0s autopkgtest [01:28:53]: starting date and time: 2024-11-14 01:28:53+0000 0s autopkgtest [01:28:53]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [01:28:53]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.x5mj34ia/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --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' -- lxd -r lxd-armhf-10.145.243.232 lxd-armhf-10.145.243.232:autopkgtest/ubuntu/plucky/armhf 52s autopkgtest [01:29:45]: testbed dpkg architecture: armhf 54s autopkgtest [01:29:47]: testbed apt version: 2.9.8 54s autopkgtest [01:29:47]: @@@@@@@@@@@@@@@@@@@@ test bed setup 62s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 62s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [990 kB] 63s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.2 kB] 63s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 63s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.6 kB] 63s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [103 kB] 63s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [667 kB] 63s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [17.2 kB] 63s Fetched 1975 kB in 1s (1643 kB/s) 63s Reading package lists... 81s tee: /proc/self/fd/2: Permission denied 103s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 103s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 103s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 103s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 104s Reading package lists... 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 105s Calculating upgrade... 106s The following NEW packages will be installed: 106s python3.13-gdbm 106s The following packages will be upgraded: 106s libgnutls30t64 libjson-glib-1.0-0 libjson-glib-1.0-common libnewt0.52 106s libpython3-stdlib libutempter0 python3 python3-gdbm python3-minimal 106s python3-newt whiptail 106s 11 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 106s Need to get 1207 kB of archives. 106s After this operation, 124 kB of additional disk space will be used. 106s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-minimal armhf 3.12.7-1 [27.4 kB] 106s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3 armhf 3.12.7-1 [24.0 kB] 106s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libpython3-stdlib armhf 3.12.7-1 [10.0 kB] 106s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libgnutls30t64 armhf 3.8.8-2ubuntu1 [955 kB] 107s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3-newt armhf 0.52.24-2ubuntu4 [19.7 kB] 107s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf libnewt0.52 armhf 0.52.24-2ubuntu4 [39.2 kB] 107s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf whiptail armhf 0.52.24-2ubuntu4 [17.2 kB] 107s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-gdbm armhf 3.13.0-2 [29.5 kB] 107s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-gdbm armhf 3.12.7-1 [8642 B] 107s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 107s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-0 armhf 1.10.0+ds-3 [61.7 kB] 107s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libutempter0 armhf 1.2.1-4 [9062 B] 107s Fetched 1207 kB in 1s (2060 kB/s) 107s (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 ... 59559 files and directories currently installed.) 107s Preparing to unpack .../python3-minimal_3.12.7-1_armhf.deb ... 107s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 107s Setting up python3-minimal (3.12.7-1) ... 107s (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 ... 59559 files and directories currently installed.) 107s Preparing to unpack .../python3_3.12.7-1_armhf.deb ... 108s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 108s Preparing to unpack .../libpython3-stdlib_3.12.7-1_armhf.deb ... 108s Unpacking libpython3-stdlib:armhf (3.12.7-1) over (3.12.6-0ubuntu1) ... 108s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_armhf.deb ... 108s Unpacking libgnutls30t64:armhf (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 108s Setting up libgnutls30t64:armhf (3.8.8-2ubuntu1) ... 108s (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 ... 59559 files and directories currently installed.) 108s Preparing to unpack .../0-python3-newt_0.52.24-2ubuntu4_armhf.deb ... 108s Unpacking python3-newt:armhf (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 108s Preparing to unpack .../1-libnewt0.52_0.52.24-2ubuntu4_armhf.deb ... 108s Unpacking libnewt0.52:armhf (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 108s Preparing to unpack .../2-whiptail_0.52.24-2ubuntu4_armhf.deb ... 108s Unpacking whiptail (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 108s Selecting previously unselected package python3.13-gdbm. 108s Preparing to unpack .../3-python3.13-gdbm_3.13.0-2_armhf.deb ... 108s Unpacking python3.13-gdbm (3.13.0-2) ... 108s Preparing to unpack .../4-python3-gdbm_3.12.7-1_armhf.deb ... 108s Unpacking python3-gdbm:armhf (3.12.7-1) over (3.12.6-1ubuntu1) ... 108s Preparing to unpack .../5-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 108s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 108s Preparing to unpack .../6-libjson-glib-1.0-0_1.10.0+ds-3_armhf.deb ... 108s Unpacking libjson-glib-1.0-0:armhf (1.10.0+ds-3) over (1.10.0+ds-2) ... 108s Preparing to unpack .../7-libutempter0_1.2.1-4_armhf.deb ... 108s Unpacking libutempter0:armhf (1.2.1-4) over (1.2.1-3build1) ... 108s Setting up libnewt0.52:armhf (0.52.24-2ubuntu4) ... 108s Setting up libutempter0:armhf (1.2.1-4) ... 108s Setting up whiptail (0.52.24-2ubuntu4) ... 108s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 108s Setting up python3.13-gdbm (3.13.0-2) ... 108s Setting up libpython3-stdlib:armhf (3.12.7-1) ... 108s Setting up python3 (3.12.7-1) ... 109s Setting up python3-newt:armhf (0.52.24-2ubuntu4) ... 109s Setting up libjson-glib-1.0-0:armhf (1.10.0+ds-3) ... 109s Setting up python3-gdbm:armhf (3.12.7-1) ... 109s Processing triggers for man-db (2.12.1-3) ... 109s Processing triggers for libc-bin (2.40-1ubuntu3) ... 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 113s autopkgtest [01:30:46]: rebooting testbed after setup commands that affected boot 180s autopkgtest [01:31:53]: testbed running kernel: Linux 6.8.0-48-generic #48~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Mon Oct 7 11:49:53 UTC 2 207s autopkgtest [01:32:20]: @@@@@@@@@@@@@@@@@@@@ apt-source python-pysam 221s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-pysam 0.22.1+ds-2 (dsc) [2563 B] 221s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-pysam 0.22.1+ds-2 (tar) [1447 kB] 221s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-pysam 0.22.1+ds-2 (diff) [10.7 kB] 222s gpgv: Signature made Wed May 29 11:37:25 2024 UTC 222s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 222s gpgv: issuer "emollier@debian.org" 222s gpgv: Can't check signature: No public key 222s dpkg-source: warning: cannot verify inline signature for ./python-pysam_0.22.1+ds-2.dsc: no acceptable signature found 222s autopkgtest [01:32:35]: testing package python-pysam version 0.22.1+ds-2 224s autopkgtest [01:32:37]: build not needed 229s autopkgtest [01:32:42]: test command1: preparing testbed 239s Reading package lists... 239s Building dependency tree... 239s Reading state information... 240s Starting pkgProblemResolver with broken count: 0 240s Starting 2 pkgProblemResolver with broken count: 0 240s Done 241s The following additional packages will be installed: 241s autoconf automake autopoint autotools-dev bcftools build-essential cpp 241s cpp-14 cpp-14-arm-linux-gnueabihf cpp-arm-linux-gnueabihf cython3 debhelper 241s debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz g++ g++-14 241s g++-14-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc gcc-14 241s gcc-14-arm-linux-gnueabihf gcc-arm-linux-gnueabihf gettext intltool-debian 241s libarchive-zip-perl libasan8 libbrotli-dev libc-dev-bin libc6-dev libcc1-0 241s libcrypt-dev libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev 241s libdeflate0 libevent-2.1-7t64 libexpat1-dev libfile-stripnondeterminism-perl 241s libgcc-14-dev libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 241s libgnutls-openssl27t64 libgnutls28-dev libgomp1 libhts-dev libhts3t64 241s libhtscodecs2 libidn2-dev libisl23 libjs-jquery libjs-sphinxdoc 241s libjs-underscore liblzma-dev libmpc3 libnghttp2-dev libp11-kit-dev 241s libpkgconf3 libpsl-dev libpython3-all-dev libpython3-dev libpython3.12-dev 241s libpython3.12t64 libpython3.13 libpython3.13-dev libpython3.13-minimal 241s libpython3.13-stdlib librtmp-dev libssh2-1-dev libssl-dev libstdc++-14-dev 241s libtasn1-6-dev libtool libubsan1 libunbound8 libzstd-dev linux-libc-dev m4 241s nettle-dev pkgconf pkgconf-bin po-debconf python3-all python3-all-dev 241s python3-dev python3-iniconfig python3-packaging python3-pluggy python3-pysam 241s python3-pytest python3.12-dev python3.13 python3.13-dev python3.13-minimal 241s rpcsvc-proto samtools tabix zlib1g-dev 241s Suggested packages: 241s autoconf-archive gnu-standards autoconf-doc python3-numpy 241s texlive-latex-recommended cpp-doc gcc-14-locales cpp-14-doc cython-doc 241s dh-make flit python3-build python3-installer python3-wheel gcc-14-doc 241s gcc-multilib manpages-dev flex bison gdb gcc-doc gdb-arm-linux-gnueabihf 241s gettext-doc libasprintf-dev libgettextpo-dev libc-devtools glibc-doc 241s libcurl4-doc libidn-dev libkrb5-dev libldap2-dev gmp-doc libgmp10-doc 241s libmpfr-dev dns-root-data gnutls-bin gnutls-doc liblzma-doc libnghttp2-doc 241s p11-kit-doc libssl-doc libstdc++-14-doc libtool-doc gfortran 241s | fortran95-compiler gcj-jdk m4-doc libmail-box-perl python3.13-venv 241s python3.13-doc binfmt-support cwltool 241s Recommended packages: 241s python3-gffutils python3-matplotlib manpages manpages-dev 241s libarchive-cpio-perl javascript-common libtasn1-doc libltdl-dev 241s libmail-sendmail-perl 241s The following NEW packages will be installed: 241s autoconf automake autopkgtest-satdep autopoint autotools-dev bcftools 241s build-essential cpp cpp-14 cpp-14-arm-linux-gnueabihf 241s cpp-arm-linux-gnueabihf cython3 debhelper debugedit dh-autoreconf dh-python 241s dh-strip-nondeterminism dwz g++ g++-14 g++-14-arm-linux-gnueabihf 241s g++-arm-linux-gnueabihf gcc gcc-14 gcc-14-arm-linux-gnueabihf 241s gcc-arm-linux-gnueabihf gettext intltool-debian libarchive-zip-perl libasan8 241s libbrotli-dev libc-dev-bin libc6-dev libcc1-0 libcrypt-dev 241s libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 241s libevent-2.1-7t64 libexpat1-dev libfile-stripnondeterminism-perl 241s libgcc-14-dev libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 241s libgnutls-openssl27t64 libgnutls28-dev libgomp1 libhts-dev libhts3t64 241s libhtscodecs2 libidn2-dev libisl23 libjs-jquery libjs-sphinxdoc 241s libjs-underscore liblzma-dev libmpc3 libnghttp2-dev libp11-kit-dev 241s libpkgconf3 libpsl-dev libpython3-all-dev libpython3-dev libpython3.12-dev 241s libpython3.12t64 libpython3.13 libpython3.13-dev libpython3.13-minimal 241s libpython3.13-stdlib librtmp-dev libssh2-1-dev libssl-dev libstdc++-14-dev 241s libtasn1-6-dev libtool libubsan1 libunbound8 libzstd-dev linux-libc-dev m4 241s nettle-dev pkgconf pkgconf-bin po-debconf python3-all python3-all-dev 241s python3-dev python3-iniconfig python3-packaging python3-pluggy python3-pysam 241s python3-pytest python3.12-dev python3.13 python3.13-dev python3.13-minimal 241s rpcsvc-proto samtools tabix zlib1g-dev 241s 0 upgraded, 102 newly installed, 0 to remove and 0 not upgraded. 241s Need to get 92.8 MB/92.8 MB of archives. 241s After this operation, 304 MB of additional disk space will be used. 241s Get:1 /tmp/autopkgtest.GaGsi7/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [816 B] 241s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13-minimal armhf 3.13.0-2 [866 kB] 242s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-minimal armhf 3.13.0-2 [1854 kB] 242s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf m4 armhf 1.4.19-4build1 [235 kB] 242s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf autoconf all 2.72-3 [382 kB] 242s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf autotools-dev all 20220109.1 [44.9 kB] 242s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf automake all 1:1.16.5-1.3ubuntu1 [558 kB] 242s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf autopoint all 0.22.5-2 [616 kB] 242s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.22-1 [38.9 kB] 242s Get:10 http://ftpmaster.internal/ubuntu plucky/universe armhf libhtscodecs2 armhf 1.6.1-1 [67.9 kB] 242s Get:11 http://ftpmaster.internal/ubuntu plucky/universe armhf libhts3t64 armhf 1.20+ds-1 [392 kB] 242s Get:12 http://ftpmaster.internal/ubuntu plucky/universe armhf bcftools armhf 1.20-2 [726 kB] 242s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libc-dev-bin armhf 2.40-1ubuntu3 [19.2 kB] 242s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf linux-libc-dev armhf 6.11.0-8.8 [1628 kB] 242s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf libcrypt-dev armhf 1:4.4.36-4build1 [120 kB] 242s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf rpcsvc-proto armhf 1.4.2-0ubuntu7 [62.2 kB] 242s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libc6-dev armhf 2.40-1ubuntu3 [1370 kB] 242s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf libisl23 armhf 0.27-1 [546 kB] 242s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf libmpc3 armhf 1.3.1-1build2 [47.1 kB] 242s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-14-arm-linux-gnueabihf armhf 14.2.0-8ubuntu1 [9219 kB] 242s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-14 armhf 14.2.0-8ubuntu1 [1032 B] 242s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-arm-linux-gnueabihf armhf 4:14.1.0-2ubuntu1 [5464 B] 242s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf cpp armhf 4:14.1.0-2ubuntu1 [22.4 kB] 242s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf libcc1-0 armhf 14.2.0-8ubuntu1 [43.3 kB] 242s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 14.2.0-8ubuntu1 [125 kB] 242s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf libasan8 armhf 14.2.0-8ubuntu1 [2901 kB] 242s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libubsan1 armhf 14.2.0-8ubuntu1 [1150 kB] 242s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf libgcc-14-dev armhf 14.2.0-8ubuntu1 [897 kB] 242s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14-arm-linux-gnueabihf armhf 14.2.0-8ubuntu1 [18.0 MB] 243s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14 armhf 14.2.0-8ubuntu1 [498 kB] 243s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-arm-linux-gnueabihf armhf 4:14.1.0-2ubuntu1 [1222 B] 243s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf gcc armhf 4:14.1.0-2ubuntu1 [5002 B] 243s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf libstdc++-14-dev armhf 14.2.0-8ubuntu1 [2569 kB] 243s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf g++-14-arm-linux-gnueabihf armhf 14.2.0-8ubuntu1 [10.5 MB] 243s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf g++-14 armhf 14.2.0-8ubuntu1 [19.9 kB] 243s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf g++-arm-linux-gnueabihf armhf 4:14.1.0-2ubuntu1 [968 B] 243s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf g++ armhf 4:14.1.0-2ubuntu1 [1084 B] 243s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf build-essential armhf 12.10ubuntu1 [4928 B] 243s Get:39 http://ftpmaster.internal/ubuntu plucky/universe armhf cython3 armhf 3.0.11+dfsg-1ubuntu1 [2391 kB] 243s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf libdebhelper-perl all 13.20ubuntu1 [94.2 kB] 243s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf libtool all 2.4.7-7build1 [166 kB] 243s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf dh-autoreconf all 20 [16.1 kB] 243s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf libarchive-zip-perl all 1.68-1 [90.2 kB] 243s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] 243s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf dh-strip-nondeterminism all 1.14.0-1 [5058 B] 243s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf debugedit armhf 1:5.1-1 [46.5 kB] 243s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf dwz armhf 0.15-1build6 [116 kB] 243s Get:48 http://ftpmaster.internal/ubuntu plucky/main armhf gettext armhf 0.22.5-2 [995 kB] 243s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf intltool-debian all 0.35.0+20060710.6 [23.2 kB] 243s Get:50 http://ftpmaster.internal/ubuntu plucky/main armhf po-debconf all 1.0.21+nmu1 [233 kB] 243s Get:51 http://ftpmaster.internal/ubuntu plucky/main armhf debhelper all 13.20ubuntu1 [893 kB] 243s Get:52 http://ftpmaster.internal/ubuntu plucky/universe armhf dh-python all 6.20241024 [112 kB] 243s Get:53 http://ftpmaster.internal/ubuntu plucky/main armhf libbrotli-dev armhf 1.1.0-2build2 [337 kB] 243s Get:54 http://ftpmaster.internal/ubuntu plucky/main armhf libevent-2.1-7t64 armhf 2.1.12-stable-10 [127 kB] 243s Get:55 http://ftpmaster.internal/ubuntu plucky/main armhf libunbound8 armhf 1.20.0-1ubuntu2.1 [416 kB] 243s Get:56 http://ftpmaster.internal/ubuntu plucky/main armhf libgnutls-dane0t64 armhf 3.8.8-2ubuntu1 [34.7 kB] 243s Get:57 http://ftpmaster.internal/ubuntu plucky/main armhf libgnutls-openssl27t64 armhf 3.8.8-2ubuntu1 [34.9 kB] 243s Get:58 http://ftpmaster.internal/ubuntu plucky/main armhf libidn2-dev armhf 2.3.7-2build2 [115 kB] 243s Get:59 http://ftpmaster.internal/ubuntu plucky/main armhf libp11-kit-dev armhf 0.25.5-2ubuntu1 [22.7 kB] 243s Get:60 http://ftpmaster.internal/ubuntu plucky/main armhf libtasn1-6-dev armhf 4.19.0-3build1 [86.0 kB] 243s Get:61 http://ftpmaster.internal/ubuntu plucky/main armhf libgmpxx4ldbl armhf 2:6.3.0+dfsg-2ubuntu7 [9124 B] 243s Get:62 http://ftpmaster.internal/ubuntu plucky/main armhf libgmp-dev armhf 2:6.3.0+dfsg-2ubuntu7 [290 kB] 244s Get:63 http://ftpmaster.internal/ubuntu plucky/main armhf nettle-dev armhf 3.10-1 [1173 kB] 244s Get:64 http://ftpmaster.internal/ubuntu plucky/main armhf libgnutls28-dev armhf 3.8.8-2ubuntu1 [1018 kB] 244s Get:65 http://ftpmaster.internal/ubuntu plucky/main armhf libpkgconf3 armhf 1.8.1-4 [26.6 kB] 244s Get:66 http://ftpmaster.internal/ubuntu plucky/main armhf pkgconf-bin armhf 1.8.1-4 [21.2 kB] 244s Get:67 http://ftpmaster.internal/ubuntu plucky/main armhf pkgconf armhf 1.8.1-4 [16.8 kB] 244s Get:68 http://ftpmaster.internal/ubuntu plucky/main armhf libnghttp2-dev armhf 1.64.0-1 [106 kB] 244s Get:69 http://ftpmaster.internal/ubuntu plucky/main armhf libpsl-dev armhf 0.21.2-1.1build1 [75.6 kB] 244s Get:70 http://ftpmaster.internal/ubuntu plucky/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1ubuntu1 [880 kB] 244s Get:71 http://ftpmaster.internal/ubuntu plucky/main armhf librtmp-dev armhf 2.4+20151223.gitfa8646d.1-2build7 [62.9 kB] 244s Get:72 http://ftpmaster.internal/ubuntu plucky/main armhf libssl-dev armhf 3.3.1-2ubuntu2 [2335 kB] 244s Get:73 http://ftpmaster.internal/ubuntu plucky/main armhf libssh2-1-dev armhf 1.11.1-1 [270 kB] 244s Get:74 http://ftpmaster.internal/ubuntu plucky/main armhf libzstd-dev armhf 1.5.6+dfsg-1 [331 kB] 244s Get:75 http://ftpmaster.internal/ubuntu plucky/main armhf libcurl4-gnutls-dev armhf 8.9.1-2ubuntu2 [443 kB] 244s Get:76 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate-dev armhf 1.22-1 [45.0 kB] 244s Get:77 http://ftpmaster.internal/ubuntu plucky/main armhf libexpat1-dev armhf 2.6.2-2 [121 kB] 244s Get:78 http://ftpmaster.internal/ubuntu plucky/main armhf liblzma-dev armhf 5.6.2-2 [166 kB] 244s Get:79 http://ftpmaster.internal/ubuntu plucky/universe armhf libhts-dev armhf 1.20+ds-1 [1744 kB] 244s Get:80 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 244s Get:81 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 244s Get:82 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-sphinxdoc all 7.4.7-4 [158 kB] 244s Get:83 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.12t64 armhf 3.12.7-3 [2075 kB] 244s Get:84 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.12-dev armhf 3.12.7-3 [4344 kB] 244s Get:85 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libpython3-dev armhf 3.12.7-1 [10.3 kB] 244s Get:86 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13-stdlib armhf 3.13.0-2 [1972 kB] 244s Get:87 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13 armhf 3.13.0-2 [2045 kB] 244s Get:88 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13-dev armhf 3.13.0-2 [4254 kB] 244s Get:89 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libpython3-all-dev armhf 3.12.7-1 [916 B] 244s Get:90 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13 armhf 3.13.0-2 [719 kB] 244s Get:91 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-all armhf 3.12.7-1 [890 B] 244s Get:92 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12-dev armhf 3.12.7-3 [505 kB] 244s Get:93 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-dev armhf 3.12.7-1 [26.7 kB] 244s Get:94 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-dev armhf 3.13.0-2 [507 kB] 244s Get:95 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-all-dev armhf 3.12.7-1 [914 B] 244s Get:96 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-iniconfig all 1.1.1-2 [6024 B] 244s Get:97 http://ftpmaster.internal/ubuntu plucky/main armhf python3-packaging all 24.1-1 [41.4 kB] 244s Get:98 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pluggy all 1.5.0-1 [21.0 kB] 244s Get:99 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pysam armhf 0.22.1+ds-2 [3383 kB] 244s Get:100 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pytest all 8.3.3-1 [251 kB] 244s Get:101 http://ftpmaster.internal/ubuntu plucky/universe armhf samtools armhf 1.20-3 [607 kB] 244s Get:102 http://ftpmaster.internal/ubuntu plucky/universe armhf tabix armhf 1.20+ds-1 [432 kB] 245s Fetched 92.8 MB in 3s (27.1 MB/s) 245s Selecting previously unselected package libpython3.13-minimal:armhf. 245s (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 ... 59567 files and directories currently installed.) 245s Preparing to unpack .../000-libpython3.13-minimal_3.13.0-2_armhf.deb ... 245s Unpacking libpython3.13-minimal:armhf (3.13.0-2) ... 245s Selecting previously unselected package python3.13-minimal. 245s Preparing to unpack .../001-python3.13-minimal_3.13.0-2_armhf.deb ... 245s Unpacking python3.13-minimal (3.13.0-2) ... 245s Selecting previously unselected package m4. 245s Preparing to unpack .../002-m4_1.4.19-4build1_armhf.deb ... 245s Unpacking m4 (1.4.19-4build1) ... 245s Selecting previously unselected package autoconf. 245s Preparing to unpack .../003-autoconf_2.72-3_all.deb ... 245s Unpacking autoconf (2.72-3) ... 245s Selecting previously unselected package autotools-dev. 245s Preparing to unpack .../004-autotools-dev_20220109.1_all.deb ... 245s Unpacking autotools-dev (20220109.1) ... 245s Selecting previously unselected package automake. 245s Preparing to unpack .../005-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 245s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 245s Selecting previously unselected package autopoint. 245s Preparing to unpack .../006-autopoint_0.22.5-2_all.deb ... 245s Unpacking autopoint (0.22.5-2) ... 245s Selecting previously unselected package libdeflate0:armhf. 245s Preparing to unpack .../007-libdeflate0_1.22-1_armhf.deb ... 245s Unpacking libdeflate0:armhf (1.22-1) ... 245s Selecting previously unselected package libhtscodecs2:armhf. 245s Preparing to unpack .../008-libhtscodecs2_1.6.1-1_armhf.deb ... 245s Unpacking libhtscodecs2:armhf (1.6.1-1) ... 245s Selecting previously unselected package libhts3t64:armhf. 245s Preparing to unpack .../009-libhts3t64_1.20+ds-1_armhf.deb ... 245s Unpacking libhts3t64:armhf (1.20+ds-1) ... 245s Selecting previously unselected package bcftools. 245s Preparing to unpack .../010-bcftools_1.20-2_armhf.deb ... 245s Unpacking bcftools (1.20-2) ... 245s Selecting previously unselected package libc-dev-bin. 245s Preparing to unpack .../011-libc-dev-bin_2.40-1ubuntu3_armhf.deb ... 245s Unpacking libc-dev-bin (2.40-1ubuntu3) ... 245s Selecting previously unselected package linux-libc-dev:armhf. 245s Preparing to unpack .../012-linux-libc-dev_6.11.0-8.8_armhf.deb ... 245s Unpacking linux-libc-dev:armhf (6.11.0-8.8) ... 246s Selecting previously unselected package libcrypt-dev:armhf. 246s Preparing to unpack .../013-libcrypt-dev_1%3a4.4.36-4build1_armhf.deb ... 246s Unpacking libcrypt-dev:armhf (1:4.4.36-4build1) ... 246s Selecting previously unselected package rpcsvc-proto. 246s Preparing to unpack .../014-rpcsvc-proto_1.4.2-0ubuntu7_armhf.deb ... 246s Unpacking rpcsvc-proto (1.4.2-0ubuntu7) ... 246s Selecting previously unselected package libc6-dev:armhf. 246s Preparing to unpack .../015-libc6-dev_2.40-1ubuntu3_armhf.deb ... 246s Unpacking libc6-dev:armhf (2.40-1ubuntu3) ... 246s Selecting previously unselected package libisl23:armhf. 246s Preparing to unpack .../016-libisl23_0.27-1_armhf.deb ... 246s Unpacking libisl23:armhf (0.27-1) ... 246s Selecting previously unselected package libmpc3:armhf. 246s Preparing to unpack .../017-libmpc3_1.3.1-1build2_armhf.deb ... 246s Unpacking libmpc3:armhf (1.3.1-1build2) ... 246s Selecting previously unselected package cpp-14-arm-linux-gnueabihf. 246s Preparing to unpack .../018-cpp-14-arm-linux-gnueabihf_14.2.0-8ubuntu1_armhf.deb ... 246s Unpacking cpp-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ... 246s Selecting previously unselected package cpp-14. 246s Preparing to unpack .../019-cpp-14_14.2.0-8ubuntu1_armhf.deb ... 246s Unpacking cpp-14 (14.2.0-8ubuntu1) ... 246s Selecting previously unselected package cpp-arm-linux-gnueabihf. 246s Preparing to unpack .../020-cpp-arm-linux-gnueabihf_4%3a14.1.0-2ubuntu1_armhf.deb ... 246s Unpacking cpp-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 246s Selecting previously unselected package cpp. 246s Preparing to unpack .../021-cpp_4%3a14.1.0-2ubuntu1_armhf.deb ... 246s Unpacking cpp (4:14.1.0-2ubuntu1) ... 246s Selecting previously unselected package libcc1-0:armhf. 246s Preparing to unpack .../022-libcc1-0_14.2.0-8ubuntu1_armhf.deb ... 246s Unpacking libcc1-0:armhf (14.2.0-8ubuntu1) ... 246s Selecting previously unselected package libgomp1:armhf. 246s Preparing to unpack .../023-libgomp1_14.2.0-8ubuntu1_armhf.deb ... 246s Unpacking libgomp1:armhf (14.2.0-8ubuntu1) ... 246s Selecting previously unselected package libasan8:armhf. 246s Preparing to unpack .../024-libasan8_14.2.0-8ubuntu1_armhf.deb ... 246s Unpacking libasan8:armhf (14.2.0-8ubuntu1) ... 246s Selecting previously unselected package libubsan1:armhf. 246s Preparing to unpack .../025-libubsan1_14.2.0-8ubuntu1_armhf.deb ... 246s Unpacking libubsan1:armhf (14.2.0-8ubuntu1) ... 246s Selecting previously unselected package libgcc-14-dev:armhf. 246s Preparing to unpack .../026-libgcc-14-dev_14.2.0-8ubuntu1_armhf.deb ... 246s Unpacking libgcc-14-dev:armhf (14.2.0-8ubuntu1) ... 247s Selecting previously unselected package gcc-14-arm-linux-gnueabihf. 247s Preparing to unpack .../027-gcc-14-arm-linux-gnueabihf_14.2.0-8ubuntu1_armhf.deb ... 247s Unpacking gcc-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ... 247s Selecting previously unselected package gcc-14. 247s Preparing to unpack .../028-gcc-14_14.2.0-8ubuntu1_armhf.deb ... 247s Unpacking gcc-14 (14.2.0-8ubuntu1) ... 247s Selecting previously unselected package gcc-arm-linux-gnueabihf. 247s Preparing to unpack .../029-gcc-arm-linux-gnueabihf_4%3a14.1.0-2ubuntu1_armhf.deb ... 247s Unpacking gcc-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 247s Selecting previously unselected package gcc. 247s Preparing to unpack .../030-gcc_4%3a14.1.0-2ubuntu1_armhf.deb ... 247s Unpacking gcc (4:14.1.0-2ubuntu1) ... 247s Selecting previously unselected package libstdc++-14-dev:armhf. 247s Preparing to unpack .../031-libstdc++-14-dev_14.2.0-8ubuntu1_armhf.deb ... 247s Unpacking libstdc++-14-dev:armhf (14.2.0-8ubuntu1) ... 247s Selecting previously unselected package g++-14-arm-linux-gnueabihf. 247s Preparing to unpack .../032-g++-14-arm-linux-gnueabihf_14.2.0-8ubuntu1_armhf.deb ... 247s Unpacking g++-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ... 247s Selecting previously unselected package g++-14. 247s Preparing to unpack .../033-g++-14_14.2.0-8ubuntu1_armhf.deb ... 247s Unpacking g++-14 (14.2.0-8ubuntu1) ... 247s Selecting previously unselected package g++-arm-linux-gnueabihf. 247s Preparing to unpack .../034-g++-arm-linux-gnueabihf_4%3a14.1.0-2ubuntu1_armhf.deb ... 247s Unpacking g++-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 247s Selecting previously unselected package g++. 248s Preparing to unpack .../035-g++_4%3a14.1.0-2ubuntu1_armhf.deb ... 248s Unpacking g++ (4:14.1.0-2ubuntu1) ... 248s Selecting previously unselected package build-essential. 248s Preparing to unpack .../036-build-essential_12.10ubuntu1_armhf.deb ... 248s Unpacking build-essential (12.10ubuntu1) ... 248s Selecting previously unselected package cython3. 248s Preparing to unpack .../037-cython3_3.0.11+dfsg-1ubuntu1_armhf.deb ... 248s Unpacking cython3 (3.0.11+dfsg-1ubuntu1) ... 248s Selecting previously unselected package libdebhelper-perl. 248s Preparing to unpack .../038-libdebhelper-perl_13.20ubuntu1_all.deb ... 248s Unpacking libdebhelper-perl (13.20ubuntu1) ... 248s Selecting previously unselected package libtool. 248s Preparing to unpack .../039-libtool_2.4.7-7build1_all.deb ... 248s Unpacking libtool (2.4.7-7build1) ... 248s Selecting previously unselected package dh-autoreconf. 248s Preparing to unpack .../040-dh-autoreconf_20_all.deb ... 248s Unpacking dh-autoreconf (20) ... 248s Selecting previously unselected package libarchive-zip-perl. 248s Preparing to unpack .../041-libarchive-zip-perl_1.68-1_all.deb ... 248s Unpacking libarchive-zip-perl (1.68-1) ... 248s Selecting previously unselected package libfile-stripnondeterminism-perl. 248s Preparing to unpack .../042-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... 248s Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... 248s Selecting previously unselected package dh-strip-nondeterminism. 248s Preparing to unpack .../043-dh-strip-nondeterminism_1.14.0-1_all.deb ... 248s Unpacking dh-strip-nondeterminism (1.14.0-1) ... 248s Selecting previously unselected package debugedit. 248s Preparing to unpack .../044-debugedit_1%3a5.1-1_armhf.deb ... 248s Unpacking debugedit (1:5.1-1) ... 248s Selecting previously unselected package dwz. 248s Preparing to unpack .../045-dwz_0.15-1build6_armhf.deb ... 248s Unpacking dwz (0.15-1build6) ... 248s Selecting previously unselected package gettext. 248s Preparing to unpack .../046-gettext_0.22.5-2_armhf.deb ... 248s Unpacking gettext (0.22.5-2) ... 248s Selecting previously unselected package intltool-debian. 248s Preparing to unpack .../047-intltool-debian_0.35.0+20060710.6_all.deb ... 248s Unpacking intltool-debian (0.35.0+20060710.6) ... 248s Selecting previously unselected package po-debconf. 248s Preparing to unpack .../048-po-debconf_1.0.21+nmu1_all.deb ... 248s Unpacking po-debconf (1.0.21+nmu1) ... 248s Selecting previously unselected package debhelper. 248s Preparing to unpack .../049-debhelper_13.20ubuntu1_all.deb ... 248s Unpacking debhelper (13.20ubuntu1) ... 248s Selecting previously unselected package dh-python. 248s Preparing to unpack .../050-dh-python_6.20241024_all.deb ... 248s Unpacking dh-python (6.20241024) ... 248s Selecting previously unselected package libbrotli-dev:armhf. 248s Preparing to unpack .../051-libbrotli-dev_1.1.0-2build2_armhf.deb ... 248s Unpacking libbrotli-dev:armhf (1.1.0-2build2) ... 248s Selecting previously unselected package libevent-2.1-7t64:armhf. 248s Preparing to unpack .../052-libevent-2.1-7t64_2.1.12-stable-10_armhf.deb ... 248s Unpacking libevent-2.1-7t64:armhf (2.1.12-stable-10) ... 248s Selecting previously unselected package libunbound8:armhf. 248s Preparing to unpack .../053-libunbound8_1.20.0-1ubuntu2.1_armhf.deb ... 248s Unpacking libunbound8:armhf (1.20.0-1ubuntu2.1) ... 248s Selecting previously unselected package libgnutls-dane0t64:armhf. 248s Preparing to unpack .../054-libgnutls-dane0t64_3.8.8-2ubuntu1_armhf.deb ... 248s Unpacking libgnutls-dane0t64:armhf (3.8.8-2ubuntu1) ... 248s Selecting previously unselected package libgnutls-openssl27t64:armhf. 248s Preparing to unpack .../055-libgnutls-openssl27t64_3.8.8-2ubuntu1_armhf.deb ... 248s Unpacking libgnutls-openssl27t64:armhf (3.8.8-2ubuntu1) ... 248s Selecting previously unselected package libidn2-dev:armhf. 248s Preparing to unpack .../056-libidn2-dev_2.3.7-2build2_armhf.deb ... 248s Unpacking libidn2-dev:armhf (2.3.7-2build2) ... 248s Selecting previously unselected package libp11-kit-dev:armhf. 248s Preparing to unpack .../057-libp11-kit-dev_0.25.5-2ubuntu1_armhf.deb ... 248s Unpacking libp11-kit-dev:armhf (0.25.5-2ubuntu1) ... 248s Selecting previously unselected package libtasn1-6-dev:armhf. 248s Preparing to unpack .../058-libtasn1-6-dev_4.19.0-3build1_armhf.deb ... 248s Unpacking libtasn1-6-dev:armhf (4.19.0-3build1) ... 249s Selecting previously unselected package libgmpxx4ldbl:armhf. 249s Preparing to unpack .../059-libgmpxx4ldbl_2%3a6.3.0+dfsg-2ubuntu7_armhf.deb ... 249s Unpacking libgmpxx4ldbl:armhf (2:6.3.0+dfsg-2ubuntu7) ... 249s Selecting previously unselected package libgmp-dev:armhf. 249s Preparing to unpack .../060-libgmp-dev_2%3a6.3.0+dfsg-2ubuntu7_armhf.deb ... 249s Unpacking libgmp-dev:armhf (2:6.3.0+dfsg-2ubuntu7) ... 249s Selecting previously unselected package nettle-dev:armhf. 249s Preparing to unpack .../061-nettle-dev_3.10-1_armhf.deb ... 249s Unpacking nettle-dev:armhf (3.10-1) ... 249s Selecting previously unselected package libgnutls28-dev:armhf. 249s Preparing to unpack .../062-libgnutls28-dev_3.8.8-2ubuntu1_armhf.deb ... 249s Unpacking libgnutls28-dev:armhf (3.8.8-2ubuntu1) ... 249s Selecting previously unselected package libpkgconf3:armhf. 249s Preparing to unpack .../063-libpkgconf3_1.8.1-4_armhf.deb ... 249s Unpacking libpkgconf3:armhf (1.8.1-4) ... 249s Selecting previously unselected package pkgconf-bin. 249s Preparing to unpack .../064-pkgconf-bin_1.8.1-4_armhf.deb ... 249s Unpacking pkgconf-bin (1.8.1-4) ... 249s Selecting previously unselected package pkgconf:armhf. 249s Preparing to unpack .../065-pkgconf_1.8.1-4_armhf.deb ... 249s Unpacking pkgconf:armhf (1.8.1-4) ... 249s Selecting previously unselected package libnghttp2-dev:armhf. 249s Preparing to unpack .../066-libnghttp2-dev_1.64.0-1_armhf.deb ... 249s Unpacking libnghttp2-dev:armhf (1.64.0-1) ... 249s Selecting previously unselected package libpsl-dev:armhf. 249s Preparing to unpack .../067-libpsl-dev_0.21.2-1.1build1_armhf.deb ... 249s Unpacking libpsl-dev:armhf (0.21.2-1.1build1) ... 249s Selecting previously unselected package zlib1g-dev:armhf. 249s Preparing to unpack .../068-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_armhf.deb ... 249s Unpacking zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 249s Selecting previously unselected package librtmp-dev:armhf. 249s Preparing to unpack .../069-librtmp-dev_2.4+20151223.gitfa8646d.1-2build7_armhf.deb ... 249s Unpacking librtmp-dev:armhf (2.4+20151223.gitfa8646d.1-2build7) ... 249s Selecting previously unselected package libssl-dev:armhf. 249s Preparing to unpack .../070-libssl-dev_3.3.1-2ubuntu2_armhf.deb ... 249s Unpacking libssl-dev:armhf (3.3.1-2ubuntu2) ... 249s Selecting previously unselected package libssh2-1-dev:armhf. 249s Preparing to unpack .../071-libssh2-1-dev_1.11.1-1_armhf.deb ... 249s Unpacking libssh2-1-dev:armhf (1.11.1-1) ... 249s Selecting previously unselected package libzstd-dev:armhf. 249s Preparing to unpack .../072-libzstd-dev_1.5.6+dfsg-1_armhf.deb ... 249s Unpacking libzstd-dev:armhf (1.5.6+dfsg-1) ... 249s Selecting previously unselected package libcurl4-gnutls-dev:armhf. 249s Preparing to unpack .../073-libcurl4-gnutls-dev_8.9.1-2ubuntu2_armhf.deb ... 249s Unpacking libcurl4-gnutls-dev:armhf (8.9.1-2ubuntu2) ... 249s Selecting previously unselected package libdeflate-dev:armhf. 249s Preparing to unpack .../074-libdeflate-dev_1.22-1_armhf.deb ... 249s Unpacking libdeflate-dev:armhf (1.22-1) ... 249s Selecting previously unselected package libexpat1-dev:armhf. 249s Preparing to unpack .../075-libexpat1-dev_2.6.2-2_armhf.deb ... 249s Unpacking libexpat1-dev:armhf (2.6.2-2) ... 249s Selecting previously unselected package liblzma-dev:armhf. 249s Preparing to unpack .../076-liblzma-dev_5.6.2-2_armhf.deb ... 249s Unpacking liblzma-dev:armhf (5.6.2-2) ... 249s Selecting previously unselected package libhts-dev:armhf. 249s Preparing to unpack .../077-libhts-dev_1.20+ds-1_armhf.deb ... 249s Unpacking libhts-dev:armhf (1.20+ds-1) ... 249s Selecting previously unselected package libjs-jquery. 249s Preparing to unpack .../078-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 249s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 249s Selecting previously unselected package libjs-underscore. 249s Preparing to unpack .../079-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 249s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 249s Selecting previously unselected package libjs-sphinxdoc. 249s Preparing to unpack .../080-libjs-sphinxdoc_7.4.7-4_all.deb ... 249s Unpacking libjs-sphinxdoc (7.4.7-4) ... 249s Selecting previously unselected package libpython3.12t64:armhf. 249s Preparing to unpack .../081-libpython3.12t64_3.12.7-3_armhf.deb ... 249s Unpacking libpython3.12t64:armhf (3.12.7-3) ... 250s Selecting previously unselected package libpython3.12-dev:armhf. 250s Preparing to unpack .../082-libpython3.12-dev_3.12.7-3_armhf.deb ... 250s Unpacking libpython3.12-dev:armhf (3.12.7-3) ... 250s Selecting previously unselected package libpython3-dev:armhf. 250s Preparing to unpack .../083-libpython3-dev_3.12.7-1_armhf.deb ... 250s Unpacking libpython3-dev:armhf (3.12.7-1) ... 250s Selecting previously unselected package libpython3.13-stdlib:armhf. 250s Preparing to unpack .../084-libpython3.13-stdlib_3.13.0-2_armhf.deb ... 250s Unpacking libpython3.13-stdlib:armhf (3.13.0-2) ... 250s Selecting previously unselected package libpython3.13:armhf. 250s Preparing to unpack .../085-libpython3.13_3.13.0-2_armhf.deb ... 250s Unpacking libpython3.13:armhf (3.13.0-2) ... 250s Selecting previously unselected package libpython3.13-dev:armhf. 250s Preparing to unpack .../086-libpython3.13-dev_3.13.0-2_armhf.deb ... 250s Unpacking libpython3.13-dev:armhf (3.13.0-2) ... 250s Selecting previously unselected package libpython3-all-dev:armhf. 250s Preparing to unpack .../087-libpython3-all-dev_3.12.7-1_armhf.deb ... 250s Unpacking libpython3-all-dev:armhf (3.12.7-1) ... 250s Selecting previously unselected package python3.13. 250s Preparing to unpack .../088-python3.13_3.13.0-2_armhf.deb ... 250s Unpacking python3.13 (3.13.0-2) ... 250s Selecting previously unselected package python3-all. 250s Preparing to unpack .../089-python3-all_3.12.7-1_armhf.deb ... 250s Unpacking python3-all (3.12.7-1) ... 250s Selecting previously unselected package python3.12-dev. 250s Preparing to unpack .../090-python3.12-dev_3.12.7-3_armhf.deb ... 250s Unpacking python3.12-dev (3.12.7-3) ... 250s Selecting previously unselected package python3-dev. 250s Preparing to unpack .../091-python3-dev_3.12.7-1_armhf.deb ... 250s Unpacking python3-dev (3.12.7-1) ... 250s Selecting previously unselected package python3.13-dev. 250s Preparing to unpack .../092-python3.13-dev_3.13.0-2_armhf.deb ... 250s Unpacking python3.13-dev (3.13.0-2) ... 250s Selecting previously unselected package python3-all-dev. 250s Preparing to unpack .../093-python3-all-dev_3.12.7-1_armhf.deb ... 250s Unpacking python3-all-dev (3.12.7-1) ... 250s Selecting previously unselected package python3-iniconfig. 250s Preparing to unpack .../094-python3-iniconfig_1.1.1-2_all.deb ... 250s Unpacking python3-iniconfig (1.1.1-2) ... 250s Selecting previously unselected package python3-packaging. 250s Preparing to unpack .../095-python3-packaging_24.1-1_all.deb ... 250s Unpacking python3-packaging (24.1-1) ... 250s Selecting previously unselected package python3-pluggy. 250s Preparing to unpack .../096-python3-pluggy_1.5.0-1_all.deb ... 250s Unpacking python3-pluggy (1.5.0-1) ... 250s Selecting previously unselected package python3-pysam. 250s Preparing to unpack .../097-python3-pysam_0.22.1+ds-2_armhf.deb ... 250s Unpacking python3-pysam (0.22.1+ds-2) ... 251s Selecting previously unselected package python3-pytest. 251s Preparing to unpack .../098-python3-pytest_8.3.3-1_all.deb ... 251s Unpacking python3-pytest (8.3.3-1) ... 251s Selecting previously unselected package samtools. 251s Preparing to unpack .../099-samtools_1.20-3_armhf.deb ... 251s Unpacking samtools (1.20-3) ... 251s Selecting previously unselected package tabix. 251s Preparing to unpack .../100-tabix_1.20+ds-1_armhf.deb ... 251s Unpacking tabix (1.20+ds-1) ... 251s Selecting previously unselected package autopkgtest-satdep. 251s Preparing to unpack .../101-1-autopkgtest-satdep.deb ... 251s Unpacking autopkgtest-satdep (0) ... 251s Setting up libhtscodecs2:armhf (1.6.1-1) ... 251s Setting up dh-python (6.20241024) ... 251s Setting up libgnutls-openssl27t64:armhf (3.8.8-2ubuntu1) ... 251s Setting up python3-iniconfig (1.1.1-2) ... 251s Setting up libzstd-dev:armhf (1.5.6+dfsg-1) ... 251s Setting up libarchive-zip-perl (1.68-1) ... 251s Setting up libdebhelper-perl (13.20ubuntu1) ... 251s Setting up libdeflate0:armhf (1.22-1) ... 251s Setting up linux-libc-dev:armhf (6.11.0-8.8) ... 251s Setting up m4 (1.4.19-4build1) ... 251s Setting up libevent-2.1-7t64:armhf (2.1.12-stable-10) ... 251s Setting up libgomp1:armhf (14.2.0-8ubuntu1) ... 251s Setting up libpsl-dev:armhf (0.21.2-1.1build1) ... 251s Setting up libpython3.12t64:armhf (3.12.7-3) ... 251s Setting up libpython3.13-minimal:armhf (3.13.0-2) ... 251s Setting up autotools-dev (20220109.1) ... 251s Setting up python3-packaging (24.1-1) ... 252s Setting up libunbound8:armhf (1.20.0-1ubuntu2.1) ... 252s Setting up libpkgconf3:armhf (1.8.1-4) ... 252s Setting up libgmpxx4ldbl:armhf (2:6.3.0+dfsg-2ubuntu7) ... 252s Setting up rpcsvc-proto (1.4.2-0ubuntu7) ... 252s Setting up libgnutls-dane0t64:armhf (3.8.8-2ubuntu1) ... 252s Setting up libssl-dev:armhf (3.3.1-2ubuntu2) ... 252s Setting up libmpc3:armhf (1.3.1-1build2) ... 252s Setting up cython3 (3.0.11+dfsg-1ubuntu1) ... 253s Setting up autopoint (0.22.5-2) ... 253s Setting up pkgconf-bin (1.8.1-4) ... 253s Setting up libidn2-dev:armhf (2.3.7-2build2) ... 253s Setting up autoconf (2.72-3) ... 253s Setting up python3-pluggy (1.5.0-1) ... 253s Setting up liblzma-dev:armhf (5.6.2-2) ... 253s Setting up libubsan1:armhf (14.2.0-8ubuntu1) ... 253s Setting up dwz (0.15-1build6) ... 253s Setting up libcrypt-dev:armhf (1:4.4.36-4build1) ... 253s Setting up libasan8:armhf (14.2.0-8ubuntu1) ... 253s Setting up debugedit (1:5.1-1) ... 253s Setting up libhts3t64:armhf (1.20+ds-1) ... 253s Setting up python3.13-minimal (3.13.0-2) ... 254s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 254s Setting up libgcc-14-dev:armhf (14.2.0-8ubuntu1) ... 254s Setting up libisl23:armhf (0.27-1) ... 254s Setting up libc-dev-bin (2.40-1ubuntu3) ... 254s Setting up libtasn1-6-dev:armhf (4.19.0-3build1) ... 254s Setting up libdeflate-dev:armhf (1.22-1) ... 254s Setting up tabix (1.20+ds-1) ... 254s Setting up libpython3.13-stdlib:armhf (3.13.0-2) ... 254s Setting up libcc1-0:armhf (14.2.0-8ubuntu1) ... 254s Setting up libbrotli-dev:armhf (1.1.0-2build2) ... 254s Setting up libp11-kit-dev:armhf (0.25.5-2ubuntu1) ... 254s Setting up cpp-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ... 254s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 254s Setting up libpython3.13:armhf (3.13.0-2) ... 254s Setting up automake (1:1.16.5-1.3ubuntu1) ... 254s update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode 254s Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... 254s Setting up gettext (0.22.5-2) ... 254s Setting up python3-pysam (0.22.1+ds-2) ... 255s Setting up libgmp-dev:armhf (2:6.3.0+dfsg-2ubuntu7) ... 255s Setting up nettle-dev:armhf (3.10-1) ... 255s Setting up python3.13 (3.13.0-2) ... 256s Setting up python3-pytest (8.3.3-1) ... 256s Setting up bcftools (1.20-2) ... 256s Setting up gcc-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ... 256s Setting up python3-all (3.12.7-1) ... 256s Setting up pkgconf:armhf (1.8.1-4) ... 256s Setting up samtools (1.20-3) ... 256s Setting up intltool-debian (0.35.0+20060710.6) ... 256s Setting up libjs-sphinxdoc (7.4.7-4) ... 256s Setting up cpp-14 (14.2.0-8ubuntu1) ... 256s Setting up dh-strip-nondeterminism (1.14.0-1) ... 256s Setting up libc6-dev:armhf (2.40-1ubuntu3) ... 256s Setting up libstdc++-14-dev:armhf (14.2.0-8ubuntu1) ... 256s Setting up cpp-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 256s Setting up gcc-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 256s Setting up libgnutls28-dev:armhf (3.8.8-2ubuntu1) ... 256s Setting up libnghttp2-dev:armhf (1.64.0-1) ... 256s Setting up g++-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ... 256s Setting up po-debconf (1.0.21+nmu1) ... 256s Setting up gcc-14 (14.2.0-8ubuntu1) ... 256s Setting up libexpat1-dev:armhf (2.6.2-2) ... 256s Setting up zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 256s Setting up cpp (4:14.1.0-2ubuntu1) ... 256s Setting up g++-14 (14.2.0-8ubuntu1) ... 256s Setting up g++-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 256s Setting up libtool (2.4.7-7build1) ... 256s Setting up libpython3.12-dev:armhf (3.12.7-3) ... 256s Setting up gcc (4:14.1.0-2ubuntu1) ... 256s Setting up dh-autoreconf (20) ... 256s Setting up libpython3.13-dev:armhf (3.13.0-2) ... 256s Setting up librtmp-dev:armhf (2.4+20151223.gitfa8646d.1-2build7) ... 256s Setting up python3.12-dev (3.12.7-3) ... 256s Setting up libssh2-1-dev:armhf (1.11.1-1) ... 256s Setting up g++ (4:14.1.0-2ubuntu1) ... 256s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 256s Setting up build-essential (12.10ubuntu1) ... 256s Setting up libpython3-dev:armhf (3.12.7-1) ... 256s Setting up python3.13-dev (3.13.0-2) ... 256s Setting up debhelper (13.20ubuntu1) ... 256s Setting up libcurl4-gnutls-dev:armhf (8.9.1-2ubuntu2) ... 256s Setting up libpython3-all-dev:armhf (3.12.7-1) ... 256s Setting up python3-dev (3.12.7-1) ... 256s Setting up python3-all-dev (3.12.7-1) ... 256s Setting up libhts-dev:armhf (1.20+ds-1) ... 256s Setting up autopkgtest-satdep (0) ... 256s Processing triggers for systemd (256.5-2ubuntu4) ... 257s Processing triggers for man-db (2.12.1-3) ... 258s Processing triggers for install-info (7.1.1-1) ... 258s Processing triggers for libc-bin (2.40-1ubuntu3) ... 276s (Reading database ... 66818 files and directories currently installed.) 276s Removing autopkgtest-satdep (0) ... 284s autopkgtest [01:33:37]: test command1: export HOME=$PWD && make -C tests/pysam_data && make -C tests/cbcf_data && pytest-3 284s autopkgtest [01:33:37]: test command1: [----------------------- 286s make: Entering directory '/tmp/autopkgtest.GaGsi7/build.WVf/src/tests/pysam_data' 286s samtools faidx ex1.fa 286s samtools view --no-PG -bo ex1.bam -t ex1.fa.fai ex1.sam.gz 286s samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz 286s [mpileup] 1 samples in 1 input files 286s gunzip < ex1.sam.gz > ex1.sam 286s samtools index ex1.bam 286s samtools view --no-PG -h ex1.bam | gzip > ex2.sam.gz 286s gunzip < ex2.sam.gz > ex2.sam 286s samtools view --no-PG -bo ex2.bam ex2.sam 286s samtools index ex2.bam 286s samtools calmd --no-PG --output-fmt BAM ex2.bam ex1.fa > with_md.sam.gz 286s [bam_fillmd1] different NM for read 'EAS139_11:7:46:695:738': 3 -> 8 286s [bam_fillmd1] different NM for read 'EAS218_4:1:48:9:409': 0 -> 5 286s [bam_fillmd1] different NM for read 'B7_591:7:200:192:373': 0 -> 5 286s [bam_fillmd1] different NM for read 'EAS56_65:1:163:846:223': 0 -> 5 286s [bam_fillmd1] different NM for read 'EAS114_30:7:283:799:560': 0 -> 5 286s [bam_fillmd1] different NM for read 'B7_595:4:84:802:737': 0 -> 4 286s [bam_fillmd1] different NM for read 'EAS51_66:5:308:400:602': 0 -> 3 286s [bam_fillmd1] different NM for read 'EAS54_81:2:285:367:932': 0 -> 3 286s [bam_fillmd1] different NM for read 'EAS114_39:1:70:147:84': 0 -> 3 286s [bam_fillmd1] different NM for read 'EAS56_53:1:124:243:35': 2 -> 5 286s [bam_fillmd1] different NM for read 'EAS1_103:2:226:302:758': 2 -> 3 286s [bam_fillmd1] different NM for read 'EAS114_28:6:175:705:982': 1 -> 0 286s [bam_fillmd1] different NM for read 'EAS51_64:4:179:389:585': 7 -> 8 286s [bam_fillmd1] different NM for read 'B7_589:1:122:337:968': 3 -> 2 286s [bam_fillmd1] different NM for read 'B7_610:4:15:805:420': 4 -> 5 286s [bam_fillmd1] different NM for read 'B7_591:2:279:124:41': 2 -> 4 286s [bam_fillmd1] different NM for read 'EAS112_32:8:89:254:332': 0 -> 1 286s [bam_fillmd1] different NM for read 'B7_597:7:103:731:697': 0 -> 2 286s [bam_fillmd1] different NM for read 'EAS139_11:2:71:83:58': 0 -> 2 286s [bam_fillmd1] different NM for read 'EAS192_3:4:63:5:870': 0 -> 2 286s [bam_fillmd1] different NM for read 'EAS139_19:2:29:1822:1881': 0 -> 2 286s [bam_fillmd1] different NM for read 'EAS188_7:3:15:568:42': 2 -> 1 286s [bam_fillmd1] different NM for read 'EAS1_95:4:176:971:874': 0 -> 1 286s [bam_fillmd1] different NM for read 'EAS1_99:1:34:649:318': 3 -> 4 286s [bam_fillmd1] different NM for read 'EAS54_65:4:61:346:384': 3 -> 4 286s [bam_fillmd1] different NM for read 'B7_597:6:20:592:496': 0 -> 1 286s [bam_fillmd1] different NM for read 'B7_597:4:38:999:463': 2 -> 1 286s gunzip < with_md.sam.gz > with_md.sam 286s samtools view --no-PG -bo with_md.bam with_md.sam 286s samtools index with_md.bam 286s samtools view --no-PG -bu -o uncompressed.bam ex2.sam 286s [bam_fillmd1] different NM for read 'EAS114_28:5:23:944:377': 0 -> 3 286s [bam_fillmd1] different NM for read 'EAS219_1:3:90:219:528': 0 -> 3 286s [bam_fillmd1] different NM for read 'EAS1_108:5:89:942:84': 0 -> 4 286s [bam_fillmd1] different NM for read 'EAS1_108:6:159:493:275': 0 -> 5 286s [bam_fillmd1] different NM for read 'EAS139_11:1:81:1019:558': 0 -> 5 286s [bam_fillmd1] different NM for read 'EAS51_62:7:162:195:761': 0 -> 4 286s [bam_fillmd1] different NM for read 'B7_597:3:115:646:430': 0 -> 4 286s [bam_fillmd1] different NM for read 'EAS114_30:6:243:209:110': 0 -> 4 286s [bam_fillmd1] different NM for read 'EAS1_108:2:266:994:429': 0 -> 4 286s [bam_fillmd1] different NM for read 'EAS114_30:5:32:461:154': 0 -> 4 286s [bam_fillmd1] different NM for read 'EAS114_39:6:7:492:1088': 0 -> 4 286s [bam_fillmd1] different NM for read 'EAS1_95:6:174:650:125': 0 -> 4 286s [bam_fillmd1] different NM for read 'EAS56_59:6:89:457:591': 1 -> 5 286s [bam_fillmd1] different NM for read 'EAS114_39:2:38:670:564': 0 -> 4 286s [bam_fillmd1] different NM for read 'EAS188_7:4:92:693:228': 1 -> 6 286s [bam_fillmd1] different NM for read 'EAS218_1:4:61:1369:440': 0 -> 4 286s [bam_fillmd1] different NM for read 'EAS114_26:4:123:1001:580': 0 -> 4 286s [bam_fillmd1] different NM for read 'EAS114_39:4:10:1312:1558': 0 -> 4 286s [bam_fillmd1] different NM for read 'EAS220_1:8:45:178:1321': 0 -> 4 286s [bam_fillmd1] different NM for read 'EAS56_59:5:125:137:58': 0 -> 4 286s [bam_fillmd1] different NM for read 'EAS192_3:3:285:349:797': 1 -> 5 286s [bam_fillmd1] different NM for read 'EAS114_45:5:56:1757:1319': 0 -> 4 286s [bam_fillmd1] different NM for read 'B7_591:3:291:404:199': 0 -> 4 286s [bam_fillmd1] different NM for read 'EAS54_65:7:159:253:353': 0 -> 4 286s [bam_fillmd1] different NM for read 'EAS56_57:1:122:38:103': 0 -> 4 286s [bam_fillmd1] different NM for read 'EAS188_4:5:103:870:105': 0 -> 4 286s [bam_fillmd1] different NM for read 'EAS1_105:8:24:718:322': 3 -> 7 286s [bam_fillmd1] different NM for read 'EAS51_64:6:118:41:489': 0 -> 4 286s [bam_fillmd1] different NM for read 'EAS56_61:3:165:665:220': 0 -> 4 286s [bam_fillmd1] different NM for read 'EAS114_30:6:238:803:383': 0 -> 4 286s [bam_fillmd1] different NM for read 'EAS1_105:3:232:364:583': 0 -> 3 286s [bam_fillmd1] different NM for read 'B7_595:2:29:729:70': 3 -> 4 286s [bam_fillmd1] different NM for read 'EAS114_30:6:220:809:850': 4 -> 6 286s [bam_fillmd1] different NM for read 'EAS54_65:2:264:157:150': 3 -> 5 286s [bam_fillmd1] different NM for read 'B7_595:8:26:242:35': 2 -> 1 286s [bam_fillmd1] different NM for read 'B7_610:7:34:144:868': 4 -> 5 286s [bam_fillmd1] different NM for read 'B7_597:8:147:360:141': 1 -> 2 286s [bam_fillmd1] different NM for read 'EAS139_19:2:82:154:1333': 0 -> 4 286s [bam_fillmd1] different NM for read 'EAS56_63:3:41:468:459': 0 -> 3 286s [bam_fillmd1] different NM for read 'EAS1_97:4:274:287:423': 0 -> 1 286s [bam_fillmd1] different NM for read 'EAS114_30:2:303:428:326': 0 -> 1 286s [bam_fillmd1] different NM for read 'EAS54_71:8:105:854:975': 0 -> 3 286s [W::bam_hdr_read] EOF marker is absent. The input is probably truncated 286s samtools view --no-PG -bo MM-chebi.bam MM-chebi.sam 286s samtools view --no-PG -bo MM-double.bam MM-double.sam 286s samtools view --no-PG -bo MM-multi.bam MM-multi.sam 286s samtools view --no-PG -bo MM-orient.bam MM-orient.sam 286s samtools view --no-PG -bo ex10.bam ex10.sam 286s samtools view --no-PG -bo ex3.bam ex3.sam 286s samtools view --no-PG -bo ex4.bam ex4.sam 286s samtools view --no-PG -bo ex5.bam ex5.sam 286s samtools view --no-PG -bo ex6.bam ex6.sam 286s samtools view --no-PG -bo ex8.bam ex8.sam 286s samtools view --no-PG -bo ex9_fail.bam ex9_fail.sam 286s samtools view --no-PG -bo ex9_nofail.bam ex9_nofail.sam 286s samtools view --no-PG -bo ex_spliced.bam ex_spliced.sam 286s samtools view --no-PG -bo example_aligned_pairs.bam example_aligned_pairs.sam 286s samtools view --no-PG -bo example_btag.bam example_btag.sam 286s samtools view --no-PG -bo example_dash_in_chr.bam example_dash_in_chr.sam 286s samtools view --no-PG -bo example_empty_header.bam example_empty_header.sam 286s samtools view --no-PG -bo example_empty_with_header.bam example_empty_with_header.sam 286s samtools view --no-PG -bo example_reverse_complement.bam example_reverse_complement.sam 286s touch tmp.list 286s samtools view --no-PG -bo example_unmapped_reads_no_sq.bam -t tmp.list example_unmapped_reads_no_sq.sam 286s rm -f tmp.list 286s samtools view --no-PG -bo issue100.bam issue100.sam 286s samtools view --no-PG -bo rg_with_tab.bam rg_with_tab.sam 287s samtools view --no-PG -bo softclip.bam softclip.sam 287s samtools view --no-PG -bo tag_bug.bam tag_bug.sam 287s samtools view --no-PG -bo test_mapped_unmapped.bam test_mapped_unmapped.sam 287s samtools view --no-PG -bo test_query_position.bam test_query_position.sam 287s samtools view --no-PG -bo test_unaligned.bam test_unaligned.sam 287s samtools index MM-chebi.bam 287s samtools index MM-double.bam 287s samtools index MM-multi.bam 287s samtools index MM-orient.bam 287s samtools index ex10.bam 287s samtools index ex3.bam 287s samtools index ex4.bam 287s samtools index ex5.bam 287s samtools index ex6.bam 287s samtools index ex8.bam 287s samtools index ex9_fail.bam 287s samtools index ex9_nofail.bam 287s samtools index ex_spliced.bam 287s samtools index example_aligned_pairs.bam 287s samtools index example_btag.bam 287s samtools index example_dash_in_chr.bam 287s samtools index example_empty_header.bam 287s samtools index example_empty_with_header.bam 287s samtools index example_reverse_complement.bam 287s samtools index example_unmapped_reads_no_sq.bam 287s samtools index issue100.bam 287s samtools index rg_with_tab.bam 287s samtools index softclip.bam 287s samtools index tag_bug.bam 287s samtools index test_mapped_unmapped.bam 287s samtools index test_query_position.bam 287s samtools index test_unaligned.bam 287s samtools view --no-PG -Co ex1.cram -T ex1.fa ex1.sam 287s samtools view --no-PG -Co ex2.cram -T ex1.fa ex2.sam 287s samtools view --no-PG -Co ex3.cram -T ex1.fa ex3.sam 287s samtools index ex1.cram 287s samtools index ex2.cram 287s samtools index ex3.cram 287s cp ex1.bam example_bai.bam 287s samtools index example_bai.bam 287s mv example_bai.bam.bai example_bai.bai 287s dd if=ex2.bam of=ex2_truncated.bam bs=$((`wc -c < ex2.bam`-512)) count=1 287s (bgzip -d < ex2.bam; printf '\37\0\0\0\1\0\0\0') | bgzip > ex2_corrupt.bam 287s 1+0 records in 287s 1+0 records out 287s 122288 bytes (122 kB, 119 KiB) copied, 0.000195363 s, 626 MB/s 287s grep "^@" ex2.sam | samtools view --no-PG -bo empty.bam - 287s samtools index empty.bam 287s cp ex1.bam explicit_index.bam 287s cp ex1.cram explicit_index.cram 287s gzip < faidx_empty_seq.fq > faidx_empty_seq.fq.gz 287s bgzip < ex1.fa > ex1.fa.gz 287s samtools faidx ex1.fa.gz 287s cp ex1.bam ex1_csi.bam 287s samtools index -c ex1_csi.bam 287s touch all.stamp 287s rm with_md.sam 287s make: Leaving directory '/tmp/autopkgtest.GaGsi7/build.WVf/src/tests/pysam_data' 287s make: Entering directory '/tmp/autopkgtest.GaGsi7/build.WVf/src/tests/cbcf_data' 287s bgzip < example_vcf40.vcf > example_vcf40.vcf.gz 287s tabix -p vcf example_vcf40.vcf.gz # create tbi index 287s bcftools index example_vcf40.vcf.gz # create csi index 287s bgzip < example_vcf42.vcf > example_vcf42.vcf.gz 287s tabix -p vcf example_vcf42.vcf.gz # create tbi index 287s bcftools index example_vcf42.vcf.gz # create csi index 287s bgzip < example_vcf42_only_header.vcf > example_vcf42_only_header.vcf.gz 287s tabix -p vcf example_vcf42_only_header.vcf.gz # create tbi index 287s bcftools index example_vcf42_only_header.vcf.gz # create csi index 287s bgzip < example_vcf42_withcontigs.vcf > example_vcf42_withcontigs.vcf.gz 287s tabix -p vcf example_vcf42_withcontigs.vcf.gz # create tbi index 287s bcftools index example_vcf42_withcontigs.vcf.gz # create csi index 287s bgzip < example_vcf43.vcf > example_vcf43.vcf.gz 287s tabix -p vcf example_vcf43.vcf.gz # create tbi index 287s bcftools index example_vcf43.vcf.gz # create csi index 287s bgzip < example_vcf43_with_utf8.vcf > example_vcf43_with_utf8.vcf.gz 287s tabix -p vcf example_vcf43_with_utf8.vcf.gz # create tbi index 287s bcftools index example_vcf43_with_utf8.vcf.gz # create csi index 287s bgzip < gnomad.vcf > gnomad.vcf.gz 287s tabix -p vcf gnomad.vcf.gz # create tbi index 287s bcftools index gnomad.vcf.gz # create csi index 287s bgzip < gnomad_fixed.vcf > gnomad_fixed.vcf.gz 287s tabix -p vcf gnomad_fixed.vcf.gz # create tbi index 287s bcftools index gnomad_fixed.vcf.gz # create csi index 287s bgzip < missing_genotypes.vcf > missing_genotypes.vcf.gz 287s tabix -p vcf missing_genotypes.vcf.gz # create tbi index 287s bcftools index missing_genotypes.vcf.gz # create csi index 287s bcftools view -O b example_vcf40.vcf.gz -o example_vcf40.bcf 287s bcftools index example_vcf40.bcf 287s bcftools view -O b example_vcf42.vcf.gz -o example_vcf42.bcf 287s bcftools index example_vcf42.bcf 287s bcftools view -O b example_vcf42_only_header.vcf.gz -o example_vcf42_only_header.bcf 287s bcftools index example_vcf42_only_header.bcf 287s bcftools view -O b example_vcf42_withcontigs.vcf.gz -o example_vcf42_withcontigs.bcf 287s bcftools index example_vcf42_withcontigs.bcf 287s bcftools view -O b example_vcf43.vcf.gz -o example_vcf43.bcf 287s bcftools index example_vcf43.bcf 287s bcftools view -O b example_vcf43_with_utf8.vcf.gz -o example_vcf43_with_utf8.bcf 287s bcftools index example_vcf43_with_utf8.bcf 287s bcftools view -O b gnomad.vcf.gz -o gnomad.bcf 287s bcftools index gnomad.bcf 287s bcftools view -O b gnomad_fixed.vcf.gz -o gnomad_fixed.bcf 287s [W::bcf_hdr_check_sanity] PL should be declared as Number=G 287s bcftools index gnomad_fixed.bcf 287s [W::bcf_hdr_check_sanity] PL should be declared as Number=G 287s bcftools view -O b missing_genotypes.vcf.gz -o missing_genotypes.bcf 287s bcftools index missing_genotypes.bcf 287s touch all.stamp 287s make: Leaving directory '/tmp/autopkgtest.GaGsi7/build.WVf/src/tests/cbcf_data' 287s ============================= test session starts ============================== 287s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3 287s cachedir: .pytest_cache 287s rootdir: /tmp/autopkgtest.GaGsi7/build.WVf/src 287s configfile: setup.cfg 287s testpaths: pysam, tests 287s plugins: typeguard-4.4.1 288s collecting ... collected 951 items 288s 288s tests/AlignedSegment_test.py::TestAlignedSegment::testBlocks PASSED 288s tests/AlignedSegment_test.py::TestAlignedSegment::testCompare PASSED 288s tests/AlignedSegment_test.py::TestAlignedSegment::testEmpty PASSED 288s tests/AlignedSegment_test.py::TestAlignedSegment::testFullReferencePositions PASSED 288s tests/AlignedSegment_test.py::TestAlignedSegment::testHashing PASSED 288s tests/AlignedSegment_test.py::TestAlignedSegment::testLargeRead PASSED 288s tests/AlignedSegment_test.py::TestAlignedSegment::testNoSequence PASSED 288s tests/AlignedSegment_test.py::TestAlignedSegment::testPositions PASSED 288s tests/AlignedSegment_test.py::TestAlignedSegment::testSettingTagInEmptyRead PASSED 288s tests/AlignedSegment_test.py::TestAlignedSegment::testStrOfEmptyRead PASSED 288s tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate PASSED 288s tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate2 PASSED 288s tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateQual PASSED 288s tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateTlen PASSED 288s tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_mapped_reads_are_updated PASSED 288s tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_unmapped_reads_ignore_length PASSED 288s tests/AlignedSegment_test.py::TestAlignedSegment::test_equivalence_matches_only_and_with_seq PASSED 288s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs PASSED 288s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_1character_md PASSED 288s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_bad_type_md PASSED 288s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_hard_clipping PASSED 288s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_lowercase_md PASSED 288s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_match_mismatch PASSED 288s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding PASSED 288s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding_with_seq PASSED 288s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip PASSED 288s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip_reference PASSED 288s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_soft_clipping PASSED 288s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_uppercase_md PASSED 288s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_with_malformed_MD_tag PASSED 288s tests/AlignedSegment_test.py::TestAlignedSegment::test_header_accessible PASSED 288s tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_query_length PASSED 288s tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_read_length PASSED 288s tests/AlignedSegment_test.py::TestAlignedSegment::test_query_length_is_limited PASSED 288s tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_asterisk PASSED 288s tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_chromosome PASSED 288s tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_none PASSED 288s tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_not_be_set_to_unknown_chromosome PASSED 288s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_chromosome PASSED 288s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing PASSED 288s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing_without_header PASSED 288s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_without_header PASSED 288s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_not_be_set_to_unknown_chromosome PASSED 288s tests/AlignedSegment_test.py::TestTidMapping::test_unmapped_tid_is_asterisk_in_output PASSED 288s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_asterisk PASSED 288s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_chromosome PASSED 288s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_none PASSED 288s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_not_be_set_to_unknown_chromosome PASSED 288s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_chromosome PASSED 288s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_equal PASSED 288s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing PASSED 288s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing_without_header PASSED 288s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_without_header PASSED 288s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_not_be_set_to_unknown_chromosome PASSED 288s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_unmapped_tid_is_asterisk_in_output PASSED 288s tests/AlignedSegment_test.py::TestCigar::testCigar PASSED 288s tests/AlignedSegment_test.py::TestCigar::testCigarString PASSED 288s tests/AlignedSegment_test.py::TestCigarStats::testStats PASSED 288s tests/AlignedSegment_test.py::TestAlignedPairs::testReferenceBases PASSED 288s tests/AlignedSegment_test.py::TestBaseModifications::testChebi PASSED 288s tests/AlignedSegment_test.py::TestBaseModifications::testDouble PASSED 288s tests/AlignedSegment_test.py::TestBaseModifications::testMulti PASSED 288s tests/AlignedSegment_test.py::TestBaseModifications::testOrient PASSED 288s tests/AlignedSegment_test.py::TestTags::testAddTags PASSED 288s tests/AlignedSegment_test.py::TestTags::testAddTagsType PASSED 288s tests/AlignedSegment_test.py::TestTags::testArrayTags PASSED 288s tests/AlignedSegment_test.py::TestTags::testEmptyTag PASSED 288s tests/AlignedSegment_test.py::TestTags::testLongTags PASSED 288s tests/AlignedSegment_test.py::TestTags::testMDTagComplex PASSED 288s tests/AlignedSegment_test.py::TestTags::testMDTagDeletions PASSED 288s tests/AlignedSegment_test.py::TestTags::testMDTagInsertions PASSED 288s tests/AlignedSegment_test.py::TestTags::testMDTagMatchOnly PASSED 288s tests/AlignedSegment_test.py::TestTags::testMDTagRefSkipping PASSED 288s tests/AlignedSegment_test.py::TestTags::testMDTagSoftClipping PASSED 288s tests/AlignedSegment_test.py::TestTags::testMissingTag PASSED 288s tests/AlignedSegment_test.py::TestTags::testNegativeIntegers PASSED 288s tests/AlignedSegment_test.py::TestTags::testNegativeIntegersWrittenToFile PASSED 288s tests/AlignedSegment_test.py::TestTags::testSetTag PASSED 288s tests/AlignedSegment_test.py::TestTags::testTagParsing PASSED 288s tests/AlignedSegment_test.py::TestTags::testTagsUpdatingFloat PASSED 288s tests/AlignedSegment_test.py::TestCopy::testCopy PASSED 288s tests/AlignedSegment_test.py::TestCopy::testDeepCopy PASSED 288s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_A PASSED 288s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_C PASSED 288s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_H PASSED 288s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_I PASSED 288s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_S PASSED 288s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_a PASSED 288s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_automated_type_detection PASSED 288s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_c PASSED 288s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_d PASSED 288s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_f PASSED 288s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_i PASSED 288s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_s PASSED 288s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_A PASSED 288s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_C PASSED 288s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_H PASSED 288s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_I PASSED 288s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_S PASSED 288s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_a PASSED 288s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_automated_type_detection PASSED 288s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_c PASSED 288s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_d PASSED 288s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_f PASSED 288s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_i PASSED 288s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_s PASSED 288s tests/AlignedSegment_test.py::TestEnums::test_cigar_enums_are_defined PASSED 288s tests/AlignedSegment_test.py::TestEnums::test_sam_flags_are_defined PASSED 288s tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_constructed_without_header PASSED 288s tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_written_to_file PASSED 288s tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_id_can_be_set PASSED 288s tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_name_is_not_available PASSED 288s tests/AlignedSegment_test.py::TestForwardStrandValues::test_qualities_are_complemented PASSED 288s tests/AlignedSegment_test.py::TestForwardStrandValues::test_sequence_is_complemented PASSED 288s tests/AlignedSegment_test.py::TestExportImport::test_dict_export PASSED 288s tests/AlignedSegment_test.py::TestExportImport::test_string_export PASSED 288s tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_with_tags PASSED 288s tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_without_tags PASSED 288s tests/AlignedSegment_test.py::TestExportImport::test_to_string_without_alignment_file PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_dict PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_header PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references_without_text PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_text PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_access_works PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_contains_works PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_get_works PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_keys_works PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_len_works PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_setting_raises_error PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_values_works PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_header_content_is_as_expected PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_name_mapping PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_text_access_works PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_contains_works PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_get_works PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_keys_works PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_len_works PASSED[E::cram_index_load] Could not retrieve index file for '/tmp/autopkgtest.GaGsi7/build.WVf/src/tests/tmp/pysamtests_tmp_check_read_write_p3z1_l0b' 288s [W::sanitise_SQ_lines] Header @SQ length mismatch for ref chr1, 2147483647 vs 1575 288s [E::cram_index_load] Could not retrieve index file for '/tmp/autopkgtest.GaGsi7/build.WVf/src/tests/tmp/pysamtests_tmp_check_read_write_1wq3f_bv' 288s 288s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_setting_raises_error PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_values_works PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_name_mapping PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_text_access_works PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_contains_works PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_get_works PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_keys_works PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_len_works PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_setting_raises_error PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_values_works PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_name_mapping PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_text_access_works PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM /tmp/autopkgtest.GaGsi7/build.WVf/src/tests/tmp/pysamtests_tmp_check_read_write_ab6ed8lm 288s PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM /tmp/autopkgtest.GaGsi7/build.WVf/src/tests/tmp/pysamtests_tmp_check_read_write_p3z1_l0b 288s PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /tmp/autopkgtest.GaGsi7/build.WVf/src/tests/tmp/pysamtests_tmp_check_read_write__6ekqn1p 288s PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM /tmp/autopkgtest.GaGsi7/build.WVf/src/tests/tmp/pysamtests_tmp_check_read_write_5wbphmb9 288s PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM /tmp/autopkgtest.GaGsi7/build.WVf/src/tests/tmp/pysamtests_tmp_check_read_write_1wq3f_bv 288s PASSED 288s tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM /tmp/autopkgtest.GaGsi7/build.WVf/src/tests/tmp/pysamtests_tmp_check_read_write_of_jdg74 288s PASSED 288s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_all_stepper PASSED 288s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_ignore_overlaps PASSED 288s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper PASSED 289s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_base_quality_threshold PASSED 289s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_ignore_orphans PASSED 289s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_mapping_quality_threshold PASSED 289s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_redo_baq PASSED 289s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_all_stepper PASSED 289s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_ignore_overlaps PASSED 289s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper PASSED 289s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_base_quality_threshold PASSED 289s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_ignore_orphans PASSED 289s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_mapping_quality_threshold PASSED 289s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_redo_baq PASSED 289s tests/AlignmentFilePileup_test.py::TestPileupQueryPosition::testPileup PASSED 289s tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope SKIPPED 289s tests/AlignmentFilePileup_test.py::TestPileupObjects::testPileupColumn PASSED 289s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testInverse PASSED 289s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateAll PASSED 289s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIteratePerContig PASSED 289s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateRanges PASSED 289s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateTruncate PASSED 289s tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testAccessOnClosedIterator PASSED 289s tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStart PASSED 289s tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStr PASSED 289s tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testTruncate PASSED 289s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_depths_are_equal PASSED 289s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_mapping_qualities_are_equal PASSED 290s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_with_reference_are_equal PASSED 290s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_without_reference_are_equal PASSED 290s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_are_equal PASSED 290s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_from_pileups_are_equal PASSED 290s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARQueryLength PASSED 290s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigar PASSED 290s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigarstring PASSED 290s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARflag PASSED 290s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmapq PASSED 290s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmpos PASSED 290s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmrnm PASSED 290s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARpos PASSED 290s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqname PASSED 290s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqqual PASSED 290s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqual PASSED 290s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARquery PASSED 290s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARrname PASSED 290s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARseq PASSED 290s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testOpt PASSED 290s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPairedBools PASSED 290s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPresentOptionalFields PASSED 290s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testTags PASSED 290s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARQueryLength PASSED 290s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigar PASSED 290s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigarstring PASSED 290s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARflag PASSED 290s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmapq PASSED 290s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmpos PASSED 290s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmrnm PASSED 290s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARpos PASSED 290s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqname PASSED 290s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqqual PASSED 290s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqual PASSED 290s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARquery PASSED 290s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARrname PASSED 290s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARseq PASSED 290s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testOpt PASSED 290s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPairedBools PASSED 290s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPresentOptionalFields PASSED 290s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testTags PASSED 290s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARQueryLength PASSED 291s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigar PASSED 291s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigarstring PASSED 292s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARflag PASSED 292s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmapq PASSED 292s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmpos PASSED 293s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmrnm PASSED 293s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARpos PASSED 293s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqname PASSED 294s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqqual PASSED 294s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqual PASSED 295s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARquery PASSED 295s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARrname PASSED 295s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARseq PASSED 296s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testOpt PASSED 296s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPairedBools PASSED 296s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPresentOptionalFields PASSED 297s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testTags PASSED 297s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARQueryLength PASSED 297s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigar PASSED 297s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigarstring PASSED 297s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARflag PASSED 297s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmapq PASSED 297s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmpos PASSED 297s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmrnm PASSED 297s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARpos PASSED 297s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqname PASSED 297s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqqual PASSED 297s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqual PASSED 297s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARquery PASSED 297s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARrname PASSED 297s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARseq PASSED 297s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testOpt PASSED 297s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPairedBools PASSED 297s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPresentOptionalFields PASSED 297s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testTags PASSED 297s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARQueryLength PASSED 298s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigar PASSED 298s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigarstring PASSED 298s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARflag PASSED 299s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmapq PASSED 299s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmpos PASSED 300s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmrnm PASSED 300s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARpos PASSED 300s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqname PASSED 301s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqqual PASSED 301s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqual PASSED 301s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARquery PASSED 302s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARrname PASSED 302s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARseq PASSED 302s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testOpt PASSED 303s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPairedBools PASSED 303s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPresentOptionalFields PASSED 304s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testTags PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARQueryLength PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigar PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigarstring PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARflag PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmapq PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmpos PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmrnm PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARpos PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqname PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqqual PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqual PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARquery PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARrname PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARseq PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testOpt PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPairedBools PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPresentOptionalFields PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testTags PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARQueryLength PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigar PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigarstring PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARflag PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmapq PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmpos PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmrnm PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARpos PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqname PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqqual PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqual PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARquery PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARrname PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARseq PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testOpt PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPairedBools PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPresentOptionalFields PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testTags PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARQueryLength PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigar PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigarstring PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARflag PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmapq PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmpos PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmrnm PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARpos PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqname PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqqual PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqual PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARquery PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARrname PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARseq PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testOpt PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPairedBools PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPresentOptionalFields PASSED 304s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testTags PASSED 304s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARQueryLength PASSED 304s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigar PASSED 304s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigarstring PASSED 304s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARflag PASSED 304s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmapq PASSED 304s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmpos PASSED 304s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmrnm PASSED 304s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARpos PASSED 304s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqname PASSED 304s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqqual PASSED 304s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqual PASSED 304s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARquery PASSED 304s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARrname PASSED 304s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARseq PASSED 304s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testOpt PASSED 304s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPairedBools PASSED 304s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPresentOptionalFields PASSED 304s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testTags PASSED 304s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARQueryLength PASSED 304s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigar PASSED 304s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigarstring PASSED 304s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARflag PASSED 304s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmapq PASSED 304s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmpos PASSED 304s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmrnm PASSED 304s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARpos PASSED 304s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqname PASSED 304s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqqual PASSED 304s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqual PASSED 304s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARquery PASSED 304s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARrname PASSED 304s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARseq PASSED 304s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testOpt PASSED 304s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPairedBools PASSED 304s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPresentOptionalFields PASSED 304s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testTags PASSED 304s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARQueryLength PASSED 304s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigar PASSED 305s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigarstring PASSED 305s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARflag PASSED 306s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmapq PASSED 306s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmpos PASSED 306s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmrnm PASSED 307s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARpos PASSED 307s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqname PASSED 307s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqqual PASSED 308s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqual PASSED 308s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARquery PASSED 309s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARrname PASSED 309s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARseq PASSED 309s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testOpt PASSED 310s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPairedBools PASSED 310s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPresentOptionalFields PASSED 310s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testTags PASSED 311s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARQueryLength PASSED 311s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigar PASSED 312s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigarstring PASSED 312s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARflag PASSED 312s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmapq PASSED 313s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmpos PASSED 313s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmrnm PASSED 314s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARpos PASSED 314s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqname PASSED 314s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqqual PASSED 315s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqual PASSED 315s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARquery PASSED 315s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARrname PASSED 316s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARseq PASSED 316s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testOpt PASSED 317s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPairedBools PASSED 317s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPresentOptionalFields PASSED 317s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testTags PASSED 317s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARQueryLength PASSED 317s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigar PASSED 317s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigarstring PASSED 317s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARflag PASSED 317s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmapq PASSED 317s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmpos PASSED 317s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmrnm PASSED 317s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARpos PASSED 317s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqname PASSED 317s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqqual PASSED 317s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqual PASSED 317s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARquery PASSED 317s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARrname PASSED 317s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARseq PASSED 317s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testOpt PASSED 317s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPairedBools PASSED 317s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPresentOptionalFields PASSED 317s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testRaises PASSED 317s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testTags PASSED 317s tests/AlignmentFile_test.py::TestIO::testBAM2BAM PASSED 318s tests/AlignmentFile_test.py::TestIO::testBAM2SAM PASSED 318s tests/AlignmentFile_test.py::TestIO::testBAMWithCSIIndex PASSED 318s tests/AlignmentFile_test.py::TestIO::testBAMWithShortBAI PASSED 318s tests/AlignmentFile_test.py::TestIO::testBAMWithoutAlignedSegments PASSED 318s tests/AlignmentFile_test.py::TestIO::testCRAM2BAM PASSED 319s tests/AlignmentFile_test.py::TestIO::testCRAM2CRAM PASSED 320s tests/AlignmentFile_test.py::TestIO::testCRAM2SAM PASSED 320s tests/AlignmentFile_test.py::TestIO::testEmptyBAM PASSED 320s tests/AlignmentFile_test.py::TestIO::testEmptyWithHeaderBAM PASSED 320s tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFile PASSED 320s tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject PASSED 320s tests/AlignmentFile_test.py::TestIO::testHead PASSED 320s tests/AlignmentFile_test.py::TestIO::testOpenFromFilename PASSED 320s tests/AlignmentFile_test.py::TestIO::testReadBamWithoutTargetNames PASSED 320s tests/AlignmentFile_test.py::TestIO::testReadSamWithoutTargetNames PASSED 320s tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex PASSED 320s tests/AlignmentFile_test.py::TestIO::testSAM2BAM PASSED 321s tests/AlignmentFile_test.py::TestIO::testSAM2CRAM PASSED 321s tests/AlignmentFile_test.py::TestIO::testSAM2SAM PASSED 321s tests/AlignmentFile_test.py::TestIO::testSAM2SAMWithoutHeader PASSED 321s tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile PASSED 321s tests/AlignmentFile_test.py::TestIO::test_accessing_attributes_in_closed_file_raises_errors PASSED 321s tests/AlignmentFile_test.py::TestIO::test_fail_read_sam_without_header PASSED 321s tests/AlignmentFile_test.py::TestIO::test_fail_when_reading_unformatted_files PASSED 321s tests/AlignmentFile_test.py::TestIO::test_fetch_by_tid PASSED 321s tests/AlignmentFile_test.py::TestIO::test_header_available_after_closing_file [E::hts_open_format] Failed to open file "missing_directory/new_file.bam" : No such file or directory 321s PASSED 321s tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_with_header_without_header_check PASSED 321s tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_without_header_with_refs PASSED 321s tests/AlignmentFile_test.py::TestIO::test_reference_name_available_after_closing_file PASSED 321s tests/AlignmentFile_test.py::TestIO::test_write_bam_to_unknown_path_fails PASSED 321s tests/AlignmentFile_test.py::TestAutoDetect::testBAM PASSED 322s tests/AlignmentFile_test.py::TestAutoDetect::testCRAM PASSED 322s tests/AlignmentFile_test.py::TestAutoDetect::testSAM PASSED 322s tests/AlignmentFile_test.py::TestIteratorRowBAM::testIteratePerContig PASSED 322s tests/AlignmentFile_test.py::TestIteratorRowBAM::testIterateRanges PASSED 322s tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate PASSED 323s tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIteratePerContig PASSED 338s tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIterateRanges PASSED 339s tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIteratePerContig PASSED 353s tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIterateRanges PASSED 353s tests/AlignmentFile_test.py::TestFloatTagBug::testFloatTagBug PASSED 353s tests/AlignmentFile_test.py::TestLargeFieldBug::testLargeFileBug PASSED 353s tests/AlignmentFile_test.py::TestClipping::testClipping PASSED 353s tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_bam_with_until_eof_reads_unmapped_reads PASSED 353s tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_sam_with_until_eof_reads_unmapped_reads [E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory 353s [E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory 353s [E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory 353s [E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory 353s PASSED 353s tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads PASSED 353s tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads_by_contig PASSED 353s tests/AlignmentFile_test.py::TestContextManager::testManager PASSED 353s tests/AlignmentFile_test.py::TestMultiThread::testSingleThreadEqualsMultithread PASSED 353s tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED 353s tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED 353s tests/AlignmentFile_test.py::TestExceptions::testBadContig PASSED 353s tests/AlignmentFile_test.py::TestExceptions::testMeaninglessCrap PASSED 353s tests/AlignmentFile_test.py::TestExceptions::testMissingFile PASSED 353s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangNewFormat PASSED 353s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeNewFormat PASSED 353s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeOldFormat PASSED 353s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeNewFormat PASSED 353s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeOldFormat PASSED 353s tests/AlignmentFile_test.py::TestExceptions::testZeroToZero PASSED 353s tests/AlignmentFile_test.py::TestWrongFormat::testOpenBamAsSam PASSED 353s tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsBam PASSED 353s tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsSam PASSED 353s tests/AlignmentFile_test.py::TestWrongFormat::testOpenSamAsBam PASSED 353s tests/AlignmentFile_test.py::TestRegionParsing::test_dash_in_chr PASSED 353s tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile PASSED 353s tests/AlignmentFile_test.py::TestDeNovoConstruction::test_pass_if_reads_binary_equal PASSED 353s tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader PASSED 353s tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_in_header PASSED 353s tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_with_null_bytes_in_header PASSED 353s tests/AlignmentFile_test.py::TestMismatchingHeader::testMismatchingHeader PASSED 353s tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader PASSED 353s tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2 PASSED 353s tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator [W::bam_hdr_read] EOF marker is absent. The input is probably truncated 353s [E::bgzf_read_block] Failed to read BGZF block data at offset 105176 expected 17578 bytes; hread returned 17094 353s [E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes 353s PASSED 353s tests/AlignmentFile_test.py::TestCorruptBAM::testCorruptBamIterator PASSED 353s tests/AlignmentFile_test.py::TestBTagSam::testReadTags PASSED 353s tests/AlignmentFile_test.py::TestBTagSam::testReadWriteTags PASSED 353s tests/AlignmentFile_test.py::TestBTagBam::testReadTags PASSED 353s tests/AlignmentFile_test.py::TestBTagBam::testReadWriteTags PASSED 353s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetch PASSED 353s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchUntilEOF PASSED 353s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionFalseTrue PASSED 353s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueFalse PASSED 353s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueTrue PASSED 353s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetch PASSED 354s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchUntilEOF PASSED 355s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionFalseTrue PASSED 356s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueFalse PASSED 357s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueTrue PASSED 358s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetch PASSED 359s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchUntilEOF PASSED 359s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionFalseTrue PASSED 360s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueFalse PASSED 361s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueTrue PASSED 362s tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetch PASSED 362s tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetchAll PASSED 362s tests/AlignmentFile_test.py::TestRemoteFileHTTP::testView PASSED 362s tests/AlignmentFile_test.py::TestLargeOptValues::testBAM PASSED 362s tests/AlignmentFile_test.py::TestLargeOptValues::testSAM PASSED 362s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_counts_as_expected PASSED 362s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_nofilter PASSED 362s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_quality_filter PASSED 362s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_all PASSED 362s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_callback PASSED 362s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_with_coordinates_works PASSED 362s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_without_coordinates_fails PASSED 362s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_wrong_coordinates_fails PASSED 362s tests/AlignmentFile_test.py::TestCountCoverage::test_counting_the_same_region_works PASSED 362s tests/AlignmentFile_test.py::TestFindIntrons::test_all PASSED 362s tests/AlignmentFile_test.py::TestFindIntrons::test_first PASSED 362s tests/AlignmentFile_test.py::TestFindIntrons::test_total PASSED 362s tests/AlignmentFile_test.py::TestLogging::testFail1 PASSED 362s tests/AlignmentFile_test.py::TestLogging::testNoFail1 PASSED 362s tests/AlignmentFile_test.py::TestLogging::testNoFail2 PASSED 363s tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testCount PASSED 363s tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testIndexStats PASSED 365s tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testMate PASSED 365s tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct PASSED 365s tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct_per_chromosome PASSED 365s tests/AlignmentFile_test.py::TestSamtoolsProxy::testIndex PASSED 365s tests/AlignmentFile_test.py::TestSamtoolsProxy::testSort PASSED 365s tests/AlignmentFile_test.py::TestSamtoolsProxy::testView [E::hts_open_format] Failed to open file "missing_file" : No such file or directory 365s [E::hts_open_format] Failed to open file "missing_file" : No such file or directory 365s PASSED 365s tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED 365s tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM [W::hts_idx_load3] The index file is older than the data file: /tmp/autopkgtest.GaGsi7/build.WVf/src/tests/pysam_data/ex1.bam.bai 365s PASSED 365s tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexCRAM PASSED 365s tests/AlignmentFile_test.py::TestExplicitIndex::testRemoteExplicitIndexBAM PASSED 365s tests/AlignmentFile_test.py::TestVerbosity::testVerbosity PASSED 365s tests/AlignmentFile_test.py::TestSanityCheckingBAM::test_empty_read_gives_value_error PASSED 365s tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_bam PASSED 365s tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_cram SKIPPED 365s tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_sam PASSED 365s tests/StreamFiledescriptors_test.py::StreamTest::test_samtools_processing SKIPPED 365s tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing PASSED 365s tests/VariantFile_test.py::TestMissingGenotypes::testVCF PASSED 365s tests/VariantFile_test.py::TestMissingGenotypes::testVCFGZ PASSED 365s tests/VariantFile_test.py::TestMissingSamples::testVCF PASSED 365s tests/VariantFile_test.py::TestMissingSamples::testVCFGZ [W::bcf_hdr_check_sanity] PL should be declared as Number=G 365s [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 365s [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) 365s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 365s [E::hts_open_format] Failed to open file "missing_file.vcf" : No such file or directory 365s [E::hts_open_format] Failed to open file "missing_file.vcf.gz" : No such file or directory 365s PASSED 365s tests/VariantFile_test.py::TestMissingSamplesFixed::testVCF PASSED 365s tests/VariantFile_test.py::TestMissingSamplesFixed::testVCFGZ PASSED 365s tests/VariantFile_test.py::TestOpening::testDetectBCF PASSED 365s tests/VariantFile_test.py::TestOpening::testDetectVCF PASSED 365s tests/VariantFile_test.py::TestOpening::testDetectVCFGZ PASSED 365s tests/VariantFile_test.py::TestOpening::testEmptyFileVCF PASSED 365s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFFromPath PASSED 365s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZOnlyHeader PASSED 365s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithIndex PASSED 365s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithoutIndex PASSED 365s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFOnlyHeader PASSED 365s tests/VariantFile_test.py::TestOpening::testMissingFile PASSED 365s tests/VariantFile_test.py::TestOpening::testMissingFileVCFGZ PASSED 365s tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_csi_index PASSED 365s tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_prebuilt_csi PASSED 365s tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_tbi_index_will_produce_csi PASSED 365s tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_csi_index PASSED 365s tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_tbi_index PASSED 365s tests/VariantFile_test.py::TestHeader::testIterator PASSED 365s tests/VariantFile_test.py::TestHeader::testStr PASSED 365s tests/VariantFile_test.py::TestParsing::testAlleles PASSED 365s tests/VariantFile_test.py::TestParsing::testAllelesVariantTypes PASSED 365s tests/VariantFile_test.py::TestParsing::testAlt PASSED 365s tests/VariantFile_test.py::TestParsing::testChrom PASSED 365s tests/VariantFile_test.py::TestParsing::testChromFromPath PASSED 365s tests/VariantFile_test.py::TestParsing::testFilter PASSED 365s tests/VariantFile_test.py::TestParsing::testFormat PASSED 366s tests/VariantFile_test.py::TestParsing::testId PASSED 366s tests/VariantFile_test.py::TestParsing::testInfo PASSED 366s tests/VariantFile_test.py::TestParsing::testPos PASSED 366s tests/VariantFile_test.py::TestParsing::testQual PASSED 366s tests/VariantFile_test.py::TestParsing::testRef PASSED 366s tests/VariantFile_test.py::TestParsing::testSampleAlleleIndices PASSED 366s tests/VariantFile_test.py::TestParsing::testSampleAlleles PASSED 366s tests/VariantFile_test.py::TestParsing::testSampleFormats PASSED 366s tests/VariantFile_test.py::TestParsing::testStart PASSED 366s tests/VariantFile_test.py::TestParsing::testStop PASSED 366s tests/VariantFile_test.py::TestIndexFilename::testOpen PASSED 366s tests/VariantFile_test.py::TestConstructionVCFWithContigs::testBase PASSED 366s tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionFromCopy PASSED 366s tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithLines PASSED 366s tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithRecords PASSED 366s tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testBase PASSED 366s tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionFromCopy PASSED 366s tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithLines PASSED 366s tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithRecords PASSED 366s tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testBase PASSED 366s tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionFromCopy PASSED 366s tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithLines PASSED 366s tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithRecords PASSED 366s tests/VariantFile_test.py::TestSettingRecordValues::testBase PASSED 366s tests/VariantFile_test.py::TestSettingRecordValues::testGenotype [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 366s [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 366s (0, 0) 366s PASSED 366s tests/VariantFile_test.py::TestSettingRecordValues::testSetQual PASSED 366s tests/VariantFile_test.py::TestMultiThreading::testNoMultiThreadingWithIgnoreTruncation PASSED 366s tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult PASSED 366s tests/VariantFile_test.py::TestSubsetting::testSubsetting [E::idx_find_and_load] Could not retrieve index file for '/tmp/autopkgtest.GaGsi7/build.WVf/src/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithreadResult_hwfzo2dh.bcf' 366s PASSED 366s 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.) 366s [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) 366s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 366s [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 366s [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) 366s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 366s PASSED 366s tests/VariantFile_test.py::TestUnicode::test_record_with_unicode PASSED 366s tests/VariantRecord_test.py::test_ascii_annotation_can_be_added PASSED 366s tests/VariantRecord_test.py::test_ascii_annotation_with_variable_length_can_be_added PASSED 366s tests/VariantRecord_test.py::test_unicode_annotation_can_be_added PASSED 366s tests/VariantRecord_test.py::test_set_sample_alleles PASSED 366s tests/compile_test.py::test_bam SKIPPED (no pyximport) 366s tests/compile_test.py::test_gtf SKIPPED (no pyximport) 366s tests/faidx_test.py::TestFastaFile::testFetch PASSED 366s tests/faidx_test.py::TestFastaFile::testFetchErrors PASSED 366s tests/faidx_test.py::TestFastaFile::testLength PASSED 366s tests/faidx_test.py::TestFastaFile::testOutOfRangeAccess PASSED 366s tests/faidx_test.py::TestFastaFile::testSequenceLengths PASSED 366s tests/faidx_test.py::TestFastaFile::test_fetch_with_region_and_contig_raises_exception PASSED 366s tests/faidx_test.py::TestFastaFile::test_fetch_with_region_is_equivalent PASSED 366s tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED 366s tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_index_succeeds PASSED 366s tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_without_index_succeeds PASSED 366s tests/faidx_test.py::TestFastaFilePathIndex::test_raise_exception_if_index_is_missing PASSED 366s tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED 366s tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_index_succeeds PASSED 366s tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_without_index_succeeds PASSED 366s tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_raise_exception_if_index_is_missing PASSED 366s tests/faidx_test.py::TestFastxFileFastq::testCounts PASSED 366s tests/faidx_test.py::TestFastxFileFastq::testManager PASSED 366s tests/faidx_test.py::TestFastxFileFastq::testMissingFile PASSED 366s tests/faidx_test.py::TestFastxFileFastq::testSequence PASSED 366s tests/faidx_test.py::TestFastqFileFastq::testCounts PASSED 366s tests/faidx_test.py::TestFastqFileFastq::testManager PASSED 366s tests/faidx_test.py::TestFastqFileFastq::testMissingFile PASSED 366s tests/faidx_test.py::TestFastqFileFastq::testSequence PASSED 366s tests/faidx_test.py::TestFastxFileFasta::testCounts PASSED 366s tests/faidx_test.py::TestFastxFileFasta::testManager PASSED 366s tests/faidx_test.py::TestFastxFileFasta::testMissingFile PASSED 366s tests/faidx_test.py::TestFastxFileFasta::testSequence PASSED 366s tests/faidx_test.py::TestFastxFileFastqStream::testCounts PASSED 366s tests/faidx_test.py::TestFastxFileFastqStream::testManager PASSED 366s tests/faidx_test.py::TestFastxFileFastqStream::testMissingFile PASSED 366s tests/faidx_test.py::TestFastxFileFastqStream::testSequence PASSED 366s tests/faidx_test.py::TestFastxFileWithEmptySequence::testIteration PASSED 366s tests/faidx_test.py::TestRemoteFileFTP::testFTPView PASSED 366s tests/faidx_test.py::TestRemoteFileFTP::test_sequence_lengths_are_available PASSED 366s tests/faidx_test.py::TestFastqRecord::test_fastx_record_can_be_created_from_scratch PASSED 366s tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_None PASSED 366s tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_modified PASSED 366s tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_name_is_None PASSED 366s tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_quality_is_wrong_length PASSED 366s tests/faidx_test.py::TestFastqRecord::test_fastx_record_name_can_be_modified PASSED 366s tests/faidx_test.py::TestFastqRecord::test_fastx_record_quality_can_be_modified PASSED 366s tests/faidx_test.py::TestFastqRecord::test_fastx_record_sequence_can_be_modified PASSED 366s tests/faidx_test.py::TestFastqProxy::test_fastq_proxy_instantiation_raises_error PASSED 366s tests/linking_test.py::TestLinking::test_package_can_be_installed SKIPPED 366s tests/linking_test.py::TestLinkWithRpath::test_package_can_be_installed SKIPPED 366s tests/linking_test.py::TestLinkWithRpath::test_package_tests_pass SKIPPED 366s tests/linking_test.py::TestLinkWithoutRpath::test_package_can_be_installed SKIPPED 366s tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_fail_on_import SKIPPED 366s tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_pass_if_ld_library_path_set SKIPPED 367s tests/samtools_test.py::SamtoolsTest::testStatements PASSED 367s tests/samtools_test.py::SamtoolsTest::testUsage SKIPPED (skipping us...) 367s tests/samtools_test.py::EmptyIndexTest::testEmptyIndex PASSED 367s tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraArg PASSED 367s tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraFlag PASSED 367s tests/samtools_test.py::TestReturnType::testReturnValueData PASSED 367s tests/samtools_test.py::TestReturnType::testReturnValueString PASSED 367s tests/samtools_test.py::StdoutTest::testDoubleCalling PASSED 367s tests/samtools_test.py::StdoutTest::testSaveStdout PASSED 367s tests/samtools_test.py::StdoutTest::testWithRedirectedStdout PASSED 367s tests/samtools_test.py::StdoutTest::testWithoutRedirectedStdout PASSED 368s tests/samtools_test.py::PysamTest::testStatements PASSED 368s tests/samtools_test.py::PysamTest::testUsage SKIPPED (skipping usage...) 368s tests/tabix_test.py::TestIndexing::test_indexing_to_custom_location_works PASSED 368s tests/tabix_test.py::TestIndexing::test_indexing_with_explict_columns_works PASSED 368s tests/tabix_test.py::TestIndexing::test_indexing_with_lineskipping_works PASSED 368s tests/tabix_test.py::TestIndexing::test_indexing_with_preset_works PASSED 368s tests/tabix_test.py::TestCompression::testCompression PASSED 368s tests/tabix_test.py::TestCompression::testIndexPresetCompressed PASSED 368s tests/tabix_test.py::TestCompression::testIndexPresetUncompressed PASSED 368s tests/tabix_test.py::TestCompressionSam::testCompression PASSED 368s tests/tabix_test.py::TestCompressionSam::testIndexPresetCompressed PASSED 368s tests/tabix_test.py::TestCompressionSam::testIndexPresetUncompressed PASSED 368s tests/tabix_test.py::TestCompressionBed::testCompression PASSED 368s tests/tabix_test.py::TestCompressionBed::testIndexPresetCompressed PASSED 368s tests/tabix_test.py::TestCompressionBed::testIndexPresetUncompressed PASSED 368s tests/tabix_test.py::TestCompressionVCF::testCompression PASSED 368s tests/tabix_test.py::TestCompressionVCF::testIndexPresetCompressed PASSED 368s tests/tabix_test.py::TestCompressionVCF::testIndexPresetUncompressed PASSED 368s tests/tabix_test.py::TestGZFile::testAll PASSED 368s tests/tabix_test.py::TestIterationWithoutComments::testAll PASSED 368s tests/tabix_test.py::TestIterationWithoutComments::testGetContigs PASSED 368s tests/tabix_test.py::TestIterationWithoutComments::testHeader PASSED 368s tests/tabix_test.py::TestIterationWithoutComments::testInvalidIntervals PASSED 368s tests/tabix_test.py::TestIterationWithoutComments::testPerContig PASSED 368s tests/tabix_test.py::TestIterationWithoutComments::testPerContig2 PASSED 369s tests/tabix_test.py::TestIterationWithoutComments::testPerContigFromStart PASSED 369s tests/tabix_test.py::TestIterationWithoutComments::testPerContigToEnd PASSED 369s tests/tabix_test.py::TestIterationWithoutComments::testPerInterval PASSED 369s tests/tabix_test.py::TestIterationWithoutComments::testRegionStrings PASSED 369s tests/tabix_test.py::TestIterationWithoutComments::testReopening PASSED 369s tests/tabix_test.py::TestIterationWithComments::testAll PASSED 369s tests/tabix_test.py::TestIterationWithComments::testGetContigs PASSED 369s tests/tabix_test.py::TestIterationWithComments::testHeader PASSED 369s tests/tabix_test.py::TestIterationWithComments::testInvalidIntervals PASSED 369s tests/tabix_test.py::TestIterationWithComments::testPerContig PASSED 369s tests/tabix_test.py::TestIterationWithComments::testPerContig2 PASSED 369s tests/tabix_test.py::TestIterationWithComments::testPerContigFromStart PASSED 369s tests/tabix_test.py::TestIterationWithComments::testPerContigToEnd PASSED 370s tests/tabix_test.py::TestIterationWithComments::testPerInterval PASSED 370s tests/tabix_test.py::TestIterationWithComments::testRegionStrings PASSED 370s tests/tabix_test.py::TestIterationWithComments::testReopening PASSED 370s tests/tabix_test.py::TestIterators::testClosedFile PASSED 370s tests/tabix_test.py::TestIterators::testClosedFileIteration PASSED 370s tests/tabix_test.py::TestIterators::testIteration PASSED 370s tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFile PASSED 370s tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFileIteration PASSED 370s tests/tabix_test.py::TestIteratorsGenericCompressed::testIteration PASSED 370s tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFile PASSED 370s tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFileIteration PASSED 370s tests/tabix_test.py::TestIteratorsFileCompressed::testIteration PASSED 370s tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFile PASSED 370s tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFileIteration PASSED 370s tests/tabix_test.py::TestIteratorsFileUncompressed::testIteration PASSED 370s tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooFewFields PASSED 370s tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooManyFields PASSED 370s tests/tabix_test.py::TestBed::testRead PASSED 370s tests/tabix_test.py::TestBed::testWrite PASSED 370s tests/tabix_test.py::TestUnicode::testFromTabix PASSED 370s tests/tabix_test.py::TestUnicode::testFromVCF PASSED 370s tests/tabix_test.py::TestVCFFromTabix::testRead PASSED 370s tests/tabix_test.py::TestVCFFromTabix::testWrite PASSED 370s tests/tabix_test.py::TestVCFFromVCF::testConnecting PASSED 370s tests/tabix_test.py::TestVCFFromVCF::testParsing PASSED 370s tests/tabix_test.py::VCFFromTabixTest_10::testRead PASSED 370s tests/tabix_test.py::VCFFromTabixTest_10::testWrite PASSED 370s tests/tabix_test.py::VCFFromVCFTest_10::testConnecting PASSED 370s tests/tabix_test.py::VCFFromVCFTest_10::testParsing PASSED 370s tests/tabix_test.py::VCFFromTabixTest_11::testRead PASSED 370s tests/tabix_test.py::VCFFromTabixTest_11::testWrite PASSED 370s tests/tabix_test.py::VCFFromVCFTest_11::testConnecting PASSED 371s tests/tabix_test.py::VCFFromVCFTest_11::testParsing PASSED 371s tests/tabix_test.py::VCFFromTabixTest_12::testRead PASSED 371s tests/tabix_test.py::VCFFromTabixTest_12::testWrite PASSED 371s tests/tabix_test.py::VCFFromVCFTest_12::testConnecting PASSED 371s tests/tabix_test.py::VCFFromVCFTest_12::testParsing PASSED 371s tests/tabix_test.py::VCFFromTabixTest_13::testRead PASSED 371s tests/tabix_test.py::VCFFromTabixTest_13::testWrite PASSED 371s tests/tabix_test.py::VCFFromVCFTest_13::testConnecting PASSED 371s tests/tabix_test.py::VCFFromVCFTest_13::testParsing PASSED 371s tests/tabix_test.py::VCFFromTabixTest_15::testRead PASSED 371s tests/tabix_test.py::VCFFromTabixTest_15::testWrite PASSED 371s tests/tabix_test.py::VCFFromVCFTest_15::testConnecting PASSED 372s tests/tabix_test.py::VCFFromVCFTest_15::testParsing PASSED 372s tests/tabix_test.py::VCFFromTabixTest_16::testRead PASSED 372s tests/tabix_test.py::VCFFromTabixTest_16::testWrite PASSED 372s tests/tabix_test.py::VCFFromVCFTest_16::testConnecting PASSED 372s tests/tabix_test.py::VCFFromVCFTest_16::testParsing PASSED 372s tests/tabix_test.py::VCFFromTabixTest_18::testRead PASSED 372s tests/tabix_test.py::VCFFromTabixTest_18::testWrite PASSED 372s tests/tabix_test.py::VCFFromVCFTest_18::testConnecting PASSED 372s tests/tabix_test.py::VCFFromVCFTest_18::testParsing PASSED 372s tests/tabix_test.py::VCFFromTabixTest_2::testRead PASSED 372s tests/tabix_test.py::VCFFromTabixTest_2::testWrite PASSED 372s tests/tabix_test.py::VCFFromVCFTest_2::testConnecting PASSED 372s tests/tabix_test.py::VCFFromVCFTest_2::testParsing PASSED 372s tests/tabix_test.py::VCFFromTabixTest_20::testRead PASSED 372s tests/tabix_test.py::VCFFromTabixTest_20::testWrite PASSED 372s tests/tabix_test.py::VCFFromVCFTest_20::testConnecting PASSED 372s tests/tabix_test.py::VCFFromVCFTest_20::testParsing PASSED 372s tests/tabix_test.py::VCFFromTabixTest_21::testRead PASSED 372s tests/tabix_test.py::VCFFromTabixTest_21::testWrite PASSED 372s tests/tabix_test.py::VCFFromVCFTest_21::testConnecting PASSED 372s tests/tabix_test.py::VCFFromVCFTest_21::testParsing PASSED 373s tests/tabix_test.py::VCFFromTabixTest_22::testRead PASSED 373s tests/tabix_test.py::VCFFromTabixTest_22::testWrite PASSED 373s tests/tabix_test.py::VCFFromVCFTest_22::testConnecting PASSED 374s tests/tabix_test.py::VCFFromVCFTest_22::testParsing PASSED 374s tests/tabix_test.py::VCFFromTabixTest_23::testRead PASSED 374s tests/tabix_test.py::VCFFromTabixTest_23::testWrite PASSED 374s tests/tabix_test.py::VCFFromVCFTest_23::testConnecting PASSED 374s tests/tabix_test.py::VCFFromVCFTest_23::testParsing PASSED 374s tests/tabix_test.py::VCFFromTabixTest_24::testRead PASSED 374s tests/tabix_test.py::VCFFromTabixTest_24::testWrite PASSED 374s tests/tabix_test.py::VCFFromVCFTest_24::testConnecting PASSED 374s tests/tabix_test.py::VCFFromVCFTest_24::testParsing PASSED 374s tests/tabix_test.py::VCFFromTabixTest_3::testRead PASSED 374s tests/tabix_test.py::VCFFromTabixTest_3::testWrite PASSED 374s tests/tabix_test.py::VCFFromVCFTest_3::testConnecting PASSED 374s tests/tabix_test.py::VCFFromVCFTest_3::testParsing PASSED 374s tests/tabix_test.py::VCFFromTabixTest_4::testRead PASSED 374s tests/tabix_test.py::VCFFromTabixTest_4::testWrite PASSED 374s tests/tabix_test.py::VCFFromVCFTest_4::testConnecting PASSED 375s tests/tabix_test.py::VCFFromVCFTest_4::testParsing PASSED 375s tests/tabix_test.py::VCFFromTabixTest_5::testRead PASSED 375s tests/tabix_test.py::VCFFromTabixTest_5::testWrite PASSED 375s tests/tabix_test.py::VCFFromVCFTest_5::testConnecting PASSED 375s tests/tabix_test.py::VCFFromVCFTest_5::testParsing PASSED 375s tests/tabix_test.py::VCFFromTabixTest_6::testRead PASSED 375s tests/tabix_test.py::VCFFromTabixTest_6::testWrite PASSED 375s tests/tabix_test.py::VCFFromVCFTest_6::testConnecting PASSED 375s tests/tabix_test.py::VCFFromVCFTest_6::testParsing PASSED 376s tests/tabix_test.py::VCFFromTabixTest_7::testRead PASSED 376s tests/tabix_test.py::VCFFromTabixTest_7::testWrite PASSED 376s tests/tabix_test.py::VCFFromVCFTest_7::testConnecting PASSED 376s tests/tabix_test.py::VCFFromVCFTest_7::testParsing PASSED 376s tests/tabix_test.py::VCFFromTabixTest_8::testRead PASSED 376s tests/tabix_test.py::VCFFromTabixTest_8::testWrite PASSED 376s tests/tabix_test.py::VCFFromVCFTest_8::testConnecting PASSED 376s tests/tabix_test.py::VCFFromVCFTest_8::testParsing PASSED 376s tests/tabix_test.py::VCFFromTabixTest_9::testRead PASSED 376s tests/tabix_test.py::VCFFromTabixTest_9::testWrite PASSED 376s tests/tabix_test.py::VCFFromVCFTest_9::testConnecting PASSED 376s tests/tabix_test.py::VCFFromVCFTest_9::testParsing PASSED 376s tests/tabix_test.py::VCFFromTabixTest_issue85::testRead PASSED 376s tests/tabix_test.py::VCFFromTabixTest_issue85::testWrite PASSED 376s tests/tabix_test.py::VCFFromVCFTest_issue85::testConnecting PASSED 376s tests/tabix_test.py::VCFFromVCFTest_issue85::testParsing PASSED 376s tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testRead PASSED 376s tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testWrite PASSED 376s tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testConnecting PASSED[W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 376s [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) 376s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 376s 376s tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testParsing PASSED 376s tests/tabix_test.py::TestVCFFromVariantFile::testConnecting PASSED 376s tests/tabix_test.py::TestVCFFromVariantFile::testParsing PASSED 376s tests/tabix_test.py::TestVCFFromVariantFile_10::testConnecting PASSED 377s 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.) 377s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:676148 is not defined in the header, assuming Type=String 377s PASSED 377s tests/tabix_test.py::TestVCFFromVariantFile_11::testConnecting PASSED 377s 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.) 377s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:669442 is not defined in the header, assuming Type=String 377s PASSED 377s tests/tabix_test.py::TestVCFFromVariantFile_12::testConnecting PASSED 377s 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.) 377s [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String 377s [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String 377s [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String 377s [W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String 377s [W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String 377s [W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String 377s [W::vcf_parse_format_dict2] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String 377s [W::vcf_parse_format_dict2] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String 377s [W::vcf_parse_format_dict2] FORMAT 'GQ' at chr1:1281168 is not defined in the header, assuming Type=String 377s [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) 377s PASSED 377s tests/tabix_test.py::TestVCFFromVariantFile_13::testConnecting PASSED 377s tests/tabix_test.py::TestVCFFromVariantFile_13::testParsing [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::bcf_hrec_check] Invalid tag name: "1000g" 377s [W::bcf_hrec_check] Invalid tag name: "GT:GL:GQ:NR" 377s [W::bcf_hdr_check_sanity] GL should be declared as Number=G 377s [W::bcf_hrec_check] Invalid tag name: "1000g" 377s [W::bcf_hrec_check] Invalid tag name: "GT:GL:GQ:NR" 377s [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse_info] INFO 'MMLQ' is not defined in the header, assuming Type=String 377s [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr17_gl000205_random' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr18' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr19' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr20' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr21' is not defined in the header. (Quick workaround: index the file with tabix.) 377s PASSED 377s tests/tabix_test.py::TestVCFFromVariantFile_15::testConnecting [W::vcf_parse] Contig 'chr22' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chrUn_gl000214' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chrUn_gl000220' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chrUn_gl000225' is not defined in the header. (Quick workaround: index the file with tabix.) 377s [W::vcf_parse] Contig 'chrX' is not defined in the header. (Quick workaround: index the file with tabix.) 377s PASSED 377s 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.) 377s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:439104 is not defined in the header, assuming Type=String 378s PASSED 378s tests/tabix_test.py::TestVCFFromVariantFile_16::testConnecting PASSED 378s 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.) 378s [W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String 378s PASSED 378s tests/tabix_test.py::TestVCFFromVariantFile_18::testConnecting PASSED 378s 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.) 378s [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String 378s [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String 378s [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String 378s [W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String 378s [W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String 378s [W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String 378s [W::vcf_parse_format_dict2] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String 378s [W::vcf_parse_format_dict2] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String 378s [W::vcf_parse_format_dict2] FORMAT 'GQ' at chr1:1281168 is not defined in the header, assuming Type=String 378s [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) 378s [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) 378s [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) 378s [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) 378s [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) 378s [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) 378s [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) 378s [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) 378s [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) 378s [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) 378s [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) 378s [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) 378s [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) 378s PASSED 378s tests/tabix_test.py::TestVCFFromVariantFile_2::testConnecting PASSED 378s tests/tabix_test.py::TestVCFFromVariantFile_2::testParsing [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) 378s [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) 378s [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) 378s [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) 378s [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) 378s [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) 378s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 378s [W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String 378s PASSED 378s tests/tabix_test.py::TestVCFFromVariantFile_20::testConnecting [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 378s PASSED 378s tests/tabix_test.py::TestVCFFromVariantFile_20::testParsing [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 378s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 378s PASSED 378s tests/tabix_test.py::TestVCFFromVariantFile_21::testConnecting PASSED 378s tests/tabix_test.py::TestVCFFromVariantFile_21::testParsing [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 378s [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 378s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 378s PASSED 378s tests/tabix_test.py::TestVCFFromVariantFile_22::testConnecting PASSED 378s 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.) 378s [W::vcf_parse_info] INFO 'refseq.name' is not defined in the header, assuming Type=String 378s [W::vcf_parse_info] INFO 'refseq.positionType' is not defined in the header, assuming Type=String 379s [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) 379s PASSED 379s tests/tabix_test.py::TestVCFFromVariantFile_23::testConnecting PASSED 379s tests/tabix_test.py::TestVCFFromVariantFile_23::testParsing [W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String 379s PASSED 379s tests/tabix_test.py::TestVCFFromVariantFile_24::testConnecting PASSED 379s tests/tabix_test.py::TestVCFFromVariantFile_24::testParsing [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: 379s #CHROM POS ID REF ALT QUAL FILTER INFO 379s 379s PASSED 379s tests/tabix_test.py::TestVCFFromVariantFile_3::testConnecting PASSED 379s tests/tabix_test.py::TestVCFFromVariantFile_3::testParsing [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) 379s PASSED 379s tests/tabix_test.py::TestVCFFromVariantFile_4::testConnecting PASSED 379s 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.) 379s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:249843 is not defined in the header, assuming Type=String 379s PASSED 379s tests/tabix_test.py::TestVCFFromVariantFile_5::testConnecting PASSED 379s 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.) 379s PASSED 379s tests/tabix_test.py::TestVCFFromVariantFile_6::testConnecting PASSED 379s 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.) 379s [W::vcf_parse_info] INFO 'CallSetAC' is not defined in the header, assuming Type=String 379s [W::vcf_parse_info] INFO 'CallSetAC2' is not defined in the header, assuming Type=String 379s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:669442 is not defined in the header, assuming Type=String 380s PASSED 380s tests/tabix_test.py::TestVCFFromVariantFile_7::testConnecting PASSED 380s 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.) 380s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:249843 is not defined in the header, assuming Type=String 380s PASSED 380s tests/tabix_test.py::TestVCFFromVariantFile_8::testConnecting PASSED 380s 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.) 380s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:676148 is not defined in the header, assuming Type=String 380s PASSED 380s tests/tabix_test.py::TestVCFFromVariantFile_9::testConnecting PASSED 380s 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.) 380s [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String 380s [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String 380s [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String 380s [W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String 380s [W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String 380s [W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String 380s [W::vcf_parse_format_dict2] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String 380s [W::vcf_parse_format_dict2] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String 380s [W::vcf_parse_format_dict2] FORMAT 'GQ' at chr1:1281168 is not defined in the header, assuming Type=String 380s [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) 380s [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) 380s PASSED 380s tests/tabix_test.py::TestVCFFromVariantFile_issue85::testConnecting PASSED 380s tests/tabix_test.py::TestVCFFromVariantFile_issue85::testParsing PASSED 380s tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testConnecting PASSED 380s tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testParsing PASSED 380s tests/tabix_test.py::TestIndexArgument::testFetchAll [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) 380s [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) 380s [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) 380s [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) 380s [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) 380s [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) 380s [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) 380s [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) 380s [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) 380s [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) 380s [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) 380s [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) 380s [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) 380s [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) 380s [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) 380s [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) 380s [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) 380s [E::bcf_hdr_parse] Could not parse the header, sample line not found 380s PASSED 380s tests/tabix_test.py::TestIndexArgument::testLoadIndexWithoutTbiExtension PASSED 380s tests/tabix_test.py::TestBackwardsCompatibility::testBED PASSED 380s tests/tabix_test.py::TestBackwardsCompatibility::testBED0v23 PASSED 380s tests/tabix_test.py::TestBackwardsCompatibility::testBED0v26 PASSED 380s tests/tabix_test.py::TestBackwardsCompatibility::testEmpty PASSED 380s tests/tabix_test.py::TestBackwardsCompatibility::testVCF PASSED 380s tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v23 PASSED 380s tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v26 PASSED 380s tests/tabix_test.py::TestMultipleIterators::testDisjointIterators PASSED 380s tests/tabix_test.py::TestMultipleIterators::testDoubleFetch PASSED 380s tests/tabix_test.py::TestMultipleIterators::testJoinedIterators PASSED 380s tests/tabix_test.py::TestMultipleIterators::testScope PASSED 380s tests/tabix_test.py::TestContextManager::testManager PASSED 380s tests/tabix_test.py::TestMultithreadTabixFile::testMultithreadEqualsSinglethread PASSED 380s tests/tabixproxies_test.py::TestBED::testAssignmentToTargetList PASSED 380s tests/tabixproxies_test.py::TestParser::testAssignmentToTargetList PASSED 380s tests/tabixproxies_test.py::TestParser::testCopy PASSED 380s tests/tabixproxies_test.py::TestParser::testIteratorCompressed PASSED 381s tests/tabixproxies_test.py::TestParser::testIteratorUncompressed PASSED 381s tests/tabixproxies_test.py::TestParser::testRead PASSED 381s tests/tabixproxies_test.py::TestParser::testUnset PASSED 381s tests/tabixproxies_test.py::TestParser::testWrite PASSED 381s tests/tabixproxies_test.py::TestGTF::testAssignmentToTargetList PASSED 381s tests/tabixproxies_test.py::TestGTF::testCopy PASSED 381s tests/tabixproxies_test.py::TestGTF::testIteratorCompressed PASSED 381s tests/tabixproxies_test.py::TestGTF::testIteratorUncompressed PASSED 381s tests/tabixproxies_test.py::TestGTF::testRead PASSED 381s tests/tabixproxies_test.py::TestGTF::testUnset PASSED 381s tests/tabixproxies_test.py::TestGTF::testWrite PASSED 381s tests/tabixproxies_test.py::TestGTF::test_added_attribute_is_output PASSED 381s tests/tabixproxies_test.py::TestGTF::test_asdict_can_be_modified PASSED 381s tests/tabixproxies_test.py::TestGTF::test_asdict_contains_attributes PASSED 381s tests/tabixproxies_test.py::TestGTF::test_setAttribute_makes_changes PASSED 381s tests/tabixproxies_test.py::TestGTF::test_setting_end_is_one_based PASSED 381s tests/tabixproxies_test.py::TestGTF::test_setting_feature_to_none_produces_dot PASSED 381s tests/tabixproxies_test.py::TestGTF::test_setting_fields PASSED 381s tests/tabixproxies_test.py::TestGTF::test_setting_frame_to_none_produces_dot PASSED 381s tests/tabixproxies_test.py::TestGTF::test_setting_score_to_none_produces_dot PASSED 381s tests/tabixproxies_test.py::TestGTF::test_setting_source_to_none_produces_dot PASSED 381s tests/tabixproxies_test.py::TestGTF::test_setting_start_is_one_based PASSED 381s tests/tabixproxies_test.py::TestGTF::test_setting_strand_to_none_produces_dot PASSED 381s tests/tabixproxies_test.py::TestGFF3::testAssignmentToTargetList PASSED 381s tests/tabixproxies_test.py::TestGFF3::testCopy PASSED 381s tests/tabixproxies_test.py::TestGFF3::testIteratorCompressed PASSED 381s tests/tabixproxies_test.py::TestGFF3::testIteratorUncompressed PASSED 381s tests/tabixproxies_test.py::TestGFF3::testRead PASSED 381s tests/tabixproxies_test.py::TestGFF3::testUnset PASSED 381s tests/tabixproxies_test.py::TestGFF3::testWrite PASSED 381s tests/tabixproxies_test.py::TestGFF3::test_added_attribute_is_output PASSED 381s tests/tabixproxies_test.py::TestGFF3::test_asdict_can_be_modified PASSED 381s tests/tabixproxies_test.py::TestGFF3::test_asdict_contains_attributes PASSED 381s tests/tabixproxies_test.py::TestGFF3::test_setAttribute_makes_changes PASSED 381s tests/tabixproxies_test.py::TestGFF3::test_setting_end_is_one_based PASSED 381s tests/tabixproxies_test.py::TestGFF3::test_setting_feature_to_none_produces_dot PASSED 381s tests/tabixproxies_test.py::TestGFF3::test_setting_fields PASSED 381s tests/tabixproxies_test.py::TestGFF3::test_setting_frame_to_none_produces_dot PASSED 381s tests/tabixproxies_test.py::TestGFF3::test_setting_score_to_none_produces_dot PASSED 381s tests/tabixproxies_test.py::TestGFF3::test_setting_source_to_none_produces_dot PASSED 381s tests/tabixproxies_test.py::TestGFF3::test_setting_start_is_one_based PASSED 381s tests/tabixproxies_test.py::TestGFF3::test_setting_strand_to_none_produces_dot PASSED 381s tests/test_samtools_python.py::test_idxstats_parse_split_lines PASSED 381s tests/test_samtools_python.py::test_bedcov_split_lines PASSED 381s tests/test_samtools_python.py::test_idxstats_parse PASSED 381s tests/test_samtools_python.py::test_bedcov PASSED 381s 381s =============================== warnings summary =============================== 381s tests/samtools_test.py::SamtoolsTest::testStatements 381s tests/samtools_test.py::PysamTest::testStatements 381s /tmp/autopkgtest.GaGsi7/build.WVf/src/tests/samtools_test.py:137: UserWarning: versions of pysam.samtools and samtools differ: 1.18 != 1.20 381s warnings.warn( 381s 381s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 381s ============ 938 passed, 13 skipped, 2 warnings in 93.47s (0:01:33) ============ 381s autopkgtest [01:35:14]: test command1: -----------------------] 385s autopkgtest [01:35:18]: test command1: - - - - - - - - - - results - - - - - - - - - - 385s command1 PASS 389s autopkgtest [01:35:22]: test autodep8-python3: preparing testbed 444s autopkgtest [01:36:17]: testbed dpkg architecture: armhf 446s autopkgtest [01:36:19]: testbed apt version: 2.9.8 446s autopkgtest [01:36:19]: @@@@@@@@@@@@@@@@@@@@ test bed setup 453s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 454s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.2 kB] 454s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 454s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.6 kB] 454s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [990 kB] 454s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [103 kB] 454s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [667 kB] 454s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [17.2 kB] 454s Fetched 1975 kB in 1s (2071 kB/s) 454s Reading package lists... 470s tee: /proc/self/fd/2: Permission denied 492s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 492s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 492s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 492s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 494s Reading package lists... 494s Reading package lists... 494s Building dependency tree... 494s Reading state information... 495s Calculating upgrade... 495s The following NEW packages will be installed: 495s python3.13-gdbm 495s The following packages will be upgraded: 495s libgnutls30t64 libjson-glib-1.0-0 libjson-glib-1.0-common libnewt0.52 495s libpython3-stdlib libutempter0 python3 python3-gdbm python3-minimal 495s python3-newt whiptail 495s 11 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 495s Need to get 1207 kB of archives. 495s After this operation, 124 kB of additional disk space will be used. 495s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-minimal armhf 3.12.7-1 [27.4 kB] 496s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3 armhf 3.12.7-1 [24.0 kB] 496s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libpython3-stdlib armhf 3.12.7-1 [10.0 kB] 496s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libgnutls30t64 armhf 3.8.8-2ubuntu1 [955 kB] 496s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3-newt armhf 0.52.24-2ubuntu4 [19.7 kB] 496s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf libnewt0.52 armhf 0.52.24-2ubuntu4 [39.2 kB] 496s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf whiptail armhf 0.52.24-2ubuntu4 [17.2 kB] 496s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-gdbm armhf 3.13.0-2 [29.5 kB] 496s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-gdbm armhf 3.12.7-1 [8642 B] 496s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 496s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-0 armhf 1.10.0+ds-3 [61.7 kB] 496s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libutempter0 armhf 1.2.1-4 [9062 B] 497s Fetched 1207 kB in 1s (1554 kB/s) 497s (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 ... 59559 files and directories currently installed.) 497s Preparing to unpack .../python3-minimal_3.12.7-1_armhf.deb ... 497s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 497s Setting up python3-minimal (3.12.7-1) ... 497s (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 ... 59559 files and directories currently installed.) 497s Preparing to unpack .../python3_3.12.7-1_armhf.deb ... 497s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 497s Preparing to unpack .../libpython3-stdlib_3.12.7-1_armhf.deb ... 497s Unpacking libpython3-stdlib:armhf (3.12.7-1) over (3.12.6-0ubuntu1) ... 497s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_armhf.deb ... 497s Unpacking libgnutls30t64:armhf (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 497s Setting up libgnutls30t64:armhf (3.8.8-2ubuntu1) ... 497s (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 ... 59559 files and directories currently installed.) 497s Preparing to unpack .../0-python3-newt_0.52.24-2ubuntu4_armhf.deb ... 497s Unpacking python3-newt:armhf (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 497s Preparing to unpack .../1-libnewt0.52_0.52.24-2ubuntu4_armhf.deb ... 497s Unpacking libnewt0.52:armhf (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 497s Preparing to unpack .../2-whiptail_0.52.24-2ubuntu4_armhf.deb ... 497s Unpacking whiptail (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 497s Selecting previously unselected package python3.13-gdbm. 497s Preparing to unpack .../3-python3.13-gdbm_3.13.0-2_armhf.deb ... 497s Unpacking python3.13-gdbm (3.13.0-2) ... 497s Preparing to unpack .../4-python3-gdbm_3.12.7-1_armhf.deb ... 497s Unpacking python3-gdbm:armhf (3.12.7-1) over (3.12.6-1ubuntu1) ... 497s Preparing to unpack .../5-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 497s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 497s Preparing to unpack .../6-libjson-glib-1.0-0_1.10.0+ds-3_armhf.deb ... 497s Unpacking libjson-glib-1.0-0:armhf (1.10.0+ds-3) over (1.10.0+ds-2) ... 498s Preparing to unpack .../7-libutempter0_1.2.1-4_armhf.deb ... 498s Unpacking libutempter0:armhf (1.2.1-4) over (1.2.1-3build1) ... 498s Setting up libnewt0.52:armhf (0.52.24-2ubuntu4) ... 498s Setting up libutempter0:armhf (1.2.1-4) ... 498s Setting up whiptail (0.52.24-2ubuntu4) ... 498s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 498s Setting up python3.13-gdbm (3.13.0-2) ... 498s Setting up libpython3-stdlib:armhf (3.12.7-1) ... 498s Setting up python3 (3.12.7-1) ... 498s Setting up python3-newt:armhf (0.52.24-2ubuntu4) ... 498s Setting up libjson-glib-1.0-0:armhf (1.10.0+ds-3) ... 498s Setting up python3-gdbm:armhf (3.12.7-1) ... 498s Processing triggers for man-db (2.12.1-3) ... 499s Processing triggers for libc-bin (2.40-1ubuntu3) ... 499s Reading package lists... 499s Building dependency tree... 499s Reading state information... 500s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 502s autopkgtest [01:37:15]: rebooting testbed after setup commands that affected boot 602s Reading package lists... 602s Building dependency tree... 602s Reading state information... 603s Starting pkgProblemResolver with broken count: 0 603s Starting 2 pkgProblemResolver with broken count: 0 603s Done 604s The following additional packages will be installed: 604s libdeflate0 libhts3t64 libhtscodecs2 libpython3.13-minimal 604s libpython3.13-stdlib python3-all python3-pysam python3.13 python3.13-minimal 604s Suggested packages: 604s python3.13-venv python3.13-doc binfmt-support 604s The following NEW packages will be installed: 604s autopkgtest-satdep libdeflate0 libhts3t64 libhtscodecs2 604s libpython3.13-minimal libpython3.13-stdlib python3-all python3-pysam 604s python3.13 python3.13-minimal 604s 0 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. 604s Need to get 9293 kB/9294 kB of archives. 604s After this operation, 53.0 MB of additional disk space will be used. 604s Get:1 /tmp/autopkgtest.GaGsi7/2-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [712 B] 604s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13-minimal armhf 3.13.0-2 [866 kB] 604s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-minimal armhf 3.13.0-2 [1854 kB] 605s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.22-1 [38.9 kB] 605s Get:5 http://ftpmaster.internal/ubuntu plucky/universe armhf libhtscodecs2 armhf 1.6.1-1 [67.9 kB] 605s Get:6 http://ftpmaster.internal/ubuntu plucky/universe armhf libhts3t64 armhf 1.20+ds-1 [392 kB] 605s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13-stdlib armhf 3.13.0-2 [1972 kB] 605s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13 armhf 3.13.0-2 [719 kB] 605s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-all armhf 3.12.7-1 [890 B] 605s Get:10 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pysam armhf 0.22.1+ds-2 [3383 kB] 606s Fetched 9293 kB in 2s (5187 kB/s) 606s Selecting previously unselected package libpython3.13-minimal:armhf. 606s (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 ... 59567 files and directories currently installed.) 606s Preparing to unpack .../0-libpython3.13-minimal_3.13.0-2_armhf.deb ... 606s Unpacking libpython3.13-minimal:armhf (3.13.0-2) ... 606s Selecting previously unselected package python3.13-minimal. 606s Preparing to unpack .../1-python3.13-minimal_3.13.0-2_armhf.deb ... 606s Unpacking python3.13-minimal (3.13.0-2) ... 606s Selecting previously unselected package libdeflate0:armhf. 606s Preparing to unpack .../2-libdeflate0_1.22-1_armhf.deb ... 606s Unpacking libdeflate0:armhf (1.22-1) ... 606s Selecting previously unselected package libhtscodecs2:armhf. 606s Preparing to unpack .../3-libhtscodecs2_1.6.1-1_armhf.deb ... 606s Unpacking libhtscodecs2:armhf (1.6.1-1) ... 606s Selecting previously unselected package libhts3t64:armhf. 606s Preparing to unpack .../4-libhts3t64_1.20+ds-1_armhf.deb ... 606s Unpacking libhts3t64:armhf (1.20+ds-1) ... 606s Selecting previously unselected package libpython3.13-stdlib:armhf. 606s Preparing to unpack .../5-libpython3.13-stdlib_3.13.0-2_armhf.deb ... 606s Unpacking libpython3.13-stdlib:armhf (3.13.0-2) ... 606s Selecting previously unselected package python3.13. 606s Preparing to unpack .../6-python3.13_3.13.0-2_armhf.deb ... 606s Unpacking python3.13 (3.13.0-2) ... 606s Selecting previously unselected package python3-all. 606s Preparing to unpack .../7-python3-all_3.12.7-1_armhf.deb ... 606s Unpacking python3-all (3.12.7-1) ... 606s Selecting previously unselected package python3-pysam. 606s Preparing to unpack .../8-python3-pysam_0.22.1+ds-2_armhf.deb ... 606s Unpacking python3-pysam (0.22.1+ds-2) ... 606s Selecting previously unselected package autopkgtest-satdep. 607s Preparing to unpack .../9-2-autopkgtest-satdep.deb ... 607s Unpacking autopkgtest-satdep (0) ... 607s Setting up libhtscodecs2:armhf (1.6.1-1) ... 607s Setting up libdeflate0:armhf (1.22-1) ... 607s Setting up libpython3.13-minimal:armhf (3.13.0-2) ... 607s Setting up libhts3t64:armhf (1.20+ds-1) ... 607s Setting up python3.13-minimal (3.13.0-2) ... 608s Setting up libpython3.13-stdlib:armhf (3.13.0-2) ... 608s Setting up python3-pysam (0.22.1+ds-2) ... 608s Setting up python3.13 (3.13.0-2) ... 609s Setting up python3-all (3.12.7-1) ... 609s Setting up autopkgtest-satdep (0) ... 609s Processing triggers for systemd (256.5-2ubuntu4) ... 609s Processing triggers for man-db (2.12.1-3) ... 610s Processing triggers for libc-bin (2.40-1ubuntu3) ... 621s (Reading database ... 60687 files and directories currently installed.) 621s Removing autopkgtest-satdep (0) ... 633s autopkgtest [01:39:26]: 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 633s autopkgtest [01:39:26]: test autodep8-python3: [----------------------- 635s Testing with python3.13: 636s Traceback (most recent call last): 636s File "", line 1, in 636s import pysam; print(pysam) 636s ^^^^^^^^^^^^ 636s File "/usr/lib/python3/dist-packages/pysam/__init__.py", line 4, in 636s from pysam.libchtslib import * 636s ModuleNotFoundError: No module named 'pysam.libchtslib' 636s autopkgtest [01:39:29]: test autodep8-python3: -----------------------] 640s autodep8-python3 FAIL non-zero exit status 1 640s autopkgtest [01:39:33]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 644s autopkgtest [01:39:37]: @@@@@@@@@@@@@@@@@@@@ summary 644s command1 PASS 644s autodep8-python3 FAIL non-zero exit status 1