0s autopkgtest [12:43:25]: starting date and time: 2024-11-04 12:43:25+0000 0s autopkgtest [12:43:25]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [12:43:25]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.93fg6dyi/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:htslib --apt-upgrade python-pysam --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=htslib/1.20+ds-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@lcy02-60.secgroup --name adt-plucky-amd64-python-pysam-20241104-124325-juju-7f2275-prod-proposed-migration-environment-15-3e398556-de9f-43ac-9ae1-c3b907ef8173 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 77s autopkgtest [12:44:42]: testbed dpkg architecture: amd64 77s autopkgtest [12:44:42]: testbed apt version: 2.9.8 77s autopkgtest [12:44:42]: @@@@@@@@@@@@@@@@@@@@ test bed setup 77s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 77s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 77s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [2268 kB] 77s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [31.2 kB] 77s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [177 kB] 77s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [165 kB] 77s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [238 kB] 77s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 77s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [1715 kB] 77s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [833 kB] 77s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [18.1 kB] 77s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [58.6 kB] 78s Fetched 5618 kB in 1s (10.1 MB/s) 78s Reading package lists... 79s Reading package lists... 80s Building dependency tree... 80s Reading state information... 80s Calculating upgrade... 80s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 80s Reading package lists... 81s Building dependency tree... 81s Reading state information... 81s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 81s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 81s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 81s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 81s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 82s Reading package lists... 82s Reading package lists... 83s Building dependency tree... 83s Reading state information... 83s Calculating upgrade... 83s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 83s Reading package lists... 83s Building dependency tree... 83s Reading state information... 84s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 84s autopkgtest [12:44:49]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 84s autopkgtest [12:44:49]: @@@@@@@@@@@@@@@@@@@@ apt-source python-pysam 85s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-pysam 0.22.1+ds-2 (dsc) [2563 B] 85s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-pysam 0.22.1+ds-2 (tar) [1447 kB] 85s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-pysam 0.22.1+ds-2 (diff) [10.7 kB] 85s gpgv: Signature made Wed May 29 11:37:25 2024 UTC 85s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 85s gpgv: issuer "emollier@debian.org" 85s gpgv: Can't check signature: No public key 85s dpkg-source: warning: cannot verify inline signature for ./python-pysam_0.22.1+ds-2.dsc: no acceptable signature found 86s autopkgtest [12:44:51]: testing package python-pysam version 0.22.1+ds-2 86s autopkgtest [12:44:51]: build not needed 86s autopkgtest [12:44:51]: test command1: preparing testbed 87s Reading package lists... 87s Building dependency tree... 87s Reading state information... 87s Starting pkgProblemResolver with broken count: 0 87s Starting 2 pkgProblemResolver with broken count: 0 87s Done 88s The following additional packages will be installed: 88s autoconf automake autopoint autotools-dev bcftools build-essential cpp 88s cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu cython3 debhelper 88s debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz g++ g++-14 88s g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14 88s gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gettext intltool-debian 88s libarchive-zip-perl libasan8 libbrotli-dev libbz2-dev libcc1-0 88s libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 88s libevent-2.1-7t64 libexpat1-dev libfile-stripnondeterminism-perl 88s libgcc-14-dev libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 88s libgnutls-openssl27t64 libgnutls28-dev libgomp1 libhts-dev libhts3t64 88s libhtscodecs2 libhwasan0 libidn2-dev libisl23 libitm1 libjs-jquery 88s libjs-sphinxdoc libjs-underscore liblsan0 liblzma-dev libmpc3 libnghttp2-dev 88s libp11-kit-dev libpkgconf3 libpsl-dev libpython3-all-dev libpython3-dev 88s libpython3.12-dev libquadmath0 librtmp-dev libssh2-1-dev libssl-dev 88s libstdc++-14-dev libtasn1-6-dev libtool libtsan2 libubsan1 libunbound8 88s libzstd-dev m4 nettle-dev pkgconf pkgconf-bin po-debconf python3-all 88s python3-all-dev python3-dev python3-iniconfig python3-packaging 88s python3-pluggy python3-pysam python3-pytest python3.12-dev samtools tabix 88s zlib1g-dev 88s Suggested packages: 88s autoconf-archive gnu-standards autoconf-doc python3-numpy 88s texlive-latex-recommended cpp-doc gcc-14-locales cpp-14-doc cython-doc 88s dh-make flit python3-build python3-installer python3-wheel g++-multilib 88s g++-14-multilib gcc-14-doc gcc-multilib manpages-dev flex bison gdb gcc-doc 88s gcc-14-multilib gdb-x86-64-linux-gnu gettext-doc libasprintf-dev 88s libgettextpo-dev libcurl4-doc libidn-dev libkrb5-dev libldap2-dev gmp-doc 88s libgmp10-doc libmpfr-dev dns-root-data gnutls-bin gnutls-doc liblzma-doc 88s libnghttp2-doc p11-kit-doc libssl-doc libstdc++-14-doc libtool-doc gfortran 88s | fortran95-compiler gcj-jdk m4-doc libmail-box-perl cwltool 88s Recommended packages: 88s python3-gffutils python3-matplotlib bzip2-doc libarchive-cpio-perl 88s javascript-common libtasn1-doc libltdl-dev libmail-sendmail-perl 88s The following NEW packages will be installed: 88s autoconf automake autopkgtest-satdep autopoint autotools-dev bcftools 88s build-essential cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu 88s cython3 debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism 88s dwz g++ g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14 88s gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gettext intltool-debian 88s libarchive-zip-perl libasan8 libbrotli-dev libbz2-dev libcc1-0 88s libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 88s libevent-2.1-7t64 libexpat1-dev libfile-stripnondeterminism-perl 88s libgcc-14-dev libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 88s libgnutls-openssl27t64 libgnutls28-dev libgomp1 libhts-dev libhts3t64 88s libhtscodecs2 libhwasan0 libidn2-dev libisl23 libitm1 libjs-jquery 88s libjs-sphinxdoc libjs-underscore liblsan0 liblzma-dev libmpc3 libnghttp2-dev 88s libp11-kit-dev libpkgconf3 libpsl-dev libpython3-all-dev libpython3-dev 88s libpython3.12-dev libquadmath0 librtmp-dev libssh2-1-dev libssl-dev 88s libstdc++-14-dev libtasn1-6-dev libtool libtsan2 libubsan1 libunbound8 88s libzstd-dev m4 nettle-dev pkgconf pkgconf-bin po-debconf python3-all 88s python3-all-dev python3-dev python3-iniconfig python3-packaging 88s python3-pluggy python3-pysam python3-pytest python3.12-dev samtools tabix 88s zlib1g-dev 88s 0 upgraded, 95 newly installed, 0 to remove and 0 not upgraded. 88s Need to get 101 MB/101 MB of archives. 88s After this operation, 375 MB of additional disk space will be used. 88s Get:1 /tmp/autopkgtest.mg0YZ7/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [816 B] 88s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 m4 amd64 1.4.19-4build1 [244 kB] 88s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 autoconf all 2.72-3 [382 kB] 88s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 autotools-dev all 20220109.1 [44.9 kB] 88s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 automake all 1:1.16.5-1.3ubuntu1 [558 kB] 88s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 autopoint all 0.22.5-2 [616 kB] 88s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.21-1 [49.8 kB] 88s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.0-1build1 [98.8 kB] 88s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libhts3t64 amd64 1.20+ds-2 [501 kB] 88s Get:10 http://ftpmaster.internal/ubuntu plucky/universe amd64 bcftools amd64 1.20-2 [810 kB] 88s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB] 88s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 88s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-7ubuntu1 [11.9 MB] 88s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-7ubuntu1 [1026 B] 88s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [5452 B] 88s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.1.0-2ubuntu1 [22.4 kB] 88s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 14.2.0-7ubuntu1 [47.6 kB] 88s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-7ubuntu1 [148 kB] 88s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 14.2.0-7ubuntu1 [29.1 kB] 88s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 14.2.0-7ubuntu1 [2998 kB] 88s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 14.2.0-7ubuntu1 [1316 kB] 88s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 14.2.0-7ubuntu1 [2733 kB] 88s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 14.2.0-7ubuntu1 [1177 kB] 88s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 14.2.0-7ubuntu1 [1634 kB] 88s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 14.2.0-7ubuntu1 [153 kB] 88s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-7ubuntu1 [2814 kB] 88s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-7ubuntu1 [23.4 MB] 88s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-7ubuntu1 [526 kB] 88s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [1214 B] 88s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.1.0-2ubuntu1 [5000 B] 88s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-7ubuntu1 [2503 kB] 88s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-7ubuntu1 [13.4 MB] 88s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-7ubuntu1 [19.8 kB] 88s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [966 B] 88s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.1.0-2ubuntu1 [1100 B] 88s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 88s Get:37 http://ftpmaster.internal/ubuntu plucky/universe amd64 cython3 amd64 3.0.11+dfsg-1ubuntu1 [2491 kB] 89s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebhelper-perl all 13.20ubuntu1 [94.2 kB] 89s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libtool all 2.4.7-7build1 [166 kB] 89s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-autoreconf all 20 [16.1 kB] 89s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] 89s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] 89s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-strip-nondeterminism all 1.14.0-1 [5058 B] 89s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 debugedit amd64 1:5.1-1 [46.9 kB] 89s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 dwz amd64 0.15-1build6 [115 kB] 89s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 gettext amd64 0.22.5-2 [948 kB] 89s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 89s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] 89s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 debhelper all 13.20ubuntu1 [893 kB] 89s Get:50 http://ftpmaster.internal/ubuntu plucky/universe amd64 dh-python all 6.20240824 [112 kB] 89s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli-dev amd64 1.1.0-2build2 [353 kB] 89s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libbz2-dev amd64 1.0.8-6 [33.8 kB] 89s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10 [144 kB] 89s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libunbound8 amd64 1.20.0-1ubuntu2.1 [447 kB] 89s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libgnutls-dane0t64 amd64 3.8.6-2ubuntu1 [24.0 kB] 89s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libgnutls-openssl27t64 amd64 3.8.6-2ubuntu1 [24.2 kB] 89s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libidn2-dev amd64 2.3.7-2build2 [120 kB] 89s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libp11-kit-dev amd64 0.25.5-2ubuntu1 [22.7 kB] 89s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libtasn1-6-dev amd64 4.19.0-3build1 [90.5 kB] 89s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-2ubuntu7 [10.0 kB] 89s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-2ubuntu7 [341 kB] 89s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 nettle-dev amd64 3.10-1 [1172 kB] 89s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 libgnutls28-dev amd64 3.8.6-2ubuntu1 [1069 kB] 89s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 libpkgconf3 amd64 1.8.1-3ubuntu1 [31.0 kB] 89s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 pkgconf-bin amd64 1.8.1-3ubuntu1 [21.2 kB] 89s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 pkgconf amd64 1.8.1-3ubuntu1 [16.8 kB] 89s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 libnghttp2-dev amd64 1.62.1-2 [118 kB] 89s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libpsl-dev amd64 0.21.2-1.1build1 [76.4 kB] 89s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB] 89s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2build7 [66.7 kB] 89s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libssl-dev amd64 3.3.1-2ubuntu2 [2686 kB] 89s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 libssh2-1-dev amd64 1.11.0-7 [260 kB] 89s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 libzstd-dev amd64 1.5.6+dfsg-1 [371 kB] 89s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4-gnutls-dev amd64 8.9.1-2ubuntu2 [476 kB] 89s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate-dev amd64 1.21-1 [56.9 kB] 89s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libexpat1-dev amd64 2.6.2-2 [140 kB] 89s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma-dev amd64 5.6.2-2 [176 kB] 89s Get:78 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libhts-dev amd64 1.20+ds-2 [6298 kB] 89s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 89s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 89s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-sphinxdoc all 7.4.7-3 [157 kB] 89s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.12-dev amd64 3.12.7-1 [5696 kB] 89s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-dev amd64 3.12.6-0ubuntu1 [10.2 kB] 89s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-all-dev amd64 3.12.6-0ubuntu1 [916 B] 89s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all amd64 3.12.6-0ubuntu1 [886 B] 89s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-dev amd64 3.12.7-1 [505 kB] 89s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dev amd64 3.12.6-0ubuntu1 [26.7 kB] 89s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all-dev amd64 3.12.6-0ubuntu1 [908 B] 89s Get:89 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 89s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 89s Get:91 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 89s Get:92 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pysam amd64 0.22.1+ds-2 [3504 kB] 89s Get:93 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.2-1 [251 kB] 89s Get:94 http://ftpmaster.internal/ubuntu plucky/universe amd64 samtools amd64 1.20-3 [599 kB] 89s Get:95 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 tabix amd64 1.20+ds-2 [640 kB] 89s Fetched 101 MB in 1s (118 MB/s) 89s Selecting previously unselected package m4. 90s (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 ... 75323 files and directories currently installed.) 90s Preparing to unpack .../00-m4_1.4.19-4build1_amd64.deb ... 90s Unpacking m4 (1.4.19-4build1) ... 90s Selecting previously unselected package autoconf. 90s Preparing to unpack .../01-autoconf_2.72-3_all.deb ... 90s Unpacking autoconf (2.72-3) ... 90s Selecting previously unselected package autotools-dev. 90s Preparing to unpack .../02-autotools-dev_20220109.1_all.deb ... 90s Unpacking autotools-dev (20220109.1) ... 90s Selecting previously unselected package automake. 90s Preparing to unpack .../03-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 90s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 90s Selecting previously unselected package autopoint. 90s Preparing to unpack .../04-autopoint_0.22.5-2_all.deb ... 90s Unpacking autopoint (0.22.5-2) ... 90s Selecting previously unselected package libdeflate0:amd64. 90s Preparing to unpack .../05-libdeflate0_1.21-1_amd64.deb ... 90s Unpacking libdeflate0:amd64 (1.21-1) ... 90s Selecting previously unselected package libhtscodecs2:amd64. 90s Preparing to unpack .../06-libhtscodecs2_1.6.0-1build1_amd64.deb ... 90s Unpacking libhtscodecs2:amd64 (1.6.0-1build1) ... 90s Selecting previously unselected package libhts3t64:amd64. 90s Preparing to unpack .../07-libhts3t64_1.20+ds-2_amd64.deb ... 90s Unpacking libhts3t64:amd64 (1.20+ds-2) ... 90s Selecting previously unselected package bcftools. 90s Preparing to unpack .../08-bcftools_1.20-2_amd64.deb ... 90s Unpacking bcftools (1.20-2) ... 90s Selecting previously unselected package libisl23:amd64. 90s Preparing to unpack .../09-libisl23_0.27-1_amd64.deb ... 90s Unpacking libisl23:amd64 (0.27-1) ... 90s Selecting previously unselected package libmpc3:amd64. 90s Preparing to unpack .../10-libmpc3_1.3.1-1build2_amd64.deb ... 90s Unpacking libmpc3:amd64 (1.3.1-1build2) ... 90s Selecting previously unselected package cpp-14-x86-64-linux-gnu. 90s Preparing to unpack .../11-cpp-14-x86-64-linux-gnu_14.2.0-7ubuntu1_amd64.deb ... 90s Unpacking cpp-14-x86-64-linux-gnu (14.2.0-7ubuntu1) ... 90s Selecting previously unselected package cpp-14. 90s Preparing to unpack .../12-cpp-14_14.2.0-7ubuntu1_amd64.deb ... 90s Unpacking cpp-14 (14.2.0-7ubuntu1) ... 90s Selecting previously unselected package cpp-x86-64-linux-gnu. 90s Preparing to unpack .../13-cpp-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ... 90s Unpacking cpp-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 90s Selecting previously unselected package cpp. 90s Preparing to unpack .../14-cpp_4%3a14.1.0-2ubuntu1_amd64.deb ... 90s Unpacking cpp (4:14.1.0-2ubuntu1) ... 90s Selecting previously unselected package libcc1-0:amd64. 90s Preparing to unpack .../15-libcc1-0_14.2.0-7ubuntu1_amd64.deb ... 90s Unpacking libcc1-0:amd64 (14.2.0-7ubuntu1) ... 90s Selecting previously unselected package libgomp1:amd64. 90s Preparing to unpack .../16-libgomp1_14.2.0-7ubuntu1_amd64.deb ... 90s Unpacking libgomp1:amd64 (14.2.0-7ubuntu1) ... 90s Selecting previously unselected package libitm1:amd64. 90s Preparing to unpack .../17-libitm1_14.2.0-7ubuntu1_amd64.deb ... 90s Unpacking libitm1:amd64 (14.2.0-7ubuntu1) ... 90s Selecting previously unselected package libasan8:amd64. 90s Preparing to unpack .../18-libasan8_14.2.0-7ubuntu1_amd64.deb ... 90s Unpacking libasan8:amd64 (14.2.0-7ubuntu1) ... 90s Selecting previously unselected package liblsan0:amd64. 90s Preparing to unpack .../19-liblsan0_14.2.0-7ubuntu1_amd64.deb ... 90s Unpacking liblsan0:amd64 (14.2.0-7ubuntu1) ... 90s Selecting previously unselected package libtsan2:amd64. 90s Preparing to unpack .../20-libtsan2_14.2.0-7ubuntu1_amd64.deb ... 90s Unpacking libtsan2:amd64 (14.2.0-7ubuntu1) ... 90s Selecting previously unselected package libubsan1:amd64. 90s Preparing to unpack .../21-libubsan1_14.2.0-7ubuntu1_amd64.deb ... 90s Unpacking libubsan1:amd64 (14.2.0-7ubuntu1) ... 91s Selecting previously unselected package libhwasan0:amd64. 91s Preparing to unpack .../22-libhwasan0_14.2.0-7ubuntu1_amd64.deb ... 91s Unpacking libhwasan0:amd64 (14.2.0-7ubuntu1) ... 91s Selecting previously unselected package libquadmath0:amd64. 91s Preparing to unpack .../23-libquadmath0_14.2.0-7ubuntu1_amd64.deb ... 91s Unpacking libquadmath0:amd64 (14.2.0-7ubuntu1) ... 91s Selecting previously unselected package libgcc-14-dev:amd64. 91s Preparing to unpack .../24-libgcc-14-dev_14.2.0-7ubuntu1_amd64.deb ... 91s Unpacking libgcc-14-dev:amd64 (14.2.0-7ubuntu1) ... 91s Selecting previously unselected package gcc-14-x86-64-linux-gnu. 91s Preparing to unpack .../25-gcc-14-x86-64-linux-gnu_14.2.0-7ubuntu1_amd64.deb ... 91s Unpacking gcc-14-x86-64-linux-gnu (14.2.0-7ubuntu1) ... 91s Selecting previously unselected package gcc-14. 91s Preparing to unpack .../26-gcc-14_14.2.0-7ubuntu1_amd64.deb ... 91s Unpacking gcc-14 (14.2.0-7ubuntu1) ... 91s Selecting previously unselected package gcc-x86-64-linux-gnu. 91s Preparing to unpack .../27-gcc-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ... 91s Unpacking gcc-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 91s Selecting previously unselected package gcc. 91s Preparing to unpack .../28-gcc_4%3a14.1.0-2ubuntu1_amd64.deb ... 91s Unpacking gcc (4:14.1.0-2ubuntu1) ... 91s Selecting previously unselected package libstdc++-14-dev:amd64. 91s Preparing to unpack .../29-libstdc++-14-dev_14.2.0-7ubuntu1_amd64.deb ... 91s Unpacking libstdc++-14-dev:amd64 (14.2.0-7ubuntu1) ... 91s Selecting previously unselected package g++-14-x86-64-linux-gnu. 91s Preparing to unpack .../30-g++-14-x86-64-linux-gnu_14.2.0-7ubuntu1_amd64.deb ... 91s Unpacking g++-14-x86-64-linux-gnu (14.2.0-7ubuntu1) ... 92s Selecting previously unselected package g++-14. 92s Preparing to unpack .../31-g++-14_14.2.0-7ubuntu1_amd64.deb ... 92s Unpacking g++-14 (14.2.0-7ubuntu1) ... 92s Selecting previously unselected package g++-x86-64-linux-gnu. 92s Preparing to unpack .../32-g++-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ... 92s Unpacking g++-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 92s Selecting previously unselected package g++. 92s Preparing to unpack .../33-g++_4%3a14.1.0-2ubuntu1_amd64.deb ... 92s Unpacking g++ (4:14.1.0-2ubuntu1) ... 92s Selecting previously unselected package build-essential. 92s Preparing to unpack .../34-build-essential_12.10ubuntu1_amd64.deb ... 92s Unpacking build-essential (12.10ubuntu1) ... 92s Selecting previously unselected package cython3. 92s Preparing to unpack .../35-cython3_3.0.11+dfsg-1ubuntu1_amd64.deb ... 92s Unpacking cython3 (3.0.11+dfsg-1ubuntu1) ... 92s Selecting previously unselected package libdebhelper-perl. 92s Preparing to unpack .../36-libdebhelper-perl_13.20ubuntu1_all.deb ... 92s Unpacking libdebhelper-perl (13.20ubuntu1) ... 92s Selecting previously unselected package libtool. 92s Preparing to unpack .../37-libtool_2.4.7-7build1_all.deb ... 92s Unpacking libtool (2.4.7-7build1) ... 92s Selecting previously unselected package dh-autoreconf. 92s Preparing to unpack .../38-dh-autoreconf_20_all.deb ... 92s Unpacking dh-autoreconf (20) ... 92s Selecting previously unselected package libarchive-zip-perl. 92s Preparing to unpack .../39-libarchive-zip-perl_1.68-1_all.deb ... 92s Unpacking libarchive-zip-perl (1.68-1) ... 92s Selecting previously unselected package libfile-stripnondeterminism-perl. 92s Preparing to unpack .../40-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... 92s Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... 92s Selecting previously unselected package dh-strip-nondeterminism. 92s Preparing to unpack .../41-dh-strip-nondeterminism_1.14.0-1_all.deb ... 92s Unpacking dh-strip-nondeterminism (1.14.0-1) ... 92s Selecting previously unselected package debugedit. 92s Preparing to unpack .../42-debugedit_1%3a5.1-1_amd64.deb ... 92s Unpacking debugedit (1:5.1-1) ... 92s Selecting previously unselected package dwz. 92s Preparing to unpack .../43-dwz_0.15-1build6_amd64.deb ... 92s Unpacking dwz (0.15-1build6) ... 92s Selecting previously unselected package gettext. 92s Preparing to unpack .../44-gettext_0.22.5-2_amd64.deb ... 92s Unpacking gettext (0.22.5-2) ... 92s Selecting previously unselected package intltool-debian. 92s Preparing to unpack .../45-intltool-debian_0.35.0+20060710.6_all.deb ... 92s Unpacking intltool-debian (0.35.0+20060710.6) ... 92s Selecting previously unselected package po-debconf. 92s Preparing to unpack .../46-po-debconf_1.0.21+nmu1_all.deb ... 92s Unpacking po-debconf (1.0.21+nmu1) ... 92s Selecting previously unselected package debhelper. 92s Preparing to unpack .../47-debhelper_13.20ubuntu1_all.deb ... 92s Unpacking debhelper (13.20ubuntu1) ... 92s Selecting previously unselected package dh-python. 92s Preparing to unpack .../48-dh-python_6.20240824_all.deb ... 92s Unpacking dh-python (6.20240824) ... 92s Selecting previously unselected package libbrotli-dev:amd64. 92s Preparing to unpack .../49-libbrotli-dev_1.1.0-2build2_amd64.deb ... 92s Unpacking libbrotli-dev:amd64 (1.1.0-2build2) ... 92s Selecting previously unselected package libbz2-dev:amd64. 92s Preparing to unpack .../50-libbz2-dev_1.0.8-6_amd64.deb ... 92s Unpacking libbz2-dev:amd64 (1.0.8-6) ... 92s Selecting previously unselected package libevent-2.1-7t64:amd64. 92s Preparing to unpack .../51-libevent-2.1-7t64_2.1.12-stable-10_amd64.deb ... 92s Unpacking libevent-2.1-7t64:amd64 (2.1.12-stable-10) ... 93s Selecting previously unselected package libunbound8:amd64. 93s 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libtasn1-6-dev:amd64. 93s Preparing to unpack .../57-libtasn1-6-dev_4.19.0-3build1_amd64.deb ... 93s Unpacking libtasn1-6-dev:amd64 (4.19.0-3build1) ... 93s Selecting previously unselected package libgmpxx4ldbl:amd64. 93s Preparing to unpack .../58-libgmpxx4ldbl_2%3a6.3.0+dfsg-2ubuntu7_amd64.deb ... 93s Unpacking libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-2ubuntu7) ... 93s Selecting previously unselected package libgmp-dev:amd64. 93s Preparing to unpack .../59-libgmp-dev_2%3a6.3.0+dfsg-2ubuntu7_amd64.deb ... 93s Unpacking libgmp-dev:amd64 (2:6.3.0+dfsg-2ubuntu7) ... 93s Selecting previously unselected package nettle-dev:amd64. 93s Preparing to unpack .../60-nettle-dev_3.10-1_amd64.deb ... 93s Unpacking nettle-dev:amd64 (3.10-1) ... 93s Selecting previously unselected package libgnutls28-dev:amd64. 93s Preparing to unpack .../61-libgnutls28-dev_3.8.6-2ubuntu1_amd64.deb ... 93s Unpacking libgnutls28-dev:amd64 (3.8.6-2ubuntu1) ... 93s Selecting previously unselected package libpkgconf3:amd64. 93s 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Setting up libhtscodecs2:amd64 (1.6.0-1build1) ... 94s Setting up dh-python (6.20240824) ... 95s Setting up libgnutls-openssl27t64:amd64 (3.8.6-2ubuntu1) ... 95s Setting up python3-iniconfig (1.1.1-2) ... 95s Setting up libzstd-dev:amd64 (1.5.6+dfsg-1) ... 95s Setting up libarchive-zip-perl (1.68-1) ... 95s Setting up libdebhelper-perl (13.20ubuntu1) ... 95s Setting up libdeflate0:amd64 (1.21-1) ... 95s Setting up m4 (1.4.19-4build1) ... 95s Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10) ... 95s Setting up python3-all (3.12.6-0ubuntu1) ... 95s Setting up libgomp1:amd64 (14.2.0-7ubuntu1) ... 95s Setting up libpsl-dev:amd64 (0.21.2-1.1build1) ... 95s Setting up autotools-dev (20220109.1) ... 95s Setting up python3-packaging (24.1-1) ... 95s Setting up libunbound8:amd64 (1.20.0-1ubuntu2.1) ... 95s Setting up libpkgconf3:amd64 (1.8.1-3ubuntu1) ... 95s Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-2ubuntu7) ... 95s Setting up libexpat1-dev:amd64 (2.6.2-2) ... 95s Setting up libgnutls-dane0t64:amd64 (3.8.6-2ubuntu1) ... 95s Setting up libquadmath0:amd64 (14.2.0-7ubuntu1) ... 95s Setting up libssl-dev:amd64 (3.3.1-2ubuntu2) ... 95s Setting up libmpc3:amd64 (1.3.1-1build2) ... 95s Setting up cython3 (3.0.11+dfsg-1ubuntu1) ... 96s Setting up autopoint (0.22.5-2) ... 96s Setting up pkgconf-bin (1.8.1-3ubuntu1) ... 96s Setting up libidn2-dev:amd64 (2.3.7-2build2) ... 96s Setting up autoconf (2.72-3) ... 96s Setting up python3-pluggy (1.5.0-1) ... 96s Setting up liblzma-dev:amd64 (5.6.2-2) ... 96s Setting up libubsan1:amd64 (14.2.0-7ubuntu1) ... 96s Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 96s Setting up dwz (0.15-1build6) ... 96s Setting up libhwasan0:amd64 (14.2.0-7ubuntu1) ... 96s Setting up libasan8:amd64 (14.2.0-7ubuntu1) ... 96s Setting up debugedit (1:5.1-1) ... 96s Setting up libhts3t64:amd64 (1.20+ds-2) ... 96s Setting up libtsan2:amd64 (14.2.0-7ubuntu1) ... 96s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 96s Setting up libisl23:amd64 (0.27-1) ... 96s Setting up libtasn1-6-dev:amd64 (4.19.0-3build1) ... 96s Setting up libdeflate-dev:amd64 (1.21-1) ... 96s Setting up tabix (1.20+ds-2) ... 96s Setting up libcc1-0:amd64 (14.2.0-7ubuntu1) ... 96s Setting up libbrotli-dev:amd64 (1.1.0-2build2) ... 96s Setting up liblsan0:amd64 (14.2.0-7ubuntu1) ... 96s Setting up libp11-kit-dev:amd64 (0.25.5-2ubuntu1) ... 96s Setting up libitm1:amd64 (14.2.0-7ubuntu1) ... 96s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 96s Setting up libbz2-dev:amd64 (1.0.8-6) ... 96s Setting up automake (1:1.16.5-1.3ubuntu1) ... 96s update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode 96s Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... 96s Setting up gettext (0.22.5-2) ... 96s Setting up python3-pysam (0.22.1+ds-2) ... 96s Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-2ubuntu7) ... 96s Setting up nettle-dev:amd64 (3.10-1) ... 96s Setting up python3-pytest (8.3.2-1) ... 96s Setting up bcftools (1.20-2) ... 96s Setting up libpython3.12-dev:amd64 (3.12.7-1) ... 96s Setting up pkgconf:amd64 (1.8.1-3ubuntu1) ... 96s Setting up samtools (1.20-3) ... 96s Setting up intltool-debian (0.35.0+20060710.6) ... 96s Setting up python3.12-dev (3.12.7-1) ... 96s Setting up cpp-14-x86-64-linux-gnu (14.2.0-7ubuntu1) ... 96s Setting up libssh2-1-dev:amd64 (1.11.0-7) ... 96s Setting up libjs-sphinxdoc (7.4.7-3) ... 96s Setting up cpp-14 (14.2.0-7ubuntu1) ... 96s Setting up dh-strip-nondeterminism (1.14.0-1) ... 96s Setting up libgcc-14-dev:amd64 (14.2.0-7ubuntu1) ... 96s Setting up libstdc++-14-dev:amd64 (14.2.0-7ubuntu1) ... 96s Setting up cpp-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 96s Setting up libgnutls28-dev:amd64 (3.8.6-2ubuntu1) ... 96s Setting up libnghttp2-dev:amd64 (1.62.1-2) ... 96s Setting up libpython3-dev:amd64 (3.12.6-0ubuntu1) ... 96s Setting up po-debconf (1.0.21+nmu1) ... 96s Setting up libpython3-all-dev:amd64 (3.12.6-0ubuntu1) ... 96s Setting up python3-dev (3.12.6-0ubuntu1) ... 96s Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2build7) ... 96s Setting up cpp (4:14.1.0-2ubuntu1) ... 96s Setting up gcc-14-x86-64-linux-gnu (14.2.0-7ubuntu1) ... 96s Setting up python3-all-dev (3.12.6-0ubuntu1) ... 96s Setting up gcc-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 96s Setting up libcurl4-gnutls-dev:amd64 (8.9.1-2ubuntu2) ... 96s Setting up gcc-14 (14.2.0-7ubuntu1) ... 96s Setting up g++-14-x86-64-linux-gnu (14.2.0-7ubuntu1) ... 96s Setting up g++-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 96s Setting up g++-14 (14.2.0-7ubuntu1) ... 96s Setting up libtool (2.4.7-7build1) ... 96s Setting up libhts-dev:amd64 (1.20+ds-2) ... 96s Setting up gcc (4:14.1.0-2ubuntu1) ... 96s Setting up dh-autoreconf (20) ... 96s Setting up g++ (4:14.1.0-2ubuntu1) ... 96s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 96s Setting up build-essential (12.10ubuntu1) ... 96s Setting up debhelper (13.20ubuntu1) ... 96s Setting up autopkgtest-satdep (0) ... 96s Processing triggers for man-db (2.12.1-3) ... 98s Processing triggers for install-info (7.1.1-1) ... 98s Processing triggers for libc-bin (2.40-1ubuntu3) ... 101s (Reading database ... 80068 files and directories currently installed.) 101s Removing autopkgtest-satdep (0) ... 101s autopkgtest [12:45:06]: test command1: export HOME=$PWD && make -C tests/pysam_data && make -C tests/cbcf_data && pytest-3 101s autopkgtest [12:45:06]: test command1: [----------------------- 101s make: Entering directory '/tmp/autopkgtest.mg0YZ7/build.ZoQ/src/tests/pysam_data' 101s samtools faidx ex1.fa 101s samtools view --no-PG -bo ex1.bam -t ex1.fa.fai ex1.sam.gz 101s samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz 101s [mpileup] 1 samples in 1 input files 101s gunzip < ex1.sam.gz > ex1.sam 101s samtools index ex1.bam 101s samtools view --no-PG -h ex1.bam | gzip > ex2.sam.gz 101s gunzip < ex2.sam.gz > ex2.sam 101s samtools view --no-PG -bo ex2.bam ex2.sam 101s samtools index ex2.bam 101s samtools calmd --no-PG --output-fmt BAM ex2.bam ex1.fa > with_md.sam.gz 101s [bam_fillmd1] different NM for read 'EAS139_11:7:46:695:738': 3 -> 8 101s [bam_fillmd1] different NM for read 'EAS218_4:1:48:9:409': 0 -> 5 101s [bam_fillmd1] different NM for read 'B7_591:7:200:192:373': 0 -> 5 101s [bam_fillmd1] different NM for read 'EAS56_65:1:163:846:223': 0 -> 5 101s [bam_fillmd1] different NM for read 'EAS114_30:7:283:799:560': 0 -> 5 101s [bam_fillmd1] different NM for read 'B7_595:4:84:802:737': 0 -> 4 101s [bam_fillmd1] different NM for read 'EAS51_66:5:308:400:602': 0 -> 3 101s [bam_fillmd1] different NM for read 'EAS54_81:2:285:367:932': 0 -> 3 101s [bam_fillmd1] different NM for read 'EAS114_39:1:70:147:84': 0 -> 3 101s [bam_fillmd1] different NM for read 'EAS56_53:1:124:243:35': 2 -> 5 101s [bam_fillmd1] different NM for read 'EAS1_103:2:226:302:758': 2 -> 3 101s [bam_fillmd1] different NM for read 'EAS114_28:6:175:705:982': 1 -> 0 101s [bam_fillmd1] different NM for read 'EAS51_64:4:179:389:585': 7 -> 8 101s [bam_fillmd1] different NM for read 'B7_589:1:122:337:968': 3 -> 2 101s [bam_fillmd1] different NM for read 'B7_610:4:15:805:420': 4 -> 5 101s [bam_fillmd1] different NM for read 'B7_591:2:279:124:41': 2 -> 4 101s [bam_fillmd1] different NM for read 'EAS112_32:8:89:254:332': 0 -> 1 101s [bam_fillmd1] different NM for read 'B7_597:7:103:731:697': 0 -> 2 101s [bam_fillmd1] different NM for read 'EAS139_11:2:71:83:58': 0 -> 2 101s [bam_fillmd1] different NM for read 'EAS192_3:4:63:5:870': 0 -> 2 101s [bam_fillmd1] different NM for read 'EAS139_19:2:29:1822:1881': 0 -> 2 101s [bam_fillmd1] different NM for read 'EAS188_7:3:15:568:42': 2 -> 1 101s [bam_fillmd1] different NM for read 'EAS1_95:4:176:971:874': 0 -> 1 101s [bam_fillmd1] different NM for read 'EAS1_99:1:34:649:318': 3 -> 4 101s [bam_fillmd1] different NM for read 'EAS54_65:4:61:346:384': 3 -> 4 101s [bam_fillmd1] different NM for read 'B7_597:6:20:592:496': 0 -> 1 101s [bam_fillmd1] different NM for read 'B7_597:4:38:999:463': 2 -> 1 101s [bam_fillmd1] different NM for read 'EAS114_28:5:23:944:377': 0 -> 3 101s [bam_fillmd1] different NM for read 'EAS219_1:3:90:219:528': 0 -> 3 101s [bam_fillmd1] different NM for read 'EAS1_108:5:89:942:84': 0 -> 4 101s [bam_fillmd1] different NM for read 'EAS1_108:6:159:493:275': 0 -> 5 101s [bam_fillmd1] different NM for read 'EAS139_11:1:81:1019:558': 0 -> 5 101s [bam_fillmd1] different NM for read 'EAS51_62:7:162:195:761': 0 -> 4 101s [bam_fillmd1] different NM for read 'B7_597:3:115:646:430': 0 -> 4 101s [bam_fillmd1] different NM for read 'EAS114_30:6:243:209:110': 0 -> 4 101s [bam_fillmd1] different NM for read 'EAS1_108:2:266:994:429': 0 -> 4 101s [bam_fillmd1] different NM for read 'EAS114_30:5:32:461:154': 0 -> 4 101s [bam_fillmd1] different NM for read 'EAS114_39:6:7:492:1088': 0 -> 4 101s [bam_fillmd1] different NM for read 'EAS1_95:6:174:650:125': 0 -> 4 101s [bam_fillmd1] different NM for read 'EAS56_59:6:89:457:591': 1 -> 5 101s [bam_fillmd1] different NM for read 'EAS114_39:2:38:670:564': 0 -> 4 101s [bam_fillmd1] different NM for read 'EAS188_7:4:92:693:228': 1 -> 6 101s [bam_fillmd1] different NM for read 'EAS218_1:4:61:1369:440': 0 -> 4 101s [bam_fillmd1] different NM for read 'EAS114_26:4:123:1001:580': 0 -> 4 101s [bam_fillmd1] different NM for read 'EAS114_39:4:10:1312:1558': 0 -> 4 101s [bam_fillmd1] different NM for read 'EAS220_1:8:45:178:1321': 0 -> 4 101s [bam_fillmd1] different NM for read 'EAS56_59:5:125:137:58': 0 -> 4 101s [bam_fillmd1] different NM for read 'EAS192_3:3:285:349:797': 1 -> 5 101s [bam_fillmd1] different NM for read 'EAS114_45:5:56:1757:1319': 0 -> 4 101s [bam_fillmd1] different NM for read 'B7_591:3:291:404:199': 0 -> 4 101s [bam_fillmd1] different NM for read 'EAS54_65:7:159:253:353': 0 -> 4 101s [bam_fillmd1] different NM for read 'EAS56_57:1:122:38:103': 0 -> 4 101s [bam_fillmd1] different NM for read 'EAS188_4:5:103:870:105': 0 -> 4 101s [bam_fillmd1] different NM for read 'EAS1_105:8:24:718:322': 3 -> 7 101s [bam_fillmd1] different NM for read 'EAS51_64:6:118:41:489': 0 -> 4 101s [bam_fillmd1] different NM for read 'EAS56_61:3:165:665:220': 0 -> 4 101s [bam_fillmd1] different NM for read 'EAS114_30:6:238:803:383': 0 -> 4 101s [bam_fillmd1] different NM for read 'EAS1_105:3:232:364:583': 0 -> 3 101s [bam_fillmd1] different NM for read 'B7_595:2:29:729:70': 3 -> 4 101s [bam_fillmd1] different NM for read 'EAS114_30:6:220:809:850': 4 -> 6 101s [bam_fillmd1] different NM for read 'EAS54_65:2:264:157:150': 3 -> 5 101s [bam_fillmd1] different NM for read 'B7_595:8:26:242:35': 2 -> 1 101s [bam_fillmd1] different NM for read 'B7_610:7:34:144:868': 4 -> 5 101s [bam_fillmd1] different NM for read 'B7_597:8:147:360:141': 1 -> 2 101s [bam_fillmd1] different NM for read 'EAS139_19:2:82:154:1333': 0 -> 4 101s [bam_fillmd1] different NM for read 'EAS56_63:3:41:468:459': 0 -> 3 101s [bam_fillmd1] different NM for read 'EAS1_97:4:274:287:423': 0 -> 1 101s [bam_fillmd1] different NM for read 'EAS114_30:2:303:428:326': 0 -> 1 101s [bam_fillmd1] different NM for read 'EAS54_71:8:105:854:975': 0 -> 3 101s gunzip < with_md.sam.gz > with_md.sam 101s samtools view --no-PG -bo with_md.bam with_md.sam 101s [W::bam_hdr_read] EOF marker is absent. The input is probably truncated 101s samtools index with_md.bam 101s samtools view --no-PG -bu -o uncompressed.bam ex2.sam 102s samtools view --no-PG -bo MM-chebi.bam MM-chebi.sam 102s samtools view --no-PG -bo MM-double.bam MM-double.sam 102s samtools view --no-PG -bo MM-multi.bam MM-multi.sam 102s samtools view --no-PG -bo MM-orient.bam MM-orient.sam 102s samtools view --no-PG -bo ex10.bam ex10.sam 102s samtools view --no-PG -bo ex3.bam ex3.sam 102s samtools view --no-PG -bo ex4.bam ex4.sam 102s samtools view --no-PG -bo ex5.bam ex5.sam 102s samtools view --no-PG -bo ex6.bam ex6.sam 102s samtools view --no-PG -bo ex8.bam ex8.sam 102s samtools view --no-PG -bo ex9_fail.bam ex9_fail.sam 102s samtools view --no-PG -bo ex9_nofail.bam ex9_nofail.sam 102s samtools view --no-PG -bo ex_spliced.bam ex_spliced.sam 102s samtools view --no-PG -bo example_aligned_pairs.bam example_aligned_pairs.sam 102s samtools view --no-PG -bo example_btag.bam example_btag.sam 102s samtools view --no-PG -bo example_dash_in_chr.bam example_dash_in_chr.sam 102s samtools view --no-PG -bo example_empty_header.bam example_empty_header.sam 102s samtools view --no-PG -bo example_empty_with_header.bam example_empty_with_header.sam 102s samtools view --no-PG -bo example_reverse_complement.bam example_reverse_complement.sam 102s touch tmp.list 102s samtools view --no-PG -bo example_unmapped_reads_no_sq.bam -t tmp.list example_unmapped_reads_no_sq.sam 102s rm -f tmp.list 102s samtools view --no-PG -bo issue100.bam issue100.sam 102s samtools view --no-PG -bo rg_with_tab.bam rg_with_tab.sam 102s samtools view --no-PG -bo softclip.bam softclip.sam 102s samtools view --no-PG -bo tag_bug.bam tag_bug.sam 102s samtools view --no-PG -bo test_mapped_unmapped.bam test_mapped_unmapped.sam 102s samtools view --no-PG -bo test_query_position.bam test_query_position.sam 102s samtools view --no-PG -bo test_unaligned.bam test_unaligned.sam 102s samtools index MM-chebi.bam 102s samtools index MM-double.bam 102s samtools index MM-multi.bam 102s samtools index MM-orient.bam 102s samtools index ex10.bam 102s samtools index ex3.bam 102s samtools index ex4.bam 102s samtools index ex5.bam 102s samtools index ex6.bam 102s samtools index ex8.bam 102s samtools index ex9_fail.bam 102s samtools index ex9_nofail.bam 102s samtools index ex_spliced.bam 102s samtools index example_aligned_pairs.bam 102s samtools index example_btag.bam 102s samtools index example_dash_in_chr.bam 102s samtools index example_empty_header.bam 102s samtools index example_empty_with_header.bam 102s samtools index example_reverse_complement.bam 102s samtools index example_unmapped_reads_no_sq.bam 102s samtools index issue100.bam 102s samtools index rg_with_tab.bam 102s samtools index softclip.bam 102s samtools index tag_bug.bam 102s samtools index test_mapped_unmapped.bam 102s samtools index test_query_position.bam 102s samtools index test_unaligned.bam 102s samtools view --no-PG -Co ex1.cram -T ex1.fa ex1.sam 102s samtools view --no-PG -Co ex2.cram -T ex1.fa ex2.sam 102s samtools view --no-PG -Co ex3.cram -T ex1.fa ex3.sam 102s samtools index ex1.cram 102s samtools index ex2.cram 102s samtools index ex3.cram 102s cp ex1.bam example_bai.bam 102s samtools index example_bai.bam 102s mv example_bai.bam.bai example_bai.bai 102s dd if=ex2.bam of=ex2_truncated.bam bs=$((`wc -c < ex2.bam`-512)) count=1 102s 1+0 records in 102s 1+0 records out 102s 122288 bytes (122 kB, 119 KiB) copied, 0.000229765 s, 532 MB/s 102s (bgzip -d < ex2.bam; printf '\37\0\0\0\1\0\0\0') | bgzip > ex2_corrupt.bam 102s grep "^@" ex2.sam | samtools view --no-PG -bo empty.bam - 102s samtools index empty.bam 102s cp ex1.bam explicit_index.bam 102s cp ex1.cram explicit_index.cram 102s gzip < faidx_empty_seq.fq > faidx_empty_seq.fq.gz 102s bgzip < ex1.fa > ex1.fa.gz 102s samtools faidx ex1.fa.gz 102s cp ex1.bam ex1_csi.bam 102s samtools index -c ex1_csi.bam 102s touch all.stamp 102s rm with_md.sam 102s make: Leaving directory '/tmp/autopkgtest.mg0YZ7/build.ZoQ/src/tests/pysam_data' 102s make: Entering directory '/tmp/autopkgtest.mg0YZ7/build.ZoQ/src/tests/cbcf_data' 102s bgzip < example_vcf40.vcf > example_vcf40.vcf.gz 102s tabix -p vcf example_vcf40.vcf.gz # create tbi index 102s bcftools index example_vcf40.vcf.gz # create csi index 102s bgzip < example_vcf42.vcf > example_vcf42.vcf.gz 102s tabix -p vcf example_vcf42.vcf.gz # create tbi index 102s bcftools index example_vcf42.vcf.gz # create csi index 102s bgzip < example_vcf42_only_header.vcf > example_vcf42_only_header.vcf.gz 102s tabix -p vcf example_vcf42_only_header.vcf.gz # create tbi index 102s bcftools index example_vcf42_only_header.vcf.gz # create csi index 102s bgzip < example_vcf42_withcontigs.vcf > example_vcf42_withcontigs.vcf.gz 102s tabix -p vcf example_vcf42_withcontigs.vcf.gz # create tbi index 102s bcftools index example_vcf42_withcontigs.vcf.gz # create csi index 102s bgzip < example_vcf43.vcf > example_vcf43.vcf.gz 102s tabix -p vcf example_vcf43.vcf.gz # create tbi index 102s bcftools index example_vcf43.vcf.gz # create csi index 102s bgzip < example_vcf43_with_utf8.vcf > example_vcf43_with_utf8.vcf.gz 102s tabix -p vcf example_vcf43_with_utf8.vcf.gz # create tbi index 102s bcftools index example_vcf43_with_utf8.vcf.gz # create csi index 102s bgzip < gnomad.vcf > gnomad.vcf.gz 102s tabix -p vcf gnomad.vcf.gz # create tbi index 102s bcftools index gnomad.vcf.gz # create csi index 102s bgzip < gnomad_fixed.vcf > gnomad_fixed.vcf.gz 102s tabix -p vcf gnomad_fixed.vcf.gz # create tbi index 102s bcftools index gnomad_fixed.vcf.gz # create csi index 102s bgzip < missing_genotypes.vcf > missing_genotypes.vcf.gz 102s tabix -p vcf missing_genotypes.vcf.gz # create tbi index 102s bcftools index missing_genotypes.vcf.gz # create csi index 102s bcftools view -O b example_vcf40.vcf.gz -o example_vcf40.bcf 102s bcftools index example_vcf40.bcf 102s bcftools view -O b example_vcf42.vcf.gz -o example_vcf42.bcf 102s bcftools index example_vcf42.bcf 102s bcftools view -O b example_vcf42_only_header.vcf.gz -o example_vcf42_only_header.bcf 102s bcftools index example_vcf42_only_header.bcf 102s bcftools view -O b example_vcf42_withcontigs.vcf.gz -o example_vcf42_withcontigs.bcf 102s bcftools index example_vcf42_withcontigs.bcf 102s bcftools view -O b example_vcf43.vcf.gz -o example_vcf43.bcf 102s bcftools index example_vcf43.bcf 102s bcftools view -O b example_vcf43_with_utf8.vcf.gz -o example_vcf43_with_utf8.bcf 102s bcftools index example_vcf43_with_utf8.bcf 102s bcftools view -O b gnomad.vcf.gz -o gnomad.bcf 102s bcftools index gnomad.bcf 102s bcftools view -O b gnomad_fixed.vcf.gz -o gnomad_fixed.bcf 102s [W::bcf_hdr_check_sanity] PL should be declared as Number=G 102s bcftools index gnomad_fixed.bcf 102s [W::bcf_hdr_check_sanity] PL should be declared as Number=G 102s bcftools view -O b missing_genotypes.vcf.gz -o missing_genotypes.bcf 102s bcftools index missing_genotypes.bcf 102s touch all.stamp 102s make: Leaving directory '/tmp/autopkgtest.mg0YZ7/build.ZoQ/src/tests/cbcf_data' 102s ============================= test session starts ============================== 102s platform linux -- Python 3.12.7, pytest-8.3.2, pluggy-1.5.0 -- /usr/bin/python3 102s cachedir: .pytest_cache 102s rootdir: /tmp/autopkgtest.mg0YZ7/build.ZoQ/src 102s configfile: setup.cfg 102s testpaths: pysam, tests 102s plugins: typeguard-4.3.0 103s collecting ... collected 951 items 103s 103s tests/AlignedSegment_test.py::TestAlignedSegment::testBlocks PASSED 103s tests/AlignedSegment_test.py::TestAlignedSegment::testCompare PASSED 103s tests/AlignedSegment_test.py::TestAlignedSegment::testEmpty PASSED 103s tests/AlignedSegment_test.py::TestAlignedSegment::testFullReferencePositions PASSED 103s tests/AlignedSegment_test.py::TestAlignedSegment::testHashing PASSED 103s tests/AlignedSegment_test.py::TestAlignedSegment::testLargeRead PASSED 103s tests/AlignedSegment_test.py::TestAlignedSegment::testNoSequence PASSED 103s tests/AlignedSegment_test.py::TestAlignedSegment::testPositions PASSED 103s tests/AlignedSegment_test.py::TestAlignedSegment::testSettingTagInEmptyRead PASSED 103s tests/AlignedSegment_test.py::TestAlignedSegment::testStrOfEmptyRead PASSED 103s tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate PASSED 103s tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate2 PASSED 103s tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateQual PASSED 103s tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateTlen PASSED 103s tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_mapped_reads_are_updated PASSED 103s tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_unmapped_reads_ignore_length PASSED 103s tests/AlignedSegment_test.py::TestAlignedSegment::test_equivalence_matches_only_and_with_seq PASSED 103s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs PASSED 103s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_1character_md PASSED 103s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_bad_type_md PASSED 103s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_hard_clipping PASSED 103s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_lowercase_md PASSED 103s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_match_mismatch PASSED 103s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding PASSED 103s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding_with_seq PASSED 103s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip PASSED 103s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip_reference PASSED 103s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_soft_clipping PASSED 103s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_uppercase_md PASSED 103s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_with_malformed_MD_tag PASSED 103s tests/AlignedSegment_test.py::TestAlignedSegment::test_header_accessible PASSED 103s tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_query_length PASSED 103s tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_read_length PASSED 103s tests/AlignedSegment_test.py::TestAlignedSegment::test_query_length_is_limited PASSED 103s tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_asterisk PASSED 103s tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_chromosome PASSED 103s tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_none PASSED 103s tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_not_be_set_to_unknown_chromosome PASSED 103s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_chromosome PASSED 103s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing PASSED 103s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing_without_header PASSED 103s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_without_header PASSED 103s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_not_be_set_to_unknown_chromosome PASSED 103s tests/AlignedSegment_test.py::TestTidMapping::test_unmapped_tid_is_asterisk_in_output PASSED 103s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_asterisk PASSED 103s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_chromosome PASSED 103s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_none PASSED 103s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_not_be_set_to_unknown_chromosome PASSED 103s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_chromosome PASSED 103s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_equal PASSED 103s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing PASSED 103s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing_without_header PASSED 103s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_without_header PASSED 103s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_not_be_set_to_unknown_chromosome PASSED 103s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_unmapped_tid_is_asterisk_in_output PASSED 103s tests/AlignedSegment_test.py::TestCigar::testCigar PASSED 103s tests/AlignedSegment_test.py::TestCigar::testCigarString PASSED 103s tests/AlignedSegment_test.py::TestCigarStats::testStats PASSED 103s tests/AlignedSegment_test.py::TestAlignedPairs::testReferenceBases PASSED 103s tests/AlignedSegment_test.py::TestBaseModifications::testChebi PASSED 103s tests/AlignedSegment_test.py::TestBaseModifications::testDouble PASSED 103s tests/AlignedSegment_test.py::TestBaseModifications::testMulti PASSED 103s tests/AlignedSegment_test.py::TestBaseModifications::testOrient PASSED 103s tests/AlignedSegment_test.py::TestTags::testAddTags PASSED 103s tests/AlignedSegment_test.py::TestTags::testAddTagsType PASSED 103s tests/AlignedSegment_test.py::TestTags::testArrayTags PASSED 103s tests/AlignedSegment_test.py::TestTags::testEmptyTag PASSED 103s tests/AlignedSegment_test.py::TestTags::testLongTags PASSED 103s tests/AlignedSegment_test.py::TestTags::testMDTagComplex PASSED 103s tests/AlignedSegment_test.py::TestTags::testMDTagDeletions PASSED 103s tests/AlignedSegment_test.py::TestTags::testMDTagInsertions PASSED 103s tests/AlignedSegment_test.py::TestTags::testMDTagMatchOnly PASSED 103s tests/AlignedSegment_test.py::TestTags::testMDTagRefSkipping PASSED 103s tests/AlignedSegment_test.py::TestTags::testMDTagSoftClipping PASSED 103s tests/AlignedSegment_test.py::TestTags::testMissingTag PASSED 103s tests/AlignedSegment_test.py::TestTags::testNegativeIntegers PASSED 103s tests/AlignedSegment_test.py::TestTags::testNegativeIntegersWrittenToFile PASSED 103s tests/AlignedSegment_test.py::TestTags::testSetTag PASSED 103s tests/AlignedSegment_test.py::TestTags::testTagParsing PASSED 103s tests/AlignedSegment_test.py::TestTags::testTagsUpdatingFloat PASSED 103s tests/AlignedSegment_test.py::TestCopy::testCopy PASSED 103s tests/AlignedSegment_test.py::TestCopy::testDeepCopy PASSED 103s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_A PASSED 103s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_C PASSED 103s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_H PASSED 103s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_I PASSED 103s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_S PASSED 103s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_a PASSED 103s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_automated_type_detection PASSED 103s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_c PASSED 103s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_d PASSED 103s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_f PASSED 103s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_i PASSED 103s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_s PASSED 103s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_A PASSED 103s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_C PASSED 103s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_H PASSED 103s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_I PASSED 103s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_S PASSED 103s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_a PASSED 103s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_automated_type_detection PASSED 103s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_c PASSED 103s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_d PASSED 103s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_f PASSED 103s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_i PASSED 103s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_s PASSED 103s tests/AlignedSegment_test.py::TestEnums::test_cigar_enums_are_defined PASSED 103s tests/AlignedSegment_test.py::TestEnums::test_sam_flags_are_defined PASSED 103s tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_constructed_without_header PASSED 103s tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_written_to_file PASSED 103s tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_id_can_be_set PASSED 103s tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_name_is_not_available PASSED 103s tests/AlignedSegment_test.py::TestForwardStrandValues::test_qualities_are_complemented PASSED 103s tests/AlignedSegment_test.py::TestForwardStrandValues::test_sequence_is_complemented PASSED 103s tests/AlignedSegment_test.py::TestExportImport::test_dict_export PASSED 103s tests/AlignedSegment_test.py::TestExportImport::test_string_export PASSED 103s tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_with_tags PASSED 103s tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_without_tags PASSED 103s tests/AlignedSegment_test.py::TestExportImport::test_to_string_without_alignment_file PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_dict PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_header PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references_without_text PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_text PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_access_works PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_contains_works PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_get_works PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_keys_works PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_len_works PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_setting_raises_error PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_values_works PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_header_content_is_as_expected PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_name_mapping PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_text_access_works PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_contains_works PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_get_works PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_keys_works PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_len_works PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_setting_raises_error PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_values_works PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_name_mapping PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_text_access_works PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_contains_works PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_get_works PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_keys_works PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_len_works PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_setting_raises_error PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_values_works PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_name_mapping PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_text_access_works PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM /tmp/autopkgtest.mg0YZ7/build.ZoQ/src/tests/tmp/pysamtests_tmp_check_read_write_flx73mcf 103s PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM [E::cram_index_load] Could not retrieve index file for '/tmp/autopkgtest.mg0YZ7/build.ZoQ/src/tests/tmp/pysamtests_tmp_check_read_write_dbzu6mrh' 103s /tmp/autopkgtest.mg0YZ7/build.ZoQ/src/tests/tmp/pysamtests_tmp_check_read_write_dbzu6mrh 103s PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /tmp/autopkgtest.mg0YZ7/build.ZoQ/src/tests/tmp/pysamtests_tmp_check_read_write_mng62h_z 103s PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM /tmp/autopkgtest.mg0YZ7/build.ZoQ/src/tests/tmp/pysamtests_tmp_check_read_write_c011jm6t 103s PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM [W::sanitise_SQ_lines] Header @SQ length mismatch for ref chr1, 2147483647 vs 1575 103s [E::cram_index_load] Could not retrieve index file for '/tmp/autopkgtest.mg0YZ7/build.ZoQ/src/tests/tmp/pysamtests_tmp_check_read_write_0ws37o60' 103s /tmp/autopkgtest.mg0YZ7/build.ZoQ/src/tests/tmp/pysamtests_tmp_check_read_write_0ws37o60 103s PASSED 103s tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM /tmp/autopkgtest.mg0YZ7/build.ZoQ/src/tests/tmp/pysamtests_tmp_check_read_write_8n4p18j8 103s PASSED 103s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_all_stepper PASSED 103s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_ignore_overlaps PASSED 103s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper PASSED 104s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_base_quality_threshold PASSED 104s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_ignore_orphans PASSED 104s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_mapping_quality_threshold PASSED 104s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_redo_baq PASSED 104s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_all_stepper PASSED 104s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_ignore_overlaps PASSED 104s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper PASSED 104s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_base_quality_threshold PASSED 104s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_ignore_orphans PASSED 104s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_mapping_quality_threshold PASSED 104s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_redo_baq PASSED 104s tests/AlignmentFilePileup_test.py::TestPileupQueryPosition::testPileup PASSED 104s tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope SKIPPED 104s tests/AlignmentFilePileup_test.py::TestPileupObjects::testPileupColumn PASSED 104s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testInverse PASSED 104s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateAll PASSED 104s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIteratePerContig PASSED 104s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateRanges PASSED 104s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateTruncate PASSED 104s tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testAccessOnClosedIterator PASSED 104s tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStart PASSED 104s tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStr PASSED 104s tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testTruncate PASSED 104s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_depths_are_equal PASSED 104s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_mapping_qualities_are_equal PASSED 104s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_with_reference_are_equal PASSED 104s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_without_reference_are_equal PASSED 104s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_are_equal PASSED 105s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_from_pileups_are_equal PASSED 105s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARQueryLength PASSED 105s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigar PASSED 105s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigarstring PASSED 105s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARflag PASSED 105s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmapq PASSED 105s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmpos PASSED 105s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmrnm PASSED 105s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARpos PASSED 105s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqname PASSED 105s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqqual PASSED 105s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqual PASSED 105s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARquery PASSED 105s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARrname PASSED 105s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARseq PASSED 105s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testOpt PASSED 105s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPairedBools PASSED 105s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPresentOptionalFields PASSED 105s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testTags PASSED 105s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARQueryLength PASSED 105s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigar PASSED 105s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigarstring PASSED 105s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARflag PASSED 105s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmapq PASSED 105s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmpos PASSED 105s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmrnm PASSED 105s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARpos PASSED 105s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqname PASSED 105s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqqual PASSED 105s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqual PASSED 105s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARquery PASSED 105s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARrname PASSED 105s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARseq PASSED 105s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testOpt PASSED 105s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPairedBools PASSED 105s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPresentOptionalFields PASSED 105s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testTags PASSED 105s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARQueryLength PASSED 105s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigar PASSED 105s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigarstring PASSED 105s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARflag PASSED 105s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmapq PASSED 105s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmpos PASSED 105s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmrnm PASSED 105s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARpos PASSED 106s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqname PASSED 106s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqqual PASSED 106s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqual PASSED 107s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARquery PASSED 107s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARrname PASSED 107s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARseq PASSED 107s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testOpt PASSED 108s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPairedBools PASSED 108s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPresentOptionalFields PASSED 113s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testTags PASSED 113s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARQueryLength PASSED 113s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigar PASSED 113s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigarstring PASSED 113s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARflag PASSED 113s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmapq PASSED 113s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmpos PASSED 113s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmrnm PASSED 113s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARpos PASSED 113s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqname PASSED 113s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqqual PASSED 113s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqual PASSED 113s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARquery PASSED 113s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARrname PASSED 113s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARseq PASSED 113s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testOpt PASSED 113s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPairedBools PASSED 113s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPresentOptionalFields PASSED 113s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testTags PASSED 113s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARQueryLength PASSED 113s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigar PASSED 113s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigarstring PASSED 113s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARflag PASSED 113s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmapq PASSED 113s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmpos PASSED 113s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmrnm PASSED 114s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARpos PASSED 114s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqname PASSED 114s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqqual PASSED 115s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqual PASSED 115s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARquery PASSED 115s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARrname PASSED 115s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARseq PASSED 116s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testOpt PASSED 116s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPairedBools PASSED 116s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPresentOptionalFields PASSED 117s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testTags PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARQueryLength PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigar PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigarstring PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARflag PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmapq PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmpos PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmrnm PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARpos PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqname PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqqual PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqual PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARquery PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARrname PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARseq PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testOpt PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPairedBools PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPresentOptionalFields PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testTags PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARQueryLength PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigar PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigarstring PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARflag PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmapq PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmpos PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmrnm PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARpos PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqname PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqqual PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqual PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARquery PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARrname PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARseq PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testOpt PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPairedBools PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPresentOptionalFields PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testTags PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARQueryLength PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigar PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigarstring PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARflag PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmapq PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmpos PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmrnm PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARpos PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqname PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqqual PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqual PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARquery PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARrname PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARseq PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testOpt PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPairedBools PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPresentOptionalFields PASSED 117s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testTags PASSED 117s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARQueryLength PASSED 117s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigar PASSED 117s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigarstring PASSED 117s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARflag PASSED 117s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmapq PASSED 117s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmpos PASSED 117s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmrnm PASSED 117s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARpos PASSED 117s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqname PASSED 117s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqqual PASSED 117s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqual PASSED 117s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARquery PASSED 117s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARrname PASSED 117s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARseq PASSED 117s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testOpt PASSED 117s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPairedBools PASSED 117s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPresentOptionalFields PASSED 117s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testTags PASSED 117s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARQueryLength PASSED 117s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigar PASSED 117s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigarstring PASSED 117s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARflag PASSED 117s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmapq PASSED 117s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmpos PASSED 117s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmrnm PASSED 117s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARpos PASSED 117s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqname PASSED 117s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqqual PASSED 117s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqual PASSED 117s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARquery PASSED 117s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARrname PASSED 117s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARseq PASSED 117s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testOpt PASSED 117s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPairedBools PASSED 117s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPresentOptionalFields PASSED 117s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testTags PASSED 117s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARQueryLength PASSED 117s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigar PASSED 118s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigarstring PASSED 118s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARflag PASSED 118s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmapq PASSED 118s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmpos PASSED 118s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmrnm PASSED 118s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARpos PASSED 119s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqname PASSED 119s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqqual PASSED 119s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqual PASSED 120s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARquery PASSED 120s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARrname PASSED 120s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARseq PASSED 120s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testOpt PASSED 121s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPairedBools PASSED 121s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPresentOptionalFields PASSED 121s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testTags PASSED 121s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARQueryLength PASSED 121s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigar PASSED 122s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigarstring PASSED 122s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARflag PASSED 122s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmapq PASSED 123s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmpos PASSED 123s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmrnm PASSED 123s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARpos PASSED 124s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqname PASSED 124s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqqual PASSED 124s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqual PASSED 124s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARquery PASSED 124s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARrname PASSED 125s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARseq PASSED 125s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testOpt PASSED 125s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPairedBools PASSED 125s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPresentOptionalFields PASSED 125s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testTags PASSED 125s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARQueryLength PASSED 125s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigar PASSED 125s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigarstring PASSED 125s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARflag PASSED 125s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmapq PASSED 125s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmpos PASSED 125s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmrnm PASSED 125s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARpos PASSED 125s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqname PASSED 125s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqqual PASSED 125s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqual PASSED 125s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARquery PASSED 125s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARrname PASSED 125s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARseq PASSED 125s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testOpt PASSED 125s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPairedBools PASSED 125s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPresentOptionalFields PASSED 125s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testRaises PASSED 125s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testTags PASSED 126s tests/AlignmentFile_test.py::TestIO::testBAM2BAM PASSED 126s tests/AlignmentFile_test.py::TestIO::testBAM2SAM PASSED 126s tests/AlignmentFile_test.py::TestIO::testBAMWithCSIIndex PASSED 126s tests/AlignmentFile_test.py::TestIO::testBAMWithShortBAI PASSED 126s tests/AlignmentFile_test.py::TestIO::testBAMWithoutAlignedSegments PASSED 126s tests/AlignmentFile_test.py::TestIO::testCRAM2BAM PASSED 127s tests/AlignmentFile_test.py::TestIO::testCRAM2CRAM PASSED 127s tests/AlignmentFile_test.py::TestIO::testCRAM2SAM PASSED 127s tests/AlignmentFile_test.py::TestIO::testEmptyBAM PASSED 127s tests/AlignmentFile_test.py::TestIO::testEmptyWithHeaderBAM PASSED 127s tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFile PASSED 127s tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject PASSED 127s tests/AlignmentFile_test.py::TestIO::testHead PASSED 127s tests/AlignmentFile_test.py::TestIO::testOpenFromFilename PASSED 127s tests/AlignmentFile_test.py::TestIO::testReadBamWithoutTargetNames PASSED 127s tests/AlignmentFile_test.py::TestIO::testReadSamWithoutTargetNames PASSED 127s tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex PASSED 127s tests/AlignmentFile_test.py::TestIO::testSAM2BAM PASSED 128s tests/AlignmentFile_test.py::TestIO::testSAM2CRAM PASSED 128s tests/AlignmentFile_test.py::TestIO::testSAM2SAM PASSED 128s tests/AlignmentFile_test.py::TestIO::testSAM2SAMWithoutHeader PASSED 128s tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile PASSED 128s tests/AlignmentFile_test.py::TestIO::test_accessing_attributes_in_closed_file_raises_errors PASSED 128s tests/AlignmentFile_test.py::TestIO::test_fail_read_sam_without_header PASSED 128s tests/AlignmentFile_test.py::TestIO::test_fail_when_reading_unformatted_files PASSED 128s tests/AlignmentFile_test.py::TestIO::test_fetch_by_tid PASSED 128s tests/AlignmentFile_test.py::TestIO::test_header_available_after_closing_file PASSED 128s tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_with_header_without_header_check PASSED 128s tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_without_header_with_refs PASSED 128s tests/AlignmentFile_test.py::TestIO::test_reference_name_available_after_closing_file PASSED 128s tests/AlignmentFile_test.py::TestIO::test_write_bam_to_unknown_path_fails PASSED 128s tests/AlignmentFile_test.py::TestAutoDetect::testBAM [E::hts_open_format] Failed to open file "missing_directory/new_file.bam" : No such file or directory 128s PASSED 128s tests/AlignmentFile_test.py::TestAutoDetect::testCRAM PASSED 128s tests/AlignmentFile_test.py::TestAutoDetect::testSAM PASSED 128s tests/AlignmentFile_test.py::TestIteratorRowBAM::testIteratePerContig PASSED 129s tests/AlignmentFile_test.py::TestIteratorRowBAM::testIterateRanges PASSED 129s tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate PASSED 129s tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIteratePerContig PASSED 138s tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIterateRanges PASSED 139s tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIteratePerContig PASSED 147s tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIterateRanges PASSED 147s tests/AlignmentFile_test.py::TestFloatTagBug::testFloatTagBug PASSED 147s tests/AlignmentFile_test.py::TestLargeFieldBug::testLargeFileBug PASSED 147s tests/AlignmentFile_test.py::TestClipping::testClipping PASSED 147s tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_bam_with_until_eof_reads_unmapped_reads PASSED 147s tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_sam_with_until_eof_reads_unmapped_reads PASSED 147s tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads PASSED 147s tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads_by_contig PASSED 147s tests/AlignmentFile_test.py::TestContextManager::testManager PASSED 147s tests/AlignmentFile_test.py::TestMultiThread::testSingleThreadEqualsMultithread PASSED 147s tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED 147s tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED 147s tests/AlignmentFile_test.py::TestExceptions::testBadContig PASSED 147s tests/AlignmentFile_test.py::TestExceptions::testMeaninglessCrap PASSED 147s tests/AlignmentFile_test.py::TestExceptions::testMissingFile [E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory 147s [E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory 147s [E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory 147s [E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory 147s PASSED 147s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangNewFormat PASSED 147s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeNewFormat PASSED 147s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeOldFormat PASSED 147s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeNewFormat PASSED 147s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeOldFormat PASSED 147s tests/AlignmentFile_test.py::TestExceptions::testZeroToZero PASSED 147s tests/AlignmentFile_test.py::TestWrongFormat::testOpenBamAsSam PASSED 147s tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsBam PASSED 147s tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsSam PASSED 147s tests/AlignmentFile_test.py::TestWrongFormat::testOpenSamAsBam PASSED 147s tests/AlignmentFile_test.py::TestRegionParsing::test_dash_in_chr PASSED 147s tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile PASSED 147s tests/AlignmentFile_test.py::TestDeNovoConstruction::test_pass_if_reads_binary_equal PASSED 147s tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader PASSED 147s tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_in_header PASSED 147s tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_with_null_bytes_in_header PASSED 147s tests/AlignmentFile_test.py::TestMismatchingHeader::testMismatchingHeader PASSED 147s tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader PASSED 147s tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2 PASSED 147s tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator [W::bam_hdr_read] EOF marker is absent. The input is probably truncated 147s [E::bgzf_read_block] Failed to read BGZF block data at offset 105176 expected 17578 bytes; hread returned 17094 147s [E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes 147s PASSED 147s tests/AlignmentFile_test.py::TestCorruptBAM::testCorruptBamIterator PASSED 147s tests/AlignmentFile_test.py::TestBTagSam::testReadTags PASSED 147s tests/AlignmentFile_test.py::TestBTagSam::testReadWriteTags PASSED 147s tests/AlignmentFile_test.py::TestBTagBam::testReadTags PASSED 147s tests/AlignmentFile_test.py::TestBTagBam::testReadWriteTags PASSED 147s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetch PASSED 147s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchUntilEOF PASSED 147s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionFalseTrue PASSED 147s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueFalse PASSED 147s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueTrue PASSED 148s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetch PASSED 148s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchUntilEOF PASSED 149s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionFalseTrue PASSED 149s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueFalse PASSED 150s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueTrue PASSED 150s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetch PASSED 151s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchUntilEOF PASSED 151s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionFalseTrue PASSED 152s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueFalse PASSED 152s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueTrue PASSED 153s tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetch PASSED 153s tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetchAll PASSED 153s tests/AlignmentFile_test.py::TestRemoteFileHTTP::testView PASSED 153s tests/AlignmentFile_test.py::TestLargeOptValues::testBAM PASSED 153s tests/AlignmentFile_test.py::TestLargeOptValues::testSAM PASSED 153s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_counts_as_expected PASSED 153s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_nofilter PASSED 153s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_quality_filter PASSED 153s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_all PASSED 153s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_callback PASSED 153s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_with_coordinates_works PASSED 153s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_without_coordinates_fails PASSED 153s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_wrong_coordinates_fails PASSED 153s tests/AlignmentFile_test.py::TestCountCoverage::test_counting_the_same_region_works PASSED 153s tests/AlignmentFile_test.py::TestFindIntrons::test_all PASSED 153s tests/AlignmentFile_test.py::TestFindIntrons::test_first PASSED 153s tests/AlignmentFile_test.py::TestFindIntrons::test_total PASSED 153s tests/AlignmentFile_test.py::TestLogging::testFail1 PASSED 153s tests/AlignmentFile_test.py::TestLogging::testNoFail1 PASSED 153s tests/AlignmentFile_test.py::TestLogging::testNoFail2 PASSED 153s tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testCount PASSED 153s tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testIndexStats PASSED 154s tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testMate PASSED 154s tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct PASSED 154s tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct_per_chromosome PASSED 154s tests/AlignmentFile_test.py::TestSamtoolsProxy::testIndex PASSED 154s tests/AlignmentFile_test.py::TestSamtoolsProxy::testSort [E::hts_open_format] Failed to open file "missing_file" : No such file or directory 154s PASSED 154s tests/AlignmentFile_test.py::TestSamtoolsProxy::testView [E::hts_open_format] Failed to open file "missing_file" : No such file or directory 154s PASSED 155s tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED 155s tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM [W::hts_idx_load3] The index file is older than the data file: /tmp/autopkgtest.mg0YZ7/build.ZoQ/src/tests/pysam_data/ex1.bam.bai 155s PASSED 155s tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexCRAM PASSED 155s tests/AlignmentFile_test.py::TestExplicitIndex::testRemoteExplicitIndexBAM PASSED 155s tests/AlignmentFile_test.py::TestVerbosity::testVerbosity PASSED 155s tests/AlignmentFile_test.py::TestSanityCheckingBAM::test_empty_read_gives_value_error PASSED 155s tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_bam PASSED 155s tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_cram SKIPPED 155s tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_sam PASSED 155s tests/StreamFiledescriptors_test.py::StreamTest::test_samtools_processing SKIPPED 155s tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing PASSED 155s tests/VariantFile_test.py::TestMissingGenotypes::testVCF PASSED 155s tests/VariantFile_test.py::TestMissingGenotypes::testVCFGZ PASSED 155s tests/VariantFile_test.py::TestMissingSamples::testVCF PASSED 155s tests/VariantFile_test.py::TestMissingSamples::testVCFGZ PASSED 155s tests/VariantFile_test.py::TestMissingSamplesFixed::testVCF [W::bcf_hdr_check_sanity] PL should be declared as Number=G 155s PASSED 155s tests/VariantFile_test.py::TestMissingSamplesFixed::testVCFGZ PASSED 155s tests/VariantFile_test.py::TestOpening::testDetectBCF PASSED 155s tests/VariantFile_test.py::TestOpening::testDetectVCF [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 155s [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) 155s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 155s PASSED 155s tests/VariantFile_test.py::TestOpening::testDetectVCFGZ PASSED 155s tests/VariantFile_test.py::TestOpening::testEmptyFileVCF PASSED 155s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFFromPath PASSED 155s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZOnlyHeader PASSED 155s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithIndex PASSED 155s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithoutIndex PASSED 155s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFOnlyHeader PASSED 155s tests/VariantFile_test.py::TestOpening::testMissingFile [E::hts_open_format] Failed to open file "missing_file.vcf" : No such file or directory 155s PASSED 155s tests/VariantFile_test.py::TestOpening::testMissingFileVCFGZ [E::hts_open_format] Failed to open file "missing_file.vcf.gz" : No such file or directory 155s PASSED 155s tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_csi_index PASSED 155s tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_prebuilt_csi PASSED 155s tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_tbi_index_will_produce_csi PASSED 155s tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_csi_index PASSED 155s tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_tbi_index PASSED 155s tests/VariantFile_test.py::TestHeader::testIterator PASSED 155s tests/VariantFile_test.py::TestHeader::testStr PASSED 155s tests/VariantFile_test.py::TestParsing::testAlleles PASSED 155s tests/VariantFile_test.py::TestParsing::testAllelesVariantTypes PASSED 155s tests/VariantFile_test.py::TestParsing::testAlt PASSED 155s tests/VariantFile_test.py::TestParsing::testChrom PASSED 155s tests/VariantFile_test.py::TestParsing::testChromFromPath PASSED 155s tests/VariantFile_test.py::TestParsing::testFilter PASSED 155s tests/VariantFile_test.py::TestParsing::testFormat PASSED 155s tests/VariantFile_test.py::TestParsing::testId PASSED 155s tests/VariantFile_test.py::TestParsing::testInfo PASSED 155s tests/VariantFile_test.py::TestParsing::testPos PASSED 155s tests/VariantFile_test.py::TestParsing::testQual PASSED 155s tests/VariantFile_test.py::TestParsing::testRef PASSED 155s tests/VariantFile_test.py::TestParsing::testSampleAlleleIndices PASSED 155s tests/VariantFile_test.py::TestParsing::testSampleAlleles PASSED 155s tests/VariantFile_test.py::TestParsing::testSampleFormats PASSED 155s tests/VariantFile_test.py::TestParsing::testStart PASSED 155s tests/VariantFile_test.py::TestParsing::testStop PASSED 155s tests/VariantFile_test.py::TestIndexFilename::testOpen PASSED 155s tests/VariantFile_test.py::TestConstructionVCFWithContigs::testBase PASSED 155s tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionFromCopy PASSED 155s tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithLines PASSED 155s tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithRecords PASSED 155s tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testBase PASSED 155s tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionFromCopy PASSED 155s tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithLines PASSED 155s tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithRecords PASSED 155s tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testBase PASSED 155s tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionFromCopy PASSED 155s tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithLines PASSED 155s tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithRecords PASSED 155s tests/VariantFile_test.py::TestSettingRecordValues::testBase PASSED 155s tests/VariantFile_test.py::TestSettingRecordValues::testGenotype [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 155s (0, 0) 155s PASSED 155s tests/VariantFile_test.py::TestSettingRecordValues::testSetQual [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 155s PASSED 155s tests/VariantFile_test.py::TestMultiThreading::testNoMultiThreadingWithIgnoreTruncation PASSED 155s tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult [E::idx_find_and_load] Could not retrieve index file for '/tmp/autopkgtest.mg0YZ7/build.ZoQ/src/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithreadResult_r1c70vqz.bcf' 155s PASSED 155s tests/VariantFile_test.py::TestSubsetting::testSubsetting PASSED 155s 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.) 155s [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) 155s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 155s [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 155s [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) 155s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 155s PASSED 155s tests/VariantFile_test.py::TestUnicode::test_record_with_unicode PASSED 155s tests/VariantRecord_test.py::test_ascii_annotation_can_be_added PASSED 155s tests/VariantRecord_test.py::test_ascii_annotation_with_variable_length_can_be_added PASSED 155s tests/VariantRecord_test.py::test_unicode_annotation_can_be_added PASSED 155s tests/VariantRecord_test.py::test_set_sample_alleles PASSED 155s tests/compile_test.py::test_bam SKIPPED (no pyximport) 155s tests/compile_test.py::test_gtf SKIPPED (no pyximport) 155s tests/faidx_test.py::TestFastaFile::testFetch PASSED 155s tests/faidx_test.py::TestFastaFile::testFetchErrors PASSED 155s tests/faidx_test.py::TestFastaFile::testLength PASSED 155s tests/faidx_test.py::TestFastaFile::testOutOfRangeAccess PASSED 155s tests/faidx_test.py::TestFastaFile::testSequenceLengths PASSED 155s tests/faidx_test.py::TestFastaFile::test_fetch_with_region_and_contig_raises_exception PASSED 155s tests/faidx_test.py::TestFastaFile::test_fetch_with_region_is_equivalent PASSED 155s tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED 155s tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_index_succeeds PASSED 155s tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_without_index_succeeds PASSED 155s tests/faidx_test.py::TestFastaFilePathIndex::test_raise_exception_if_index_is_missing PASSED 155s tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED 155s tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_index_succeeds PASSED 155s tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_without_index_succeeds PASSED 155s tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_raise_exception_if_index_is_missing PASSED 155s tests/faidx_test.py::TestFastxFileFastq::testCounts PASSED 155s tests/faidx_test.py::TestFastxFileFastq::testManager PASSED 155s tests/faidx_test.py::TestFastxFileFastq::testMissingFile PASSED 155s tests/faidx_test.py::TestFastxFileFastq::testSequence PASSED 155s tests/faidx_test.py::TestFastqFileFastq::testCounts PASSED 155s tests/faidx_test.py::TestFastqFileFastq::testManager PASSED 155s tests/faidx_test.py::TestFastqFileFastq::testMissingFile PASSED 155s tests/faidx_test.py::TestFastqFileFastq::testSequence PASSED 155s tests/faidx_test.py::TestFastxFileFasta::testCounts PASSED 155s tests/faidx_test.py::TestFastxFileFasta::testManager PASSED 155s tests/faidx_test.py::TestFastxFileFasta::testMissingFile PASSED 155s tests/faidx_test.py::TestFastxFileFasta::testSequence PASSED 155s tests/faidx_test.py::TestFastxFileFastqStream::testCounts PASSED 155s tests/faidx_test.py::TestFastxFileFastqStream::testManager PASSED 155s tests/faidx_test.py::TestFastxFileFastqStream::testMissingFile PASSED 155s tests/faidx_test.py::TestFastxFileFastqStream::testSequence PASSED 155s tests/faidx_test.py::TestFastxFileWithEmptySequence::testIteration PASSED 157s tests/faidx_test.py::TestRemoteFileFTP::testFTPView PASSED 158s tests/faidx_test.py::TestRemoteFileFTP::test_sequence_lengths_are_available PASSED 158s tests/faidx_test.py::TestFastqRecord::test_fastx_record_can_be_created_from_scratch PASSED 158s tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_None PASSED 158s tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_modified PASSED 158s tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_name_is_None PASSED 158s tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_quality_is_wrong_length PASSED 158s tests/faidx_test.py::TestFastqRecord::test_fastx_record_name_can_be_modified PASSED 158s tests/faidx_test.py::TestFastqRecord::test_fastx_record_quality_can_be_modified PASSED 158s tests/faidx_test.py::TestFastqRecord::test_fastx_record_sequence_can_be_modified PASSED 158s tests/faidx_test.py::TestFastqProxy::test_fastq_proxy_instantiation_raises_error PASSED 158s tests/linking_test.py::TestLinking::test_package_can_be_installed SKIPPED 158s tests/linking_test.py::TestLinkWithRpath::test_package_can_be_installed SKIPPED 158s tests/linking_test.py::TestLinkWithRpath::test_package_tests_pass SKIPPED 158s tests/linking_test.py::TestLinkWithoutRpath::test_package_can_be_installed SKIPPED 158s tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_fail_on_import SKIPPED 158s tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_pass_if_ld_library_path_set SKIPPED 159s tests/samtools_test.py::SamtoolsTest::testStatements PASSED 159s tests/samtools_test.py::SamtoolsTest::testUsage SKIPPED (skipping us...) 159s tests/samtools_test.py::EmptyIndexTest::testEmptyIndex PASSED 159s tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraArg PASSED 159s tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraFlag PASSED 159s tests/samtools_test.py::TestReturnType::testReturnValueData PASSED 159s tests/samtools_test.py::TestReturnType::testReturnValueString PASSED 159s tests/samtools_test.py::StdoutTest::testDoubleCalling PASSED 159s tests/samtools_test.py::StdoutTest::testSaveStdout PASSED 159s tests/samtools_test.py::StdoutTest::testWithRedirectedStdout PASSED 159s tests/samtools_test.py::StdoutTest::testWithoutRedirectedStdout PASSED 160s tests/samtools_test.py::PysamTest::testStatements PASSED 160s tests/samtools_test.py::PysamTest::testUsage SKIPPED (skipping usage...) 160s tests/tabix_test.py::TestIndexing::test_indexing_to_custom_location_works PASSED 160s tests/tabix_test.py::TestIndexing::test_indexing_with_explict_columns_works PASSED 160s tests/tabix_test.py::TestIndexing::test_indexing_with_lineskipping_works PASSED 160s tests/tabix_test.py::TestIndexing::test_indexing_with_preset_works PASSED 160s tests/tabix_test.py::TestCompression::testCompression PASSED 160s tests/tabix_test.py::TestCompression::testIndexPresetCompressed PASSED 160s tests/tabix_test.py::TestCompression::testIndexPresetUncompressed PASSED 160s tests/tabix_test.py::TestCompressionSam::testCompression PASSED 160s tests/tabix_test.py::TestCompressionSam::testIndexPresetCompressed PASSED 160s tests/tabix_test.py::TestCompressionSam::testIndexPresetUncompressed PASSED 160s tests/tabix_test.py::TestCompressionBed::testCompression PASSED 160s tests/tabix_test.py::TestCompressionBed::testIndexPresetCompressed PASSED 160s tests/tabix_test.py::TestCompressionBed::testIndexPresetUncompressed PASSED 160s tests/tabix_test.py::TestCompressionVCF::testCompression PASSED 160s tests/tabix_test.py::TestCompressionVCF::testIndexPresetCompressed PASSED 160s tests/tabix_test.py::TestCompressionVCF::testIndexPresetUncompressed PASSED 160s tests/tabix_test.py::TestGZFile::testAll PASSED 160s tests/tabix_test.py::TestIterationWithoutComments::testAll PASSED 160s tests/tabix_test.py::TestIterationWithoutComments::testGetContigs PASSED 160s tests/tabix_test.py::TestIterationWithoutComments::testHeader PASSED 160s tests/tabix_test.py::TestIterationWithoutComments::testInvalidIntervals PASSED 160s tests/tabix_test.py::TestIterationWithoutComments::testPerContig PASSED 160s tests/tabix_test.py::TestIterationWithoutComments::testPerContig2 PASSED 160s tests/tabix_test.py::TestIterationWithoutComments::testPerContigFromStart PASSED 160s tests/tabix_test.py::TestIterationWithoutComments::testPerContigToEnd PASSED 160s tests/tabix_test.py::TestIterationWithoutComments::testPerInterval PASSED 160s tests/tabix_test.py::TestIterationWithoutComments::testRegionStrings PASSED 160s tests/tabix_test.py::TestIterationWithoutComments::testReopening PASSED 160s tests/tabix_test.py::TestIterationWithComments::testAll PASSED 160s tests/tabix_test.py::TestIterationWithComments::testGetContigs PASSED 160s tests/tabix_test.py::TestIterationWithComments::testHeader PASSED 160s tests/tabix_test.py::TestIterationWithComments::testInvalidIntervals PASSED 160s tests/tabix_test.py::TestIterationWithComments::testPerContig PASSED 160s tests/tabix_test.py::TestIterationWithComments::testPerContig2 PASSED 161s tests/tabix_test.py::TestIterationWithComments::testPerContigFromStart PASSED 161s tests/tabix_test.py::TestIterationWithComments::testPerContigToEnd PASSED 161s tests/tabix_test.py::TestIterationWithComments::testPerInterval PASSED 161s tests/tabix_test.py::TestIterationWithComments::testRegionStrings PASSED 161s tests/tabix_test.py::TestIterationWithComments::testReopening PASSED 161s tests/tabix_test.py::TestIterators::testClosedFile PASSED 161s tests/tabix_test.py::TestIterators::testClosedFileIteration PASSED 161s tests/tabix_test.py::TestIterators::testIteration PASSED 161s tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFile PASSED 161s tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFileIteration PASSED 161s tests/tabix_test.py::TestIteratorsGenericCompressed::testIteration PASSED 161s tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFile PASSED 161s tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFileIteration PASSED 161s tests/tabix_test.py::TestIteratorsFileCompressed::testIteration PASSED 161s tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFile PASSED 161s tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFileIteration PASSED 161s tests/tabix_test.py::TestIteratorsFileUncompressed::testIteration PASSED 161s tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooFewFields PASSED 161s tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooManyFields PASSED 161s tests/tabix_test.py::TestBed::testRead PASSED 161s tests/tabix_test.py::TestBed::testWrite PASSED 161s tests/tabix_test.py::TestUnicode::testFromTabix PASSED 161s tests/tabix_test.py::TestUnicode::testFromVCF PASSED 161s tests/tabix_test.py::TestVCFFromTabix::testRead PASSED 161s tests/tabix_test.py::TestVCFFromTabix::testWrite PASSED 161s tests/tabix_test.py::TestVCFFromVCF::testConnecting PASSED 161s tests/tabix_test.py::TestVCFFromVCF::testParsing PASSED 161s tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testRead PASSED 161s tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testWrite PASSED 161s tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testConnecting PASSED 161s tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testParsing PASSED 161s tests/tabix_test.py::VCFFromTabixTest_4::testRead PASSED 161s tests/tabix_test.py::VCFFromTabixTest_4::testWrite PASSED 161s tests/tabix_test.py::VCFFromVCFTest_4::testConnecting PASSED 162s tests/tabix_test.py::VCFFromVCFTest_4::testParsing PASSED 162s tests/tabix_test.py::VCFFromTabixTest_12::testRead PASSED 162s tests/tabix_test.py::VCFFromTabixTest_12::testWrite PASSED 162s tests/tabix_test.py::VCFFromVCFTest_12::testConnecting PASSED 162s tests/tabix_test.py::VCFFromVCFTest_12::testParsing PASSED 162s tests/tabix_test.py::VCFFromTabixTest_20::testRead PASSED 162s tests/tabix_test.py::VCFFromTabixTest_20::testWrite PASSED 162s tests/tabix_test.py::VCFFromVCFTest_20::testConnecting PASSED 162s tests/tabix_test.py::VCFFromVCFTest_20::testParsing PASSED 162s tests/tabix_test.py::VCFFromTabixTest_8::testRead PASSED 162s tests/tabix_test.py::VCFFromTabixTest_8::testWrite PASSED 162s tests/tabix_test.py::VCFFromVCFTest_8::testConnecting PASSED 162s tests/tabix_test.py::VCFFromVCFTest_8::testParsing PASSED 162s tests/tabix_test.py::VCFFromTabixTest_16::testRead PASSED 162s tests/tabix_test.py::VCFFromTabixTest_16::testWrite PASSED 162s tests/tabix_test.py::VCFFromVCFTest_16::testConnecting PASSED 162s tests/tabix_test.py::VCFFromVCFTest_16::testParsing PASSED 162s tests/tabix_test.py::VCFFromTabixTest_5::testRead PASSED 162s tests/tabix_test.py::VCFFromTabixTest_5::testWrite PASSED 162s tests/tabix_test.py::VCFFromVCFTest_5::testConnecting PASSED 162s tests/tabix_test.py::VCFFromVCFTest_5::testParsing PASSED 162s tests/tabix_test.py::VCFFromTabixTest_11::testRead PASSED 163s tests/tabix_test.py::VCFFromTabixTest_11::testWrite PASSED 163s tests/tabix_test.py::VCFFromVCFTest_11::testConnecting PASSED 163s tests/tabix_test.py::VCFFromVCFTest_11::testParsing PASSED 163s tests/tabix_test.py::VCFFromTabixTest_9::testRead PASSED 163s tests/tabix_test.py::VCFFromTabixTest_9::testWrite PASSED 163s tests/tabix_test.py::VCFFromVCFTest_9::testConnecting PASSED 163s tests/tabix_test.py::VCFFromVCFTest_9::testParsing PASSED 163s tests/tabix_test.py::VCFFromTabixTest_24::testRead PASSED 163s tests/tabix_test.py::VCFFromTabixTest_24::testWrite PASSED 163s tests/tabix_test.py::VCFFromVCFTest_24::testConnecting PASSED 163s tests/tabix_test.py::VCFFromVCFTest_24::testParsing PASSED 163s tests/tabix_test.py::VCFFromTabixTest_13::testRead PASSED 163s tests/tabix_test.py::VCFFromTabixTest_13::testWrite PASSED 163s tests/tabix_test.py::VCFFromVCFTest_13::testConnecting PASSED 163s tests/tabix_test.py::VCFFromVCFTest_13::testParsing PASSED 163s tests/tabix_test.py::VCFFromTabixTest_18::testRead PASSED 163s tests/tabix_test.py::VCFFromTabixTest_18::testWrite PASSED 163s tests/tabix_test.py::VCFFromVCFTest_18::testConnecting PASSED 163s tests/tabix_test.py::VCFFromVCFTest_18::testParsing PASSED 163s tests/tabix_test.py::VCFFromTabixTest_23::testRead PASSED 163s tests/tabix_test.py::VCFFromTabixTest_23::testWrite PASSED 163s tests/tabix_test.py::VCFFromVCFTest_23::testConnecting PASSED 163s tests/tabix_test.py::VCFFromVCFTest_23::testParsing PASSED 164s tests/tabix_test.py::VCFFromTabixTest_22::testRead PASSED 164s tests/tabix_test.py::VCFFromTabixTest_22::testWrite PASSED 164s tests/tabix_test.py::VCFFromVCFTest_22::testConnecting PASSED 165s tests/tabix_test.py::VCFFromVCFTest_22::testParsing PASSED 165s tests/tabix_test.py::VCFFromTabixTest_issue85::testRead PASSED 165s tests/tabix_test.py::VCFFromTabixTest_issue85::testWrite PASSED 165s tests/tabix_test.py::VCFFromVCFTest_issue85::testConnecting PASSED 165s tests/tabix_test.py::VCFFromVCFTest_issue85::testParsing PASSED 165s tests/tabix_test.py::VCFFromTabixTest_7::testRead PASSED 165s tests/tabix_test.py::VCFFromTabixTest_7::testWrite PASSED 165s tests/tabix_test.py::VCFFromVCFTest_7::testConnecting PASSED 165s tests/tabix_test.py::VCFFromVCFTest_7::testParsing PASSED 165s tests/tabix_test.py::VCFFromTabixTest_3::testRead PASSED 165s tests/tabix_test.py::VCFFromTabixTest_3::testWrite PASSED 165s tests/tabix_test.py::VCFFromVCFTest_3::testConnecting PASSED 165s tests/tabix_test.py::VCFFromVCFTest_3::testParsing PASSED 166s tests/tabix_test.py::VCFFromTabixTest_6::testRead PASSED 166s tests/tabix_test.py::VCFFromTabixTest_6::testWrite PASSED 166s tests/tabix_test.py::VCFFromVCFTest_6::testConnecting PASSED 166s tests/tabix_test.py::VCFFromVCFTest_6::testParsing PASSED 166s tests/tabix_test.py::VCFFromTabixTest_2::testRead PASSED 166s tests/tabix_test.py::VCFFromTabixTest_2::testWrite PASSED 166s tests/tabix_test.py::VCFFromVCFTest_2::testConnecting PASSED 166s tests/tabix_test.py::VCFFromVCFTest_2::testParsing PASSED 166s tests/tabix_test.py::VCFFromTabixTest_15::testRead PASSED 167s tests/tabix_test.py::VCFFromTabixTest_15::testWrite PASSED 167s tests/tabix_test.py::VCFFromVCFTest_15::testConnecting PASSED 167s tests/tabix_test.py::VCFFromVCFTest_15::testParsing PASSED 167s tests/tabix_test.py::VCFFromTabixTest_10::testRead PASSED 167s tests/tabix_test.py::VCFFromTabixTest_10::testWrite PASSED 167s tests/tabix_test.py::VCFFromVCFTest_10::testConnecting PASSED 167s tests/tabix_test.py::VCFFromVCFTest_10::testParsing PASSED 167s tests/tabix_test.py::VCFFromTabixTest_21::testRead PASSED 167s tests/tabix_test.py::VCFFromTabixTest_21::testWrite PASSED 167s tests/tabix_test.py::VCFFromVCFTest_21::testConnecting PASSED 167s tests/tabix_test.py::VCFFromVCFTest_21::testParsing PASSED 167s tests/tabix_test.py::TestVCFFromVariantFile::testConnecting PASSED 167s tests/tabix_test.py::TestVCFFromVariantFile::testParsing [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 167s [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) 167s PASSED[W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 167s 167s tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testConnecting PASSED 167s tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testParsing PASSED 167s tests/tabix_test.py::TestVCFFromVariantFile_4::testConnecting PASSED 167s 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.) 167s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:249843 is not defined in the header, assuming Type=String 168s PASSED 168s tests/tabix_test.py::TestVCFFromVariantFile_12::testConnecting PASSED 168s 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.) 168s [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String 168s [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String 168s [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String 168s [W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String 168s [W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String 168s [W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String 168s [W::vcf_parse_format_dict2] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String 168s [W::vcf_parse_format_dict2] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String 168s [W::vcf_parse_format_dict2] FORMAT 'GQ' at chr1:1281168 is not defined in the header, assuming Type=String 168s [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) 168s [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) 168s [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) 168s [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) 168s [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) 168s [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) 168s [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) 168s [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) 168s [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) 168s [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) 168s [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) 168s [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) 168s [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) 168s [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) 168s [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) 168s [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) 168s [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) 168s [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) 168s PASSED 168s tests/tabix_test.py::TestVCFFromVariantFile_20::testConnecting [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) 168s [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 168s PASSED 168s tests/tabix_test.py::TestVCFFromVariantFile_20::testParsing [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 168s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 168s PASSED 168s tests/tabix_test.py::TestVCFFromVariantFile_8::testConnecting PASSED 168s 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.) 168s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:676148 is not defined in the header, assuming Type=String 168s PASSED 168s tests/tabix_test.py::TestVCFFromVariantFile_16::testConnecting [W::bcf_hdr_check_sanity] GL should be declared as Number=G 168s PASSED 168s 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.) 168s [W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String 168s PASSED 168s tests/tabix_test.py::TestVCFFromVariantFile_5::testConnecting PASSED 168s 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.) 168s PASSED 168s tests/tabix_test.py::TestVCFFromVariantFile_11::testConnecting PASSED 168s 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.) 168s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:669442 is not defined in the header, assuming Type=String 169s PASSED 169s tests/tabix_test.py::TestVCFFromVariantFile_9::testConnecting PASSED 169s 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.) 169s [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String 169s [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String 169s [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String 169s [W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String 169s [W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String 169s [W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String 169s [W::vcf_parse_format_dict2] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String 169s [W::vcf_parse_format_dict2] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String 169s [W::vcf_parse_format_dict2] FORMAT 'GQ' at chr1:1281168 is not defined in the header, assuming Type=String 169s [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) 169s PASSED 169s tests/tabix_test.py::TestVCFFromVariantFile_24::testConnecting PASSED[E::bcf_hdr_parse_sample_line] 169s tests/tabix_test.py::TestVCFFromVariantFile_24::testParsing Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: 169s #CHROM POS ID REF ALT QUAL FILTER INFO 169s 169s PASSED 169s tests/tabix_test.py::TestVCFFromVariantFile_13::testConnecting [W::bcf_hrec_check] Invalid tag name: "1000g" 169s [W::bcf_hrec_check] Invalid tag name: "GT:GL:GQ:NR" 169s PASSED 169s tests/tabix_test.py::TestVCFFromVariantFile_13::testParsing [W::bcf_hrec_check] Invalid tag name: "1000g" 169s [W::bcf_hrec_check] Invalid tag name: "GT:GL:GQ:NR" 169s [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse_info] INFO 'MMLQ' is not defined in the header, assuming Type=String 169s [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr17_gl000205_random' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr18' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr19' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr20' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr21' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr22' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chrUn_gl000214' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chrUn_gl000220' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chrUn_gl000225' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chrX' is not defined in the header. (Quick workaround: index the file with tabix.) 169s PASSED 169s tests/tabix_test.py::TestVCFFromVariantFile_18::testConnecting PASSED 169s 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.) 169s [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String 169s [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String 169s [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String 169s [W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String 169s [W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String 169s [W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String 169s [W::vcf_parse_format_dict2] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String 169s [W::vcf_parse_format_dict2] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String 169s [W::vcf_parse_format_dict2] FORMAT 'GQ' at chr1:1281168 is not defined in the header, assuming Type=String 169s [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) 169s [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) 169s PASSED 169s tests/tabix_test.py::TestVCFFromVariantFile_23::testConnecting PASSED 169s tests/tabix_test.py::TestVCFFromVariantFile_23::testParsing [W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String 169s PASSED 169s tests/tabix_test.py::TestVCFFromVariantFile_22::testConnecting PASSED 169s 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.) 169s [W::vcf_parse_info] INFO 'refseq.name' is not defined in the header, assuming Type=String 169s [W::vcf_parse_info] INFO 'refseq.positionType' is not defined in the header, assuming Type=String 170s [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) 170s PASSED 170s tests/tabix_test.py::TestVCFFromVariantFile_issue85::testConnecting [E::bcf_hdr_parse] Could not parse the header, sample line not found 170s PASSED 170s tests/tabix_test.py::TestVCFFromVariantFile_issue85::testParsing PASSED 170s tests/tabix_test.py::TestVCFFromVariantFile_7::testConnecting PASSED 170s 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.) 170s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:249843 is not defined in the header, assuming Type=String 170s PASSED 170s tests/tabix_test.py::TestVCFFromVariantFile_3::testConnecting PASSED 170s 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.) 170s PASSED 170s tests/tabix_test.py::TestVCFFromVariantFile_6::testConnecting PASSED 170s 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.) 170s [W::vcf_parse_info] INFO 'CallSetAC' is not defined in the header, assuming Type=String 170s [W::vcf_parse_info] INFO 'CallSetAC2' is not defined in the header, assuming Type=String 170s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:669442 is not defined in the header, assuming Type=String 171s PASSED 171s tests/tabix_test.py::TestVCFFromVariantFile_2::testConnecting PASSED 171s tests/tabix_test.py::TestVCFFromVariantFile_2::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 171s [W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String 171s PASSED 171s tests/tabix_test.py::TestVCFFromVariantFile_15::testConnecting PASSED 171s 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.) 171s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:439104 is not defined in the header, assuming Type=String 171s PASSED 171s tests/tabix_test.py::TestVCFFromVariantFile_10::testConnecting PASSED 171s 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.) 171s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:676148 is not defined in the header, assuming Type=String 171s PASSED 171s tests/tabix_test.py::TestVCFFromVariantFile_21::testConnecting [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 171s PASSED 171s tests/tabix_test.py::TestVCFFromVariantFile_21::testParsing [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 171s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 171s PASSED 171s tests/tabix_test.py::TestIndexArgument::testFetchAll PASSED 171s tests/tabix_test.py::TestIndexArgument::testLoadIndexWithoutTbiExtension PASSED 171s tests/tabix_test.py::TestBackwardsCompatibility::testBED PASSED 171s tests/tabix_test.py::TestBackwardsCompatibility::testBED0v23 PASSED 171s tests/tabix_test.py::TestBackwardsCompatibility::testBED0v26 PASSED 171s tests/tabix_test.py::TestBackwardsCompatibility::testEmpty PASSED 171s tests/tabix_test.py::TestBackwardsCompatibility::testVCF PASSED 171s tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v23 PASSED 171s tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v26 PASSED 171s tests/tabix_test.py::TestMultipleIterators::testDisjointIterators PASSED 171s tests/tabix_test.py::TestMultipleIterators::testDoubleFetch PASSED 171s tests/tabix_test.py::TestMultipleIterators::testJoinedIterators PASSED 171s tests/tabix_test.py::TestMultipleIterators::testScope PASSED 171s tests/tabix_test.py::TestContextManager::testManager PASSED 171s tests/tabix_test.py::TestMultithreadTabixFile::testMultithreadEqualsSinglethread PASSED 171s tests/tabixproxies_test.py::TestBED::testAssignmentToTargetList PASSED 171s tests/tabixproxies_test.py::TestParser::testAssignmentToTargetList PASSED 171s tests/tabixproxies_test.py::TestParser::testCopy PASSED 171s tests/tabixproxies_test.py::TestParser::testIteratorCompressed PASSED 172s tests/tabixproxies_test.py::TestParser::testIteratorUncompressed PASSED 172s tests/tabixproxies_test.py::TestParser::testRead PASSED 172s tests/tabixproxies_test.py::TestParser::testUnset PASSED 172s tests/tabixproxies_test.py::TestParser::testWrite PASSED 172s tests/tabixproxies_test.py::TestGTF::testAssignmentToTargetList PASSED 172s tests/tabixproxies_test.py::TestGTF::testCopy PASSED 172s tests/tabixproxies_test.py::TestGTF::testIteratorCompressed PASSED 172s tests/tabixproxies_test.py::TestGTF::testIteratorUncompressed PASSED 172s tests/tabixproxies_test.py::TestGTF::testRead PASSED 172s tests/tabixproxies_test.py::TestGTF::testUnset PASSED 172s tests/tabixproxies_test.py::TestGTF::testWrite PASSED 172s tests/tabixproxies_test.py::TestGTF::test_added_attribute_is_output PASSED 172s tests/tabixproxies_test.py::TestGTF::test_asdict_can_be_modified PASSED 172s tests/tabixproxies_test.py::TestGTF::test_asdict_contains_attributes PASSED 172s tests/tabixproxies_test.py::TestGTF::test_setAttribute_makes_changes PASSED 172s tests/tabixproxies_test.py::TestGTF::test_setting_end_is_one_based PASSED 172s tests/tabixproxies_test.py::TestGTF::test_setting_feature_to_none_produces_dot PASSED 172s tests/tabixproxies_test.py::TestGTF::test_setting_fields PASSED 172s tests/tabixproxies_test.py::TestGTF::test_setting_frame_to_none_produces_dot PASSED 172s tests/tabixproxies_test.py::TestGTF::test_setting_score_to_none_produces_dot PASSED 172s tests/tabixproxies_test.py::TestGTF::test_setting_source_to_none_produces_dot PASSED 172s tests/tabixproxies_test.py::TestGTF::test_setting_start_is_one_based PASSED 172s tests/tabixproxies_test.py::TestGTF::test_setting_strand_to_none_produces_dot PASSED 172s tests/tabixproxies_test.py::TestGFF3::testAssignmentToTargetList PASSED 172s tests/tabixproxies_test.py::TestGFF3::testCopy PASSED 172s tests/tabixproxies_test.py::TestGFF3::testIteratorCompressed PASSED 172s tests/tabixproxies_test.py::TestGFF3::testIteratorUncompressed PASSED 172s tests/tabixproxies_test.py::TestGFF3::testRead PASSED 172s tests/tabixproxies_test.py::TestGFF3::testUnset PASSED 172s tests/tabixproxies_test.py::TestGFF3::testWrite PASSED 172s tests/tabixproxies_test.py::TestGFF3::test_added_attribute_is_output PASSED 172s tests/tabixproxies_test.py::TestGFF3::test_asdict_can_be_modified PASSED 172s tests/tabixproxies_test.py::TestGFF3::test_asdict_contains_attributes PASSED 172s tests/tabixproxies_test.py::TestGFF3::test_setAttribute_makes_changes PASSED 172s tests/tabixproxies_test.py::TestGFF3::test_setting_end_is_one_based PASSED 172s tests/tabixproxies_test.py::TestGFF3::test_setting_feature_to_none_produces_dot PASSED 172s tests/tabixproxies_test.py::TestGFF3::test_setting_fields PASSED 172s tests/tabixproxies_test.py::TestGFF3::test_setting_frame_to_none_produces_dot PASSED 172s tests/tabixproxies_test.py::TestGFF3::test_setting_score_to_none_produces_dot PASSED 172s tests/tabixproxies_test.py::TestGFF3::test_setting_source_to_none_produces_dot PASSED 172s tests/tabixproxies_test.py::TestGFF3::test_setting_start_is_one_based PASSED 172s tests/tabixproxies_test.py::TestGFF3::test_setting_strand_to_none_produces_dot PASSED 172s tests/test_samtools_python.py::test_idxstats_parse_split_lines PASSED 172s tests/test_samtools_python.py::test_bedcov_split_lines PASSED 172s tests/test_samtools_python.py::test_idxstats_parse PASSED 172s tests/test_samtools_python.py::test_bedcov PASSED 172s 172s =============================== warnings summary =============================== 172s tests/samtools_test.py::SamtoolsTest::testStatements 172s tests/samtools_test.py::PysamTest::testStatements 172s /tmp/autopkgtest.mg0YZ7/build.ZoQ/src/tests/samtools_test.py:137: UserWarning: versions of pysam.samtools and samtools differ: 1.18 != 1.20 172s warnings.warn( 172s 172s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 172s ============ 938 passed, 13 skipped, 2 warnings in 69.33s (0:01:09) ============ 172s autopkgtest [12:46:17]: test command1: -----------------------] 172s command1 PASS 172s autopkgtest [12:46:17]: test command1: - - - - - - - - - - results - - - - - - - - - - 172s autopkgtest [12:46:17]: test autodep8-python3: preparing testbed 1809s autopkgtest [13:13:34]: testbed dpkg architecture: amd64 1809s autopkgtest [13:13:34]: testbed apt version: 2.9.8 1809s autopkgtest [13:13:34]: @@@@@@@@@@@@@@@@@@@@ test bed setup 1809s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 1809s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [2268 kB] 1809s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [177 kB] 1809s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 1809s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [31.2 kB] 1809s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [238 kB] 1809s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [165 kB] 1809s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 1809s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [833 kB] 1809s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [1715 kB] 1809s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [58.6 kB] 1809s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [18.1 kB] 1810s Fetched 5618 kB in 1s (9357 kB/s) 1810s Reading package lists... 1811s Reading package lists... 1811s Building dependency tree... 1811s Reading state information... 1812s Calculating upgrade... 1812s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1812s Reading package lists... 1812s Building dependency tree... 1812s Reading state information... 1812s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1812s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 1812s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 1812s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 1812s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 1814s Reading package lists... 1814s Reading package lists... 1814s Building dependency tree... 1814s Reading state information... 1814s Calculating upgrade... 1814s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1814s Reading package lists... 1815s Building dependency tree... 1815s Reading state information... 1815s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1816s Reading package lists... 1816s Building dependency tree... 1816s Reading state information... 1816s Starting pkgProblemResolver with broken count: 0 1816s Starting 2 pkgProblemResolver with broken count: 0 1816s Done 1817s The following additional packages will be installed: 1817s libdeflate0 libhts3t64 libhtscodecs2 python3-all python3-pysam 1817s The following NEW packages will be installed: 1817s autopkgtest-satdep libdeflate0 libhts3t64 libhtscodecs2 python3-all 1817s python3-pysam 1817s 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. 1817s Need to get 4155 kB/4155 kB of archives. 1817s After this operation, 36.6 MB of additional disk space will be used. 1817s Get:1 /tmp/autopkgtest.mg0YZ7/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [720 B] 1817s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.21-1 [49.8 kB] 1817s Get:3 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.0-1build1 [98.8 kB] 1817s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libhts3t64 amd64 1.20+ds-2 [501 kB] 1817s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all amd64 3.12.6-0ubuntu1 [886 B] 1817s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pysam amd64 0.22.1+ds-2 [3504 kB] 1817s Fetched 4155 kB in 0s (27.8 MB/s) 1817s Selecting previously unselected package libdeflate0:amd64. 1817s (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 ... 75323 files and directories currently installed.) 1817s Preparing to unpack .../0-libdeflate0_1.21-1_amd64.deb ... 1817s Unpacking libdeflate0:amd64 (1.21-1) ... 1818s Selecting previously unselected package libhtscodecs2:amd64. 1818s Preparing to unpack .../1-libhtscodecs2_1.6.0-1build1_amd64.deb ... 1818s Unpacking libhtscodecs2:amd64 (1.6.0-1build1) ... 1818s Selecting previously unselected package libhts3t64:amd64. 1818s Preparing to unpack .../2-libhts3t64_1.20+ds-2_amd64.deb ... 1818s Unpacking libhts3t64:amd64 (1.20+ds-2) ... 1818s Selecting previously unselected package python3-all. 1818s Preparing to unpack .../3-python3-all_3.12.6-0ubuntu1_amd64.deb ... 1818s Unpacking python3-all (3.12.6-0ubuntu1) ... 1818s Selecting previously unselected package python3-pysam. 1818s Preparing to unpack .../4-python3-pysam_0.22.1+ds-2_amd64.deb ... 1818s Unpacking python3-pysam (0.22.1+ds-2) ... 1818s Selecting previously unselected package autopkgtest-satdep. 1818s Preparing to unpack .../5-2-autopkgtest-satdep.deb ... 1818s Unpacking autopkgtest-satdep (0) ... 1818s Setting up libhtscodecs2:amd64 (1.6.0-1build1) ... 1818s Setting up libdeflate0:amd64 (1.21-1) ... 1818s Setting up python3-all (3.12.6-0ubuntu1) ... 1818s Setting up libhts3t64:amd64 (1.20+ds-2) ... 1818s Setting up python3-pysam (0.22.1+ds-2) ... 1818s Setting up autopkgtest-satdep (0) ... 1818s Processing triggers for man-db (2.12.1-3) ... 1818s Processing triggers for libc-bin (2.40-1ubuntu3) ... 1820s (Reading database ... 75709 files and directories currently installed.) 1820s Removing autopkgtest-satdep (0) ... 1821s autopkgtest [13:13:46]: 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 1821s autopkgtest [13:13:46]: test autodep8-python3: [----------------------- 1821s Testing with python3.12: 1821s 1821s autopkgtest [13:13:46]: test autodep8-python3: -----------------------] 1822s autodep8-python3 PASS (superficial) 1822s autopkgtest [13:13:47]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 1822s autopkgtest [13:13:47]: @@@@@@@@@@@@@@@@@@@@ summary 1822s command1 PASS 1822s autodep8-python3 PASS (superficial) 1831s nova [W] Skipping flock for amd64 1831s Creating nova instance adt-plucky-amd64-python-pysam-20241104-124325-juju-7f2275-prod-proposed-migration-environment-15-3e398556-de9f-43ac-9ae1-c3b907ef8173 from image adt/ubuntu-plucky-amd64-server-20241104.img (UUID 0ab90577-a6b7-4a72-9ab8-957838d495c0)... 1831s nova [W] Skipping flock for amd64 1831s Creating nova instance adt-plucky-amd64-python-pysam-20241104-124325-juju-7f2275-prod-proposed-migration-environment-15-3e398556-de9f-43ac-9ae1-c3b907ef8173 from image adt/ubuntu-plucky-amd64-server-20241104.img (UUID 0ab90577-a6b7-4a72-9ab8-957838d495c0)...