0s autopkgtest [10:50:09]: starting date and time: 2024-11-13 10:50:09+0000 0s autopkgtest [10:50:09]: git checkout: 0acbae0a WIP show VirtSubproc stderr in real-time 0s autopkgtest [10:50:09]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.mwva4r0_/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-2@bos03-arm64-16.secgroup --name adt-plucky-arm64-python-pysam-20241113-105009-juju-7f2275-prod-proposed-migration-environment-2-c55ae399-79e1-4064-a8c5-754bcf65ae23 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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/ 103s autopkgtest [10:51:52]: testbed dpkg architecture: arm64 103s autopkgtest [10:51:52]: testbed apt version: 2.9.8 103s autopkgtest [10:51:52]: @@@@@@@@@@@@@@@@@@@@ test bed setup 104s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 104s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 104s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 104s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 105s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 105s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB] 105s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 105s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB] 105s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB] 105s Fetched 1794 kB in 1s (1965 kB/s) 105s Reading package lists... 107s Reading package lists... 108s Building dependency tree... 108s Reading state information... 108s Calculating upgrade... 109s The following NEW packages will be installed: 109s python3.13-gdbm 109s The following packages will be upgraded: 109s libpython3-stdlib python3 python3-gdbm python3-minimal 109s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 109s Need to get 101 kB of archives. 109s After this operation, 141 kB of additional disk space will be used. 109s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB] 109s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB] 109s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB] 109s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB] 109s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B] 110s Fetched 101 kB in 0s (282 kB/s) 110s (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 ... 79924 files and directories currently installed.) 110s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ... 110s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 110s Setting up python3-minimal (3.12.7-1) ... 110s (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 ... 79924 files and directories currently installed.) 110s Preparing to unpack .../python3_3.12.7-1_arm64.deb ... 110s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 110s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ... 110s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 110s Selecting previously unselected package python3.13-gdbm. 110s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ... 110s Unpacking python3.13-gdbm (3.13.0-2) ... 111s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ... 111s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 111s Setting up python3.13-gdbm (3.13.0-2) ... 111s Setting up libpython3-stdlib:arm64 (3.12.7-1) ... 111s Setting up python3 (3.12.7-1) ... 111s Setting up python3-gdbm:arm64 (3.12.7-1) ... 111s Processing triggers for man-db (2.12.1-3) ... 112s Reading package lists... 112s Building dependency tree... 112s Reading state information... 113s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 113s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 113s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 113s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 113s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 114s Reading package lists... 114s Reading package lists... 115s Building dependency tree... 115s Reading state information... 115s Calculating upgrade... 116s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 116s Reading package lists... 116s Building dependency tree... 116s Reading state information... 117s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 120s autopkgtest [10:52:09]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 120s autopkgtest [10:52:09]: @@@@@@@@@@@@@@@@@@@@ apt-source python-pysam 123s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-pysam 0.22.1+ds-2 (dsc) [2563 B] 123s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-pysam 0.22.1+ds-2 (tar) [1447 kB] 123s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-pysam 0.22.1+ds-2 (diff) [10.7 kB] 123s gpgv: Signature made Wed May 29 11:37:25 2024 UTC 123s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 123s gpgv: issuer "emollier@debian.org" 123s gpgv: Can't check signature: No public key 123s dpkg-source: warning: cannot verify inline signature for ./python-pysam_0.22.1+ds-2.dsc: no acceptable signature found 123s autopkgtest [10:52:12]: testing package python-pysam version 0.22.1+ds-2 124s autopkgtest [10:52:13]: build not needed 127s autopkgtest [10:52:16]: test command1: preparing testbed 129s Reading package lists... 129s Building dependency tree... 129s Reading state information... 130s Starting pkgProblemResolver with broken count: 0 130s Starting 2 pkgProblemResolver with broken count: 0 130s Done 130s The following additional packages will be installed: 130s autoconf automake autopoint autotools-dev bcftools build-essential cpp 130s cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu cython3 debhelper 130s debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz g++ g++-14 130s g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14 130s gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext intltool-debian 130s libarchive-zip-perl libasan8 libbrotli-dev libcc1-0 libcurl4-gnutls-dev 130s libdebhelper-perl libdeflate-dev libdeflate0 libevent-2.1-7t64 libexpat1-dev 130s libfile-stripnondeterminism-perl libgcc-14-dev libgmp-dev libgmpxx4ldbl 130s libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev libgomp1 130s libhts-dev libhts3t64 libhtscodecs2 libhwasan0 libidn2-dev libisl23 libitm1 130s libjs-jquery libjs-sphinxdoc libjs-underscore liblsan0 liblzma-dev libmpc3 130s libnghttp2-dev libp11-kit-dev libpkgconf3 libpsl-dev libpython3-all-dev 130s libpython3-dev libpython3.12-dev libpython3.13 libpython3.13-dev 130s libpython3.13-minimal libpython3.13-stdlib librtmp-dev libssh2-1-dev 130s libssl-dev libstdc++-14-dev libtasn1-6-dev libtool libtsan2 libubsan1 130s libunbound8 libzstd-dev m4 nettle-dev pkgconf pkgconf-bin po-debconf 130s python3-all python3-all-dev python3-dev python3-iniconfig python3-packaging 130s python3-pluggy python3-pysam python3-pytest python3.12-dev python3.13 130s python3.13-dev python3.13-minimal samtools tabix zlib1g-dev 130s Suggested packages: 130s autoconf-archive gnu-standards autoconf-doc python3-numpy 130s texlive-latex-recommended cpp-doc gcc-14-locales cpp-14-doc cython-doc 130s dh-make flit python3-build python3-installer python3-wheel gcc-14-doc 130s gcc-multilib manpages-dev flex bison gdb gcc-doc gdb-aarch64-linux-gnu 130s gettext-doc libasprintf-dev libgettextpo-dev libcurl4-doc libidn-dev 130s libkrb5-dev libldap2-dev gmp-doc libgmp10-doc libmpfr-dev dns-root-data 130s gnutls-bin gnutls-doc liblzma-doc libnghttp2-doc p11-kit-doc libssl-doc 130s libstdc++-14-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc 130s libmail-box-perl python3.13-venv python3.13-doc binfmt-support cwltool 130s Recommended packages: 130s python3-gffutils python3-matplotlib libarchive-cpio-perl javascript-common 130s libtasn1-doc libltdl-dev libmail-sendmail-perl 130s The following NEW packages will be installed: 130s autoconf automake autopkgtest-satdep autopoint autotools-dev bcftools 130s build-essential cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu 130s cython3 debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism 130s dwz g++ g++-14 g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14 130s gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext intltool-debian 130s libarchive-zip-perl libasan8 libbrotli-dev libcc1-0 libcurl4-gnutls-dev 130s libdebhelper-perl libdeflate-dev libdeflate0 libevent-2.1-7t64 libexpat1-dev 130s libfile-stripnondeterminism-perl libgcc-14-dev libgmp-dev libgmpxx4ldbl 130s libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev libgomp1 130s libhts-dev libhts3t64 libhtscodecs2 libhwasan0 libidn2-dev libisl23 libitm1 130s libjs-jquery libjs-sphinxdoc libjs-underscore liblsan0 liblzma-dev libmpc3 130s libnghttp2-dev libp11-kit-dev libpkgconf3 libpsl-dev libpython3-all-dev 130s libpython3-dev libpython3.12-dev libpython3.13 libpython3.13-dev 130s libpython3.13-minimal libpython3.13-stdlib librtmp-dev libssh2-1-dev 130s libssl-dev libstdc++-14-dev libtasn1-6-dev libtool libtsan2 libubsan1 130s libunbound8 libzstd-dev m4 nettle-dev pkgconf pkgconf-bin po-debconf 130s python3-all python3-all-dev python3-dev python3-iniconfig python3-packaging 130s python3-pluggy python3-pysam python3-pytest python3.12-dev python3.13 130s python3.13-dev python3.13-minimal samtools tabix zlib1g-dev 130s 0 upgraded, 100 newly installed, 0 to remove and 0 not upgraded. 130s Need to get 109 MB/109 MB of archives. 130s After this operation, 416 MB of additional disk space will be used. 130s Get:1 /tmp/autopkgtest.GNnawt/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [816 B] 131s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-minimal arm64 3.13.0-2 [877 kB] 131s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-minimal arm64 3.13.0-2 [2100 kB] 131s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 m4 arm64 1.4.19-4build1 [240 kB] 131s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 autoconf all 2.72-3 [382 kB] 131s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 autotools-dev all 20220109.1 [44.9 kB] 131s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 automake all 1:1.16.5-1.3ubuntu1 [558 kB] 131s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 autopoint all 0.22.5-2 [616 kB] 131s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB] 131s Get:10 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.1-1 [82.5 kB] 131s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts3t64 arm64 1.20+ds-1 [431 kB] 131s Get:12 http://ftpmaster.internal/ubuntu plucky/universe arm64 bcftools arm64 1.20-2 [776 kB] 131s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libisl23 arm64 0.27-1 [676 kB] 131s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB] 131s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-8ubuntu1 [10.6 MB] 132s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14 arm64 14.2.0-8ubuntu1 [1028 B] 132s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [5452 B] 132s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp arm64 4:14.1.0-2ubuntu1 [22.5 kB] 132s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libcc1-0 arm64 14.2.0-8ubuntu1 [49.7 kB] 132s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-8ubuntu1 [145 kB] 132s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 14.2.0-8ubuntu1 [27.8 kB] 132s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 14.2.0-8ubuntu1 [2893 kB] 132s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 14.2.0-8ubuntu1 [1283 kB] 132s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 14.2.0-8ubuntu1 [2686 kB] 132s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 14.2.0-8ubuntu1 [1151 kB] 132s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 14.2.0-8ubuntu1 [1598 kB] 132s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-8ubuntu1 [2594 kB] 132s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-8ubuntu1 [20.9 MB] 132s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14 arm64 14.2.0-8ubuntu1 [518 kB] 132s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [1200 B] 132s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc arm64 4:14.1.0-2ubuntu1 [4994 B] 132s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-8ubuntu1 [2476 kB] 132s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-8ubuntu1 [12.1 MB] 133s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14 arm64 14.2.0-8ubuntu1 [19.9 kB] 133s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [958 B] 133s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 g++ arm64 4:14.1.0-2ubuntu1 [1080 B] 133s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 133s Get:38 http://ftpmaster.internal/ubuntu plucky/universe arm64 cython3 arm64 3.0.11+dfsg-1ubuntu1 [2355 kB] 133s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libdebhelper-perl all 13.20ubuntu1 [94.2 kB] 133s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libtool all 2.4.7-7build1 [166 kB] 133s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 dh-autoreconf all 20 [16.1 kB] 133s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] 133s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] 133s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 dh-strip-nondeterminism all 1.14.0-1 [5058 B] 133s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 debugedit arm64 1:5.1-1 [45.9 kB] 133s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 dwz arm64 0.15-1build6 [113 kB] 133s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 gettext arm64 0.22.5-2 [930 kB] 133s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 133s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] 133s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 debhelper all 13.20ubuntu1 [893 kB] 133s Get:51 http://ftpmaster.internal/ubuntu plucky/universe arm64 dh-python all 6.20241024 [112 kB] 133s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 libbrotli-dev arm64 1.1.0-2build2 [360 kB] 133s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10 [140 kB] 133s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 libunbound8 arm64 1.20.0-1ubuntu2.1 [431 kB] 133s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 libgnutls-dane0t64 arm64 3.8.6-2ubuntu1 [24.0 kB] 133s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 libgnutls-openssl27t64 arm64 3.8.6-2ubuntu1 [24.0 kB] 133s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 libidn2-dev arm64 2.3.7-2build2 [120 kB] 133s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 libp11-kit-dev arm64 0.25.5-2ubuntu1 [22.7 kB] 133s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 libtasn1-6-dev arm64 4.19.0-3build1 [90.6 kB] 133s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-2ubuntu7 [10.1 kB] 133s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-2ubuntu7 [335 kB] 133s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 nettle-dev arm64 3.10-1 [1189 kB] 133s Get:63 http://ftpmaster.internal/ubuntu plucky/main arm64 libgnutls28-dev arm64 3.8.6-2ubuntu1 [1132 kB] 133s Get:64 http://ftpmaster.internal/ubuntu plucky/main arm64 libpkgconf3 arm64 1.8.1-4 [31.4 kB] 133s Get:65 http://ftpmaster.internal/ubuntu plucky/main arm64 pkgconf-bin arm64 1.8.1-4 [20.9 kB] 133s Get:66 http://ftpmaster.internal/ubuntu plucky/main arm64 pkgconf arm64 1.8.1-4 [16.7 kB] 133s Get:67 http://ftpmaster.internal/ubuntu plucky/main arm64 libnghttp2-dev arm64 1.64.0-1 [120 kB] 133s Get:68 http://ftpmaster.internal/ubuntu plucky/main arm64 libpsl-dev arm64 0.21.2-1.1build1 [77.2 kB] 133s Get:69 http://ftpmaster.internal/ubuntu plucky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB] 133s Get:70 http://ftpmaster.internal/ubuntu plucky/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-2build7 [69.4 kB] 133s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 libssl-dev arm64 3.3.1-2ubuntu2 [3176 kB] 133s Get:72 http://ftpmaster.internal/ubuntu plucky/main arm64 libssh2-1-dev arm64 1.11.1-1 [286 kB] 133s Get:73 http://ftpmaster.internal/ubuntu plucky/main arm64 libzstd-dev arm64 1.5.6+dfsg-1 [352 kB] 133s Get:74 http://ftpmaster.internal/ubuntu plucky/main arm64 libcurl4-gnutls-dev arm64 8.9.1-2ubuntu2 [485 kB] 133s Get:75 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate-dev arm64 1.22-1 [53.8 kB] 133s Get:76 http://ftpmaster.internal/ubuntu plucky/main arm64 libexpat1-dev arm64 2.6.2-2 [128 kB] 133s Get:77 http://ftpmaster.internal/ubuntu plucky/main arm64 liblzma-dev arm64 5.6.2-2 [179 kB] 133s Get:78 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts-dev arm64 1.20+ds-1 [5908 kB] 133s Get:79 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 133s Get:80 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 133s Get:81 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-sphinxdoc all 7.4.7-4 [158 kB] 133s Get:82 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.12-dev arm64 3.12.7-3 [5565 kB] 134s Get:83 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-dev arm64 3.12.7-1 [10.3 kB] 134s Get:84 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-stdlib arm64 3.13.0-2 [2073 kB] 134s Get:85 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13 arm64 3.13.0-2 [2262 kB] 134s Get:86 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-dev arm64 3.13.0-2 [5386 kB] 134s Get:87 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-all-dev arm64 3.12.7-1 [916 B] 134s Get:88 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13 arm64 3.13.0-2 [719 kB] 134s Get:89 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-all arm64 3.12.7-1 [890 B] 134s Get:90 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-dev arm64 3.12.7-3 [505 kB] 134s Get:91 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-dev arm64 3.12.7-1 [26.7 kB] 134s Get:92 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-dev arm64 3.13.0-2 [507 kB] 134s Get:93 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-all-dev arm64 3.12.7-1 [914 B] 134s Get:94 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 134s Get:95 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.1-1 [41.4 kB] 134s Get:96 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 134s Get:97 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pysam arm64 0.22.1+ds-2 [3412 kB] 134s Get:98 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.3-1 [251 kB] 134s Get:99 http://ftpmaster.internal/ubuntu plucky/universe arm64 samtools arm64 1.20-3 [590 kB] 134s Get:100 http://ftpmaster.internal/ubuntu plucky/universe arm64 tabix arm64 1.20+ds-1 [515 kB] 134s Fetched 109 MB in 4s (31.1 MB/s) 134s Selecting previously unselected package libpython3.13-minimal:arm64. 135s (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 ... 79931 files and directories currently installed.) 135s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_arm64.deb ... 135s Unpacking libpython3.13-minimal:arm64 (3.13.0-2) ... 135s Selecting previously unselected package python3.13-minimal. 135s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_arm64.deb ... 135s Unpacking python3.13-minimal (3.13.0-2) ... 135s Selecting previously unselected package m4. 135s Preparing to unpack .../02-m4_1.4.19-4build1_arm64.deb ... 135s Unpacking m4 (1.4.19-4build1) ... 135s Selecting previously unselected package autoconf. 135s Preparing to unpack .../03-autoconf_2.72-3_all.deb ... 135s Unpacking autoconf (2.72-3) ... 135s Selecting previously unselected package autotools-dev. 135s Preparing to unpack .../04-autotools-dev_20220109.1_all.deb ... 135s Unpacking autotools-dev (20220109.1) ... 135s Selecting previously unselected package automake. 135s Preparing to unpack .../05-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 135s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 135s Selecting previously unselected package autopoint. 135s Preparing to unpack .../06-autopoint_0.22.5-2_all.deb ... 135s Unpacking autopoint (0.22.5-2) ... 135s Selecting previously unselected package libdeflate0:arm64. 135s Preparing to unpack .../07-libdeflate0_1.22-1_arm64.deb ... 135s Unpacking libdeflate0:arm64 (1.22-1) ... 135s Selecting previously unselected package libhtscodecs2:arm64. 135s Preparing to unpack .../08-libhtscodecs2_1.6.1-1_arm64.deb ... 135s Unpacking libhtscodecs2:arm64 (1.6.1-1) ... 135s Selecting previously unselected package libhts3t64:arm64. 135s Preparing to unpack .../09-libhts3t64_1.20+ds-1_arm64.deb ... 135s Unpacking libhts3t64:arm64 (1.20+ds-1) ... 135s Selecting previously unselected package bcftools. 135s Preparing to unpack .../10-bcftools_1.20-2_arm64.deb ... 135s Unpacking bcftools (1.20-2) ... 135s Selecting previously unselected package libisl23:arm64. 135s Preparing to unpack .../11-libisl23_0.27-1_arm64.deb ... 135s Unpacking libisl23:arm64 (0.27-1) ... 135s Selecting previously unselected package libmpc3:arm64. 135s Preparing to unpack .../12-libmpc3_1.3.1-1build2_arm64.deb ... 135s Unpacking libmpc3:arm64 (1.3.1-1build2) ... 135s Selecting previously unselected package cpp-14-aarch64-linux-gnu. 135s Preparing to unpack .../13-cpp-14-aarch64-linux-gnu_14.2.0-8ubuntu1_arm64.deb ... 135s Unpacking cpp-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 135s Selecting previously unselected package cpp-14. 135s Preparing to unpack .../14-cpp-14_14.2.0-8ubuntu1_arm64.deb ... 135s Unpacking cpp-14 (14.2.0-8ubuntu1) ... 135s Selecting previously unselected package cpp-aarch64-linux-gnu. 135s Preparing to unpack .../15-cpp-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ... 135s Unpacking cpp-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 135s Selecting previously unselected package cpp. 136s Preparing to unpack .../16-cpp_4%3a14.1.0-2ubuntu1_arm64.deb ... 136s Unpacking cpp (4:14.1.0-2ubuntu1) ... 136s Selecting previously unselected package libcc1-0:arm64. 136s Preparing to unpack .../17-libcc1-0_14.2.0-8ubuntu1_arm64.deb ... 136s Unpacking libcc1-0:arm64 (14.2.0-8ubuntu1) ... 136s Selecting previously unselected package libgomp1:arm64. 136s Preparing to unpack .../18-libgomp1_14.2.0-8ubuntu1_arm64.deb ... 136s Unpacking libgomp1:arm64 (14.2.0-8ubuntu1) ... 136s Selecting previously unselected package libitm1:arm64. 136s Preparing to unpack .../19-libitm1_14.2.0-8ubuntu1_arm64.deb ... 136s Unpacking libitm1:arm64 (14.2.0-8ubuntu1) ... 136s Selecting previously unselected package libasan8:arm64. 136s Preparing to unpack .../20-libasan8_14.2.0-8ubuntu1_arm64.deb ... 136s Unpacking libasan8:arm64 (14.2.0-8ubuntu1) ... 136s Selecting previously unselected package liblsan0:arm64. 136s Preparing to unpack .../21-liblsan0_14.2.0-8ubuntu1_arm64.deb ... 136s Unpacking liblsan0:arm64 (14.2.0-8ubuntu1) ... 136s Selecting previously unselected package libtsan2:arm64. 136s Preparing to unpack .../22-libtsan2_14.2.0-8ubuntu1_arm64.deb ... 136s Unpacking libtsan2:arm64 (14.2.0-8ubuntu1) ... 136s Selecting previously unselected package libubsan1:arm64. 136s Preparing to unpack .../23-libubsan1_14.2.0-8ubuntu1_arm64.deb ... 136s Unpacking libubsan1:arm64 (14.2.0-8ubuntu1) ... 136s Selecting previously unselected package libhwasan0:arm64. 136s Preparing to unpack .../24-libhwasan0_14.2.0-8ubuntu1_arm64.deb ... 136s Unpacking libhwasan0:arm64 (14.2.0-8ubuntu1) ... 136s Selecting previously unselected package libgcc-14-dev:arm64. 136s Preparing to unpack .../25-libgcc-14-dev_14.2.0-8ubuntu1_arm64.deb ... 136s Unpacking libgcc-14-dev:arm64 (14.2.0-8ubuntu1) ... 136s Selecting previously unselected package gcc-14-aarch64-linux-gnu. 136s Preparing to unpack .../26-gcc-14-aarch64-linux-gnu_14.2.0-8ubuntu1_arm64.deb ... 136s Unpacking gcc-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 137s Selecting previously unselected package gcc-14. 137s Preparing to unpack .../27-gcc-14_14.2.0-8ubuntu1_arm64.deb ... 137s Unpacking gcc-14 (14.2.0-8ubuntu1) ... 137s Selecting previously unselected package gcc-aarch64-linux-gnu. 137s Preparing to unpack .../28-gcc-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ... 137s Unpacking gcc-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 137s Selecting previously unselected package gcc. 137s Preparing to unpack .../29-gcc_4%3a14.1.0-2ubuntu1_arm64.deb ... 137s Unpacking gcc (4:14.1.0-2ubuntu1) ... 137s Selecting previously unselected package libstdc++-14-dev:arm64. 137s Preparing to unpack .../30-libstdc++-14-dev_14.2.0-8ubuntu1_arm64.deb ... 137s Unpacking libstdc++-14-dev:arm64 (14.2.0-8ubuntu1) ... 137s Selecting previously unselected package g++-14-aarch64-linux-gnu. 137s Preparing to unpack .../31-g++-14-aarch64-linux-gnu_14.2.0-8ubuntu1_arm64.deb ... 137s Unpacking g++-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 137s Selecting previously unselected package g++-14. 137s Preparing to unpack .../32-g++-14_14.2.0-8ubuntu1_arm64.deb ... 137s Unpacking g++-14 (14.2.0-8ubuntu1) ... 137s Selecting previously unselected package g++-aarch64-linux-gnu. 137s Preparing to unpack .../33-g++-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ... 137s Unpacking g++-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 137s Selecting previously unselected package g++. 137s Preparing to unpack .../34-g++_4%3a14.1.0-2ubuntu1_arm64.deb ... 137s Unpacking g++ (4:14.1.0-2ubuntu1) ... 137s Selecting previously unselected package build-essential. 137s Preparing to unpack .../35-build-essential_12.10ubuntu1_arm64.deb ... 137s Unpacking build-essential (12.10ubuntu1) ... 137s Selecting previously unselected package cython3. 137s Preparing to unpack .../36-cython3_3.0.11+dfsg-1ubuntu1_arm64.deb ... 137s Unpacking cython3 (3.0.11+dfsg-1ubuntu1) ... 138s Selecting previously unselected package libdebhelper-perl. 138s Preparing to unpack .../37-libdebhelper-perl_13.20ubuntu1_all.deb ... 138s Unpacking libdebhelper-perl (13.20ubuntu1) ... 138s Selecting previously unselected package libtool. 138s Preparing to unpack .../38-libtool_2.4.7-7build1_all.deb ... 138s Unpacking libtool (2.4.7-7build1) ... 138s Selecting previously unselected package dh-autoreconf. 138s Preparing to unpack .../39-dh-autoreconf_20_all.deb ... 138s Unpacking dh-autoreconf (20) ... 138s Selecting previously unselected package libarchive-zip-perl. 138s Preparing to unpack .../40-libarchive-zip-perl_1.68-1_all.deb ... 138s Unpacking libarchive-zip-perl (1.68-1) ... 138s Selecting previously unselected package libfile-stripnondeterminism-perl. 138s Preparing to unpack .../41-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... 138s Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... 138s Selecting previously unselected package dh-strip-nondeterminism. 138s Preparing to unpack .../42-dh-strip-nondeterminism_1.14.0-1_all.deb ... 138s Unpacking dh-strip-nondeterminism (1.14.0-1) ... 138s Selecting previously unselected package debugedit. 138s Preparing to unpack .../43-debugedit_1%3a5.1-1_arm64.deb ... 138s Unpacking debugedit (1:5.1-1) ... 138s Selecting previously unselected package dwz. 138s Preparing to unpack .../44-dwz_0.15-1build6_arm64.deb ... 138s Unpacking dwz (0.15-1build6) ... 138s Selecting previously unselected package gettext. 138s Preparing to unpack .../45-gettext_0.22.5-2_arm64.deb ... 138s Unpacking gettext (0.22.5-2) ... 138s Selecting previously unselected package intltool-debian. 138s Preparing to unpack .../46-intltool-debian_0.35.0+20060710.6_all.deb ... 138s Unpacking intltool-debian (0.35.0+20060710.6) ... 138s Selecting previously unselected package po-debconf. 138s Preparing to unpack .../47-po-debconf_1.0.21+nmu1_all.deb ... 138s Unpacking po-debconf (1.0.21+nmu1) ... 138s Selecting previously unselected package debhelper. 138s Preparing to unpack .../48-debhelper_13.20ubuntu1_all.deb ... 138s Unpacking debhelper (13.20ubuntu1) ... 138s Selecting previously unselected package dh-python. 138s Preparing to unpack .../49-dh-python_6.20241024_all.deb ... 138s Unpacking dh-python (6.20241024) ... 138s Selecting previously unselected package libbrotli-dev:arm64. 138s Preparing to unpack .../50-libbrotli-dev_1.1.0-2build2_arm64.deb ... 138s Unpacking libbrotli-dev:arm64 (1.1.0-2build2) ... 138s Selecting previously unselected package libevent-2.1-7t64:arm64. 138s Preparing to unpack .../51-libevent-2.1-7t64_2.1.12-stable-10_arm64.deb ... 138s Unpacking libevent-2.1-7t64:arm64 (2.1.12-stable-10) ... 138s Selecting previously unselected package libunbound8:arm64. 138s Preparing to unpack .../52-libunbound8_1.20.0-1ubuntu2.1_arm64.deb ... 138s Unpacking libunbound8:arm64 (1.20.0-1ubuntu2.1) ... 138s Selecting previously unselected package libgnutls-dane0t64:arm64. 138s Preparing to unpack .../53-libgnutls-dane0t64_3.8.6-2ubuntu1_arm64.deb ... 138s Unpacking libgnutls-dane0t64:arm64 (3.8.6-2ubuntu1) ... 138s Selecting previously unselected package libgnutls-openssl27t64:arm64. 138s Preparing to unpack .../54-libgnutls-openssl27t64_3.8.6-2ubuntu1_arm64.deb ... 138s Unpacking libgnutls-openssl27t64:arm64 (3.8.6-2ubuntu1) ... 138s Selecting previously unselected package libidn2-dev:arm64. 138s Preparing to unpack .../55-libidn2-dev_2.3.7-2build2_arm64.deb ... 138s Unpacking libidn2-dev:arm64 (2.3.7-2build2) ... 138s Selecting previously unselected package libp11-kit-dev:arm64. 138s Preparing to unpack .../56-libp11-kit-dev_0.25.5-2ubuntu1_arm64.deb ... 138s Unpacking libp11-kit-dev:arm64 (0.25.5-2ubuntu1) ... 138s Selecting previously unselected package libtasn1-6-dev:arm64. 139s Preparing to unpack .../57-libtasn1-6-dev_4.19.0-3build1_arm64.deb ... 139s Unpacking libtasn1-6-dev:arm64 (4.19.0-3build1) ... 139s Selecting previously unselected package libgmpxx4ldbl:arm64. 139s Preparing to unpack .../58-libgmpxx4ldbl_2%3a6.3.0+dfsg-2ubuntu7_arm64.deb ... 139s Unpacking libgmpxx4ldbl:arm64 (2:6.3.0+dfsg-2ubuntu7) ... 139s Selecting previously unselected package libgmp-dev:arm64. 139s Preparing to unpack .../59-libgmp-dev_2%3a6.3.0+dfsg-2ubuntu7_arm64.deb ... 139s Unpacking libgmp-dev:arm64 (2:6.3.0+dfsg-2ubuntu7) ... 139s Selecting previously unselected package nettle-dev:arm64. 139s Preparing to unpack .../60-nettle-dev_3.10-1_arm64.deb ... 139s Unpacking nettle-dev:arm64 (3.10-1) ... 139s Selecting previously unselected package libgnutls28-dev:arm64. 139s Preparing to unpack .../61-libgnutls28-dev_3.8.6-2ubuntu1_arm64.deb ... 139s Unpacking libgnutls28-dev:arm64 (3.8.6-2ubuntu1) ... 139s Selecting previously unselected package libpkgconf3:arm64. 139s Preparing to unpack .../62-libpkgconf3_1.8.1-4_arm64.deb ... 139s Unpacking libpkgconf3:arm64 (1.8.1-4) ... 139s Selecting previously unselected package pkgconf-bin. 139s Preparing to unpack .../63-pkgconf-bin_1.8.1-4_arm64.deb ... 139s Unpacking pkgconf-bin (1.8.1-4) ... 139s Selecting previously unselected package pkgconf:arm64. 139s Preparing to unpack .../64-pkgconf_1.8.1-4_arm64.deb ... 139s Unpacking pkgconf:arm64 (1.8.1-4) ... 139s Selecting previously unselected package libnghttp2-dev:arm64. 139s Preparing to unpack .../65-libnghttp2-dev_1.64.0-1_arm64.deb ... 139s Unpacking libnghttp2-dev:arm64 (1.64.0-1) ... 139s Selecting previously unselected package libpsl-dev:arm64. 139s Preparing to unpack .../66-libpsl-dev_0.21.2-1.1build1_arm64.deb ... 139s Unpacking libpsl-dev:arm64 (0.21.2-1.1build1) ... 139s Selecting previously unselected package zlib1g-dev:arm64. 139s Preparing to unpack .../67-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_arm64.deb ... 139s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 139s Selecting previously unselected package librtmp-dev:arm64. 139s Preparing to unpack .../68-librtmp-dev_2.4+20151223.gitfa8646d.1-2build7_arm64.deb ... 139s Unpacking librtmp-dev:arm64 (2.4+20151223.gitfa8646d.1-2build7) ... 139s Selecting previously unselected package libssl-dev:arm64. 139s Preparing to unpack .../69-libssl-dev_3.3.1-2ubuntu2_arm64.deb ... 139s Unpacking libssl-dev:arm64 (3.3.1-2ubuntu2) ... 139s Selecting previously unselected package libssh2-1-dev:arm64. 139s Preparing to unpack .../70-libssh2-1-dev_1.11.1-1_arm64.deb ... 139s Unpacking libssh2-1-dev:arm64 (1.11.1-1) ... 139s Selecting previously unselected package libzstd-dev:arm64. 139s Preparing to unpack .../71-libzstd-dev_1.5.6+dfsg-1_arm64.deb ... 139s Unpacking libzstd-dev:arm64 (1.5.6+dfsg-1) ... 139s Selecting previously unselected package libcurl4-gnutls-dev:arm64. 139s Preparing to unpack .../72-libcurl4-gnutls-dev_8.9.1-2ubuntu2_arm64.deb ... 139s Unpacking libcurl4-gnutls-dev:arm64 (8.9.1-2ubuntu2) ... 139s Selecting previously unselected package libdeflate-dev:arm64. 139s Preparing to unpack .../73-libdeflate-dev_1.22-1_arm64.deb ... 139s Unpacking libdeflate-dev:arm64 (1.22-1) ... 139s Selecting previously unselected package libexpat1-dev:arm64. 139s Preparing to unpack .../74-libexpat1-dev_2.6.2-2_arm64.deb ... 139s Unpacking libexpat1-dev:arm64 (2.6.2-2) ... 139s Selecting previously unselected package liblzma-dev:arm64. 139s Preparing to unpack .../75-liblzma-dev_5.6.2-2_arm64.deb ... 139s Unpacking liblzma-dev:arm64 (5.6.2-2) ... 139s Selecting previously unselected package libhts-dev:arm64. 140s Preparing to unpack .../76-libhts-dev_1.20+ds-1_arm64.deb ... 140s Unpacking libhts-dev:arm64 (1.20+ds-1) ... 140s Selecting previously unselected package libjs-jquery. 140s Preparing to unpack .../77-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 140s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 140s Selecting previously unselected package libjs-underscore. 140s Preparing to unpack .../78-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 140s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 140s Selecting previously unselected package libjs-sphinxdoc. 140s Preparing to unpack .../79-libjs-sphinxdoc_7.4.7-4_all.deb ... 140s Unpacking libjs-sphinxdoc (7.4.7-4) ... 140s Selecting previously unselected package libpython3.12-dev:arm64. 140s Preparing to unpack .../80-libpython3.12-dev_3.12.7-3_arm64.deb ... 140s Unpacking libpython3.12-dev:arm64 (3.12.7-3) ... 140s Selecting previously unselected package libpython3-dev:arm64. 140s Preparing to unpack .../81-libpython3-dev_3.12.7-1_arm64.deb ... 140s Unpacking libpython3-dev:arm64 (3.12.7-1) ... 140s Selecting previously unselected package libpython3.13-stdlib:arm64. 140s Preparing to unpack .../82-libpython3.13-stdlib_3.13.0-2_arm64.deb ... 140s Unpacking libpython3.13-stdlib:arm64 (3.13.0-2) ... 140s Selecting previously unselected package libpython3.13:arm64. 140s Preparing to unpack .../83-libpython3.13_3.13.0-2_arm64.deb ... 140s Unpacking libpython3.13:arm64 (3.13.0-2) ... 140s Selecting previously unselected package libpython3.13-dev:arm64. 140s Preparing to unpack .../84-libpython3.13-dev_3.13.0-2_arm64.deb ... 140s Unpacking libpython3.13-dev:arm64 (3.13.0-2) ... 141s Selecting previously unselected package libpython3-all-dev:arm64. 141s Preparing to unpack .../85-libpython3-all-dev_3.12.7-1_arm64.deb ... 141s Unpacking libpython3-all-dev:arm64 (3.12.7-1) ... 141s Selecting previously unselected package python3.13. 141s Preparing to unpack .../86-python3.13_3.13.0-2_arm64.deb ... 141s Unpacking python3.13 (3.13.0-2) ... 141s Selecting previously unselected package python3-all. 141s Preparing to unpack .../87-python3-all_3.12.7-1_arm64.deb ... 141s Unpacking python3-all (3.12.7-1) ... 141s Selecting previously unselected package python3.12-dev. 141s Preparing to unpack .../88-python3.12-dev_3.12.7-3_arm64.deb ... 141s Unpacking python3.12-dev (3.12.7-3) ... 141s Selecting previously unselected package python3-dev. 141s Preparing to unpack .../89-python3-dev_3.12.7-1_arm64.deb ... 141s Unpacking python3-dev (3.12.7-1) ... 141s Selecting previously unselected package python3.13-dev. 141s Preparing to unpack .../90-python3.13-dev_3.13.0-2_arm64.deb ... 141s Unpacking python3.13-dev (3.13.0-2) ... 141s Selecting previously unselected package python3-all-dev. 141s Preparing to unpack .../91-python3-all-dev_3.12.7-1_arm64.deb ... 141s Unpacking python3-all-dev (3.12.7-1) ... 141s Selecting previously unselected package python3-iniconfig. 141s Preparing to unpack .../92-python3-iniconfig_1.1.1-2_all.deb ... 141s Unpacking python3-iniconfig (1.1.1-2) ... 141s Selecting previously unselected package python3-packaging. 141s Preparing to unpack .../93-python3-packaging_24.1-1_all.deb ... 141s Unpacking python3-packaging (24.1-1) ... 141s Selecting previously unselected package python3-pluggy. 141s Preparing to unpack .../94-python3-pluggy_1.5.0-1_all.deb ... 141s Unpacking python3-pluggy (1.5.0-1) ... 141s Selecting previously unselected package python3-pysam. 141s Preparing to unpack .../95-python3-pysam_0.22.1+ds-2_arm64.deb ... 141s Unpacking python3-pysam (0.22.1+ds-2) ... 141s Selecting previously unselected package python3-pytest. 141s Preparing to unpack .../96-python3-pytest_8.3.3-1_all.deb ... 141s Unpacking python3-pytest (8.3.3-1) ... 141s Selecting previously unselected package samtools. 141s Preparing to unpack .../97-samtools_1.20-3_arm64.deb ... 141s Unpacking samtools (1.20-3) ... 141s Selecting previously unselected package tabix. 141s Preparing to unpack .../98-tabix_1.20+ds-1_arm64.deb ... 141s Unpacking tabix (1.20+ds-1) ... 141s Selecting previously unselected package autopkgtest-satdep. 141s Preparing to unpack .../99-1-autopkgtest-satdep.deb ... 141s Unpacking autopkgtest-satdep (0) ... 141s Setting up libhtscodecs2:arm64 (1.6.1-1) ... 141s Setting up dh-python (6.20241024) ... 142s Setting up libgnutls-openssl27t64:arm64 (3.8.6-2ubuntu1) ... 142s Setting up python3-iniconfig (1.1.1-2) ... 142s Setting up libzstd-dev:arm64 (1.5.6+dfsg-1) ... 142s Setting up libarchive-zip-perl (1.68-1) ... 142s Setting up libdebhelper-perl (13.20ubuntu1) ... 142s Setting up libdeflate0:arm64 (1.22-1) ... 142s Setting up m4 (1.4.19-4build1) ... 142s Setting up libevent-2.1-7t64:arm64 (2.1.12-stable-10) ... 142s Setting up libgomp1:arm64 (14.2.0-8ubuntu1) ... 142s Setting up libpsl-dev:arm64 (0.21.2-1.1build1) ... 142s Setting up libpython3.13-minimal:arm64 (3.13.0-2) ... 142s Setting up autotools-dev (20220109.1) ... 142s Setting up python3-packaging (24.1-1) ... 142s Setting up libunbound8:arm64 (1.20.0-1ubuntu2.1) ... 142s Setting up libpkgconf3:arm64 (1.8.1-4) ... 142s Setting up libgmpxx4ldbl:arm64 (2:6.3.0+dfsg-2ubuntu7) ... 142s Setting up libexpat1-dev:arm64 (2.6.2-2) ... 142s Setting up libgnutls-dane0t64:arm64 (3.8.6-2ubuntu1) ... 142s Setting up libssl-dev:arm64 (3.3.1-2ubuntu2) ... 142s Setting up libmpc3:arm64 (1.3.1-1build2) ... 142s Setting up cython3 (3.0.11+dfsg-1ubuntu1) ... 144s Setting up autopoint (0.22.5-2) ... 144s Setting up pkgconf-bin (1.8.1-4) ... 144s Setting up libidn2-dev:arm64 (2.3.7-2build2) ... 144s Setting up autoconf (2.72-3) ... 144s Setting up python3-pluggy (1.5.0-1) ... 144s Setting up liblzma-dev:arm64 (5.6.2-2) ... 144s Setting up libubsan1:arm64 (14.2.0-8ubuntu1) ... 144s Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 144s Setting up dwz (0.15-1build6) ... 144s Setting up libhwasan0:arm64 (14.2.0-8ubuntu1) ... 144s Setting up libasan8:arm64 (14.2.0-8ubuntu1) ... 144s Setting up debugedit (1:5.1-1) ... 144s Setting up libhts3t64:arm64 (1.20+ds-1) ... 144s Setting up python3.13-minimal (3.13.0-2) ... 145s Setting up libtsan2:arm64 (14.2.0-8ubuntu1) ... 145s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 145s Setting up libisl23:arm64 (0.27-1) ... 145s Setting up libtasn1-6-dev:arm64 (4.19.0-3build1) ... 145s Setting up libdeflate-dev:arm64 (1.22-1) ... 145s Setting up tabix (1.20+ds-1) ... 145s Setting up libpython3.13-stdlib:arm64 (3.13.0-2) ... 145s Setting up libcc1-0:arm64 (14.2.0-8ubuntu1) ... 145s Setting up libbrotli-dev:arm64 (1.1.0-2build2) ... 145s Setting up liblsan0:arm64 (14.2.0-8ubuntu1) ... 145s Setting up libp11-kit-dev:arm64 (0.25.5-2ubuntu1) ... 145s Setting up libitm1:arm64 (14.2.0-8ubuntu1) ... 145s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 145s Setting up libpython3.13:arm64 (3.13.0-2) ... 145s Setting up automake (1:1.16.5-1.3ubuntu1) ... 145s update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode 145s Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... 145s Setting up gettext (0.22.5-2) ... 145s Setting up python3-pysam (0.22.1+ds-2) ... 145s Setting up libgmp-dev:arm64 (2:6.3.0+dfsg-2ubuntu7) ... 145s Setting up nettle-dev:arm64 (3.10-1) ... 145s Setting up python3.13 (3.13.0-2) ... 147s Setting up python3-pytest (8.3.3-1) ... 147s Setting up bcftools (1.20-2) ... 147s Setting up python3-all (3.12.7-1) ... 147s Setting up libpython3.12-dev:arm64 (3.12.7-3) ... 147s Setting up pkgconf:arm64 (1.8.1-4) ... 147s Setting up samtools (1.20-3) ... 147s Setting up intltool-debian (0.35.0+20060710.6) ... 147s Setting up libpython3.13-dev:arm64 (3.13.0-2) ... 147s Setting up python3.12-dev (3.12.7-3) ... 147s Setting up libssh2-1-dev:arm64 (1.11.1-1) ... 147s Setting up libjs-sphinxdoc (7.4.7-4) ... 147s Setting up dh-strip-nondeterminism (1.14.0-1) ... 147s Setting up cpp-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 147s Setting up libgcc-14-dev:arm64 (14.2.0-8ubuntu1) ... 147s Setting up libstdc++-14-dev:arm64 (14.2.0-8ubuntu1) ... 147s Setting up libgnutls28-dev:arm64 (3.8.6-2ubuntu1) ... 147s Setting up libnghttp2-dev:arm64 (1.64.0-1) ... 147s Setting up libpython3-dev:arm64 (3.12.7-1) ... 147s Setting up python3.13-dev (3.13.0-2) ... 147s Setting up po-debconf (1.0.21+nmu1) ... 147s Setting up cpp-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 147s Setting up libpython3-all-dev:arm64 (3.12.7-1) ... 147s Setting up python3-dev (3.12.7-1) ... 147s Setting up librtmp-dev:arm64 (2.4+20151223.gitfa8646d.1-2build7) ... 147s Setting up cpp-14 (14.2.0-8ubuntu1) ... 147s Setting up cpp (4:14.1.0-2ubuntu1) ... 147s Setting up gcc-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 147s Setting up python3-all-dev (3.12.7-1) ... 147s Setting up gcc-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 147s Setting up g++-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 147s Setting up libcurl4-gnutls-dev:arm64 (8.9.1-2ubuntu2) ... 147s Setting up gcc-14 (14.2.0-8ubuntu1) ... 147s Setting up g++-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 147s Setting up g++-14 (14.2.0-8ubuntu1) ... 147s Setting up libtool (2.4.7-7build1) ... 147s Setting up libhts-dev:arm64 (1.20+ds-1) ... 147s Setting up gcc (4:14.1.0-2ubuntu1) ... 147s Setting up dh-autoreconf (20) ... 147s Setting up g++ (4:14.1.0-2ubuntu1) ... 147s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 147s Setting up build-essential (12.10ubuntu1) ... 147s Setting up debhelper (13.20ubuntu1) ... 147s Setting up autopkgtest-satdep (0) ... 147s Processing triggers for systemd (256.5-2ubuntu4) ... 147s Processing triggers for man-db (2.12.1-3) ... 149s Processing triggers for install-info (7.1.1-1) ... 149s Processing triggers for libc-bin (2.40-1ubuntu3) ... 155s (Reading database ... 85602 files and directories currently installed.) 155s Removing autopkgtest-satdep (0) ... 156s autopkgtest [10:52:45]: test command1: export HOME=$PWD && make -C tests/pysam_data && make -C tests/cbcf_data && pytest-3 156s autopkgtest [10:52:45]: test command1: [----------------------- 156s make: Entering directory '/tmp/autopkgtest.GNnawt/build.dpD/src/tests/pysam_data' 156s samtools faidx ex1.fa 156s samtools view --no-PG -bo ex1.bam -t ex1.fa.fai ex1.sam.gz 156s samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz 156s [mpileup] 1 samples in 1 input files 156s gunzip < ex1.sam.gz > ex1.sam 156s samtools index ex1.bam 156s samtools view --no-PG -h ex1.bam | gzip > ex2.sam.gz 156s gunzip < ex2.sam.gz > ex2.sam 156s samtools view --no-PG -bo ex2.bam ex2.sam 156s samtools index ex2.bam 156s samtools calmd --no-PG --output-fmt BAM ex2.bam ex1.fa > with_md.sam.gz 156s [bam_fillmd1] different NM for read 'EAS139_11:7:46:695:738': 3 -> 8 156s [bam_fillmd1] different NM for read 'EAS218_4:1:48:9:409': 0 -> 5 156s [bam_fillmd1] different NM for read 'B7_591:7:200:192:373': 0 -> 5 156s [bam_fillmd1] different NM for read 'EAS56_65:1:163:846:223': 0 -> 5 156s [bam_fillmd1] different NM for read 'EAS114_30:7:283:799:560': 0 -> 5 156s [bam_fillmd1] different NM for read 'B7_595:4:84:802:737': 0 -> 4 156s [bam_fillmd1] different NM for read 'EAS51_66:5:308:400:602': 0 -> 3 156s [bam_fillmd1] different NM for read 'EAS54_81:2:285:367:932': 0 -> 3 156s [bam_fillmd1] different NM for read 'EAS114_39:1:70:147:84': 0 -> 3 156s [bam_fillmd1] different NM for read 'EAS56_53:1:124:243:35': 2 -> 5 156s [bam_fillmd1] different NM for read 'EAS1_103:2:226:302:758': 2 -> 3 156s [bam_fillmd1] different NM for read 'EAS114_28:6:175:705:982': 1 -> 0 156s [bam_fillmd1] different NM for read 'EAS51_64:4:179:389:585': 7 -> 8 156s [bam_fillmd1] different NM for read 'B7_589:1:122:337:968': 3 -> 2 156s [bam_fillmd1] different NM for read 'B7_610:4:15:805:420': 4 -> 5 156s [bam_fillmd1] different NM for read 'B7_591:2:279:124:41': 2 -> 4 156s [bam_fillmd1] different NM for read 'EAS112_32:8:89:254:332': 0 -> 1 156s [bam_fillmd1] different NM for read 'B7_597:7:103:731:697': 0 -> 2 156s [bam_fillmd1] different NM for read 'EAS139_11:2:71:83:58': 0 -> 2 156s [bam_fillmd1] different NM for read 'EAS192_3:4:63:5:870': 0 -> 2 156s [bam_fillmd1] different NM for read 'EAS139_19:2:29:1822:1881': 0 -> 2 156s [bam_fillmd1] different NM for read 'EAS188_7:3:15:568:42': 2 -> 1 156s [bam_fillmd1] different NM for read 'EAS1_95:4:176:971:874': 0 -> 1 156s [bam_fillmd1] different NM for read 'EAS1_99:1:34:649:318': 3 -> 4 156s [bam_fillmd1] different NM for read 'EAS54_65:4:61:346:384': 3 -> 4 156s [bam_fillmd1] different NM for read 'B7_597:6:20:592:496': 0 -> 1 156s [bam_fillmd1] different NM for read 'B7_597:4:38:999:463': 2 -> 1 156s [bam_fillmd1] different NM for read 'EAS114_28:5:23:944:377': 0 -> 3 156s [bam_fillmd1] different NM for read 'EAS219_1:3:90:219:528': 0 -> 3 156s [bam_fillmd1] different NM for read 'EAS1_108:5:89:942:84': 0 -> 4 156s [bam_fillmd1] different NM for read 'EAS1_108:6:159:493:275': 0 -> 5 156s [bam_fillmd1] different NM for read 'EAS139_11:1:81:1019:558': 0 -> 5 156s [bam_fillmd1] different NM for read 'EAS51_62:7:162:195:761': 0 -> 4 156s [bam_fillmd1] different NM for read 'B7_597:3:115:646:430': 0 -> 4 156s [bam_fillmd1] different NM for read 'EAS114_30:6:243:209:110': 0 -> 4 156s [bam_fillmd1] different NM for read 'EAS1_108:2:266:994:429': 0 -> 4 156s [bam_fillmd1] different NM for read 'EAS114_30:5:32:461:154': 0 -> 4 156s [bam_fillmd1] different NM for read 'EAS114_39:6:7:492:1088': 0 -> 4 156s [bam_fillmd1] different NM for read 'EAS1_95:6:174:650:125': 0 -> 4 156s [bam_fillmd1] different NM for read 'EAS56_59:6:89:457:591': 1 -> 5 156s [bam_fillmd1] different NM for read 'EAS114_39:2:38:670:564': 0 -> 4 156s [bam_fillmd1] different NM for read 'EAS188_7:4:92:693:228': 1 -> 6 156s [bam_fillmd1] different NM for read 'EAS218_1:4:61:1369:440': 0 -> 4 156s [bam_fillmd1] different NM for read 'EAS114_26:4:123:1001:580': 0 -> 4 156s [bam_fillmd1] different NM for read 'EAS114_39:4:10:1312:1558': 0 -> 4 156s [bam_fillmd1] different NM for read 'EAS220_1:8:45:178:1321': 0 -> 4 156s [bam_fillmd1] different NM for read 'EAS56_59:5:125:137:58': 0 -> 4 156s [bam_fillmd1] different NM for read 'EAS192_3:3:285:349:797': 1 -> 5 156s [bam_fillmd1] different NM for read 'EAS114_45:5:56:1757:1319': 0 -> 4 156s [bam_fillmd1] different NM for read 'B7_591:3:291:404:199': 0 -> 4 156s [bam_fillmd1] different NM for read 'EAS54_65:7:159:253:353': 0 -> 4 156s [bam_fillmd1] different NM for read 'EAS56_57:1:122:38:103': 0 -> 4 156s [bam_fillmd1] different NM for read 'EAS188_4:5:103:870:105': 0 -> 4 156s [bam_fillmd1] different NM for read 'EAS1_105:8:24:718:322': 3 -> 7 156s [bam_fillmd1] different NM for read 'EAS51_64:6:118:41:489': 0 -> 4 156s [bam_fillmd1] different NM for read 'EAS56_61:3:165:665:220': 0 -> 4 156s [bam_fillmd1] different NM for read 'EAS114_30:6:238:803:383': 0 -> 4 156s [bam_fillmd1] different NM for read 'EAS1_105:3:232:364:583': 0 -> 3 156s [bam_fillmd1] different NM for read 'B7_595:2:29:729:70': 3 -> 4 156s [bam_fillmd1] different NM for read 'EAS114_30:6:220:809:850': 4 -> 6 156s [bam_fillmd1] different NM for read 'EAS54_65:2:264:157:150': 3 -> 5 156s [bam_fillmd1] different NM for read 'B7_595:8:26:242:35': 2 -> 1 156s [bam_fillmd1] different NM for read 'B7_610:7:34:144:868': 4 -> 5 156s [bam_fillmd1] different NM for read 'B7_597:8:147:360:141': 1 -> 2 156s [bam_fillmd1] different NM for read 'EAS139_19:2:82:154:1333': 0 -> 4 156s [bam_fillmd1] different NM for read 'EAS56_63:3:41:468:459': 0 -> 3 156s [bam_fillmd1] different NM for read 'EAS1_97:4:274:287:423': 0 -> 1 156s [bam_fillmd1] different NM for read 'EAS114_30:2:303:428:326': 0 -> 1 156s [bam_fillmd1] different NM for read 'EAS54_71:8:105:854:975': 0 -> 3 156s gunzip < with_md.sam.gz > with_md.sam 156s samtools view --no-PG -bo with_md.bam with_md.sam 156s [W::bam_hdr_read] EOF marker is absent. The input is probably truncated 156s samtools index with_md.bam 156s samtools view --no-PG -bu -o uncompressed.bam ex2.sam 156s samtools view --no-PG -bo MM-chebi.bam MM-chebi.sam 156s samtools view --no-PG -bo MM-double.bam MM-double.sam 156s samtools view --no-PG -bo MM-multi.bam MM-multi.sam 156s samtools view --no-PG -bo MM-orient.bam MM-orient.sam 156s samtools view --no-PG -bo ex10.bam ex10.sam 157s samtools view --no-PG -bo ex3.bam ex3.sam 157s samtools view --no-PG -bo ex4.bam ex4.sam 157s samtools view --no-PG -bo ex5.bam ex5.sam 157s samtools view --no-PG -bo ex6.bam ex6.sam 157s samtools view --no-PG -bo ex8.bam ex8.sam 157s samtools view --no-PG -bo ex9_fail.bam ex9_fail.sam 157s samtools view --no-PG -bo ex9_nofail.bam ex9_nofail.sam 157s samtools view --no-PG -bo ex_spliced.bam ex_spliced.sam 157s samtools view --no-PG -bo example_aligned_pairs.bam example_aligned_pairs.sam 157s samtools view --no-PG -bo example_btag.bam example_btag.sam 157s samtools view --no-PG -bo example_dash_in_chr.bam example_dash_in_chr.sam 157s samtools view --no-PG -bo example_empty_header.bam example_empty_header.sam 157s samtools view --no-PG -bo example_empty_with_header.bam example_empty_with_header.sam 157s samtools view --no-PG -bo example_reverse_complement.bam example_reverse_complement.sam 157s touch tmp.list 157s samtools view --no-PG -bo example_unmapped_reads_no_sq.bam -t tmp.list example_unmapped_reads_no_sq.sam 157s rm -f tmp.list 157s samtools view --no-PG -bo issue100.bam issue100.sam 157s samtools view --no-PG -bo rg_with_tab.bam rg_with_tab.sam 157s samtools view --no-PG -bo softclip.bam softclip.sam 157s samtools view --no-PG -bo tag_bug.bam tag_bug.sam 157s samtools view --no-PG -bo test_mapped_unmapped.bam test_mapped_unmapped.sam 157s samtools view --no-PG -bo test_query_position.bam test_query_position.sam 157s samtools view --no-PG -bo test_unaligned.bam test_unaligned.sam 157s samtools index MM-chebi.bam 157s samtools index MM-double.bam 157s samtools index MM-multi.bam 157s samtools index MM-orient.bam 157s samtools index ex10.bam 157s samtools index ex3.bam 157s samtools index ex4.bam 157s samtools index ex5.bam 157s samtools index ex6.bam 157s samtools index ex8.bam 157s samtools index ex9_fail.bam 157s samtools index ex9_nofail.bam 157s samtools index ex_spliced.bam 157s samtools index example_aligned_pairs.bam 157s samtools index example_btag.bam 157s samtools index example_dash_in_chr.bam 157s samtools index example_empty_header.bam 157s samtools index example_empty_with_header.bam 157s samtools index example_reverse_complement.bam 157s samtools index example_unmapped_reads_no_sq.bam 157s samtools index issue100.bam 157s samtools index rg_with_tab.bam 157s samtools index softclip.bam 157s samtools index tag_bug.bam 157s samtools index test_mapped_unmapped.bam 157s samtools index test_query_position.bam 157s samtools index test_unaligned.bam 157s samtools view --no-PG -Co ex1.cram -T ex1.fa ex1.sam 157s samtools view --no-PG -Co ex2.cram -T ex1.fa ex2.sam 157s samtools view --no-PG -Co ex3.cram -T ex1.fa ex3.sam 157s samtools index ex1.cram 157s samtools index ex2.cram 157s samtools index ex3.cram 157s cp ex1.bam example_bai.bam 157s samtools index example_bai.bam 157s mv example_bai.bam.bai example_bai.bai 157s dd if=ex2.bam of=ex2_truncated.bam bs=$((`wc -c < ex2.bam`-512)) count=1 157s 1+0 records in 157s 1+0 records out 157s 122288 bytes (122 kB, 119 KiB) copied, 0.000202963 s, 603 MB/s 157s (bgzip -d < ex2.bam; printf '\37\0\0\0\1\0\0\0') | bgzip > ex2_corrupt.bam 157s grep "^@" ex2.sam | samtools view --no-PG -bo empty.bam - 157s samtools index empty.bam 157s cp ex1.bam explicit_index.bam 157s cp ex1.cram explicit_index.cram 157s gzip < faidx_empty_seq.fq > faidx_empty_seq.fq.gz 157s bgzip < ex1.fa > ex1.fa.gz 157s samtools faidx ex1.fa.gz 157s cp ex1.bam ex1_csi.bam 157s samtools index -c ex1_csi.bam 157s touch all.stamp 157s rm with_md.sam 157s make: Leaving directory '/tmp/autopkgtest.GNnawt/build.dpD/src/tests/pysam_data' 157s make: Entering directory '/tmp/autopkgtest.GNnawt/build.dpD/src/tests/cbcf_data' 157s bgzip < example_vcf40.vcf > example_vcf40.vcf.gz 157s tabix -p vcf example_vcf40.vcf.gz # create tbi index 157s bcftools index example_vcf40.vcf.gz # create csi index 157s bgzip < example_vcf42.vcf > example_vcf42.vcf.gz 157s tabix -p vcf example_vcf42.vcf.gz # create tbi index 157s bcftools index example_vcf42.vcf.gz # create csi index 157s bgzip < example_vcf42_only_header.vcf > example_vcf42_only_header.vcf.gz 157s tabix -p vcf example_vcf42_only_header.vcf.gz # create tbi index 157s bcftools index example_vcf42_only_header.vcf.gz # create csi index 157s bgzip < example_vcf42_withcontigs.vcf > example_vcf42_withcontigs.vcf.gz 157s tabix -p vcf example_vcf42_withcontigs.vcf.gz # create tbi index 157s bcftools index example_vcf42_withcontigs.vcf.gz # create csi index 157s bgzip < example_vcf43.vcf > example_vcf43.vcf.gz 157s tabix -p vcf example_vcf43.vcf.gz # create tbi index 157s bcftools index example_vcf43.vcf.gz # create csi index 157s bgzip < example_vcf43_with_utf8.vcf > example_vcf43_with_utf8.vcf.gz 157s tabix -p vcf example_vcf43_with_utf8.vcf.gz # create tbi index 157s bcftools index example_vcf43_with_utf8.vcf.gz # create csi index 157s bgzip < gnomad.vcf > gnomad.vcf.gz 157s tabix -p vcf gnomad.vcf.gz # create tbi index 157s bcftools index gnomad.vcf.gz # create csi index 157s bgzip < gnomad_fixed.vcf > gnomad_fixed.vcf.gz 157s tabix -p vcf gnomad_fixed.vcf.gz # create tbi index 157s bcftools index gnomad_fixed.vcf.gz # create csi index 157s bgzip < missing_genotypes.vcf > missing_genotypes.vcf.gz 157s tabix -p vcf missing_genotypes.vcf.gz # create tbi index 157s bcftools index missing_genotypes.vcf.gz # create csi index 157s bcftools view -O b example_vcf40.vcf.gz -o example_vcf40.bcf 157s bcftools index example_vcf40.bcf 157s bcftools view -O b example_vcf42.vcf.gz -o example_vcf42.bcf 157s bcftools index example_vcf42.bcf 157s bcftools view -O b example_vcf42_only_header.vcf.gz -o example_vcf42_only_header.bcf 157s bcftools index example_vcf42_only_header.bcf 157s bcftools view -O b example_vcf42_withcontigs.vcf.gz -o example_vcf42_withcontigs.bcf 157s bcftools index example_vcf42_withcontigs.bcf 157s bcftools view -O b example_vcf43.vcf.gz -o example_vcf43.bcf 157s bcftools index example_vcf43.bcf 157s bcftools view -O b example_vcf43_with_utf8.vcf.gz -o example_vcf43_with_utf8.bcf 157s bcftools index example_vcf43_with_utf8.bcf 157s bcftools view -O b gnomad.vcf.gz -o gnomad.bcf 157s bcftools index gnomad.bcf 157s bcftools view -O b gnomad_fixed.vcf.gz -o gnomad_fixed.bcf 157s [W::bcf_hdr_check_sanity] PL should be declared as Number=G 157s bcftools index gnomad_fixed.bcf 157s [W::bcf_hdr_check_sanity] PL should be declared as Number=G 157s bcftools view -O b missing_genotypes.vcf.gz -o missing_genotypes.bcf 157s bcftools index missing_genotypes.bcf 157s touch all.stamp 157s make: Leaving directory '/tmp/autopkgtest.GNnawt/build.dpD/src/tests/cbcf_data' 158s ============================= test session starts ============================== 158s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3 158s cachedir: .pytest_cache 158s rootdir: /tmp/autopkgtest.GNnawt/build.dpD/src 158s configfile: setup.cfg 158s testpaths: pysam, tests 158s plugins: typeguard-4.4.1 158s collecting ... collected 951 items 158s 158s tests/AlignedSegment_test.py::TestAlignedSegment::testBlocks PASSED 158s tests/AlignedSegment_test.py::TestAlignedSegment::testCompare PASSED 158s tests/AlignedSegment_test.py::TestAlignedSegment::testEmpty PASSED 158s tests/AlignedSegment_test.py::TestAlignedSegment::testFullReferencePositions PASSED 158s tests/AlignedSegment_test.py::TestAlignedSegment::testHashing PASSED 158s tests/AlignedSegment_test.py::TestAlignedSegment::testLargeRead PASSED 158s tests/AlignedSegment_test.py::TestAlignedSegment::testNoSequence PASSED 158s tests/AlignedSegment_test.py::TestAlignedSegment::testPositions PASSED 158s tests/AlignedSegment_test.py::TestAlignedSegment::testSettingTagInEmptyRead PASSED 158s tests/AlignedSegment_test.py::TestAlignedSegment::testStrOfEmptyRead PASSED 158s tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate PASSED 158s tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate2 PASSED 158s tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateQual PASSED 158s tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateTlen PASSED 158s tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_mapped_reads_are_updated PASSED 158s tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_unmapped_reads_ignore_length PASSED 158s tests/AlignedSegment_test.py::TestAlignedSegment::test_equivalence_matches_only_and_with_seq PASSED 158s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs PASSED 158s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_1character_md PASSED 158s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_bad_type_md PASSED 158s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_hard_clipping PASSED 158s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_lowercase_md PASSED 158s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_match_mismatch PASSED 158s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding PASSED 158s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding_with_seq PASSED 158s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip PASSED 158s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip_reference PASSED 158s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_soft_clipping PASSED 158s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_uppercase_md PASSED 158s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_with_malformed_MD_tag PASSED 158s tests/AlignedSegment_test.py::TestAlignedSegment::test_header_accessible PASSED 158s tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_query_length PASSED 158s tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_read_length PASSED 158s tests/AlignedSegment_test.py::TestAlignedSegment::test_query_length_is_limited PASSED 158s tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_asterisk PASSED 158s tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_chromosome PASSED 158s tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_none PASSED 158s tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_not_be_set_to_unknown_chromosome PASSED 158s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_chromosome PASSED 158s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing PASSED 158s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing_without_header PASSED 158s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_without_header PASSED 158s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_not_be_set_to_unknown_chromosome PASSED 158s tests/AlignedSegment_test.py::TestTidMapping::test_unmapped_tid_is_asterisk_in_output PASSED 158s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_asterisk PASSED 158s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_chromosome PASSED 158s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_none PASSED 158s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_not_be_set_to_unknown_chromosome PASSED 158s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_chromosome PASSED 158s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_equal PASSED 158s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing PASSED 158s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing_without_header PASSED 158s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_without_header PASSED 158s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_not_be_set_to_unknown_chromosome PASSED 158s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_unmapped_tid_is_asterisk_in_output PASSED 158s tests/AlignedSegment_test.py::TestCigar::testCigar PASSED 158s tests/AlignedSegment_test.py::TestCigar::testCigarString PASSED 158s tests/AlignedSegment_test.py::TestCigarStats::testStats PASSED 158s tests/AlignedSegment_test.py::TestAlignedPairs::testReferenceBases PASSED 158s tests/AlignedSegment_test.py::TestBaseModifications::testChebi PASSED 158s tests/AlignedSegment_test.py::TestBaseModifications::testDouble PASSED 158s tests/AlignedSegment_test.py::TestBaseModifications::testMulti PASSED 158s tests/AlignedSegment_test.py::TestBaseModifications::testOrient PASSED 158s tests/AlignedSegment_test.py::TestTags::testAddTags PASSED 158s tests/AlignedSegment_test.py::TestTags::testAddTagsType PASSED 158s tests/AlignedSegment_test.py::TestTags::testArrayTags PASSED 158s tests/AlignedSegment_test.py::TestTags::testEmptyTag PASSED 158s tests/AlignedSegment_test.py::TestTags::testLongTags PASSED 158s tests/AlignedSegment_test.py::TestTags::testMDTagComplex PASSED 158s tests/AlignedSegment_test.py::TestTags::testMDTagDeletions PASSED 158s tests/AlignedSegment_test.py::TestTags::testMDTagInsertions PASSED 158s tests/AlignedSegment_test.py::TestTags::testMDTagMatchOnly PASSED 158s tests/AlignedSegment_test.py::TestTags::testMDTagRefSkipping PASSED 158s tests/AlignedSegment_test.py::TestTags::testMDTagSoftClipping PASSED 158s tests/AlignedSegment_test.py::TestTags::testMissingTag PASSED 158s tests/AlignedSegment_test.py::TestTags::testNegativeIntegers PASSED 158s tests/AlignedSegment_test.py::TestTags::testNegativeIntegersWrittenToFile PASSED 158s tests/AlignedSegment_test.py::TestTags::testSetTag PASSED 158s tests/AlignedSegment_test.py::TestTags::testTagParsing PASSED 158s tests/AlignedSegment_test.py::TestTags::testTagsUpdatingFloat PASSED 158s tests/AlignedSegment_test.py::TestCopy::testCopy PASSED 158s tests/AlignedSegment_test.py::TestCopy::testDeepCopy PASSED 158s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_A PASSED 158s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_C PASSED 158s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_H PASSED 158s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_I PASSED 158s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_S PASSED 158s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_a PASSED 158s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_automated_type_detection PASSED 158s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_c PASSED 158s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_d PASSED 158s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_f PASSED 158s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_i PASSED 158s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_s PASSED 158s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_A PASSED 158s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_C PASSED 158s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_H PASSED 158s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_I PASSED 158s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_S PASSED 158s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_a PASSED 158s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_automated_type_detection PASSED 158s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_c PASSED 158s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_d PASSED 158s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_f PASSED 158s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_i PASSED 158s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_s PASSED 158s tests/AlignedSegment_test.py::TestEnums::test_cigar_enums_are_defined PASSED 158s tests/AlignedSegment_test.py::TestEnums::test_sam_flags_are_defined PASSED 158s tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_constructed_without_header PASSED 158s tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_written_to_file PASSED 158s tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_id_can_be_set PASSED 158s tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_name_is_not_available PASSED 158s tests/AlignedSegment_test.py::TestForwardStrandValues::test_qualities_are_complemented PASSED 158s tests/AlignedSegment_test.py::TestForwardStrandValues::test_sequence_is_complemented PASSED 158s tests/AlignedSegment_test.py::TestExportImport::test_dict_export PASSED 158s tests/AlignedSegment_test.py::TestExportImport::test_string_export PASSED 158s tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_with_tags PASSED 158s tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_without_tags PASSED 158s tests/AlignedSegment_test.py::TestExportImport::test_to_string_without_alignment_file PASSED 158s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_dict PASSED 158s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_header PASSED 158s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references PASSED 158s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references_without_text PASSED 158s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_text PASSED 158s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_access_works PASSED 158s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_contains_works PASSED 158s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_get_works PASSED 158s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_keys_works PASSED 158s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_len_works PASSED 158s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_setting_raises_error PASSED 158s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_values_works PASSED 158s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_header_content_is_as_expected PASSED 159s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_name_mapping PASSED 159s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_text_access_works PASSED 159s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works PASSED 159s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_contains_works PASSED 159s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_get_works PASSED 159s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_keys_works PASSED 159s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_len_works PASSED 159s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_setting_raises_error PASSED 159s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_values_works PASSED 159s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected PASSED 159s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_name_mapping PASSED 159s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_text_access_works PASSED 159s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works PASSED 159s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_contains_works PASSED 159s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_get_works PASSED 159s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_keys_works PASSED 159s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_len_works PASSED 159s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_setting_raises_error PASSED 159s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_values_works PASSED 159s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected PASSED 159s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_name_mapping PASSED 159s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_text_access_works PASSED 159s tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM /tmp/autopkgtest.GNnawt/build.dpD/src/tests/tmp/pysamtests_tmp_check_read_write_w_7f7prh 159s PASSED 159s tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM /tmp/autopkgtest.GNnawt/build.dpD/src/tests/tmp/pysamtests_tmp_check_read_write_5cye19qn 159s PASSED 159s tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /tmp/autopkgtest.GNnawt/build.dpD/src/tests/tmp/pysamtests_tmp_check_read_write_9q08v7t4 159s PASSED 159s tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM /tmp/autopkgtest.GNnawt/build.dpD/src/tests/tmp/pysamtests_tmp_check_read_write_bei9sp6f 159s PASSED 159s tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM /tmp/autopkgtest.GNnawt/build.dpD/src/tests/tmp/pysamtests_tmp_check_read_write_1y7x2xug 159s PASSED 159s tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM [E::cram_index_load] Could not retrieve index file for '/tmp/autopkgtest.GNnawt/build.dpD/src/tests/tmp/pysamtests_tmp_check_read_write_5cye19qn' 159s [W::sanitise_SQ_lines] Header @SQ length mismatch for ref chr1, 2147483647 vs 1575 159s [E::cram_index_load] Could not retrieve index file for '/tmp/autopkgtest.GNnawt/build.dpD/src/tests/tmp/pysamtests_tmp_check_read_write_1y7x2xug' 159s /tmp/autopkgtest.GNnawt/build.dpD/src/tests/tmp/pysamtests_tmp_check_read_write_7u2p3xeg 159s PASSED 159s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_all_stepper PASSED 159s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_ignore_overlaps PASSED 159s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper PASSED 159s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_base_quality_threshold PASSED 159s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_ignore_orphans PASSED 159s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_mapping_quality_threshold PASSED 159s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_redo_baq PASSED 159s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_all_stepper PASSED 159s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_ignore_overlaps PASSED 159s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper PASSED 159s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_base_quality_threshold PASSED 159s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_ignore_orphans PASSED 159s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_mapping_quality_threshold PASSED 159s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_redo_baq PASSED 159s tests/AlignmentFilePileup_test.py::TestPileupQueryPosition::testPileup PASSED 159s tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope SKIPPED 159s tests/AlignmentFilePileup_test.py::TestPileupObjects::testPileupColumn PASSED 159s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testInverse PASSED 159s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateAll PASSED 159s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIteratePerContig PASSED 159s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateRanges PASSED 159s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateTruncate PASSED 159s tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testAccessOnClosedIterator PASSED 159s tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStart PASSED 159s tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStr PASSED 159s tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testTruncate PASSED 159s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_depths_are_equal PASSED 159s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_mapping_qualities_are_equal PASSED 160s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_with_reference_are_equal PASSED 160s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_without_reference_are_equal PASSED 160s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_are_equal PASSED 160s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_from_pileups_are_equal PASSED 160s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARQueryLength PASSED 160s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigar PASSED 160s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigarstring PASSED 160s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARflag PASSED 160s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmapq PASSED 160s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmpos PASSED 160s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmrnm PASSED 160s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARpos PASSED 160s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqname PASSED 160s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqqual PASSED 160s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqual PASSED 160s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARquery PASSED 160s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARrname PASSED 160s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARseq PASSED 160s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testOpt PASSED 160s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPairedBools PASSED 160s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPresentOptionalFields PASSED 160s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testTags PASSED 160s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARQueryLength PASSED 160s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigar PASSED 160s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigarstring PASSED 160s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARflag PASSED 160s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmapq PASSED 160s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmpos PASSED 160s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmrnm PASSED 160s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARpos PASSED 160s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqname PASSED 160s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqqual PASSED 160s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqual PASSED 160s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARquery PASSED 160s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARrname PASSED 160s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARseq PASSED 160s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testOpt PASSED 160s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPairedBools PASSED 160s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPresentOptionalFields PASSED 160s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testTags PASSED 160s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARQueryLength PASSED 161s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigar PASSED 161s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigarstring PASSED 161s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARflag PASSED 162s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmapq PASSED 162s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmpos PASSED 163s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmrnm PASSED 163s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARpos PASSED 163s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqname PASSED 164s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqqual PASSED 164s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqual PASSED 165s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARquery PASSED 165s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARrname PASSED 165s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARseq PASSED 166s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testOpt PASSED 166s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPairedBools PASSED 166s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPresentOptionalFields PASSED 167s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testTags PASSED 167s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARQueryLength PASSED 167s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigar PASSED 167s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigarstring PASSED 167s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARflag PASSED 167s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmapq PASSED 167s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmpos PASSED 167s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmrnm PASSED 167s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARpos PASSED 167s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqname PASSED 167s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqqual PASSED 167s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqual PASSED 167s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARquery PASSED 167s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARrname PASSED 167s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARseq PASSED 167s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testOpt PASSED 167s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPairedBools PASSED 167s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPresentOptionalFields PASSED 167s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testTags PASSED 167s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARQueryLength PASSED 168s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigar PASSED 168s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigarstring PASSED 169s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARflag PASSED 169s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmapq PASSED 169s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmpos PASSED 170s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmrnm PASSED 170s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARpos PASSED 171s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqname PASSED 171s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqqual PASSED 171s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqual PASSED 172s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARquery PASSED 172s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARrname PASSED 173s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARseq PASSED 173s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testOpt PASSED 174s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPairedBools PASSED 174s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPresentOptionalFields PASSED 174s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testTags PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARQueryLength PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigar PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigarstring PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARflag PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmapq PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmpos PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmrnm PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARpos PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqname PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqqual PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqual PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARquery PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARrname PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARseq PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testOpt PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPairedBools PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPresentOptionalFields PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testTags PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARQueryLength PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigar PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigarstring PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARflag PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmapq PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmpos PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmrnm PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARpos PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqname PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqqual PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqual PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARquery PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARrname PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARseq PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testOpt PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPairedBools PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPresentOptionalFields PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testTags PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARQueryLength PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigar PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigarstring PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARflag PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmapq PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmpos PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmrnm PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARpos PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqname PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqqual PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqual PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARquery PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARrname PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARseq PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testOpt PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPairedBools PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPresentOptionalFields PASSED 174s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testTags PASSED 174s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARQueryLength PASSED 174s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigar PASSED 174s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigarstring PASSED 174s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARflag PASSED 174s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmapq PASSED 174s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmpos PASSED 174s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmrnm PASSED 174s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARpos PASSED 174s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqname PASSED 174s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqqual PASSED 174s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqual PASSED 174s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARquery PASSED 174s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARrname PASSED 174s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARseq PASSED 174s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testOpt PASSED 174s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPairedBools PASSED 174s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPresentOptionalFields PASSED 174s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testTags PASSED 174s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARQueryLength PASSED 174s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigar PASSED 174s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigarstring PASSED 174s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARflag PASSED 174s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmapq PASSED 174s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmpos PASSED 174s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmrnm PASSED 174s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARpos PASSED 174s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqname PASSED 174s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqqual PASSED 174s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqual PASSED 174s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARquery PASSED 174s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARrname PASSED 174s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARseq PASSED 174s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testOpt PASSED 174s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPairedBools PASSED 174s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPresentOptionalFields PASSED 174s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testTags PASSED 175s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARQueryLength PASSED 175s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigar PASSED 176s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigarstring PASSED 176s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARflag PASSED 176s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmapq PASSED 177s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmpos PASSED 177s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmrnm PASSED 178s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARpos PASSED 178s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqname PASSED 178s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqqual PASSED 179s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqual PASSED 179s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARquery PASSED 180s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARrname PASSED 180s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARseq PASSED 180s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testOpt PASSED 181s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPairedBools PASSED 181s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPresentOptionalFields PASSED 182s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testTags PASSED 182s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARQueryLength PASSED 182s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigar PASSED 183s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigarstring PASSED 183s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARflag PASSED 184s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmapq PASSED 184s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmpos PASSED 184s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmrnm PASSED 185s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARpos PASSED 185s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqname PASSED 186s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqqual PASSED 186s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqual PASSED 186s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARquery PASSED 187s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARrname PASSED 187s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARseq PASSED 187s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testOpt PASSED 188s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPairedBools PASSED 188s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPresentOptionalFields PASSED 189s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testTags PASSED 189s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARQueryLength PASSED 189s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigar PASSED 189s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigarstring PASSED 189s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARflag PASSED 189s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmapq PASSED 189s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmpos PASSED 189s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmrnm PASSED 189s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARpos PASSED 189s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqname PASSED 189s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqqual PASSED 189s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqual PASSED 189s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARquery PASSED 189s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARrname PASSED 189s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARseq PASSED 189s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testOpt PASSED 189s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPairedBools PASSED 189s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPresentOptionalFields PASSED 189s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testRaises PASSED 189s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testTags PASSED 189s tests/AlignmentFile_test.py::TestIO::testBAM2BAM PASSED 189s tests/AlignmentFile_test.py::TestIO::testBAM2SAM PASSED 189s tests/AlignmentFile_test.py::TestIO::testBAMWithCSIIndex PASSED 189s tests/AlignmentFile_test.py::TestIO::testBAMWithShortBAI PASSED 189s tests/AlignmentFile_test.py::TestIO::testBAMWithoutAlignedSegments PASSED 189s tests/AlignmentFile_test.py::TestIO::testCRAM2BAM PASSED 190s tests/AlignmentFile_test.py::TestIO::testCRAM2CRAM PASSED 191s tests/AlignmentFile_test.py::TestIO::testCRAM2SAM PASSED 191s tests/AlignmentFile_test.py::TestIO::testEmptyBAM PASSED 191s tests/AlignmentFile_test.py::TestIO::testEmptyWithHeaderBAM PASSED 191s tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFile PASSED 191s tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject PASSED 191s tests/AlignmentFile_test.py::TestIO::testHead PASSED 191s tests/AlignmentFile_test.py::TestIO::testOpenFromFilename PASSED 191s tests/AlignmentFile_test.py::TestIO::testReadBamWithoutTargetNames PASSED 191s tests/AlignmentFile_test.py::TestIO::testReadSamWithoutTargetNames PASSED 191s tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex PASSED 191s tests/AlignmentFile_test.py::TestIO::testSAM2BAM PASSED 192s tests/AlignmentFile_test.py::TestIO::testSAM2CRAM PASSED 192s tests/AlignmentFile_test.py::TestIO::testSAM2SAM PASSED 192s tests/AlignmentFile_test.py::TestIO::testSAM2SAMWithoutHeader PASSED 193s tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile PASSED 193s tests/AlignmentFile_test.py::TestIO::test_accessing_attributes_in_closed_file_raises_errors PASSED 193s tests/AlignmentFile_test.py::TestIO::test_fail_read_sam_without_header PASSED 193s tests/AlignmentFile_test.py::TestIO::test_fail_when_reading_unformatted_files PASSED 193s tests/AlignmentFile_test.py::TestIO::test_fetch_by_tid PASSED 193s tests/AlignmentFile_test.py::TestIO::test_header_available_after_closing_file PASSED 193s tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_with_header_without_header_check PASSED 193s tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_without_header_with_refs PASSED 193s tests/AlignmentFile_test.py::TestIO::test_reference_name_available_after_closing_file PASSED 193s tests/AlignmentFile_test.py::TestIO::test_write_bam_to_unknown_path_fails PASSED 193s tests/AlignmentFile_test.py::TestAutoDetect::testBAM PASSED 193s tests/AlignmentFile_test.py::TestAutoDetect::testCRAM [E::hts_open_format] Failed to open file "missing_directory/new_file.bam" : No such file or directory 193s PASSED 193s tests/AlignmentFile_test.py::TestAutoDetect::testSAM PASSED 193s tests/AlignmentFile_test.py::TestIteratorRowBAM::testIteratePerContig PASSED 193s tests/AlignmentFile_test.py::TestIteratorRowBAM::testIterateRanges PASSED 194s tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate PASSED 195s tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIteratePerContig PASSED 210s tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIterateRanges PASSED 211s tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIteratePerContig PASSED 225s tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIterateRanges PASSED 225s tests/AlignmentFile_test.py::TestFloatTagBug::testFloatTagBug PASSED 225s tests/AlignmentFile_test.py::TestLargeFieldBug::testLargeFileBug PASSED 225s tests/AlignmentFile_test.py::TestClipping::testClipping PASSED 225s tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_bam_with_until_eof_reads_unmapped_reads PASSED 225s tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_sam_with_until_eof_reads_unmapped_reads PASSED 225s tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads PASSED 225s tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads_by_contig PASSED 225s tests/AlignmentFile_test.py::TestContextManager::testManager PASSED 225s tests/AlignmentFile_test.py::TestMultiThread::testSingleThreadEqualsMultithread PASSED 225s tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED 225s tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED 225s tests/AlignmentFile_test.py::TestExceptions::testBadContig PASSED 225s tests/AlignmentFile_test.py::TestExceptions::testMeaninglessCrap PASSED 225s tests/AlignmentFile_test.py::TestExceptions::testMissingFile PASSED 225s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangNewFormat PASSED 225s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeNewFormat PASSED 225s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeOldFormat PASSED 225s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeNewFormat PASSED 225s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeOldFormat PASSED 225s tests/AlignmentFile_test.py::TestExceptions::testZeroToZero PASSED 225s tests/AlignmentFile_test.py::TestWrongFormat::testOpenBamAsSam PASSED 225s tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsBam PASSED 225s tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsSam PASSED 225s tests/AlignmentFile_test.py::TestWrongFormat::testOpenSamAsBam PASSED 225s tests/AlignmentFile_test.py::TestRegionParsing::test_dash_in_chr PASSED 225s tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile [E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory 225s [E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory 225s [E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory 225s [E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory 225s PASSED 225s tests/AlignmentFile_test.py::TestDeNovoConstruction::test_pass_if_reads_binary_equal PASSED 225s tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader PASSED 225s tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_in_header PASSED 225s tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_with_null_bytes_in_header PASSED 225s tests/AlignmentFile_test.py::TestMismatchingHeader::testMismatchingHeader PASSED 225s tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader PASSED 225s tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2 PASSED 225s tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator [W::bam_hdr_read] EOF marker is absent. The input is probably truncated 225s PASSED 225s tests/AlignmentFile_test.py::TestCorruptBAM::testCorruptBamIterator PASSED 225s tests/AlignmentFile_test.py::TestBTagSam::testReadTags PASSED 225s tests/AlignmentFile_test.py::TestBTagSam::testReadWriteTags PASSED 225s tests/AlignmentFile_test.py::TestBTagBam::testReadTags PASSED 225s tests/AlignmentFile_test.py::TestBTagBam::testReadWriteTags PASSED 225s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetch PASSED 225s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchUntilEOF PASSED 225s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionFalseTrue PASSED 225s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueFalse PASSED 225s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueTrue PASSED 225s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetch [E::bgzf_read_block] Failed to read BGZF block data at offset 105176 expected 17578 bytes; hread returned 17094 225s [E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes 226s PASSED 227s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchUntilEOF PASSED 228s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionFalseTrue PASSED 229s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueFalse PASSED 230s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueTrue PASSED 230s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetch PASSED 231s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchUntilEOF PASSED 232s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionFalseTrue PASSED 233s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueFalse PASSED 234s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueTrue PASSED 234s tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetch PASSED 235s tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetchAll PASSED 235s tests/AlignmentFile_test.py::TestRemoteFileHTTP::testView PASSED 235s tests/AlignmentFile_test.py::TestLargeOptValues::testBAM PASSED 235s tests/AlignmentFile_test.py::TestLargeOptValues::testSAM PASSED 235s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_counts_as_expected PASSED 235s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_nofilter PASSED 235s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_quality_filter PASSED 235s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_all PASSED 235s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_callback PASSED 235s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_with_coordinates_works PASSED 235s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_without_coordinates_fails PASSED 235s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_wrong_coordinates_fails PASSED 235s tests/AlignmentFile_test.py::TestCountCoverage::test_counting_the_same_region_works PASSED 235s tests/AlignmentFile_test.py::TestFindIntrons::test_all PASSED 235s tests/AlignmentFile_test.py::TestFindIntrons::test_first PASSED 235s tests/AlignmentFile_test.py::TestFindIntrons::test_total PASSED 235s tests/AlignmentFile_test.py::TestLogging::testFail1 PASSED 235s tests/AlignmentFile_test.py::TestLogging::testNoFail1 PASSED 235s tests/AlignmentFile_test.py::TestLogging::testNoFail2 PASSED 236s tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testCount PASSED 236s tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testIndexStats PASSED 237s tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testMate PASSED 237s tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct PASSED 237s tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct_per_chromosome PASSED 237s tests/AlignmentFile_test.py::TestSamtoolsProxy::testIndex PASSED 237s tests/AlignmentFile_test.py::TestSamtoolsProxy::testSort [E::hts_open_format] Failed to open file "missing_file" : No such file or directory 237s PASSED 237s tests/AlignmentFile_test.py::TestSamtoolsProxy::testView PASSED 237s tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex [E::hts_open_format] Failed to open file "missing_file" : No such file or directory 237s PASSED 237s tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM [W::hts_idx_load3] The index file is older than the data file: /tmp/autopkgtest.GNnawt/build.dpD/src/tests/pysam_data/ex1.bam.bai 237s PASSED 237s tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexCRAM PASSED 237s tests/AlignmentFile_test.py::TestExplicitIndex::testRemoteExplicitIndexBAM PASSED 237s tests/AlignmentFile_test.py::TestVerbosity::testVerbosity PASSED 237s tests/AlignmentFile_test.py::TestSanityCheckingBAM::test_empty_read_gives_value_error PASSED 237s tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_bam PASSED 237s tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_cram SKIPPED 237s tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_sam PASSED 237s tests/StreamFiledescriptors_test.py::StreamTest::test_samtools_processing SKIPPED 237s tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing PASSED 237s tests/VariantFile_test.py::TestMissingGenotypes::testVCF PASSED 237s tests/VariantFile_test.py::TestMissingGenotypes::testVCFGZ PASSED 237s tests/VariantFile_test.py::TestMissingSamples::testVCF PASSED 237s tests/VariantFile_test.py::TestMissingSamples::testVCFGZ PASSED 237s tests/VariantFile_test.py::TestMissingSamplesFixed::testVCF PASSED[W::bcf_hdr_check_sanity] PL should be declared as Number=G 237s 237s tests/VariantFile_test.py::TestMissingSamplesFixed::testVCFGZ PASSED 237s tests/VariantFile_test.py::TestOpening::testDetectBCF PASSED 237s tests/VariantFile_test.py::TestOpening::testDetectVCF PASSED 237s tests/VariantFile_test.py::TestOpening::testDetectVCFGZ PASSED 237s tests/VariantFile_test.py::TestOpening::testEmptyFileVCF PASSED 237s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFFromPath PASSED 237s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZOnlyHeader PASSED 237s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithIndex PASSED 237s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithoutIndex PASSED 237s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFOnlyHeader PASSED 237s tests/VariantFile_test.py::TestOpening::testMissingFile PASSED 237s tests/VariantFile_test.py::TestOpening::testMissingFileVCFGZ PASSED 237s tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_csi_index PASSED 237s tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_prebuilt_csi PASSED 237s tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_tbi_index_will_produce_csi [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 237s [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) 237s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 237s [E::hts_open_format] Failed to open file "missing_file.vcf" : No such file or directory 237s [E::hts_open_format] Failed to open file "missing_file.vcf.gz" : No such file or directory 237s PASSED 237s tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_csi_index PASSED 237s tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_tbi_index PASSED 237s tests/VariantFile_test.py::TestHeader::testIterator PASSED 237s tests/VariantFile_test.py::TestHeader::testStr PASSED 237s tests/VariantFile_test.py::TestParsing::testAlleles PASSED 237s tests/VariantFile_test.py::TestParsing::testAllelesVariantTypes PASSED 237s tests/VariantFile_test.py::TestParsing::testAlt PASSED 237s tests/VariantFile_test.py::TestParsing::testChrom PASSED 237s tests/VariantFile_test.py::TestParsing::testChromFromPath PASSED 237s tests/VariantFile_test.py::TestParsing::testFilter PASSED 237s tests/VariantFile_test.py::TestParsing::testFormat PASSED 237s tests/VariantFile_test.py::TestParsing::testId PASSED 237s tests/VariantFile_test.py::TestParsing::testInfo PASSED 237s tests/VariantFile_test.py::TestParsing::testPos PASSED 237s tests/VariantFile_test.py::TestParsing::testQual PASSED 237s tests/VariantFile_test.py::TestParsing::testRef PASSED 237s tests/VariantFile_test.py::TestParsing::testSampleAlleleIndices PASSED 237s tests/VariantFile_test.py::TestParsing::testSampleAlleles PASSED 237s tests/VariantFile_test.py::TestParsing::testSampleFormats PASSED 237s tests/VariantFile_test.py::TestParsing::testStart PASSED 237s tests/VariantFile_test.py::TestParsing::testStop PASSED 237s tests/VariantFile_test.py::TestIndexFilename::testOpen PASSED 237s tests/VariantFile_test.py::TestConstructionVCFWithContigs::testBase PASSED 237s tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionFromCopy PASSED 237s tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithLines PASSED 237s tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithRecords PASSED 237s tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testBase PASSED 237s tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionFromCopy PASSED 237s tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithLines PASSED 237s tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithRecords PASSED 237s tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testBase PASSED 237s tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionFromCopy PASSED 237s tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithLines PASSED 237s tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithRecords PASSED 237s tests/VariantFile_test.py::TestSettingRecordValues::testBase PASSED 237s tests/VariantFile_test.py::TestSettingRecordValues::testGenotype (0, 0) 237s PASSED[W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 237s 237s tests/VariantFile_test.py::TestSettingRecordValues::testSetQual PASSED[W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 237s 237s tests/VariantFile_test.py::TestMultiThreading::testNoMultiThreadingWithIgnoreTruncation PASSED 237s tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult PASSED[E::idx_find_and_load] Could not retrieve index file for '/tmp/autopkgtest.GNnawt/build.dpD/src/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithreadResult_pqhtcpjh.bcf' 237s 237s tests/VariantFile_test.py::TestSubsetting::testSubsetting PASSED 237s 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.) 237s [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) 237s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 237s [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 237s [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) 237s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 237s PASSED 237s tests/VariantFile_test.py::TestUnicode::test_record_with_unicode PASSED 237s tests/VariantRecord_test.py::test_ascii_annotation_can_be_added PASSED 237s tests/VariantRecord_test.py::test_ascii_annotation_with_variable_length_can_be_added PASSED 237s tests/VariantRecord_test.py::test_unicode_annotation_can_be_added PASSED 237s tests/VariantRecord_test.py::test_set_sample_alleles PASSED 237s tests/compile_test.py::test_bam SKIPPED (no pyximport) 237s tests/compile_test.py::test_gtf SKIPPED (no pyximport) 237s tests/faidx_test.py::TestFastaFile::testFetch PASSED 237s tests/faidx_test.py::TestFastaFile::testFetchErrors PASSED 237s tests/faidx_test.py::TestFastaFile::testLength PASSED 237s tests/faidx_test.py::TestFastaFile::testOutOfRangeAccess PASSED 237s tests/faidx_test.py::TestFastaFile::testSequenceLengths PASSED 237s tests/faidx_test.py::TestFastaFile::test_fetch_with_region_and_contig_raises_exception PASSED 237s tests/faidx_test.py::TestFastaFile::test_fetch_with_region_is_equivalent PASSED 237s tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED 237s tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_index_succeeds PASSED 237s tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_without_index_succeeds PASSED 237s tests/faidx_test.py::TestFastaFilePathIndex::test_raise_exception_if_index_is_missing PASSED 237s tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED 237s tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_index_succeeds PASSED 237s tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_without_index_succeeds PASSED 237s tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_raise_exception_if_index_is_missing PASSED 237s tests/faidx_test.py::TestFastxFileFastq::testCounts PASSED 237s tests/faidx_test.py::TestFastxFileFastq::testManager PASSED 237s tests/faidx_test.py::TestFastxFileFastq::testMissingFile PASSED 237s tests/faidx_test.py::TestFastxFileFastq::testSequence PASSED 237s tests/faidx_test.py::TestFastqFileFastq::testCounts PASSED 237s tests/faidx_test.py::TestFastqFileFastq::testManager PASSED 237s tests/faidx_test.py::TestFastqFileFastq::testMissingFile PASSED 238s tests/faidx_test.py::TestFastqFileFastq::testSequence PASSED 238s tests/faidx_test.py::TestFastxFileFasta::testCounts PASSED 238s tests/faidx_test.py::TestFastxFileFasta::testManager PASSED 238s tests/faidx_test.py::TestFastxFileFasta::testMissingFile PASSED 238s tests/faidx_test.py::TestFastxFileFasta::testSequence PASSED 238s tests/faidx_test.py::TestFastxFileFastqStream::testCounts PASSED 238s tests/faidx_test.py::TestFastxFileFastqStream::testManager PASSED 238s tests/faidx_test.py::TestFastxFileFastqStream::testMissingFile PASSED 238s tests/faidx_test.py::TestFastxFileFastqStream::testSequence PASSED 238s tests/faidx_test.py::TestFastxFileWithEmptySequence::testIteration PASSED 238s tests/faidx_test.py::TestRemoteFileFTP::testFTPView PASSED 238s tests/faidx_test.py::TestRemoteFileFTP::test_sequence_lengths_are_available PASSED 238s tests/faidx_test.py::TestFastqRecord::test_fastx_record_can_be_created_from_scratch PASSED 238s tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_None PASSED 238s tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_modified PASSED 238s tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_name_is_None PASSED 238s tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_quality_is_wrong_length PASSED 238s tests/faidx_test.py::TestFastqRecord::test_fastx_record_name_can_be_modified PASSED 238s tests/faidx_test.py::TestFastqRecord::test_fastx_record_quality_can_be_modified PASSED 238s tests/faidx_test.py::TestFastqRecord::test_fastx_record_sequence_can_be_modified PASSED 238s tests/faidx_test.py::TestFastqProxy::test_fastq_proxy_instantiation_raises_error PASSED 238s tests/linking_test.py::TestLinking::test_package_can_be_installed SKIPPED 238s tests/linking_test.py::TestLinkWithRpath::test_package_can_be_installed SKIPPED 238s tests/linking_test.py::TestLinkWithRpath::test_package_tests_pass SKIPPED 238s tests/linking_test.py::TestLinkWithoutRpath::test_package_can_be_installed SKIPPED 238s tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_fail_on_import SKIPPED 238s tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_pass_if_ld_library_path_set SKIPPED 239s tests/samtools_test.py::SamtoolsTest::testStatements PASSED 239s tests/samtools_test.py::SamtoolsTest::testUsage SKIPPED (skipping us...) 239s tests/samtools_test.py::EmptyIndexTest::testEmptyIndex PASSED 239s tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraArg PASSED 239s tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraFlag PASSED 239s tests/samtools_test.py::TestReturnType::testReturnValueData PASSED 239s tests/samtools_test.py::TestReturnType::testReturnValueString PASSED 239s tests/samtools_test.py::StdoutTest::testDoubleCalling PASSED 239s tests/samtools_test.py::StdoutTest::testSaveStdout PASSED 239s tests/samtools_test.py::StdoutTest::testWithRedirectedStdout PASSED 239s tests/samtools_test.py::StdoutTest::testWithoutRedirectedStdout PASSED 240s tests/samtools_test.py::PysamTest::testStatements PASSED 240s tests/samtools_test.py::PysamTest::testUsage SKIPPED (skipping usage...) 240s tests/tabix_test.py::TestIndexing::test_indexing_to_custom_location_works PASSED 240s tests/tabix_test.py::TestIndexing::test_indexing_with_explict_columns_works PASSED 240s tests/tabix_test.py::TestIndexing::test_indexing_with_lineskipping_works PASSED 240s tests/tabix_test.py::TestIndexing::test_indexing_with_preset_works PASSED 240s tests/tabix_test.py::TestCompression::testCompression PASSED 240s tests/tabix_test.py::TestCompression::testIndexPresetCompressed PASSED 240s tests/tabix_test.py::TestCompression::testIndexPresetUncompressed PASSED 240s tests/tabix_test.py::TestCompressionSam::testCompression PASSED 240s tests/tabix_test.py::TestCompressionSam::testIndexPresetCompressed PASSED 240s tests/tabix_test.py::TestCompressionSam::testIndexPresetUncompressed PASSED 240s tests/tabix_test.py::TestCompressionBed::testCompression PASSED 240s tests/tabix_test.py::TestCompressionBed::testIndexPresetCompressed PASSED 240s tests/tabix_test.py::TestCompressionBed::testIndexPresetUncompressed PASSED 240s tests/tabix_test.py::TestCompressionVCF::testCompression PASSED 240s tests/tabix_test.py::TestCompressionVCF::testIndexPresetCompressed PASSED 240s tests/tabix_test.py::TestCompressionVCF::testIndexPresetUncompressed PASSED 240s tests/tabix_test.py::TestGZFile::testAll PASSED 240s tests/tabix_test.py::TestIterationWithoutComments::testAll PASSED 240s tests/tabix_test.py::TestIterationWithoutComments::testGetContigs PASSED 240s tests/tabix_test.py::TestIterationWithoutComments::testHeader PASSED 240s tests/tabix_test.py::TestIterationWithoutComments::testInvalidIntervals PASSED 240s tests/tabix_test.py::TestIterationWithoutComments::testPerContig PASSED 240s tests/tabix_test.py::TestIterationWithoutComments::testPerContig2 PASSED 241s tests/tabix_test.py::TestIterationWithoutComments::testPerContigFromStart PASSED 241s tests/tabix_test.py::TestIterationWithoutComments::testPerContigToEnd PASSED 241s tests/tabix_test.py::TestIterationWithoutComments::testPerInterval PASSED 241s tests/tabix_test.py::TestIterationWithoutComments::testRegionStrings PASSED 241s tests/tabix_test.py::TestIterationWithoutComments::testReopening PASSED 241s tests/tabix_test.py::TestIterationWithComments::testAll PASSED 241s tests/tabix_test.py::TestIterationWithComments::testGetContigs PASSED 241s tests/tabix_test.py::TestIterationWithComments::testHeader PASSED 241s tests/tabix_test.py::TestIterationWithComments::testInvalidIntervals PASSED 241s tests/tabix_test.py::TestIterationWithComments::testPerContig PASSED 241s tests/tabix_test.py::TestIterationWithComments::testPerContig2 PASSED 241s tests/tabix_test.py::TestIterationWithComments::testPerContigFromStart PASSED 241s tests/tabix_test.py::TestIterationWithComments::testPerContigToEnd PASSED 241s tests/tabix_test.py::TestIterationWithComments::testPerInterval PASSED 241s tests/tabix_test.py::TestIterationWithComments::testRegionStrings PASSED 241s tests/tabix_test.py::TestIterationWithComments::testReopening PASSED 241s tests/tabix_test.py::TestIterators::testClosedFile PASSED 241s tests/tabix_test.py::TestIterators::testClosedFileIteration PASSED 241s tests/tabix_test.py::TestIterators::testIteration PASSED 241s tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFile PASSED 241s tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFileIteration PASSED 241s tests/tabix_test.py::TestIteratorsGenericCompressed::testIteration PASSED 241s tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFile PASSED 241s tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFileIteration PASSED 241s tests/tabix_test.py::TestIteratorsFileCompressed::testIteration PASSED 241s tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFile PASSED 241s tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFileIteration PASSED 242s tests/tabix_test.py::TestIteratorsFileUncompressed::testIteration PASSED 242s tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooFewFields PASSED 242s tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooManyFields PASSED 242s tests/tabix_test.py::TestBed::testRead PASSED 242s tests/tabix_test.py::TestBed::testWrite PASSED 242s tests/tabix_test.py::TestUnicode::testFromTabix PASSED 242s tests/tabix_test.py::TestUnicode::testFromVCF PASSED 242s tests/tabix_test.py::TestVCFFromTabix::testRead PASSED 242s tests/tabix_test.py::TestVCFFromTabix::testWrite PASSED 242s tests/tabix_test.py::TestVCFFromVCF::testConnecting PASSED 242s tests/tabix_test.py::TestVCFFromVCF::testParsing PASSED 242s tests/tabix_test.py::VCFFromTabixTest_24::testRead PASSED 242s tests/tabix_test.py::VCFFromTabixTest_24::testWrite PASSED 242s tests/tabix_test.py::VCFFromVCFTest_24::testConnecting PASSED 242s tests/tabix_test.py::VCFFromVCFTest_24::testParsing PASSED 242s tests/tabix_test.py::VCFFromTabixTest_9::testRead PASSED 242s tests/tabix_test.py::VCFFromTabixTest_9::testWrite PASSED 242s tests/tabix_test.py::VCFFromVCFTest_9::testConnecting PASSED 242s tests/tabix_test.py::VCFFromVCFTest_9::testParsing PASSED 242s tests/tabix_test.py::VCFFromTabixTest_2::testRead PASSED 242s tests/tabix_test.py::VCFFromTabixTest_2::testWrite PASSED 242s tests/tabix_test.py::VCFFromVCFTest_2::testConnecting PASSED 242s tests/tabix_test.py::VCFFromVCFTest_2::testParsing PASSED 242s tests/tabix_test.py::VCFFromTabixTest_18::testRead PASSED 242s tests/tabix_test.py::VCFFromTabixTest_18::testWrite PASSED 242s tests/tabix_test.py::VCFFromVCFTest_18::testConnecting PASSED 242s tests/tabix_test.py::VCFFromVCFTest_18::testParsing PASSED 242s tests/tabix_test.py::VCFFromTabixTest_15::testRead PASSED 243s tests/tabix_test.py::VCFFromTabixTest_15::testWrite PASSED 243s tests/tabix_test.py::VCFFromVCFTest_15::testConnecting PASSED 243s tests/tabix_test.py::VCFFromVCFTest_15::testParsing PASSED 243s tests/tabix_test.py::VCFFromTabixTest_22::testRead PASSED 244s tests/tabix_test.py::VCFFromTabixTest_22::testWrite PASSED 244s tests/tabix_test.py::VCFFromVCFTest_22::testConnecting PASSED 244s tests/tabix_test.py::VCFFromVCFTest_22::testParsing PASSED 245s tests/tabix_test.py::VCFFromTabixTest_10::testRead PASSED 245s tests/tabix_test.py::VCFFromTabixTest_10::testWrite PASSED 245s tests/tabix_test.py::VCFFromVCFTest_10::testConnecting PASSED 245s tests/tabix_test.py::VCFFromVCFTest_10::testParsing PASSED 245s tests/tabix_test.py::VCFFromTabixTest_5::testRead PASSED 245s tests/tabix_test.py::VCFFromTabixTest_5::testWrite PASSED 245s tests/tabix_test.py::VCFFromVCFTest_5::testConnecting PASSED 245s tests/tabix_test.py::VCFFromVCFTest_5::testParsing PASSED 245s tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testRead PASSED 245s tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testWrite PASSED 245s tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testConnecting PASSED 245s tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testParsing PASSED 245s tests/tabix_test.py::VCFFromTabixTest_4::testRead PASSED 245s tests/tabix_test.py::VCFFromTabixTest_4::testWrite PASSED 245s tests/tabix_test.py::VCFFromVCFTest_4::testConnecting PASSED 246s tests/tabix_test.py::VCFFromVCFTest_4::testParsing PASSED 246s tests/tabix_test.py::VCFFromTabixTest_8::testRead PASSED 246s tests/tabix_test.py::VCFFromTabixTest_8::testWrite PASSED 246s tests/tabix_test.py::VCFFromVCFTest_8::testConnecting PASSED 246s tests/tabix_test.py::VCFFromVCFTest_8::testParsing PASSED 246s tests/tabix_test.py::VCFFromTabixTest_23::testRead PASSED 246s tests/tabix_test.py::VCFFromTabixTest_23::testWrite PASSED 246s tests/tabix_test.py::VCFFromVCFTest_23::testConnecting PASSED 246s tests/tabix_test.py::VCFFromVCFTest_23::testParsing PASSED 246s tests/tabix_test.py::VCFFromTabixTest_13::testRead PASSED 246s tests/tabix_test.py::VCFFromTabixTest_13::testWrite PASSED 246s tests/tabix_test.py::VCFFromVCFTest_13::testConnecting PASSED 246s tests/tabix_test.py::VCFFromVCFTest_13::testParsing PASSED 246s tests/tabix_test.py::VCFFromTabixTest_16::testRead PASSED 246s tests/tabix_test.py::VCFFromTabixTest_16::testWrite PASSED 246s tests/tabix_test.py::VCFFromVCFTest_16::testConnecting PASSED 246s tests/tabix_test.py::VCFFromVCFTest_16::testParsing PASSED 246s tests/tabix_test.py::VCFFromTabixTest_12::testRead PASSED 246s tests/tabix_test.py::VCFFromTabixTest_12::testWrite PASSED 246s tests/tabix_test.py::VCFFromVCFTest_12::testConnecting PASSED 246s tests/tabix_test.py::VCFFromVCFTest_12::testParsing PASSED 246s tests/tabix_test.py::VCFFromTabixTest_11::testRead PASSED 247s tests/tabix_test.py::VCFFromTabixTest_11::testWrite PASSED 247s tests/tabix_test.py::VCFFromVCFTest_11::testConnecting PASSED 247s tests/tabix_test.py::VCFFromVCFTest_11::testParsing PASSED 247s tests/tabix_test.py::VCFFromTabixTest_21::testRead PASSED 247s tests/tabix_test.py::VCFFromTabixTest_21::testWrite PASSED 247s tests/tabix_test.py::VCFFromVCFTest_21::testConnecting PASSED 247s tests/tabix_test.py::VCFFromVCFTest_21::testParsing PASSED 247s tests/tabix_test.py::VCFFromTabixTest_6::testRead PASSED 247s tests/tabix_test.py::VCFFromTabixTest_6::testWrite PASSED 247s tests/tabix_test.py::VCFFromVCFTest_6::testConnecting PASSED 248s tests/tabix_test.py::VCFFromVCFTest_6::testParsing PASSED 248s tests/tabix_test.py::VCFFromTabixTest_7::testRead PASSED 248s tests/tabix_test.py::VCFFromTabixTest_7::testWrite PASSED 248s tests/tabix_test.py::VCFFromVCFTest_7::testConnecting PASSED 248s tests/tabix_test.py::VCFFromVCFTest_7::testParsing PASSED 248s tests/tabix_test.py::VCFFromTabixTest_20::testRead PASSED 248s tests/tabix_test.py::VCFFromTabixTest_20::testWrite PASSED 248s tests/tabix_test.py::VCFFromVCFTest_20::testConnecting PASSED 248s tests/tabix_test.py::VCFFromVCFTest_20::testParsing PASSED 248s tests/tabix_test.py::VCFFromTabixTest_issue85::testRead PASSED 248s tests/tabix_test.py::VCFFromTabixTest_issue85::testWrite PASSED 248s tests/tabix_test.py::VCFFromVCFTest_issue85::testConnecting PASSED 248s tests/tabix_test.py::VCFFromVCFTest_issue85::testParsing PASSED 249s tests/tabix_test.py::VCFFromTabixTest_3::testRead PASSED 249s tests/tabix_test.py::VCFFromTabixTest_3::testWrite PASSED 249s tests/tabix_test.py::VCFFromVCFTest_3::testConnecting PASSED 249s tests/tabix_test.py::VCFFromVCFTest_3::testParsing PASSED 249s tests/tabix_test.py::TestVCFFromVariantFile::testConnecting PASSED 249s tests/tabix_test.py::TestVCFFromVariantFile::testParsing [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 249s PASSED 249s tests/tabix_test.py::TestVCFFromVariantFile_24::testConnecting [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: 249s #CHROM POS ID REF ALT QUAL FILTER INFO 249s 249s PASSED 249s tests/tabix_test.py::TestVCFFromVariantFile_24::testParsing PASSED 249s tests/tabix_test.py::TestVCFFromVariantFile_9::testConnecting PASSED 249s 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.) 249s [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String 249s [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String 249s [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String 249s [W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String 249s [W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String 249s [W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String 249s [W::vcf_parse_format_dict2] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String 249s [W::vcf_parse_format_dict2] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String 249s [W::vcf_parse_format_dict2] FORMAT 'GQ' at chr1:1281168 is not defined in the header, assuming Type=String 249s [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) 249s PASSED 249s tests/tabix_test.py::TestVCFFromVariantFile_2::testConnecting [W::bcf_hdr_check_sanity] GL should be declared as Number=G 249s PASSED 249s 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.) 249s [W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String 249s PASSED 249s tests/tabix_test.py::TestVCFFromVariantFile_18::testConnecting PASSED 249s 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.) 249s [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String 249s [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String 249s [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String 249s [W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String 249s [W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String 249s [W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String 249s [W::vcf_parse_format_dict2] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String 249s [W::vcf_parse_format_dict2] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String 249s [W::vcf_parse_format_dict2] FORMAT 'GQ' at chr1:1281168 is not defined in the header, assuming Type=String 249s [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) 249s PASSED 249s tests/tabix_test.py::TestVCFFromVariantFile_15::testConnecting [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) 249s [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) 249s PASSED 249s 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.) 249s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:439104 is not defined in the header, assuming Type=String 250s PASSED 250s tests/tabix_test.py::TestVCFFromVariantFile_22::testConnecting PASSED 250s 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.) 250s [W::vcf_parse_info] INFO 'refseq.name' is not defined in the header, assuming Type=String 250s [W::vcf_parse_info] INFO 'refseq.positionType' is not defined in the header, assuming Type=String 250s [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) 250s PASSED 250s tests/tabix_test.py::TestVCFFromVariantFile_10::testConnecting PASSED 250s 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.) 250s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:676148 is not defined in the header, assuming Type=String 250s PASSED 251s tests/tabix_test.py::TestVCFFromVariantFile_5::testConnecting PASSED 251s 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.) 251s PASSED 251s tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testConnecting PASSED 251s tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testParsing PASSED 251s tests/tabix_test.py::TestVCFFromVariantFile_4::testConnecting PASSED 251s tests/tabix_test.py::TestVCFFromVariantFile_4::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:249843 is not defined in the header, assuming Type=String 251s PASSED 251s tests/tabix_test.py::TestVCFFromVariantFile_8::testConnecting PASSED 251s 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.) 251s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:676148 is not defined in the header, assuming Type=String 251s PASSED 251s tests/tabix_test.py::TestVCFFromVariantFile_23::testConnecting PASSED 251s tests/tabix_test.py::TestVCFFromVariantFile_23::testParsing [W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String 251s PASSED 251s tests/tabix_test.py::TestVCFFromVariantFile_13::testConnecting [W::bcf_hrec_check] Invalid tag name: "1000g" 251s [W::bcf_hrec_check] Invalid tag name: "GT:GL:GQ:NR" 251s PASSED 251s tests/tabix_test.py::TestVCFFromVariantFile_13::testParsing [W::bcf_hrec_check] Invalid tag name: "1000g" 251s [W::bcf_hrec_check] Invalid tag name: "GT:GL:GQ:NR" 251s [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse_info] INFO 'MMLQ' is not defined in the header, assuming Type=String 251s [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr17_gl000205_random' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr18' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr19' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr20' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr21' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr22' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chrUn_gl000214' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chrUn_gl000220' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chrUn_gl000225' is not defined in the header. (Quick workaround: index the file with tabix.) 251s PASSED[W::vcf_parse] Contig 'chrX' is not defined in the header. (Quick workaround: index the file with tabix.) 251s 251s tests/tabix_test.py::TestVCFFromVariantFile_16::testConnecting PASSED 251s 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.) 251s [W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String 251s PASSED 251s tests/tabix_test.py::TestVCFFromVariantFile_12::testConnecting PASSED 251s 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.) 251s [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String 251s [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String 251s [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String 251s [W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String 251s [W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String 251s [W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String 251s [W::vcf_parse_format_dict2] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String 251s [W::vcf_parse_format_dict2] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String 251s [W::vcf_parse_format_dict2] FORMAT 'GQ' at chr1:1281168 is not defined in the header, assuming Type=String 251s [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) 251s [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) 251s PASSED 251s tests/tabix_test.py::TestVCFFromVariantFile_11::testConnecting PASSED 251s 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.) 251s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:669442 is not defined in the header, assuming Type=String 252s PASSED 252s tests/tabix_test.py::TestVCFFromVariantFile_21::testConnecting PASSED 252s tests/tabix_test.py::TestVCFFromVariantFile_21::testParsing [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 252s [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 252s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 252s PASSED 252s tests/tabix_test.py::TestVCFFromVariantFile_6::testConnecting PASSED 252s 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.) 252s [W::vcf_parse_info] INFO 'CallSetAC' is not defined in the header, assuming Type=String 252s [W::vcf_parse_info] INFO 'CallSetAC2' is not defined in the header, assuming Type=String 252s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:669442 is not defined in the header, assuming Type=String 252s PASSED 252s tests/tabix_test.py::TestVCFFromVariantFile_7::testConnecting PASSED 252s 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.) 252s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:249843 is not defined in the header, assuming Type=String 253s PASSED 253s tests/tabix_test.py::TestVCFFromVariantFile_20::testConnecting PASSED 253s tests/tabix_test.py::TestVCFFromVariantFile_20::testParsing [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 253s PASSED 253s tests/tabix_test.py::TestVCFFromVariantFile_issue85::testConnecting [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 253s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 253s PASSED 253s tests/tabix_test.py::TestVCFFromVariantFile_issue85::testParsing PASSED 253s tests/tabix_test.py::TestVCFFromVariantFile_3::testConnecting PASSED 253s tests/tabix_test.py::TestVCFFromVariantFile_3::testParsing [E::bcf_hdr_parse] Could not parse the header, sample line not found 253s [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) 253s PASSED 253s tests/tabix_test.py::TestIndexArgument::testFetchAll PASSED 253s tests/tabix_test.py::TestIndexArgument::testLoadIndexWithoutTbiExtension PASSED 253s tests/tabix_test.py::TestBackwardsCompatibility::testBED PASSED 253s tests/tabix_test.py::TestBackwardsCompatibility::testBED0v23 PASSED 253s tests/tabix_test.py::TestBackwardsCompatibility::testBED0v26 PASSED 253s tests/tabix_test.py::TestBackwardsCompatibility::testEmpty PASSED 253s tests/tabix_test.py::TestBackwardsCompatibility::testVCF PASSED 253s tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v23 PASSED 253s tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v26 PASSED 253s tests/tabix_test.py::TestMultipleIterators::testDisjointIterators PASSED 253s tests/tabix_test.py::TestMultipleIterators::testDoubleFetch PASSED 253s tests/tabix_test.py::TestMultipleIterators::testJoinedIterators PASSED 253s tests/tabix_test.py::TestMultipleIterators::testScope PASSED 253s tests/tabix_test.py::TestContextManager::testManager PASSED 253s tests/tabix_test.py::TestMultithreadTabixFile::testMultithreadEqualsSinglethread PASSED 253s tests/tabixproxies_test.py::TestBED::testAssignmentToTargetList PASSED 253s tests/tabixproxies_test.py::TestParser::testAssignmentToTargetList PASSED 253s tests/tabixproxies_test.py::TestParser::testCopy PASSED 253s tests/tabixproxies_test.py::TestParser::testIteratorCompressed PASSED 253s tests/tabixproxies_test.py::TestParser::testIteratorUncompressed PASSED 253s tests/tabixproxies_test.py::TestParser::testRead PASSED 253s tests/tabixproxies_test.py::TestParser::testUnset PASSED 253s tests/tabixproxies_test.py::TestParser::testWrite PASSED 253s tests/tabixproxies_test.py::TestGTF::testAssignmentToTargetList PASSED 253s tests/tabixproxies_test.py::TestGTF::testCopy PASSED 253s tests/tabixproxies_test.py::TestGTF::testIteratorCompressed PASSED 253s tests/tabixproxies_test.py::TestGTF::testIteratorUncompressed PASSED 253s tests/tabixproxies_test.py::TestGTF::testRead PASSED 253s tests/tabixproxies_test.py::TestGTF::testUnset PASSED 253s tests/tabixproxies_test.py::TestGTF::testWrite PASSED 253s tests/tabixproxies_test.py::TestGTF::test_added_attribute_is_output PASSED 253s tests/tabixproxies_test.py::TestGTF::test_asdict_can_be_modified PASSED 253s tests/tabixproxies_test.py::TestGTF::test_asdict_contains_attributes PASSED 253s tests/tabixproxies_test.py::TestGTF::test_setAttribute_makes_changes PASSED 253s tests/tabixproxies_test.py::TestGTF::test_setting_end_is_one_based PASSED 253s tests/tabixproxies_test.py::TestGTF::test_setting_feature_to_none_produces_dot PASSED 253s tests/tabixproxies_test.py::TestGTF::test_setting_fields PASSED 253s tests/tabixproxies_test.py::TestGTF::test_setting_frame_to_none_produces_dot PASSED 253s tests/tabixproxies_test.py::TestGTF::test_setting_score_to_none_produces_dot PASSED 253s tests/tabixproxies_test.py::TestGTF::test_setting_source_to_none_produces_dot PASSED 253s tests/tabixproxies_test.py::TestGTF::test_setting_start_is_one_based PASSED 253s tests/tabixproxies_test.py::TestGTF::test_setting_strand_to_none_produces_dot PASSED 253s tests/tabixproxies_test.py::TestGFF3::testAssignmentToTargetList PASSED 253s tests/tabixproxies_test.py::TestGFF3::testCopy PASSED 253s tests/tabixproxies_test.py::TestGFF3::testIteratorCompressed PASSED 253s tests/tabixproxies_test.py::TestGFF3::testIteratorUncompressed PASSED 253s tests/tabixproxies_test.py::TestGFF3::testRead PASSED 253s tests/tabixproxies_test.py::TestGFF3::testUnset PASSED 253s tests/tabixproxies_test.py::TestGFF3::testWrite PASSED 253s tests/tabixproxies_test.py::TestGFF3::test_added_attribute_is_output PASSED 253s tests/tabixproxies_test.py::TestGFF3::test_asdict_can_be_modified PASSED 253s tests/tabixproxies_test.py::TestGFF3::test_asdict_contains_attributes PASSED 253s tests/tabixproxies_test.py::TestGFF3::test_setAttribute_makes_changes PASSED 253s tests/tabixproxies_test.py::TestGFF3::test_setting_end_is_one_based PASSED 253s tests/tabixproxies_test.py::TestGFF3::test_setting_feature_to_none_produces_dot PASSED 253s tests/tabixproxies_test.py::TestGFF3::test_setting_fields PASSED 253s tests/tabixproxies_test.py::TestGFF3::test_setting_frame_to_none_produces_dot PASSED 253s tests/tabixproxies_test.py::TestGFF3::test_setting_score_to_none_produces_dot PASSED 253s tests/tabixproxies_test.py::TestGFF3::test_setting_source_to_none_produces_dot PASSED 253s tests/tabixproxies_test.py::TestGFF3::test_setting_start_is_one_based PASSED 253s tests/tabixproxies_test.py::TestGFF3::test_setting_strand_to_none_produces_dot PASSED 253s tests/test_samtools_python.py::test_idxstats_parse_split_lines PASSED 253s tests/test_samtools_python.py::test_bedcov_split_lines PASSED 253s tests/test_samtools_python.py::test_idxstats_parse PASSED 253s tests/test_samtools_python.py::test_bedcov PASSED 253s 253s =============================== warnings summary =============================== 253s tests/samtools_test.py::SamtoolsTest::testStatements 253s tests/samtools_test.py::PysamTest::testStatements 253s /tmp/autopkgtest.GNnawt/build.dpD/src/tests/samtools_test.py:137: UserWarning: versions of pysam.samtools and samtools differ: 1.18 != 1.20 253s warnings.warn( 253s 253s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 253s ============ 938 passed, 13 skipped, 2 warnings in 95.70s (0:01:35) ============ 254s autopkgtest [10:54:23]: test command1: -----------------------] 254s command1 PASS 254s autopkgtest [10:54:23]: test command1: - - - - - - - - - - results - - - - - - - - - - 255s autopkgtest [10:54:24]: test autodep8-python3: preparing testbed 347s autopkgtest [10:55:56]: testbed dpkg architecture: arm64 347s autopkgtest [10:55:56]: testbed apt version: 2.9.8 347s autopkgtest [10:55:56]: @@@@@@@@@@@@@@@@@@@@ test bed setup 348s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 348s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 348s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 348s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 349s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 349s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB] 349s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 349s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB] 349s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB] 349s Fetched 1794 kB in 1s (2010 kB/s) 349s Reading package lists... 352s Reading package lists... 352s Building dependency tree... 352s Reading state information... 353s Calculating upgrade... 353s The following NEW packages will be installed: 353s python3.13-gdbm 353s The following packages will be upgraded: 353s libpython3-stdlib python3 python3-gdbm python3-minimal 354s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 354s Need to get 101 kB of archives. 354s After this operation, 141 kB of additional disk space will be used. 354s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB] 354s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB] 354s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB] 354s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB] 354s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B] 354s Fetched 101 kB in 0s (287 kB/s) 355s (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 ... 79924 files and directories currently installed.) 355s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ... 355s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 355s Setting up python3-minimal (3.12.7-1) ... 355s (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 ... 79924 files and directories currently installed.) 355s Preparing to unpack .../python3_3.12.7-1_arm64.deb ... 355s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 355s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ... 355s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 355s Selecting previously unselected package python3.13-gdbm. 355s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ... 355s Unpacking python3.13-gdbm (3.13.0-2) ... 355s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ... 355s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 355s Setting up python3.13-gdbm (3.13.0-2) ... 355s Setting up libpython3-stdlib:arm64 (3.12.7-1) ... 355s Setting up python3 (3.12.7-1) ... 355s Setting up python3-gdbm:arm64 (3.12.7-1) ... 355s Processing triggers for man-db (2.12.1-3) ... 356s Reading package lists... 357s Building dependency tree... 357s Reading state information... 357s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 358s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 358s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 358s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 358s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 359s Reading package lists... 359s Reading package lists... 359s Building dependency tree... 359s Reading state information... 360s Calculating upgrade... 360s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 360s Reading package lists... 361s Building dependency tree... 361s Reading state information... 362s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 366s Reading package lists... 366s Building dependency tree... 366s Reading state information... 367s Starting pkgProblemResolver with broken count: 0 367s Starting 2 pkgProblemResolver with broken count: 0 367s Done 368s The following additional packages will be installed: 368s libdeflate0 libhts3t64 libhtscodecs2 libpython3.13-minimal 368s libpython3.13-stdlib python3-all python3-pysam python3.13 python3.13-minimal 368s Suggested packages: 368s python3.13-venv python3.13-doc binfmt-support 368s The following NEW packages will be installed: 368s autopkgtest-satdep libdeflate0 libhts3t64 libhtscodecs2 368s libpython3.13-minimal libpython3.13-stdlib python3-all python3-pysam 368s python3.13 python3.13-minimal 368s 0 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. 368s Need to get 9742 kB/9742 kB of archives. 368s After this operation, 60.5 MB of additional disk space will be used. 368s Get:1 /tmp/autopkgtest.GNnawt/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [712 B] 368s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-minimal arm64 3.13.0-2 [877 kB] 368s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-minimal arm64 3.13.0-2 [2100 kB] 368s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB] 368s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.1-1 [82.5 kB] 368s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts3t64 arm64 1.20+ds-1 [431 kB] 368s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-stdlib arm64 3.13.0-2 [2073 kB] 369s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13 arm64 3.13.0-2 [719 kB] 369s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-all arm64 3.12.7-1 [890 B] 369s Get:10 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pysam arm64 0.22.1+ds-2 [3412 kB] 369s Fetched 9742 kB in 1s (11.0 MB/s) 369s Selecting previously unselected package libpython3.13-minimal:arm64. 369s (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 ... 79931 files and directories currently installed.) 369s Preparing to unpack .../0-libpython3.13-minimal_3.13.0-2_arm64.deb ... 369s Unpacking libpython3.13-minimal:arm64 (3.13.0-2) ... 369s Selecting previously unselected package python3.13-minimal. 369s Preparing to unpack .../1-python3.13-minimal_3.13.0-2_arm64.deb ... 369s Unpacking python3.13-minimal (3.13.0-2) ... 369s Selecting previously unselected package libdeflate0:arm64. 369s Preparing to unpack .../2-libdeflate0_1.22-1_arm64.deb ... 369s Unpacking libdeflate0:arm64 (1.22-1) ... 369s Selecting previously unselected package libhtscodecs2:arm64. 369s Preparing to unpack .../3-libhtscodecs2_1.6.1-1_arm64.deb ... 369s Unpacking libhtscodecs2:arm64 (1.6.1-1) ... 369s Selecting previously unselected package libhts3t64:arm64. 369s Preparing to unpack .../4-libhts3t64_1.20+ds-1_arm64.deb ... 369s Unpacking libhts3t64:arm64 (1.20+ds-1) ... 369s Selecting previously unselected package libpython3.13-stdlib:arm64. 369s Preparing to unpack .../5-libpython3.13-stdlib_3.13.0-2_arm64.deb ... 369s Unpacking libpython3.13-stdlib:arm64 (3.13.0-2) ... 369s Selecting previously unselected package python3.13. 369s Preparing to unpack .../6-python3.13_3.13.0-2_arm64.deb ... 369s Unpacking python3.13 (3.13.0-2) ... 370s Selecting previously unselected package python3-all. 370s Preparing to unpack .../7-python3-all_3.12.7-1_arm64.deb ... 370s Unpacking python3-all (3.12.7-1) ... 370s Selecting previously unselected package python3-pysam. 370s Preparing to unpack .../8-python3-pysam_0.22.1+ds-2_arm64.deb ... 370s Unpacking python3-pysam (0.22.1+ds-2) ... 370s Selecting previously unselected package autopkgtest-satdep. 370s Preparing to unpack .../9-2-autopkgtest-satdep.deb ... 370s Unpacking autopkgtest-satdep (0) ... 370s Setting up libhtscodecs2:arm64 (1.6.1-1) ... 370s Setting up libdeflate0:arm64 (1.22-1) ... 370s Setting up libpython3.13-minimal:arm64 (3.13.0-2) ... 370s Setting up libhts3t64:arm64 (1.20+ds-1) ... 370s Setting up python3.13-minimal (3.13.0-2) ... 372s Setting up libpython3.13-stdlib:arm64 (3.13.0-2) ... 372s Setting up python3-pysam (0.22.1+ds-2) ... 372s Setting up python3.13 (3.13.0-2) ... 373s Setting up python3-all (3.12.7-1) ... 373s Setting up autopkgtest-satdep (0) ... 373s Processing triggers for systemd (256.5-2ubuntu4) ... 373s Processing triggers for man-db (2.12.1-3) ... 374s Processing triggers for libc-bin (2.40-1ubuntu3) ... 377s (Reading database ... 81051 files and directories currently installed.) 377s Removing autopkgtest-satdep (0) ... 381s autopkgtest [10:56:30]: 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 381s autopkgtest [10:56:30]: test autodep8-python3: [----------------------- 381s Testing with python3.13: 381s Traceback (most recent call last): 381s File "", line 1, in 381s import pysam; print(pysam) 381s ^^^^^^^^^^^^ 381s File "/usr/lib/python3/dist-packages/pysam/__init__.py", line 4, in 381s from pysam.libchtslib import * 381s ModuleNotFoundError: No module named 'pysam.libchtslib' 382s autopkgtest [10:56:31]: test autodep8-python3: -----------------------] 382s autodep8-python3 FAIL non-zero exit status 1 382s autopkgtest [10:56:31]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 383s autopkgtest [10:56:32]: @@@@@@@@@@@@@@@@@@@@ summary 383s command1 PASS 383s autodep8-python3 FAIL non-zero exit status 1 397s virt: nova [W] Skipping flock in bos03-arm64 397s virt: Creating nova instance adt-plucky-arm64-python-pysam-20241113-105009-juju-7f2275-prod-proposed-migration-environment-2-c55ae399-79e1-4064-a8c5-754bcf65ae23 from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)... 397s virt: nova [W] Skipping flock in bos03-arm64 397s virt: Creating nova instance adt-plucky-arm64-python-pysam-20241113-105009-juju-7f2275-prod-proposed-migration-environment-2-c55ae399-79e1-4064-a8c5-754bcf65ae23 from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)...