 | a | 0 | - | | chr1 | 7070471 | 7079248 | a | 0 | - | | chr1 | 3829950 | 3833669 | a | 0 | - | | chr1 | 5160956 | 5169817 | 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 | 9883936 | 9884154 | a | 0 | - | | chr1 | 4054457 | 4054889 | a | 0 | - | | chr3 | 8025515 | 8030594 | a | 0 | - | | chr12 | 2042329 | 2048666 | a | 0 | + | | chr21 | 5920772 | 5926501 | a | 0 | + | | chr21 | 8772524 | 8779524 | a | 0 | + | | chr21 | 8977965 | 8977966 | a | 0 | - | | chr21 | 7576029 | 7578727 | 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/tmp789u4zvc/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4054457 4054889 a 0 - 1 1 chr1 9883936 9884154 a 0 - 2 2 chr12 2042329 2048666 a 0 + 3 3 chr21 5920772 5926501 a 0 + 4 4 chr21 7576029 7578727 a 0 - 5 5 chr21 8772524 8779524 a 0 + 6 6 chr21 8977965 8977966 a 0 - 7 7 chr3 8025515 8030594 a 0 - 8 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9883936 | 9884154 | a | 0 | - | | chr1 | 4054457 | 4054889 | a | 0 | - | | chr3 | 8025515 | 8030594 | a | 0 | - | | chr12 | 2042329 | 2048666 | a | 0 | + | | chr21 | 5920772 | 5926501 | a | 0 | + | | chr21 | 8772524 | 8779524 | a | 0 | + | | chr21 | 8977965 | 8977966 | a | 0 | - | | chr21 | 7576029 | 7578727 | 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 | 9038622 | 9041382 | a | 0 | - | | chrX | 8624888 | 8627648 | 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/tmp6iiety6c/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 9038622 9041382 a 0 - 1 1 chrX 8624888 8627648 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9038622 | 9041382 | a | 0 | - | | chrX | 8624888 | 8627648 | 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 | 9991816 | 9997901 | a | 0 | + | | chr1 | 2446413 | 2453946 | a | 0 | - | | chr1 | 6435355 | 6443795 | 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/tmpxrhch99u/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2446413 2453946 a 0 - 1 1 chr1 6435355 6443795 a 0 - 2 2 chr1 9991816 9997901 a 0 + 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9991816 | 9997901 | a | 0 | + | | chr1 | 2446413 | 2453946 | a | 0 | - | | chr1 | 6435355 | 6443795 | 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 | 3867531 | 3868774 | a | 0 | + | | chr1 | 3867531 | 3868774 | a | 0 | + | | chr1 | 1693946 | 1695042 | a | 0 | - | | chr1 | 1948766 | 1954031 | a | 0 | - | | chr1 | 10000000 | 10001243 | a | 0 | - | | chr1 | 3867531 | 3867532 | a | 0 | - | | chr1 | 6674986 | 6676229 | a | 0 | - | | chr17 | 350802 | 352045 | 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/tmpg6ndp8q5/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1693946 1695042 a 0 - 1 1 chr1 1948766 1954031 a 0 - 2 2 chr1 3867531 3867532 a 0 - 3 3 chr1 3867531 3868774 a 0 + 3 4 chr1 3867531 3868774 a 0 + 3 5 chr1 6674986 6676229 a 0 - 4 6 chr1 10000000 10001243 a 0 - 5 7 chr17 350802 352045 a 0 - 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3867531 | 3868774 | a | 0 | + | | chr1 | 3867531 | 3868774 | a | 0 | + | | chr1 | 1693946 | 1695042 | a | 0 | - | | chr1 | 1948766 | 1954031 | a | 0 | - | | chr1 | 10000000 | 10001243 | a | 0 | - | | chr1 | 3867531 | 3867532 | a | 0 | - | | chr1 | 6674986 | 6676229 | a | 0 | - | | chr17 | 350802 | 352045 | 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 | 9637058 | 9643450 | a | 0 | - | | chr17 | 7188128 | 7197277 | 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/tmptiy4e2x_/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 9637058 9643450 a 0 - 1 1 chr17 7188128 7197277 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9637058 | 9643450 | a | 0 | - | | chr17 | 7188128 | 7197277 | 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 | 9004329 | 9007317 | 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/tmprztsslal/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 9004329 9007317 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9004329 | 9007317 | 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 | 833681 | 835177 | a | 0 | - | | chr1 | 4366139 | 4368832 | a | 0 | - | | chr2 | 3394393 | 3402390 | 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/tmpvvemafzp/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 833681 835177 a 0 - 1 1 chr1 4366139 4368832 a 0 - 2 2 chr2 3394393 3402390 a 0 - 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 833681 | 835177 | a | 0 | - | | chr1 | 4366139 | 4368832 | a | 0 | - | | chr2 | 3394393 | 3402390 | 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 | 1013856 | 1016116 | a | 0 | + | | chr1 | 3099111 | 3103683 | a | 0 | + | | chr1 | 8454313 | 8460166 | a | 0 | + | | chr1 | 3692411 | 3697854 | a | 0 | + | | chr1 | 6292876 | 6293381 | a | 0 | - | | chr19 | 7169697 | 7171957 | a | 0 | + | | chr22 | 5260174 | 5268193 | 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 -i <(sort -k1,1 -k2,2n /tmp/tmph5a1ay7f/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1013856 1016116 a 0 + 1 1 chr1 3099111 3103683 a 0 + 2 2 chr1 3692411 3697854 a 0 + 3 3 chr1 6292876 6293381 a 0 - 4 4 chr1 8454313 8460166 a 0 + 5 5 chr19 7169697 7171957 a 0 + 6 6 chr22 5260174 5268193 a 0 - 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1013856 | 1016116 | a | 0 | + | | chr1 | 3099111 | 3103683 | a | 0 | + | | chr1 | 8454313 | 8460166 | a | 0 | + | | chr1 | 3692411 | 3697854 | a | 0 | + | | chr1 | 6292876 | 6293381 | a | 0 | - | | chr19 | 7169697 | 7171957 | a | 0 | + | | chr22 | 5260174 | 5268193 | 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 | 1774876 | 1778743 | a | 0 | + | | chr1 | 9537772 | 9541191 | a | 0 | + | | chr1 | 3245797 | 3248273 | a | 0 | + | | chr1 | 9953400 | 9953885 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr8 | 8746001 | 8751993 | a | 0 | + | | chr9 | 4829836 | 4832312 | a | 0 | + | | chr10 | 553120 | 558443 | a | 0 | + | | chr15 | 9733006 | 9735482 | 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/tmpuv5o7tx1/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1774876 1778743 a 0 + 1 1 chr1 3245797 3248273 a 0 + 2 2 chr1 8685080 8691148 a 0 - 3 3 chr1 9537772 9541191 a 0 + 4 4 chr1 9953400 9953885 a 0 + 5 5 chr10 553120 558443 a 0 + 6 6 chr15 9733006 9735482 a 0 + 7 7 chr8 8746001 8751993 a 0 + 8 8 chr9 4829836 4832312 a 0 + 9 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1774876 | 1778743 | a | 0 | + | | chr1 | 9537772 | 9541191 | a | 0 | + | | chr1 | 3245797 | 3248273 | a | 0 | + | | chr1 | 9953400 | 9953885 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr8 | 8746001 | 8751993 | a | 0 | + | | chr9 | 4829836 | 4832312 | a | 0 | + | | chr10 | 553120 | 558443 | a | 0 | + | | chr15 | 9733006 | 9735482 | 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 | 6682967 | 6687836 | a | 0 | + | | chr1 | 8491998 | 8500550 | a | 0 | + | | chr1 | 7059626 | 7064106 | a | 0 | + | | chr1 | 2493690 | 2503436 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 7533289 | 7537769 | a | 0 | + | | chr1 | 1759230 | 1759231 | a | 0 | + | | chr1 | 1453409 | 1460193 | a | 0 | + | | chr1 | 856646 | 863310 | 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/tmptiunbcua/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 856646 863310 a 0 - 1 1 chr1 1453409 1460193 a 0 + 2 2 chr1 1759230 1759231 a 0 + 3 3 chr1 2493690 2503436 a 0 + 4 4 chr1 6682967 6687836 a 0 + 5 5 chr1 7059626 7064106 a 0 + 6 6 chr1 7533289 7537769 a 0 + 7 7 chr1 8034431 8037216 a 0 + 8 8 chr1 8491998 8500550 a 0 + 9 9 chr1 8764108 8764970 a 0 + 10 10 chr3 6403138 6407394 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6682967 | 6687836 | a | 0 | + | | chr1 | 8491998 | 8500550 | a | 0 | + | | chr1 | 7059626 | 7064106 | a | 0 | + | | chr1 | 2493690 | 2503436 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 7533289 | 7537769 | a | 0 | + | | chr1 | 1759230 | 1759231 | a | 0 | + | | chr1 | 1453409 | 1460193 | a | 0 | + | | chr1 | 856646 | 863310 | 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 | 8722192 | 8722625 | a | 0 | + | | chr1 | 8722192 | 8728775 | a | 0 | - | | chr1 | 4374295 | 4380878 | a | 0 | - | | chrX | 8722192 | 8732047 | 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/tmpta9oyen3/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4374295 4380878 a 0 - 1 1 chr1 8722192 8722625 a 0 + 2 2 chr1 8722192 8728775 a 0 - 2 3 chrX 8722192 8732047 a 0 - 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8722192 | 8722625 | a | 0 | + | | chr1 | 8722192 | 8728775 | a | 0 | - | | chr1 | 4374295 | 4380878 | a | 0 | - | | chrX | 8722192 | 8732047 | 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 | 8484984 | 8489612 | a | 0 | + | | chr16 | 3308642 | 3313270 | 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/tmpwwlh_bij/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 8484984 8489612 a 0 + 1 1 chr16 3308642 3313270 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8484984 | 8489612 | a | 0 | + | | chr16 | 3308642 | 3313270 | 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 | 8769630 | 8773106 | a | 0 | + | | chr1 | 4927898 | 4932218 | a | 0 | - | | chr18 | 8627541 | 8634164 | a | 0 | + | | chr20 | 1587796 | 1594658 | 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/tmpkanl92z5/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4927898 4932218 a 0 - 1 1 chr1 8769630 8773106 a 0 + 2 2 chr18 8627541 8634164 a 0 + 3 3 chr20 1587796 1594658 a 0 - 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8769630 | 8773106 | a | 0 | + | | chr1 | 4927898 | 4932218 | a | 0 | - | | chr18 | 8627541 | 8634164 | a | 0 | + | | chr20 | 1587796 | 1594658 | 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 | 4598096 | 4602584 | 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/tmp0_x012av/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4598096 4602584 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4598096 | 4602584 | 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 | 4820102 | 4827147 | a | 0 | - | | chr2 | 1728533 | 1729515 | a | 0 | - | | chr4 | 1628544 | 1637169 | a | 0 | - | | chr5 | 9482700 | 9488083 | a | 0 | + | | chr11 | 9716848 | 9726764 | a | 0 | + | | chr12 | 7294875 | 7301581 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 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/tmp0_8vcni3/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4820102 4827147 a 0 - 1 1 chr11 9716848 9726764 a 0 + 2 2 chr12 7294875 7301581 a 0 - 3 3 chr2 1728533 1729515 a 0 - 4 4 chr4 1628544 1637169 a 0 - 5 5 chr5 9482700 9488083 a 0 + 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4820102 | 4827147 | a | 0 | - | | chr2 | 1728533 | 1729515 | a | 0 | - | | chr4 | 1628544 | 1637169 | a | 0 | - | | chr5 | 9482700 | 9488083 | a | 0 | + | | chr11 | 9716848 | 9726764 | a | 0 | + | | chr12 | 7294875 | 7301581 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 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 | 7135705 | 7139828 | 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/tmpfpmr37r8/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 7135705 7139828 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7135705 | 7139828 | 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 | 4157360 | 4157362 | a | 0 | + | | chr14 | 9632961 | 9640586 | a | 0 | - | | chr15 | 2854065 | 2864065 | a | 0 | - | | chrM | 2854065 | 2860530 | a | 0 | + | | chrM | 4358440 | 4362994 | 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/tmpgrd00eu1/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4157360 4157362 a 0 + 1 1 chr14 9632961 9640586 a 0 - 2 2 chr15 2854065 2864065 a 0 - 3 3 chrM 2854065 2860530 a 0 + 4 4 chrM 4358440 4362994 a 0 + 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4157360 | 4157362 | a | 0 | + | | chr14 | 9632961 | 9640586 | a | 0 | - | | chr15 | 2854065 | 2864065 | a | 0 | - | | chrM | 2854065 | 2860530 | a | 0 | + | | chrM | 4358440 | 4362994 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chr5 | 7094966 | 7102651 | a | 0 | + | | chr5 | 4003409 | 4012024 | a | 0 | + | | chr5 | 3963713 | 3971907 | a | 0 | + | | chr5 | 7164186 | 7170622 | a | 0 | + | | chr5 | 2343242 | 2344028 | a | 0 | - | | chr5 | 8229547 | 8234052 | 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/tmpe3hj9zwl/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr5 2343242 2344028 a 0 - 1 1 chr5 3963713 3971907 a 0 + 2 2 chr5 4003409 4012024 a 0 + 3 3 chr5 7094966 7102651 a 0 + 4 4 chr5 7164186 7170622 a 0 + 5 5 chr5 8229547 8234052 a 0 - 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr5 | 7094966 | 7102651 | a | 0 | + | | chr5 | 4003409 | 4012024 | a | 0 | + | | chr5 | 3963713 | 3971907 | a | 0 | + | | chr5 | 7164186 | 7170622 | a | 0 | + | | chr5 | 2343242 | 2344028 | a | 0 | - | | chr5 | 8229547 | 8234052 | 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 | 3751317 | 3751570 | a | 0 | + | | chr1 | 8398440 | 8400627 | a | 0 | + | | chr1 | 9439804 | 9439938 | a | 0 | - | | chr11 | 3632981 | 3639666 | 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/tmpsurbcqkg/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3751317 3751570 a 0 + 1 1 chr1 8398440 8400627 a 0 + 2 2 chr1 9439804 9439938 a 0 - 3 3 chr11 3632981 3639666 a 0 - 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3751317 | 3751570 | a | 0 | + | | chr1 | 8398440 | 8400627 | a | 0 | + | | chr1 | 9439804 | 9439938 | a | 0 | - | | chr11 | 3632981 | 3639666 | 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 | 2678193 | 2687842 | a | 0 | - | | chr1 | 3902313 | 3907004 | a | 0 | - | | chr1 | 1256846 | 1263363 | a | 0 | - | | chr2 | 3856217 | 3860465 | a | 0 | + | | chr14 | 1767874 | 1770026 | a | 0 | - | | chr16 | 2620686 | 2629083 | 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/tmpcw12ygiz/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1256846 1263363 a 0 - 1 1 chr1 2678193 2687842 a 0 - 2 2 chr1 3902313 3907004 a 0 - 3 3 chr14 1767874 1770026 a 0 - 4 4 chr16 2620686 2629083 a 0 - 5 5 chr2 3856217 3860465 a 0 + 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2678193 | 2687842 | a | 0 | - | | chr1 | 3902313 | 3907004 | a | 0 | - | | chr1 | 1256846 | 1263363 | a | 0 | - | | chr2 | 3856217 | 3860465 | a | 0 | + | | chr14 | 1767874 | 1770026 | a | 0 | - | | chr16 | 2620686 | 2629083 | 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 | 3512897 | 3521909 | a | 0 | + | | chr1 | 7741175 | 7749401 | a | 0 | + | | chr1 | 7124968 | 7127062 | a | 0 | - | | chr8 | 9400648 | 9404857 | 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/tmpzfaijnmh/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3512897 3521909 a 0 + 1 1 chr1 7124968 7127062 a 0 - 2 2 chr1 7741175 7749401 a 0 + 3 3 chr8 9400648 9404857 a 0 - 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3512897 | 3521909 | a | 0 | + | | chr1 | 7741175 | 7749401 | a | 0 | + | | chr1 | 7124968 | 7127062 | a | 0 | - | | chr8 | 9400648 | 9404857 | 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) | |--------------+-----------+-----------+------------+-----------+--------------| | chrY | 9658492 | 9663521 | 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/tmprunmmvma/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chrY 9658492 9663521 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chrY | 9658492 | 9663521 | 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/tmpl3lu8jny/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. ---------------------------------- 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_summary _________________________________ [gw0] linux -- Python 3.12.3 /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('6.100.4', b'AXicY2QAA0YGBAAAADIAAw==') 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', 'chr1', 'chr7', 'chr7', 'chr8', 'chr17', 'chrM'], 'Start': [8354667, 9907638, 4817408, 3831500, 9510401, 2748559, 8482154, 2241514, 6290428, 5055242], 'End': [8355327, 9914159, 4823929, 3832455, 9516922, 2755080, 8488675, 2248035, 6296949, 5058601], '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', 'chr1', 'chr2', 'chr7', 'chr12'], 'Start': [2818074, 2818074, 2818074, 2818074, 2818074, 1902386, 71942, 2818074, 460555, 1179922], 'End': [2819872, 2819872, 2822457, 2819112, 2819872, 1904184, 73740, 2819872, 462353, 1179969], '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', 'chr1', 'chr2', 'chr7', 'chr12'], 'Start': [2818074, 1902386, 2818074, 71942, 2818074, 2818074, 2818074, 2818074, 460555, 1179922], 'End': [2820898, 1909818, 2820898, 72465, 2820905, 2820898, 2820898, 2819868, 462355, 1184532], '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', 'chr7', 'chr8', 'chr12', 'chr17'], 'Start': [460546, 67342, 918017, 724495, 918017, 396552, 918017, 723976, 918017, 1051393], 'End': [461315, 70936, 919141, 725024, 923919, 406167, 918287, 726284, 919466, 1057029], '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', 'chr7', 'chr8', 'chr12', 'chr17'], 'Start': [13836, 67342, 918017, 918017, 460546, 396552, 918017, 723976, 918017, 1051393], 'End': [15629, 70936, 919141, 923919, 461315, 406167, 918287, 726284, 919466, 1057029], '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', 'chr7', 'chr8', 'chr12', 'chr17'], 'Start': [67342, 918017, 918017, 460546, 13836, 396552, 918017, 723976, 918017, 1051393], 'End': [70936, 919141, 923919, 461315, 15629, 397577, 918287, 726284, 921388, 1057029], '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', 'chr7', 'chr8', 'chr12', 'chr17'], 'Start': [67342, 918017, 918017, 460546, 13836, 396552, 918017, 723976, 918017, 1051393], 'End': [70936, 919141, 923919, 461315, 15629, 397577, 918287, 726284, 921388, 1057029], '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', 'chrX'], 'Start': [1737305, 3475333, 678415, 6544193, 4512584, 8641412], 'End': [1744168, 3475650, 681880, 6548693, 4516049, 8647820], 'Name': ['a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '-', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr14', 'chrX'], 'Start': [678415, 1737305, 3475333, 6544193, 4512584, 8641412], 'End': [681880, 1744168, 3475650, 6548693, 4516049, 8647820], 'Name': ['a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 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'], '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'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr3', 'chr5', 'chr13', 'chr13', 'chr13', 'chr13', 'chr13'], 'Start': [3585029, 10000000, 4908527, 6235736, 4011546, 2335748, 417013], 'End': [3588107, 10005754, 4918527, 6242246, 4017902, 2342260, 417268], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '+', '+', '+', '-']} {'Chromosome': ['chr1', 'chr7', 'chr15', 'chrM', 'chrY'], 'Start': [6385186, 9186843, 8482632, 5555618, 9325236], 'End': [6387834, 9193432, 8482687, 5565617, 9327981], 'Name': ['a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0], 'Strand': ['-', '-', '+', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr9', 'chr9', 'chr11', 'chr12', 'chr22'], 'Start': [4723808, 4723808, 4723808, 4723808, 4723808, 4723808, 4723808, 4723808, 4723808, 4723808], 'End': [4733384, 4727516, 4732737, 4723885, 4733569, 4733384, 4725769, 4728468, 4728876, 4727942], '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': [9152252], 'End': [9153598], 'Name': ['a'], 'Score': [0], 'Strand': ['-']} {'Chromosome': ['chr1', 'chr11', 'chr15', 'chr20'], 'Start': [1383906, 3026912, 2857665, 580359], 'End': [1390431, 3031736, 2857954, 588671], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['+', '+', '+', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr2', 'chr18', 'chrY'], 'Start': [5272236, 4906940, 1566042, 10000000, 6858071, 7894281, 8917791, 9841968, 9256849, 5246961], 'End': [5280437, 4915141, 1574243, 10008201, 6866272, 7902482, 8925992, 9850169, 9265050, 5255162], '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': [5340374], 'End': [5343946], 'Name': ['a'], 'Score': [0], 'Strand': ['-']} {'Chromosome': ['chr5'], 'Start': [8977217], 'End': [8983420], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [4007], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr8', 'chr11'], 'Start': [3161792, 2843980, 9999999, 8174746, 3730545, 1871008, 1136962, 3628572], 'End': [3167265, 2844899, 10002681, 8181029, 3735673, 1879133, 1136964, 3634022], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['-', '-', '-', '-', '-', '-', '+', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr9', 'chr10', 'chr11', 'chr13', 'chr19'], 'Start': [2694515, 6957677, 6206801, 8383968, 6176360, 5868120, 9922596, 8656968], 'End': [2704515, 6960667, 6209005, 8387711, 6180158, 5869313, 9925747, 8666238], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '+', '+', '-', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr5', 'chr9', 'chr13', 'chr14', 'chr15', 'chr19'], 'Start': [4631212, 628467, 9501811, 1687404, 4414603, 7596205, 829, 1154799, 9284313, 2376223], 'End': [4638951, 635564, 9501812, 1693188, 4416344, 7597183, 4758, 1163319, 9293663, 2383604], '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', 'chr9', 'chr10', 'chr15', 'chr17', 'chrY'], 'Start': [5956207, 1757999, 8081765, 200625, 2195594, 7067012, 7410878, 1, 1704299, 541639], 'End': [5957555, 1766090, 8085952, 208949, 2200851, 7074485, 7417501, 3098, 1706519, 546189], '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', 'chr16'], 'Start': [2680827, 6423304, 4935665, 551043], 'End': [2683323, 6425800, 4938161, 554524], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['+', '+', '-', '-']} {'Chromosome': ['chr1'], 'Start': [5021835], 'End': [5028022], 'Name': ['a'], 'Score': [0], 'Strand': ['-']} {'Chromosome': ['chr1'], 'Start': [683589], 'End': [693589], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr5', 'chr5', 'chr16', 'chr19', 'chr22'], 'Start': [2889818, 649664, 4473619, 3299770, 7171912, 6186751, 15117, 6465405, 7021200, 5608474], 'End': [2893261, 656509, 4478720, 3308160, 7172294, 6195461, 21555, 6469858, 7023580, 5616297], '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'], 'Start': [5149759, 8612603], 'End': [5159665, 8622603], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr14', 'chrY'], 'Start': [247228, 2564724], 'End': [255494, 2570132], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chrY'], 'Start': [7759629, 7759629, 7759629, 7759629, 7759629, 5301326], 'End': [7760538, 7765377, 7765073, 7762430, 7763541, 5308887], 'Name': ['a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0], 'Strand': ['+', '-', '-', '-', '-', '+']} {'Chromosome': ['chr1', 'chr1', 'chr22'], 'Start': [4481101, 2876009, 2876009], 'End': [4483562, 2878243, 2885032], 'Name': ['a', 'a', 'a'], 'Score': [0, 0, 0], 'Strand': ['+', '-', '-']} {'Chromosome': ['chr1'], 'Start': [3741101], 'End': [3741980], 'Name': ['a'], 'Score': [0], 'Strand': ['-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1'], 'Start': [3511474, 9252482, 3360885, 1339499], 'End': [3518110, 9254883, 3370885, 1347164], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['+', '+', '+', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr9', 'chr18', 'chr19', 'chr21', 'chrX'], 'Start': [1905663, 6314401, 3152043, 7727986, 5641832, 1116171, 9712163, 9990178, 9271186, 5974110], 'End': [1913822, 6322560, 3160202, 7736145, 5649991, 1120890, 9720322, 9991206, 9279345, 5982269], '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', 'chr8', 'chr12', 'chr13', 'chr14'], 'Start': [4009882, 579235, 6618786, 1720725, 4425596, 73326, 10000000, 6897634, 4009882, 8490274], 'End': [4011007, 587682, 6628785, 1723658, 4432051, 75122, 10000867, 6899885, 4019203, 8494852], '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', 'chr8', 'chr20'], 'Start': [1202406, 5292133, 1202406, 1202406], 'End': [1210317, 5292135, 1207990, 1209736], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['+', '-', '+', '+']} {'Chromosome': ['chr1', 'chr6', 'chr12', 'chr15', 'chr18', 'chr19', 'chr19'], 'Start': [1, 7054813, 3603447, 492018, 9180600, 492018, 492018], 'End': [10000, 7059844, 3609802, 493851, 9184176, 495041, 493953], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '+', '+', '+', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr3', 'chr13', 'chr15'], 'Start': [878093, 932274, 1034079, 128003, 2626053, 1714301], 'End': [887820, 937622, 1040822, 130977, 2629941, 1714302], 'Name': ['a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0], 'Strand': ['-', '-', '-', '-', '-', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr4'], 'Start': [6292326, 3738930, 1, 6235888, 6220320, 1833067], 'End': [6294815, 3743101, 9256, 6236724, 6229620, 1833240], 'Name': ['a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0], 'Strand': ['+', '-', '-', '-', '-', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr3', 'chr14'], 'Start': [382989, 7109110, 590840, 7258936, 1733338], 'End': [387131, 7114029, 598044, 7261945, 1740245], 'Name': ['a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '-']} {'Chromosome': ['chr1'], 'Start': [9201548], 'End': [9205619], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1'], 'Start': [3425607, 2761761, 5652756, 6424439], 'End': [3429819, 2765130, 5656179, 6427572], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['+', '+', '+', '-']} {'Chromosome': ['chr18'], 'Start': [9646637], 'End': [9656452], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chrY'], 'Start': [6880260, 2668447, 3640233, 8533896], 'End': [6882932, 2674427, 3643052, 8542255], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['+', '+', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1'], 'Start': [1, 6036635, 2, 9999999], 'End': [6179, 6039069, 2358, 10008117], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['-', '-', '-', '-']} {'Chromosome': ['chr1', 'chr1'], 'Start': [5668673, 5668673], 'End': [5678673, 5674677], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr4', 'chrX'], 'Start': [9588035, 10000000], 'End': [9594919, 10006884], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '-']} {'Chromosome': ['chr21'], 'Start': [1477565], 'End': [1479014], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chrY'], 'Start': [7934141], 'End': [7934168], 'Name': ['a'], 'Score': [0], 'Strand': ['-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr12', 'chrY'], 'Start': [77021, 2442022, 481349, 4392078, 5836849, 4897416], 'End': [81441, 2444028, 485594, 4395542, 5846807, 4898283], 'Name': ['a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0], 'Strand': ['+', '-', '-', '-', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr21'], 'Start': [1722913, 9091738, 1722913], 'End': [1722914, 9096611, 1731141], 'Name': ['a', 'a', 'a'], 'Score': [0, 0, 0], 'Strand': ['+', '+', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1'], 'Start': [1355537, 3603496, 393149], 'End': [1355948, 3603907, 393560], 'Name': ['a', 'a', 'a'], 'Score': [0, 0, 0], 'Strand': ['+', '+', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr6', 'chr6', 'chr14', 'chr21'], 'Start': [5879044, 3605866, 8810801, 3998574, 8492233, 8644974, 8983866, 8912997], 'End': [5880007, 3607836, 8816468, 4007718, 8495550, 8648651, 8987543, 8916674], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '-', '-', '-', '-', '+']} {'Chromosome': ['chr1'], 'Start': [8678463], 'End': [8680336], 'Name': ['a'], 'Score': [0], 'Strand': ['-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr5', 'chr8', 'chr15', 'chr19'], 'Start': [8918577, 2, 7644453, 6183142, 3255739, 9182567, 9227320, 3566989, 9182567, 9768876], 'End': [8925118, 3690, 7645733, 6192325, 3258379, 9186622, 9234364, 3570362, 9188655, 9773456], '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': [4623439], 'End': [4630987], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr10', 'chr19', 'chr22'], 'Start': [7001853, 3997501, 6473389, 7642835, 7771189, 5045567, 1681118, 5045567], 'End': [7008512, 3999408, 6479528, 7650405, 7779839, 5046103, 1681977, 5052605], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '-', '+', '-', '+']} {'Chromosome': ['chr1', 'chr1'], 'Start': [7755548, 7543391], 'End': [7763497, 7545553], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr9', 'chr14', 'chr19'], 'Start': [6493934, 9255905, 7553619, 2082263, 1452841, 5503271], 'End': [6497933, 9259112, 7559509, 2087225, 1457307, 5504993], 'Name': ['a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '+', '+', '+']} {'Chromosome': ['chr5', 'chr6', 'chr19', 'chr20'], 'Start': [4811733, 516053, 8628468, 3615575], 'End': [4818151, 517083, 8636161, 3624033], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['-', '-', '+', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr2', 'chr20', 'chrY'], 'Start': [600619, 1304508, 4046527, 760320, 1, 4441977], 'End': [605515, 1306178, 4048388, 760451, 9449, 4447400], 'Name': ['a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0], 'Strand': ['+', '-', '-', '+', '+', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr10', 'chr16', 'chr21', 'chrM'], 'Start': [4640620, 2, 280446, 5654707, 4320185, 7570732, 8281576, 1434943, 6058833, 5951806], 'End': [4645799, 436, 283204, 5658034, 4326236, 7571773, 8288993, 1443889, 6060420, 5958181], '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', 'chr3', 'chr7'], 'Start': [5778055, 5889214, 1118788, 4481066, 1], 'End': [5788055, 5894179, 1120779, 4487988, 6131], 'Name': ['a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0], 'Strand': ['-', '-', '-', '+', '-']} {'Chromosome': ['chr1', 'chr4', 'chr6', 'chr10', 'chr11', 'chr14', 'chr14', 'chr18', 'chr21'], 'Start': [1578465, 569973, 587429, 3131619, 6472071, 7557545, 1209898, 1590843, 6065028], 'End': [1588465, 575333, 589836, 3139530, 6475532, 7567454, 1216109, 1592641, 6073261], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['-', '+', '-', '+', '-', '-', '-', '+', '+']} {'Chromosome': ['chr20'], 'Start': [9690509], 'End': [9698612], 'Name': ['a'], 'Score': [0], 'Strand': ['-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr3', 'chr4', 'chr12', 'chr16', 'chr19'], 'Start': [5276355, 7873550, 9632007, 294924, 5487033, 4093204, 9577577, 342242, 2287737, 8264268], 'End': [5276356, 7882124, 9632482, 303558, 5494605, 4097092, 9584160, 346532, 2291546, 8268456], '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', 'chr15', 'chr20'], 'Start': [7919355, 1050156, 3897868, 8362126, 4107447, 9583815], 'End': [7924639, 1054248, 3907868, 8372126, 4116356, 9588595], 'Name': ['a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '-', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr7', 'chrX', 'chrX', 'chrX', 'chrX', 'chrY'], 'Start': [7800909, 3534513, 3534513, 7265511, 1774064, 3534513, 3534513, 3534513, 5875884], 'End': [7803838, 3537758, 3538037, 7274028, 1774855, 3534669, 3541345, 3537209, 5878699], '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', 'chr18'], 'Start': [524051, 10000000, 524051, 524051, 8666947], 'End': [532037, 10008784, 529140, 525476, 8672283], 'Name': ['a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0], 'Strand': ['+', '-', '-', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr6', 'chr16', 'chr18', 'chr19'], 'Start': [2086681, 1, 761861, 8330458, 4451006, 7695697, 3849657], 'End': [2089494, 5371, 764674, 8335394, 4453819, 7696956, 3852470], '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': [8627159, 9472905, 6826535, 9999999, 8144715, 6807547], 'End': [8636926, 9482256, 6830812, 10001973, 8150970, 6817314], 'Name': ['a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0], 'Strand': ['+', '-', '-', '-', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr16', 'chr22'], 'Start': [5431767, 5329226, 7384328, 3441575, 1116421, 1370628, 4682935], 'End': [5439357, 5331280, 7384864, 3442452, 1116957, 1372696, 4689582], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '-', '+', '+']} {'Chromosome': ['chr1', 'chr12', 'chr22'], 'Start': [3378271, 3109819, 5975394], 'End': [3383669, 3112772, 5983609], 'Name': ['a', 'a', 'a'], 'Score': [0, 0, 0], 'Strand': ['+', '-', '+']} {'Chromosome': ['chr6', 'chrX'], 'Start': [1573611, 1573611], 'End': [1574177, 1574177], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '+']} {'Chromosome': ['chr1', 'chr4', 'chr14', 'chr14', 'chr14', 'chr14', 'chr14'], 'Start': [4688592, 4688592, 4688592, 4688592, 4688592, 4688592, 3812887], 'End': [4697932, 4692792, 4694726, 4691496, 4696196, 4697188, 3821903], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '-', '+', '-', '-', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr13', 'chr22'], 'Start': [5644323, 2, 9602133, 1879037, 2146841], 'End': [5648964, 598, 9606629, 1883914, 2147111], 'Name': ['a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '+', '-']} {'Chromosome': ['chr1', 'chr9', 'chr21', 'chr21', 'chr21', 'chr21', 'chr21'], 'Start': [543361, 2441328, 1305500, 3752816, 6461139, 2679882, 3752816], 'End': [549524, 2445610, 1311008, 3762705, 6469046, 2683529, 3758324], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0], 'Strand': ['-', '+', '+', '+', '-', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr6', 'chr22'], 'Start': [1928452, 10000000, 7754830, 5724069, 454169], 'End': [1935980, 10008729, 7763559, 5732798, 462898], 'Name': ['a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0], 'Strand': ['+', '-', '-', '-', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chrY'], 'Start': [1142252, 1142252, 2650881, 1142252], 'End': [1143932, 1152252, 2660881, 1145217], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['-', '-', '-', '+']} {'Chromosome': ['chrM', 'chrM', 'chrM'], 'Start': [10000000, 4894310, 1607323], 'End': [10005000, 4901275, 1616510], 'Name': ['a', 'a', 'a'], 'Score': [0, 0, 0], 'Strand': ['+', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr6', 'chr10', 'chr11', 'chr20', 'chr21'], 'Start': [2085881, 7136249, 5604857, 4556985, 3360336, 4677132, 5415247, 3087928, 7086718, 9310501], 'End': [2095880, 7143187, 5611657, 4560190, 3362395, 4682704, 5418854, 3088200, 7091563, 9317800], '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', 'chr19'], 'Start': [3627040, 1526634, 3221754], 'End': [3631706, 1527074, 3231709], 'Name': ['a', 'a', 'a'], 'Score': [0, 0, 0], 'Strand': ['+', '+', '+']} {'Chromosome': ['chr1'], 'Start': [8816549], 'End': [8817410], 'Name': ['a'], 'Score': [0], 'Strand': ['-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr5', 'chr7', 'chr19', 'chrM'], 'Start': [4299979, 6611390, 4709589, 1627906, 4384785, 1273244, 5138890, 6795088, 7259393], 'End': [4301778, 6619385, 4712442, 1634367, 4384896, 1282803, 5146917, 6796983, 7260510], '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', 'chr7', 'chr9', 'chr12', 'chr19'], 'Start': [7834265, 9668991, 4722250, 8745654, 3733213, 5809421, 9713102, 2215774, 1793357, 4357211], 'End': [7836430, 9673232, 4723655, 8755303, 3743162, 5813662, 9714780, 2225732, 1797598, 4360990], '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', 'chr2', 'chrM'], 'Start': [1695551, 7638508, 7827606], 'End': [1704238, 7640919, 7829945], 'Name': ['a', 'a', 'a'], 'Score': [0, 0, 0], 'Strand': ['-', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1'], 'Start': [1272615, 1380525, 6410612, 9438087, 7709871, 7875425, 5600297, 3738109, 763098, 2885905], 'End': [1277734, 1388307, 6413386, 9441663, 7717874, 7878901, 5608578, 3741200, 770587, 2892860], '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', 'chr8', 'chr12', 'chr12'], 'Start': [2741597, 1, 4767424, 4474843, 7212728], 'End': [2743659, 1947, 4769224, 4479775, 7216683], 'Name': ['a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0], 'Strand': ['-', '-', '-', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1'], 'Start': [4474688, 196700, 1340965, 4474688], 'End': [4482760, 200896, 1345161, 4478884], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['-', '-', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr9', 'chrX'], 'Start': [2954108, 1117663, 5001884, 3252606], 'End': [2959183, 1125733, 5009831, 3261893], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['+', '-', '+', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr4', 'chr19', 'chrM'], 'Start': [903876, 2859279, 9997304, 903876, 10000000, 903876, 9481609, 903876, 230350, 903876], 'End': [905441, 2863208, 10000296, 905441, 10001565, 910409, 9487412, 908303, 231915, 904846], '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', 'chr8', 'chr9', 'chr15', 'chr20'], 'Start': [5774429, 6990427, 3191166, 1046599, 8954810, 5210373, 2553406, 7969648, 6371405, 9555994], 'End': [5777832, 6998014, 3197434, 1049766, 8955657, 5216520, 2562347, 7973908, 6376615, 9558444], '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', 'chr8', 'chr13', 'chr16', 'chr22'], 'Start': [1439089, 5302935, 2309083, 6026081, 5167957, 290374, 8196496, 4327911, 4723481, 7144171], 'End': [1446401, 5304703, 2314567, 6034979, 5168536, 297563, 8203280, 4330997, 4727838, 7146288], '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', 'chr21', 'chrX'], 'Start': [9790084, 1654797, 8523361, 8409339, 2134778, 3488668], 'End': [9798953, 1662845, 8526572, 8412189, 2140186, 3488971], 'Name': ['a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '-', '-']} {'Chromosome': ['chr1', 'chr17', 'chr22'], 'Start': [6459927, 2844047, 2541841], 'End': [6462574, 2846435, 2543221], 'Name': ['a', 'a', 'a'], 'Score': [0, 0, 0], 'Strand': ['+', '-', '+']} {'Chromosome': ['chr21'], 'Start': [2330509], 'End': [2340202], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr9', 'chr12', 'chr16', 'chr18'], 'Start': [6216806, 5778285, 8516062, 3739378, 3357728], 'End': [6226411, 5778286, 8518705, 3742021, 3360371], 'Name': ['a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0], 'Strand': ['-', '-', '-', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr7', 'chrY'], 'Start': [213221, 5494327, 3875511, 2], 'End': [221966, 5501961, 3880063, 2024], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['+', '-', '+', '-']} {'Chromosome': ['chr1', 'chr14', 'chr14', 'chr14'], 'Start': [3299675, 837439, 4115700, 1045619], 'End': [3303992, 846538, 4116856, 1048360], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['-', '+', '-', '-']} {'Chromosome': ['chr21', 'chr21', 'chr21', 'chr21'], 'Start': [8891905, 2920859, 9679625, 4817070], 'End': [8893246, 2927627, 9686306, 4823529], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['+', '+', '+', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr3', 'chr8', 'chr10', 'chr22', 'chrX', 'chrX'], 'Start': [2, 2, 7014490, 7082486, 7329079, 7850039, 2, 2, 2, 6373744], 'End': [1689, 2090, 7023180, 7085024, 7336127, 7857783, 5635, 2540, 2169, 6378185], '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', 'chr10', 'chr10', 'chr19', 'chr22'], 'Start': [1168438, 6545651, 4045510, 5685375, 5758807], 'End': [1169452, 6552125, 4048132, 5685757, 5762995], 'Name': ['a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0], 'Strand': ['-', '+', '+', '+', '+']} {'Chromosome': ['chr12', 'chr15', 'chr15', 'chr15'], 'Start': [1015976, 6463765, 1812449, 9163876], 'End': [1020658, 6463766, 1814088, 9170834], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['-', '+', '-', '-']} {'Chromosome': ['chr1', 'chr3', 'chr18', 'chrX', 'chrX'], 'Start': [6140076, 3672847, 7932368, 8844733, 6006956], 'End': [6146939, 3675477, 7939224, 8847614, 6013632], 'Name': ['a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0], 'Strand': ['-', '+', '-', '+', '-']} {'Chromosome': ['chr4', 'chr14', 'chrY'], 'Start': [7093104, 7093104, 7093104], 'End': [7095999, 7098767, 7098332], 'Name': ['a', 'a', 'a'], 'Score': [0, 0, 0], 'Strand': ['-', '-', '+']} {'Chromosome': ['chr1'], 'Start': [4157144], 'End': [4157224], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chrM'], 'Start': [9999999, 7254009], 'End': [10004302, 7254010], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr3', 'chr9', 'chr18', 'chrX', 'chrY', 'chrY'], 'Start': [3161997, 4097507, 2907097, 4732142, 174533, 2025875, 2907097, 2943658, 9877457, 6619348], 'End': [3165963, 4101557, 2910239, 4736305, 182298, 2030271, 2914428, 2946263, 9877458, 6623744], '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'], 'Start': [3416678, 301225, 8652608, 4648688, 7140732], 'End': [3425932, 310754, 8659488, 4655001, 7149184], 'Name': ['a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '+', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1'], 'Start': [9020875, 4274773, 8452444, 10000000, 2500576, 2900600, 5875747, 6970276, 4721347, 1], 'End': [9025649, 4276617, 8453167, 10008534, 2506958, 2910415, 5876029, 6971283, 4726551, 2422], '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': ['+']} _________________________________ test_windows _________________________________ [gw0] linux -- Python 3.12.3 /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_windows2 _________________________________ [gw0] linux -- Python 3.12.3 /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 _________________________________ [gw2] linux -- Python 3.12.3 /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('6.100.4', b'AXicY2QAA0YGBAAAADIAAw==') 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/tmpgwuvjw70/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpeh7_uepb/f1.bed) bedtools_df Chromosome Start End 0 chr1 448620 448630 1 chr1 448630 448640 2 chr1 448640 448650 3 chr1 448650 448660 4 chr1 448660 448670 ... ... ... ... 1847 chr22 8617900 8617910 1848 chr22 8617910 8617920 1849 chr22 8617920 8617930 1850 chr22 8617930 8617940 1851 chr22 8617940 8617944 [1852 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp6pagsijr/f1.bed) bedtools_df Chromosome Start End 0 chr1 448620 448630 1 chr1 448630 448640 2 chr1 448640 448650 3 chr1 448650 448660 4 chr1 448660 448670 ... ... ... ... 1589 chr22 8616610 8616620 1590 chr22 8616620 8616630 1591 chr22 8616630 8616640 1592 chr22 8616640 8616650 1593 chr22 8616650 8616659 [1594 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp8wcgposv/f1.bed) bedtools_df Chromosome Start End 0 chr1 448620 448630 1 chr1 448630 448640 2 chr1 448640 448642 3 chr1 4142280 4142290 4 chr1 4142290 4142300 ... ... ... ... 2588 chr22 8618350 8618360 2589 chr22 8618360 8618370 2590 chr22 8618370 8618380 2591 chr22 8618380 8618390 2592 chr22 8618390 8618400 [2593 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpzyp6bs94/f1.bed) bedtools_df Chromosome Start End 0 chr1 448620 448630 1 chr1 448630 448640 2 chr1 448640 448642 3 chr1 4142280 4142290 4 chr1 4142290 4142300 ... ... ... ... 2588 chr22 8618350 8618360 2589 chr22 8618360 8618370 2590 chr22 8618370 8618380 2591 chr22 8618380 8618390 2592 chr22 8618390 8618400 [2593 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmprm41ocgx/f1.bed) bedtools_df Chromosome Start End 0 chr1 67340 67350 1 chr1 67350 67360 2 chr1 67360 67370 3 chr1 67370 67380 4 chr1 67380 67390 ... ... ... ... 1318 chr1 4006890 4006900 1319 chr1 4006900 4006910 1320 chr1 4006910 4006920 1321 chr1 4006920 4006930 1322 chr1 4006930 4006935 [1323 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp6y7a0j8l/f1.bed) bedtools_df Chromosome Start End 0 chr1 67340 67350 1 chr1 67350 67360 2 chr1 67360 67370 3 chr1 67370 67380 4 chr1 67380 67390 ... ... ... ... 1318 chr1 4006890 4006900 1319 chr1 4006900 4006910 1320 chr1 4006910 4006920 1321 chr1 4006920 4006930 1322 chr1 4006930 4006935 [1323 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpvz6fylr6/f1.bed) bedtools_df Chromosome Start End 0 chr1 75016 75026 1 chr1 75026 75036 2 chr1 75036 75046 3 chr1 75046 75056 4 chr1 75056 75066 ... ... ... ... 2521 chr3 5714712 5714722 2522 chr3 5714722 5714732 2523 chr3 5714732 5714742 2524 chr3 5714742 5714752 2525 chr3 5714752 5714762 [2526 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp2rrx_ueh/f1.bed) bedtools_df Chromosome Start End 0 chr1 128863 128873 1 chr1 128873 128883 2 chr1 128883 128893 3 chr1 128893 128903 4 chr1 128903 128913 ... ... ... ... 3318 chr4 134693 134703 3319 chr4 134703 134713 3320 chr4 134713 134723 3321 chr4 134723 134733 3322 chr4 134733 134743 [3323 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpk1se6svl/f1.bed) bedtools_df Chromosome Start End 0 chr1 3277591 3277601 1 chr1 3277601 3277611 2 chr1 3277611 3277621 3 chr1 3277621 3277631 4 chr1 3277631 3277641 ... ... ... ... 2515 chr6 466190 466200 2516 chr6 466200 466210 2517 chr6 466210 466220 2518 chr6 466220 466230 2519 chr6 466230 466236 [2520 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmphrjw388c/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmptxc2gavq/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp9gp34geq/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpq8x287_1/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpxco8t2k7/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp_v1_49an/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp8hm3agzb/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpf6zrpehd/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp3tu98duk/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpvcnlve7n/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpry5jbc7y/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpi5qyi9bz/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp5iofqkf5/f1.bed) bedtools_df Chromosome Start End 0 chr1 1166252 1166262 1 chr1 1166262 1166272 2 chr1 1166272 1166282 3 chr1 1166282 1166292 4 chr1 1166292 1166302 .. ... ... ... 208 chr6 5250022 5250032 209 chr6 5250032 5250042 210 chr6 5250042 5250052 211 chr6 5250052 5250062 212 chr6 5250062 5250067 [213 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp_m2yvoub/f1.bed) bedtools_df Chromosome Start End 0 chr1 1171970 1171980 1 chr1 1171980 1171990 2 chr1 1171990 1172000 3 chr1 1172000 1172010 4 chr1 1172010 1172020 ... ... ... ... 3983 chr1 4864879 4864889 3984 chr1 4864889 4864899 3985 chr1 4864899 4864909 3986 chr1 4864909 4864919 3987 chr1 4864919 4864929 [3988 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpcaty6p17/f1.bed) bedtools_df Chromosome Start End 0 chr1 3376990 3377000 1 chr1 3377000 3377010 2 chr1 3377010 3377020 3 chr1 3377020 3377030 4 chr1 3377030 3377040 ... ... ... ... 1142 chrY 6177852 6177862 1143 chrY 6177862 6177872 1144 chrY 6177872 6177882 1145 chrY 6177882 6177892 1146 chrY 6177892 6177898 [1147 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp10j2r3r4/f1.bed) bedtools_df Chromosome Start End 0 chr1 601260 601270 1 chr1 601270 601280 2 chr1 601280 601290 3 chr1 601290 601300 4 chr1 601300 601310 ... ... ... ... 3468 chr22 8083873 8083883 3469 chr22 8083883 8083893 3470 chr22 8083893 8083903 3471 chr22 8083903 8083913 3472 chr22 8083913 8083917 [3473 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmplgi60_9j/f1.bed) bedtools_df Chromosome Start End 0 chr1 1801670 1801680 1 chr1 1801680 1801690 2 chr1 1801690 1801700 3 chr1 1801700 1801710 4 chr1 1801710 1801720 ... ... ... ... 2863 chrX 4668760 4668770 2864 chrX 4668770 4668780 2865 chrX 4668780 4668790 2866 chrX 4668790 4668800 2867 chrX 4668800 4668803 [2868 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp11_x3ae3/f1.bed) bedtools_df Chromosome Start End 0 chr1 5416074 5416084 1 chr1 5416084 5416094 2 chr1 5416094 5416104 3 chr1 5416104 5416114 4 chr1 5416114 5416124 ... ... ... ... 1496 chr22 8051001 8051011 1497 chr22 8051011 8051021 1498 chr22 8051021 8051031 1499 chr22 8051031 8051041 1500 chr22 8051041 8051044 [1501 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpp4bkwk1s/f1.bed) bedtools_df Chromosome Start End 0 chr1 5583221 5583231 1 chr1 5583231 5583241 2 chr1 5583241 5583251 3 chr1 5583251 5583261 4 chr1 5583261 5583271 ... ... ... ... 5073 chrY 5621649 5621659 5074 chrY 5621659 5621669 5075 chrY 5621669 5621679 5076 chrY 5621679 5621689 5077 chrY 5621689 5621697 [5078 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpuhioe071/f1.bed) bedtools_df Chromosome Start End 0 chr1 273330 273340 1 chr1 273340 273350 2 chr1 273350 273360 3 chr1 273360 273370 4 chr1 273370 273380 ... ... ... ... 2400 chr9 3758400 3758410 2401 chr9 3758410 3758420 2402 chr9 3758420 3758430 2403 chr9 3758430 3758440 2404 chr9 3758440 3758442 [2405 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpcsjj75uo/f1.bed) bedtools_df Chromosome Start End 0 chr1 9803685 9803686 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpr0xsofhx/f1.bed) bedtools_df Chromosome Start End 0 chr1 5899004 5899014 1 chr1 5899014 5899024 2 chr1 5899024 5899034 3 chr1 5899034 5899044 4 chr1 5899044 5899054 .. ... ... ... 835 chr1 5904784 5904794 836 chr1 5904794 5904804 837 chr1 5904804 5904814 838 chr1 5904814 5904824 839 chr1 5904824 5904834 [840 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmprkbqhaa7/f1.bed) bedtools_df Chromosome Start End 0 chr1 1920636 1920646 1 chr1 1920646 1920656 2 chr1 1920656 1920666 3 chr1 1920666 1920676 4 chr1 1920676 1920686 ... ... ... ... 5132 chrX 6971839 6971849 5133 chrX 6971849 6971859 5134 chrX 6971859 6971869 5135 chrX 6971869 6971879 5136 chrX 6971879 6971880 [5137 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpuovytxik/f1.bed) bedtools_df Chromosome Start End 0 chr1 2436638 2436648 1 chr1 2436648 2436658 2 chr1 2436658 2436668 3 chr1 2436668 2436678 4 chr1 2436678 2436688 .. ... ... ... 323 chr1 2439868 2439878 324 chr1 2439878 2439888 325 chr1 2439888 2439898 326 chr1 2439898 2439908 327 chr1 2439908 2439911 [328 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpr88_9urt/f1.bed) bedtools_df Chromosome Start End 0 chr1 7006691 7006701 1 chr1 7006701 7006711 2 chr1 7006711 7006721 3 chr1 7006721 7006731 4 chr1 7006731 7006741 .. ... ... ... 151 chr1 7008201 7008211 152 chr1 7008211 7008221 153 chr1 7008221 7008231 154 chr1 7008231 7008241 155 chr1 7008241 7008250 [156 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp2gto70i1/f1.bed) bedtools_df Chromosome Start End 0 chr1 3546347 3546357 1 chr1 3546357 3546367 2 chr1 3546367 3546377 3 chr1 3546377 3546387 4 chr1 3546387 3546397 ... ... ... ... 5511 chr18 7678382 7678392 5512 chr18 7678392 7678402 5513 chr18 7678402 7678412 5514 chr18 7678412 7678422 5515 chr18 7678422 7678424 [5516 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp10kbk902/f1.bed) bedtools_df Chromosome Start End 0 chr1 6419312 6419322 1 chr1 6419322 6419332 2 chr1 6419332 6419342 3 chr1 6419342 6419352 4 chr1 6419352 6419362 ... ... ... ... 996 chr5 7612349 7612359 997 chr5 7612359 7612369 998 chr5 7612369 7612379 999 chr5 7612379 7612389 1000 chr5 7612389 7612391 [1001 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpexfo7i3k/f1.bed) bedtools_df Chromosome Start End 0 chr1 1177313 1177323 1 chr1 1177323 1177333 2 chr1 1177333 1177343 3 chr1 1177343 1177353 4 chr1 1177353 1177363 ... ... ... ... 1797 chr1 7940032 7940042 1798 chr1 7940042 7940052 1799 chr1 7940052 7940062 1800 chr1 7940062 7940072 1801 chr1 7940072 7940077 [1802 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpm565jvwl/f1.bed) bedtools_df Chromosome Start End 0 chr18 462448 462458 1 chr18 462458 462468 2 chr18 462468 462478 3 chr18 462478 462488 4 chr18 462488 462498 ... ... ... ... 1022 chr3 7043631 7043641 1023 chr3 7043641 7043651 1024 chr3 7043651 7043661 1025 chr3 7043661 7043671 1026 chr3 7043671 7043680 [1027 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpmsf62srr/f1.bed) bedtools_df Chromosome Start End 0 chr1 9546951 9546961 1 chr1 9546961 9546971 2 chr1 9546971 9546981 3 chr1 9546981 9546991 4 chr1 9546991 9547001 ... ... ... ... 1441 chrX 5021930 5021940 1442 chrX 5021940 5021950 1443 chrX 5021950 5021960 1444 chrX 5021960 5021970 1445 chrX 5021970 5021973 [1446 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpapl5hvhl/f1.bed) bedtools_df Chromosome Start End 0 chr1 2413282 2413292 1 chr1 2413292 2413302 2 chr1 2413302 2413312 3 chr1 2413312 2413322 4 chr1 2413322 2413332 ... ... ... ... 5629 chr8 7280187 7280197 5630 chr8 7280197 7280207 5631 chr8 7280207 7280217 5632 chr8 7280217 7280227 5633 chr8 7280227 7280234 [5634 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp2kp501aq/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 ... ... ... ... 6018 chr8 1230645 1230655 6019 chr8 1230655 1230665 6020 chr8 1230665 1230675 6021 chr8 1230675 1230685 6022 chr8 1230685 1230692 [6023 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpm1gpjsg8/f1.bed) bedtools_df Chromosome Start End 0 chr1 925022 925032 1 chr1 925032 925042 2 chr1 925042 925052 3 chr1 925052 925062 4 chr1 925062 925072 ... ... ... ... 10995 chrM 3562514 3562524 10996 chrM 3562524 3562534 10997 chrM 3562534 3562544 10998 chrM 3562544 3562554 10999 chrM 3562554 3562563 [11000 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmptkagvmch/f1.bed) bedtools_df Chromosome Start End 0 chr1 1053689 1053690 1 chr1 1053689 1053699 2 chr1 1053699 1053709 3 chr1 1053709 1053719 4 chr1 1053719 1053729 ... ... ... ... 2754 chr21 1062879 1062889 2755 chr21 1062889 1062899 2756 chr21 1062899 1062909 2757 chr21 1062909 1062919 2758 chr21 1062919 1062920 [2759 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpgo05w3z6/f1.bed) bedtools_df Chromosome Start End 0 chr1 3830425 3830435 1 chr1 3830435 3830445 2 chr1 3830445 3830455 3 chr1 3830455 3830465 4 chr1 3830465 3830475 ... ... ... ... 1570 chr17 8149396 8149406 1571 chr17 8149406 8149416 1572 chr17 8149416 8149426 1573 chr17 8149426 8149436 1574 chr17 8149436 8149442 [1575 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmptme99jrk/f1.bed) bedtools_df Chromosome Start End 0 chr1 799775 799785 1 chr1 799785 799795 2 chr1 799795 799805 3 chr1 799805 799815 4 chr1 799815 799825 ... ... ... ... 6224 chrX 921824 921834 6225 chrX 921834 921844 6226 chrX 921844 921854 6227 chrX 921854 921864 6228 chrX 921864 921874 [6229 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp5_c_l_nw/f1.bed) bedtools_df Chromosome Start End 0 chr1 2927814 2927824 1 chr1 2927824 2927834 2 chr1 2927834 2927844 3 chr1 2927844 2927854 4 chr1 2927854 2927864 ... ... ... ... 2466 chr18 10009410 10009420 2467 chr18 10009420 10009430 2468 chr18 10009430 10009440 2469 chr18 10009440 10009450 2470 chr18 10009450 10009453 [2471 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpjx5gek31/f1.bed) bedtools_df Chromosome Start End 0 chr11 3961154 3961164 1 chr11 3961164 3961174 2 chr11 3961174 3961184 3 chr11 3961184 3961194 4 chr11 3961194 3961204 .. ... ... ... 805 chr11 3969204 3969214 806 chr11 3969214 3969224 807 chr11 3969224 3969234 808 chr11 3969234 3969244 809 chr11 3969244 3969247 [810 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpb2ti5ds5/f1.bed) bedtools_df Chromosome Start End 0 chr1 1787892 1787902 1 chr1 1787902 1787912 2 chr1 1787912 1787922 3 chr1 1787922 1787932 4 chr1 1787932 1787942 ... ... ... ... 1114 chr1 9835474 9835484 1115 chr1 9835484 9835494 1116 chr1 9835494 9835504 1117 chr1 9835504 9835514 1118 chr1 9835514 9835517 [1119 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmper03koj6/f1.bed) bedtools_df Chromosome Start End 0 chr1 2364338 2364348 1 chr1 2364348 2364356 2 chr1 3447104 3447105 3 chr1 5862386 5862396 4 chr1 5862396 5862406 ... ... ... ... 1053 chr13 9919533 9919543 1054 chr13 9919543 9919546 1055 chr14 2366225 2366226 1056 chr16 6413251 6413252 1057 chr5 4708844 4708845 [1058 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp2zd77xer/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 ... ... ... ... 5752 chr8 4907377 4907387 5753 chr8 4907387 4907397 5754 chr8 4907397 4907407 5755 chr8 4907407 4907417 5756 chr8 4907417 4907418 [5757 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpnjgq6_8t/f1.bed) bedtools_df Chromosome Start End 0 chr1 1716019 1716029 1 chr1 1716029 1716039 2 chr1 1716039 1716049 3 chr1 1716049 1716059 4 chr1 1716059 1716069 .. ... ... ... 414 chr7 4004985 4004995 415 chr7 4004995 4005005 416 chr7 4005005 4005015 417 chr7 4005015 4005025 418 chr7 4005025 4005026 [419 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp1ppp6u0_/f1.bed) bedtools_df Chromosome Start End 0 chr1 2592772 2592782 1 chr1 2592782 2592792 2 chr1 2592792 2592802 3 chr1 2592802 2592812 4 chr1 2592812 2592822 ... ... ... ... 6017 chr19 2673464 2673474 6018 chr19 2673474 2673484 6019 chr19 2673484 2673494 6020 chr19 2673494 2673504 6021 chr19 2673504 2673509 [6022 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpkl19r1j5/f1.bed) bedtools_df Chromosome Start End 0 chr1 2876789 2876799 1 chr1 2876799 2876809 2 chr1 2876809 2876819 3 chr1 2876819 2876829 4 chr1 2876829 2876839 ... ... ... ... 7258 chr4 5388163 5388173 7259 chr4 5388173 5388183 7260 chr4 5388183 5388193 7261 chr4 5388193 5388203 7262 chr4 5388203 5388212 [7263 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpi5qobf6p/f1.bed) bedtools_df Chromosome Start End 0 chr1 864069 864079 1 chr1 864079 864089 2 chr1 864089 864099 3 chr1 864099 864109 4 chr1 864109 864119 ... ... ... ... 4023 chr3 5586984 5586994 4024 chr3 5586994 5587004 4025 chr3 5587004 5587014 4026 chr3 5587014 5587024 4027 chr3 5587024 5587034 [4028 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp10feroo6/f1.bed) bedtools_df Chromosome Start End 0 chr1 118708 118718 1 chr1 118718 118728 2 chr1 118728 118738 3 chr1 118738 118748 4 chr1 118748 118758 ... ... ... ... 5028 chrM 8593956 8593966 5029 chrM 8593966 8593976 5030 chrM 8593976 8593986 5031 chrM 8593986 8593996 5032 chrM 8593996 8594004 [5033 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpweun7_pt/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 ... ... ... ... 3931 chr4 3916235 3916245 3932 chr4 3916245 3916255 3933 chr4 3916255 3916265 3934 chr4 3916265 3916275 3935 chr4 3916275 3916280 [3936 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpb_1zwo6k/f1.bed) bedtools_df Chromosome Start End 0 chr1 732425 732435 1 chr1 732435 732445 2 chr1 732445 732455 3 chr1 732455 732465 4 chr1 732465 732475 ... ... ... ... 1034 chr5 1590328 1590338 1035 chr5 1590338 1590348 1036 chr5 1590348 1590358 1037 chr5 1590358 1590368 1038 chr5 1590368 1590371 [1039 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpifcysi65/f1.bed) bedtools_df Chromosome Start End 0 chr1 1367837 1367847 1 chr1 1367847 1367857 2 chr1 1367857 1367867 3 chr1 1367867 1367877 4 chr1 1367877 1367887 ... ... ... ... 5123 chr7 10006939 10006949 5124 chr7 10006949 10006959 5125 chr7 10006959 10006969 5126 chr7 10006969 10006975 5127 chr8 9570595 9570597 [5128 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmppljnregn/f1.bed) bedtools_df Chromosome Start End 0 chr1 5578323 5578333 1 chr1 5578333 5578343 2 chr1 5578343 5578353 3 chr1 5578353 5578363 4 chr1 5578363 5578373 .. ... ... ... 985 chr1 7676175 7676185 986 chr1 7676185 7676195 987 chr1 7676195 7676205 988 chr1 7676205 7676215 989 chr1 7676215 7676220 [990 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmplu8t1sdo/f1.bed) bedtools_df Chromosome Start End 0 chr1 9137752 9137762 1 chr1 9137762 9137772 2 chr1 9137772 9137782 3 chr1 9137782 9137792 4 chr1 9137792 9137802 .. ... ... ... 719 chr3 5855205 5855215 720 chr3 5855215 5855225 721 chr3 5855225 5855235 722 chr3 5855235 5855245 723 chr3 5855245 5855250 [724 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmph_uy9rna/f1.bed) bedtools_df Chromosome Start End 0 chr1 5290630 5290640 1 chr1 5290640 5290650 2 chr1 5290650 5290660 3 chr1 5290660 5290670 4 chr1 5290670 5290680 ... ... ... ... 5745 chr4 5295740 5295750 5746 chr4 5295750 5295760 5747 chr4 5295760 5295770 5748 chr4 5295770 5295780 5749 chr4 5295780 5295790 [5750 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp5ckyb613/f1.bed) bedtools_df Chromosome Start End 0 chr16 8601704 8601714 1 chr16 8601714 8601724 2 chr16 8601724 8601734 3 chr16 8601734 8601744 4 chr16 8601744 8601754 .. ... ... ... 926 chr16 8610964 8610974 927 chr16 8610974 8610984 928 chr16 8610984 8610994 929 chr16 8610994 8611004 930 chr16 8611004 8611009 [931 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpqoakw0od/f1.bed) bedtools_df Chromosome Start End 0 chr16 5862710 5862720 1 chr16 5862720 5862730 2 chr16 5862730 5862740 3 chr16 5862740 5862750 4 chr16 5862750 5862760 ... ... ... ... 4609 chr4 8152931 8152941 4610 chr4 8152941 8152951 4611 chr4 8152951 8152961 4612 chr4 8152961 8152971 4613 chr4 8152971 8152972 [4614 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpv7l36vh5/f1.bed) bedtools_df Chromosome Start End 0 chr1 938656 938666 1 chr1 938666 938676 2 chr1 938676 938686 3 chr1 938686 938696 4 chr1 938696 938706 ... ... ... ... 5162 chrM 6301103 6301113 5163 chrM 6301113 6301123 5164 chrM 6301123 6301133 5165 chrM 6301133 6301143 5166 chrM 6301143 6301147 [5167 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp81hafhnq/f1.bed) bedtools_df Chromosome Start End 0 chr1 1080750 1080760 1 chr1 1080760 1080770 2 chr1 1080770 1080780 3 chr1 1080780 1080790 4 chr1 1080790 1080800 ... ... ... ... 7245 chr8 6962 6972 7246 chr8 6972 6982 7247 chr8 6982 6992 7248 chr8 6992 7002 7249 chr8 7002 7011 [7250 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpkgek1qx8/f1.bed) bedtools_df Chromosome Start End 0 chr1 1610606 1610616 1 chr1 1610616 1610626 2 chr1 1610626 1610636 3 chr1 1610636 1610646 4 chr1 1610646 1610656 ... ... ... ... 4426 chr4 3583541 3583551 4427 chr4 3583551 3583561 4428 chr4 3583561 3583571 4429 chr4 3583571 3583576 4430 chrY 207416 207417 [4431 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpxt8qwqst/f1.bed) bedtools_df Chromosome Start End 0 chr1 427020 427030 1 chr1 427030 427040 2 chr1 427040 427050 3 chr1 427050 427060 4 chr1 427060 427070 ... ... ... ... 2949 chr3 8405580 8405590 2950 chr3 8405590 8405600 2951 chr3 8405600 8405610 2952 chr3 8405610 8405620 2953 chr3 8405620 8405626 [2954 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpt8ckbtw8/f1.bed) bedtools_df Chromosome Start End 0 chr1 5420636 5420646 1 chr1 5420646 5420656 2 chr1 5420656 5420666 3 chr1 5420666 5420676 4 chr1 5420676 5420686 ... ... ... ... 1979 chr5 4273001 4273011 1980 chr5 4273011 4273021 1981 chr5 4273021 4273031 1982 chr5 4273031 4273041 1983 chr5 4273041 4273051 [1984 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp4f6ppsjh/f1.bed) bedtools_df Chromosome Start End 0 chr10 9050357 9050367 1 chr10 9050367 9050377 2 chr10 9050377 9050387 3 chr10 9050387 9050397 4 chr10 9050397 9050407 ... ... ... ... 5202 chrM 8350336 8350346 5203 chrM 8350346 8350356 5204 chrM 8350356 8350366 5205 chrM 8350366 8350376 5206 chrM 8350376 8350386 [5207 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpuj607z8j/f1.bed) bedtools_df Chromosome Start End 0 chr1 7069315 7069325 1 chr1 7069325 7069335 2 chr1 7069335 7069345 3 chr1 7069345 7069355 4 chr1 7069355 7069365 .. ... ... ... 975 chr1 7079065 7079075 976 chr1 7079075 7079085 977 chr1 7079085 7079095 978 chr1 7079095 7079105 979 chr1 7079105 7079110 [980 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpj4gxif5c/f1.bed) bedtools_df Chromosome Start End 0 chr1 2626838 2626848 1 chr1 2626848 2626858 2 chr1 2626858 2626868 3 chr1 2626868 2626878 4 chr1 2626878 2626888 ... ... ... ... 5785 chr1 7851726 7851736 5786 chr1 7851736 7851746 5787 chr1 7851746 7851756 5788 chr1 7851756 7851766 5789 chr1 7851766 7851768 [5790 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmppo0klfle/f1.bed) bedtools_df Chromosome Start End 0 chr16 9586328 9586338 1 chr16 9586338 9586348 2 chr16 9586348 9586358 3 chr16 9586358 9586368 4 chr16 9586368 9586378 .. ... ... ... 901 chr5 4058431 4058441 902 chr5 4058441 4058451 903 chr5 4058451 4058461 904 chr5 4058461 4058471 905 chr5 4058471 4058481 [906 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp38bctao2/f1.bed) bedtools_df Chromosome Start End 0 chr1 338190 338200 1 chr1 338200 338210 2 chr1 338210 338220 3 chr1 338220 338230 4 chr1 338230 338240 ... ... ... ... 2866 chr4 5132426 5132436 2867 chr4 5132436 5132446 2868 chr4 5132446 5132456 2869 chr4 5132456 5132466 2870 chr4 5132466 5132471 [2871 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpqwbse828/f1.bed) bedtools_df Chromosome Start End 0 chr1 408670 408680 1 chr1 408680 408690 2 chr1 408690 408700 3 chr1 408700 408710 4 chr1 408710 408720 ... ... ... ... 2626 chr4 5895882 5895892 2627 chr4 5895892 5895902 2628 chr4 5895902 5895912 2629 chr4 5895912 5895922 2630 chr4 5895922 5895924 [2631 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpr5ctytza/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 ... ... ... ... 6052 chr21 3464599 3464609 6053 chr21 3464609 3464619 6054 chr21 3464619 3464629 6055 chr21 3464629 3464639 6056 chr21 3464639 3464640 [6057 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp57iy7wjr/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 ... ... ... ... 5897 chrM 8593728 8593738 5898 chrM 8593738 8593748 5899 chrM 8593748 8593758 5900 chrM 8593758 8593768 5901 chrM 8593768 8593769 [5902 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpbpspk7cz/f1.bed) bedtools_df Chromosome Start End 0 chr1 4733944 4733954 1 chr1 4733954 4733964 2 chr1 4733964 4733974 3 chr1 4733974 4733984 4 chr1 4733984 4733994 .. ... ... ... 737 chr1 7432266 7432276 738 chr1 7432276 7432286 739 chr1 7432286 7432296 740 chr1 7432296 7432306 741 chr1 7432306 7432314 [742 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmptoiq31v_/f1.bed) bedtools_df Chromosome Start End 0 chr1 237586 237596 1 chr1 237596 237606 2 chr1 237606 237616 3 chr1 237616 237626 4 chr1 237626 237636 ... ... ... ... 6145 chr16 1177391 1177401 6146 chr16 1177401 1177411 6147 chr16 1177411 1177421 6148 chr16 1177421 1177431 6149 chr16 1177431 1177437 [6150 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpc28jm2ia/f1.bed) bedtools_df Chromosome Start End 0 chr1 9159695 9159705 1 chr1 9159705 9159715 2 chr1 9159715 9159725 3 chr1 9159725 9159735 4 chr1 9159735 9159745 .. ... ... ... 942 chr18 6616944 6616954 943 chr18 6616954 6616964 944 chr18 6616964 6616974 945 chr18 6616974 6616984 946 chr18 6616984 6616986 [947 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp49u7eva9/f1.bed) bedtools_df Chromosome Start End 0 chr1 1032042 1032052 1 chr1 1032052 1032062 2 chr1 1032062 1032072 3 chr1 1032072 1032082 4 chr1 1032082 1032092 .. ... ... ... 727 chr1 1039312 1039322 728 chr1 1039322 1039332 729 chr1 1039332 1039342 730 chr1 1039342 1039352 731 chr1 1039352 1039362 [732 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpzcphdm8a/f1.bed) bedtools_df Chromosome Start End 0 chr1 2685374 2685384 1 chr1 2685384 2685394 2 chr1 2685394 2685404 3 chr1 2685404 2685414 4 chr1 2685414 2685424 ... ... ... ... 2305 chr9 163928 163938 2306 chr9 163938 163948 2307 chr9 163948 163958 2308 chr9 163958 163968 2309 chr9 163968 163974 [2310 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpfb3wrgdw/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 ... ... ... ... 1303 chr1 8410684 8410694 1304 chr1 8410694 8410704 1305 chr1 8410704 8410714 1306 chr1 8410714 8410724 1307 chr1 8410724 8410726 [1308 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpm65e9_ja/f1.bed) bedtools_df Chromosome Start End 0 chr1 5267780 5267790 1 chr1 5267790 5267800 2 chr1 5267800 5267810 3 chr1 5267810 5267820 4 chr1 5267820 5267830 ... ... ... ... 1807 chr21 255133 255143 1808 chr21 255143 255153 1809 chr21 255153 255163 1810 chr21 255163 255173 1811 chr21 255173 255176 [1812 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpxw6_t_wk/f1.bed) bedtools_df Chromosome Start End 0 chr1 5549290 5549300 1 chr1 5549300 5549310 2 chr1 5549310 5549320 3 chr1 5549320 5549330 4 chr1 5549330 5549340 ... ... ... ... 4233 chr9 5836056 5836066 4234 chr9 5836066 5836076 4235 chr9 5836076 5836086 4236 chr9 5836086 5836096 4237 chr9 5836096 5836102 [4238 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpe0v8wan4/f1.bed) bedtools_df Chromosome Start End 0 chr1 389206 389216 1 chr1 389216 389226 2 chr1 389226 389236 3 chr1 389236 389246 4 chr1 389246 389256 ... ... ... ... 4438 chrY 3876745 3876755 4439 chrY 3876755 3876765 4440 chrY 3876765 3876775 4441 chrY 3876775 3876785 4442 chrY 3876785 3876792 [4443 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp6zjxosyy/f1.bed) bedtools_df Chromosome Start End 0 chr1 6180896 6180906 1 chr1 6180906 6180916 2 chr1 6180916 6180926 3 chr1 6180926 6180936 4 chr1 6180936 6180946 .. ... ... ... 285 chr6 7307250 7307260 286 chr6 7307260 7307270 287 chr6 7307270 7307280 288 chr6 7307280 7307290 289 chr6 7307290 7307296 [290 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmplach2pi_/f1.bed) bedtools_df Chromosome Start End 0 chr1 2592636 2592646 1 chr1 2592646 2592656 2 chr1 2592656 2592666 3 chr1 2592666 2592676 4 chr1 2592676 2592686 ... ... ... ... 5105 chrM 2594256 2594266 5106 chrM 2594266 2594276 5107 chrM 2594276 2594286 5108 chrM 2594286 2594296 5109 chrM 2594296 2594297 [5110 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp5ll9wtau/f1.bed) bedtools_df Chromosome Start End 0 chr1 7318396 7318406 1 chr1 7318406 7318416 2 chr1 7318416 7318426 3 chr1 7318426 7318436 4 chr1 7318436 7318446 ... ... ... ... 2111 chr4 856573 856583 2112 chr4 856583 856593 2113 chr4 856593 856603 2114 chr4 856603 856613 2115 chr4 856613 856619 [2116 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpr5lbcinz/f1.bed) bedtools_df Chromosome Start End 0 chr1 4286793 4286803 1 chr1 4286803 4286813 2 chr1 4286813 4286823 3 chr1 4286823 4286833 4 chr1 4286833 4286843 ... ... ... ... 4510 chr8 7133686 7133696 4511 chr8 7133696 7133706 4512 chr8 7133706 7133716 4513 chr8 7133716 7133726 4514 chr8 7133726 7133736 [4515 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp6e6k4on2/f1.bed) bedtools_df Chromosome Start End 0 chr10 1718773 1718774 1 chr10 3031588 3031598 2 chr10 3031598 3031608 3 chr10 3031608 3031618 4 chr10 3031618 3031628 ... ... ... ... 2803 chr5 425071 425081 2804 chr5 425081 425091 2805 chr5 425091 425101 2806 chr5 425101 425111 2807 chr5 425111 425114 [2808 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp4hlvwc69/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 ... ... ... ... 5562 chrM 5151 5161 5563 chrM 5161 5171 5564 chrM 5171 5181 5565 chrM 5181 5191 5566 chrM 5191 5196 [5567 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmptc8a63fw/f1.bed) bedtools_df Chromosome Start End 0 chr1 2021018 2021028 1 chr1 2021028 2021038 2 chr1 2021038 2021048 3 chr1 2021048 2021058 4 chr1 2021058 2021068 ... ... ... ... 1863 chr13 2036478 2036488 1864 chr13 2036488 2036498 1865 chr13 2036498 2036508 1866 chr13 2036508 2036518 1867 chr13 2036518 2036524 [1868 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp7ke8e6es/f1.bed) bedtools_df Chromosome Start End 0 chr1 1250629 1250639 1 chr1 1250639 1250649 2 chr1 1250649 1250659 3 chr1 1250659 1250669 4 chr1 1250669 1250679 ... ... ... ... 4707 chrM 3707545 3707555 4708 chrM 3707555 3707565 4709 chrM 3707565 3707575 4710 chrM 3707575 3707585 4711 chrM 3707585 3707586 [4712 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpyk6r5ecp/f1.bed) bedtools_df Chromosome Start End 0 chr1 5338511 5338521 1 chr1 5338521 5338531 2 chr1 5338531 5338541 3 chr1 5338541 5338551 4 chr1 5338551 5338561 ... ... ... ... 3111 chr9 6402945 6402955 3112 chr9 6402955 6402965 3113 chr9 6402965 6402975 3114 chr9 6402975 6402985 3115 chr9 6402985 6402988 [3116 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpbqmuvxrs/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 ... ... ... ... 3216 chrM 8010229 8010239 3217 chrM 8010239 8010249 3218 chrM 8010249 8010259 3219 chrM 8010259 8010269 3220 chrM 8010269 8010271 [3221 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp4j0ftfqf/f1.bed) bedtools_df Chromosome Start End 0 chr1 7098255 7098265 1 chr1 7098265 7098275 2 chr1 7098275 7098285 3 chr1 7098285 7098295 4 chr1 7098295 7098305 ... ... ... ... 1938 chrY 8346154 8346164 1939 chrY 8346164 8346174 1940 chrY 8346174 8346184 1941 chrY 8346184 8346194 1942 chrY 8346194 8346197 [1943 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpbko1udfl/f1.bed) bedtools_df Chromosome Start End 0 chr1 1282357 1282367 1 chr1 1282367 1282377 2 chr1 1282377 1282387 3 chr1 1282387 1282397 4 chr1 1282397 1282407 ... ... ... ... 5121 chr9 7344854 7344864 5122 chr9 7344864 7344874 5123 chr9 7344874 7344884 5124 chr9 7344884 7344894 5125 chr9 7344894 7344898 [5126 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpkqzdymw3/f1.bed) bedtools_df Chromosome Start End 0 chr1 6603344 6603354 1 chr1 6603354 6603364 2 chr1 6603364 6603374 3 chr1 6603374 6603384 4 chr1 6603384 6603394 ... ... ... ... 1254 chr4 8925620 8925630 1255 chr4 8925630 8925640 1256 chr4 8925640 8925650 1257 chr4 8925650 8925660 1258 chr4 8925660 8925662 [1259 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpqvvin2rl/f1.bed) bedtools_df Chromosome Start End 0 chr1 9149751 9149761 1 chr1 9149761 9149771 2 chr1 9149771 9149781 3 chr1 9149781 9149791 4 chr1 9149791 9149801 ... ... ... ... 3036 chrY 9157321 9157331 3037 chrY 9157331 9157341 3038 chrY 9157341 9157351 3039 chrY 9157351 9157361 3040 chrY 9157361 9157364 [3041 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpsqi53tv0/f1.bed) bedtools_df Chromosome Start End 0 chr1 1110584 1110594 1 chr1 1110594 1110604 2 chr1 1110604 1110614 3 chr1 1110614 1110624 4 chr1 1110624 1110634 ... ... ... ... 6297 chr1 9947357 9947367 6298 chr1 9947367 9947377 6299 chr1 9947377 9947387 6300 chr1 9947387 9947397 6301 chr1 9947397 9947407 [6302 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp1xo12nm1/f1.bed) bedtools_df Chromosome Start End 0 chr1 2083910 2083920 1 chr1 2083920 2083930 2 chr1 2083930 2083940 3 chr1 2083940 2083950 4 chr1 2083950 2083960 ... ... ... ... 2564 chr6 4470168 4470178 2565 chr6 4470178 4470188 2566 chr6 4470188 4470198 2567 chr6 4470198 4470208 2568 chr6 4470208 4470215 [2569 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmple61hhk6/f1.bed) bedtools_df Chromosome Start End 0 chr1 6585326 6585336 1 chr1 6585336 6585346 2 chr1 6585346 6585356 3 chr1 6585356 6585366 4 chr1 6585366 6585376 ... ... ... ... 4557 chrM 1622779 1622789 4558 chrM 1622789 1622799 4559 chrM 1622799 1622809 4560 chrM 1622809 1622819 4561 chrM 1622819 1622829 [4562 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp7biptn5p/f1.bed) bedtools_df Chromosome Start End 0 chr1 6432272 6432282 1 chr1 6432282 6432292 2 chr1 6432292 6432302 3 chr1 6432302 6432312 4 chr1 6432312 6432322 .. ... ... ... 744 chr19 8447354 8447364 745 chr19 8447364 8447374 746 chr19 8447374 8447384 747 chr19 8447384 8447394 748 chr19 8447394 8447404 [749 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpom0xci7i/f1.bed) bedtools_df Chromosome Start End 0 chrY 2718339 2718349 1 chrY 2718349 2718359 2 chrY 2718359 2718369 3 chrY 2718369 2718379 4 chrY 2718379 2718389 .. ... ... ... 352 chrY 2721859 2721869 353 chrY 2721869 2721879 354 chrY 2721879 2721889 355 chrY 2721889 2721899 356 chrY 2721899 2721904 [357 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp_cm327jv/f1.bed) bedtools_df Chromosome Start End 0 chr1 4435910 4435920 1 chr1 4435920 4435930 2 chr1 4435930 4435940 3 chr1 4435940 4435950 4 chr1 4435950 4435960 .. ... ... ... 794 chr1 8398674 8398684 795 chr1 8398684 8398694 796 chr1 8398694 8398704 797 chr1 8398704 8398714 798 chr1 8398714 8398715 [799 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp0y3bx67y/f1.bed) bedtools_df Chromosome Start End 0 chr1 3302336 3302346 1 chr1 3302346 3302356 2 chr1 3302356 3302366 3 chr1 3302366 3302376 4 chr1 3302376 3302386 ... ... ... ... 1602 chr1 9888830 9888840 1603 chr1 9888840 9888850 1604 chr1 9888850 9888860 1605 chr1 9888860 9888870 1606 chr1 9888870 9888872 [1607 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpt6z72eqj/f1.bed) bedtools_df Chromosome Start End 0 chr1 3281450 3281460 1 chr1 3281460 3281470 2 chr1 3281470 3281480 3 chr1 3281480 3281490 4 chr1 3281490 3281500 ... ... ... ... 1690 chr4 9597327 9597337 1691 chr4 9597337 9597347 1692 chr4 9597347 9597357 1693 chr4 9597357 9597367 1694 chr4 9597367 9597372 [1695 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpjb3_el_d/f1.bed) bedtools_df Chromosome Start End 0 chr1 9895371 9895381 1 chr1 9895381 9895391 2 chr1 9895391 9895401 3 chr1 9895401 9895411 4 chr1 9895411 9895421 .. ... ... ... 635 chr17 4992153 4992163 636 chr17 4992163 4992173 637 chr17 4992173 4992183 638 chr17 4992183 4992193 639 chr17 4992193 4992202 [640 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpt9gggmvr/f1.bed) bedtools_df Chromosome Start End 0 chr1 218381 218391 1 chr1 218391 218401 2 chr1 218401 218411 3 chr1 218411 218421 4 chr1 218421 218431 ... ... ... ... 2525 chr21 2145478 2145488 2526 chr21 2145488 2145498 2527 chr21 2145498 2145508 2528 chr21 2145508 2145518 2529 chr21 2145518 2145519 [2530 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpejlmzjol/f1.bed) bedtools_df Chromosome Start End 0 chr1 1757765 1757775 1 chr1 1757775 1757785 2 chr1 1757785 1757795 3 chr1 1757795 1757805 4 chr1 1757805 1757815 ... ... ... ... 1804 chr18 9977600 9977610 1805 chr18 9977610 9977620 1806 chr18 9977620 9977630 1807 chr18 9977630 9977640 1808 chr18 9977640 9977641 [1809 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmppj37rebd/f1.bed) bedtools_df Chromosome Start End 0 chr1 44716 44726 1 chr1 44726 44736 2 chr1 44736 44746 3 chr1 44746 44756 4 chr1 44756 44766 ... ... ... ... 5991 chr8 9180390 9180400 5992 chr8 9180400 9180410 5993 chr8 9180410 9180420 5994 chr8 9180420 9180430 5995 chr8 9180430 9180434 [5996 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpemyq6bwh/f1.bed) bedtools_df Chromosome Start End 0 chr1 1571947 1571957 1 chr1 1571957 1571967 2 chr1 1571967 1571977 3 chr1 1571977 1571987 4 chr1 1571987 1571997 ... ... ... ... 5043 chr21 10002370 10002380 5044 chr21 10002380 10002390 5045 chr21 10002390 10002400 5046 chr21 10002400 10002410 5047 chr21 10002410 10002416 [5048 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp3vct1d1g/f1.bed) bedtools_df Chromosome Start End 0 chr1 1437705 1437715 1 chr1 1437715 1437725 2 chr1 1437725 1437735 3 chr1 1437735 1437745 4 chr1 1437745 1437755 .. ... ... ... 692 chr1 1444625 1444635 693 chr1 1444635 1444645 694 chr1 1444645 1444655 695 chr1 1444655 1444665 696 chr1 1444665 1444668 [697 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp7y1ote2z/f1.bed) bedtools_df Chromosome Start End 0 chr1 486187 486197 1 chr1 486197 486207 2 chr1 486207 486217 3 chr1 486217 486227 4 chr1 486227 486237 ... ... ... ... 3837 chr9 5718292 5718302 3838 chr9 5718302 5718312 3839 chr9 5718312 5718322 3840 chr9 5718322 5718332 3841 chr9 5718332 5718333 [3842 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpecn33fis/f1.bed) bedtools_df Chromosome Start End 0 chr1 5377207 5377217 1 chr1 5377217 5377227 2 chr1 5377227 5377237 3 chr1 5377237 5377247 4 chr1 5377247 5377257 ... ... ... ... 4811 chrY 4507503 4507513 4812 chrY 4507513 4507523 4813 chrY 4507523 4507533 4814 chrY 4507533 4507543 4815 chrY 4507543 4507550 [4816 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp4ftf1509/f1.bed) bedtools_df Chromosome Start End 0 chr1 2149915 2149925 1 chr1 2149925 2149935 2 chr1 2149935 2149945 3 chr1 2149945 2149955 4 chr1 2149955 2149965 ... ... ... ... 4935 chr5 6974038 6974048 4936 chr5 6974048 6974058 4937 chr5 6974058 6974068 4938 chr5 6974068 6974078 4939 chr5 6974078 6974087 [4940 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp497t9_zh/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 ... ... ... ... 3187 chr5 8326368 8326378 3188 chr5 8326378 8326388 3189 chr5 8326388 8326398 3190 chr5 8326398 8326408 3191 chr5 8326408 8326414 [3192 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpckxff1k1/f1.bed) bedtools_df Chromosome Start End 0 chr1 7082447 7082457 1 chr1 7082457 7082467 2 chr1 7082467 7082477 3 chr1 7082477 7082487 4 chr1 7082487 7082497 ... ... ... ... 1372 chr17 8323382 8323392 1373 chr17 8323392 8323402 1374 chr17 8323402 8323412 1375 chr17 8323412 8323422 1376 chr17 8323422 8323423 [1377 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmps8ix6xfz/f1.bed) bedtools_df Chromosome Start End 0 chr8 5984282 5984292 1 chr8 5984292 5984302 2 chr8 5984302 5984312 3 chr8 5984312 5984322 4 chr8 5984322 5984332 .. ... ... ... 884 chr8 5993122 5993132 885 chr8 5993132 5993142 886 chr8 5993142 5993152 887 chr8 5993152 5993162 888 chr8 5993162 5993166 [889 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpk_v1aqj3/f1.bed) bedtools_df Chromosome Start End 0 chr15 3041551 3041561 1 chr15 3041561 3041571 2 chr15 3041571 3041581 3 chr15 3041581 3041591 4 chr15 3041591 3041601 .. ... ... ... 82 chr15 3042371 3042381 83 chr15 3042381 3042391 84 chr15 3042391 3042401 85 chr15 3042401 3042411 86 chr15 3042411 3042414 [87 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmptc0css7g/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 ... ... ... ... 5367 chr7 8256072 8256082 5368 chr7 8256082 8256092 5369 chr7 8256092 8256102 5370 chr7 8256102 8256112 5371 chr7 8256112 8256118 [5372 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpz138cy8p/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 =============================== 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 pyranges/__init__.py:18 pyranges/__init__.py:18 pyranges/__init__.py:18 pyranges/__init__.py:18 /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 tests/test_binary.py:118 tests/test_binary.py:118 tests/test_binary.py:118 /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 tests/test_binary.py:139 tests/test_binary.py:139 tests/test_binary.py:139 /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 tests/test_binary.py:160 tests/test_binary.py:160 tests/test_binary.py:160 /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 tests/test_binary.py:187 tests/test_binary.py:187 tests/test_binary.py:187 /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 tests/test_binary.py:212 tests/test_binary.py:212 tests/test_binary.py:212 /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 tests/test_binary.py:291 tests/test_binary.py:291 tests/test_binary.py:291 /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 tests/test_binary.py:329 tests/test_binary.py:329 tests/test_binary.py:329 /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 tests/test_binary.py:368 tests/test_binary.py:368 tests/test_binary.py:368 /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 tests/test_binary.py:392 tests/test_binary.py:392 tests/test_binary.py:392 /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 tests/test_binary.py:426 tests/test_binary.py:426 tests/test_binary.py:426 /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 tests/test_binary.py:516 tests/test_binary.py:516 tests/test_binary.py:516 /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 tests/test_binary.py:579 tests/test_binary.py:579 tests/test_binary.py:579 /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: 20 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py: 44444 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py: 235223 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/test_genomicfeatures.py: 4 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_getset_attr.py: 3 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py: 24350 warnings .pybuild/cpython3_3.12_pyranges/build/tests/data/test_data.py: 9 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: 16 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py: 1965 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py: 132 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_stranded.py: 2 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py: 5296 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 tests/test_do_not_error.py:46 tests/test_do_not_error.py:46 tests/test_do_not_error.py:46 /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 tests/test_unary.py:35 tests/test_unary.py:35 tests/test_unary.py:35 /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 tests/test_unary.py:100 tests/test_unary.py:100 tests/test_unary.py:100 /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 tests/test_unary.py:163 tests/test_unary.py:163 tests/test_unary.py:163 /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 tests/test_unary.py:205 tests/test_unary.py:205 tests/test_unary.py:205 /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 tests/test_unary.py:234 tests/test_unary.py:234 tests/test_unary.py:234 /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 tests/test_unary.py:272 tests/test_unary.py:272 tests/test_unary.py:272 /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 tests/test_unary.py:287 tests/test_unary.py:287 tests/test_unary.py:287 /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 tests/test_unary.py:315 tests/test_unary.py:315 tests/test_unary.py:315 /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_do_not_error.py: 28201 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py: 3186 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py: 6983 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_concat.py: 1 warning .pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py: 2355 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: 5209 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_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_nearest[downstream-False-opposite] - Except... FAILED tests/test_binary.py::test_set_intersect[False] - Exception: Starts/En... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain2-method_chain2] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain35-method_chain35] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain3-method_chain3] 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_chain36-method_chain36] FAILED tests/test_binary.py::test_set_intersect[same] - Exception: Starts/End... FAILED tests/test_binary.py::test_jaccard[same] - Exception: Starts/Ends not ... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain4-method_chain4] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain37-method_chain37] 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_chain5-method_chain5] 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_chain38-method_chain38] 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_chain39-method_chain39] 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_chain40-method_chain40] 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_chain9-method_chain9] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain41-method_chain41] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain10-method_chain10] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain42-method_chain42] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain11-method_chain11] 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_chain12-method_chain12] 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_chain13-method_chain13] 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_chain45-method_chain45] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain14-method_chain14] 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_chain47-method_chain47] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain15-method_chain15] 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_chain49-method_chain49] FAILED tests/test_binary.py::test_k_nearest[downstream-True-same-last] - Exce... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain17-method_chain17] 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_chain50-method_chain50] 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_chain19-method_chain19] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain51-method_chain51] FAILED tests/test_binary.py::test_coverage[same] - Exception: Starts/Ends not... FAILED tests/test_binary.py::test_k_nearest[upstream-False-opposite-last] - V... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain21-method_chain21] FAILED tests/test_binary.py::test_coverage[opposite] - Exception: Starts/Ends... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain52-method_chain52] FAILED tests/test_binary.py::test_k_nearest[upstream-False-same-last] - Excep... FAILED tests/test_binary.py::test_subtraction[same] - Exception: Starts/Ends ... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain53-method_chain53] FAILED tests/test_binary.py::test_k_nearest[upstream-False-False-last] - Valu... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain22-method_chain22] FAILED tests/test_binary.py::test_subtraction[opposite] - Exception: Starts/E... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain54-method_chain54] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain23-method_chain23] FAILED tests/test_binary.py::test_k_nearest[upstream-True-opposite-last] - Ex... FAILED tests/test_binary.py::test_subtraction[False] - Exception: Starts/Ends... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain55-method_chain55] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain24-method_chain24] 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_chain56-method_chain56] FAILED tests/test_binary.py::test_nearest[None-True-False] - ExceptionGroup: ... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain25-method_chain25] FAILED tests/test_binary.py::test_k_nearest[upstream-True-False-last] - Excep... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain57-method_chain57] FAILED tests/test_binary.py::test_nearest[None-True-same] - ExceptionGroup: H... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain26-method_chain26] FAILED tests/test_binary.py::test_k_nearest[None-False-opposite-last] - Value... FAILED tests/test_binary.py::test_k_nearest[None-False-same-last] - ValueErro... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain58-method_chain58] FAILED tests/test_binary.py::test_nearest[None-True-opposite] - ValueError: B... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain27-method_chain27] FAILED tests/test_binary.py::test_k_nearest[None-False-False-last] - ValueErr... 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_chain59-method_chain59] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain28-method_chain28] FAILED tests/test_binary.py::test_nearest[None-False-same] - ValueError: Buff... FAILED tests/test_binary.py::test_k_nearest[None-True-opposite-last] - ValueE... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain60-method_chain60] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain29-method_chain29] FAILED tests/test_binary.py::test_k_nearest[None-True-same-last] - ValueError... FAILED tests/test_binary.py::test_nearest[None-False-opposite] - ValueError: ... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain61-method_chain61] FAILED tests/test_binary.py::test_k_nearest[None-True-False-last] - ValueErro... FAILED tests/test_binary.py::test_nearest[upstream-True-False] - ExceptionGro... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain62-method_chain62] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain31-method_chain31] FAILED tests/test_binary.py::test_k_nearest_1_vs_nearest - ValueError: Buffer... FAILED tests/test_binary.py::test_nearest[upstream-True-same] - ExceptionGrou... 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_chain0-method_chain0] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain33-method_chain33] FAILED tests/test_binary.py::test_nearest[upstream-True-opposite] - Exception... FAILED tests/test_binary.py::test_nearest[upstream-False-False] - ValueError:... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain64-method_chain64] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain1-method_chain1] FAILED tests/test_binary.py::test_nearest[upstream-False-same] - ExceptionGro... 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_chain68-method_chain68] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain158-method_chain158] FAILED tests/test_binary.py::test_nearest[upstream-False-opposite] - Exceptio... 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_chain70-method_chain70] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain159-method_chain159] FAILED tests/test_binary.py::test_nearest[downstream-True-False] - ExceptionG... 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_chain160-method_chain160] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain71-method_chain71] FAILED tests/test_binary.py::test_nearest[downstream-True-same] - ExceptionGr... 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_chain161-method_chain161] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain72-method_chain72] FAILED tests/test_binary.py::test_nearest[downstream-True-opposite] - Excepti... 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_chain162-method_chain162] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain73-method_chain73] FAILED tests/test_binary.py::test_nearest[downstream-False-False] - ValueErro... FAILED tests/test_binary.py::test_nearest[downstream-False-same] - ValueError... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain123-method_chain123] 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_chain164-method_chain164] 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_chain124-method_chain124] 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_chain166-method_chain166] 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_chain125-method_chain125] 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_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_chain126-method_chain126] 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_chain199-method_chain199] 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_chain127-method_chain127] 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_chain78-method_chain78] 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_chain201-method_chain201] 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_chain171-method_chain171] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain80-method_chain80] 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_chain131-method_chain131] 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_chain82-method_chain82] 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_chain133-method_chain133] 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_chain204-method_chain204] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain84-method_chain84] 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_chain205-method_chain205] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain85-method_chain85] 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_chain135-method_chain135] 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_chain175-method_chain175] 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_chain207-method_chain207] 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_chain176-method_chain176] 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_chain208-method_chain208] 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_chain88-method_chain88] 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_chain180-method_chain180] 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_chain89-method_chain89] 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_chain139-method_chain139] 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_chain90-method_chain90] 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_chain140-method_chain140] 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_chain91-method_chain91] 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_chain215-method_chain215] 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_chain185-method_chain185] 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_chain217-method_chain217] 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_chain186-method_chain186] 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_chain96-method_chain96] 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_chain187-method_chain187] 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_chain147-method_chain147] 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_chain188-method_chain188] 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_chain99-method_chain99] 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_chain189-method_chain189] 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_chain100-method_chain100] 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_chain190-method_chain190] 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_chain101-method_chain101] 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_chain151-method_chain151] 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_chain192-method_chain192] 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_chain152-method_chain152] 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_chain224-method_chain224] 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_chain153-method_chain153] 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_chain225-method_chain225] 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_chain154-method_chain154] 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_chain231-method_chain231] 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_chain106-method_chain106] 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_chain232-method_chain232] 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_chain156-method_chain156] 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_chain233-method_chain233] 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_chain157-method_chain157] 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_chain234-method_chain234] 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_chain109-method_chain109] 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_chain235-method_chain235] 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_chain259-method_chain259] 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_chain111-method_chain111] 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_chain283-method_chain283] 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_chain112-method_chain112] 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_chain284-method_chain284] 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_chain238-method_chain238] 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_chain264-method_chain264] 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_chain239-method_chain239] 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_chain266-method_chain266] 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_chain303-method_chain303] 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_chain243-method_chain243] 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_chain288-method_chain288] 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_chain245-method_chain245] 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_chain290-method_chain290] 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_chain306-method_chain306] 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_chain270-method_chain270] 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_chain307-method_chain307] 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_chain308-method_chain308] 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_chain248-method_chain248] 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_chain309-method_chain309] 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_chain272-method_chain272] 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_chain250-method_chain250] 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_chain311-method_chain311] 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_chain251-method_chain251] 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_chain313-method_chain313] 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_chain252-method_chain252] 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_chain315-method_chain315] 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_chain253-method_chain253] 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_chain280-method_chain280] 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_chain254-method_chain254] 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_chain300-method_chain300] 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_chain322-method_chain322] 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_chain318-method_chain318] 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_chain339-method_chain339] 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_chain319-method_chain319] 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_chain325-method_chain325] 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_chain320-method_chain320] 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_chain327-method_chain327] 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_chain321-method_chain321] 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_chain356-method_chain356] 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_chain367-method_chain367] 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_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_chain368-method_chain368] 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_chain358-method_chain358] 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_chain347-method_chain347] 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_chain332-method_chain332] 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_chain348-method_chain348] 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_chain333-method_chain333] 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_chain362-method_chain362] 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_chain334-method_chain334] 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_chain372-method_chain372] 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_chain335-method_chain335] 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_chain365-method_chain365] 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_chain352-method_chain352] 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_chain366-method_chain366] 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_chain337-method_chain337] 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_chain376-method_chain376] 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_chain379-method_chain379] 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_chain403-method_chain403] 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_chain380-method_chain380] 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_chain404-method_chain404] 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_chain398-method_chain398] 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_chain392-method_chain392] 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_chain382-method_chain382] 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_chain406-method_chain406] 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_chain383-method_chain383] 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_chain401-method_chain401] 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_chain395-method_chain395] 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_chain385-method_chain385] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain409-method_chain409] 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_chain386-method_chain386] 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_chain421-method_chain421] 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_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_chain423-method_chain423] 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_chain418-method_chain418] 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_chain429-method_chain429] 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_chain428-method_chain428] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain419-method_chain419] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain430-method_chain430] 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_chain435-method_chain435] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain420-method_chain420] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain431-method_chain431] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain433-method_chain433] FAILED tests/test_genomicfeatures.py::test_introns_single - ValueError: Buffe... 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_chain437-method_chain437] 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_chain434-method_chain434] FAILED tests/test_unary.py::test_cluster[True] - Exception: Starts/Ends not i... FAILED tests/test_unary.py::test_merge[False] - Exception: Starts/Ends not in... 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... FAILED tests/windows/test_windows.py::test_windows - ValueError: Buffer dtype... FAILED tests/windows/test_windows.py::test_windows2 - ValueError: Buffer dtyp... FAILED tests/test_unary.py::test_windows - Exception: Starts/Ends not int64 o... ======= 412 failed, 119 passed, 359524 warnings in 42385.26s (11:46:25) ======== 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 4 I: pybuild pybuild:308: mkdir -pv /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_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_3.11_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_3.11_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_3.11_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_3.11_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_3.11_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_3.11_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_3.11_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_3.11_pyranges/build/tests/test_data' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/test_sorted.bam' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_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_3.11_pyranges/build/tests/test_data/test_sorted.bam.bai' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/ensembl.gtf' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_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_3.11_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_3.11_pyranges/build/tests/test_data/ucsc_df_to_parse.txt' '/build/reproducible-path/pyranges-0.0.111+ds/tests/data' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_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_3.11_pyranges/build/tests/data/test_data.py' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/control.bam' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_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_3.11_pyranges/build/pyranges/example_data/control.bam.bai' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/exons.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_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_3.11_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_3.11_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_3.11_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_3.11_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_3.11_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_3.11_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_3.11_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_3.11_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_3.11_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_3.11_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_3.11_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_3.11_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_3.11_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_3.11_pyranges/build/pyranges/example_data/aorta2.bed' I: pybuild base:311: cd /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build; python3.11 -m pytest -v -n 4 ============================= test session starts ============================== platform linux -- Python 3.11.9, pytest-7.4.4, pluggy-1.5.0 -- /usr/bin/python3.11 cachedir: .pytest_cache hypothesis profile 'default' -> database=DirectoryBasedExampleDatabase(PosixPath('/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/.hypothesis/examples')) rootdir: /build/reproducible-path/pyranges-0.0.111+ds plugins: hypothesis-6.100.4, xdist-3.5.0 created: 4/4 workers 4 workers [531 items] scheduling tests via LoadScheduling tests/test_binary.py::test_set_intersect[False] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain35-method_chain35] tests/test_binary.py::test_nearest[downstream-False-opposite] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain2-method_chain2] [gw2] [ 0%] 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] [gw1] [ 0%] 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_chain36-method_chain36] [gw3] [ 0%] FAILED tests/test_binary.py::test_set_intersect[False] tests/test_binary.py::test_set_intersect[same] [gw0] [ 0%] FAILED tests/test_binary.py::test_nearest[downstream-False-opposite] tests/test_binary.py::test_jaccard[False] [gw1] [ 0%] 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] [gw2] [ 1%] 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] [gw3] [ 1%] FAILED tests/test_binary.py::test_set_intersect[same] tests/test_binary.py::test_set_union[False] [gw0] [ 1%] FAILED tests/test_binary.py::test_jaccard[False] tests/test_binary.py::test_jaccard[same] [gw1] [ 1%] 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] [gw0] [ 1%] FAILED tests/test_binary.py::test_jaccard[same] tests/test_binary.py::test_join[False] [gw3] [ 2%] FAILED tests/test_binary.py::test_set_union[False] tests/test_binary.py::test_set_union[same] [gw2] [ 2%] 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] [gw3] [ 2%] FAILED tests/test_binary.py::test_set_union[same] tests/test_binary.py::test_overlap[False] [gw2] [ 2%] 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] [gw1] [ 2%] 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] [gw0] [ 3%] PASSED tests/test_binary.py::test_join[False] tests/test_binary.py::test_join[same] [gw2] [ 3%] 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_chain7-method_chain7] [gw1] [ 3%] 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] [gw3] [ 3%] PASSED tests/test_binary.py::test_overlap[False] tests/test_binary.py::test_overlap[same] [gw2] [ 3%] 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] [gw0] [ 3%] PASSED tests/test_binary.py::test_join[same] tests/test_binary.py::test_join[opposite] [gw1] [ 4%] 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] [gw2] [ 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] [gw3] [ 4%] PASSED tests/test_binary.py::test_overlap[same] tests/test_binary.py::test_overlap[opposite] [gw1] [ 4%] 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] [gw2] [ 4%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain9-method_chain9] [gw0] [ 5%] PASSED tests/test_binary.py::test_join[opposite] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain10-method_chain10] tests/test_binary.py::test_reldist [gw1] [ 5%] 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_chain43-method_chain43] [gw3] [ 5%] PASSED tests/test_binary.py::test_overlap[opposite] tests/test_binary.py::test_intersect[False] [gw2] [ 5%] 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] [gw1] [ 5%] 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] [gw0] [ 6%] PASSED tests/test_binary.py::test_reldist tests/test_binary.py::test_k_nearest[downstream-False-opposite-last] [gw1] [ 6%] 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] [gw2] [ 6%] 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] [gw3] [ 6%] PASSED tests/test_binary.py::test_intersect[False] tests/test_binary.py::test_intersect[same] [gw0] [ 6%] FAILED tests/test_binary.py::test_k_nearest[downstream-False-opposite-last] tests/test_binary.py::test_k_nearest[downstream-False-same-last] [gw1] [ 6%] 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] [gw2] [ 7%] 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] [gw1] [ 7%] 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] [gw0] [ 7%] FAILED tests/test_binary.py::test_k_nearest[downstream-False-same-last] tests/test_binary.py::test_k_nearest[downstream-False-False-last] [gw2] [ 7%] 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] [gw1] [ 7%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain47-method_chain47] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain48-method_chain48] [gw1] [ 8%] 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] [gw3] [ 8%] PASSED tests/test_binary.py::test_intersect[same] tests/test_binary.py::test_intersect[opposite] [gw0] [ 8%] FAILED tests/test_binary.py::test_k_nearest[downstream-False-False-last] tests/test_binary.py::test_k_nearest[downstream-True-opposite-last] [gw2] [ 8%] 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] [gw1] [ 8%] 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] [gw0] [ 9%] FAILED tests/test_binary.py::test_k_nearest[downstream-True-opposite-last] tests/test_binary.py::test_k_nearest[downstream-True-same-last] [gw2] [ 9%] 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] [gw2] [ 9%] 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] [gw1] [ 9%] 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] [gw3] [ 9%] PASSED tests/test_binary.py::test_intersect[opposite] tests/test_binary.py::test_coverage[False] [gw0] [ 9%] FAILED tests/test_binary.py::test_k_nearest[downstream-True-same-last] tests/test_binary.py::test_k_nearest[downstream-True-False-last] [gw1] [ 10%] 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] [gw3] [ 10%] FAILED tests/test_binary.py::test_coverage[False] tests/test_binary.py::test_coverage[same] [gw2] [ 10%] 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] [gw2] [ 10%] 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_chain19-method_chain19] [gw0] [ 10%] FAILED tests/test_binary.py::test_k_nearest[downstream-True-False-last] tests/test_binary.py::test_k_nearest[upstream-False-opposite-last] [gw1] [ 11%] 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] [gw3] [ 11%] FAILED tests/test_binary.py::test_coverage[same] tests/test_binary.py::test_coverage[opposite] [gw0] [ 11%] FAILED tests/test_binary.py::test_k_nearest[upstream-False-opposite-last] tests/test_binary.py::test_k_nearest[upstream-False-same-last] [gw2] [ 11%] 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] [gw2] [ 11%] 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] [gw1] [ 12%] 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] [gw3] [ 12%] FAILED tests/test_binary.py::test_coverage[opposite] tests/test_binary.py::test_subtraction[same] [gw0] [ 12%] FAILED tests/test_binary.py::test_k_nearest[upstream-False-same-last] tests/test_binary.py::test_k_nearest[upstream-False-False-last] [gw1] [ 12%] 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_chain55-method_chain55] [gw2] [ 12%] 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] [ 12%] FAILED tests/test_binary.py::test_subtraction[same] tests/test_binary.py::test_subtraction[opposite] [gw0] [ 13%] FAILED tests/test_binary.py::test_k_nearest[upstream-False-False-last] tests/test_binary.py::test_k_nearest[upstream-True-opposite-last] [gw1] [ 13%] 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] [gw2] [ 13%] 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] [gw3] [ 13%] FAILED tests/test_binary.py::test_subtraction[opposite] tests/test_binary.py::test_subtraction[False] [gw0] [ 13%] FAILED tests/test_binary.py::test_k_nearest[upstream-True-opposite-last] tests/test_binary.py::test_k_nearest[upstream-True-same-last] [gw1] [ 14%] 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] [gw2] [ 14%] 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] [gw3] [ 14%] FAILED tests/test_binary.py::test_subtraction[False] tests/test_binary.py::test_nearest[None-True-False] [gw0] [ 14%] FAILED tests/test_binary.py::test_k_nearest[upstream-True-same-last] tests/test_binary.py::test_k_nearest[upstream-True-False-last] [gw1] [ 14%] 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] [gw0] [ 15%] FAILED tests/test_binary.py::test_k_nearest[upstream-True-False-last] tests/test_binary.py::test_k_nearest[None-False-opposite-last] [gw3] [ 15%] FAILED tests/test_binary.py::test_nearest[None-True-False] tests/test_binary.py::test_nearest[None-True-same] [gw2] [ 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] [gw1] [ 15%] 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] [gw3] [ 15%] FAILED tests/test_binary.py::test_nearest[None-True-same] tests/test_binary.py::test_nearest[None-True-opposite] [gw2] [ 16%] 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] [gw0] [ 16%] FAILED tests/test_binary.py::test_k_nearest[None-False-opposite-last] tests/test_binary.py::test_k_nearest[None-False-same-last] [gw1] [ 16%] 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] [gw3] [ 16%] FAILED tests/test_binary.py::test_nearest[None-True-opposite] tests/test_binary.py::test_nearest[None-False-False] [gw0] [ 16%] FAILED tests/test_binary.py::test_k_nearest[None-False-same-last] tests/test_binary.py::test_k_nearest[None-False-False-last] [gw2] [ 16%] 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] [gw1] [ 17%] 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] [gw0] [ 17%] FAILED tests/test_binary.py::test_k_nearest[None-False-False-last] tests/test_binary.py::test_k_nearest[None-True-opposite-last] [gw3] [ 17%] FAILED tests/test_binary.py::test_nearest[None-False-False] tests/test_binary.py::test_nearest[None-False-same] [gw2] [ 17%] 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] [gw1] [ 17%] 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] [gw3] [ 18%] FAILED tests/test_binary.py::test_nearest[None-False-same] tests/test_binary.py::test_nearest[None-False-opposite] [gw0] [ 18%] FAILED tests/test_binary.py::test_k_nearest[None-True-opposite-last] tests/test_binary.py::test_k_nearest[None-True-same-last] [gw2] [ 18%] 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] [gw1] [ 18%] 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] [gw0] [ 18%] FAILED tests/test_binary.py::test_k_nearest[None-True-same-last] tests/test_binary.py::test_k_nearest[None-True-False-last] [gw3] [ 19%] FAILED tests/test_binary.py::test_nearest[None-False-opposite] tests/test_binary.py::test_nearest[upstream-True-False] [gw2] [ 19%] 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] [gw0] [ 19%] FAILED tests/test_binary.py::test_k_nearest[None-True-False-last] tests/test_binary.py::test_k_nearest_1_vs_nearest [gw2] [ 19%] 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_chain31-method_chain31] [gw1] [ 19%] 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] [gw3] [ 19%] FAILED tests/test_binary.py::test_nearest[upstream-True-False] tests/test_binary.py::test_nearest[upstream-True-same] [gw0] [ 20%] FAILED tests/test_binary.py::test_k_nearest_1_vs_nearest tests/test_change_chromosome_custom.py::test_change_chromosomes [gw0] [ 20%] PASSED tests/test_change_chromosome_custom.py::test_change_chromosomes tests/test_concat.py::test_concat_stranded_unstranded [gw0] [ 20%] PASSED tests/test_concat.py::test_concat_stranded_unstranded tests/test_concat.py::test_concat_unstranded_unstranded [gw0] [ 20%] PASSED tests/test_concat.py::test_concat_unstranded_unstranded tests/test_concat.py::test_concat_unstranded_stranded [gw0] [ 20%] PASSED tests/test_concat.py::test_concat_unstranded_stranded tests/test_count_overlaps.py::test_strand_vs_strand_same [gw0] [ 21%] 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] [gw3] [ 21%] FAILED tests/test_binary.py::test_nearest[upstream-True-same] tests/test_binary.py::test_nearest[upstream-True-opposite] [gw1] [ 21%] 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] [gw2] [ 21%] 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] [gw1] [ 21%] 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] [gw2] [ 22%] 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] [gw0] [ 22%] 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] [ 22%] FAILED tests/test_binary.py::test_nearest[upstream-True-opposite] tests/test_binary.py::test_nearest[upstream-False-False] [gw0] [ 22%] 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_chain68-method_chain68] [gw2] [ 22%] 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] [gw1] [ 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_chain67-method_chain67] [gw3] [ 23%] FAILED tests/test_binary.py::test_nearest[upstream-False-False] tests/test_binary.py::test_nearest[upstream-False-same] [gw2] [ 23%] 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_chain116-method_chain116] [gw1] [ 23%] 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_chain158-method_chain158] [gw2] [ 23%] 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] [gw0] [ 23%] 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] [gw3] [ 24%] FAILED tests/test_binary.py::test_nearest[upstream-False-same] tests/test_binary.py::test_nearest[upstream-False-opposite] [gw0] [ 24%] 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] [gw1] [ 24%] 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] [gw2] [ 24%] 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] [gw2] [ 24%] 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] [ 25%] 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] [gw1] [ 25%] 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] [gw3] [ 25%] FAILED tests/test_binary.py::test_nearest[upstream-False-opposite] tests/test_binary.py::test_nearest[downstream-True-False] [gw2] [ 25%] 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] [ 25%] 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] [gw3] [ 25%] FAILED tests/test_binary.py::test_nearest[downstream-True-False] tests/test_binary.py::test_nearest[downstream-True-same] [gw0] [ 26%] 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] [gw3] [ 26%] FAILED tests/test_binary.py::test_nearest[downstream-True-same] tests/test_binary.py::test_nearest[downstream-True-opposite] [gw1] [ 26%] 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] [gw2] [ 26%] 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] [gw0] [ 26%] 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] [gw3] [ 27%] FAILED tests/test_binary.py::test_nearest[downstream-True-opposite] tests/test_binary.py::test_nearest[downstream-False-False] [gw1] [ 27%] 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_chain163-method_chain163] [gw2] [ 27%] 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] [gw1] [ 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] [gw0] [ 27%] 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] [gw3] [ 28%] FAILED tests/test_binary.py::test_nearest[downstream-False-False] tests/test_binary.py::test_nearest[downstream-False-same] [gw2] [ 28%] 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_chain123-method_chain123] [gw0] [ 28%] 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] [gw1] [ 28%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain164-method_chain164] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain165-method_chain165] [gw1] [ 28%] 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] [gw3] [ 29%] FAILED tests/test_binary.py::test_nearest[downstream-False-same] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain195-method_chain195] [gw3] [ 29%] 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] [gw2] [ 29%] 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] [gw1] [ 29%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain166-method_chain166] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain167-method_chain167] [gw0] [ 29%] 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] [gw1] [ 29%] 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] [gw3] [ 30%] 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] [gw2] [ 30%] 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] [gw0] [ 30%] 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_chain77-method_chain77] [gw1] [ 30%] 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] [gw3] [ 30%] 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_chain198-method_chain198] [gw2] [ 31%] 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] [gw0] [ 31%] 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] [gw3] [ 31%] 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] [ 31%] 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] [gw2] [ 31%] 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] [gw0] [ 32%] 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] [gw3] [ 32%] 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] [gw0] [ 32%] 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] [gw1] [ 32%] 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] [gw2] [ 32%] 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] [gw3] [ 32%] 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] [ 33%] 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] [gw1] [ 33%] 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] [ 33%] 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] [gw0] [ 33%] 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] [gw3] [ 33%] 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] [gw2] [ 34%] 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] [gw2] [ 34%] 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] [gw1] [ 34%] 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] [gw0] [ 34%] 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] [gw3] [ 34%] 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] [gw0] [ 35%] 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] [ 35%] 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] [gw2] [ 35%] 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] [gw2] [ 35%] 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] [gw3] [ 35%] 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] [gw0] [ 35%] 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] [gw1] [ 36%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain174-method_chain174] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain175-method_chain175] [gw2] [ 36%] 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] [gw3] [ 36%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain204-method_chain204] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain205-method_chain205] [gw0] [ 36%] 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] [ 36%] 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_chain176-method_chain176] [gw2] [ 37%] 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] [gw3] [ 37%] 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] [gw0] [ 37%] 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] [gw1] [ 37%] 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] [gw2] [ 37%] 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] [gw3] [ 38%] 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] [gw1] [ 38%] 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] [gw1] [ 38%] PASSED 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] [gw0] [ 38%] 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] [gw1] [ 38%] 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] [gw3] [ 38%] 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] [gw2] [ 39%] 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_chain137-method_chain137] [gw0] [ 39%] 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] [gw1] [ 39%] 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] [ 39%] 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] [gw3] [ 39%] 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_chain209-method_chain209] [gw0] [ 40%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain89-method_chain89] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain90-method_chain90] [gw2] [ 40%] 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] [gw1] [ 40%] 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] [gw3] [ 40%] 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] [gw0] [ 40%] 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] [gw1] [ 41%] 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] [gw2] [ 41%] 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] [gw3] [ 41%] 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] [gw0] [ 41%] 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] [gw2] [ 41%] 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] [gw1] [ 41%] 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] [gw3] [ 42%] 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] [gw3] [ 42%] 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] [gw0] [ 42%] 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_chain93-method_chain93] [gw3] [ 42%] PASSED 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] [gw0] [ 42%] 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] [gw3] [ 43%] 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] [gw1] [ 43%] 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_chain186-method_chain186] [gw2] [ 43%] 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] [gw3] [ 43%] 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] [gw1] [ 43%] 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_chain187-method_chain187] [gw2] [ 44%] 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] [gw3] [ 44%] 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] [gw0] [ 44%] 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] [gw2] [ 44%] 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_chain143-method_chain143] [gw0] [ 44%] 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] [gw1] [ 45%] 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] [gw3] [ 45%] 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] [gw0] [ 45%] 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] [gw0] [ 45%] 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] [gw2] [ 45%] 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] [gw2] [ 45%] 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] [gw1] [ 46%] 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] [gw3] [ 46%] 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_chain219-method_chain219] [gw0] [ 46%] 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] [gw2] [ 46%] 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] [gw2] [ 46%] 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] [ 47%] 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] [gw3] [ 47%] 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] [gw0] [ 47%] 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] [gw2] [ 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] [gw1] [ 47%] 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] [gw1] [ 48%] 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] [gw0] [ 48%] 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] [ 48%] 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] [gw2] [ 48%] 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] [gw1] [ 48%] 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] [gw0] [ 48%] 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] [gw1] [ 49%] 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] [gw3] [ 49%] 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] [gw2] [ 49%] 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_chain150-method_chain150] [gw0] [ 49%] 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] [gw1] [ 49%] 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_chain228-method_chain228] [gw3] [ 50%] 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] [gw2] [ 50%] 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] [gw1] [ 50%] 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_chain229-method_chain229] [gw0] [ 50%] 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] [gw3] [ 50%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain223-method_chain223] [gw2] [ 51%] 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_chain224-method_chain224] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain152-method_chain152] [gw1] [ 51%] 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] [gw1] [ 51%] 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] [gw0] [ 51%] 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] [gw3] [ 51%] 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] [gw2] [ 51%] 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] [gw1] [ 52%] 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_chain232-method_chain232] [gw0] [ 52%] 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] Sat May 11 14:02:41 UTC 2024 - pbuilder was killed by timeout after 18h.