0s autopkgtest [15:01:18]: starting date and time: 2024-11-14 15:01:18+0000
  0s autopkgtest [15:01:18]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky
  0s autopkgtest [15:01:18]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.6ht6zncf/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade python-pysam --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@lcy02-6.secgroup --name adt-plucky-amd64-python-pysam-20241114-150118-juju-7f2275-prod-proposed-migration-environment-15-7b4efa4a-7a59-4460-a467-711b98796903 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
 51s autopkgtest [15:02:09]: testbed dpkg architecture: amd64
 51s autopkgtest [15:02:09]: testbed apt version: 2.9.8
 51s autopkgtest [15:02:09]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 51s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
 51s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [105 kB]
 51s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
 51s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [966 kB]
 51s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB]
 51s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [81.3 kB]
 51s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [141 kB]
 51s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB]
 51s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [741 kB]
 51s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [290 kB]
 51s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [1084 B]
 51s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [9252 B]
 52s Fetched 2463 kB in 0s (7494 kB/s)
 52s Reading package lists...
 54s Reading package lists...
 54s Building dependency tree...
 54s Reading state information...
 54s Calculating upgrade...
 55s The following NEW packages will be installed:
 55s   python3.13-gdbm
 55s The following packages will be upgraded:
 55s   libpython3-stdlib pastebinit python3 python3-gdbm python3-minimal
 55s   python3-systemd
 55s 6 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
 55s Need to get 162 kB of archives.
 55s After this operation, 251 kB of additional disk space will be used.
 55s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB]
 55s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB]
 55s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB]
 55s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB]
 55s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B]
 55s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 pastebinit all 1.7.1-1 [14.9 kB]
 55s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build5 [45.7 kB]
 55s Fetched 162 kB in 0s (7187 kB/s)
 55s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
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(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
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(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 75542 files and directories currently installed.)
 55s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ...
 55s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ...
 55s Setting up python3-minimal (3.12.7-1) ...
 55s (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 ... 75542 files and directories currently installed.)
 56s Preparing to unpack .../0-python3_3.12.7-1_amd64.deb ...
 56s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ...
 56s Preparing to unpack .../1-libpython3-stdlib_3.12.7-1_amd64.deb ...
 56s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ...
 56s Selecting previously unselected package python3.13-gdbm.
 56s Preparing to unpack .../2-python3.13-gdbm_3.13.0-2_amd64.deb ...
 56s Unpacking python3.13-gdbm (3.13.0-2) ...
 56s Preparing to unpack .../3-python3-gdbm_3.12.7-1_amd64.deb ...
 56s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ...
 56s Preparing to unpack .../4-pastebinit_1.7.1-1_all.deb ...
 56s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ...
 56s Preparing to unpack .../5-python3-systemd_235-1build5_amd64.deb ...
 56s Unpacking python3-systemd (235-1build5) over (235-1build4) ...
 56s Setting up python3.13-gdbm (3.13.0-2) ...
 56s Setting up libpython3-stdlib:amd64 (3.12.7-1) ...
 56s Setting up python3 (3.12.7-1) ...
 56s Setting up python3-systemd (235-1build5) ...
 56s Setting up python3-gdbm:amd64 (3.12.7-1) ...
 56s Setting up pastebinit (1.7.1-1) ...
 56s Processing triggers for man-db (2.12.1-3) ...
 57s Reading package lists...
 57s Building dependency tree...
 57s Reading state information...
 58s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 58s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
 58s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
 58s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
 58s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
 59s Reading package lists...
 59s Reading package lists...
 59s Building dependency tree...
 59s Reading state information...
 59s Calculating upgrade...
 60s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 60s Reading package lists...
 60s Building dependency tree...
 60s Reading state information...
 60s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 61s autopkgtest [15:02:19]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024
 61s autopkgtest [15:02:19]: @@@@@@@@@@@@@@@@@@@@ apt-source python-pysam
 62s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-pysam 0.22.1+ds-2 (dsc) [2563 B]
 62s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-pysam 0.22.1+ds-2 (tar) [1447 kB]
 62s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-pysam 0.22.1+ds-2 (diff) [10.7 kB]
 62s gpgv: Signature made Wed May 29 11:37:25 2024 UTC
 62s gpgv:                using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
 62s gpgv:                issuer "emollier@debian.org"
 62s gpgv: Can't check signature: No public key
 62s dpkg-source: warning: cannot verify inline signature for ./python-pysam_0.22.1+ds-2.dsc: no acceptable signature found
 62s autopkgtest [15:02:20]: testing package python-pysam version 0.22.1+ds-2
 62s autopkgtest [15:02:20]: build not needed
 63s autopkgtest [15:02:21]: test command1: preparing testbed
 64s Reading package lists...
 64s Building dependency tree...
 64s Reading state information...
 65s Starting pkgProblemResolver with broken count: 0
 65s Starting 2 pkgProblemResolver with broken count: 0
 65s Done
 65s The following additional packages will be installed:
 65s   autoconf automake autopoint autotools-dev bcftools build-essential cpp
 65s   cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu cython3 debhelper
 65s   debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz g++ g++-14
 65s   g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14
 65s   gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gettext intltool-debian
 65s   libarchive-zip-perl libasan8 libbrotli-dev libcc1-0 libcurl4-gnutls-dev
 65s   libdebhelper-perl libdeflate-dev libdeflate0 libevent-2.1-7t64 libexpat1-dev
 65s   libfile-stripnondeterminism-perl libgcc-14-dev libgmp-dev libgmpxx4ldbl
 65s   libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev libgomp1
 65s   libhts-dev libhts3t64 libhtscodecs2 libhwasan0 libidn2-dev libisl23 libitm1
 65s   libjs-jquery libjs-sphinxdoc libjs-underscore liblsan0 liblzma-dev libmpc3
 65s   libnghttp2-dev libp11-kit-dev libpkgconf3 libpsl-dev libpython3-all-dev
 65s   libpython3-dev libpython3.12-dev libpython3.13 libpython3.13-dev
 65s   libpython3.13-minimal libpython3.13-stdlib libquadmath0 librtmp-dev
 65s   libssh2-1-dev libssl-dev libstdc++-14-dev libtasn1-6-dev libtool libtsan2
 65s   libubsan1 libunbound8 libzstd-dev m4 nettle-dev pkgconf pkgconf-bin
 65s   po-debconf python3-all python3-all-dev python3-dev python3-iniconfig
 65s   python3-packaging python3-pluggy python3-pysam python3-pytest python3.12-dev
 65s   python3.13 python3.13-dev python3.13-minimal samtools tabix zlib1g-dev
 65s Suggested packages:
 65s   autoconf-archive gnu-standards autoconf-doc python3-numpy
 65s   texlive-latex-recommended cpp-doc gcc-14-locales cpp-14-doc cython-doc
 65s   dh-make flit python3-build python3-installer python3-wheel g++-multilib
 65s   g++-14-multilib gcc-14-doc gcc-multilib manpages-dev flex bison gdb gcc-doc
 65s   gcc-14-multilib gdb-x86-64-linux-gnu gettext-doc libasprintf-dev
 65s   libgettextpo-dev libcurl4-doc libidn-dev libkrb5-dev libldap2-dev gmp-doc
 65s   libgmp10-doc libmpfr-dev dns-root-data gnutls-bin gnutls-doc liblzma-doc
 65s   libnghttp2-doc p11-kit-doc libssl-doc libstdc++-14-doc libtool-doc gfortran
 65s   | fortran95-compiler gcj-jdk m4-doc libmail-box-perl python3.13-venv
 65s   python3.13-doc binfmt-support cwltool
 65s Recommended packages:
 65s   python3-gffutils python3-matplotlib libarchive-cpio-perl javascript-common
 65s   libtasn1-doc libltdl-dev libmail-sendmail-perl
 65s The following NEW packages will be installed:
 65s   autoconf automake autopkgtest-satdep autopoint autotools-dev bcftools
 65s   build-essential cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu
 65s   cython3 debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism
 65s   dwz g++ g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14
 65s   gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gettext intltool-debian
 65s   libarchive-zip-perl libasan8 libbrotli-dev libcc1-0 libcurl4-gnutls-dev
 65s   libdebhelper-perl libdeflate-dev libdeflate0 libevent-2.1-7t64 libexpat1-dev
 65s   libfile-stripnondeterminism-perl libgcc-14-dev libgmp-dev libgmpxx4ldbl
 65s   libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev libgomp1
 65s   libhts-dev libhts3t64 libhtscodecs2 libhwasan0 libidn2-dev libisl23 libitm1
 65s   libjs-jquery libjs-sphinxdoc libjs-underscore liblsan0 liblzma-dev libmpc3
 65s   libnghttp2-dev libp11-kit-dev libpkgconf3 libpsl-dev libpython3-all-dev
 65s   libpython3-dev libpython3.12-dev libpython3.13 libpython3.13-dev
 65s   libpython3.13-minimal libpython3.13-stdlib libquadmath0 librtmp-dev
 65s   libssh2-1-dev libssl-dev libstdc++-14-dev libtasn1-6-dev libtool libtsan2
 65s   libubsan1 libunbound8 libzstd-dev m4 nettle-dev pkgconf pkgconf-bin
 65s   po-debconf python3-all python3-all-dev python3-dev python3-iniconfig
 65s   python3-packaging python3-pluggy python3-pysam python3-pytest python3.12-dev
 65s   python3.13 python3.13-dev python3.13-minimal samtools tabix zlib1g-dev
 65s 0 upgraded, 101 newly installed, 0 to remove and 0 not upgraded.
 65s Need to get 115 MB/115 MB of archives.
 65s After this operation, 430 MB of additional disk space will be used.
 65s Get:1 /tmp/autopkgtest.kUrCsn/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [816 B]
 65s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.0-2 [879 kB]
 65s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.0-2 [2188 kB]
 65s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 m4 amd64 1.4.19-4build1 [244 kB]
 65s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 autoconf all 2.72-3 [382 kB]
 65s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 autotools-dev all 20220109.1 [44.9 kB]
 65s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 automake all 1:1.16.5-1.3ubuntu1 [558 kB]
 65s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 autopoint all 0.22.5-2 [616 kB]
 65s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB]
 65s Get:10 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-1 [132 kB]
 65s Get:11 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.20+ds-1 [439 kB]
 65s Get:12 http://ftpmaster.internal/ubuntu plucky/universe amd64 bcftools amd64 1.20-2 [810 kB]
 65s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB]
 65s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB]
 65s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [11.9 MB]
 65s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-8ubuntu1 [1030 B]
 65s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [5452 B]
 66s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.1.0-2ubuntu1 [22.4 kB]
 66s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 14.2.0-8ubuntu1 [47.6 kB]
 66s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB]
 66s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 14.2.0-8ubuntu1 [29.1 kB]
 66s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 14.2.0-8ubuntu1 [2998 kB]
 66s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 14.2.0-8ubuntu1 [1317 kB]
 66s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 14.2.0-8ubuntu1 [2732 kB]
 66s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 14.2.0-8ubuntu1 [1177 kB]
 66s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 14.2.0-8ubuntu1 [1634 kB]
 66s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 14.2.0-8ubuntu1 [153 kB]
 66s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-8ubuntu1 [2814 kB]
 66s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [23.3 MB]
 66s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-8ubuntu1 [528 kB]
 66s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [1214 B]
 66s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.1.0-2ubuntu1 [5000 B]
 66s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-8ubuntu1 [2504 kB]
 66s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [13.3 MB]
 66s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-8ubuntu1 [19.9 kB]
 66s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [966 B]
 66s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.1.0-2ubuntu1 [1100 B]
 66s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B]
 66s Get:39 http://ftpmaster.internal/ubuntu plucky/universe amd64 cython3 amd64 3.0.11+dfsg-1ubuntu1 [2491 kB]
 66s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebhelper-perl all 13.20ubuntu1 [94.2 kB]
 66s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libtool all 2.4.7-7build1 [166 kB]
 66s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-autoreconf all 20 [16.1 kB]
 66s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB]
 66s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB]
 66s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-strip-nondeterminism all 1.14.0-1 [5058 B]
 66s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 debugedit amd64 1:5.1-1 [46.9 kB]
 66s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 dwz amd64 0.15-1build6 [115 kB]
 66s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 gettext amd64 0.22.5-2 [948 kB]
 66s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB]
 66s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 po-debconf all 1.0.21+nmu1 [233 kB]
 66s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 debhelper all 13.20ubuntu1 [893 kB]
 66s Get:52 http://ftpmaster.internal/ubuntu plucky/universe amd64 dh-python all 6.20241024 [112 kB]
 66s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli-dev amd64 1.1.0-2build2 [353 kB]
 66s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10 [144 kB]
 66s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libunbound8 amd64 1.20.0-1ubuntu2.1 [447 kB]
 66s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libgnutls-dane0t64 amd64 3.8.8-2ubuntu1 [24.3 kB]
 66s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libgnutls-openssl27t64 amd64 3.8.8-2ubuntu1 [24.5 kB]
 66s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libidn2-dev amd64 2.3.7-2build2 [120 kB]
 66s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libp11-kit-dev amd64 0.25.5-2ubuntu1 [22.7 kB]
 66s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libtasn1-6-dev amd64 4.19.0-3build1 [90.5 kB]
 66s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-2ubuntu7 [10.0 kB]
 66s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-2ubuntu7 [341 kB]
 66s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 nettle-dev amd64 3.10-1 [1172 kB]
 66s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 libgnutls28-dev amd64 3.8.8-2ubuntu1 [1108 kB]
 66s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 libpkgconf3 amd64 1.8.1-4 [32.3 kB]
 66s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 pkgconf-bin amd64 1.8.1-4 [21.6 kB]
 66s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 pkgconf amd64 1.8.1-4 [16.8 kB]
 66s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libnghttp2-dev amd64 1.64.0-1 [123 kB]
 66s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 libpsl-dev amd64 0.21.2-1.1build1 [76.4 kB]
 66s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB]
 66s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2build7 [66.7 kB]
 66s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 libssl-dev amd64 3.3.1-2ubuntu2 [2686 kB]
 66s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 libssh2-1-dev amd64 1.11.1-1 [292 kB]
 66s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libzstd-dev amd64 1.5.6+dfsg-1 [371 kB]
 66s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4-gnutls-dev amd64 8.9.1-2ubuntu2 [476 kB]
 66s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate-dev amd64 1.22-1 [72.2 kB]
 66s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 libexpat1-dev amd64 2.6.2-2 [140 kB]
 66s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma-dev amd64 5.6.2-2 [176 kB]
 66s Get:79 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts-dev amd64 1.20+ds-1 [5944 kB]
 66s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
 66s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB]
 66s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-sphinxdoc all 7.4.7-4 [158 kB]
 66s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.12-dev amd64 3.12.7-3 [5699 kB]
 66s Get:84 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-dev amd64 3.12.7-1 [10.3 kB]
 66s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [2107 kB]
 66s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13 amd64 3.13.0-2 [2321 kB]
 66s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-dev amd64 3.13.0-2 [5488 kB]
 66s Get:88 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-all-dev amd64 3.12.7-1 [916 B]
 66s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.0-2 [719 kB]
 66s Get:90 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all amd64 3.12.7-1 [890 B]
 66s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-dev amd64 3.12.7-3 [505 kB]
 66s Get:92 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-dev amd64 3.12.7-1 [26.7 kB]
 66s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-dev amd64 3.13.0-2 [507 kB]
 66s Get:94 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all-dev amd64 3.12.7-1 [914 B]
 66s Get:95 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B]
 66s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB]
 66s Get:97 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB]
 66s Get:98 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pysam amd64 0.22.1+ds-2 [3504 kB]
 66s Get:99 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.3-1 [251 kB]
 66s Get:100 http://ftpmaster.internal/ubuntu plucky/universe amd64 samtools amd64 1.20-3 [599 kB]
 66s Get:101 http://ftpmaster.internal/ubuntu plucky/universe amd64 tabix amd64 1.20+ds-1 [510 kB]
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 77s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
 77s Setting up build-essential (12.10ubuntu1) ...
 77s Setting up debhelper (13.20ubuntu1) ...
 77s Setting up autopkgtest-satdep (0) ...
 77s Processing triggers for systemd (256.5-2ubuntu4) ...
 77s Processing triggers for man-db (2.12.1-3) ...
 78s Processing triggers for install-info (7.1.1-1) ...
 78s Processing triggers for libc-bin (2.40-1ubuntu3) ...
 81s (Reading database ... 81342 files and directories currently installed.)
 81s Removing autopkgtest-satdep (0) ...
 81s autopkgtest [15:02:39]: test command1: export HOME=$PWD && make -C tests/pysam_data && make -C tests/cbcf_data && pytest-3
 81s autopkgtest [15:02:39]: test command1: [-----------------------
 81s make: Entering directory '/tmp/autopkgtest.kUrCsn/build.Qdd/src/tests/pysam_data'
 81s samtools faidx ex1.fa
 81s samtools view --no-PG -bo ex1.bam -t ex1.fa.fai ex1.sam.gz
 81s samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz
 81s [mpileup] 1 samples in 1 input files
 81s gunzip < ex1.sam.gz > ex1.sam
 81s samtools index ex1.bam
 81s samtools view --no-PG -h ex1.bam | gzip > ex2.sam.gz
 81s gunzip < ex2.sam.gz > ex2.sam
 81s samtools view --no-PG -bo ex2.bam ex2.sam
 81s samtools index ex2.bam
 81s samtools calmd --no-PG --output-fmt BAM ex2.bam ex1.fa > with_md.sam.gz
 81s [bam_fillmd1] different NM for read 'EAS139_11:7:46:695:738': 3 -> 8
 81s [bam_fillmd1] different NM for read 'EAS218_4:1:48:9:409': 0 -> 5
 81s [bam_fillmd1] different NM for read 'B7_591:7:200:192:373': 0 -> 5
 81s [bam_fillmd1] different NM for read 'EAS56_65:1:163:846:223': 0 -> 5
 81s [bam_fillmd1] different NM for read 'EAS114_30:7:283:799:560': 0 -> 5
 81s [bam_fillmd1] different NM for read 'B7_595:4:84:802:737': 0 -> 4
 81s [bam_fillmd1] different NM for read 'EAS51_66:5:308:400:602': 0 -> 3
 81s [bam_fillmd1] different NM for read 'EAS54_81:2:285:367:932': 0 -> 3
 81s [bam_fillmd1] different NM for read 'EAS114_39:1:70:147:84': 0 -> 3
 81s [bam_fillmd1] different NM for read 'EAS56_53:1:124:243:35': 2 -> 5
 81s [bam_fillmd1] different NM for read 'EAS1_103:2:226:302:758': 2 -> 3
 81s [bam_fillmd1] different NM for read 'EAS114_28:6:175:705:982': 1 -> 0
 81s [bam_fillmd1] different NM for read 'EAS51_64:4:179:389:585': 7 -> 8
 81s [bam_fillmd1] different NM for read 'B7_589:1:122:337:968': 3 -> 2
 81s [bam_fillmd1] different NM for read 'B7_610:4:15:805:420': 4 -> 5
 81s [bam_fillmd1] different NM for read 'B7_591:2:279:124:41': 2 -> 4
 81s [bam_fillmd1] different NM for read 'EAS112_32:8:89:254:332': 0 -> 1
 81s [bam_fillmd1] different NM for read 'B7_597:7:103:731:697': 0 -> 2
 81s [bam_fillmd1] different NM for read 'EAS139_11:2:71:83:58': 0 -> 2
 81s [bam_fillmd1] different NM for read 'EAS192_3:4:63:5:870': 0 -> 2
 81s [bam_fillmd1] different NM for read 'EAS139_19:2:29:1822:1881': 0 -> 2
 81s [bam_fillmd1] different NM for read 'EAS188_7:3:15:568:42': 2 -> 1
 81s [bam_fillmd1] different NM for read 'EAS1_95:4:176:971:874': 0 -> 1
 81s [bam_fillmd1] different NM for read 'EAS1_99:1:34:649:318': 3 -> 4
 81s [bam_fillmd1] different NM for read 'EAS54_65:4:61:346:384': 3 -> 4
 81s [bam_fillmd1] different NM for read 'B7_597:6:20:592:496': 0 -> 1
 81s [bam_fillmd1] different NM for read 'B7_597:4:38:999:463': 2 -> 1
 81s [bam_fillmd1] different NM for read 'EAS114_28:5:23:944:377': 0 -> 3
 81s [bam_fillmd1] different NM for read 'EAS219_1:3:90:219:528': 0 -> 3
 81s [bam_fillmd1] different NM for read 'EAS1_108:5:89:942:84': 0 -> 4
 81s [bam_fillmd1] different NM for read 'EAS1_108:6:159:493:275': 0 -> 5
 81s [bam_fillmd1] different NM for read 'EAS139_11:1:81:1019:558': 0 -> 5
 81s [bam_fillmd1] different NM for read 'EAS51_62:7:162:195:761': 0 -> 4
 81s [bam_fillmd1] different NM for read 'B7_597:3:115:646:430': 0 -> 4
 81s [bam_fillmd1] different NM for read 'EAS114_30:6:243:209:110': 0 -> 4
 81s [bam_fillmd1] different NM for read 'EAS1_108:2:266:994:429': 0 -> 4
 81s [bam_fillmd1] different NM for read 'EAS114_30:5:32:461:154': 0 -> 4
 81s [bam_fillmd1] different NM for read 'EAS114_39:6:7:492:1088': 0 -> 4
 81s [bam_fillmd1] different NM for read 'EAS1_95:6:174:650:125': 0 -> 4
 81s [bam_fillmd1] different NM for read 'EAS56_59:6:89:457:591': 1 -> 5
 81s [bam_fillmd1] different NM for read 'EAS114_39:2:38:670:564': 0 -> 4
 81s [bam_fillmd1] different NM for read 'EAS188_7:4:92:693:228': 1 -> 6
 81s [bam_fillmd1] different NM for read 'EAS218_1:4:61:1369:440': 0 -> 4
 81s [bam_fillmd1] different NM for read 'EAS114_26:4:123:1001:580': 0 -> 4
 81s [bam_fillmd1] different NM for read 'EAS114_39:4:10:1312:1558': 0 -> 4
 81s [bam_fillmd1] different NM for read 'EAS220_1:8:45:178:1321': 0 -> 4
 81s [bam_fillmd1] different NM for read 'EAS56_59:5:125:137:58': 0 -> 4
 81s [bam_fillmd1] different NM for read 'EAS192_3:3:285:349:797': 1 -> 5
 81s [bam_fillmd1] different NM for read 'EAS114_45:5:56:1757:1319': 0 -> 4
 81s [bam_fillmd1] different NM for read 'B7_591:3:291:404:199': 0 -> 4
 81s [bam_fillmd1] different NM for read 'EAS54_65:7:159:253:353': 0 -> 4
 81s [bam_fillmd1] different NM for read 'EAS56_57:1:122:38:103': 0 -> 4
 81s [bam_fillmd1] different NM for read 'EAS188_4:5:103:870:105': 0 -> 4
 81s [bam_fillmd1] different NM for read 'EAS1_105:8:24:718:322': 3 -> 7
 81s [bam_fillmd1] different NM for read 'EAS51_64:6:118:41:489': 0 -> 4
 81s [bam_fillmd1] different NM for read 'EAS56_61:3:165:665:220': 0 -> 4
 81s [bam_fillmd1] different NM for read 'EAS114_30:6:238:803:383': 0 -> 4
 81s [bam_fillmd1] different NM for read 'EAS1_105:3:232:364:583': 0 -> 3
 81s [bam_fillmd1] different NM for read 'B7_595:2:29:729:70': 3 -> 4
 81s [bam_fillmd1] different NM for read 'EAS114_30:6:220:809:850': 4 -> 6
 81s [bam_fillmd1] different NM for read 'EAS54_65:2:264:157:150': 3 -> 5
 81s [bam_fillmd1] different NM for read 'B7_595:8:26:242:35': 2 -> 1
 81s [bam_fillmd1] different NM for read 'B7_610:7:34:144:868': 4 -> 5
 81s [bam_fillmd1] different NM for read 'B7_597:8:147:360:141': 1 -> 2
 81s [bam_fillmd1] different NM for read 'EAS139_19:2:82:154:1333': 0 -> 4
 81s [bam_fillmd1] different NM for read 'EAS56_63:3:41:468:459': 0 -> 3
 81s [bam_fillmd1] different NM for read 'EAS1_97:4:274:287:423': 0 -> 1
 81s [bam_fillmd1] different NM for read 'EAS114_30:2:303:428:326': 0 -> 1
 81s [bam_fillmd1] different NM for read 'EAS54_71:8:105:854:975': 0 -> 3
 81s gunzip < with_md.sam.gz > with_md.sam
 81s samtools view --no-PG -bo with_md.bam with_md.sam
 81s [W::bam_hdr_read] EOF marker is absent. The input is probably truncated
 81s samtools index with_md.bam
 81s samtools view --no-PG -bu -o uncompressed.bam ex2.sam
 81s samtools view --no-PG -bo MM-chebi.bam MM-chebi.sam
 81s samtools view --no-PG -bo MM-double.bam MM-double.sam
 82s samtools view --no-PG -bo MM-multi.bam MM-multi.sam
 82s samtools view --no-PG -bo MM-orient.bam MM-orient.sam
 82s samtools view --no-PG -bo ex10.bam ex10.sam
 82s samtools view --no-PG -bo ex3.bam ex3.sam
 82s samtools view --no-PG -bo ex4.bam ex4.sam
 82s samtools view --no-PG -bo ex5.bam ex5.sam
 82s samtools view --no-PG -bo ex6.bam ex6.sam
 82s samtools view --no-PG -bo ex8.bam ex8.sam
 82s samtools view --no-PG -bo ex9_fail.bam ex9_fail.sam
 82s samtools view --no-PG -bo ex9_nofail.bam ex9_nofail.sam
 82s samtools view --no-PG -bo ex_spliced.bam ex_spliced.sam
 82s samtools view --no-PG -bo example_aligned_pairs.bam example_aligned_pairs.sam
 82s samtools view --no-PG -bo example_btag.bam example_btag.sam
 82s samtools view --no-PG -bo example_dash_in_chr.bam example_dash_in_chr.sam
 82s samtools view --no-PG -bo example_empty_header.bam example_empty_header.sam
 82s samtools view --no-PG -bo example_empty_with_header.bam example_empty_with_header.sam
 82s samtools view --no-PG -bo example_reverse_complement.bam example_reverse_complement.sam
 82s touch tmp.list
 82s samtools view --no-PG -bo example_unmapped_reads_no_sq.bam -t tmp.list example_unmapped_reads_no_sq.sam
 82s rm -f tmp.list
 82s samtools view --no-PG -bo issue100.bam issue100.sam
 82s samtools view --no-PG -bo rg_with_tab.bam rg_with_tab.sam
 82s samtools view --no-PG -bo softclip.bam softclip.sam
 82s samtools view --no-PG -bo tag_bug.bam tag_bug.sam
 82s samtools view --no-PG -bo test_mapped_unmapped.bam test_mapped_unmapped.sam
 82s samtools view --no-PG -bo test_query_position.bam test_query_position.sam
 82s samtools view --no-PG -bo test_unaligned.bam test_unaligned.sam
 82s samtools index MM-chebi.bam
 82s samtools index MM-double.bam
 82s samtools index MM-multi.bam
 82s samtools index MM-orient.bam
 82s samtools index ex10.bam
 82s samtools index ex3.bam
 82s samtools index ex4.bam
 82s samtools index ex5.bam
 82s samtools index ex6.bam
 82s samtools index ex8.bam
 82s samtools index ex9_fail.bam
 82s samtools index ex9_nofail.bam
 82s samtools index ex_spliced.bam
 82s samtools index example_aligned_pairs.bam
 82s samtools index example_btag.bam
 82s samtools index example_dash_in_chr.bam
 82s samtools index example_empty_header.bam
 82s samtools index example_empty_with_header.bam
 82s samtools index example_reverse_complement.bam
 82s samtools index example_unmapped_reads_no_sq.bam
 82s samtools index issue100.bam
 82s samtools index rg_with_tab.bam
 82s samtools index softclip.bam
 82s samtools index tag_bug.bam
 82s samtools index test_mapped_unmapped.bam
 82s samtools index test_query_position.bam
 82s samtools index test_unaligned.bam
 82s samtools view --no-PG -Co ex1.cram -T ex1.fa ex1.sam
 82s samtools view --no-PG -Co ex2.cram -T ex1.fa ex2.sam
 82s samtools view --no-PG -Co ex3.cram -T ex1.fa ex3.sam
 82s samtools index ex1.cram
 82s samtools index ex2.cram
 82s samtools index ex3.cram
 82s cp ex1.bam example_bai.bam
 82s samtools index example_bai.bam
 82s mv example_bai.bam.bai example_bai.bai
 82s dd if=ex2.bam of=ex2_truncated.bam bs=$((`wc -c < ex2.bam`-512)) count=1
 82s 1+0 records in
 82s 1+0 records out
 82s 122288 bytes (122 kB, 119 KiB) copied, 0.000261716 s, 467 MB/s
 82s (bgzip -d < ex2.bam; printf '\37\0\0\0\1\0\0\0') | bgzip > ex2_corrupt.bam
 82s grep "^@" ex2.sam | samtools view --no-PG -bo empty.bam -
 82s samtools index empty.bam
 82s cp ex1.bam explicit_index.bam
 82s cp ex1.cram explicit_index.cram
 82s gzip < faidx_empty_seq.fq > faidx_empty_seq.fq.gz
 82s bgzip < ex1.fa > ex1.fa.gz
 82s samtools faidx ex1.fa.gz
 82s cp ex1.bam ex1_csi.bam
 82s samtools index -c ex1_csi.bam
 82s touch all.stamp
 82s rm with_md.sam
 82s make: Leaving directory '/tmp/autopkgtest.kUrCsn/build.Qdd/src/tests/pysam_data'
 82s make: Entering directory '/tmp/autopkgtest.kUrCsn/build.Qdd/src/tests/cbcf_data'
 82s bgzip < example_vcf40.vcf > example_vcf40.vcf.gz
 82s tabix -p vcf example_vcf40.vcf.gz    # create tbi index
 82s bcftools index example_vcf40.vcf.gz  # create csi index
 82s bgzip < example_vcf42.vcf > example_vcf42.vcf.gz
 82s tabix -p vcf example_vcf42.vcf.gz    # create tbi index
 82s bcftools index example_vcf42.vcf.gz  # create csi index
 82s bgzip < example_vcf42_only_header.vcf > example_vcf42_only_header.vcf.gz
 82s tabix -p vcf example_vcf42_only_header.vcf.gz    # create tbi index
 82s bcftools index example_vcf42_only_header.vcf.gz  # create csi index
 82s bgzip < example_vcf42_withcontigs.vcf > example_vcf42_withcontigs.vcf.gz
 82s tabix -p vcf example_vcf42_withcontigs.vcf.gz    # create tbi index
 82s bcftools index example_vcf42_withcontigs.vcf.gz  # create csi index
 82s bgzip < example_vcf43.vcf > example_vcf43.vcf.gz
 82s tabix -p vcf example_vcf43.vcf.gz    # create tbi index
 82s bcftools index example_vcf43.vcf.gz  # create csi index
 82s bgzip < example_vcf43_with_utf8.vcf > example_vcf43_with_utf8.vcf.gz
 82s tabix -p vcf example_vcf43_with_utf8.vcf.gz    # create tbi index
 82s bcftools index example_vcf43_with_utf8.vcf.gz  # create csi index
 82s bgzip < gnomad.vcf > gnomad.vcf.gz
 82s tabix -p vcf gnomad.vcf.gz    # create tbi index
 82s bcftools index gnomad.vcf.gz  # create csi index
 82s bgzip < gnomad_fixed.vcf > gnomad_fixed.vcf.gz
 82s tabix -p vcf gnomad_fixed.vcf.gz    # create tbi index
 82s bcftools index gnomad_fixed.vcf.gz  # create csi index
 82s bgzip < missing_genotypes.vcf > missing_genotypes.vcf.gz
 82s tabix -p vcf missing_genotypes.vcf.gz    # create tbi index
 82s bcftools index missing_genotypes.vcf.gz  # create csi index
 82s bcftools view -O b example_vcf40.vcf.gz -o example_vcf40.bcf
 82s bcftools index example_vcf40.bcf
 82s bcftools view -O b example_vcf42.vcf.gz -o example_vcf42.bcf
 82s bcftools index example_vcf42.bcf
 82s bcftools view -O b example_vcf42_only_header.vcf.gz -o example_vcf42_only_header.bcf
 82s bcftools index example_vcf42_only_header.bcf
 82s bcftools view -O b example_vcf42_withcontigs.vcf.gz -o example_vcf42_withcontigs.bcf
 82s bcftools index example_vcf42_withcontigs.bcf
 82s bcftools view -O b example_vcf43.vcf.gz -o example_vcf43.bcf
 82s bcftools index example_vcf43.bcf
 82s bcftools view -O b example_vcf43_with_utf8.vcf.gz -o example_vcf43_with_utf8.bcf
 82s bcftools index example_vcf43_with_utf8.bcf
 82s bcftools view -O b gnomad.vcf.gz -o gnomad.bcf
 82s bcftools index gnomad.bcf
 82s bcftools view -O b gnomad_fixed.vcf.gz -o gnomad_fixed.bcf
 82s [W::bcf_hdr_check_sanity] PL should be declared as Number=G
 82s bcftools index gnomad_fixed.bcf
 82s [W::bcf_hdr_check_sanity] PL should be declared as Number=G
 82s bcftools view -O b missing_genotypes.vcf.gz -o missing_genotypes.bcf
 82s bcftools index missing_genotypes.bcf
 82s touch all.stamp
 82s make: Leaving directory '/tmp/autopkgtest.kUrCsn/build.Qdd/src/tests/cbcf_data'
 82s ============================= test session starts ==============================
 82s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3
 82s cachedir: .pytest_cache
 82s rootdir: /tmp/autopkgtest.kUrCsn/build.Qdd/src
 82s configfile: setup.cfg
 82s testpaths: pysam, tests
 82s plugins: typeguard-4.4.1
 83s collecting ... collected 951 items
 83s 
 83s tests/AlignedSegment_test.py::TestAlignedSegment::testBlocks PASSED
 83s tests/AlignedSegment_test.py::TestAlignedSegment::testCompare PASSED
 83s tests/AlignedSegment_test.py::TestAlignedSegment::testEmpty PASSED
 83s tests/AlignedSegment_test.py::TestAlignedSegment::testFullReferencePositions PASSED
 83s tests/AlignedSegment_test.py::TestAlignedSegment::testHashing PASSED
 83s tests/AlignedSegment_test.py::TestAlignedSegment::testLargeRead PASSED
 83s tests/AlignedSegment_test.py::TestAlignedSegment::testNoSequence PASSED
 83s tests/AlignedSegment_test.py::TestAlignedSegment::testPositions PASSED
 83s tests/AlignedSegment_test.py::TestAlignedSegment::testSettingTagInEmptyRead PASSED
 83s tests/AlignedSegment_test.py::TestAlignedSegment::testStrOfEmptyRead PASSED
 83s tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate PASSED
 83s tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate2 PASSED
 83s tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateQual PASSED
 83s tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateTlen PASSED
 83s tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_mapped_reads_are_updated PASSED
 83s tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_unmapped_reads_ignore_length PASSED
 83s tests/AlignedSegment_test.py::TestAlignedSegment::test_equivalence_matches_only_and_with_seq PASSED
 83s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs PASSED
 83s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_1character_md PASSED
 83s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_bad_type_md PASSED
 83s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_hard_clipping PASSED
 83s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_lowercase_md PASSED
 83s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_match_mismatch PASSED
 83s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding PASSED
 83s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding_with_seq PASSED
 83s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip PASSED
 83s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip_reference PASSED
 83s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_soft_clipping PASSED
 83s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_uppercase_md PASSED
 83s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_with_malformed_MD_tag PASSED
 83s tests/AlignedSegment_test.py::TestAlignedSegment::test_header_accessible PASSED
 83s tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_query_length PASSED
 83s tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_read_length PASSED
 83s tests/AlignedSegment_test.py::TestAlignedSegment::test_query_length_is_limited PASSED
 83s tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_asterisk PASSED
 83s tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_chromosome PASSED
 83s tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_none PASSED
 83s tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_not_be_set_to_unknown_chromosome PASSED
 83s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_chromosome PASSED
 83s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing PASSED
 83s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing_without_header PASSED
 83s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_without_header PASSED
 83s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_not_be_set_to_unknown_chromosome PASSED
 83s tests/AlignedSegment_test.py::TestTidMapping::test_unmapped_tid_is_asterisk_in_output PASSED
 83s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_asterisk PASSED
 83s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_chromosome PASSED
 83s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_none PASSED
 83s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_not_be_set_to_unknown_chromosome PASSED
 83s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_chromosome PASSED
 83s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_equal PASSED
 83s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing PASSED
 83s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing_without_header PASSED
 83s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_without_header PASSED
 83s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_not_be_set_to_unknown_chromosome PASSED
 83s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_unmapped_tid_is_asterisk_in_output PASSED
 83s tests/AlignedSegment_test.py::TestCigar::testCigar PASSED
 83s tests/AlignedSegment_test.py::TestCigar::testCigarString PASSED
 83s tests/AlignedSegment_test.py::TestCigarStats::testStats PASSED
 83s tests/AlignedSegment_test.py::TestAlignedPairs::testReferenceBases PASSED
 83s tests/AlignedSegment_test.py::TestBaseModifications::testChebi PASSED
 83s tests/AlignedSegment_test.py::TestBaseModifications::testDouble PASSED
 83s tests/AlignedSegment_test.py::TestBaseModifications::testMulti PASSED
 83s tests/AlignedSegment_test.py::TestBaseModifications::testOrient PASSED
 83s tests/AlignedSegment_test.py::TestTags::testAddTags PASSED
 83s tests/AlignedSegment_test.py::TestTags::testAddTagsType PASSED
 83s tests/AlignedSegment_test.py::TestTags::testArrayTags PASSED
 83s tests/AlignedSegment_test.py::TestTags::testEmptyTag PASSED
 83s tests/AlignedSegment_test.py::TestTags::testLongTags PASSED
 83s tests/AlignedSegment_test.py::TestTags::testMDTagComplex PASSED
 83s tests/AlignedSegment_test.py::TestTags::testMDTagDeletions PASSED
 83s tests/AlignedSegment_test.py::TestTags::testMDTagInsertions PASSED
 83s tests/AlignedSegment_test.py::TestTags::testMDTagMatchOnly PASSED
 83s tests/AlignedSegment_test.py::TestTags::testMDTagRefSkipping PASSED
 83s tests/AlignedSegment_test.py::TestTags::testMDTagSoftClipping PASSED
 83s tests/AlignedSegment_test.py::TestTags::testMissingTag PASSED
 83s tests/AlignedSegment_test.py::TestTags::testNegativeIntegers PASSED
 83s tests/AlignedSegment_test.py::TestTags::testNegativeIntegersWrittenToFile PASSED
 83s tests/AlignedSegment_test.py::TestTags::testSetTag PASSED
 83s tests/AlignedSegment_test.py::TestTags::testTagParsing PASSED
 83s tests/AlignedSegment_test.py::TestTags::testTagsUpdatingFloat PASSED
 83s tests/AlignedSegment_test.py::TestCopy::testCopy PASSED
 83s tests/AlignedSegment_test.py::TestCopy::testDeepCopy PASSED
 83s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_A PASSED
 83s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_C PASSED
 83s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_H PASSED
 83s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_I PASSED
 83s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_S PASSED
 83s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_a PASSED
 83s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_automated_type_detection PASSED
 83s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_c PASSED
 83s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_d PASSED
 83s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_f PASSED
 83s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_i PASSED
 83s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_s PASSED
 83s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_A PASSED
 83s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_C PASSED
 83s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_H PASSED
 83s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_I PASSED
 83s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_S PASSED
 83s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_a PASSED
 83s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_automated_type_detection PASSED
 83s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_c PASSED
 83s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_d PASSED
 83s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_f PASSED
 83s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_i PASSED
 83s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_s PASSED
 83s tests/AlignedSegment_test.py::TestEnums::test_cigar_enums_are_defined PASSED
 83s tests/AlignedSegment_test.py::TestEnums::test_sam_flags_are_defined PASSED
 83s tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_constructed_without_header PASSED
 83s tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_written_to_file PASSED
 83s tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_id_can_be_set PASSED
 83s tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_name_is_not_available PASSED
 83s tests/AlignedSegment_test.py::TestForwardStrandValues::test_qualities_are_complemented PASSED
 83s tests/AlignedSegment_test.py::TestForwardStrandValues::test_sequence_is_complemented PASSED
 83s tests/AlignedSegment_test.py::TestExportImport::test_dict_export PASSED
 83s tests/AlignedSegment_test.py::TestExportImport::test_string_export PASSED
 83s tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_with_tags PASSED
 83s tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_without_tags PASSED
 83s tests/AlignedSegment_test.py::TestExportImport::test_to_string_without_alignment_file PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_dict PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_header PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references_without_text PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_text PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_access_works PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_contains_works PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_get_works PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_keys_works PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_len_works PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_setting_raises_error PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_values_works PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_header_content_is_as_expected PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_name_mapping PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_text_access_works PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_contains_works PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_get_works PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_keys_works PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_len_works PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_setting_raises_error PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_values_works PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_name_mapping PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_text_access_works PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_contains_works PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_get_works PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_keys_works PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_len_works PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_setting_raises_error PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_values_works PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_name_mapping PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_text_access_works PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM /tmp/autopkgtest.kUrCsn/build.Qdd/src/tests/tmp/pysamtests_tmp_check_read_write_t_jbg_as
 83s PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM [E::cram_index_load] Could not retrieve index file for '/tmp/autopkgtest.kUrCsn/build.Qdd/src/tests/tmp/pysamtests_tmp_check_read_write_j6fxvwy9'
 83s /tmp/autopkgtest.kUrCsn/build.Qdd/src/tests/tmp/pysamtests_tmp_check_read_write_j6fxvwy9
 83s PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /tmp/autopkgtest.kUrCsn/build.Qdd/src/tests/tmp/pysamtests_tmp_check_read_write_705o5ww7
 83s PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM [W::sanitise_SQ_lines] Header @SQ length mismatch for ref chr1, 2147483647 vs 1575
 83s /tmp/autopkgtest.kUrCsn/build.Qdd/src/tests/tmp/pysamtests_tmp_check_read_write_0od0g8d9
 83s PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM [E::cram_index_load] Could not retrieve index file for '/tmp/autopkgtest.kUrCsn/build.Qdd/src/tests/tmp/pysamtests_tmp_check_read_write_77g56hjb'
 83s /tmp/autopkgtest.kUrCsn/build.Qdd/src/tests/tmp/pysamtests_tmp_check_read_write_77g56hjb
 83s PASSED
 83s tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM /tmp/autopkgtest.kUrCsn/build.Qdd/src/tests/tmp/pysamtests_tmp_check_read_write_v1n7xyio
 83s PASSED
 83s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_all_stepper PASSED
 83s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_ignore_overlaps PASSED
 83s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper PASSED
 83s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_base_quality_threshold PASSED
 83s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_ignore_orphans PASSED
 83s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_mapping_quality_threshold PASSED
 84s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_redo_baq PASSED
 84s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_all_stepper PASSED
 84s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_ignore_overlaps PASSED
 84s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper PASSED
 84s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_base_quality_threshold PASSED
 84s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_ignore_orphans PASSED
 84s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_mapping_quality_threshold PASSED
 84s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_redo_baq PASSED
 84s tests/AlignmentFilePileup_test.py::TestPileupQueryPosition::testPileup PASSED
 84s tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope SKIPPED
 84s tests/AlignmentFilePileup_test.py::TestPileupObjects::testPileupColumn PASSED
 84s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testInverse PASSED
 84s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateAll PASSED
 84s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIteratePerContig PASSED
 84s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateRanges PASSED
 84s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateTruncate PASSED
 84s tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testAccessOnClosedIterator PASSED
 84s tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStart PASSED
 84s tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStr PASSED
 84s tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testTruncate PASSED
 84s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_depths_are_equal PASSED
 84s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_mapping_qualities_are_equal PASSED
 84s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_with_reference_are_equal PASSED
 84s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_without_reference_are_equal PASSED
 84s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_are_equal PASSED
 84s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_from_pileups_are_equal PASSED
 84s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARQueryLength PASSED
 84s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigar PASSED
 84s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigarstring PASSED
 84s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARflag PASSED
 84s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmapq PASSED
 84s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmpos PASSED
 84s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmrnm PASSED
 84s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARpos PASSED
 84s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqname PASSED
 84s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqqual PASSED
 84s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqual PASSED
 84s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARquery PASSED
 84s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARrname PASSED
 84s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARseq PASSED
 84s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testOpt PASSED
 84s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPairedBools PASSED
 84s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPresentOptionalFields PASSED
 84s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testTags PASSED
 84s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARQueryLength PASSED
 84s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigar PASSED
 84s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigarstring PASSED
 84s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARflag PASSED
 84s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmapq PASSED
 84s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmpos PASSED
 84s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmrnm PASSED
 84s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARpos PASSED
 84s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqname PASSED
 84s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqqual PASSED
 84s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqual PASSED
 84s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARquery PASSED
 84s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARrname PASSED
 84s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARseq PASSED
 84s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testOpt PASSED
 84s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPairedBools PASSED
 84s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPresentOptionalFields PASSED
 84s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testTags PASSED
 84s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARQueryLength PASSED
 85s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigar PASSED
 85s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigarstring PASSED
 85s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARflag PASSED
 85s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmapq PASSED
 85s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmpos PASSED
 86s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmrnm PASSED
 86s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARpos PASSED
 86s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqname PASSED
 86s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqqual PASSED
 87s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqual PASSED
 87s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARquery PASSED
 87s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARrname PASSED
 87s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARseq PASSED
 87s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testOpt PASSED
 88s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPairedBools PASSED
 88s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPresentOptionalFields PASSED
 89s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testTags PASSED
 89s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARQueryLength PASSED
 89s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigar PASSED
 89s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigarstring PASSED
 89s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARflag PASSED
 89s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmapq PASSED
 89s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmpos PASSED
 89s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmrnm PASSED
 89s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARpos PASSED
 89s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqname PASSED
 89s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqqual PASSED
 89s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqual PASSED
 89s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARquery PASSED
 89s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARrname PASSED
 89s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARseq PASSED
 89s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testOpt PASSED
 89s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPairedBools PASSED
 89s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPresentOptionalFields PASSED
 89s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testTags PASSED
 89s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARQueryLength PASSED
 89s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigar PASSED
 89s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigarstring PASSED
 90s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARflag PASSED
 90s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmapq PASSED
 90s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmpos PASSED
 90s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmrnm PASSED
 90s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARpos PASSED
 90s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqname PASSED
 91s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqqual PASSED
 91s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqual PASSED
 91s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARquery PASSED
 92s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARrname PASSED
 92s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARseq PASSED
 92s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testOpt PASSED
 92s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPairedBools PASSED
 93s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPresentOptionalFields PASSED
 93s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testTags PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARQueryLength PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigar PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigarstring PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARflag PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmapq PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmpos PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmrnm PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARpos PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqname PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqqual PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqual PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARquery PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARrname PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARseq PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testOpt PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPairedBools PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPresentOptionalFields PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testTags PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARQueryLength PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigar PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigarstring PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARflag PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmapq PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmpos PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmrnm PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARpos PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqname PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqqual PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqual PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARquery PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARrname PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARseq PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testOpt PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPairedBools PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPresentOptionalFields PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testTags PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARQueryLength PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigar PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigarstring PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARflag PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmapq PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmpos PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmrnm PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARpos PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqname PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqqual PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqual PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARquery PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARrname PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARseq PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testOpt PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPairedBools PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPresentOptionalFields PASSED
 93s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testTags PASSED
 93s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARQueryLength PASSED
 93s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigar PASSED
 93s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigarstring PASSED
 93s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARflag PASSED
 93s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmapq PASSED
 93s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmpos PASSED
 93s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmrnm PASSED
 93s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARpos PASSED
 93s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqname PASSED
 93s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqqual PASSED
 93s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqual PASSED
 93s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARquery PASSED
 93s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARrname PASSED
 93s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARseq PASSED
 93s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testOpt PASSED
 93s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPairedBools PASSED
 93s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPresentOptionalFields PASSED
 93s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testTags PASSED
 93s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARQueryLength PASSED
 93s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigar PASSED
 93s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigarstring PASSED
 93s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARflag PASSED
 93s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmapq PASSED
 93s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmpos PASSED
 93s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmrnm PASSED
 93s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARpos PASSED
 93s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqname PASSED
 93s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqqual PASSED
 93s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqual PASSED
 93s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARquery PASSED
 93s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARrname PASSED
 93s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARseq PASSED
 93s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testOpt PASSED
 93s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPairedBools PASSED
 93s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPresentOptionalFields PASSED
 93s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testTags PASSED
 93s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARQueryLength PASSED
 93s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigar PASSED
 94s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigarstring PASSED
 94s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARflag PASSED
 94s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmapq PASSED
 94s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmpos PASSED
 94s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmrnm PASSED
 95s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARpos PASSED
 95s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqname PASSED
 95s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqqual PASSED
 96s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqual PASSED
 96s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARquery PASSED
 96s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARrname PASSED
 96s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARseq PASSED
 96s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testOpt PASSED
 97s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPairedBools PASSED
 97s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPresentOptionalFields PASSED
 97s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testTags PASSED
 98s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARQueryLength PASSED
 98s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigar PASSED
 98s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigarstring PASSED
 99s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARflag PASSED
 99s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmapq PASSED
 99s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmpos PASSED
 99s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmrnm PASSED
 99s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARpos PASSED
100s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqname PASSED
100s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqqual PASSED
100s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqual PASSED
101s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARquery PASSED
101s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARrname PASSED
101s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARseq PASSED
101s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testOpt PASSED
101s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPairedBools PASSED
102s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPresentOptionalFields PASSED
102s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testTags PASSED
102s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARQueryLength PASSED
102s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigar PASSED
102s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigarstring PASSED
102s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARflag PASSED
102s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmapq PASSED
102s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmpos PASSED
102s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmrnm PASSED
102s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARpos PASSED
102s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqname PASSED
102s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqqual PASSED
102s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqual PASSED
102s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARquery PASSED
102s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARrname PASSED
102s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARseq PASSED
102s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testOpt PASSED
102s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPairedBools PASSED
102s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPresentOptionalFields PASSED
102s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testRaises PASSED
102s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testTags PASSED
102s tests/AlignmentFile_test.py::TestIO::testBAM2BAM PASSED
102s tests/AlignmentFile_test.py::TestIO::testBAM2SAM PASSED
102s tests/AlignmentFile_test.py::TestIO::testBAMWithCSIIndex PASSED
102s tests/AlignmentFile_test.py::TestIO::testBAMWithShortBAI PASSED
102s tests/AlignmentFile_test.py::TestIO::testBAMWithoutAlignedSegments PASSED
102s tests/AlignmentFile_test.py::TestIO::testCRAM2BAM PASSED
103s tests/AlignmentFile_test.py::TestIO::testCRAM2CRAM PASSED
103s tests/AlignmentFile_test.py::TestIO::testCRAM2SAM PASSED
103s tests/AlignmentFile_test.py::TestIO::testEmptyBAM PASSED
103s tests/AlignmentFile_test.py::TestIO::testEmptyWithHeaderBAM PASSED
103s tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFile PASSED
103s tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject PASSED
103s tests/AlignmentFile_test.py::TestIO::testHead PASSED
103s tests/AlignmentFile_test.py::TestIO::testOpenFromFilename PASSED
103s tests/AlignmentFile_test.py::TestIO::testReadBamWithoutTargetNames PASSED
103s tests/AlignmentFile_test.py::TestIO::testReadSamWithoutTargetNames PASSED
103s tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex PASSED
103s tests/AlignmentFile_test.py::TestIO::testSAM2BAM PASSED
104s tests/AlignmentFile_test.py::TestIO::testSAM2CRAM PASSED
104s tests/AlignmentFile_test.py::TestIO::testSAM2SAM PASSED
104s tests/AlignmentFile_test.py::TestIO::testSAM2SAMWithoutHeader PASSED
104s tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile PASSED
104s tests/AlignmentFile_test.py::TestIO::test_accessing_attributes_in_closed_file_raises_errors PASSED
104s tests/AlignmentFile_test.py::TestIO::test_fail_read_sam_without_header PASSED
104s tests/AlignmentFile_test.py::TestIO::test_fail_when_reading_unformatted_files PASSED
104s tests/AlignmentFile_test.py::TestIO::test_fetch_by_tid PASSED
104s tests/AlignmentFile_test.py::TestIO::test_header_available_after_closing_file PASSED
104s tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_with_header_without_header_check PASSED
104s tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_without_header_with_refs PASSED
104s tests/AlignmentFile_test.py::TestIO::test_reference_name_available_after_closing_file PASSED
104s tests/AlignmentFile_test.py::TestIO::test_write_bam_to_unknown_path_fails [E::hts_open_format] Failed to open file "missing_directory/new_file.bam" : No such file or directory
104s PASSED
104s tests/AlignmentFile_test.py::TestAutoDetect::testBAM PASSED
104s tests/AlignmentFile_test.py::TestAutoDetect::testCRAM PASSED
104s tests/AlignmentFile_test.py::TestAutoDetect::testSAM PASSED
104s tests/AlignmentFile_test.py::TestIteratorRowBAM::testIteratePerContig PASSED
105s tests/AlignmentFile_test.py::TestIteratorRowBAM::testIterateRanges PASSED
105s tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate PASSED
105s tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIteratePerContig PASSED
114s tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIterateRanges PASSED
115s tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIteratePerContig PASSED
123s tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIterateRanges PASSED
123s tests/AlignmentFile_test.py::TestFloatTagBug::testFloatTagBug PASSED
123s tests/AlignmentFile_test.py::TestLargeFieldBug::testLargeFileBug PASSED
123s tests/AlignmentFile_test.py::TestClipping::testClipping PASSED
123s tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_bam_with_until_eof_reads_unmapped_reads PASSED
123s tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_sam_with_until_eof_reads_unmapped_reads PASSED
123s tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads PASSED
123s tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads_by_contig PASSED
123s tests/AlignmentFile_test.py::TestContextManager::testManager PASSED
123s tests/AlignmentFile_test.py::TestMultiThread::testSingleThreadEqualsMultithread PASSED
123s tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED
123s tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED
123s tests/AlignmentFile_test.py::TestExceptions::testBadContig PASSED
123s tests/AlignmentFile_test.py::TestExceptions::testMeaninglessCrap PASSED
123s tests/AlignmentFile_test.py::TestExceptions::testMissingFile PASSED
123s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangNewFormat PASSED
123s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeNewFormat PASSED
123s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeOldFormat PASSED
123s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeNewFormat PASSED
123s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeOldFormat PASSED
123s tests/AlignmentFile_test.py::TestExceptions::testZeroToZero PASSED
123s tests/AlignmentFile_test.py::TestWrongFormat::testOpenBamAsSam PASSED
123s tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsBam PASSED
123s tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsSam PASSED
123s tests/AlignmentFile_test.py::TestWrongFormat::testOpenSamAsBam PASSED
123s tests/AlignmentFile_test.py::TestRegionParsing::test_dash_in_chr PASSED
123s tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile PASSED
123s tests/AlignmentFile_test.py::TestDeNovoConstruction::test_pass_if_reads_binary_equal PASSED
123s tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader PASSED
123s tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_in_header PASSED
123s tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_with_null_bytes_in_header [E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory
123s [E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory
123s [E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory
123s [E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory
123s PASSED
123s tests/AlignmentFile_test.py::TestMismatchingHeader::testMismatchingHeader PASSED
124s tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader [W::bam_hdr_read] EOF marker is absent. The input is probably truncated
124s PASSED
124s tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2 PASSED
124s tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator [E::bgzf_read_block] Failed to read BGZF block data at offset 105176 expected 17578 bytes; hread returned 17094
124s [E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes
124s PASSED
124s tests/AlignmentFile_test.py::TestCorruptBAM::testCorruptBamIterator PASSED
124s tests/AlignmentFile_test.py::TestBTagSam::testReadTags PASSED
124s tests/AlignmentFile_test.py::TestBTagSam::testReadWriteTags PASSED
124s tests/AlignmentFile_test.py::TestBTagBam::testReadTags PASSED
124s tests/AlignmentFile_test.py::TestBTagBam::testReadWriteTags PASSED
124s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetch PASSED
124s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchUntilEOF PASSED
124s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionFalseTrue PASSED
124s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueFalse PASSED
124s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueTrue PASSED
124s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetch PASSED
124s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchUntilEOF PASSED
125s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionFalseTrue PASSED
125s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueFalse PASSED
126s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueTrue PASSED
126s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetch PASSED
127s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchUntilEOF PASSED
128s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionFalseTrue PASSED
128s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueFalse PASSED
129s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueTrue PASSED
129s tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetch PASSED
129s tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetchAll PASSED
129s tests/AlignmentFile_test.py::TestRemoteFileHTTP::testView PASSED
129s tests/AlignmentFile_test.py::TestLargeOptValues::testBAM PASSED
129s tests/AlignmentFile_test.py::TestLargeOptValues::testSAM PASSED
129s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_counts_as_expected PASSED
129s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_nofilter PASSED
129s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_quality_filter PASSED
129s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_all PASSED
129s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_callback PASSED
129s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_with_coordinates_works PASSED
129s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_without_coordinates_fails PASSED
129s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_wrong_coordinates_fails PASSED
129s tests/AlignmentFile_test.py::TestCountCoverage::test_counting_the_same_region_works PASSED
129s tests/AlignmentFile_test.py::TestFindIntrons::test_all PASSED
129s tests/AlignmentFile_test.py::TestFindIntrons::test_first PASSED
129s tests/AlignmentFile_test.py::TestFindIntrons::test_total PASSED
129s tests/AlignmentFile_test.py::TestLogging::testFail1 PASSED
129s tests/AlignmentFile_test.py::TestLogging::testNoFail1 PASSED
129s tests/AlignmentFile_test.py::TestLogging::testNoFail2 PASSED
129s tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testCount PASSED
129s tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testIndexStats PASSED
131s tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testMate PASSED
131s tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct PASSED
131s tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct_per_chromosome PASSED
131s tests/AlignmentFile_test.py::TestSamtoolsProxy::testIndex PASSED
131s tests/AlignmentFile_test.py::TestSamtoolsProxy::testSort [E::hts_open_format] Failed to open file "missing_file" : No such file or directory
131s PASSED
131s tests/AlignmentFile_test.py::TestSamtoolsProxy::testView PASSED[E::hts_open_format] Failed to open file "missing_file" : No such file or directory
131s 
131s tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED
131s tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM PASSED[W::hts_idx_load3] The index file is older than the data file: /tmp/autopkgtest.kUrCsn/build.Qdd/src/tests/pysam_data/ex1.bam.bai
131s 
131s tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexCRAM PASSED
131s tests/AlignmentFile_test.py::TestExplicitIndex::testRemoteExplicitIndexBAM PASSED
131s tests/AlignmentFile_test.py::TestVerbosity::testVerbosity PASSED
131s tests/AlignmentFile_test.py::TestSanityCheckingBAM::test_empty_read_gives_value_error PASSED
131s tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_bam PASSED
131s tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_cram SKIPPED
131s tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_sam PASSED
131s tests/StreamFiledescriptors_test.py::StreamTest::test_samtools_processing SKIPPED
131s tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing PASSED
131s tests/VariantFile_test.py::TestMissingGenotypes::testVCF PASSED
131s tests/VariantFile_test.py::TestMissingGenotypes::testVCFGZ PASSED
131s tests/VariantFile_test.py::TestMissingSamples::testVCF PASSED
131s tests/VariantFile_test.py::TestMissingSamples::testVCFGZ PASSED
131s tests/VariantFile_test.py::TestMissingSamplesFixed::testVCF PASSED
131s tests/VariantFile_test.py::TestMissingSamplesFixed::testVCFGZ [W::bcf_hdr_check_sanity] PL should be declared as Number=G
131s PASSED
131s tests/VariantFile_test.py::TestOpening::testDetectBCF PASSED
131s tests/VariantFile_test.py::TestOpening::testDetectVCF PASSED
131s tests/VariantFile_test.py::TestOpening::testDetectVCFGZ PASSED
131s tests/VariantFile_test.py::TestOpening::testEmptyFileVCF [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
131s [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.)
131s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
131s PASSED
131s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFFromPath PASSED
131s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZOnlyHeader PASSED
131s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithIndex PASSED
131s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithoutIndex PASSED
131s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFOnlyHeader PASSED
131s tests/VariantFile_test.py::TestOpening::testMissingFile PASSED[E::hts_open_format] Failed to open file "missing_file.vcf" : No such file or directory
131s 
131s tests/VariantFile_test.py::TestOpening::testMissingFileVCFGZ PASSED[E::hts_open_format] Failed to open file "missing_file.vcf.gz" : No such file or directory
131s 
131s tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_csi_index PASSED
131s tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_prebuilt_csi PASSED
131s tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_tbi_index_will_produce_csi PASSED
131s tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_csi_index PASSED
131s tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_tbi_index PASSED
131s tests/VariantFile_test.py::TestHeader::testIterator PASSED
131s tests/VariantFile_test.py::TestHeader::testStr PASSED
131s tests/VariantFile_test.py::TestParsing::testAlleles PASSED
131s tests/VariantFile_test.py::TestParsing::testAllelesVariantTypes PASSED
131s tests/VariantFile_test.py::TestParsing::testAlt PASSED
131s tests/VariantFile_test.py::TestParsing::testChrom PASSED
131s tests/VariantFile_test.py::TestParsing::testChromFromPath PASSED
131s tests/VariantFile_test.py::TestParsing::testFilter PASSED
131s tests/VariantFile_test.py::TestParsing::testFormat PASSED
131s tests/VariantFile_test.py::TestParsing::testId PASSED
131s tests/VariantFile_test.py::TestParsing::testInfo PASSED
131s tests/VariantFile_test.py::TestParsing::testPos PASSED
131s tests/VariantFile_test.py::TestParsing::testQual PASSED
131s tests/VariantFile_test.py::TestParsing::testRef PASSED
131s tests/VariantFile_test.py::TestParsing::testSampleAlleleIndices PASSED
131s tests/VariantFile_test.py::TestParsing::testSampleAlleles PASSED
131s tests/VariantFile_test.py::TestParsing::testSampleFormats PASSED
131s tests/VariantFile_test.py::TestParsing::testStart PASSED
131s tests/VariantFile_test.py::TestParsing::testStop PASSED
131s tests/VariantFile_test.py::TestIndexFilename::testOpen PASSED
131s tests/VariantFile_test.py::TestConstructionVCFWithContigs::testBase PASSED
131s tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionFromCopy PASSED
131s tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithLines PASSED
131s tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithRecords PASSED
131s tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testBase PASSED
131s tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionFromCopy PASSED
131s tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithLines PASSED
131s tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithRecords PASSED
131s tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testBase PASSED
131s tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionFromCopy PASSED
131s tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithLines PASSED
131s tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithRecords PASSED
131s tests/VariantFile_test.py::TestSettingRecordValues::testBase PASSED
131s tests/VariantFile_test.py::TestSettingRecordValues::testGenotype (0, 0)
131s PASSED[W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
131s 
131s tests/VariantFile_test.py::TestSettingRecordValues::testSetQual [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
131s PASSED
131s tests/VariantFile_test.py::TestMultiThreading::testNoMultiThreadingWithIgnoreTruncation PASSED
131s tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult PASSED[E::idx_find_and_load] Could not retrieve index file for '/tmp/autopkgtest.kUrCsn/build.Qdd/src/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithreadResult_64fuf2eg.bcf'
131s 
131s tests/VariantFile_test.py::TestSubsetting::testSubsetting PASSED
131s tests/VariantFile_test.py::TestVCFVersions::test_all_records_can_be_fetched [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
131s [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.)
131s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
131s [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
131s [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.)
131s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
131s PASSED
131s tests/VariantFile_test.py::TestUnicode::test_record_with_unicode PASSED
131s tests/VariantRecord_test.py::test_ascii_annotation_can_be_added PASSED
131s tests/VariantRecord_test.py::test_ascii_annotation_with_variable_length_can_be_added PASSED
131s tests/VariantRecord_test.py::test_unicode_annotation_can_be_added PASSED
131s tests/VariantRecord_test.py::test_set_sample_alleles PASSED
131s tests/compile_test.py::test_bam SKIPPED (no pyximport)
131s tests/compile_test.py::test_gtf SKIPPED (no pyximport)
131s tests/faidx_test.py::TestFastaFile::testFetch PASSED
131s tests/faidx_test.py::TestFastaFile::testFetchErrors PASSED
131s tests/faidx_test.py::TestFastaFile::testLength PASSED
131s tests/faidx_test.py::TestFastaFile::testOutOfRangeAccess PASSED
131s tests/faidx_test.py::TestFastaFile::testSequenceLengths PASSED
131s tests/faidx_test.py::TestFastaFile::test_fetch_with_region_and_contig_raises_exception PASSED
131s tests/faidx_test.py::TestFastaFile::test_fetch_with_region_is_equivalent PASSED
131s tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED
131s tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_index_succeeds PASSED
131s tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_without_index_succeeds PASSED
131s tests/faidx_test.py::TestFastaFilePathIndex::test_raise_exception_if_index_is_missing PASSED
131s tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED
131s tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_index_succeeds PASSED
131s tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_without_index_succeeds PASSED
131s tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_raise_exception_if_index_is_missing PASSED
131s tests/faidx_test.py::TestFastxFileFastq::testCounts PASSED
131s tests/faidx_test.py::TestFastxFileFastq::testManager PASSED
131s tests/faidx_test.py::TestFastxFileFastq::testMissingFile PASSED
131s tests/faidx_test.py::TestFastxFileFastq::testSequence PASSED
131s tests/faidx_test.py::TestFastqFileFastq::testCounts PASSED
131s tests/faidx_test.py::TestFastqFileFastq::testManager PASSED
131s tests/faidx_test.py::TestFastqFileFastq::testMissingFile PASSED
131s tests/faidx_test.py::TestFastqFileFastq::testSequence PASSED
131s tests/faidx_test.py::TestFastxFileFasta::testCounts PASSED
131s tests/faidx_test.py::TestFastxFileFasta::testManager PASSED
131s tests/faidx_test.py::TestFastxFileFasta::testMissingFile PASSED
131s tests/faidx_test.py::TestFastxFileFasta::testSequence PASSED
131s tests/faidx_test.py::TestFastxFileFastqStream::testCounts PASSED
131s tests/faidx_test.py::TestFastxFileFastqStream::testManager PASSED
131s tests/faidx_test.py::TestFastxFileFastqStream::testMissingFile PASSED
131s tests/faidx_test.py::TestFastxFileFastqStream::testSequence PASSED
131s tests/faidx_test.py::TestFastxFileWithEmptySequence::testIteration PASSED
133s tests/faidx_test.py::TestRemoteFileFTP::testFTPView PASSED
134s tests/faidx_test.py::TestRemoteFileFTP::test_sequence_lengths_are_available PASSED
134s tests/faidx_test.py::TestFastqRecord::test_fastx_record_can_be_created_from_scratch PASSED
134s tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_None PASSED
134s tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_modified PASSED
134s tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_name_is_None PASSED
134s tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_quality_is_wrong_length PASSED
134s tests/faidx_test.py::TestFastqRecord::test_fastx_record_name_can_be_modified PASSED
134s tests/faidx_test.py::TestFastqRecord::test_fastx_record_quality_can_be_modified PASSED
134s tests/faidx_test.py::TestFastqRecord::test_fastx_record_sequence_can_be_modified PASSED
134s tests/faidx_test.py::TestFastqProxy::test_fastq_proxy_instantiation_raises_error PASSED
134s tests/linking_test.py::TestLinking::test_package_can_be_installed SKIPPED
134s tests/linking_test.py::TestLinkWithRpath::test_package_can_be_installed SKIPPED
134s tests/linking_test.py::TestLinkWithRpath::test_package_tests_pass SKIPPED
134s tests/linking_test.py::TestLinkWithoutRpath::test_package_can_be_installed SKIPPED
134s tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_fail_on_import SKIPPED
134s tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_pass_if_ld_library_path_set SKIPPED
135s tests/samtools_test.py::SamtoolsTest::testStatements PASSED
135s tests/samtools_test.py::SamtoolsTest::testUsage SKIPPED (skipping us...)
135s tests/samtools_test.py::EmptyIndexTest::testEmptyIndex PASSED
135s tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraArg PASSED
135s tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraFlag PASSED
135s tests/samtools_test.py::TestReturnType::testReturnValueData PASSED
135s tests/samtools_test.py::TestReturnType::testReturnValueString PASSED
135s tests/samtools_test.py::StdoutTest::testDoubleCalling PASSED
135s tests/samtools_test.py::StdoutTest::testSaveStdout PASSED
135s tests/samtools_test.py::StdoutTest::testWithRedirectedStdout PASSED
135s tests/samtools_test.py::StdoutTest::testWithoutRedirectedStdout PASSED
136s tests/samtools_test.py::PysamTest::testStatements PASSED
136s tests/samtools_test.py::PysamTest::testUsage SKIPPED (skipping usage...)
136s tests/tabix_test.py::TestIndexing::test_indexing_to_custom_location_works PASSED
136s tests/tabix_test.py::TestIndexing::test_indexing_with_explict_columns_works PASSED
136s tests/tabix_test.py::TestIndexing::test_indexing_with_lineskipping_works PASSED
136s tests/tabix_test.py::TestIndexing::test_indexing_with_preset_works PASSED
136s tests/tabix_test.py::TestCompression::testCompression PASSED
136s tests/tabix_test.py::TestCompression::testIndexPresetCompressed PASSED
136s tests/tabix_test.py::TestCompression::testIndexPresetUncompressed PASSED
136s tests/tabix_test.py::TestCompressionSam::testCompression PASSED
136s tests/tabix_test.py::TestCompressionSam::testIndexPresetCompressed PASSED
136s tests/tabix_test.py::TestCompressionSam::testIndexPresetUncompressed PASSED
136s tests/tabix_test.py::TestCompressionBed::testCompression PASSED
136s tests/tabix_test.py::TestCompressionBed::testIndexPresetCompressed PASSED
136s tests/tabix_test.py::TestCompressionBed::testIndexPresetUncompressed PASSED
136s tests/tabix_test.py::TestCompressionVCF::testCompression PASSED
136s tests/tabix_test.py::TestCompressionVCF::testIndexPresetCompressed PASSED
136s tests/tabix_test.py::TestCompressionVCF::testIndexPresetUncompressed PASSED
136s tests/tabix_test.py::TestGZFile::testAll PASSED
136s tests/tabix_test.py::TestIterationWithoutComments::testAll PASSED
136s tests/tabix_test.py::TestIterationWithoutComments::testGetContigs PASSED
136s tests/tabix_test.py::TestIterationWithoutComments::testHeader PASSED
136s tests/tabix_test.py::TestIterationWithoutComments::testInvalidIntervals PASSED
136s tests/tabix_test.py::TestIterationWithoutComments::testPerContig PASSED
136s tests/tabix_test.py::TestIterationWithoutComments::testPerContig2 PASSED
136s tests/tabix_test.py::TestIterationWithoutComments::testPerContigFromStart PASSED
136s tests/tabix_test.py::TestIterationWithoutComments::testPerContigToEnd PASSED
136s tests/tabix_test.py::TestIterationWithoutComments::testPerInterval PASSED
136s tests/tabix_test.py::TestIterationWithoutComments::testRegionStrings PASSED
136s tests/tabix_test.py::TestIterationWithoutComments::testReopening PASSED
136s tests/tabix_test.py::TestIterationWithComments::testAll PASSED
136s tests/tabix_test.py::TestIterationWithComments::testGetContigs PASSED
136s tests/tabix_test.py::TestIterationWithComments::testHeader PASSED
136s tests/tabix_test.py::TestIterationWithComments::testInvalidIntervals PASSED
137s tests/tabix_test.py::TestIterationWithComments::testPerContig PASSED
137s tests/tabix_test.py::TestIterationWithComments::testPerContig2 PASSED
137s tests/tabix_test.py::TestIterationWithComments::testPerContigFromStart PASSED
137s tests/tabix_test.py::TestIterationWithComments::testPerContigToEnd PASSED
137s tests/tabix_test.py::TestIterationWithComments::testPerInterval PASSED
137s tests/tabix_test.py::TestIterationWithComments::testRegionStrings PASSED
137s tests/tabix_test.py::TestIterationWithComments::testReopening PASSED
137s tests/tabix_test.py::TestIterators::testClosedFile PASSED
137s tests/tabix_test.py::TestIterators::testClosedFileIteration PASSED
137s tests/tabix_test.py::TestIterators::testIteration PASSED
137s tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFile PASSED
137s tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFileIteration PASSED
137s tests/tabix_test.py::TestIteratorsGenericCompressed::testIteration PASSED
137s tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFile PASSED
137s tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFileIteration PASSED
137s tests/tabix_test.py::TestIteratorsFileCompressed::testIteration PASSED
137s tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFile PASSED
137s tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFileIteration PASSED
137s tests/tabix_test.py::TestIteratorsFileUncompressed::testIteration PASSED
137s tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooFewFields PASSED
137s tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooManyFields PASSED
137s tests/tabix_test.py::TestBed::testRead PASSED
137s tests/tabix_test.py::TestBed::testWrite PASSED
137s tests/tabix_test.py::TestUnicode::testFromTabix PASSED
137s tests/tabix_test.py::TestUnicode::testFromVCF PASSED
137s tests/tabix_test.py::TestVCFFromTabix::testRead PASSED
137s tests/tabix_test.py::TestVCFFromTabix::testWrite PASSED
137s tests/tabix_test.py::TestVCFFromVCF::testConnecting PASSED
137s tests/tabix_test.py::TestVCFFromVCF::testParsing PASSED
137s tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testRead PASSED
137s tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testWrite PASSED
137s tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testConnecting PASSED
137s tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testParsing PASSED
137s tests/tabix_test.py::VCFFromTabixTest_4::testRead PASSED
137s tests/tabix_test.py::VCFFromTabixTest_4::testWrite PASSED
137s tests/tabix_test.py::VCFFromVCFTest_4::testConnecting PASSED
138s tests/tabix_test.py::VCFFromVCFTest_4::testParsing PASSED
138s tests/tabix_test.py::VCFFromTabixTest_12::testRead PASSED
138s tests/tabix_test.py::VCFFromTabixTest_12::testWrite PASSED
138s tests/tabix_test.py::VCFFromVCFTest_12::testConnecting PASSED
138s tests/tabix_test.py::VCFFromVCFTest_12::testParsing PASSED
138s tests/tabix_test.py::VCFFromTabixTest_20::testRead PASSED
138s tests/tabix_test.py::VCFFromTabixTest_20::testWrite PASSED
138s tests/tabix_test.py::VCFFromVCFTest_20::testConnecting PASSED
138s tests/tabix_test.py::VCFFromVCFTest_20::testParsing PASSED
138s tests/tabix_test.py::VCFFromTabixTest_8::testRead PASSED
138s tests/tabix_test.py::VCFFromTabixTest_8::testWrite PASSED
138s tests/tabix_test.py::VCFFromVCFTest_8::testConnecting PASSED
138s tests/tabix_test.py::VCFFromVCFTest_8::testParsing PASSED
138s tests/tabix_test.py::VCFFromTabixTest_16::testRead PASSED
138s tests/tabix_test.py::VCFFromTabixTest_16::testWrite PASSED
138s tests/tabix_test.py::VCFFromVCFTest_16::testConnecting PASSED
138s tests/tabix_test.py::VCFFromVCFTest_16::testParsing PASSED
138s tests/tabix_test.py::VCFFromTabixTest_5::testRead PASSED
138s tests/tabix_test.py::VCFFromTabixTest_5::testWrite PASSED
138s tests/tabix_test.py::VCFFromVCFTest_5::testConnecting PASSED
138s tests/tabix_test.py::VCFFromVCFTest_5::testParsing PASSED
138s tests/tabix_test.py::VCFFromTabixTest_11::testRead PASSED
139s tests/tabix_test.py::VCFFromTabixTest_11::testWrite PASSED
139s tests/tabix_test.py::VCFFromVCFTest_11::testConnecting PASSED
139s tests/tabix_test.py::VCFFromVCFTest_11::testParsing PASSED
139s tests/tabix_test.py::VCFFromTabixTest_9::testRead PASSED
139s tests/tabix_test.py::VCFFromTabixTest_9::testWrite PASSED
139s tests/tabix_test.py::VCFFromVCFTest_9::testConnecting PASSED
139s tests/tabix_test.py::VCFFromVCFTest_9::testParsing PASSED
139s tests/tabix_test.py::VCFFromTabixTest_24::testRead PASSED
139s tests/tabix_test.py::VCFFromTabixTest_24::testWrite PASSED
139s tests/tabix_test.py::VCFFromVCFTest_24::testConnecting PASSED
139s tests/tabix_test.py::VCFFromVCFTest_24::testParsing PASSED
139s tests/tabix_test.py::VCFFromTabixTest_13::testRead PASSED
139s tests/tabix_test.py::VCFFromTabixTest_13::testWrite PASSED
139s tests/tabix_test.py::VCFFromVCFTest_13::testConnecting PASSED
139s tests/tabix_test.py::VCFFromVCFTest_13::testParsing PASSED
139s tests/tabix_test.py::VCFFromTabixTest_18::testRead PASSED
139s tests/tabix_test.py::VCFFromTabixTest_18::testWrite PASSED
139s tests/tabix_test.py::VCFFromVCFTest_18::testConnecting PASSED
139s tests/tabix_test.py::VCFFromVCFTest_18::testParsing PASSED
139s tests/tabix_test.py::VCFFromTabixTest_23::testRead PASSED
139s tests/tabix_test.py::VCFFromTabixTest_23::testWrite PASSED
139s tests/tabix_test.py::VCFFromVCFTest_23::testConnecting PASSED
139s tests/tabix_test.py::VCFFromVCFTest_23::testParsing PASSED
140s tests/tabix_test.py::VCFFromTabixTest_22::testRead PASSED
140s tests/tabix_test.py::VCFFromTabixTest_22::testWrite PASSED
140s tests/tabix_test.py::VCFFromVCFTest_22::testConnecting PASSED
141s tests/tabix_test.py::VCFFromVCFTest_22::testParsing PASSED
141s tests/tabix_test.py::VCFFromTabixTest_issue85::testRead PASSED
141s tests/tabix_test.py::VCFFromTabixTest_issue85::testWrite PASSED
141s tests/tabix_test.py::VCFFromVCFTest_issue85::testConnecting PASSED
141s tests/tabix_test.py::VCFFromVCFTest_issue85::testParsing PASSED
141s tests/tabix_test.py::VCFFromTabixTest_7::testRead PASSED
141s tests/tabix_test.py::VCFFromTabixTest_7::testWrite PASSED
141s tests/tabix_test.py::VCFFromVCFTest_7::testConnecting PASSED
141s tests/tabix_test.py::VCFFromVCFTest_7::testParsing PASSED
141s tests/tabix_test.py::VCFFromTabixTest_3::testRead PASSED
141s tests/tabix_test.py::VCFFromTabixTest_3::testWrite PASSED
141s tests/tabix_test.py::VCFFromVCFTest_3::testConnecting PASSED
142s tests/tabix_test.py::VCFFromVCFTest_3::testParsing PASSED
142s tests/tabix_test.py::VCFFromTabixTest_6::testRead PASSED
142s tests/tabix_test.py::VCFFromTabixTest_6::testWrite PASSED
142s tests/tabix_test.py::VCFFromVCFTest_6::testConnecting PASSED
142s tests/tabix_test.py::VCFFromVCFTest_6::testParsing PASSED
142s tests/tabix_test.py::VCFFromTabixTest_2::testRead PASSED
142s tests/tabix_test.py::VCFFromTabixTest_2::testWrite PASSED
142s tests/tabix_test.py::VCFFromVCFTest_2::testConnecting PASSED
142s tests/tabix_test.py::VCFFromVCFTest_2::testParsing PASSED
142s tests/tabix_test.py::VCFFromTabixTest_15::testRead PASSED
143s tests/tabix_test.py::VCFFromTabixTest_15::testWrite PASSED
143s tests/tabix_test.py::VCFFromVCFTest_15::testConnecting PASSED
143s tests/tabix_test.py::VCFFromVCFTest_15::testParsing PASSED
143s tests/tabix_test.py::VCFFromTabixTest_10::testRead PASSED
143s tests/tabix_test.py::VCFFromTabixTest_10::testWrite PASSED
143s tests/tabix_test.py::VCFFromVCFTest_10::testConnecting PASSED
143s tests/tabix_test.py::VCFFromVCFTest_10::testParsing PASSED
143s tests/tabix_test.py::VCFFromTabixTest_21::testRead PASSED
143s tests/tabix_test.py::VCFFromTabixTest_21::testWrite PASSED
143s tests/tabix_test.py::VCFFromVCFTest_21::testConnecting PASSED
143s tests/tabix_test.py::VCFFromVCFTest_21::testParsing PASSED
143s tests/tabix_test.py::TestVCFFromVariantFile::testConnecting PASSED
143s tests/tabix_test.py::TestVCFFromVariantFile::testParsing [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
143s [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.)
143s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
143s PASSED
143s tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testConnecting PASSED
143s tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testParsing PASSED
143s tests/tabix_test.py::TestVCFFromVariantFile_4::testConnecting [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
143s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:249843 is not defined in the header, assuming Type=String
143s PASSED
144s tests/tabix_test.py::TestVCFFromVariantFile_4::testParsing PASSED
144s tests/tabix_test.py::TestVCFFromVariantFile_12::testConnecting PASSED
144s tests/tabix_test.py::TestVCFFromVariantFile_12::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
144s [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String
144s [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String
144s [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String
144s [W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String
144s [W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String
144s [W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String
144s [W::vcf_parse_format_dict2] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String
144s [W::vcf_parse_format_dict2] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String
144s [W::vcf_parse_format_dict2] FORMAT 'GQ' at chr1:1281168 is not defined in the header, assuming Type=String
144s [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.)
144s [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.)
144s [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
144s [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.)
144s [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.)
144s [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.)
144s [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.)
144s [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.)
144s [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.)
144s [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.)
144s [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.)
144s [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.)
144s [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.)
144s [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.)
144s [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.)
144s [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.)
144s [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.)
144s [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.)
144s [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.)
144s PASSED
144s tests/tabix_test.py::TestVCFFromVariantFile_20::testConnecting [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0
144s PASSED
144s tests/tabix_test.py::TestVCFFromVariantFile_20::testParsing [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0
144s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
144s PASSED
144s tests/tabix_test.py::TestVCFFromVariantFile_8::testConnecting PASSED
144s tests/tabix_test.py::TestVCFFromVariantFile_8::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
144s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:676148 is not defined in the header, assuming Type=String
144s PASSED
144s tests/tabix_test.py::TestVCFFromVariantFile_16::testConnecting [W::bcf_hdr_check_sanity] GL should be declared as Number=G
144s PASSED
144s tests/tabix_test.py::TestVCFFromVariantFile_16::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
144s [W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String
144s PASSED
144s tests/tabix_test.py::TestVCFFromVariantFile_5::testConnecting PASSED
144s tests/tabix_test.py::TestVCFFromVariantFile_5::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
144s PASSED
144s tests/tabix_test.py::TestVCFFromVariantFile_11::testConnecting PASSED
144s tests/tabix_test.py::TestVCFFromVariantFile_11::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
144s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:669442 is not defined in the header, assuming Type=String
145s PASSED
145s tests/tabix_test.py::TestVCFFromVariantFile_9::testConnecting PASSED
145s tests/tabix_test.py::TestVCFFromVariantFile_9::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String
145s [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String
145s [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String
145s [W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String
145s [W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String
145s [W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String
145s [W::vcf_parse_format_dict2] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String
145s [W::vcf_parse_format_dict2] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String
145s [W::vcf_parse_format_dict2] FORMAT 'GQ' at chr1:1281168 is not defined in the header, assuming Type=String
145s [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.)
145s PASSED
145s tests/tabix_test.py::TestVCFFromVariantFile_24::testConnecting PASSED
145s tests/tabix_test.py::TestVCFFromVariantFile_24::testParsing [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs:
145s 	#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
145s 
145s PASSED
145s tests/tabix_test.py::TestVCFFromVariantFile_13::testConnecting PASSED
145s tests/tabix_test.py::TestVCFFromVariantFile_13::testParsing [W::bcf_hrec_check] Invalid tag name: "1000g"
145s [W::bcf_hrec_check] Invalid tag name: "GT:GL:GQ:NR"
145s [W::bcf_hrec_check] Invalid tag name: "1000g"
145s [W::bcf_hrec_check] Invalid tag name: "GT:GL:GQ:NR"
145s [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse_info] INFO 'MMLQ' is not defined in the header, assuming Type=String
145s [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr17_gl000205_random' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr18' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr19' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr20' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr21' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr22' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chrUn_gl000214' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chrUn_gl000220' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chrUn_gl000225' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chrX' is not defined in the header. (Quick workaround: index the file with tabix.)
145s PASSED
145s tests/tabix_test.py::TestVCFFromVariantFile_18::testConnecting PASSED
145s tests/tabix_test.py::TestVCFFromVariantFile_18::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String
145s [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String
145s [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String
145s [W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String
145s [W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String
145s [W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String
145s [W::vcf_parse_format_dict2] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String
145s [W::vcf_parse_format_dict2] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String
145s [W::vcf_parse_format_dict2] FORMAT 'GQ' at chr1:1281168 is not defined in the header, assuming Type=String
145s [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.)
145s PASSED
145s tests/tabix_test.py::TestVCFFromVariantFile_23::testConnecting PASSED
145s tests/tabix_test.py::TestVCFFromVariantFile_23::testParsing [W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String
145s PASSED
145s tests/tabix_test.py::TestVCFFromVariantFile_22::testConnecting PASSED
145s tests/tabix_test.py::TestVCFFromVariantFile_22::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
145s [W::vcf_parse_info] INFO 'refseq.name' is not defined in the header, assuming Type=String
145s [W::vcf_parse_info] INFO 'refseq.positionType' is not defined in the header, assuming Type=String
145s [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.)
146s PASSED
146s tests/tabix_test.py::TestVCFFromVariantFile_issue85::testConnecting [E::bcf_hdr_parse] Could not parse the header, sample line not found
146s PASSED
146s tests/tabix_test.py::TestVCFFromVariantFile_issue85::testParsing PASSED
146s tests/tabix_test.py::TestVCFFromVariantFile_7::testConnecting PASSED
146s tests/tabix_test.py::TestVCFFromVariantFile_7::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
146s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:249843 is not defined in the header, assuming Type=String
146s PASSED
146s tests/tabix_test.py::TestVCFFromVariantFile_3::testConnecting PASSED
146s tests/tabix_test.py::TestVCFFromVariantFile_3::testParsing [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.)
146s PASSED
146s tests/tabix_test.py::TestVCFFromVariantFile_6::testConnecting PASSED
146s tests/tabix_test.py::TestVCFFromVariantFile_6::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
146s [W::vcf_parse_info] INFO 'CallSetAC' is not defined in the header, assuming Type=String
146s [W::vcf_parse_info] INFO 'CallSetAC2' is not defined in the header, assuming Type=String
146s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:669442 is not defined in the header, assuming Type=String
146s PASSED
146s tests/tabix_test.py::TestVCFFromVariantFile_2::testConnecting PASSED
146s tests/tabix_test.py::TestVCFFromVariantFile_2::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
146s [W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String
146s PASSED
147s tests/tabix_test.py::TestVCFFromVariantFile_15::testConnecting PASSED
147s tests/tabix_test.py::TestVCFFromVariantFile_15::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
147s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:439104 is not defined in the header, assuming Type=String
147s PASSED
147s tests/tabix_test.py::TestVCFFromVariantFile_10::testConnecting PASSED
147s tests/tabix_test.py::TestVCFFromVariantFile_10::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
147s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:676148 is not defined in the header, assuming Type=String
147s PASSED
147s tests/tabix_test.py::TestVCFFromVariantFile_21::testConnecting [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0
147s PASSED
147s tests/tabix_test.py::TestVCFFromVariantFile_21::testParsing [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0
147s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
147s PASSED
147s tests/tabix_test.py::TestIndexArgument::testFetchAll PASSED
147s tests/tabix_test.py::TestIndexArgument::testLoadIndexWithoutTbiExtension PASSED
147s tests/tabix_test.py::TestBackwardsCompatibility::testBED PASSED
147s tests/tabix_test.py::TestBackwardsCompatibility::testBED0v23 PASSED
147s tests/tabix_test.py::TestBackwardsCompatibility::testBED0v26 PASSED
147s tests/tabix_test.py::TestBackwardsCompatibility::testEmpty PASSED
147s tests/tabix_test.py::TestBackwardsCompatibility::testVCF PASSED
147s tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v23 PASSED
147s tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v26 PASSED
147s tests/tabix_test.py::TestMultipleIterators::testDisjointIterators PASSED
147s tests/tabix_test.py::TestMultipleIterators::testDoubleFetch PASSED
147s tests/tabix_test.py::TestMultipleIterators::testJoinedIterators PASSED
147s tests/tabix_test.py::TestMultipleIterators::testScope PASSED
147s tests/tabix_test.py::TestContextManager::testManager PASSED
147s tests/tabix_test.py::TestMultithreadTabixFile::testMultithreadEqualsSinglethread PASSED
147s tests/tabixproxies_test.py::TestBED::testAssignmentToTargetList PASSED
147s tests/tabixproxies_test.py::TestParser::testAssignmentToTargetList PASSED
147s tests/tabixproxies_test.py::TestParser::testCopy PASSED
147s tests/tabixproxies_test.py::TestParser::testIteratorCompressed PASSED
147s tests/tabixproxies_test.py::TestParser::testIteratorUncompressed PASSED
147s tests/tabixproxies_test.py::TestParser::testRead PASSED
147s tests/tabixproxies_test.py::TestParser::testUnset PASSED
147s tests/tabixproxies_test.py::TestParser::testWrite PASSED
147s tests/tabixproxies_test.py::TestGTF::testAssignmentToTargetList PASSED
147s tests/tabixproxies_test.py::TestGTF::testCopy PASSED
147s tests/tabixproxies_test.py::TestGTF::testIteratorCompressed PASSED
147s tests/tabixproxies_test.py::TestGTF::testIteratorUncompressed PASSED
147s tests/tabixproxies_test.py::TestGTF::testRead PASSED
147s tests/tabixproxies_test.py::TestGTF::testUnset PASSED
147s tests/tabixproxies_test.py::TestGTF::testWrite PASSED
147s tests/tabixproxies_test.py::TestGTF::test_added_attribute_is_output PASSED
147s tests/tabixproxies_test.py::TestGTF::test_asdict_can_be_modified PASSED
147s tests/tabixproxies_test.py::TestGTF::test_asdict_contains_attributes PASSED
147s tests/tabixproxies_test.py::TestGTF::test_setAttribute_makes_changes PASSED
147s tests/tabixproxies_test.py::TestGTF::test_setting_end_is_one_based PASSED
147s tests/tabixproxies_test.py::TestGTF::test_setting_feature_to_none_produces_dot PASSED
147s tests/tabixproxies_test.py::TestGTF::test_setting_fields PASSED
147s tests/tabixproxies_test.py::TestGTF::test_setting_frame_to_none_produces_dot PASSED
147s tests/tabixproxies_test.py::TestGTF::test_setting_score_to_none_produces_dot PASSED
147s tests/tabixproxies_test.py::TestGTF::test_setting_source_to_none_produces_dot PASSED
147s tests/tabixproxies_test.py::TestGTF::test_setting_start_is_one_based PASSED
147s tests/tabixproxies_test.py::TestGTF::test_setting_strand_to_none_produces_dot PASSED
147s tests/tabixproxies_test.py::TestGFF3::testAssignmentToTargetList PASSED
147s tests/tabixproxies_test.py::TestGFF3::testCopy PASSED
147s tests/tabixproxies_test.py::TestGFF3::testIteratorCompressed PASSED
147s tests/tabixproxies_test.py::TestGFF3::testIteratorUncompressed PASSED
147s tests/tabixproxies_test.py::TestGFF3::testRead PASSED
147s tests/tabixproxies_test.py::TestGFF3::testUnset PASSED
147s tests/tabixproxies_test.py::TestGFF3::testWrite PASSED
147s tests/tabixproxies_test.py::TestGFF3::test_added_attribute_is_output PASSED
147s tests/tabixproxies_test.py::TestGFF3::test_asdict_can_be_modified PASSED
147s tests/tabixproxies_test.py::TestGFF3::test_asdict_contains_attributes PASSED
147s tests/tabixproxies_test.py::TestGFF3::test_setAttribute_makes_changes PASSED
147s tests/tabixproxies_test.py::TestGFF3::test_setting_end_is_one_based PASSED
147s tests/tabixproxies_test.py::TestGFF3::test_setting_feature_to_none_produces_dot PASSED
147s tests/tabixproxies_test.py::TestGFF3::test_setting_fields PASSED
147s tests/tabixproxies_test.py::TestGFF3::test_setting_frame_to_none_produces_dot PASSED
147s tests/tabixproxies_test.py::TestGFF3::test_setting_score_to_none_produces_dot PASSED
147s tests/tabixproxies_test.py::TestGFF3::test_setting_source_to_none_produces_dot PASSED
147s tests/tabixproxies_test.py::TestGFF3::test_setting_start_is_one_based PASSED
147s tests/tabixproxies_test.py::TestGFF3::test_setting_strand_to_none_produces_dot PASSED
147s tests/test_samtools_python.py::test_idxstats_parse_split_lines PASSED
147s tests/test_samtools_python.py::test_bedcov_split_lines PASSED
147s tests/test_samtools_python.py::test_idxstats_parse PASSED
147s tests/test_samtools_python.py::test_bedcov PASSED
147s 
147s =============================== warnings summary ===============================
147s tests/samtools_test.py::SamtoolsTest::testStatements
147s tests/samtools_test.py::PysamTest::testStatements
147s   /tmp/autopkgtest.kUrCsn/build.Qdd/src/tests/samtools_test.py:137: UserWarning: versions of pysam.samtools and samtools differ: 1.18 != 1.20
147s     warnings.warn(
147s 
147s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
147s ============ 938 passed, 13 skipped, 2 warnings in 65.10s (0:01:05) ============
148s autopkgtest [15:03:46]: test command1: -----------------------]
148s command1             PASSautopkgtest [15:03:46]: test command1:  - - - - - - - - - - results - - - - - - - - - -
148s 
148s autopkgtest [15:03:46]: test autodep8-python3: preparing testbed
204s autopkgtest [15:04:42]: testbed dpkg architecture: amd64
204s autopkgtest [15:04:42]: testbed apt version: 2.9.8
204s autopkgtest [15:04:42]: @@@@@@@@@@@@@@@@@@@@ test bed setup
204s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
204s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB]
204s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [966 kB]
204s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [105 kB]
204s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
204s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [81.3 kB]
204s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [141 kB]
204s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB]
204s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [741 kB]
204s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [290 kB]
204s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [1084 B]
204s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [9252 B]
204s Fetched 2463 kB in 0s (7655 kB/s)
204s Reading package lists...
206s Reading package lists...
206s Building dependency tree...
206s Reading state information...
206s Calculating upgrade...
207s The following NEW packages will be installed:
207s   python3.13-gdbm
207s The following packages will be upgraded:
207s   libpython3-stdlib pastebinit python3 python3-gdbm python3-minimal
207s   python3-systemd
207s 6 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
207s Need to get 162 kB of archives.
207s After this operation, 251 kB of additional disk space will be used.
207s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB]
207s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB]
207s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB]
207s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB]
207s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B]
207s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 pastebinit all 1.7.1-1 [14.9 kB]
207s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build5 [45.7 kB]
207s Fetched 162 kB in 0s (7663 kB/s)
207s (Reading database ... 
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(Reading database ... 75542 files and directories currently installed.)
207s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ...
207s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ...
207s Setting up python3-minimal (3.12.7-1) ...
207s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 75542 files and directories currently installed.)
207s Preparing to unpack .../0-python3_3.12.7-1_amd64.deb ...
207s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ...
208s Preparing to unpack .../1-libpython3-stdlib_3.12.7-1_amd64.deb ...
208s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ...
208s Selecting previously unselected package python3.13-gdbm.
208s Preparing to unpack .../2-python3.13-gdbm_3.13.0-2_amd64.deb ...
208s Unpacking python3.13-gdbm (3.13.0-2) ...
208s Preparing to unpack .../3-python3-gdbm_3.12.7-1_amd64.deb ...
208s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ...
208s Preparing to unpack .../4-pastebinit_1.7.1-1_all.deb ...
208s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ...
208s Preparing to unpack .../5-python3-systemd_235-1build5_amd64.deb ...
208s Unpacking python3-systemd (235-1build5) over (235-1build4) ...
208s Setting up python3.13-gdbm (3.13.0-2) ...
208s Setting up libpython3-stdlib:amd64 (3.12.7-1) ...
208s Setting up python3 (3.12.7-1) ...
208s Setting up python3-systemd (235-1build5) ...
208s Setting up python3-gdbm:amd64 (3.12.7-1) ...
208s Setting up pastebinit (1.7.1-1) ...
208s Processing triggers for man-db (2.12.1-3) ...
209s Reading package lists...
209s Building dependency tree...
209s Reading state information...
209s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
210s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
210s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
210s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
210s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
211s Reading package lists...
211s Reading package lists...
211s Building dependency tree...
211s Reading state information...
212s Calculating upgrade...
212s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
212s Reading package lists...
212s Building dependency tree...
212s Reading state information...
212s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
215s Reading package lists...
215s Building dependency tree...
215s Reading state information...
215s Starting pkgProblemResolver with broken count: 0
215s Starting 2 pkgProblemResolver with broken count: 0
215s Done
216s The following additional packages will be installed:
216s   libdeflate0 libhts3t64 libhtscodecs2 libpython3.13-minimal
216s   libpython3.13-stdlib python3-all python3-pysam python3.13 python3.13-minimal
216s Suggested packages:
216s   python3.13-venv python3.13-doc binfmt-support
216s The following NEW packages will be installed:
216s   autopkgtest-satdep libdeflate0 libhts3t64 libhtscodecs2
216s   libpython3.13-minimal libpython3.13-stdlib python3-all python3-pysam
216s   python3.13 python3.13-minimal
216s 0 upgraded, 10 newly installed, 0 to remove and 0 not upgraded.
216s Need to get 10.0 MB/10.0 MB of archives.
216s After this operation, 59.0 MB of additional disk space will be used.
216s Get:1 /tmp/autopkgtest.kUrCsn/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [712 B]
216s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.0-2 [879 kB]
216s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.0-2 [2188 kB]
216s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB]
216s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-1 [132 kB]
216s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.20+ds-1 [439 kB]
216s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [2107 kB]
216s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.0-2 [719 kB]
216s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all amd64 3.12.7-1 [890 B]
216s Get:10 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pysam amd64 0.22.1+ds-2 [3504 kB]
217s Fetched 10.0 MB in 0s (35.2 MB/s)
217s Selecting previously unselected package libpython3.13-minimal:amd64.
217s (Reading database ... 
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(Reading database ... 75554 files and directories currently installed.)
217s Preparing to unpack .../0-libpython3.13-minimal_3.13.0-2_amd64.deb ...
217s Unpacking libpython3.13-minimal:amd64 (3.13.0-2) ...
217s Selecting previously unselected package python3.13-minimal.
217s Preparing to unpack .../1-python3.13-minimal_3.13.0-2_amd64.deb ...
217s Unpacking python3.13-minimal (3.13.0-2) ...
217s Selecting previously unselected package libdeflate0:amd64.
217s Preparing to unpack .../2-libdeflate0_1.22-1_amd64.deb ...
217s Unpacking libdeflate0:amd64 (1.22-1) ...
217s Selecting previously unselected package libhtscodecs2:amd64.
217s Preparing to unpack .../3-libhtscodecs2_1.6.1-1_amd64.deb ...
217s Unpacking libhtscodecs2:amd64 (1.6.1-1) ...
217s Selecting previously unselected package libhts3t64:amd64.
217s Preparing to unpack .../4-libhts3t64_1.20+ds-1_amd64.deb ...
217s Unpacking libhts3t64:amd64 (1.20+ds-1) ...
217s Selecting previously unselected package libpython3.13-stdlib:amd64.
217s Preparing to unpack .../5-libpython3.13-stdlib_3.13.0-2_amd64.deb ...
217s Unpacking libpython3.13-stdlib:amd64 (3.13.0-2) ...
217s Selecting previously unselected package python3.13.
217s Preparing to unpack .../6-python3.13_3.13.0-2_amd64.deb ...
217s Unpacking python3.13 (3.13.0-2) ...
217s Selecting previously unselected package python3-all.
217s Preparing to unpack .../7-python3-all_3.12.7-1_amd64.deb ...
217s Unpacking python3-all (3.12.7-1) ...
217s Selecting previously unselected package python3-pysam.
217s Preparing to unpack .../8-python3-pysam_0.22.1+ds-2_amd64.deb ...
217s Unpacking python3-pysam (0.22.1+ds-2) ...
217s Selecting previously unselected package autopkgtest-satdep.
217s Preparing to unpack .../9-2-autopkgtest-satdep.deb ...
217s Unpacking autopkgtest-satdep (0) ...
217s Setting up libhtscodecs2:amd64 (1.6.1-1) ...
217s Setting up libdeflate0:amd64 (1.22-1) ...
217s Setting up libpython3.13-minimal:amd64 (3.13.0-2) ...
217s Setting up libhts3t64:amd64 (1.20+ds-1) ...
217s Setting up python3.13-minimal (3.13.0-2) ...
218s Setting up libpython3.13-stdlib:amd64 (3.13.0-2) ...
218s Setting up python3-pysam (0.22.1+ds-2) ...
218s Setting up python3.13 (3.13.0-2) ...
219s Setting up python3-all (3.12.7-1) ...
219s Setting up autopkgtest-satdep (0) ...
219s Processing triggers for systemd (256.5-2ubuntu4) ...
219s Processing triggers for man-db (2.12.1-3) ...
220s Processing triggers for libc-bin (2.40-1ubuntu3) ...
222s (Reading database ... 76674 files and directories currently installed.)
222s Removing autopkgtest-satdep (0) ...
225s autopkgtest [15:05:03]: test autodep8-python3: set -e ; for py in $(py3versions -r 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c "import pysam; print(pysam)" ; done
225s autopkgtest [15:05:03]: test autodep8-python3: [-----------------------
225s Testing with python3.13:
225s Traceback (most recent call last):
225s   File "<string>", line 1, in <module>
225s     import pysam; print(pysam)
225s     ^^^^^^^^^^^^
225s   File "/usr/lib/python3/dist-packages/pysam/__init__.py", line 4, in <module>
225s     from pysam.libchtslib import *
225s ModuleNotFoundError: No module named 'pysam.libchtslib'
226s autopkgtest [15:05:04]: test autodep8-python3: -----------------------]
226s autopkgtest [15:05:04]: test autodep8-python3:  - - - - - - - - - - results - - - - - - - - - -
226s autodep8-python3     FAIL non-zero exit status 1
226s autopkgtest [15:05:04]: @@@@@@@@@@@@@@@@@@@@ summary
226s command1             PASS
226s autodep8-python3     FAIL non-zero exit status 1
239s nova [W] Skipping flock for amd64
239s Creating nova instance adt-plucky-amd64-python-pysam-20241114-150118-juju-7f2275-prod-proposed-migration-environment-15-7b4efa4a-7a59-4460-a467-711b98796903 from image adt/ubuntu-plucky-amd64-server-20241114.img (UUID 86f72d39-d3f4-462e-8625-4ce3a06b44aa)...
239s nova [W] Skipping flock for amd64
239s Creating nova instance adt-plucky-amd64-python-pysam-20241114-150118-juju-7f2275-prod-proposed-migration-environment-15-7b4efa4a-7a59-4460-a467-711b98796903 from image adt/ubuntu-plucky-amd64-server-20241114.img (UUID 86f72d39-d3f4-462e-8625-4ce3a06b44aa)...