Thu Feb 10 01:21:50 UTC 2022 I: starting to build python-deeptools/bullseye/amd64 on jenkins on '2022-02-10 01:21' Thu Feb 10 01:21:50 UTC 2022 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_11/101810/console.log Thu Feb 10 01:21:50 UTC 2022 I: Downloading source for bullseye/python-deeptools=3.5.0-1 --2022-02-10 01:21:51-- http://cdn-fastly.deb.debian.org/debian/pool/main/p/python-deeptools/python-deeptools_3.5.0-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2399 (2.3K) Saving to: ‘python-deeptools_3.5.0-1.dsc’ 0K .. 100% 124M=0s 2022-02-10 01:21:51 (124 MB/s) - ‘python-deeptools_3.5.0-1.dsc’ saved [2399/2399] Thu Feb 10 01:21:51 UTC 2022 I: python-deeptools_3.5.0-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: python-deeptools Binary: python3-deeptools Architecture: all Version: 3.5.0-1 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller Homepage: https://github.com/deeptools/deepTools Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/python-deeptools Vcs-Git: https://salsa.debian.org/med-team/python-deeptools.git Testsuite: autopkgtest, autopkgtest-pkg-python Testsuite-Triggers: python3-nose Build-Depends: debhelper-compat (= 13), dh-python, python3-all, python3-setuptools, python3-numpy, python3-scipy (>= 0.17.0), python3-matplotlib (>= 2.1.2), python3-pysam (>= 0.14.0), python3-py2bit, python3-numpydoc, python3-pybigwig, python3-plotly (>= 2.0.0), python3-deeptoolsintervals, python3-nose Package-List: python3-deeptools deb python optional arch=all Checksums-Sha1: 3fd42d68db28a4dbe19dcb534fe07117a09a6d43 24598524 python-deeptools_3.5.0.orig.tar.xz b33a427218bb57fde514ac62357909fe7e812df8 5724 python-deeptools_3.5.0-1.debian.tar.xz Checksums-Sha256: 532a5a8fd4de4a66158e1061dcb667b780e91fa78627c7a074c6d56171491759 24598524 python-deeptools_3.5.0.orig.tar.xz 110bebc7a39f7c504c6a55680fc10ee7fb53be18d34b4c7d6a9de4ecb1b2f4b1 5724 python-deeptools_3.5.0-1.debian.tar.xz Files: 1d1cc2a78f1e17b0a1a557593312f1dd 24598524 python-deeptools_3.5.0.orig.tar.xz 178f5c8b5699fb2e61291df5aec0be1b 5724 python-deeptools_3.5.0-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJHBAEBCAAxFiEEhMGXeonn7+0+XKYuL9i+2sAg7tEFAl9jafYTHG1vZWxsZXJA ZGViaWFuLm9yZwAKCRAv2L7awCDu0fa4D/0fVc0g2psKDPwZy+mX4/AIUa+YPDAf W+JoALr9gXdzNaIbpxsfBkmI5xvB24Z451fCKUqGyKs4ESEchrxUp0cF3owr8yIc dMEk8PWwxHTmVq7fhE/y7MHLSCqBiLGoZpxDUo0ojG76U+Cd4UFnnWTcO0sgNB3Q 9E9ZmyGkNmxjIpHfb4oYXpUa/bfgadhr+NV9lq7ujkJiCADELSqH3NiA3cI4G4PH V92dTU2XpP24BadBmWoZwvfglVOlmlVRDhBuaIfWbNrp9+jZfMOSgdJmUbioD26B aZKPIrnHd9IgLjwzlPb69l9gnNw0+MmMseYG4HxXy5v2RDydSHtLeQuIxwhveWBJ HlmGFCgZC8tU3v93TaG1sThC2c1lRIdC5NgFeN99sKw2ZMd+6efmUBvg007d/8kP H6ilzpODJLVqcEde25yL8YfEPIauwGfPelPv1uGhLIvrm9yaOCfcBF4LauNH++y0 OZ4c8HOasd4CH2IfrnZp4KtsJpQaiOLtUjqxqZaU9DFWwvw9mb9hwqw+9yVXFyId 1ZU+ctRr2wizybhV6T8IOuUhcYsJ6CvvVbivnHE7JO5SuV7T+5k3AX/7KRXadCbN +XfLqE2WcU2q+yAtgDYdFVsLDCU1F1UdK2fwDlmryT2938ex6aZhhn+68mwGmraS mX6f+Jax0Q+Jng== =9Ma+ -----END PGP SIGNATURE----- Thu Feb 10 01:21:51 UTC 2022 I: Checking whether the package is not for us Thu Feb 10 01:21:51 UTC 2022 I: Starting 1st build on remote node ionos1-amd64.debian.net. Thu Feb 10 01:21:51 UTC 2022 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Thu Feb 10 01:24:19 UTC 2022 I: Deleting $TMPDIR on ionos1-amd64.debian.net. W: cgroups are not available on the host, not using them. I: pbuilder: network access will be disabled during build I: Current time: Wed Feb 9 13:21:53 -12 2022 I: pbuilder-time-stamp: 1644456113 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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 [python-deeptools_3.5.0-1.dsc] I: copying [./python-deeptools_3.5.0.orig.tar.xz] I: copying [./python-deeptools_3.5.0-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.uHdPjS9j/trustedkeys.kbx': General error gpgv: Signature made Thu Sep 17 01:51:50 2020 -12 gpgv: using RSA key 84C1977A89E7EFED3E5CA62E2FD8BEDAC020EED1 gpgv: issuer "moeller@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./python-deeptools_3.5.0-1.dsc dpkg-source: info: extracting python-deeptools in python-deeptools-3.5.0 dpkg-source: info: unpacking python-deeptools_3.5.0.orig.tar.xz dpkg-source: info: unpacking python-deeptools_3.5.0-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying tmp_inhibit_test_readFiltering.patch dpkg-source: info: applying python2to3_for_executables.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2476865/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=15' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' IFS=' ' 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='2476865' 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/tmp.NgiJCkrLq2/pbuilderrc_jn3v --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.NgiJCkrLq2/b1 --logfile b1/build.log python-deeptools_3.5.0-1.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/sbin/chroot' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos1-amd64 5.10.0-11-amd64 #1 SMP Debian 5.10.92-1 (2022-01-18) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Aug 4 2021 bash -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash -rwxr-xr-x 1 root root 113664 Sep 23 2020 date -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd -rwxr-xr-x 1 root root 93936 Sep 23 2020 df -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir -rwxr-xr-x 1 root root 84440 Jul 28 2021 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 39680 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 69032 Jul 28 2021 findmnt -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 203072 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe -rwxr-xr-x 1 root root 98048 Mar 2 2021 gzip -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln -rwxr-xr-x 1 root root 56952 Feb 7 2020 login -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls -rwxr-xr-x 1 root root 149736 Jul 28 2021 lsblk -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 59632 Jul 28 2021 more -rwsr-xr-x 1 root root 55528 Jul 28 2021 mount -rwxr-xr-x 1 root root 18664 Jul 28 2021 mountpoint -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Aug 4 2021 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Feb 6 21:25 sh -> dash -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty -rwsr-xr-x 1 root root 71912 Jul 28 2021 su -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch -rwxr-xr-x 1 root root 39680 Sep 23 2020 true -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jul 28 2021 umount -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir -rwxr-xr-x 1 root root 63744 Jul 28 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew I: user script /srv/workspace/pbuilder/2476865/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: amd64 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-python, python3-all, python3-setuptools, python3-numpy, python3-scipy (>= 0.17.0), python3-matplotlib (>= 2.1.2), python3-pysam (>= 0.14.0), python3-py2bit, python3-numpydoc, python3-pybigwig, python3-plotly (>= 2.0.0), python3-deeptoolsintervals, python3-nose dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19655 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-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy (>= 0.17.0); however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib (>= 2.1.2); however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-pysam (>= 0.14.0); however: Package python3-pysam is not installed. pbuilder-satisfydepends-dummy depends on python3-py2bit; however: Package python3-py2bit is not installed. pbuilder-satisfydepends-dummy depends on python3-numpydoc; however: Package python3-numpydoc is not installed. pbuilder-satisfydepends-dummy depends on python3-pybigwig; however: Package python3-pybigwig is not installed. pbuilder-satisfydepends-dummy depends on python3-plotly (>= 2.0.0); however: Package python3-plotly is not installed. pbuilder-satisfydepends-dummy depends on python3-deeptoolsintervals; however: Package python3-deeptoolsintervals is not installed. pbuilder-satisfydepends-dummy depends on python3-nose; however: Package python3-nose 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} bsdextrautils{a} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} fonts-lyx{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbigwig0{a} libblas3{a} libbrotli1{a} libbsd0{a} libcurl3-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfreetype6{a} libgfortran5{a} libhts3{a} libicu67{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.4-2{a} libmagic-mgc{a} libmagic1{a} libmd0{a} libmpdec3{a} libnghttp2-14{a} libpipeline1{a} libpng16-16{a} libpsl5{a} libpython3-stdlib{a} libpython3.9{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libsub-override-perl{a} libtiff5{a} libtool{a} libuchardet0{a} libwebp6{a} libwebpdemux2{a} libwebpmux3{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxml2{a} m4{a} mailcap{a} man-db{a} media-types{a} mime-support{a} openssl{a} po-debconf{a} python-babel-localedata{a} python-matplotlib-data{a} python3{a} python3-alabaster{a} python3-all{a} python3-attr{a} python3-babel{a} python3-certifi{a} python3-chardet{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-deeptoolsintervals{a} python3-distutils{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-importlib-metadata{a} python3-ipython-genutils{a} python3-jinja2{a} python3-jsonschema{a} python3-jupyter-core{a} python3-kiwisolver{a} python3-lib2to3{a} python3-markupsafe{a} python3-matplotlib{a} python3-minimal{a} python3-more-itertools{a} python3-nbformat{a} python3-nose{a} python3-numpy{a} python3-numpydoc{a} python3-packaging{a} python3-pil{a} python3-pkg-resources{a} python3-plotly{a} python3-py2bit{a} python3-pybigwig{a} python3-pygments{a} python3-pyparsing{a} python3-pyrsistent{a} python3-pysam{a} python3-requests{a} python3-retrying{a} python3-roman{a} python3-scipy{a} python3-setuptools{a} python3-six{a} python3-snowballstemmer{a} python3-sphinx{a} python3-traitlets{a} python3-tz{a} python3-urllib3{a} python3-zipp{a} python3.9{a} python3.9-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} ttf-bitstream-vera{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libpaper-utils libsasl2-modules lynx publicsuffix python3-olefile python3-tk wget 0 packages upgraded, 142 newly installed, 0 to remove and 0 not upgraded. Need to get 72.5 MB of archives. After unpacking 308 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2 [96.9 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 mailcap all 3.69 [31.7 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 mime-support all 3.66 [10.9 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 sgml-base all 1.30 [15.1 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 openssl amd64 1.1.1k-1+deb11u1 [851 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 ca-certificates all 20210119 [158 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7 [693 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 python3-distutils all 3.9.2-1 [143 kB] Get: 51 http://deb.debian.org/debian bullseye/main amd64 dh-python all 4.20201102+nmu1 [99.4 kB] Get: 52 http://deb.debian.org/debian bullseye/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get: 53 http://deb.debian.org/debian bullseye/main amd64 docutils-common all 0.16+dfsg-4 [129 kB] Get: 54 http://deb.debian.org/debian bullseye/main amd64 fonts-lyx all 2.3.6-1 [205 kB] Get: 55 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get: 56 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1 [69.1 kB] Get: 57 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1 [106 kB] Get: 58 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3 [232 kB] Get: 59 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1 [77.1 kB] Get: 60 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get: 61 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 62 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2 [156 kB] Get: 63 http://deb.debian.org/debian bullseye/main amd64 libcurl3-gnutls amd64 7.74.0-1.3+deb11u1 [338 kB] Get: 64 http://deb.debian.org/debian bullseye/main amd64 libbigwig0 amd64 0.4.4+dfsg-2 [27.1 kB] Get: 65 http://deb.debian.org/debian bullseye/main amd64 libblas3 amd64 3.9.0-3 [153 kB] Get: 66 http://deb.debian.org/debian bullseye/main amd64 libmd0 amd64 1.0.3-3 [28.0 kB] Get: 67 http://deb.debian.org/debian bullseye/main amd64 libbsd0 amd64 0.11.3-1 [108 kB] Get: 68 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get: 69 http://deb.debian.org/debian bullseye/main amd64 libpng16-16 amd64 1.6.37-3 [294 kB] Get: 70 http://deb.debian.org/debian bullseye/main amd64 libfreetype6 amd64 2.10.4+dfsg-1 [418 kB] Get: 71 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get: 72 http://deb.debian.org/debian bullseye/main amd64 libhts3 amd64 1.11-4 [378 kB] Get: 73 http://deb.debian.org/debian bullseye/main amd64 libimagequant0 amd64 2.12.2-1.1 [32.5 kB] Get: 74 http://deb.debian.org/debian bullseye/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get: 75 http://deb.debian.org/debian bullseye/main amd64 libjpeg62-turbo amd64 1:2.0.6-4 [151 kB] Get: 76 http://deb.debian.org/debian bullseye/main amd64 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 77 http://deb.debian.org/debian bullseye/main amd64 libjs-jquery-ui all 1.12.1+dfsg-8+deb11u1 [232 kB] Get: 78 http://deb.debian.org/debian bullseye/main amd64 libjs-underscore all 1.9.1~dfsg-3 [100 kB] Get: 79 http://deb.debian.org/debian bullseye/main amd64 libjs-sphinxdoc all 3.4.3-2 [127 kB] Get: 80 http://deb.debian.org/debian bullseye/main amd64 liblapack3 amd64 3.9.0-3 [2166 kB] Get: 81 http://deb.debian.org/debian bullseye/main amd64 liblbfgsb0 amd64 3.0+dfsg.3-9 [28.5 kB] Get: 82 http://deb.debian.org/debian bullseye/main amd64 liblcms2-2 amd64 2.12~rc1-2 [150 kB] Get: 83 http://deb.debian.org/debian bullseye/main amd64 libpython3.9 amd64 3.9.2-1 [1691 kB] Get: 84 http://deb.debian.org/debian bullseye/main amd64 libwebp6 amd64 0.6.1-2.1 [258 kB] Get: 85 http://deb.debian.org/debian bullseye/main amd64 libtiff5 amd64 4.2.0-1 [289 kB] Get: 86 http://deb.debian.org/debian bullseye/main amd64 libwebpdemux2 amd64 0.6.1-2.1 [87.7 kB] Get: 87 http://deb.debian.org/debian bullseye/main amd64 libwebpmux3 amd64 0.6.1-2.1 [97.6 kB] Get: 88 http://deb.debian.org/debian bullseye/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 89 http://deb.debian.org/debian bullseye/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 90 http://deb.debian.org/debian bullseye/main amd64 libxcb1 amd64 1.14-3 [140 kB] Get: 91 http://deb.debian.org/debian bullseye/main amd64 python-babel-localedata all 2.8.0+dfsg.1-7 [4997 kB] Get: 92 http://deb.debian.org/debian bullseye/main amd64 ttf-bitstream-vera all 1.10-8.1 [223 kB] Get: 93 http://deb.debian.org/debian bullseye/main amd64 python-matplotlib-data all 3.3.4-1 [4153 kB] Get: 94 http://deb.debian.org/debian bullseye/main amd64 python3-alabaster all 0.7.8-1.1 [18.6 kB] Get: 95 http://deb.debian.org/debian bullseye/main amd64 python3-all amd64 3.9.2-3 [1056 B] Get: 96 http://deb.debian.org/debian bullseye/main amd64 python3-attr all 20.3.0-1 [52.9 kB] Get: 97 http://deb.debian.org/debian bullseye/main amd64 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 98 http://deb.debian.org/debian bullseye/main amd64 python3-tz all 2021.1-1 [34.8 kB] Get: 99 http://deb.debian.org/debian bullseye/main amd64 python3-babel all 2.8.0+dfsg.1-7 [100 kB] Get: 100 http://deb.debian.org/debian bullseye/main amd64 python3-certifi all 2020.6.20-1 [151 kB] Get: 101 http://deb.debian.org/debian bullseye/main amd64 python3-chardet all 4.0.0-1 [99.0 kB] Get: 102 http://deb.debian.org/debian bullseye/main amd64 python3-six all 1.16.0-2 [17.5 kB] Get: 103 http://deb.debian.org/debian bullseye/main amd64 python3-cycler all 0.10.0-3 [8084 B] Get: 104 http://deb.debian.org/debian bullseye/main amd64 python3-dateutil all 2.8.1-6 [79.2 kB] Get: 105 http://deb.debian.org/debian bullseye/main amd64 python3-decorator all 4.4.2-2 [15.8 kB] Get: 106 http://deb.debian.org/debian bullseye/main amd64 python3-deeptoolsintervals amd64 0.1.9-3+b2 [50.6 kB] Get: 107 http://deb.debian.org/debian bullseye/main amd64 python3-roman all 2.0.0-5 [9064 B] Get: 108 http://deb.debian.org/debian bullseye/main amd64 python3-docutils all 0.16+dfsg-4 [384 kB] Get: 109 http://deb.debian.org/debian bullseye/main amd64 python3-idna all 2.10-1 [37.4 kB] Get: 110 http://deb.debian.org/debian bullseye/main amd64 python3-imagesize all 1.2.0-2 [5824 B] Get: 111 http://deb.debian.org/debian bullseye/main amd64 python3-more-itertools all 4.2.0-3 [42.7 kB] Get: 112 http://deb.debian.org/debian bullseye/main amd64 python3-zipp all 1.0.0-3 [6060 B] Get: 113 http://deb.debian.org/debian bullseye/main amd64 python3-importlib-metadata all 1.6.0-2 [10.3 kB] Get: 114 http://deb.debian.org/debian bullseye/main amd64 python3-ipython-genutils all 0.2.0-4 [21.4 kB] Get: 115 http://deb.debian.org/debian bullseye/main amd64 python3-markupsafe amd64 1.1.1-1+b3 [15.2 kB] Get: 116 http://deb.debian.org/debian bullseye/main amd64 python3-jinja2 all 2.11.3-1 [114 kB] Get: 117 http://deb.debian.org/debian bullseye/main amd64 python3-setuptools all 52.0.0-4 [366 kB] Get: 118 http://deb.debian.org/debian bullseye/main amd64 python3-pyrsistent amd64 0.15.5-1+b3 [59.1 kB] Get: 119 http://deb.debian.org/debian bullseye/main amd64 python3-jsonschema all 3.2.0-3 [46.3 kB] Get: 120 http://deb.debian.org/debian bullseye/main amd64 python3-traitlets all 5.0.5-1 [84.4 kB] Get: 121 http://deb.debian.org/debian bullseye/main amd64 python3-jupyter-core all 4.7.1-1 [44.0 kB] Get: 122 http://deb.debian.org/debian bullseye/main amd64 python3-kiwisolver amd64 1.3.1-1+b1 [55.7 kB] Get: 123 http://deb.debian.org/debian bullseye/main amd64 python3-pyparsing all 2.4.7-1 [109 kB] Get: 124 http://deb.debian.org/debian bullseye/main amd64 python3-numpy amd64 1:1.19.5-1 [2693 kB] Get: 125 http://deb.debian.org/debian bullseye/main amd64 python3-pil amd64 8.1.2+dfsg-0.3 [445 kB] Get: 126 http://deb.debian.org/debian bullseye/main amd64 python3-matplotlib amd64 3.3.4-1 [4163 kB] Get: 127 http://deb.debian.org/debian bullseye/main amd64 python3-nbformat all 5.1.2-1 [51.6 kB] Get: 128 http://deb.debian.org/debian bullseye/main amd64 python3-nose all 1.3.7-7 [133 kB] Get: 129 http://deb.debian.org/debian bullseye/main amd64 sphinx-common all 3.4.3-2 [578 kB] Get: 130 http://deb.debian.org/debian bullseye/main amd64 python3-packaging all 20.9-2 [33.5 kB] Get: 131 http://deb.debian.org/debian bullseye/main amd64 python3-pygments all 2.7.1+dfsg-2.1 [657 kB] Get: 132 http://deb.debian.org/debian bullseye/main amd64 python3-urllib3 all 1.26.5-1~exp1 [114 kB] Get: 133 http://deb.debian.org/debian bullseye/main amd64 python3-requests all 2.25.1+dfsg-2 [69.3 kB] Get: 134 http://deb.debian.org/debian bullseye/main amd64 python3-snowballstemmer all 2.1.0-1 [58.7 kB] Get: 135 http://deb.debian.org/debian bullseye/main amd64 python3-sphinx all 3.4.3-2 [545 kB] Get: 136 http://deb.debian.org/debian bullseye/main amd64 python3-numpydoc all 1.1.0-3 [40.0 kB] Get: 137 http://deb.debian.org/debian bullseye/main amd64 python3-retrying all 1.3.3-4 [8876 B] Get: 138 http://deb.debian.org/debian bullseye/main amd64 python3-plotly all 4.14.3+dfsg-1 [2450 kB] Get: 139 http://deb.debian.org/debian bullseye/main amd64 python3-py2bit amd64 0.3.0-6+b1 [18.3 kB] Get: 140 http://deb.debian.org/debian bullseye/main amd64 python3-pybigwig amd64 0.3.17-1+b4 [35.8 kB] Get: 141 http://deb.debian.org/debian bullseye/main amd64 python3-pysam amd64 0.15.4+ds-3+b2 [1536 kB] Get: 142 http://deb.debian.org/debian bullseye/main amd64 python3-scipy amd64 1.6.0-2 [12.3 MB] Fetched 72.5 MB in 1s (59.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19655 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8_amd64.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../1-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_amd64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../3-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../4-man-db_2.9.4-2_amd64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package libpython3.9-minimal:amd64. Preparing to unpack .../5-libpython3.9-minimal_3.9.2-1_amd64.deb ... Unpacking libpython3.9-minimal:amd64 (3.9.2-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../6-libexpat1_2.2.10-2_amd64.deb ... Unpacking libexpat1:amd64 (2.2.10-2) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../7-python3.9-minimal_3.9.2-1_amd64.deb ... Unpacking python3.9-minimal (3.9.2-1) ... Setting up libpython3.9-minimal:amd64 (3.9.2-1) ... Setting up libexpat1:amd64 (2.2.10-2) ... Setting up python3.9-minimal (3.9.2-1) ... 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 ... 20522 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_amd64.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package mailcap. Preparing to unpack .../2-mailcap_3.69_all.deb ... Unpacking mailcap (3.69) ... Selecting previously unselected package mime-support. Preparing to unpack .../3-mime-support_3.66_all.deb ... Unpacking mime-support (3.66) ... Selecting previously unselected package libmpdec3:amd64. Preparing to unpack .../4-libmpdec3_2.5.1-1_amd64.deb ... Unpacking libmpdec3:amd64 (2.5.1-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../6-libreadline8_8.1-1_amd64.deb ... Unpacking libreadline8:amd64 (8.1-1) ... Selecting previously unselected package libpython3.9-stdlib:amd64. Preparing to unpack .../7-libpython3.9-stdlib_3.9.2-1_amd64.deb ... Unpacking libpython3.9-stdlib:amd64 (3.9.2-1) ... Selecting previously unselected package python3.9. Preparing to unpack .../8-python3.9_3.9.2-1_amd64.deb ... Unpacking python3.9 (3.9.2-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.9.2-3_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.9.2-3) ... Setting up python3-minimal (3.9.2-3) ... 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 ... 20967 files and directories currently installed.) Preparing to unpack .../000-python3_3.9.2-3_amd64.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.30_all.deb ... Unpacking sgml-base (1.30) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package openssl. Preparing to unpack .../003-openssl_1.1.1k-1+deb11u1_amd64.deb ... Unpacking openssl (1.1.1k-1+deb11u1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../004-ca-certificates_20210119_all.deb ... Unpacking ca-certificates (20210119) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-libmagic-mgc_1%3a5.39-3_amd64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../006-libmagic1_1%3a5.39-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.39-3) ... 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Setting up liblcms2-2:amd64 (2.12~rc1-2) ... Setting up libxau6:amd64 (1:1.0.9-1) ... Setting up libpsl5:amd64 (0.21.0-1.2) ... Setting up ttf-bitstream-vera (1.10-8.1) ... Setting up bsdextrautils (2.36.1-8) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:amd64 (67.1-7) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up fonts-lyx (2.3.6-1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:amd64 (1.0.9-2+b2) ... Setting up libnghttp2-14:amd64 (1.43.0-1) ... Setting up libmagic1:amd64 (1:5.39-3) ... Setting up libdeflate0:amd64 (1.7-1) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up libjbig0:amd64 (2.1-3.1+b2) ... Setting up python-babel-localedata (2.8.0+dfsg.1-7) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libblas3:amd64 (3.9.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libjpeg62-turbo:amd64 (1:2.0.6-4) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libsigsegv2:amd64 (2.13-1) ... Setting up libimagequant0:amd64 (2.12.2-1.1) ... Setting up libpng16-16:amd64 (1.6.37-3) ... Setting up autopoint (0.21-4) ... Setting up libwebp6:amd64 (0.6.1-2.1) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-2.1) ... Setting up libgfortran5:amd64 (10.2.1-6) ... Setting up libmd0:amd64 (1.0.3-3) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libmpdec3:amd64 (2.5.1-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libssh2-1:amd64 (1.9.0-2) ... Setting up sgml-base (1.30) ... Setting up libtiff5:amd64 (4.2.0-1) ... Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-7) ... Setting up python-matplotlib-data (3.3.4-1) ... Setting up openssl (1.1.1k-1+deb11u1) ... Setting up libwebpmux3:amd64 (0.6.1-2.1) ... Setting up libbsd0:amd64 (0.11.3-1) ... Setting up mailcap (3.69) ... Setting up libelf1:amd64 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7) ... Setting up libjs-underscore (1.9.1~dfsg-3) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up liblapack3:amd64 (3.9.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb1:amd64 (1.14-3) ... Setting up gettext (0.21-4) ... Setting up mime-support (3.66) ... Setting up libtool (2.4.6-15) ... Setting up libwebpdemux2:amd64 (0.6.1-2.1) ... Setting up libreadline8:amd64 (8.1-1) ... Setting up libldap-2.4-2:amd64 (2.4.57+dfsg-3) ... Setting up m4 (1.4.18-5) ... Setting up libcurl3-gnutls:amd64 (7.74.0-1.3+deb11u1) ... Setting up libbigwig0:amd64 (0.4.4+dfsg-2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 129 added, 0 removed; done. Setting up libjs-jquery-ui (1.12.1+dfsg-8+deb11u1) ... Setting up libfreetype6:amd64 (2.10.4+dfsg-1) ... Setting up libjs-sphinxdoc (3.4.3-2) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up xml-core (0.18+nmu1) ... Setting up libpython3.9-stdlib:amd64 (3.9.2-1) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.3-9) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libhts3:amd64 (1.11-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up libpython3.9:amd64 (3.9.2-1) ... Setting up sphinx-common (3.4.3-2) ... Setting up python3.9 (3.9.2-1) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Setting up python3-markupsafe (1.1.1-1+b3) ... Setting up python3-tz (2021.1-1) ... Setting up python3-six (1.16.0-2) ... Setting up python3-pil:amd64 (8.1.2+dfsg-0.3) ... Setting up python3-roman (2.0.0-5) ... Setting up python3-decorator (4.4.2-2) ... Setting up python3-jinja2 (2.11.3-1) ... Setting up python3-pyparsing (2.4.7-1) ... Setting up python3-certifi (2020.6.20-1) ... Setting up python3-snowballstemmer (2.1.0-1) ... Setting up python3-cycler (0.10.0-3) ... Setting up python3-kiwisolver (1.3.1-1+b1) ... Setting up python3-idna (2.10-1) ... Setting up python3-urllib3 (1.26.5-1~exp1) ... Setting up python3-pyrsistent:amd64 (0.15.5-1+b3) ... Setting up python3-dateutil (2.8.1-6) ... Setting up python3-py2bit (0.3.0-6+b1) ... Setting up python3-lib2to3 (3.9.2-1) ... Setting up python3-imagesize (1.2.0-2) ... Setting up python3-pkg-resources (52.0.0-4) ... Setting up python3-distutils (3.9.2-1) ... Setting up dh-python (4.20201102+nmu1) ... Setting up python3-more-itertools (4.2.0-3) ... Setting up python3-attr (20.3.0-1) ... Setting up python3-pysam (0.15.4+ds-3+b2) ... Setting up python3-setuptools (52.0.0-4) ... Setting up python3-babel (2.8.0+dfsg.1-7) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-deeptoolsintervals (0.1.9-3+b2) ... Setting up python3-ipython-genutils (0.2.0-4) ... Setting up python3-alabaster (0.7.8-1.1) ... Setting up python3-retrying (1.3.3-4) ... Setting up python3-all (3.9.2-3) ... Setting up python3-zipp (1.0.0-3) ... Setting up python3-nose (1.3.7-7) ... Setting up python3-pygments (2.7.1+dfsg-2.1) ... Setting up python3-packaging (20.9-2) ... Setting up python3-chardet (4.0.0-1) ... Setting up python3-requests (2.25.1+dfsg-2) ... Setting up python3-numpy (1:1.19.5-1) ... Setting up python3-pybigwig (0.3.17-1+b4) ... Setting up python3-traitlets (5.0.5-1) ... Setting up python3-jupyter-core (4.7.1-1) ... Setting up python3-matplotlib (3.3.4-1) ... Setting up python3-scipy (1.6.0-2) ... Setting up python3-importlib-metadata (1.6.0-2) ... Setting up python3-jsonschema (3.2.0-3) ... Setting up python3-nbformat (5.1.2-1) ... Setting up python3-plotly (4.14.3+dfsg-1) ... Processing triggers for libc-bin (2.31-13+deb11u2) ... Processing triggers for sgml-base (1.30) ... Setting up docutils-common (0.16+dfsg-4) ... Processing triggers for sgml-base (1.30) ... Setting up python3-docutils (0.16+dfsg-4) ... update-alternatives: using /usr/share/docutils/scripts/python3/rst-buildhtml to provide /usr/bin/rst-buildhtml (rst-buildhtml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html to provide /usr/bin/rst2html (rst2html) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html4 to provide /usr/bin/rst2html4 (rst2html4) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html5 to provide /usr/bin/rst2html5 (rst2html5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2latex to provide /usr/bin/rst2latex (rst2latex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2man to provide /usr/bin/rst2man (rst2man) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt to provide /usr/bin/rst2odt (rst2odt) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt_prepstyles to provide /usr/bin/rst2odt_prepstyles (rst2odt_prepstyles) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2pseudoxml to provide /usr/bin/rst2pseudoxml (rst2pseudoxml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2s5 to provide /usr/bin/rst2s5 (rst2s5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2xetex to provide /usr/bin/rst2xetex (rst2xetex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2xml to provide /usr/bin/rst2xml (rst2xml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rstpep2html to provide /usr/bin/rstpep2html (rstpep2html) in auto mode Setting up python3-sphinx (3.4.3-2) ... Setting up python3-numpydoc (1.1.0-3) ... Processing triggers for ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 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/python-deeptools-3.5.0/ && 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 > ../python-deeptools_3.5.0-1_source.changes dpkg-buildpackage: info: source package python-deeptools dpkg-buildpackage: info: source version 3.5.0-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Steffen Moeller dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from python-deeptools-3.5.0/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/python-deeptools-3.5.0' dh_auto_clean install -d /build/python-deeptools-3.5.0/debian/.debhelper/generated/_source/home pybuild --clean --test-nose -i python{version} -p 3.9 I: pybuild base:232: python3.9 setup.py clean running clean removing '/build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.9' does not exist -- can't clean it rm -rf .pybuild/ find . -name \*.pyc -exec rm {} \; rm -rf .pytest_cache deeptools/__pycache__ make[1]: Leaving directory '/build/python-deeptools-3.5.0' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/python3-deeptools.substvars debian/files rm -fr -- debian/python3-deeptools/ debian/tmp/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild install -d /build/python-deeptools-3.5.0/debian/.debhelper/generated/_source/home pybuild --configure --test-nose -i python{version} -p 3.9 I: pybuild base:232: python3.9 setup.py config running config dh_auto_build -O--buildsystem=pybuild pybuild --build --test-nose -i python{version} -p 3.9 I: pybuild base:232: /usr/bin/python3 setup.py build running build running build_py creating /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/writeBedGraph_bam_and_bw.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/plotProfile.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/plotHeatmap.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/plotFingerprint.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/plotEnrichment.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/plotCoverage.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/plotCorrelation.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/multiBigwigSummary.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/multiBamSummary.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/getScaleFactor.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/estimateReadFiltering.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/deeptools_list_tools.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/deepBlue.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/correctGCBias.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/computeMatrixOperations.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/computeMatrix.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/computeGCBias.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/bigwigCompare.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/bamPEFragmentSize.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/bamCoverage.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/bamCompare.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/alignmentSieve.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/SES_scaleFactor.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/plotPCA.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/writeBedGraph.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/utilities.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/sumCoveragePerBin.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/parserCommon.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/misc.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/mapReduce.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/heatmapper_utilities.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/heatmapper.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/getScorePerBigWigBin.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/getRatio.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/getFragmentAndReadSize.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/countReadsPerBin.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/correlation_heatmap.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/correlation.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/cm.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/bamHandler.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/_version.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools copying deeptools/__init__.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools creating /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/test copying deeptools/test/test_readFiltering.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/test copying deeptools/test/testskip_heatmapper_images.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/test copying deeptools/test/test_writeBedGraph.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/test copying deeptools/test/test_tools.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/test copying deeptools/test/test_plotCoverage.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/test copying deeptools/test/test_multiBamSummary.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/test copying deeptools/test/test_heatmapper.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/test copying deeptools/test/test_countReadsPerBin.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/test copying deeptools/test/test_computeMatrixOperations.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/test copying deeptools/test/test_bigwigCompare_and_multiBigwigSummary.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/test copying deeptools/test/test_bamCoverage_and_bamCompare.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/test copying deeptools/test/__init__.py -> /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/test running egg_info creating deepTools.egg-info writing deepTools.egg-info/PKG-INFO writing dependency_links to deepTools.egg-info/dependency_links.txt writing requirements to deepTools.egg-info/requires.txt writing top-level names to deepTools.egg-info/top_level.txt writing manifest file 'deepTools.egg-info/SOURCES.txt' reading manifest file 'deepTools.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files found matching 'examples/*' warning: no previously-included files found matching 'galaxy/*' warning: no previously-included files found matching 'gallery/*' writing manifest file 'deepTools.egg-info/SOURCES.txt' running build_scripts creating build creating build/scripts-3.9 copying and adjusting bin/bamCompare -> build/scripts-3.9 copying and adjusting bin/bamCoverage -> build/scripts-3.9 copying and adjusting bin/multiBamSummary -> build/scripts-3.9 copying and adjusting bin/plotHeatmap -> build/scripts-3.9 copying and adjusting bin/plotFingerprint -> build/scripts-3.9 copying and adjusting bin/estimateScaleFactor -> build/scripts-3.9 copying and adjusting bin/bamPEFragmentSize -> build/scripts-3.9 copying and adjusting bin/computeMatrix -> build/scripts-3.9 copying and adjusting bin/plotProfile -> build/scripts-3.9 copying and adjusting bin/computeGCBias -> build/scripts-3.9 copying and adjusting bin/correctGCBias -> build/scripts-3.9 copying and adjusting bin/multiBigwigSummary -> build/scripts-3.9 copying and adjusting bin/bigwigCompare -> build/scripts-3.9 copying and adjusting bin/plotCoverage -> build/scripts-3.9 copying and adjusting bin/plotPCA -> build/scripts-3.9 copying and adjusting bin/plotCorrelation -> build/scripts-3.9 copying and adjusting bin/plotEnrichment -> build/scripts-3.9 copying and adjusting bin/deeptools -> build/scripts-3.9 copying and adjusting bin/computeMatrixOperations -> build/scripts-3.9 copying and adjusting bin/estimateReadFiltering -> build/scripts-3.9 copying and adjusting bin/alignmentSieve -> build/scripts-3.9 changing mode of build/scripts-3.9/bamCompare from 644 to 755 changing mode of build/scripts-3.9/bamCoverage from 644 to 755 changing mode of build/scripts-3.9/multiBamSummary from 644 to 755 changing mode of build/scripts-3.9/plotHeatmap from 644 to 755 changing mode of build/scripts-3.9/plotFingerprint from 644 to 755 changing mode of build/scripts-3.9/estimateScaleFactor from 644 to 755 changing mode of build/scripts-3.9/bamPEFragmentSize from 644 to 755 changing mode of build/scripts-3.9/computeMatrix from 644 to 755 changing mode of build/scripts-3.9/plotProfile from 644 to 755 changing mode of build/scripts-3.9/computeGCBias from 644 to 755 changing mode of build/scripts-3.9/correctGCBias from 644 to 755 changing mode of build/scripts-3.9/multiBigwigSummary from 644 to 755 changing mode of build/scripts-3.9/bigwigCompare from 644 to 755 changing mode of build/scripts-3.9/plotCoverage from 644 to 755 changing mode of build/scripts-3.9/plotPCA from 644 to 755 changing mode of build/scripts-3.9/plotCorrelation from 644 to 755 changing mode of build/scripts-3.9/plotEnrichment from 644 to 755 changing mode of build/scripts-3.9/deeptools from 644 to 755 changing mode of build/scripts-3.9/computeMatrixOperations from 644 to 755 changing mode of build/scripts-3.9/estimateReadFiltering from 644 to 755 changing mode of build/scripts-3.9/alignmentSieve from 644 to 755 debian/rules override_dh_auto_test make[1]: Entering directory '/build/python-deeptools-3.5.0' PYTHONPATH=/build/python-deeptools-3.5.0 nosetests3 -x -v -s deeptools Test minimal command line args for bamCoverage ... bamFilesList: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/testB.bam'] binLength: 50 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 50 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 bamFilesList: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/testB.cram'] binLength: 50 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 50 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 ok deeptools.test.test_bamCoverage_and_bamCompare.test_bam_coverage_extend ... bamFilesList: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/testB.bam'] binLength: 50 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: 100 numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 50 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 400 bamFilesList: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/testB.cram'] binLength: 50 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: 100 numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 50 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 400 ok deeptools.test.test_bamCoverage_and_bamCompare.test_bam_coverage_extend_and_normalizeUsingRPGC ... normalization: 1x (effective genome size 200) bamFilesList: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/testB.bam'] binLength: 50 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: 100 numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 50 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 400 normalization: 1x (effective genome size 200) bamFilesList: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/testB.cram'] binLength: 50 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: 100 numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 50 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 400 ok deeptools.test.test_bamCoverage_and_bamCompare.test_bam_coverage_skipnas ... bamFilesList: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/testB.bam'] binLength: 50 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 50 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: True smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 bamFilesList: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/testB.cram'] binLength: 50 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 50 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: True smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 ok deeptools.test.test_bamCoverage_and_bamCompare.test_bam_coverage_filtering ... Specified --scaleFactor: 1.0 bamFilesList: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/testB.bam'] binLength: 50 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: True region: None bedFile: None minMappingQuality: None ignoreDuplicates: True chrsToSkip: [] stepSize: 50 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 Specified --scaleFactor: 1.0 bamFilesList: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/testB.cram'] binLength: 50 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: True region: None bedFile: None minMappingQuality: None ignoreDuplicates: True chrsToSkip: [] stepSize: 50 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 ok Test minimal command line args for bamCoverage. The ratio ... bamFilesList: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/testB.bam', '/build/python-deeptools-3.5.0/deeptools/test/test_data/testB.bam'] binLength: 50 numberOfSamples: 0 blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 50 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 bamFilesList: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/testB.cram', '/build/python-deeptools-3.5.0/deeptools/test/test_data/testB.cram'] binLength: 50 numberOfSamples: 0 blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 50 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 ok Test with two different files ... The following chromosome names did not match between the the bam files chromosome length chr_cigar 200 bamFilesList: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/testA.bam', '/build/python-deeptools-3.5.0/deeptools/test/test_data/testB.bam'] binLength: 50 numberOfSamples: 0 blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 50 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 The following chromosome names did not match between the the bam files chromosome length chr_cigar 200 bamFilesList: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/testA.cram', '/build/python-deeptools-3.5.0/deeptools/test/test_data/testB.cram'] binLength: 50 numberOfSamples: 0 blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 50 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 ok Test with different pseudocounts ... The following chromosome names did not match between the the bam files chromosome length chr_cigar 200 bamFilesList: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/testA.bam', '/build/python-deeptools-3.5.0/deeptools/test/test_data/testB.bam'] binLength: 50 numberOfSamples: 0 blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 50 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 ok Ensure --skipZeroOverZero works in bamCompare ... The following chromosome names did not match between the the bam files chromosome length chr_cigar 200 bamFilesList: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/testA.bam', '/build/python-deeptools-3.5.0/deeptools/test/test_data/testB.bam'] binLength: 50 numberOfSamples: 0 blackListFileName: None skipZeroOverZero: True bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 50 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 ok Test the scale factor functions ... ok Test skipnas ... The following chromosome names did not match between the the bam files chromosome length chr_cigar 200 bamFilesList: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/testA.bam', '/build/python-deeptools-3.5.0/deeptools/test/test_data/testB.bam'] binLength: 50 numberOfSamples: 0 blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 50 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: True smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 The following chromosome names did not match between the the bam files chromosome length chr_cigar 200 bamFilesList: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/testA.cram', '/build/python-deeptools-3.5.0/deeptools/test/test_data/testB.cram'] binLength: 50 numberOfSamples: 0 blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 50 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: True smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 ok Test read extension ... The following chromosome names did not match between the the bam files chromosome length chr_cigar 200 bamFilesList: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/testA.bam', '/build/python-deeptools-3.5.0/deeptools/test/test_data/testB.bam'] binLength: 50 numberOfSamples: 0 blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: 100 numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 50 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 400 The following chromosome names did not match between the the bam files chromosome length chr_cigar 200 bamFilesList: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/testA.cram', '/build/python-deeptools-3.5.0/deeptools/test/test_data/testB.cram'] binLength: 50 numberOfSamples: 0 blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: 100 numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 50 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 400 ok Test scale factor ... The following chromosome names did not match between the the bam files chromosome length chr_cigar 200 bamFilesList: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/testA.bam', '/build/python-deeptools-3.5.0/deeptools/test/test_data/testB.bam'] binLength: 50 numberOfSamples: 0 blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: ['chr_cigar'] stepSize: 50 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 The following chromosome names did not match between the the bam files chromosome length chr_cigar 200 bamFilesList: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/testA.cram', '/build/python-deeptools-3.5.0/deeptools/test/test_data/testB.cram'] binLength: 50 numberOfSamples: 0 blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: ['chr_cigar'] stepSize: 50 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 ok Test scale factor ... normalization: CPM normalization: CPM The following chromosome names did not match between the the bam files chromosome length chr_cigar 200 bamFilesList: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/testA.bam', '/build/python-deeptools-3.5.0/deeptools/test/test_data/testB.bam'] binLength: 50 numberOfSamples: 0 blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: ['chr_cigar'] stepSize: 50 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 normalization: CPM normalization: CPM The following chromosome names did not match between the the bam files chromosome length chr_cigar 200 bamFilesList: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/testA.cram', '/build/python-deeptools-3.5.0/deeptools/test/test_data/testB.cram'] binLength: 50 numberOfSamples: 0 blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: ['chr_cigar'] stepSize: 50 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 ok Test --samFlagInclude --samFlagExclude --minMappingQuality --ignoreDuplicates and --blackListFileName ... normalization: 1x (effective genome size 1400) bamFilesList: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/test_filtering.bam'] binLength: 50 numberOfSamples: None blackListFileName: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/test_filtering.blacklist.bed'] skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: 5 ignoreDuplicates: True chrsToSkip: [] stepSize: 50 center_read: False samFlag_include: 512 samFlag_exclude: 256 minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 normalization: 1x (effective genome size 1400) bamFilesList: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/test_filtering.cram'] binLength: 50 numberOfSamples: None blackListFileName: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/test_filtering.blacklist.bed'] skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: 5 ignoreDuplicates: True chrsToSkip: [] stepSize: 50 center_read: False samFlag_include: 512 samFlag_exclude: 256 minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 ok Test -bs 1 --Offset 1 ... bamFilesList: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/testA.bam'] binLength: 1 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 1 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 filter_strand: None Offset: [1] bamFilesList: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/testA.cram'] binLength: 1 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 1 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 filter_strand: None Offset: [1] ok Test -bs 1 --Offset 1 10 ... bamFilesList: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/testA.bam'] binLength: 1 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 1 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 filter_strand: None Offset: [1, 10] bamFilesList: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/testA.cram'] binLength: 1 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 1 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 filter_strand: None Offset: [1, 10] ok Test -bs 1 --Offset -1 ... bamFilesList: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/testA.bam'] binLength: 1 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 1 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 filter_strand: None Offset: [-1] bamFilesList: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/testA.cram'] binLength: 1 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 1 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 filter_strand: None Offset: [-1] ok Test -bs 1 --Offset 20 -4 ... bamFilesList: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/testA.bam'] binLength: 1 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 1 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 filter_strand: None Offset: [20, -4] bamFilesList: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/testA.cram'] binLength: 1 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 1 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 filter_strand: None Offset: [20, -4] ok Test --samFlagInclude --samFlagExclude --minMappingQuality --ignoreDuplicates and --blackListFileName ... bamFilesList: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/test_filtering.bam', '/build/python-deeptools-3.5.0/deeptools/test/test_data/test_filtering2.bam'] binLength: 50 numberOfSamples: 0 blackListFileName: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/test_filtering.blacklist.bed'] skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: 5 ignoreDuplicates: True chrsToSkip: [] stepSize: 50 center_read: False samFlag_include: 512 samFlag_exclude: 256 minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 bamFilesList: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/test_filtering.cram', '/build/python-deeptools-3.5.0/deeptools/test/test_data/test_filtering2.cram'] binLength: 50 numberOfSamples: 0 blackListFileName: ['/build/python-deeptools-3.5.0/deeptools/test/test_data/test_filtering.blacklist.bed'] skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: 5 ignoreDuplicates: True chrsToSkip: [] stepSize: 50 center_read: False samFlag_include: 512 samFlag_exclude: 256 minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 ok deeptools.test.test_bigwigCompare_and_multiBigwigSummary.test_bigwigCompare ... ok deeptools.test.test_bigwigCompare_and_multiBigwigSummary.test_bigwigCompare_skipnas ... ok deeptools.test.test_bigwigCompare_and_multiBigwigSummary.test_bigwigCompare_skipZeroOverZero ... ok deeptools.test.test_bigwigCompare_and_multiBigwigSummary.test_multiBigwigSummary ... The following chromosome names did not match between the bigwig files chromosome length chr_cigar 200 Number of bins found: 4 ok Test multiBigwigSummary raw counts output ... The following chromosome names did not match between the bigwig files chromosome length chr_cigar 200 *Warning* The resulting bed file does not contain information for the chromosomes that were not common between the bigwig files Number of bins found: 4 ok deeptools.test.test_bigwigCompare_and_multiBigwigSummary.test_multiBigwigSummary_gtf ... Number of bins found: 2 ok deeptools.test.test_bigwigCompare_and_multiBigwigSummary.test_multiBigwigSummary_metagene ... Number of bins found: 2 ok computeMatrixOperations relabel ... ok computeMatrixOperations subset ... ok computeMatrixOperations cbind ... ok computeMatrixOperations filterStrand ... ok computeMatrixOperations rbind ... ok computeMatrixOperations rbind with different groups ... ok computeMatrixOperations sort ... ok deeptools.test.test_countReadsPerBin.TestCountReadsPerBin.test_bed_file ... ok deeptools.test.test_countReadsPerBin.TestCountReadsPerBin.test_countReadsInRegions_min_mapping_quality ... ok deeptools.test.test_countReadsPerBin.TestCountReadsPerBin.test_count_reads_in_region ... ok In this case when read extension is smaller than read length ... *WARNING*: read extension is smaller than read length (read length = 50). Reads will not be extended. ok deeptools.test.test_countReadsPerBin.TestCountReadsPerBin.test_count_reads_in_region_ignore_bed_regions ... ok deeptools.test.test_countReadsPerBin.TestCountReadsPerBin.test_count_reads_in_region_ignore_duplicates ... ok count the reads over the whole region ... ok deeptools.test.test_countReadsPerBin.TestCountReadsPerBin.test_get_coverage_of_region_ignore_duplicates ... ok deeptools.test.test_countReadsPerBin.TestCountReadsPerBin.test_get_coverage_of_region_large_bin ... ok deeptools.test.test_countReadsPerBin.TestCountReadsPerBin.test_get_coverage_of_region_sam_flag_exclude ... ok deeptools.test.test_countReadsPerBin.TestCountReadsPerBin.test_get_coverage_of_region_sam_flag_include ... ok The bamFile1 contains a read at position 10 ... ok deeptools.test.test_countReadsPerBin.TestCountReadsPerBin.test_get_coverage_of_region_zeros_to_nan ... ok deeptools.test.test_countReadsPerBin.TestCountReadsPerBinCRAM.test_bed_file ... ok deeptools.test.test_countReadsPerBin.TestCountReadsPerBinCRAM.test_countReadsInRegions_min_mapping_quality ... ok deeptools.test.test_countReadsPerBin.TestCountReadsPerBinCRAM.test_count_reads_in_region ... ok In this case when read extension is smaller than read length ... *WARNING*: read extension is smaller than read length (read length = 50). Reads will not be extended. ok deeptools.test.test_countReadsPerBin.TestCountReadsPerBinCRAM.test_count_reads_in_region_ignore_bed_regions ... ok deeptools.test.test_countReadsPerBin.TestCountReadsPerBinCRAM.test_count_reads_in_region_ignore_duplicates ... ok count the reads over the whole region ... ok deeptools.test.test_countReadsPerBin.TestCountReadsPerBinCRAM.test_get_coverage_of_region_ignore_duplicates ... ok deeptools.test.test_countReadsPerBin.TestCountReadsPerBinCRAM.test_get_coverage_of_region_large_bin ... ok deeptools.test.test_countReadsPerBin.TestCountReadsPerBinCRAM.test_get_coverage_of_region_sam_flag_exclude ... ok deeptools.test.test_countReadsPerBin.TestCountReadsPerBinCRAM.test_get_coverage_of_region_sam_flag_include ... ok The bamFile1 contains a read at position 10 ... ok deeptools.test.test_countReadsPerBin.TestCountReadsPerBinCRAM.test_get_coverage_of_region_zeros_to_nan ... ok deeptools.test.test_heatmapper.test_computeMatrix_reference_point ... ok deeptools.test.test_heatmapper.test_computeMatrix_reference_point_center ... ok deeptools.test.test_heatmapper.test_computeMatrix_reference_point_tes ... ok deeptools.test.test_heatmapper.test_computeMatrix_reference_point_missing_data_as_zero ... ok deeptools.test.test_heatmapper.test_computeMatrix_scale_regions ... ok deeptools.test.test_heatmapper.test_computeMatrix_multiple_bed ... ok deeptools.test.test_heatmapper.test_computeMatrix_region_extend_over_chr_end ... ok deeptools.test.test_heatmapper.test_computeMatrix_unscaled ... ok deeptools.test.test_heatmapper.test_computeMatrix_gtf ... ok deeptools.test.test_heatmapper.test_computeMatrix_metagene ... ok deeptools.test.test_heatmapper.test_chopRegions_body ... ok deeptools.test.test_heatmapper.test_chopRegions_TSS ... ok deeptools.test.test_heatmapper.test_chopRegions_TES ... ok deeptools.test.test_heatmapper.test_chopRegionsFromMiddle ... ok deeptools.test.test_multiBamSummary.test_multiBamSummary_gtf ... Number of bins found: 2 Number of bins found: 2 ok deeptools.test.test_multiBamSummary.test_multiBamSummary_metagene ... Number of bins found: 2 Number of bins found: 2 ok deeptools.test.test_multiBamSummary.test_multiBamSummary_scalingFactors ... The following chromosome names did not match between the the bam files chromosome length chr_cigar 200 Number of bins found: 4 /build/python-deeptools-3.5.0/deeptools/test/test_multiBamSummary.py:54: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/test.scalingFactors.txt' mode='r' encoding='UTF-8'> ok deeptools.test.test_plotCoverage.test_plotCoverage_default ... ok Minimal testing ... ok --minMappingQuality 10 --samFlagExclude 512 --ignoreDuplicates -bl ... ok Test alignmentSieve with the --BED option ... [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_9je26u1l.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_k50b7jr7.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_dh8_rl8_.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_d182vsml.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_nigzlg9w.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_p8g4dfnb.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_rxezhlf3.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_f8htz5wx.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_561u06zw.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools__qjbs_bv.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_mxcpwrnl.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_meg2uqfh.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_scneuqeg.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_6f1rb2g6.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_ahtjoyhp.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_z4nllytf.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_hsbss4kp.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_n6m7ztmg.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_w757q1ny.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_pa2cy5jv.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_fc6jvz07.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_d6b068rd.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_y4f9jbxr.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_c9mficmh.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_ygx127_l.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_zkw8vcx6.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_kxhw0fcq.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_9x3ekiuk.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_gcsxqz4t.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_ygx_034s.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_pzhgbb4d.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_952_mwsz.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools__akdnhp2.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_3hi6hi08.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_nlpmlpv_.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_45c87a51.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_ppt9x_7l.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_gxy3ko4d.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_88irbcr7.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_ceolufwe.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_y11l6tsn.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_axr1rvji.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_kl1j8ghj.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_tj840ty_.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools__k0x8w33.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_v7o61q0y.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_j17dz7kf.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_jf_w5oo2.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_rsnwdgm7.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools__rmojdj6.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_v1f3uiyf.bam' ok Test filtering a BAM file by MAPQ, flag, and blacklist ... SKIP: Skip this test (see )https://github.com/deeptools/deepTools/issues/903 Test alignmentSieve --BED --shift ... [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_lttn1bkf.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools__hv3p674.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_li__akx1.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_ti_fcf_g.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_5s09513p.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_qhkuvsot.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_58oecwkh.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_eapwgxcy.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_vy3qbxgj.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_lregf_tf.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_bvkjq0wm.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_z23qlgkx.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_la9cwyy2.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_9g3wz7tj.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_1oxvg7sa.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools__ehn3jc3.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_74uqp61j.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_yi_8q5us.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_t0p2q5ih.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_heciihn2.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_34qfgakk.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_s_w_123w.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_p8paxara.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_o1qd2au2.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_9b7boot2.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_btdz438m.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_u3gy9zhf.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_uioezakm.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_17m69rch.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_f5fv2h9z.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_75360w9n.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_b38i2_uk.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_3j_af5dt.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_a1lz0qf6.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_nbxpnngc.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_2_tz4k4b.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_vpmosyqn.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_7ev45kmf.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_mlabdawr.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_7i_51ui5.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_dgdzkatj.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_zdlaemt2.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_n3dj3214.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_8fz0fydp.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_yk1gabbu.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_byp74qse.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_2uxqkqnz.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_rnb9aeqm.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_q91k4lxr.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_nj7ppav2.bam' [E::idx_find_and_load] Could not retrieve index file for '/tmp/_deeptools_rf2vmih_.bam' ok Checks everything that is in /bin/ ... plotProfile 3.5.0 plotPCA 3.5.0 plotHeatmap 3.5.0 plotFingerprint 3.5.0 plotEnrichment 3.5.0 plotCoverage 3.5.0 plotCorrelation 3.5.0 multiBigwigSummary 3.5.0 multiBamSummary 3.5.0 estimateScaleFactor 3.5.0 estimateReadFiltering 3.5.0 deeptools 3.5.0 correctGCBias 3.5.0 computeMatrixOperations 3.5.0 computeMatrix 3.5.0 computeGCBias 3.5.0 bigwigCompare 3.5.0 bamPEFragmentSize 3.5.0 bamCoverage 3.5.0 bamCompare 3.5.0 alignmentSieve 3.5.0 ok The bamFile1 contains a read at position 10 ... ok test_writeBedGraph_worker (deeptools.test.test_writeBedGraph.TestWriteBedGraph) ... ok test_writeBedGraph_worker_ignore_duplicates (deeptools.test.test_writeBedGraph.TestWriteBedGraph) ... ok test_writeBedGraph_worker_scaling (deeptools.test.test_writeBedGraph.TestWriteBedGraph) ... ok test_writeBedGraph_worker_smoothing (deeptools.test.test_writeBedGraph.TestWriteBedGraph) ... ok test_writeBedGraph_worker_zerotonan (deeptools.test.test_writeBedGraph.TestWriteBedGraph) ... ok The bamFile1 contains a read at position 10 ... ok test_writeBedGraph_worker (deeptools.test.test_writeBedGraph.TestWriteBedGraphCRAM) ... ok test_writeBedGraph_worker_ignore_duplicates (deeptools.test.test_writeBedGraph.TestWriteBedGraphCRAM) ... ok test_writeBedGraph_worker_scaling (deeptools.test.test_writeBedGraph.TestWriteBedGraphCRAM) ... ok test_writeBedGraph_worker_smoothing (deeptools.test.test_writeBedGraph.TestWriteBedGraphCRAM) ... ok test_writeBedGraph_worker_zerotonan (deeptools.test.test_writeBedGraph.TestWriteBedGraphCRAM) ... ok Test a simple plot generated using a matrix from ... ok deeptools.test.testskip_heatmapper_images.test_plotHeatmap_rename_labels ... ok deeptools.test.testskip_heatmapper_images.test_plotHeatmap_scale_regions ... ok deeptools.test.testskip_heatmapper_images.test_plotHeatmap_multi_bigwig_pergroup ... ok deeptools.test.testskip_heatmapper_images.test_plotHeatmap_multiple_colors_muti_scales ... ok deeptools.test.testskip_heatmapper_images.test_plotHeatmap_multiple_colormap_no_boxes ... ok deeptools.test.testskip_heatmapper_images.test_plotHeatmap_interpolation ... ok deeptools.test.testskip_heatmapper_images.test_plotProfiler ... ok deeptools.test.testskip_heatmapper_images.test_plotProfiler_heatmap ... ok deeptools.test.testskip_heatmapper_images.test_plotProfiler_overlapped_lines ... ok deeptools.test.testskip_heatmapper_images.test_plotProfiler_multibigwig ... ok deeptools.test.testskip_heatmapper_images.test_plotProfiler_multibigwig_pergroup ... ok ---------------------------------------------------------------------- Ran 108 tests in 18.022s OK (SKIP=1) MainProcess, processing 3 (11501.7 per sec) reads @ 3R:0-200 MainProcess countReadsInRegions_worker: processing 4 (8464.8 per sec) @ 3R:0-200 MainProcess, processing 3 (9701.6 per sec) reads @ 3R:0-200 MainProcess countReadsInRegions_worker: processing 4 (7070.0 per sec) @ 3R:0-200 Due to filtering, 50.0% of the aforementioned alignments will be used 1.0 Due to filtering, 50.0% of the aforementioned alignments will be used 1.0 There are 193 alignments, of which 7 are completely within a blacklist region. Due to filtering, 72.58064516129032% of the aforementioned alignments will be used 135.0 There are 193 alignments, of which 7 are completely within a blacklist region. Due to filtering, 72.58064516129032% of the aforementioned alignments will be used 135.0 There are 193 alignments, of which 7 are completely within a blacklist region. Due to filtering, 72.58064516129032% of the aforementioned alignments will be used 135.0 There are 97 alignments, of which 4 are completely within a blacklist region. Due to filtering, 86.02150537634408% of the aforementioned alignments will be used 80.0 There are 193 alignments, of which 7 are completely within a blacklist region. Due to filtering, 72.58064516129032% of the aforementioned alignments will be used 135.0 There are 97 alignments, of which 4 are completely within a blacklist region. Due to filtering, 86.02150537634408% of the aforementioned alignments will be used 80.0 sample mean std min 25% 50% 75% max test1.bam 4.90 5.63 0 0.0 3.0 8.0 25 test2.bam 6.56 6.63 0 0.0 5.0 11.0 25 sample mean std min 25% 50% 75% max test1.cram 4.90 5.63 0 0.0 3.0 8.0 25 test2.cram 6.56 6.63 0 0.0 5.0 11.0 25 plotProfile plotPCA plotHeatmap plotFingerprint plotEnrichment plotCoverage plotCorrelation multiBigwigSummary multiBamSummary estimateScaleFactor estimateReadFiltering deeptools correctGCBias computeMatrixOperations computeMatrix computeGCBias bigwigCompare bamPEFragmentSize bamCoverage bamCompare alignmentSieve make[1]: Leaving directory '/build/python-deeptools-3.5.0' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild rm -f -- debian/python3-deeptools.substvars rm -fr -- debian/.debhelper/generated/python3-deeptools/ debian/python3-deeptools/ debian/tmp/ dh_auto_install -O--buildsystem=pybuild install -d /build/python-deeptools-3.5.0/debian/python3-deeptools pybuild --install --test-nose -i python{version} -p 3.9 --dest-dir /build/python-deeptools-3.5.0/debian/python3-deeptools I: pybuild base:232: /usr/bin/python3 setup.py install --root /build/python-deeptools-3.5.0/debian/python3-deeptools running install running build running build_py running egg_info writing deepTools.egg-info/PKG-INFO writing dependency_links to deepTools.egg-info/dependency_links.txt writing requirements to deepTools.egg-info/requires.txt writing top-level names to deepTools.egg-info/top_level.txt reading manifest file 'deepTools.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files found matching 'examples/*' warning: no previously-included files found matching 'galaxy/*' warning: no previously-included files found matching 'gallery/*' writing manifest file 'deepTools.egg-info/SOURCES.txt' running build_scripts running install_lib creating /build/python-deeptools-3.5.0/debian/python3-deeptools/usr creating /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib creating /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9 creating /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages creating /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools creating /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/test copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/test/__init__.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/test copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/test/test_bamCoverage_and_bamCompare.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/test copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/test/test_bigwigCompare_and_multiBigwigSummary.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/test copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/test/test_computeMatrixOperations.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/test copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/test/test_countReadsPerBin.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/test copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/test/test_heatmapper.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/test copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/test/test_multiBamSummary.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/test copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/test/test_plotCoverage.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/test copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/test/test_tools.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/test copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/test/test_writeBedGraph.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/test copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/test/testskip_heatmapper_images.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/test copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/test/test_readFiltering.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/test copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/__init__.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/_version.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/bamHandler.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/cm.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/correlation.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/correlation_heatmap.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/countReadsPerBin.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/getFragmentAndReadSize.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/getRatio.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/getScorePerBigWigBin.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/heatmapper.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/heatmapper_utilities.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/mapReduce.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/misc.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/parserCommon.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/sumCoveragePerBin.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/utilities.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/writeBedGraph.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/plotPCA.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/SES_scaleFactor.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/alignmentSieve.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/bamCompare.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/bamCoverage.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/bamPEFragmentSize.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/bigwigCompare.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/computeGCBias.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/computeMatrix.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/computeMatrixOperations.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/correctGCBias.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/deepBlue.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/deeptools_list_tools.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/estimateReadFiltering.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/getScaleFactor.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/multiBamSummary.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/multiBigwigSummary.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/plotCorrelation.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/plotCoverage.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/plotEnrichment.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/plotFingerprint.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/plotHeatmap.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/plotProfile.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools copying /build/python-deeptools-3.5.0/.pybuild/cpython3_3.9_deeptools/build/deeptools/writeBedGraph_bam_and_bw.py -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/test/__init__.py to __init__.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/test/test_bamCoverage_and_bamCompare.py to test_bamCoverage_and_bamCompare.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/test/test_bigwigCompare_and_multiBigwigSummary.py to test_bigwigCompare_and_multiBigwigSummary.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/test/test_computeMatrixOperations.py to test_computeMatrixOperations.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/test/test_countReadsPerBin.py to test_countReadsPerBin.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/test/test_heatmapper.py to test_heatmapper.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/test/test_multiBamSummary.py to test_multiBamSummary.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/test/test_plotCoverage.py to test_plotCoverage.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/test/test_tools.py to test_tools.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/test/test_writeBedGraph.py to test_writeBedGraph.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/test/testskip_heatmapper_images.py to testskip_heatmapper_images.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/test/test_readFiltering.py to test_readFiltering.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/__init__.py to __init__.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/_version.py to _version.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/bamHandler.py to bamHandler.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/cm.py to cm.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/correlation.py to correlation.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/correlation_heatmap.py to correlation_heatmap.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/countReadsPerBin.py to countReadsPerBin.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/getFragmentAndReadSize.py to getFragmentAndReadSize.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/getRatio.py to getRatio.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/getScorePerBigWigBin.py to getScorePerBigWigBin.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/heatmapper.py to heatmapper.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/heatmapper_utilities.py to heatmapper_utilities.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/mapReduce.py to mapReduce.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/misc.py to misc.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/parserCommon.py to parserCommon.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/sumCoveragePerBin.py to sumCoveragePerBin.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/utilities.py to utilities.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/writeBedGraph.py to writeBedGraph.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/plotPCA.py to plotPCA.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/SES_scaleFactor.py to SES_scaleFactor.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/alignmentSieve.py to alignmentSieve.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/bamCompare.py to bamCompare.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/bamCoverage.py to bamCoverage.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/bamPEFragmentSize.py to bamPEFragmentSize.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/bigwigCompare.py to bigwigCompare.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/computeGCBias.py to computeGCBias.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/computeMatrix.py to computeMatrix.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/computeMatrixOperations.py to computeMatrixOperations.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/correctGCBias.py to correctGCBias.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/deepBlue.py to deepBlue.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/deeptools_list_tools.py to deeptools_list_tools.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/estimateReadFiltering.py to estimateReadFiltering.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/getScaleFactor.py to getScaleFactor.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/multiBamSummary.py to multiBamSummary.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/multiBigwigSummary.py to multiBigwigSummary.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/plotCorrelation.py to plotCorrelation.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/plotCoverage.py to plotCoverage.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/plotEnrichment.py to plotEnrichment.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/plotFingerprint.py to plotFingerprint.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/plotHeatmap.py to plotHeatmap.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/plotProfile.py to plotProfile.cpython-39.pyc byte-compiling /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deeptools/writeBedGraph_bam_and_bw.py to writeBedGraph_bam_and_bw.cpython-39.pyc running install_egg_info Copying deepTools.egg-info to /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/lib/python3.9/dist-packages/deepTools-3.5.0.egg-info Skipping SOURCES.txt running install_scripts creating /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin copying build/scripts-3.9/alignmentSieve -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin copying build/scripts-3.9/estimateReadFiltering -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin copying build/scripts-3.9/computeMatrixOperations -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin copying build/scripts-3.9/deeptools -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin copying build/scripts-3.9/plotEnrichment -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin copying build/scripts-3.9/plotCorrelation -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin copying build/scripts-3.9/plotPCA -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin copying build/scripts-3.9/plotCoverage -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin copying build/scripts-3.9/bigwigCompare -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin copying build/scripts-3.9/multiBigwigSummary -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin copying build/scripts-3.9/correctGCBias -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin copying build/scripts-3.9/computeGCBias -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin copying build/scripts-3.9/plotProfile -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin copying build/scripts-3.9/computeMatrix -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin copying build/scripts-3.9/bamPEFragmentSize -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin copying build/scripts-3.9/estimateScaleFactor -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin copying build/scripts-3.9/plotFingerprint -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin copying build/scripts-3.9/plotHeatmap -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin copying build/scripts-3.9/multiBamSummary -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin copying build/scripts-3.9/bamCoverage -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin copying build/scripts-3.9/bamCompare -> /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin changing mode of /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin/alignmentSieve to 755 changing mode of /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin/estimateReadFiltering to 755 changing mode of /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin/computeMatrixOperations to 755 changing mode of /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin/deeptools to 755 changing mode of /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin/plotEnrichment to 755 changing mode of /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin/plotCorrelation to 755 changing mode of /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin/plotPCA to 755 changing mode of /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin/plotCoverage to 755 changing mode of /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin/bigwigCompare to 755 changing mode of /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin/multiBigwigSummary to 755 changing mode of /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin/correctGCBias to 755 changing mode of /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin/computeGCBias to 755 changing mode of /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin/plotProfile to 755 changing mode of /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin/computeMatrix to 755 changing mode of /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin/bamPEFragmentSize to 755 changing mode of /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin/estimateScaleFactor to 755 changing mode of /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin/plotFingerprint to 755 changing mode of /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin/plotHeatmap to 755 changing mode of /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin/multiBamSummary to 755 changing mode of /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin/bamCoverage to 755 changing mode of /build/python-deeptools-3.5.0/debian/python3-deeptools/usr/bin/bamCompare to 755 dh_installdocs -O--buildsystem=pybuild install -d debian/python3-deeptools/usr/share/doc/python3-deeptools install -d debian/.debhelper/generated/python3-deeptools install -p -m0644 debian/TODO debian/python3-deeptools/usr/share/doc/python3-deeptools/TODO.Debian install -p -m0644 debian/copyright debian/python3-deeptools/usr/share/doc/python3-deeptools/copyright dh_installchangelogs -O--buildsystem=pybuild install -p -m0644 debian/changelog debian/python3-deeptools/usr/share/doc/python3-deeptools/changelog.Debian install -p -m0644 ./CHANGES.txt debian/python3-deeptools/usr/share/doc/python3-deeptools/changelog dh_python3 -O--buildsystem=pybuild D: dh_python3 dh_python3:161: version: 4.20201102+nmu1 D: dh_python3 dh_python3:162: argv: ['/usr/bin/dh_python3', '-O--buildsystem=pybuild'] D: dh_python3 dh_python3:163: options: {'guess_deps': True, 'skip_private': False, 'verbose': False, 'arch': None, 'package': None, 'no_package': None, 'compile_all': False, 'vrange': None, 'regexpr': None, 'accept_upstream_versions': False, 'depends': None, 'depends_section': None, 'recommends': None, 'recommends_section': None, 'suggests': None, 'suggests_section': None, 'requires': None, 'shebang': None, 'ignore_shebangs': False, 'clean_dbg_pkg': True, 'no_ext_rename': False, 'no_shebang_rewrite': False, 'O': '--buildsystem=pybuild'} D: dh_python3 dh_python3:164: args: [] D: dh_python3 dh_python3:165: supported Python versions: 3.9 (default=3.9) D: dh_python3 debhelper:152: source=python-deeptools, binary packages=['python3-deeptools'] D: dh_python3 dh_python3:183: processing package python3-deeptools... D: dh_python3 fs:49: moving files from debian/python3-deeptools/usr/lib/python3.9/dist-packages to debian/python3-deeptools/usr/lib/python3/dist-packages/ D: dh_python3 fs:260: package python3-deeptools details = {'requires.txt': {'debian/python3-deeptools/usr/lib/python3/dist-packages/deepTools-3.5.0.egg-info/requires.txt'}, 'egg-info': set(), 'nsp.txt': set(), 'shebangs': {/usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3}, 'public_vers': {Version('3')}, 'private_dirs': {}, 'compile': True, 'ext_vers': set(), 'ext_no_version': set()} D: dh_python3 depends:117: generating dependencies for package python3-deeptools D: dh_python3 pydist:142: trying to find dependency for deeptoolsintervals>=0.1.8 (python=None) D: dh_python3 pydist:142: trying to find dependency for matplotlib>=3.1.0 (python=None) D: dh_python3 pydist:142: trying to find dependency for numpy>=1.9.0 (python=None) D: dh_python3 pydist:142: trying to find dependency for numpydoc>=0.5 (python=None) D: dh_python3 pydist:142: trying to find dependency for plotly>=2.0.0 (python=None) D: dh_python3 pydist:142: trying to find dependency for py2bit>=0.2.0 (python=None) D: dh_python3 pydist:142: trying to find dependency for pyBigWig>=0.2.1 (python=None) D: dh_python3 pydist:142: trying to find dependency for pysam>=0.14.0 (python=None) D: dh_python3 pydist:142: trying to find dependency for scipy>=0.17.0 (python=None) D: dh_python3 depends:275: D={'python3:any', 'python3-numpy', 'python3-plotly (>=2.0.0)', 'python3-pybigwig', 'python3-pysam (>=0.14.0)', 'python3-deeptoolsintervals', 'python3-scipy (>=0.17.0)', 'python3-numpydoc', 'python3-matplotlib (>=2.1.2)', 'python3-py2bit'}; R=[]; S=[]; E=[], B=[]; RT=[] dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild cd debian/python3-deeptools chmod a-x usr/share/doc/python3-deeptools/changelog usr/share/doc/python3-deeptools/changelog.Debian gzip -9nf usr/share/doc/python3-deeptools/changelog usr/share/doc/python3-deeptools/changelog.Debian cd '/build/python-deeptools-3.5.0' dh_fixperms -O--buildsystem=pybuild find debian/python3-deeptools ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/python3-deeptools/usr/share/doc -type f -a -true -a ! -regex 'debian/python3-deeptools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-deeptools/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/python3-deeptools -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-deeptools/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/python3-deeptools/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w dh_missing -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild install -d debian/python3-deeptools/DEBIAN printf '#!/bin/sh\nset -e\n' > debian/python3-deeptools/DEBIAN/postinst cat debian/python3-deeptools.postinst.debhelper >> debian/python3-deeptools/DEBIAN/postinst chmod 0755 -- debian/python3-deeptools/DEBIAN/postinst printf '#!/bin/sh\nset -e\n' > debian/python3-deeptools/DEBIAN/prerm cat debian/python3-deeptools.prerm.debhelper >> debian/python3-deeptools/DEBIAN/prerm chmod 0755 -- debian/python3-deeptools/DEBIAN/prerm dh_gencontrol -O--buildsystem=pybuild echo misc:Depends= >> debian/python3-deeptools.substvars echo misc:Pre-Depends= >> debian/python3-deeptools.substvars dpkg-gencontrol -ppython3-deeptools -ldebian/changelog -Tdebian/python3-deeptools.substvars -Pdebian/python3-deeptools chmod 0644 -- debian/python3-deeptools/DEBIAN/control dh_md5sums -O--buildsystem=pybuild cd debian/python3-deeptools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/python3-deeptools/DEBIAN/md5sums dh_builddeb -O--buildsystem=pybuild dpkg-deb --root-owner-group --build debian/python3-deeptools .. dpkg-deb: building package 'python3-deeptools' in '../python3-deeptools_3.5.0-1_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../python-deeptools_3.5.0-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from python-deeptools-3.5.0/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2476865 and its subdirectories I: Current time: Wed Feb 9 13:24:18 -12 2022 I: pbuilder-time-stamp: 1644456258 Thu Feb 10 01:24:19 UTC 2022 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Thu Feb 10 01:24:19 UTC 2022 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Thu Feb 10 01:25:51 UTC 2022 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Thu Feb 10 01:25:51 UTC 2022 I: python-deeptools_3.5.0-1_amd64.changes: Format: 1.8 Date: Tue, 15 Sep 2020 11:10:31 +0200 Source: python-deeptools Binary: python3-deeptools Architecture: all Version: 3.5.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Steffen Moeller Description: python3-deeptools - platform for exploring biological deep-sequencing data Changes: python-deeptools (3.5.0-1) unstable; urgency=medium . * New upstream version * debhelper-compat 13 (routine-update) Checksums-Sha1: 083377ae957f41f27764fbec696ac8205682f921 8458 python-deeptools_3.5.0-1_amd64.buildinfo a90b02da171c92cb5653f3a715e5c83f7c26f88d 158080 python3-deeptools_3.5.0-1_all.deb Checksums-Sha256: 9abd9e5f45bb08e824f931143b02df4656c8c1f9ab995a624f598bec30353cbd 8458 python-deeptools_3.5.0-1_amd64.buildinfo 9ac8fc72495dd02cad02153306197eda259b2d24528553237d661e0bda8b1f93 158080 python3-deeptools_3.5.0-1_all.deb Files: bd5720be240929fb2186dab3f0ac4953 8458 science optional python-deeptools_3.5.0-1_amd64.buildinfo 30855e746cdad5115d78edae0aa179cb 158080 python optional python3-deeptools_3.5.0-1_all.deb Thu Feb 10 01:25:54 UTC 2022 I: diffoscope 203 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 5400 --html /srv/reproducible-results/rbuild-debian/tmp.NgiJCkrLq2/python-deeptools_3.5.0-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.NgiJCkrLq2/python-deeptools_3.5.0-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.NgiJCkrLq2/python-deeptools_3.5.0-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.NgiJCkrLq2/b1/python-deeptools_3.5.0-1_amd64.changes /srv/reproducible-results/rbuild-debian/tmp.NgiJCkrLq2/b2/python-deeptools_3.5.0-1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.429s) 0.429s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.028s) 0.027s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile ## specialize (total time: 0.001s) 0.001s 1 call specialize Thu Feb 10 01:25:56 UTC 2022 I: diffoscope 203 found no differences in the changes files, and a .buildinfo file also exists. Thu Feb 10 01:25:56 UTC 2022 I: python-deeptools from bullseye built successfully and reproducibly on amd64. Thu Feb 10 01:25:58 UTC 2022 I: Submitting .buildinfo files to external archives: Thu Feb 10 01:25:58 UTC 2022 I: Submitting 12K b1/python-deeptools_3.5.0-1_amd64.buildinfo.asc Thu Feb 10 01:25:59 UTC 2022 I: Submitting 12K b2/python-deeptools_3.5.0-1_amd64.buildinfo.asc Thu Feb 10 01:26:00 UTC 2022 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Feb 10 01:26:00 UTC 2022 I: Done submitting .buildinfo files. Thu Feb 10 01:26:00 UTC 2022 I: Removing signed python-deeptools_3.5.0-1_amd64.buildinfo.asc files: removed './b1/python-deeptools_3.5.0-1_amd64.buildinfo.asc' removed './b2/python-deeptools_3.5.0-1_amd64.buildinfo.asc'