0s autopkgtest [07:42:40]: starting date and time: 2024-11-03 07:42:40+0000 0s autopkgtest [07:42:40]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [07:42:40]: host juju-7f2275-prod-proposed-migration-environment-14; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.xo916lx7/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-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-14@bos03-ppc64el-24.secgroup --name adt-plucky-ppc64el-python-pysam-20241103-074240-juju-7f2275-prod-proposed-migration-environment-14-ba3a0410-7bb9-4a9a-ac5f-32af078039a1 --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-14 --net-id=net_prod-proposed-migration-ppc64el -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/ 112s autopkgtest [07:44:32]: testbed dpkg architecture: ppc64el 112s autopkgtest [07:44:32]: testbed apt version: 2.9.8 112s autopkgtest [07:44:32]: @@@@@@@@@@@@@@@@@@@@ test bed setup 113s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 113s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [177 kB] 114s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 114s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [2268 kB] 119s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [31.2 kB] 119s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [213 kB] 120s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [1576 kB] 128s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [37.8 kB] 128s Fetched 4384 kB in 15s (290 kB/s) 128s Reading package lists... 131s Reading package lists... 131s Building dependency tree... 131s Reading state information... 131s Calculating upgrade... 131s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 131s Reading package lists... 131s Building dependency tree... 131s Reading state information... 132s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 132s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 132s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 132s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 132s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 133s Reading package lists... 133s Reading package lists... 133s Building dependency tree... 133s Reading state information... 133s Calculating upgrade... 134s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 134s Reading package lists... 134s Building dependency tree... 134s Reading state information... 134s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 137s autopkgtest [07:44:57]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 13:49:23 UTC 2024 137s autopkgtest [07:44:57]: @@@@@@@@@@@@@@@@@@@@ apt-source python-pysam 150s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-pysam 0.22.1+ds-2 (dsc) [2563 B] 150s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-pysam 0.22.1+ds-2 (tar) [1447 kB] 150s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-pysam 0.22.1+ds-2 (diff) [10.7 kB] 150s gpgv: Signature made Wed May 29 11:37:25 2024 UTC 150s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 150s gpgv: issuer "emollier@debian.org" 150s gpgv: Can't check signature: No public key 150s dpkg-source: warning: cannot verify inline signature for ./python-pysam_0.22.1+ds-2.dsc: no acceptable signature found 150s autopkgtest [07:45:10]: testing package python-pysam version 0.22.1+ds-2 150s autopkgtest [07:45:10]: build not needed 151s autopkgtest [07:45:11]: test command1: preparing testbed 153s Reading package lists... 153s Building dependency tree... 153s Reading state information... 153s Starting pkgProblemResolver with broken count: 0 153s Starting 2 pkgProblemResolver with broken count: 0 153s Done 153s The following additional packages will be installed: 153s autoconf automake autopoint autotools-dev bcftools build-essential cpp 153s cpp-14 cpp-14-powerpc64le-linux-gnu cpp-powerpc64le-linux-gnu cython3 153s debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz g++ 153s g++-14 g++-14-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc gcc-14 153s gcc-14-powerpc64le-linux-gnu gcc-powerpc64le-linux-gnu gettext 153s intltool-debian libarchive-zip-perl libasan8 libbrotli-dev libbz2-dev 153s libcc1-0 libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 153s libevent-2.1-7t64 libexpat1-dev libfile-stripnondeterminism-perl 153s libgcc-14-dev libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 153s libgnutls-openssl27t64 libgnutls28-dev libgomp1 libhts-dev libhts3t64 153s libhtscodecs2 libidn2-dev libisl23 libitm1 libjs-jquery libjs-sphinxdoc 153s libjs-underscore liblsan0 liblzma-dev libmpc3 libnghttp2-dev libp11-kit-dev 153s libpkgconf3 libpsl-dev libpython3-all-dev libpython3-dev libpython3.12-dev 153s libquadmath0 librtmp-dev libssh2-1-dev libssl-dev libstdc++-14-dev 153s libtasn1-6-dev libtool libtsan2 libubsan1 libunbound8 libzstd-dev m4 153s nettle-dev pkgconf pkgconf-bin po-debconf python3-all python3-all-dev 153s python3-dev python3-iniconfig python3-packaging python3-pluggy python3-pysam 153s python3-pytest python3.12-dev samtools tabix zlib1g-dev 153s Suggested packages: 153s autoconf-archive gnu-standards autoconf-doc python3-numpy 153s texlive-latex-recommended cpp-doc gcc-14-locales cpp-14-doc cython-doc 153s dh-make flit python3-build python3-installer python3-wheel gcc-14-doc 153s gcc-multilib manpages-dev flex bison gdb gcc-doc gdb-powerpc64le-linux-gnu 153s gettext-doc libasprintf-dev libgettextpo-dev libcurl4-doc libidn-dev 153s libkrb5-dev libldap2-dev gmp-doc libgmp10-doc libmpfr-dev dns-root-data 153s gnutls-bin gnutls-doc liblzma-doc libnghttp2-doc p11-kit-doc libssl-doc 153s libstdc++-14-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc 153s libmail-box-perl cwltool 153s Recommended packages: 153s python3-gffutils python3-matplotlib bzip2-doc libarchive-cpio-perl 153s javascript-common libtasn1-doc libltdl-dev libmail-sendmail-perl 153s The following NEW packages will be installed: 153s autoconf automake autopkgtest-satdep autopoint autotools-dev bcftools 153s build-essential cpp cpp-14 cpp-14-powerpc64le-linux-gnu 153s cpp-powerpc64le-linux-gnu cython3 debhelper debugedit dh-autoreconf 153s dh-python dh-strip-nondeterminism dwz g++ g++-14 153s g++-14-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc gcc-14 153s gcc-14-powerpc64le-linux-gnu gcc-powerpc64le-linux-gnu gettext 153s intltool-debian libarchive-zip-perl libasan8 libbrotli-dev libbz2-dev 153s libcc1-0 libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 153s libevent-2.1-7t64 libexpat1-dev libfile-stripnondeterminism-perl 153s libgcc-14-dev libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 153s libgnutls-openssl27t64 libgnutls28-dev libgomp1 libhts-dev libhts3t64 153s libhtscodecs2 libidn2-dev libisl23 libitm1 libjs-jquery libjs-sphinxdoc 153s libjs-underscore liblsan0 liblzma-dev libmpc3 libnghttp2-dev libp11-kit-dev 153s libpkgconf3 libpsl-dev libpython3-all-dev libpython3-dev libpython3.12-dev 153s libquadmath0 librtmp-dev libssh2-1-dev libssl-dev libstdc++-14-dev 153s libtasn1-6-dev libtool libtsan2 libubsan1 libunbound8 libzstd-dev m4 153s nettle-dev pkgconf pkgconf-bin po-debconf python3-all python3-all-dev 153s python3-dev python3-iniconfig python3-packaging python3-pluggy python3-pysam 153s python3-pytest python3.12-dev samtools tabix zlib1g-dev 153s 0 upgraded, 94 newly installed, 0 to remove and 0 not upgraded. 153s Need to get 96.1 MB/96.1 MB of archives. 153s After this operation, 378 MB of additional disk space will be used. 153s Get:1 /tmp/autopkgtest.TIYAUm/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [820 B] 153s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el m4 ppc64el 1.4.19-4build1 [278 kB] 154s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el autoconf all 2.72-3 [382 kB] 155s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el autotools-dev all 20220109.1 [44.9 kB] 155s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el automake all 1:1.16.5-1.3ubuntu1 [558 kB] 156s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el autopoint all 0.22.5-2 [616 kB] 156s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdeflate0 ppc64el 1.21-1 [63.3 kB] 156s Get:8 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1build1 [110 kB] 156s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el libhts3t64 ppc64el 1.20+ds-2 [574 kB] 156s Get:10 http://ftpmaster.internal/ubuntu plucky/universe ppc64el bcftools ppc64el 1.20-2 [1014 kB] 157s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el libisl23 ppc64el 0.27-1 [882 kB] 157s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el libmpc3 ppc64el 1.3.1-1build2 [62.1 kB] 157s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el cpp-14-powerpc64le-linux-gnu ppc64el 14.2.0-7ubuntu1 [10.5 MB] 159s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el cpp-14 ppc64el 14.2.0-7ubuntu1 [1030 B] 159s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el cpp-powerpc64le-linux-gnu ppc64el 4:14.1.0-2ubuntu1 [5456 B] 159s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el cpp ppc64el 4:14.1.0-2ubuntu1 [22.5 kB] 159s Get:17 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcc1-0 ppc64el 14.2.0-7ubuntu1 [48.1 kB] 159s Get:18 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgomp1 ppc64el 14.2.0-7ubuntu1 [161 kB] 159s Get:19 http://ftpmaster.internal/ubuntu plucky/main ppc64el libitm1 ppc64el 14.2.0-7ubuntu1 [31.9 kB] 159s Get:20 http://ftpmaster.internal/ubuntu plucky/main ppc64el libasan8 ppc64el 14.2.0-7ubuntu1 [2945 kB] 159s Get:21 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblsan0 ppc64el 14.2.0-7ubuntu1 [1322 kB] 159s Get:22 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtsan2 ppc64el 14.2.0-7ubuntu1 [2694 kB] 159s Get:23 http://ftpmaster.internal/ubuntu plucky/main ppc64el libubsan1 ppc64el 14.2.0-7ubuntu1 [1191 kB] 159s Get:24 http://ftpmaster.internal/ubuntu plucky/main ppc64el libquadmath0 ppc64el 14.2.0-7ubuntu1 [158 kB] 159s Get:25 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgcc-14-dev ppc64el 14.2.0-7ubuntu1 [1620 kB] 159s Get:26 http://ftpmaster.internal/ubuntu plucky/main ppc64el gcc-14-powerpc64le-linux-gnu ppc64el 14.2.0-7ubuntu1 [20.6 MB] 161s Get:27 http://ftpmaster.internal/ubuntu plucky/main ppc64el gcc-14 ppc64el 14.2.0-7ubuntu1 [526 kB] 161s Get:28 http://ftpmaster.internal/ubuntu plucky/main ppc64el gcc-powerpc64le-linux-gnu ppc64el 4:14.1.0-2ubuntu1 [1222 B] 161s Get:29 http://ftpmaster.internal/ubuntu plucky/main ppc64el gcc ppc64el 4:14.1.0-2ubuntu1 [5006 B] 161s Get:30 http://ftpmaster.internal/ubuntu plucky/main ppc64el libstdc++-14-dev ppc64el 14.2.0-7ubuntu1 [2672 kB] 161s Get:31 http://ftpmaster.internal/ubuntu plucky/main ppc64el g++-14-powerpc64le-linux-gnu ppc64el 14.2.0-7ubuntu1 [12.0 MB] 162s Get:32 http://ftpmaster.internal/ubuntu plucky/main ppc64el g++-14 ppc64el 14.2.0-7ubuntu1 [19.8 kB] 162s Get:33 http://ftpmaster.internal/ubuntu plucky/main ppc64el g++-powerpc64le-linux-gnu ppc64el 4:14.1.0-2ubuntu1 [968 B] 162s Get:34 http://ftpmaster.internal/ubuntu plucky/main ppc64el g++ ppc64el 4:14.1.0-2ubuntu1 [1090 B] 162s Get:35 http://ftpmaster.internal/ubuntu plucky/main ppc64el build-essential ppc64el 12.10ubuntu1 [4936 B] 162s Get:36 http://ftpmaster.internal/ubuntu plucky/universe ppc64el cython3 ppc64el 3.0.11+dfsg-1ubuntu1 [2579 kB] 162s Get:37 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdebhelper-perl all 13.20ubuntu1 [94.2 kB] 162s Get:38 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtool all 2.4.7-7build1 [166 kB] 162s Get:39 http://ftpmaster.internal/ubuntu plucky/main ppc64el dh-autoreconf all 20 [16.1 kB] 162s Get:40 http://ftpmaster.internal/ubuntu plucky/main ppc64el libarchive-zip-perl all 1.68-1 [90.2 kB] 162s Get:41 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] 162s Get:42 http://ftpmaster.internal/ubuntu plucky/main ppc64el dh-strip-nondeterminism all 1.14.0-1 [5058 B] 162s Get:43 http://ftpmaster.internal/ubuntu plucky/main ppc64el debugedit ppc64el 1:5.1-1 [52.1 kB] 162s Get:44 http://ftpmaster.internal/ubuntu plucky/main ppc64el dwz ppc64el 0.15-1build6 [142 kB] 162s Get:45 http://ftpmaster.internal/ubuntu plucky/main ppc64el gettext ppc64el 0.22.5-2 [1082 kB] 162s Get:46 http://ftpmaster.internal/ubuntu plucky/main ppc64el intltool-debian all 0.35.0+20060710.6 [23.2 kB] 162s Get:47 http://ftpmaster.internal/ubuntu plucky/main ppc64el po-debconf all 1.0.21+nmu1 [233 kB] 162s Get:48 http://ftpmaster.internal/ubuntu plucky/main ppc64el debhelper all 13.20ubuntu1 [893 kB] 162s Get:49 http://ftpmaster.internal/ubuntu plucky/universe ppc64el dh-python all 6.20240824 [112 kB] 162s Get:50 http://ftpmaster.internal/ubuntu plucky/main ppc64el libbrotli-dev ppc64el 1.1.0-2build2 [423 kB] 162s Get:51 http://ftpmaster.internal/ubuntu plucky/main ppc64el libbz2-dev ppc64el 1.0.8-6 [50.2 kB] 162s Get:52 http://ftpmaster.internal/ubuntu plucky/main ppc64el libevent-2.1-7t64 ppc64el 2.1.12-stable-10 [172 kB] 162s Get:53 http://ftpmaster.internal/ubuntu plucky/main ppc64el libunbound8 ppc64el 1.20.0-1ubuntu2.1 [546 kB] 162s Get:54 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgnutls-dane0t64 ppc64el 3.8.6-2ubuntu1 [25.0 kB] 162s Get:55 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgnutls-openssl27t64 ppc64el 3.8.6-2ubuntu1 [24.5 kB] 162s Get:56 http://ftpmaster.internal/ubuntu plucky/main ppc64el libidn2-dev ppc64el 2.3.7-2build2 [124 kB] 162s Get:57 http://ftpmaster.internal/ubuntu plucky/main ppc64el libp11-kit-dev ppc64el 0.25.5-2ubuntu1 [22.7 kB] 162s Get:58 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtasn1-6-dev ppc64el 4.19.0-3build1 [104 kB] 162s Get:59 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgmpxx4ldbl ppc64el 2:6.3.0+dfsg-2ubuntu7 [10.2 kB] 162s Get:60 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgmp-dev ppc64el 2:6.3.0+dfsg-2ubuntu7 [371 kB] 162s Get:61 http://ftpmaster.internal/ubuntu plucky/main ppc64el nettle-dev ppc64el 3.10-1 [1231 kB] 162s Get:62 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgnutls28-dev ppc64el 3.8.6-2ubuntu1 [1211 kB] 162s Get:63 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpkgconf3 ppc64el 1.8.1-3ubuntu1 [37.1 kB] 162s Get:64 http://ftpmaster.internal/ubuntu plucky/main ppc64el pkgconf-bin ppc64el 1.8.1-3ubuntu1 [22.5 kB] 162s Get:65 http://ftpmaster.internal/ubuntu plucky/main ppc64el pkgconf ppc64el 1.8.1-3ubuntu1 [16.8 kB] 162s Get:66 http://ftpmaster.internal/ubuntu plucky/main ppc64el libnghttp2-dev ppc64el 1.62.1-2 [138 kB] 162s Get:67 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpsl-dev ppc64el 0.21.2-1.1build1 [79.1 kB] 162s Get:68 http://ftpmaster.internal/ubuntu plucky/main ppc64el zlib1g-dev ppc64el 1:1.3.dfsg+really1.3.1-1ubuntu1 [902 kB] 162s Get:69 http://ftpmaster.internal/ubuntu plucky/main ppc64el librtmp-dev ppc64el 2.4+20151223.gitfa8646d.1-2build7 [76.1 kB] 162s Get:70 http://ftpmaster.internal/ubuntu plucky/main ppc64el libssl-dev ppc64el 3.3.1-2ubuntu2 [2985 kB] 162s Get:71 http://ftpmaster.internal/ubuntu plucky/main ppc64el libssh2-1-dev ppc64el 1.11.0-7 [293 kB] 162s Get:72 http://ftpmaster.internal/ubuntu plucky/main ppc64el libzstd-dev ppc64el 1.5.6+dfsg-1 [489 kB] 162s Get:73 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcurl4-gnutls-dev ppc64el 8.9.1-2ubuntu2 [578 kB] 163s Get:74 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdeflate-dev ppc64el 1.21-1 [70.8 kB] 163s Get:75 http://ftpmaster.internal/ubuntu plucky/main ppc64el libexpat1-dev ppc64el 2.6.2-2 [149 kB] 163s Get:76 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblzma-dev ppc64el 5.6.2-2 [206 kB] 163s Get:77 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el libhts-dev ppc64el 1.20+ds-2 [6379 kB] 163s Get:78 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 163s Get:79 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 163s Get:80 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-sphinxdoc all 7.4.7-3 [157 kB] 163s Get:81 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3.12-dev ppc64el 3.12.7-1 [6133 kB] 163s Get:82 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3-dev ppc64el 3.12.6-0ubuntu1 [10.2 kB] 163s Get:83 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3-all-dev ppc64el 3.12.6-0ubuntu1 [916 B] 163s Get:84 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-all ppc64el 3.12.6-0ubuntu1 [888 B] 163s Get:85 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.12-dev ppc64el 3.12.7-1 [505 kB] 163s Get:86 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-dev ppc64el 3.12.6-0ubuntu1 [26.7 kB] 163s Get:87 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-all-dev ppc64el 3.12.6-0ubuntu1 [908 B] 163s Get:88 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-iniconfig all 1.1.1-2 [6024 B] 163s Get:89 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-packaging all 24.1-1 [41.4 kB] 163s Get:90 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pluggy all 1.5.0-1 [21.0 kB] 163s Get:91 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pysam ppc64el 0.22.1+ds-2 [3818 kB] 163s Get:92 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pytest all 8.3.2-1 [251 kB] 164s Get:93 http://ftpmaster.internal/ubuntu plucky/universe ppc64el samtools ppc64el 1.20-3 [676 kB] 164s Get:94 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el tabix ppc64el 1.20+ds-2 [724 kB] 164s Fetched 96.1 MB in 10s (9200 kB/s) 164s Selecting previously unselected package m4. 164s (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 ... 73549 files and directories currently installed.) 164s Preparing to unpack .../00-m4_1.4.19-4build1_ppc64el.deb ... 164s Unpacking m4 (1.4.19-4build1) ... 164s Selecting previously unselected package autoconf. 164s Preparing to unpack .../01-autoconf_2.72-3_all.deb ... 164s Unpacking autoconf (2.72-3) ... 164s Selecting previously unselected package autotools-dev. 164s Preparing to unpack .../02-autotools-dev_20220109.1_all.deb ... 164s Unpacking autotools-dev (20220109.1) ... 164s Selecting previously unselected package automake. 164s Preparing to unpack .../03-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 164s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 164s Selecting previously unselected package autopoint. 164s Preparing to unpack .../04-autopoint_0.22.5-2_all.deb ... 164s Unpacking autopoint (0.22.5-2) ... 164s Selecting previously unselected package libdeflate0:ppc64el. 164s Preparing to unpack .../05-libdeflate0_1.21-1_ppc64el.deb ... 164s Unpacking libdeflate0:ppc64el (1.21-1) ... 164s Selecting previously unselected package libhtscodecs2:ppc64el. 164s Preparing to unpack .../06-libhtscodecs2_1.6.0-1build1_ppc64el.deb ... 164s Unpacking libhtscodecs2:ppc64el (1.6.0-1build1) ... 164s Selecting previously unselected package libhts3t64:ppc64el. 164s Preparing to unpack .../07-libhts3t64_1.20+ds-2_ppc64el.deb ... 164s Unpacking libhts3t64:ppc64el (1.20+ds-2) ... 164s Selecting previously unselected package bcftools. 164s Preparing to unpack .../08-bcftools_1.20-2_ppc64el.deb ... 164s Unpacking bcftools (1.20-2) ... 164s Selecting previously unselected package libisl23:ppc64el. 164s Preparing to unpack .../09-libisl23_0.27-1_ppc64el.deb ... 164s Unpacking libisl23:ppc64el (0.27-1) ... 164s Selecting previously unselected package libmpc3:ppc64el. 164s Preparing to unpack .../10-libmpc3_1.3.1-1build2_ppc64el.deb ... 164s Unpacking libmpc3:ppc64el (1.3.1-1build2) ... 164s Selecting previously unselected package cpp-14-powerpc64le-linux-gnu. 164s Preparing to unpack .../11-cpp-14-powerpc64le-linux-gnu_14.2.0-7ubuntu1_ppc64el.deb ... 164s Unpacking cpp-14-powerpc64le-linux-gnu (14.2.0-7ubuntu1) ... 165s Selecting previously unselected package cpp-14. 165s Preparing to unpack .../12-cpp-14_14.2.0-7ubuntu1_ppc64el.deb ... 165s Unpacking cpp-14 (14.2.0-7ubuntu1) ... 165s Selecting previously unselected package cpp-powerpc64le-linux-gnu. 165s Preparing to unpack .../13-cpp-powerpc64le-linux-gnu_4%3a14.1.0-2ubuntu1_ppc64el.deb ... 165s Unpacking cpp-powerpc64le-linux-gnu (4:14.1.0-2ubuntu1) ... 165s Selecting previously unselected package cpp. 165s Preparing to unpack .../14-cpp_4%3a14.1.0-2ubuntu1_ppc64el.deb ... 165s Unpacking cpp (4:14.1.0-2ubuntu1) ... 165s Selecting previously unselected package libcc1-0:ppc64el. 165s Preparing to unpack .../15-libcc1-0_14.2.0-7ubuntu1_ppc64el.deb ... 165s Unpacking libcc1-0:ppc64el (14.2.0-7ubuntu1) ... 165s Selecting previously unselected package libgomp1:ppc64el. 165s Preparing to unpack .../16-libgomp1_14.2.0-7ubuntu1_ppc64el.deb ... 165s Unpacking libgomp1:ppc64el (14.2.0-7ubuntu1) ... 165s Selecting previously unselected package libitm1:ppc64el. 165s Preparing to unpack .../17-libitm1_14.2.0-7ubuntu1_ppc64el.deb ... 165s Unpacking libitm1:ppc64el (14.2.0-7ubuntu1) ... 165s Selecting previously unselected package libasan8:ppc64el. 165s Preparing to unpack .../18-libasan8_14.2.0-7ubuntu1_ppc64el.deb ... 165s Unpacking libasan8:ppc64el (14.2.0-7ubuntu1) ... 165s Selecting previously unselected package liblsan0:ppc64el. 165s Preparing to unpack .../19-liblsan0_14.2.0-7ubuntu1_ppc64el.deb ... 165s Unpacking liblsan0:ppc64el (14.2.0-7ubuntu1) ... 165s Selecting previously unselected package libtsan2:ppc64el. 165s Preparing to unpack .../20-libtsan2_14.2.0-7ubuntu1_ppc64el.deb ... 165s Unpacking libtsan2:ppc64el (14.2.0-7ubuntu1) ... 165s Selecting previously unselected package libubsan1:ppc64el. 165s Preparing to unpack .../21-libubsan1_14.2.0-7ubuntu1_ppc64el.deb ... 165s Unpacking libubsan1:ppc64el (14.2.0-7ubuntu1) ... 165s Selecting previously unselected package libquadmath0:ppc64el. 165s Preparing to unpack .../22-libquadmath0_14.2.0-7ubuntu1_ppc64el.deb ... 165s Unpacking libquadmath0:ppc64el (14.2.0-7ubuntu1) ... 165s Selecting previously unselected package libgcc-14-dev:ppc64el. 165s Preparing to unpack .../23-libgcc-14-dev_14.2.0-7ubuntu1_ppc64el.deb ... 165s Unpacking libgcc-14-dev:ppc64el (14.2.0-7ubuntu1) ... 165s Selecting previously unselected package gcc-14-powerpc64le-linux-gnu. 165s Preparing to unpack .../24-gcc-14-powerpc64le-linux-gnu_14.2.0-7ubuntu1_ppc64el.deb ... 165s Unpacking gcc-14-powerpc64le-linux-gnu (14.2.0-7ubuntu1) ... 165s Selecting previously unselected package gcc-14. 165s Preparing to unpack .../25-gcc-14_14.2.0-7ubuntu1_ppc64el.deb ... 165s Unpacking gcc-14 (14.2.0-7ubuntu1) ... 165s Selecting previously unselected package gcc-powerpc64le-linux-gnu. 165s Preparing to unpack .../26-gcc-powerpc64le-linux-gnu_4%3a14.1.0-2ubuntu1_ppc64el.deb ... 165s Unpacking gcc-powerpc64le-linux-gnu (4:14.1.0-2ubuntu1) ... 165s Selecting previously unselected package gcc. 165s Preparing to unpack .../27-gcc_4%3a14.1.0-2ubuntu1_ppc64el.deb ... 165s Unpacking gcc (4:14.1.0-2ubuntu1) ... 165s Selecting previously unselected package libstdc++-14-dev:ppc64el. 165s Preparing to unpack .../28-libstdc++-14-dev_14.2.0-7ubuntu1_ppc64el.deb ... 165s Unpacking libstdc++-14-dev:ppc64el (14.2.0-7ubuntu1) ... 166s Selecting previously unselected package g++-14-powerpc64le-linux-gnu. 166s Preparing to unpack .../29-g++-14-powerpc64le-linux-gnu_14.2.0-7ubuntu1_ppc64el.deb ... 166s Unpacking g++-14-powerpc64le-linux-gnu (14.2.0-7ubuntu1) ... 166s Selecting previously unselected package g++-14. 166s Preparing to unpack .../30-g++-14_14.2.0-7ubuntu1_ppc64el.deb ... 166s Unpacking g++-14 (14.2.0-7ubuntu1) ... 166s Selecting previously unselected package g++-powerpc64le-linux-gnu. 166s Preparing to unpack .../31-g++-powerpc64le-linux-gnu_4%3a14.1.0-2ubuntu1_ppc64el.deb ... 166s Unpacking g++-powerpc64le-linux-gnu (4:14.1.0-2ubuntu1) ... 166s Selecting previously unselected package g++. 166s Preparing to unpack .../32-g++_4%3a14.1.0-2ubuntu1_ppc64el.deb ... 166s Unpacking g++ (4:14.1.0-2ubuntu1) ... 166s Selecting previously unselected package build-essential. 166s Preparing to unpack .../33-build-essential_12.10ubuntu1_ppc64el.deb ... 166s Unpacking build-essential (12.10ubuntu1) ... 166s Selecting previously unselected package cython3. 166s Preparing to unpack .../34-cython3_3.0.11+dfsg-1ubuntu1_ppc64el.deb ... 166s Unpacking cython3 (3.0.11+dfsg-1ubuntu1) ... 166s Selecting previously unselected package libdebhelper-perl. 166s Preparing to unpack .../35-libdebhelper-perl_13.20ubuntu1_all.deb ... 166s Unpacking libdebhelper-perl (13.20ubuntu1) ... 166s Selecting previously unselected package libtool. 166s Preparing to unpack .../36-libtool_2.4.7-7build1_all.deb ... 166s Unpacking libtool (2.4.7-7build1) ... 166s Selecting previously unselected package dh-autoreconf. 166s Preparing to unpack .../37-dh-autoreconf_20_all.deb ... 166s Unpacking dh-autoreconf (20) ... 166s Selecting previously unselected package libarchive-zip-perl. 166s Preparing to unpack .../38-libarchive-zip-perl_1.68-1_all.deb ... 166s Unpacking libarchive-zip-perl (1.68-1) ... 166s Selecting previously unselected package libfile-stripnondeterminism-perl. 166s Preparing to unpack .../39-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... 166s Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... 166s Selecting previously unselected package dh-strip-nondeterminism. 166s Preparing to unpack .../40-dh-strip-nondeterminism_1.14.0-1_all.deb ... 166s Unpacking dh-strip-nondeterminism (1.14.0-1) ... 166s Selecting previously unselected package debugedit. 166s Preparing to unpack .../41-debugedit_1%3a5.1-1_ppc64el.deb ... 166s Unpacking debugedit (1:5.1-1) ... 166s Selecting previously unselected package dwz. 166s Preparing to unpack .../42-dwz_0.15-1build6_ppc64el.deb ... 166s Unpacking dwz (0.15-1build6) ... 166s Selecting previously unselected package gettext. 166s Preparing to unpack .../43-gettext_0.22.5-2_ppc64el.deb ... 166s Unpacking gettext (0.22.5-2) ... 166s Selecting previously unselected package intltool-debian. 166s Preparing to unpack .../44-intltool-debian_0.35.0+20060710.6_all.deb ... 166s Unpacking intltool-debian (0.35.0+20060710.6) ... 166s Selecting previously unselected package po-debconf. 166s Preparing to unpack .../45-po-debconf_1.0.21+nmu1_all.deb ... 166s Unpacking po-debconf (1.0.21+nmu1) ... 166s Selecting previously unselected package debhelper. 166s Preparing to unpack .../46-debhelper_13.20ubuntu1_all.deb ... 166s Unpacking debhelper (13.20ubuntu1) ... 166s Selecting previously unselected package dh-python. 166s Preparing to unpack .../47-dh-python_6.20240824_all.deb ... 166s Unpacking dh-python (6.20240824) ... 166s Selecting previously unselected package libbrotli-dev:ppc64el. 166s Preparing to unpack .../48-libbrotli-dev_1.1.0-2build2_ppc64el.deb ... 166s Unpacking libbrotli-dev:ppc64el (1.1.0-2build2) ... 166s Selecting previously unselected package libbz2-dev:ppc64el. 166s Preparing to unpack .../49-libbz2-dev_1.0.8-6_ppc64el.deb ... 166s Unpacking libbz2-dev:ppc64el (1.0.8-6) ... 166s Selecting previously unselected package libevent-2.1-7t64:ppc64el. 166s Preparing to unpack .../50-libevent-2.1-7t64_2.1.12-stable-10_ppc64el.deb ... 166s Unpacking libevent-2.1-7t64:ppc64el (2.1.12-stable-10) ... 166s Selecting previously unselected package libunbound8:ppc64el. 166s Preparing to unpack .../51-libunbound8_1.20.0-1ubuntu2.1_ppc64el.deb ... 166s Unpacking libunbound8:ppc64el (1.20.0-1ubuntu2.1) ... 166s Selecting previously unselected package libgnutls-dane0t64:ppc64el. 166s Preparing to unpack .../52-libgnutls-dane0t64_3.8.6-2ubuntu1_ppc64el.deb ... 166s Unpacking libgnutls-dane0t64:ppc64el (3.8.6-2ubuntu1) ... 166s Selecting previously unselected package libgnutls-openssl27t64:ppc64el. 166s Preparing to unpack .../53-libgnutls-openssl27t64_3.8.6-2ubuntu1_ppc64el.deb ... 166s Unpacking libgnutls-openssl27t64:ppc64el (3.8.6-2ubuntu1) ... 166s Selecting previously unselected package libidn2-dev:ppc64el. 166s Preparing to unpack .../54-libidn2-dev_2.3.7-2build2_ppc64el.deb ... 166s Unpacking libidn2-dev:ppc64el (2.3.7-2build2) ... 166s Selecting previously unselected package libp11-kit-dev:ppc64el. 166s Preparing to unpack .../55-libp11-kit-dev_0.25.5-2ubuntu1_ppc64el.deb ... 166s Unpacking libp11-kit-dev:ppc64el (0.25.5-2ubuntu1) ... 166s Selecting previously unselected package libtasn1-6-dev:ppc64el. 166s Preparing to unpack .../56-libtasn1-6-dev_4.19.0-3build1_ppc64el.deb ... 166s Unpacking libtasn1-6-dev:ppc64el (4.19.0-3build1) ... 166s Selecting previously unselected package libgmpxx4ldbl:ppc64el. 166s Preparing to unpack .../57-libgmpxx4ldbl_2%3a6.3.0+dfsg-2ubuntu7_ppc64el.deb ... 166s Unpacking libgmpxx4ldbl:ppc64el (2:6.3.0+dfsg-2ubuntu7) ... 166s Selecting previously unselected package libgmp-dev:ppc64el. 166s Preparing to unpack .../58-libgmp-dev_2%3a6.3.0+dfsg-2ubuntu7_ppc64el.deb ... 166s Unpacking libgmp-dev:ppc64el (2:6.3.0+dfsg-2ubuntu7) ... 166s Selecting previously unselected package nettle-dev:ppc64el. 166s Preparing to unpack .../59-nettle-dev_3.10-1_ppc64el.deb ... 166s Unpacking nettle-dev:ppc64el (3.10-1) ... 167s Selecting previously unselected package libgnutls28-dev:ppc64el. 167s Preparing to unpack .../60-libgnutls28-dev_3.8.6-2ubuntu1_ppc64el.deb ... 167s Unpacking libgnutls28-dev:ppc64el (3.8.6-2ubuntu1) ... 167s Selecting previously unselected package libpkgconf3:ppc64el. 167s Preparing to unpack .../61-libpkgconf3_1.8.1-3ubuntu1_ppc64el.deb ... 167s Unpacking libpkgconf3:ppc64el (1.8.1-3ubuntu1) ... 167s Selecting previously unselected package pkgconf-bin. 167s Preparing to unpack .../62-pkgconf-bin_1.8.1-3ubuntu1_ppc64el.deb ... 167s Unpacking pkgconf-bin (1.8.1-3ubuntu1) ... 167s Selecting previously unselected package pkgconf:ppc64el. 167s Preparing to unpack .../63-pkgconf_1.8.1-3ubuntu1_ppc64el.deb ... 167s Unpacking pkgconf:ppc64el (1.8.1-3ubuntu1) ... 167s Selecting previously unselected package libnghttp2-dev:ppc64el. 167s Preparing to unpack .../64-libnghttp2-dev_1.62.1-2_ppc64el.deb ... 167s Unpacking libnghttp2-dev:ppc64el (1.62.1-2) ... 167s Selecting previously unselected package libpsl-dev:ppc64el. 167s Preparing to unpack .../65-libpsl-dev_0.21.2-1.1build1_ppc64el.deb ... 167s Unpacking libpsl-dev:ppc64el (0.21.2-1.1build1) ... 167s Selecting previously unselected package zlib1g-dev:ppc64el. 167s Preparing to unpack .../66-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_ppc64el.deb ... 167s Unpacking zlib1g-dev:ppc64el (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 167s Selecting previously unselected package librtmp-dev:ppc64el. 167s Preparing to unpack .../67-librtmp-dev_2.4+20151223.gitfa8646d.1-2build7_ppc64el.deb ... 167s Unpacking librtmp-dev:ppc64el (2.4+20151223.gitfa8646d.1-2build7) ... 167s Selecting previously unselected package libssl-dev:ppc64el. 167s Preparing to unpack .../68-libssl-dev_3.3.1-2ubuntu2_ppc64el.deb ... 167s Unpacking libssl-dev:ppc64el (3.3.1-2ubuntu2) ... 167s Selecting previously unselected package libssh2-1-dev:ppc64el. 167s Preparing to unpack .../69-libssh2-1-dev_1.11.0-7_ppc64el.deb ... 167s Unpacking libssh2-1-dev:ppc64el (1.11.0-7) ... 167s Selecting previously unselected package libzstd-dev:ppc64el. 167s Preparing to unpack .../70-libzstd-dev_1.5.6+dfsg-1_ppc64el.deb ... 167s Unpacking libzstd-dev:ppc64el (1.5.6+dfsg-1) ... 167s Selecting previously unselected package libcurl4-gnutls-dev:ppc64el. 167s Preparing to unpack .../71-libcurl4-gnutls-dev_8.9.1-2ubuntu2_ppc64el.deb ... 167s Unpacking libcurl4-gnutls-dev:ppc64el (8.9.1-2ubuntu2) ... 167s Selecting previously unselected package libdeflate-dev:ppc64el. 167s Preparing to unpack .../72-libdeflate-dev_1.21-1_ppc64el.deb ... 167s Unpacking libdeflate-dev:ppc64el (1.21-1) ... 167s Selecting previously unselected package libexpat1-dev:ppc64el. 167s Preparing to unpack .../73-libexpat1-dev_2.6.2-2_ppc64el.deb ... 167s Unpacking libexpat1-dev:ppc64el (2.6.2-2) ... 167s Selecting previously unselected package liblzma-dev:ppc64el. 167s Preparing to unpack .../74-liblzma-dev_5.6.2-2_ppc64el.deb ... 167s Unpacking liblzma-dev:ppc64el (5.6.2-2) ... 167s Selecting previously unselected package libhts-dev:ppc64el. 167s Preparing to unpack .../75-libhts-dev_1.20+ds-2_ppc64el.deb ... 167s Unpacking libhts-dev:ppc64el (1.20+ds-2) ... 167s Selecting previously unselected package libjs-jquery. 167s Preparing to unpack .../76-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 167s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 167s Selecting previously unselected package libjs-underscore. 167s Preparing to unpack .../77-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 167s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 167s Selecting previously unselected package libjs-sphinxdoc. 167s Preparing to unpack .../78-libjs-sphinxdoc_7.4.7-3_all.deb ... 167s Unpacking libjs-sphinxdoc (7.4.7-3) ... 167s Selecting previously unselected package libpython3.12-dev:ppc64el. 167s Preparing to unpack .../79-libpython3.12-dev_3.12.7-1_ppc64el.deb ... 167s Unpacking libpython3.12-dev:ppc64el (3.12.7-1) ... 167s Selecting previously unselected package libpython3-dev:ppc64el. 167s Preparing to unpack .../80-libpython3-dev_3.12.6-0ubuntu1_ppc64el.deb ... 167s Unpacking libpython3-dev:ppc64el (3.12.6-0ubuntu1) ... 167s Selecting previously unselected package libpython3-all-dev:ppc64el. 167s Preparing to unpack .../81-libpython3-all-dev_3.12.6-0ubuntu1_ppc64el.deb ... 167s Unpacking libpython3-all-dev:ppc64el (3.12.6-0ubuntu1) ... 167s Selecting previously unselected package python3-all. 167s Preparing to unpack .../82-python3-all_3.12.6-0ubuntu1_ppc64el.deb ... 167s Unpacking python3-all (3.12.6-0ubuntu1) ... 167s Selecting previously unselected package python3.12-dev. 167s Preparing to unpack .../83-python3.12-dev_3.12.7-1_ppc64el.deb ... 167s Unpacking python3.12-dev (3.12.7-1) ... 167s Selecting previously unselected package python3-dev. 167s Preparing to unpack .../84-python3-dev_3.12.6-0ubuntu1_ppc64el.deb ... 167s Unpacking python3-dev (3.12.6-0ubuntu1) ... 167s Selecting previously unselected package python3-all-dev. 167s Preparing to unpack .../85-python3-all-dev_3.12.6-0ubuntu1_ppc64el.deb ... 167s Unpacking python3-all-dev (3.12.6-0ubuntu1) ... 167s Selecting previously unselected package python3-iniconfig. 167s Preparing to unpack .../86-python3-iniconfig_1.1.1-2_all.deb ... 167s Unpacking python3-iniconfig (1.1.1-2) ... 167s Selecting previously unselected package python3-packaging. 167s Preparing to unpack .../87-python3-packaging_24.1-1_all.deb ... 167s Unpacking python3-packaging (24.1-1) ... 167s Selecting previously unselected package python3-pluggy. 167s Preparing to unpack .../88-python3-pluggy_1.5.0-1_all.deb ... 167s Unpacking python3-pluggy (1.5.0-1) ... 167s Selecting previously unselected package python3-pysam. 167s Preparing to unpack .../89-python3-pysam_0.22.1+ds-2_ppc64el.deb ... 167s Unpacking python3-pysam (0.22.1+ds-2) ... 168s Selecting previously unselected package python3-pytest. 168s Preparing to unpack .../90-python3-pytest_8.3.2-1_all.deb ... 168s Unpacking python3-pytest (8.3.2-1) ... 168s Selecting previously unselected package samtools. 168s Preparing to unpack .../91-samtools_1.20-3_ppc64el.deb ... 168s Unpacking samtools (1.20-3) ... 168s Selecting previously unselected package tabix. 168s Preparing to unpack .../92-tabix_1.20+ds-2_ppc64el.deb ... 168s Unpacking tabix (1.20+ds-2) ... 168s Selecting previously unselected package autopkgtest-satdep. 168s Preparing to unpack .../93-1-autopkgtest-satdep.deb ... 168s Unpacking autopkgtest-satdep (0) ... 168s Setting up libhtscodecs2:ppc64el (1.6.0-1build1) ... 168s Setting up dh-python (6.20240824) ... 168s Setting up libgnutls-openssl27t64:ppc64el (3.8.6-2ubuntu1) ... 168s Setting up python3-iniconfig (1.1.1-2) ... 168s Setting up libzstd-dev:ppc64el (1.5.6+dfsg-1) ... 168s Setting up libarchive-zip-perl (1.68-1) ... 168s Setting up libdebhelper-perl (13.20ubuntu1) ... 168s Setting up libdeflate0:ppc64el (1.21-1) ... 168s Setting up m4 (1.4.19-4build1) ... 168s Setting up libevent-2.1-7t64:ppc64el (2.1.12-stable-10) ... 168s Setting up python3-all (3.12.6-0ubuntu1) ... 168s Setting up libgomp1:ppc64el (14.2.0-7ubuntu1) ... 168s Setting up libpsl-dev:ppc64el (0.21.2-1.1build1) ... 168s Setting up autotools-dev (20220109.1) ... 168s Setting up python3-packaging (24.1-1) ... 168s Setting up libunbound8:ppc64el (1.20.0-1ubuntu2.1) ... 168s Setting up libpkgconf3:ppc64el (1.8.1-3ubuntu1) ... 168s Setting up libgmpxx4ldbl:ppc64el (2:6.3.0+dfsg-2ubuntu7) ... 168s Setting up libexpat1-dev:ppc64el (2.6.2-2) ... 168s Setting up libgnutls-dane0t64:ppc64el (3.8.6-2ubuntu1) ... 168s Setting up libquadmath0:ppc64el (14.2.0-7ubuntu1) ... 168s Setting up libssl-dev:ppc64el (3.3.1-2ubuntu2) ... 168s Setting up libmpc3:ppc64el (1.3.1-1build2) ... 168s Setting up cython3 (3.0.11+dfsg-1ubuntu1) ... 169s Setting up autopoint (0.22.5-2) ... 169s Setting up pkgconf-bin (1.8.1-3ubuntu1) ... 169s Setting up libidn2-dev:ppc64el (2.3.7-2build2) ... 169s Setting up autoconf (2.72-3) ... 169s Setting up python3-pluggy (1.5.0-1) ... 169s Setting up liblzma-dev:ppc64el (5.6.2-2) ... 169s Setting up libubsan1:ppc64el (14.2.0-7ubuntu1) ... 169s Setting up zlib1g-dev:ppc64el (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 169s Setting up dwz (0.15-1build6) ... 169s Setting up libasan8:ppc64el (14.2.0-7ubuntu1) ... 169s Setting up debugedit (1:5.1-1) ... 169s Setting up libhts3t64:ppc64el (1.20+ds-2) ... 169s Setting up libtsan2:ppc64el (14.2.0-7ubuntu1) ... 169s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 169s Setting up libisl23:ppc64el (0.27-1) ... 169s Setting up libtasn1-6-dev:ppc64el (4.19.0-3build1) ... 169s Setting up libdeflate-dev:ppc64el (1.21-1) ... 169s Setting up tabix (1.20+ds-2) ... 169s Setting up libcc1-0:ppc64el (14.2.0-7ubuntu1) ... 169s Setting up libbrotli-dev:ppc64el (1.1.0-2build2) ... 169s Setting up liblsan0:ppc64el (14.2.0-7ubuntu1) ... 169s Setting up libp11-kit-dev:ppc64el (0.25.5-2ubuntu1) ... 169s Setting up libitm1:ppc64el (14.2.0-7ubuntu1) ... 169s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 169s Setting up libbz2-dev:ppc64el (1.0.8-6) ... 169s Setting up automake (1:1.16.5-1.3ubuntu1) ... 169s update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode 169s Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... 169s Setting up gettext (0.22.5-2) ... 169s Setting up python3-pysam (0.22.1+ds-2) ... 169s Setting up libgmp-dev:ppc64el (2:6.3.0+dfsg-2ubuntu7) ... 169s Setting up nettle-dev:ppc64el (3.10-1) ... 169s Setting up python3-pytest (8.3.2-1) ... 170s Setting up bcftools (1.20-2) ... 170s Setting up libpython3.12-dev:ppc64el (3.12.7-1) ... 170s Setting up pkgconf:ppc64el (1.8.1-3ubuntu1) ... 170s Setting up samtools (1.20-3) ... 170s Setting up intltool-debian (0.35.0+20060710.6) ... 170s Setting up python3.12-dev (3.12.7-1) ... 170s Setting up cpp-14-powerpc64le-linux-gnu (14.2.0-7ubuntu1) ... 170s Setting up libssh2-1-dev:ppc64el (1.11.0-7) ... 170s Setting up libjs-sphinxdoc (7.4.7-3) ... 170s Setting up cpp-14 (14.2.0-7ubuntu1) ... 170s Setting up dh-strip-nondeterminism (1.14.0-1) ... 170s Setting up libgcc-14-dev:ppc64el (14.2.0-7ubuntu1) ... 170s Setting up libstdc++-14-dev:ppc64el (14.2.0-7ubuntu1) ... 170s Setting up cpp-powerpc64le-linux-gnu (4:14.1.0-2ubuntu1) ... 170s Setting up gcc-14-powerpc64le-linux-gnu (14.2.0-7ubuntu1) ... 170s Setting up libgnutls28-dev:ppc64el (3.8.6-2ubuntu1) ... 170s Setting up libnghttp2-dev:ppc64el (1.62.1-2) ... 170s Setting up libpython3-dev:ppc64el (3.12.6-0ubuntu1) ... 170s Setting up g++-14-powerpc64le-linux-gnu (14.2.0-7ubuntu1) ... 170s Setting up po-debconf (1.0.21+nmu1) ... 170s Setting up gcc-14 (14.2.0-7ubuntu1) ... 170s Setting up gcc-powerpc64le-linux-gnu (4:14.1.0-2ubuntu1) ... 170s Setting up libpython3-all-dev:ppc64el (3.12.6-0ubuntu1) ... 170s Setting up python3-dev (3.12.6-0ubuntu1) ... 170s Setting up librtmp-dev:ppc64el (2.4+20151223.gitfa8646d.1-2build7) ... 170s Setting up cpp (4:14.1.0-2ubuntu1) ... 170s Setting up g++-14 (14.2.0-7ubuntu1) ... 170s Setting up g++-powerpc64le-linux-gnu (4:14.1.0-2ubuntu1) ... 170s Setting up python3-all-dev (3.12.6-0ubuntu1) ... 170s Setting up libtool (2.4.7-7build1) ... 170s Setting up libcurl4-gnutls-dev:ppc64el (8.9.1-2ubuntu2) ... 170s Setting up gcc (4:14.1.0-2ubuntu1) ... 170s Setting up dh-autoreconf (20) ... 170s Setting up g++ (4:14.1.0-2ubuntu1) ... 170s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 170s Setting up build-essential (12.10ubuntu1) ... 170s Setting up libhts-dev:ppc64el (1.20+ds-2) ... 170s Setting up debhelper (13.20ubuntu1) ... 170s Setting up autopkgtest-satdep (0) ... 170s Processing triggers for man-db (2.12.1-3) ... 171s Processing triggers for install-info (7.1.1-1) ... 171s Processing triggers for libc-bin (2.40-1ubuntu3) ... 175s (Reading database ... 78200 files and directories currently installed.) 175s Removing autopkgtest-satdep (0) ... 176s autopkgtest [07:45:36]: test command1: export HOME=$PWD && make -C tests/pysam_data && make -C tests/cbcf_data && pytest-3 176s autopkgtest [07:45:36]: test command1: [----------------------- 176s make: Entering directory '/tmp/autopkgtest.TIYAUm/build.Rhj/src/tests/pysam_data' 176s samtools faidx ex1.fa 176s samtools view --no-PG -bo ex1.bam -t ex1.fa.fai ex1.sam.gz 176s samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz 176s [mpileup] 1 samples in 1 input files 176s gunzip < ex1.sam.gz > ex1.sam 176s samtools index ex1.bam 176s samtools view --no-PG -h ex1.bam | gzip > ex2.sam.gz 176s gunzip < ex2.sam.gz > ex2.sam 176s samtools view --no-PG -bo ex2.bam ex2.sam 176s samtools index ex2.bam 176s samtools calmd --no-PG --output-fmt BAM ex2.bam ex1.fa > with_md.sam.gz 176s [bam_fillmd1] different NM for read 'EAS139_11:7:46:695:738': 3 -> 8 176s [bam_fillmd1] different NM for read 'EAS218_4:1:48:9:409': 0 -> 5 176s [bam_fillmd1] different NM for read 'B7_591:7:200:192:373': 0 -> 5 176s [bam_fillmd1] different NM for read 'EAS56_65:1:163:846:223': 0 -> 5 176s [bam_fillmd1] different NM for read 'EAS114_30:7:283:799:560': 0 -> 5 176s [bam_fillmd1] different NM for read 'B7_595:4:84:802:737': 0 -> 4 176s [bam_fillmd1] different NM for read 'EAS51_66:5:308:400:602': 0 -> 3 176s [bam_fillmd1] different NM for read 'EAS54_81:2:285:367:932': 0 -> 3 176s [bam_fillmd1] different NM for read 'EAS114_39:1:70:147:84': 0 -> 3 176s [bam_fillmd1] different NM for read 'EAS56_53:1:124:243:35': 2 -> 5 176s [bam_fillmd1] different NM for read 'EAS1_103:2:226:302:758': 2 -> 3 176s [bam_fillmd1] different NM for read 'EAS114_28:6:175:705:982': 1 -> 0 176s [bam_fillmd1] different NM for read 'EAS51_64:4:179:389:585': 7 -> 8 176s [bam_fillmd1] different NM for read 'B7_589:1:122:337:968': 3 -> 2 176s [bam_fillmd1] different NM for read 'B7_610:4:15:805:420': 4 -> 5 176s [bam_fillmd1] different NM for read 'B7_591:2:279:124:41': 2 -> 4 176s [bam_fillmd1] different NM for read 'EAS112_32:8:89:254:332': 0 -> 1 176s [bam_fillmd1] different NM for read 'B7_597:7:103:731:697': 0 -> 2 176s [bam_fillmd1] different NM for read 'EAS139_11:2:71:83:58': 0 -> 2 176s [bam_fillmd1] different NM for read 'EAS192_3:4:63:5:870': 0 -> 2 176s [bam_fillmd1] different NM for read 'EAS139_19:2:29:1822:1881': 0 -> 2 176s [bam_fillmd1] different NM for read 'EAS188_7:3:15:568:42': 2 -> 1 176s [bam_fillmd1] different NM for read 'EAS1_95:4:176:971:874': 0 -> 1 176s [bam_fillmd1] different NM for read 'EAS1_99:1:34:649:318': 3 -> 4 176s [bam_fillmd1] different NM for read 'EAS54_65:4:61:346:384': 3 -> 4 176s [bam_fillmd1] different NM for read 'B7_597:6:20:592:496': 0 -> 1 176s [bam_fillmd1] different NM for read 'B7_597:4:38:999:463': 2 -> 1 176s [bam_fillmd1] different NM for read 'EAS114_28:5:23:944:377': 0 -> 3 176s [bam_fillmd1] different NM for read 'EAS219_1:3:90:219:528': 0 -> 3 176s [bam_fillmd1] different NM for read 'EAS1_108:5:89:942:84': 0 -> 4 176s [bam_fillmd1] different NM for read 'EAS1_108:6:159:493:275': 0 -> 5 176s [bam_fillmd1] different NM for read 'EAS139_11:1:81:1019:558': 0 -> 5 176s [bam_fillmd1] different NM for read 'EAS51_62:7:162:195:761': 0 -> 4 176s [bam_fillmd1] different NM for read 'B7_597:3:115:646:430': 0 -> 4 176s [bam_fillmd1] different NM for read 'EAS114_30:6:243:209:110': 0 -> 4 176s [bam_fillmd1] different NM for read 'EAS1_108:2:266:994:429': 0 -> 4 176s [bam_fillmd1] different NM for read 'EAS114_30:5:32:461:154': 0 -> 4 176s [bam_fillmd1] different NM for read 'EAS114_39:6:7:492:1088': 0 -> 4 176s [bam_fillmd1] different NM for read 'EAS1_95:6:174:650:125': 0 -> 4 176s [bam_fillmd1] different NM for read 'EAS56_59:6:89:457:591': 1 -> 5 176s [bam_fillmd1] different NM for read 'EAS114_39:2:38:670:564': 0 -> 4 176s [bam_fillmd1] different NM for read 'EAS188_7:4:92:693:228': 1 -> 6 176s [bam_fillmd1] different NM for read 'EAS218_1:4:61:1369:440': 0 -> 4 176s [bam_fillmd1] different NM for read 'EAS114_26:4:123:1001:580': 0 -> 4 176s [bam_fillmd1] different NM for read 'EAS114_39:4:10:1312:1558': 0 -> 4 176s [bam_fillmd1] different NM for read 'EAS220_1:8:45:178:1321': 0 -> 4 176s [bam_fillmd1] different NM for read 'EAS56_59:5:125:137:58': 0 -> 4 176s [bam_fillmd1] different NM for read 'EAS192_3:3:285:349:797': 1 -> 5 176s [bam_fillmd1] different NM for read 'EAS114_45:5:56:1757:1319': 0 -> 4 176s [bam_fillmd1] different NM for read 'B7_591:3:291:404:199': 0 -> 4 176s [bam_fillmd1] different NM for read 'EAS54_65:7:159:253:353': 0 -> 4 176s [bam_fillmd1] different NM for read 'EAS56_57:1:122:38:103': 0 -> 4 176s [bam_fillmd1] different NM for read 'EAS188_4:5:103:870:105': 0 -> 4 176s [bam_fillmd1] different NM for read 'EAS1_105:8:24:718:322': 3 -> 7 176s [bam_fillmd1] different NM for read 'EAS51_64:6:118:41:489': 0 -> 4 176s [bam_fillmd1] different NM for read 'EAS56_61:3:165:665:220': 0 -> 4 176s [bam_fillmd1] different NM for read 'EAS114_30:6:238:803:383': 0 -> 4 176s [bam_fillmd1] different NM for read 'EAS1_105:3:232:364:583': 0 -> 3 176s [bam_fillmd1] different NM for read 'B7_595:2:29:729:70': 3 -> 4 176s [bam_fillmd1] different NM for read 'EAS114_30:6:220:809:850': 4 -> 6 176s [bam_fillmd1] different NM for read 'EAS54_65:2:264:157:150': 3 -> 5 176s [bam_fillmd1] different NM for read 'B7_595:8:26:242:35': 2 -> 1 176s [bam_fillmd1] different NM for read 'B7_610:7:34:144:868': 4 -> 5 176s [bam_fillmd1] different NM for read 'B7_597:8:147:360:141': 1 -> 2 176s [bam_fillmd1] different NM for read 'EAS139_19:2:82:154:1333': 0 -> 4 176s [bam_fillmd1] different NM for read 'EAS56_63:3:41:468:459': 0 -> 3 176s [bam_fillmd1] different NM for read 'EAS1_97:4:274:287:423': 0 -> 1 176s [bam_fillmd1] different NM for read 'EAS114_30:2:303:428:326': 0 -> 1 176s [bam_fillmd1] different NM for read 'EAS54_71:8:105:854:975': 0 -> 3 176s gunzip < with_md.sam.gz > with_md.sam 176s samtools view --no-PG -bo with_md.bam with_md.sam 176s [W::bam_hdr_read] EOF marker is absent. The input is probably truncated 176s samtools index with_md.bam 176s samtools view --no-PG -bu -o uncompressed.bam ex2.sam 176s samtools view --no-PG -bo MM-chebi.bam MM-chebi.sam 176s samtools view --no-PG -bo MM-double.bam MM-double.sam 176s samtools view --no-PG -bo MM-multi.bam MM-multi.sam 176s samtools view --no-PG -bo MM-orient.bam MM-orient.sam 176s samtools view --no-PG -bo ex10.bam ex10.sam 176s samtools view --no-PG -bo ex3.bam ex3.sam 176s samtools view --no-PG -bo ex4.bam ex4.sam 176s samtools view --no-PG -bo ex5.bam ex5.sam 176s samtools view --no-PG -bo ex6.bam ex6.sam 176s samtools view --no-PG -bo ex8.bam ex8.sam 176s samtools view --no-PG -bo ex9_fail.bam ex9_fail.sam 176s samtools view --no-PG -bo ex9_nofail.bam ex9_nofail.sam 176s samtools view --no-PG -bo ex_spliced.bam ex_spliced.sam 176s samtools view --no-PG -bo example_aligned_pairs.bam example_aligned_pairs.sam 176s samtools view --no-PG -bo example_btag.bam example_btag.sam 176s samtools view --no-PG -bo example_dash_in_chr.bam example_dash_in_chr.sam 176s samtools view --no-PG -bo example_empty_header.bam example_empty_header.sam 176s samtools view --no-PG -bo example_empty_with_header.bam example_empty_with_header.sam 176s samtools view --no-PG -bo example_reverse_complement.bam example_reverse_complement.sam 176s touch tmp.list 176s samtools view --no-PG -bo example_unmapped_reads_no_sq.bam -t tmp.list example_unmapped_reads_no_sq.sam 176s rm -f tmp.list 176s samtools view --no-PG -bo issue100.bam issue100.sam 176s samtools view --no-PG -bo rg_with_tab.bam rg_with_tab.sam 176s samtools view --no-PG -bo softclip.bam softclip.sam 176s samtools view --no-PG -bo tag_bug.bam tag_bug.sam 176s samtools view --no-PG -bo test_mapped_unmapped.bam test_mapped_unmapped.sam 176s samtools view --no-PG -bo test_query_position.bam test_query_position.sam 176s samtools view --no-PG -bo test_unaligned.bam test_unaligned.sam 176s samtools index MM-chebi.bam 176s samtools index MM-double.bam 176s samtools index MM-multi.bam 176s samtools index MM-orient.bam 176s samtools index ex10.bam 176s samtools index ex3.bam 176s samtools index ex4.bam 176s samtools index ex5.bam 176s samtools index ex6.bam 176s samtools index ex8.bam 176s samtools index ex9_fail.bam 176s samtools index ex9_nofail.bam 176s samtools index ex_spliced.bam 176s samtools index example_aligned_pairs.bam 176s samtools index example_btag.bam 176s samtools index example_dash_in_chr.bam 176s samtools index example_empty_header.bam 176s samtools index example_empty_with_header.bam 176s samtools index example_reverse_complement.bam 176s samtools index example_unmapped_reads_no_sq.bam 176s samtools index issue100.bam 176s samtools index rg_with_tab.bam 176s samtools index softclip.bam 176s samtools index tag_bug.bam 176s samtools index test_mapped_unmapped.bam 176s samtools index test_query_position.bam 176s samtools index test_unaligned.bam 176s samtools view --no-PG -Co ex1.cram -T ex1.fa ex1.sam 176s samtools view --no-PG -Co ex2.cram -T ex1.fa ex2.sam 176s samtools view --no-PG -Co ex3.cram -T ex1.fa ex3.sam 176s samtools index ex1.cram 176s samtools index ex2.cram 177s samtools index ex3.cram 177s cp ex1.bam example_bai.bam 177s samtools index example_bai.bam 177s mv example_bai.bam.bai example_bai.bai 177s dd if=ex2.bam of=ex2_truncated.bam bs=$((`wc -c < ex2.bam`-512)) count=1 177s 1+0 records in 177s 1+0 records out 177s 122288 bytes (122 kB, 119 KiB) copied, 0.000121638 s, 1.0 GB/s 177s (bgzip -d < ex2.bam; printf '\37\0\0\0\1\0\0\0') | bgzip > ex2_corrupt.bam 177s grep "^@" ex2.sam | samtools view --no-PG -bo empty.bam - 177s samtools index empty.bam 177s cp ex1.bam explicit_index.bam 177s cp ex1.cram explicit_index.cram 177s gzip < faidx_empty_seq.fq > faidx_empty_seq.fq.gz 177s bgzip < ex1.fa > ex1.fa.gz 177s samtools faidx ex1.fa.gz 177s cp ex1.bam ex1_csi.bam 177s samtools index -c ex1_csi.bam 177s touch all.stamp 177s rm with_md.sam 177s make: Leaving directory '/tmp/autopkgtest.TIYAUm/build.Rhj/src/tests/pysam_data' 177s make: Entering directory '/tmp/autopkgtest.TIYAUm/build.Rhj/src/tests/cbcf_data' 177s bgzip < example_vcf40.vcf > example_vcf40.vcf.gz 177s tabix -p vcf example_vcf40.vcf.gz # create tbi index 177s bcftools index example_vcf40.vcf.gz # create csi index 177s bgzip < example_vcf42.vcf > example_vcf42.vcf.gz 177s tabix -p vcf example_vcf42.vcf.gz # create tbi index 177s bcftools index example_vcf42.vcf.gz # create csi index 177s bgzip < example_vcf42_only_header.vcf > example_vcf42_only_header.vcf.gz 177s tabix -p vcf example_vcf42_only_header.vcf.gz # create tbi index 177s bcftools index example_vcf42_only_header.vcf.gz # create csi index 177s bgzip < example_vcf42_withcontigs.vcf > example_vcf42_withcontigs.vcf.gz 177s tabix -p vcf example_vcf42_withcontigs.vcf.gz # create tbi index 177s bcftools index example_vcf42_withcontigs.vcf.gz # create csi index 177s bgzip < example_vcf43.vcf > example_vcf43.vcf.gz 177s tabix -p vcf example_vcf43.vcf.gz # create tbi index 177s bcftools index example_vcf43.vcf.gz # create csi index 177s bgzip < example_vcf43_with_utf8.vcf > example_vcf43_with_utf8.vcf.gz 177s tabix -p vcf example_vcf43_with_utf8.vcf.gz # create tbi index 177s bcftools index example_vcf43_with_utf8.vcf.gz # create csi index 177s bgzip < gnomad.vcf > gnomad.vcf.gz 177s tabix -p vcf gnomad.vcf.gz # create tbi index 177s bcftools index gnomad.vcf.gz # create csi index 177s bgzip < gnomad_fixed.vcf > gnomad_fixed.vcf.gz 177s tabix -p vcf gnomad_fixed.vcf.gz # create tbi index 177s bcftools index gnomad_fixed.vcf.gz # create csi index 177s bgzip < missing_genotypes.vcf > missing_genotypes.vcf.gz 177s tabix -p vcf missing_genotypes.vcf.gz # create tbi index 177s bcftools index missing_genotypes.vcf.gz # create csi index 177s bcftools view -O b example_vcf40.vcf.gz -o example_vcf40.bcf 177s bcftools index example_vcf40.bcf 177s bcftools view -O b example_vcf42.vcf.gz -o example_vcf42.bcf 177s bcftools index example_vcf42.bcf 177s bcftools view -O b example_vcf42_only_header.vcf.gz -o example_vcf42_only_header.bcf 177s bcftools index example_vcf42_only_header.bcf 177s bcftools view -O b example_vcf42_withcontigs.vcf.gz -o example_vcf42_withcontigs.bcf 177s bcftools index example_vcf42_withcontigs.bcf 177s bcftools view -O b example_vcf43.vcf.gz -o example_vcf43.bcf 177s bcftools index example_vcf43.bcf 177s bcftools view -O b example_vcf43_with_utf8.vcf.gz -o example_vcf43_with_utf8.bcf 177s bcftools index example_vcf43_with_utf8.bcf 177s bcftools view -O b gnomad.vcf.gz -o gnomad.bcf 177s bcftools index gnomad.bcf 177s bcftools view -O b gnomad_fixed.vcf.gz -o gnomad_fixed.bcf 177s [W::bcf_hdr_check_sanity] PL should be declared as Number=G 177s bcftools index gnomad_fixed.bcf 177s [W::bcf_hdr_check_sanity] PL should be declared as Number=G 177s bcftools view -O b missing_genotypes.vcf.gz -o missing_genotypes.bcf 177s bcftools index missing_genotypes.bcf 177s touch all.stamp 177s make: Leaving directory '/tmp/autopkgtest.TIYAUm/build.Rhj/src/tests/cbcf_data' 177s ============================= test session starts ============================== 177s platform linux -- Python 3.12.7, pytest-8.3.2, pluggy-1.5.0 -- /usr/bin/python3 177s cachedir: .pytest_cache 177s rootdir: /tmp/autopkgtest.TIYAUm/build.Rhj/src 177s configfile: setup.cfg 177s testpaths: pysam, tests 177s plugins: typeguard-4.3.0 178s collecting ... collected 951 items 178s 178s tests/AlignedSegment_test.py::TestAlignedSegment::testBlocks PASSED 178s tests/AlignedSegment_test.py::TestAlignedSegment::testCompare PASSED 178s tests/AlignedSegment_test.py::TestAlignedSegment::testEmpty PASSED 178s tests/AlignedSegment_test.py::TestAlignedSegment::testFullReferencePositions PASSED 178s tests/AlignedSegment_test.py::TestAlignedSegment::testHashing PASSED 178s tests/AlignedSegment_test.py::TestAlignedSegment::testLargeRead PASSED 178s tests/AlignedSegment_test.py::TestAlignedSegment::testNoSequence PASSED 178s tests/AlignedSegment_test.py::TestAlignedSegment::testPositions PASSED 178s tests/AlignedSegment_test.py::TestAlignedSegment::testSettingTagInEmptyRead PASSED 178s tests/AlignedSegment_test.py::TestAlignedSegment::testStrOfEmptyRead PASSED 178s tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate PASSED 178s tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate2 PASSED 178s tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateQual PASSED 178s tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateTlen PASSED 178s tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_mapped_reads_are_updated PASSED 178s tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_unmapped_reads_ignore_length PASSED 178s tests/AlignedSegment_test.py::TestAlignedSegment::test_equivalence_matches_only_and_with_seq PASSED 178s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs PASSED 178s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_1character_md PASSED 178s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_bad_type_md PASSED 178s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_hard_clipping PASSED 178s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_lowercase_md PASSED 178s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_match_mismatch PASSED 178s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding PASSED 178s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding_with_seq PASSED 178s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip PASSED 178s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip_reference PASSED 178s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_soft_clipping PASSED 178s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_uppercase_md PASSED 178s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_with_malformed_MD_tag PASSED 178s tests/AlignedSegment_test.py::TestAlignedSegment::test_header_accessible PASSED 178s tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_query_length PASSED 178s tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_read_length PASSED 178s tests/AlignedSegment_test.py::TestAlignedSegment::test_query_length_is_limited PASSED 178s tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_asterisk PASSED 178s tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_chromosome PASSED 178s tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_none PASSED 178s tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_not_be_set_to_unknown_chromosome PASSED 178s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_chromosome PASSED 178s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing PASSED 178s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing_without_header PASSED 178s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_without_header PASSED 178s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_not_be_set_to_unknown_chromosome PASSED 178s tests/AlignedSegment_test.py::TestTidMapping::test_unmapped_tid_is_asterisk_in_output PASSED 178s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_asterisk PASSED 178s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_chromosome PASSED 178s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_none PASSED 178s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_not_be_set_to_unknown_chromosome PASSED 178s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_chromosome PASSED 178s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_equal PASSED 178s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing PASSED 178s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing_without_header PASSED 178s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_without_header PASSED 178s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_not_be_set_to_unknown_chromosome PASSED 178s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_unmapped_tid_is_asterisk_in_output PASSED 178s tests/AlignedSegment_test.py::TestCigar::testCigar PASSED 178s tests/AlignedSegment_test.py::TestCigar::testCigarString PASSED 178s tests/AlignedSegment_test.py::TestCigarStats::testStats PASSED 178s tests/AlignedSegment_test.py::TestAlignedPairs::testReferenceBases PASSED 178s tests/AlignedSegment_test.py::TestBaseModifications::testChebi PASSED 178s tests/AlignedSegment_test.py::TestBaseModifications::testDouble PASSED 178s tests/AlignedSegment_test.py::TestBaseModifications::testMulti PASSED 178s tests/AlignedSegment_test.py::TestBaseModifications::testOrient PASSED 178s tests/AlignedSegment_test.py::TestTags::testAddTags PASSED 178s tests/AlignedSegment_test.py::TestTags::testAddTagsType PASSED 178s tests/AlignedSegment_test.py::TestTags::testArrayTags PASSED 178s tests/AlignedSegment_test.py::TestTags::testEmptyTag PASSED 178s tests/AlignedSegment_test.py::TestTags::testLongTags PASSED 178s tests/AlignedSegment_test.py::TestTags::testMDTagComplex PASSED 178s tests/AlignedSegment_test.py::TestTags::testMDTagDeletions PASSED 178s tests/AlignedSegment_test.py::TestTags::testMDTagInsertions PASSED 178s tests/AlignedSegment_test.py::TestTags::testMDTagMatchOnly PASSED 178s tests/AlignedSegment_test.py::TestTags::testMDTagRefSkipping PASSED 178s tests/AlignedSegment_test.py::TestTags::testMDTagSoftClipping PASSED 178s tests/AlignedSegment_test.py::TestTags::testMissingTag PASSED 178s tests/AlignedSegment_test.py::TestTags::testNegativeIntegers PASSED 178s tests/AlignedSegment_test.py::TestTags::testNegativeIntegersWrittenToFile PASSED 178s tests/AlignedSegment_test.py::TestTags::testSetTag PASSED 178s tests/AlignedSegment_test.py::TestTags::testTagParsing PASSED 178s tests/AlignedSegment_test.py::TestTags::testTagsUpdatingFloat PASSED 178s tests/AlignedSegment_test.py::TestCopy::testCopy PASSED 178s tests/AlignedSegment_test.py::TestCopy::testDeepCopy PASSED 178s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_A PASSED 178s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_C PASSED 178s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_H PASSED 178s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_I PASSED 178s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_S PASSED 178s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_a PASSED 178s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_automated_type_detection PASSED 178s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_c PASSED 178s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_d PASSED 178s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_f PASSED 178s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_i PASSED 178s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_s PASSED 178s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_A PASSED 178s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_C PASSED 178s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_H PASSED 178s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_I PASSED 178s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_S PASSED 178s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_a PASSED 178s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_automated_type_detection PASSED 178s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_c PASSED 178s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_d PASSED 178s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_f PASSED 178s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_i PASSED 178s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_s PASSED 178s tests/AlignedSegment_test.py::TestEnums::test_cigar_enums_are_defined PASSED 178s tests/AlignedSegment_test.py::TestEnums::test_sam_flags_are_defined PASSED 178s tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_constructed_without_header PASSED 178s tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_written_to_file PASSED 178s tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_id_can_be_set PASSED 178s tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_name_is_not_available PASSED 178s tests/AlignedSegment_test.py::TestForwardStrandValues::test_qualities_are_complemented PASSED 178s tests/AlignedSegment_test.py::TestForwardStrandValues::test_sequence_is_complemented PASSED 178s tests/AlignedSegment_test.py::TestExportImport::test_dict_export PASSED 178s tests/AlignedSegment_test.py::TestExportImport::test_string_export PASSED 178s tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_with_tags PASSED 178s tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_without_tags PASSED 178s tests/AlignedSegment_test.py::TestExportImport::test_to_string_without_alignment_file PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_dict PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_header PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references_without_text PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_text PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_access_works PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_contains_works PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_get_works PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_keys_works PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_len_works PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_setting_raises_error PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_values_works PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_header_content_is_as_expected PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_name_mapping PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_text_access_works PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_contains_works PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_get_works PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_keys_works PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_len_works PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_setting_raises_error PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_values_works PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_name_mapping PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_text_access_works PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_contains_works PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_get_works PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_keys_works PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_len_works PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_setting_raises_error PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_values_works PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_name_mapping PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_text_access_works PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM /tmp/autopkgtest.TIYAUm/build.Rhj/src/tests/tmp/pysamtests_tmp_check_read_write_wbe0eowj 178s PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM /tmp/autopkgtest.TIYAUm/build.Rhj/src/tests/tmp/pysamtests_tmp_check_read_write_oysgiaqg 178s PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /tmp/autopkgtest.TIYAUm/build.Rhj/src/tests/tmp/pysamtests_tmp_check_read_write_csswjy_7 178s PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM /tmp/autopkgtest.TIYAUm/build.Rhj/src/tests/tmp/pysamtests_tmp_check_read_write_hl08ya0y 178s PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM /tmp/autopkgtest.TIYAUm/build.Rhj/src/tests/tmp/pysamtests_tmp_check_read_write_4gm2fs57 178s PASSED 178s tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM [E::cram_index_load] Could not retrieve index file for '/tmp/autopkgtest.TIYAUm/build.Rhj/src/tests/tmp/pysamtests_tmp_check_read_write_oysgiaqg' 178s [W::sanitise_SQ_lines] Header @SQ length mismatch for ref chr1, 2147483647 vs 1575 178s [E::cram_index_load] Could not retrieve index file for '/tmp/autopkgtest.TIYAUm/build.Rhj/src/tests/tmp/pysamtests_tmp_check_read_write_4gm2fs57' 178s /tmp/autopkgtest.TIYAUm/build.Rhj/src/tests/tmp/pysamtests_tmp_check_read_write_zx3s_io1 178s PASSED 178s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_all_stepper PASSED 178s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_ignore_overlaps PASSED 178s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper PASSED 178s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_base_quality_threshold PASSED 178s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_ignore_orphans PASSED 178s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_mapping_quality_threshold PASSED 179s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_redo_baq PASSED 179s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_all_stepper PASSED 179s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_ignore_overlaps PASSED 179s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper PASSED 179s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_base_quality_threshold PASSED 179s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_ignore_orphans PASSED 179s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_mapping_quality_threshold PASSED 179s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_redo_baq PASSED 179s tests/AlignmentFilePileup_test.py::TestPileupQueryPosition::testPileup PASSED 179s tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope SKIPPED 179s tests/AlignmentFilePileup_test.py::TestPileupObjects::testPileupColumn PASSED 179s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testInverse PASSED 179s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateAll PASSED 179s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIteratePerContig PASSED 179s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateRanges PASSED 179s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateTruncate PASSED 179s tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testAccessOnClosedIterator PASSED 179s tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStart PASSED 179s tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStr PASSED 179s tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testTruncate PASSED 179s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_depths_are_equal PASSED 179s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_mapping_qualities_are_equal PASSED 179s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_with_reference_are_equal PASSED 179s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_without_reference_are_equal PASSED 179s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_are_equal PASSED 180s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_from_pileups_are_equal PASSED 180s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARQueryLength PASSED 180s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigar PASSED 180s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigarstring PASSED 180s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARflag PASSED 180s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmapq PASSED 180s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmpos PASSED 180s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmrnm PASSED 180s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARpos PASSED 180s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqname PASSED 180s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqqual PASSED 180s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqual PASSED 180s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARquery PASSED 180s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARrname PASSED 180s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARseq PASSED 180s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testOpt PASSED 180s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPairedBools PASSED 180s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPresentOptionalFields PASSED 180s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testTags PASSED 180s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARQueryLength PASSED 180s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigar PASSED 180s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigarstring PASSED 180s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARflag PASSED 180s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmapq PASSED 180s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmpos PASSED 180s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmrnm PASSED 180s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARpos PASSED 180s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqname PASSED 180s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqqual PASSED 180s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqual PASSED 180s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARquery PASSED 180s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARrname PASSED 180s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARseq PASSED 180s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testOpt PASSED 180s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPairedBools PASSED 180s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPresentOptionalFields PASSED 180s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testTags PASSED 180s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARQueryLength PASSED 181s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigar PASSED 181s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigarstring PASSED 182s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARflag PASSED 182s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmapq PASSED 183s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmpos PASSED 183s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmrnm PASSED 183s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARpos PASSED 184s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqname PASSED 184s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqqual PASSED 185s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqual PASSED 185s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARquery PASSED 186s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARrname PASSED 186s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARseq PASSED 186s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testOpt PASSED 187s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPairedBools PASSED 188s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPresentOptionalFields PASSED 188s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testTags PASSED 188s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARQueryLength PASSED 188s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigar PASSED 188s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigarstring PASSED 188s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARflag PASSED 188s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmapq PASSED 188s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmpos PASSED 188s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmrnm PASSED 188s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARpos PASSED 188s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqname PASSED 188s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqqual PASSED 188s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqual PASSED 188s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARquery PASSED 188s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARrname PASSED 188s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARseq PASSED 188s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testOpt PASSED 188s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPairedBools PASSED 188s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPresentOptionalFields PASSED 188s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testTags PASSED 189s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARQueryLength PASSED 189s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigar PASSED 189s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigarstring PASSED 190s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARflag PASSED 190s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmapq PASSED 191s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmpos PASSED 191s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmrnm PASSED 192s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARpos PASSED 192s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqname PASSED 192s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqqual PASSED 193s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqual PASSED 193s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARquery PASSED 194s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARrname PASSED 194s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARseq PASSED 195s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testOpt PASSED 195s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPairedBools PASSED 196s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPresentOptionalFields PASSED 196s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testTags PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARQueryLength PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigar PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigarstring PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARflag PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmapq PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmpos PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmrnm PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARpos PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqname PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqqual PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqual PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARquery PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARrname PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARseq PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testOpt PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPairedBools PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPresentOptionalFields PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testTags PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARQueryLength PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigar PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigarstring PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARflag PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmapq PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmpos PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmrnm PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARpos PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqname PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqqual PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqual PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARquery PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARrname PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARseq PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testOpt PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPairedBools PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPresentOptionalFields PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testTags PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARQueryLength PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigar PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigarstring PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARflag PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmapq PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmpos PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmrnm PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARpos PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqname PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqqual PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqual PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARquery PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARrname PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARseq PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testOpt PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPairedBools PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPresentOptionalFields PASSED 196s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testTags PASSED 196s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARQueryLength PASSED 196s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigar PASSED 196s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigarstring PASSED 196s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARflag PASSED 196s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmapq PASSED 196s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmpos PASSED 196s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmrnm PASSED 196s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARpos PASSED 196s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqname PASSED 196s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqqual PASSED 196s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqual PASSED 196s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARquery PASSED 196s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARrname PASSED 196s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARseq PASSED 196s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testOpt PASSED 196s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPairedBools PASSED 196s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPresentOptionalFields PASSED 196s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testTags PASSED 196s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARQueryLength PASSED 196s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigar PASSED 196s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigarstring PASSED 196s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARflag PASSED 196s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmapq PASSED 196s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmpos PASSED 196s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmrnm PASSED 196s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARpos PASSED 196s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqname PASSED 196s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqqual PASSED 196s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqual PASSED 196s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARquery PASSED 196s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARrname PASSED 196s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARseq PASSED 196s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testOpt PASSED 196s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPairedBools PASSED 196s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPresentOptionalFields PASSED 196s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testTags PASSED 196s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARQueryLength PASSED 197s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigar PASSED 197s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigarstring PASSED 198s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARflag PASSED 198s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmapq PASSED 199s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmpos PASSED 199s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmrnm PASSED 199s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARpos PASSED 200s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqname PASSED 200s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqqual PASSED 201s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqual PASSED 201s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARquery PASSED 202s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARrname PASSED 202s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARseq PASSED 203s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testOpt PASSED 203s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPairedBools PASSED 204s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPresentOptionalFields PASSED 204s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testTags PASSED 205s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARQueryLength PASSED 205s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigar PASSED 205s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigarstring PASSED 206s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARflag PASSED 206s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmapq PASSED 207s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmpos PASSED 208s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmrnm PASSED 208s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARpos PASSED 209s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqname PASSED 209s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqqual PASSED 210s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqual PASSED 210s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARquery PASSED 210s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARrname PASSED 211s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARseq PASSED 211s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testOpt PASSED 212s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPairedBools PASSED 212s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPresentOptionalFields PASSED 213s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testTags PASSED 213s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARQueryLength PASSED 213s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigar PASSED 213s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigarstring PASSED 213s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARflag PASSED 213s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmapq PASSED 213s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmpos PASSED 213s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmrnm PASSED 213s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARpos PASSED 213s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqname PASSED 213s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqqual PASSED 213s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqual PASSED 213s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARquery PASSED 213s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARrname PASSED 213s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARseq PASSED 213s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testOpt PASSED 213s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPairedBools PASSED 213s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPresentOptionalFields PASSED 213s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testRaises PASSED 213s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testTags PASSED 213s tests/AlignmentFile_test.py::TestIO::testBAM2BAM PASSED 213s tests/AlignmentFile_test.py::TestIO::testBAM2SAM PASSED 213s tests/AlignmentFile_test.py::TestIO::testBAMWithCSIIndex PASSED 213s tests/AlignmentFile_test.py::TestIO::testBAMWithShortBAI PASSED 213s tests/AlignmentFile_test.py::TestIO::testBAMWithoutAlignedSegments PASSED 213s tests/AlignmentFile_test.py::TestIO::testCRAM2BAM PASSED 215s tests/AlignmentFile_test.py::TestIO::testCRAM2CRAM PASSED 215s tests/AlignmentFile_test.py::TestIO::testCRAM2SAM PASSED 215s tests/AlignmentFile_test.py::TestIO::testEmptyBAM PASSED 215s tests/AlignmentFile_test.py::TestIO::testEmptyWithHeaderBAM PASSED 215s tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFile PASSED 215s tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject PASSED 215s tests/AlignmentFile_test.py::TestIO::testHead PASSED 215s tests/AlignmentFile_test.py::TestIO::testOpenFromFilename PASSED 215s tests/AlignmentFile_test.py::TestIO::testReadBamWithoutTargetNames PASSED 215s tests/AlignmentFile_test.py::TestIO::testReadSamWithoutTargetNames PASSED 215s tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex PASSED 215s tests/AlignmentFile_test.py::TestIO::testSAM2BAM PASSED 216s tests/AlignmentFile_test.py::TestIO::testSAM2CRAM PASSED 216s tests/AlignmentFile_test.py::TestIO::testSAM2SAM PASSED 216s tests/AlignmentFile_test.py::TestIO::testSAM2SAMWithoutHeader PASSED 217s tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile PASSED 217s tests/AlignmentFile_test.py::TestIO::test_accessing_attributes_in_closed_file_raises_errors PASSED 217s tests/AlignmentFile_test.py::TestIO::test_fail_read_sam_without_header PASSED 217s tests/AlignmentFile_test.py::TestIO::test_fail_when_reading_unformatted_files PASSED 217s tests/AlignmentFile_test.py::TestIO::test_fetch_by_tid PASSED 217s tests/AlignmentFile_test.py::TestIO::test_header_available_after_closing_file PASSED 217s tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_with_header_without_header_check PASSED 217s tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_without_header_with_refs PASSED 217s tests/AlignmentFile_test.py::TestIO::test_reference_name_available_after_closing_file PASSED 217s tests/AlignmentFile_test.py::TestIO::test_write_bam_to_unknown_path_fails PASSED 217s tests/AlignmentFile_test.py::TestAutoDetect::testBAM PASSED 217s tests/AlignmentFile_test.py::TestAutoDetect::testCRAM [E::hts_open_format] Failed to open file "missing_directory/new_file.bam" : No such file or directory 217s PASSED 217s tests/AlignmentFile_test.py::TestAutoDetect::testSAM PASSED 217s tests/AlignmentFile_test.py::TestIteratorRowBAM::testIteratePerContig PASSED 219s tests/AlignmentFile_test.py::TestIteratorRowBAM::testIterateRanges PASSED 219s tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate PASSED 219s tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIteratePerContig PASSED 234s tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIterateRanges PASSED 236s tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIteratePerContig PASSED 254s tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIterateRanges PASSED 254s tests/AlignmentFile_test.py::TestFloatTagBug::testFloatTagBug PASSED 254s tests/AlignmentFile_test.py::TestLargeFieldBug::testLargeFileBug PASSED 254s tests/AlignmentFile_test.py::TestClipping::testClipping PASSED 254s tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_bam_with_until_eof_reads_unmapped_reads PASSED 254s tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_sam_with_until_eof_reads_unmapped_reads PASSED 254s tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads PASSED 254s tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads_by_contig PASSED 254s tests/AlignmentFile_test.py::TestContextManager::testManager PASSED 254s tests/AlignmentFile_test.py::TestMultiThread::testSingleThreadEqualsMultithread PASSED 254s tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED 254s tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED 254s tests/AlignmentFile_test.py::TestExceptions::testBadContig PASSED 254s tests/AlignmentFile_test.py::TestExceptions::testMeaninglessCrap PASSED 254s tests/AlignmentFile_test.py::TestExceptions::testMissingFile PASSED 254s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangNewFormat PASSED 254s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeNewFormat PASSED 254s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeOldFormat PASSED 254s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeNewFormat PASSED 254s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeOldFormat PASSED 254s tests/AlignmentFile_test.py::TestExceptions::testZeroToZero PASSED 254s tests/AlignmentFile_test.py::TestWrongFormat::testOpenBamAsSam PASSED 254s tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsBam [E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory 254s [E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory 254s [E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory 254s [E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory 254s PASSED 254s tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsSam PASSED 254s tests/AlignmentFile_test.py::TestWrongFormat::testOpenSamAsBam PASSED 254s tests/AlignmentFile_test.py::TestRegionParsing::test_dash_in_chr PASSED 254s tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile PASSED 254s tests/AlignmentFile_test.py::TestDeNovoConstruction::test_pass_if_reads_binary_equal PASSED 254s tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader PASSED 254s tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_in_header PASSED 254s tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_with_null_bytes_in_header PASSED 254s tests/AlignmentFile_test.py::TestMismatchingHeader::testMismatchingHeader PASSED 254s tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader PASSED 254s tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2 PASSED 254s tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator [W::bam_hdr_read] EOF marker is absent. The input is probably truncated 254s [E::bgzf_read_block] Failed to read BGZF block data at offset 105176 expected 17578 bytes; hread returned 17094 254s [E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes 254s PASSED 254s tests/AlignmentFile_test.py::TestCorruptBAM::testCorruptBamIterator PASSED 254s tests/AlignmentFile_test.py::TestBTagSam::testReadTags PASSED 254s tests/AlignmentFile_test.py::TestBTagSam::testReadWriteTags PASSED 254s tests/AlignmentFile_test.py::TestBTagBam::testReadTags PASSED 254s tests/AlignmentFile_test.py::TestBTagBam::testReadWriteTags PASSED 254s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetch PASSED 254s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchUntilEOF PASSED 254s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionFalseTrue PASSED 254s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueFalse PASSED 254s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueTrue PASSED 255s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetch PASSED 256s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchUntilEOF PASSED 257s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionFalseTrue PASSED 258s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueFalse PASSED 259s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueTrue PASSED 260s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetch PASSED 261s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchUntilEOF PASSED 262s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionFalseTrue PASSED 263s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueFalse PASSED 264s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueTrue PASSED 265s tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetch PASSED 265s tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetchAll PASSED 265s tests/AlignmentFile_test.py::TestRemoteFileHTTP::testView PASSED 265s tests/AlignmentFile_test.py::TestLargeOptValues::testBAM PASSED 265s tests/AlignmentFile_test.py::TestLargeOptValues::testSAM PASSED 265s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_counts_as_expected PASSED 265s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_nofilter PASSED 265s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_quality_filter PASSED 265s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_all PASSED 266s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_callback PASSED 266s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_with_coordinates_works PASSED 266s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_without_coordinates_fails PASSED 266s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_wrong_coordinates_fails PASSED 266s tests/AlignmentFile_test.py::TestCountCoverage::test_counting_the_same_region_works PASSED 266s tests/AlignmentFile_test.py::TestFindIntrons::test_all PASSED 266s tests/AlignmentFile_test.py::TestFindIntrons::test_first PASSED 266s tests/AlignmentFile_test.py::TestFindIntrons::test_total PASSED 266s tests/AlignmentFile_test.py::TestLogging::testFail1 PASSED 266s tests/AlignmentFile_test.py::TestLogging::testNoFail1 PASSED 266s tests/AlignmentFile_test.py::TestLogging::testNoFail2 PASSED 266s tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testCount PASSED 266s tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testIndexStats PASSED 268s tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testMate PASSED 268s tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct PASSED 268s tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct_per_chromosome PASSED 268s tests/AlignmentFile_test.py::TestSamtoolsProxy::testIndex PASSED 268s tests/AlignmentFile_test.py::TestSamtoolsProxy::testSort [E::hts_open_format] Failed to open file "missing_file" : No such file or directory 268s PASSED[E::hts_open_format] Failed to open file "missing_file" : No such file or directory 268s 268s tests/AlignmentFile_test.py::TestSamtoolsProxy::testView PASSED 268s tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED 268s tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM [W::hts_idx_load3] The index file is older than the data file: /tmp/autopkgtest.TIYAUm/build.Rhj/src/tests/pysam_data/ex1.bam.bai 268s PASSED 268s tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexCRAM PASSED 269s tests/AlignmentFile_test.py::TestExplicitIndex::testRemoteExplicitIndexBAM PASSED 269s tests/AlignmentFile_test.py::TestVerbosity::testVerbosity PASSED 269s tests/AlignmentFile_test.py::TestSanityCheckingBAM::test_empty_read_gives_value_error PASSED 269s tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_bam PASSED 269s tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_cram SKIPPED 269s tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_sam PASSED 269s tests/StreamFiledescriptors_test.py::StreamTest::test_samtools_processing SKIPPED 269s tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing PASSED 269s tests/VariantFile_test.py::TestMissingGenotypes::testVCF PASSED 269s tests/VariantFile_test.py::TestMissingGenotypes::testVCFGZ PASSED 269s tests/VariantFile_test.py::TestMissingSamples::testVCF PASSED 269s tests/VariantFile_test.py::TestMissingSamples::testVCFGZ [W::bcf_hdr_check_sanity] PL should be declared as Number=G 269s [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 269s [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) 269s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 269s [E::hts_open_format] Failed to open file "missing_file.vcf" : No such file or directory 269s [E::hts_open_format] Failed to open file "missing_file.vcf.gz" : No such file or directory 269s PASSED 269s tests/VariantFile_test.py::TestMissingSamplesFixed::testVCF PASSED 269s tests/VariantFile_test.py::TestMissingSamplesFixed::testVCFGZ PASSED 269s tests/VariantFile_test.py::TestOpening::testDetectBCF PASSED 269s tests/VariantFile_test.py::TestOpening::testDetectVCF PASSED 269s tests/VariantFile_test.py::TestOpening::testDetectVCFGZ PASSED 269s tests/VariantFile_test.py::TestOpening::testEmptyFileVCF PASSED 269s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFFromPath PASSED 269s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZOnlyHeader PASSED 269s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithIndex PASSED 269s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithoutIndex PASSED 269s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFOnlyHeader PASSED 269s tests/VariantFile_test.py::TestOpening::testMissingFile PASSED 269s tests/VariantFile_test.py::TestOpening::testMissingFileVCFGZ PASSED 269s tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_csi_index PASSED 269s tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_prebuilt_csi PASSED 269s tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_tbi_index_will_produce_csi PASSED 269s tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_csi_index PASSED 269s tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_tbi_index PASSED 269s tests/VariantFile_test.py::TestHeader::testIterator PASSED 269s tests/VariantFile_test.py::TestHeader::testStr PASSED 269s tests/VariantFile_test.py::TestParsing::testAlleles PASSED 269s tests/VariantFile_test.py::TestParsing::testAllelesVariantTypes PASSED 269s tests/VariantFile_test.py::TestParsing::testAlt PASSED 269s tests/VariantFile_test.py::TestParsing::testChrom PASSED 269s tests/VariantFile_test.py::TestParsing::testChromFromPath PASSED 269s tests/VariantFile_test.py::TestParsing::testFilter PASSED 269s tests/VariantFile_test.py::TestParsing::testFormat PASSED 269s tests/VariantFile_test.py::TestParsing::testId PASSED 269s tests/VariantFile_test.py::TestParsing::testInfo PASSED 269s tests/VariantFile_test.py::TestParsing::testPos PASSED 269s tests/VariantFile_test.py::TestParsing::testQual PASSED 269s tests/VariantFile_test.py::TestParsing::testRef PASSED 269s tests/VariantFile_test.py::TestParsing::testSampleAlleleIndices PASSED 269s tests/VariantFile_test.py::TestParsing::testSampleAlleles PASSED 269s tests/VariantFile_test.py::TestParsing::testSampleFormats PASSED 269s tests/VariantFile_test.py::TestParsing::testStart PASSED 269s tests/VariantFile_test.py::TestParsing::testStop PASSED 269s tests/VariantFile_test.py::TestIndexFilename::testOpen PASSED 269s tests/VariantFile_test.py::TestConstructionVCFWithContigs::testBase PASSED 269s tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionFromCopy PASSED 269s tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithLines PASSED 269s tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithRecords PASSED 269s tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testBase PASSED 269s tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionFromCopy PASSED 269s tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithLines PASSED 269s tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithRecords PASSED 269s tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testBase PASSED 269s tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionFromCopy PASSED 269s tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithLines PASSED 269s tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithRecords PASSED 269s tests/VariantFile_test.py::TestSettingRecordValues::testBase PASSED 269s tests/VariantFile_test.py::TestSettingRecordValues::testGenotype [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 269s (0, 0) 269s PASSED 269s tests/VariantFile_test.py::TestSettingRecordValues::testSetQual [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 269s PASSED 269s tests/VariantFile_test.py::TestMultiThreading::testNoMultiThreadingWithIgnoreTruncation PASSED 269s tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult [E::idx_find_and_load] Could not retrieve index file for '/tmp/autopkgtest.TIYAUm/build.Rhj/src/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithreadResult_0xkp2pzh.bcf' 269s PASSED 269s tests/VariantFile_test.py::TestSubsetting::testSubsetting [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)PASSED 269s tests/VariantFile_test.py::TestVCFVersions::test_all_records_can_be_fetched 269s [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) 269s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 269s [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 269s [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) 269s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 269s PASSED 269s tests/VariantFile_test.py::TestUnicode::test_record_with_unicode PASSED 269s tests/VariantRecord_test.py::test_ascii_annotation_can_be_added PASSED 269s tests/VariantRecord_test.py::test_ascii_annotation_with_variable_length_can_be_added PASSED 269s tests/VariantRecord_test.py::test_unicode_annotation_can_be_added PASSED 269s tests/VariantRecord_test.py::test_set_sample_alleles PASSED 269s tests/compile_test.py::test_bam SKIPPED (no pyximport) 269s tests/compile_test.py::test_gtf SKIPPED (no pyximport) 269s tests/faidx_test.py::TestFastaFile::testFetch PASSED 269s tests/faidx_test.py::TestFastaFile::testFetchErrors PASSED 269s tests/faidx_test.py::TestFastaFile::testLength PASSED 269s tests/faidx_test.py::TestFastaFile::testOutOfRangeAccess PASSED 269s tests/faidx_test.py::TestFastaFile::testSequenceLengths PASSED 269s tests/faidx_test.py::TestFastaFile::test_fetch_with_region_and_contig_raises_exception PASSED 269s tests/faidx_test.py::TestFastaFile::test_fetch_with_region_is_equivalent PASSED 269s tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED 269s tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_index_succeeds PASSED 269s tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_without_index_succeeds PASSED 269s tests/faidx_test.py::TestFastaFilePathIndex::test_raise_exception_if_index_is_missing PASSED 269s tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED 269s tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_index_succeeds PASSED 269s tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_without_index_succeeds PASSED 269s tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_raise_exception_if_index_is_missing PASSED 269s tests/faidx_test.py::TestFastxFileFastq::testCounts PASSED 269s tests/faidx_test.py::TestFastxFileFastq::testManager PASSED 269s tests/faidx_test.py::TestFastxFileFastq::testMissingFile PASSED 269s tests/faidx_test.py::TestFastxFileFastq::testSequence PASSED 269s tests/faidx_test.py::TestFastqFileFastq::testCounts PASSED 269s tests/faidx_test.py::TestFastqFileFastq::testManager PASSED 269s tests/faidx_test.py::TestFastqFileFastq::testMissingFile PASSED 269s tests/faidx_test.py::TestFastqFileFastq::testSequence PASSED 269s tests/faidx_test.py::TestFastxFileFasta::testCounts PASSED 269s tests/faidx_test.py::TestFastxFileFasta::testManager PASSED 269s tests/faidx_test.py::TestFastxFileFasta::testMissingFile PASSED 269s tests/faidx_test.py::TestFastxFileFasta::testSequence PASSED 269s tests/faidx_test.py::TestFastxFileFastqStream::testCounts PASSED 269s tests/faidx_test.py::TestFastxFileFastqStream::testManager PASSED 269s tests/faidx_test.py::TestFastxFileFastqStream::testMissingFile PASSED 269s tests/faidx_test.py::TestFastxFileFastqStream::testSequence PASSED 269s tests/faidx_test.py::TestFastxFileWithEmptySequence::testIteration PASSED 270s tests/faidx_test.py::TestRemoteFileFTP::testFTPView PASSED 270s tests/faidx_test.py::TestRemoteFileFTP::test_sequence_lengths_are_available PASSED 270s tests/faidx_test.py::TestFastqRecord::test_fastx_record_can_be_created_from_scratch PASSED 270s tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_None PASSED 270s tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_modified PASSED 270s tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_name_is_None PASSED 270s tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_quality_is_wrong_length PASSED 270s tests/faidx_test.py::TestFastqRecord::test_fastx_record_name_can_be_modified PASSED 270s tests/faidx_test.py::TestFastqRecord::test_fastx_record_quality_can_be_modified PASSED 270s tests/faidx_test.py::TestFastqRecord::test_fastx_record_sequence_can_be_modified PASSED 270s tests/faidx_test.py::TestFastqProxy::test_fastq_proxy_instantiation_raises_error PASSED 270s tests/linking_test.py::TestLinking::test_package_can_be_installed SKIPPED 270s tests/linking_test.py::TestLinkWithRpath::test_package_can_be_installed SKIPPED 270s tests/linking_test.py::TestLinkWithRpath::test_package_tests_pass SKIPPED 270s tests/linking_test.py::TestLinkWithoutRpath::test_package_can_be_installed SKIPPED 270s tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_fail_on_import SKIPPED 270s tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_pass_if_ld_library_path_set SKIPPED 271s tests/samtools_test.py::SamtoolsTest::testStatements PASSED 271s tests/samtools_test.py::SamtoolsTest::testUsage SKIPPED (skipping us...) 271s tests/samtools_test.py::EmptyIndexTest::testEmptyIndex PASSED 271s tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraArg PASSED 271s tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraFlag PASSED 271s tests/samtools_test.py::TestReturnType::testReturnValueData PASSED 271s tests/samtools_test.py::TestReturnType::testReturnValueString PASSED 271s tests/samtools_test.py::StdoutTest::testDoubleCalling PASSED 271s tests/samtools_test.py::StdoutTest::testSaveStdout PASSED 271s tests/samtools_test.py::StdoutTest::testWithRedirectedStdout PASSED 271s tests/samtools_test.py::StdoutTest::testWithoutRedirectedStdout PASSED 272s tests/samtools_test.py::PysamTest::testStatements PASSED 272s tests/samtools_test.py::PysamTest::testUsage SKIPPED (skipping usage...) 273s tests/tabix_test.py::TestIndexing::test_indexing_to_custom_location_works PASSED 273s tests/tabix_test.py::TestIndexing::test_indexing_with_explict_columns_works PASSED 273s tests/tabix_test.py::TestIndexing::test_indexing_with_lineskipping_works PASSED 273s tests/tabix_test.py::TestIndexing::test_indexing_with_preset_works PASSED 273s tests/tabix_test.py::TestCompression::testCompression PASSED 273s tests/tabix_test.py::TestCompression::testIndexPresetCompressed PASSED 273s tests/tabix_test.py::TestCompression::testIndexPresetUncompressed PASSED 273s tests/tabix_test.py::TestCompressionSam::testCompression PASSED 273s tests/tabix_test.py::TestCompressionSam::testIndexPresetCompressed PASSED 273s tests/tabix_test.py::TestCompressionSam::testIndexPresetUncompressed PASSED 273s tests/tabix_test.py::TestCompressionBed::testCompression PASSED 273s tests/tabix_test.py::TestCompressionBed::testIndexPresetCompressed PASSED 273s tests/tabix_test.py::TestCompressionBed::testIndexPresetUncompressed PASSED 273s tests/tabix_test.py::TestCompressionVCF::testCompression PASSED 273s tests/tabix_test.py::TestCompressionVCF::testIndexPresetCompressed PASSED 273s tests/tabix_test.py::TestCompressionVCF::testIndexPresetUncompressed PASSED 273s tests/tabix_test.py::TestGZFile::testAll PASSED 273s tests/tabix_test.py::TestIterationWithoutComments::testAll PASSED 273s tests/tabix_test.py::TestIterationWithoutComments::testGetContigs PASSED 273s tests/tabix_test.py::TestIterationWithoutComments::testHeader PASSED 273s tests/tabix_test.py::TestIterationWithoutComments::testInvalidIntervals PASSED 273s tests/tabix_test.py::TestIterationWithoutComments::testPerContig PASSED 273s tests/tabix_test.py::TestIterationWithoutComments::testPerContig2 PASSED 273s tests/tabix_test.py::TestIterationWithoutComments::testPerContigFromStart PASSED 273s tests/tabix_test.py::TestIterationWithoutComments::testPerContigToEnd PASSED 273s tests/tabix_test.py::TestIterationWithoutComments::testPerInterval PASSED 273s tests/tabix_test.py::TestIterationWithoutComments::testRegionStrings PASSED 273s tests/tabix_test.py::TestIterationWithoutComments::testReopening PASSED 273s tests/tabix_test.py::TestIterationWithComments::testAll PASSED 273s tests/tabix_test.py::TestIterationWithComments::testGetContigs PASSED 273s tests/tabix_test.py::TestIterationWithComments::testHeader PASSED 273s tests/tabix_test.py::TestIterationWithComments::testInvalidIntervals PASSED 273s tests/tabix_test.py::TestIterationWithComments::testPerContig PASSED 273s tests/tabix_test.py::TestIterationWithComments::testPerContig2 PASSED 274s tests/tabix_test.py::TestIterationWithComments::testPerContigFromStart PASSED 274s tests/tabix_test.py::TestIterationWithComments::testPerContigToEnd PASSED 274s tests/tabix_test.py::TestIterationWithComments::testPerInterval PASSED 274s tests/tabix_test.py::TestIterationWithComments::testRegionStrings PASSED 274s tests/tabix_test.py::TestIterationWithComments::testReopening PASSED 274s tests/tabix_test.py::TestIterators::testClosedFile PASSED 274s tests/tabix_test.py::TestIterators::testClosedFileIteration PASSED 274s tests/tabix_test.py::TestIterators::testIteration PASSED 274s tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFile PASSED 274s tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFileIteration PASSED 274s tests/tabix_test.py::TestIteratorsGenericCompressed::testIteration PASSED 274s tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFile PASSED 274s tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFileIteration PASSED 274s tests/tabix_test.py::TestIteratorsFileCompressed::testIteration PASSED 274s tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFile PASSED 274s tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFileIteration PASSED 274s tests/tabix_test.py::TestIteratorsFileUncompressed::testIteration PASSED 274s tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooFewFields PASSED 274s tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooManyFields PASSED 274s tests/tabix_test.py::TestBed::testRead PASSED 274s tests/tabix_test.py::TestBed::testWrite PASSED 274s tests/tabix_test.py::TestUnicode::testFromTabix PASSED 274s tests/tabix_test.py::TestUnicode::testFromVCF PASSED 274s tests/tabix_test.py::TestVCFFromTabix::testRead PASSED 274s tests/tabix_test.py::TestVCFFromTabix::testWrite PASSED 274s tests/tabix_test.py::TestVCFFromVCF::testConnecting PASSED 274s tests/tabix_test.py::TestVCFFromVCF::testParsing PASSED 274s tests/tabix_test.py::VCFFromTabixTest_21::testRead PASSED 274s tests/tabix_test.py::VCFFromTabixTest_21::testWrite PASSED 274s tests/tabix_test.py::VCFFromVCFTest_21::testConnecting PASSED 274s tests/tabix_test.py::VCFFromVCFTest_21::testParsing PASSED 275s tests/tabix_test.py::VCFFromTabixTest_11::testRead PASSED 275s tests/tabix_test.py::VCFFromTabixTest_11::testWrite PASSED 275s tests/tabix_test.py::VCFFromVCFTest_11::testConnecting PASSED 275s tests/tabix_test.py::VCFFromVCFTest_11::testParsing PASSED 275s tests/tabix_test.py::VCFFromTabixTest_issue85::testRead PASSED 275s tests/tabix_test.py::VCFFromTabixTest_issue85::testWrite PASSED 275s tests/tabix_test.py::VCFFromVCFTest_issue85::testConnecting PASSED 275s tests/tabix_test.py::VCFFromVCFTest_issue85::testParsing PASSED 275s tests/tabix_test.py::VCFFromTabixTest_8::testRead PASSED 275s tests/tabix_test.py::VCFFromTabixTest_8::testWrite PASSED 275s tests/tabix_test.py::VCFFromVCFTest_8::testConnecting PASSED 276s tests/tabix_test.py::VCFFromVCFTest_8::testParsing PASSED 276s tests/tabix_test.py::VCFFromTabixTest_23::testRead PASSED 276s tests/tabix_test.py::VCFFromTabixTest_23::testWrite PASSED 276s tests/tabix_test.py::VCFFromVCFTest_23::testConnecting PASSED 276s tests/tabix_test.py::VCFFromVCFTest_23::testParsing PASSED 276s tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testRead PASSED 276s tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testWrite PASSED 276s tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testConnecting PASSED 276s tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testParsing PASSED 276s tests/tabix_test.py::VCFFromTabixTest_3::testRead PASSED 276s tests/tabix_test.py::VCFFromTabixTest_3::testWrite PASSED 276s tests/tabix_test.py::VCFFromVCFTest_3::testConnecting PASSED 276s tests/tabix_test.py::VCFFromVCFTest_3::testParsing PASSED 276s tests/tabix_test.py::VCFFromTabixTest_2::testRead PASSED 276s tests/tabix_test.py::VCFFromTabixTest_2::testWrite PASSED 276s tests/tabix_test.py::VCFFromVCFTest_2::testConnecting PASSED 276s tests/tabix_test.py::VCFFromVCFTest_2::testParsing PASSED 276s tests/tabix_test.py::VCFFromTabixTest_15::testRead PASSED 277s tests/tabix_test.py::VCFFromTabixTest_15::testWrite PASSED 277s tests/tabix_test.py::VCFFromVCFTest_15::testConnecting PASSED 277s tests/tabix_test.py::VCFFromVCFTest_15::testParsing PASSED 277s tests/tabix_test.py::VCFFromTabixTest_7::testRead PASSED 278s tests/tabix_test.py::VCFFromTabixTest_7::testWrite PASSED 278s tests/tabix_test.py::VCFFromVCFTest_7::testConnecting PASSED 278s tests/tabix_test.py::VCFFromVCFTest_7::testParsing PASSED 278s tests/tabix_test.py::VCFFromTabixTest_10::testRead PASSED 278s tests/tabix_test.py::VCFFromTabixTest_10::testWrite PASSED 278s tests/tabix_test.py::VCFFromVCFTest_10::testConnecting PASSED 278s tests/tabix_test.py::VCFFromVCFTest_10::testParsing PASSED 279s tests/tabix_test.py::VCFFromTabixTest_12::testRead PASSED 279s tests/tabix_test.py::VCFFromTabixTest_12::testWrite PASSED 279s tests/tabix_test.py::VCFFromVCFTest_12::testConnecting PASSED 279s tests/tabix_test.py::VCFFromVCFTest_12::testParsing PASSED 279s tests/tabix_test.py::VCFFromTabixTest_4::testRead PASSED 279s tests/tabix_test.py::VCFFromTabixTest_4::testWrite PASSED 279s tests/tabix_test.py::VCFFromVCFTest_4::testConnecting PASSED 280s tests/tabix_test.py::VCFFromVCFTest_4::testParsing PASSED 280s tests/tabix_test.py::VCFFromTabixTest_13::testRead PASSED 280s tests/tabix_test.py::VCFFromTabixTest_13::testWrite PASSED 280s tests/tabix_test.py::VCFFromVCFTest_13::testConnecting PASSED 280s tests/tabix_test.py::VCFFromVCFTest_13::testParsing PASSED 280s tests/tabix_test.py::VCFFromTabixTest_18::testRead PASSED 280s tests/tabix_test.py::VCFFromTabixTest_18::testWrite PASSED 280s tests/tabix_test.py::VCFFromVCFTest_18::testConnecting PASSED 280s tests/tabix_test.py::VCFFromVCFTest_18::testParsing PASSED 280s tests/tabix_test.py::VCFFromTabixTest_22::testRead PASSED 281s tests/tabix_test.py::VCFFromTabixTest_22::testWrite PASSED 281s tests/tabix_test.py::VCFFromVCFTest_22::testConnecting PASSED 282s tests/tabix_test.py::VCFFromVCFTest_22::testParsing PASSED 282s tests/tabix_test.py::VCFFromTabixTest_16::testRead PASSED 282s tests/tabix_test.py::VCFFromTabixTest_16::testWrite PASSED 282s tests/tabix_test.py::VCFFromVCFTest_16::testConnecting PASSED 282s tests/tabix_test.py::VCFFromVCFTest_16::testParsing PASSED 282s tests/tabix_test.py::VCFFromTabixTest_9::testRead PASSED 282s tests/tabix_test.py::VCFFromTabixTest_9::testWrite PASSED 282s tests/tabix_test.py::VCFFromVCFTest_9::testConnecting PASSED 282s tests/tabix_test.py::VCFFromVCFTest_9::testParsing PASSED 282s tests/tabix_test.py::VCFFromTabixTest_5::testRead PASSED 282s tests/tabix_test.py::VCFFromTabixTest_5::testWrite PASSED 282s tests/tabix_test.py::VCFFromVCFTest_5::testConnecting PASSED 282s tests/tabix_test.py::VCFFromVCFTest_5::testParsing PASSED 282s tests/tabix_test.py::VCFFromTabixTest_24::testRead PASSED 282s tests/tabix_test.py::VCFFromTabixTest_24::testWrite PASSED 282s tests/tabix_test.py::VCFFromVCFTest_24::testConnecting PASSED 282s tests/tabix_test.py::VCFFromVCFTest_24::testParsing PASSED 282s tests/tabix_test.py::VCFFromTabixTest_20::testRead PASSED 282s tests/tabix_test.py::VCFFromTabixTest_20::testWrite PASSED 282s tests/tabix_test.py::VCFFromVCFTest_20::testConnecting PASSED 282s tests/tabix_test.py::VCFFromVCFTest_20::testParsing PASSED 283s tests/tabix_test.py::VCFFromTabixTest_6::testRead PASSED 283s tests/tabix_test.py::VCFFromTabixTest_6::testWrite PASSED 283s tests/tabix_test.py::VCFFromVCFTest_6::testConnecting PASSED 284s tests/tabix_test.py::VCFFromVCFTest_6::testParsing PASSED 284s tests/tabix_test.py::TestVCFFromVariantFile::testConnecting PASSED 284s tests/tabix_test.py::TestVCFFromVariantFile::testParsing [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 284s [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) 284s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 284s PASSED 284s tests/tabix_test.py::TestVCFFromVariantFile_21::testConnecting [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 284s [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 284s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 284s PASSED 284s tests/tabix_test.py::TestVCFFromVariantFile_21::testParsing PASSED 284s tests/tabix_test.py::TestVCFFromVariantFile_11::testConnecting PASSED 284s 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.) 284s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:669442 is not defined in the header, assuming Type=String 284s PASSED 284s tests/tabix_test.py::TestVCFFromVariantFile_issue85::testConnecting [E::bcf_hdr_parse] Could not parse the header, sample line not found 284s PASSED 284s tests/tabix_test.py::TestVCFFromVariantFile_issue85::testParsing PASSED 284s tests/tabix_test.py::TestVCFFromVariantFile_8::testConnecting PASSED 284s 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.) 284s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:676148 is not defined in the header, assuming Type=String 285s PASSED 285s tests/tabix_test.py::TestVCFFromVariantFile_23::testConnecting [W::bcf_hdr_check_sanity] GL should be declared as Number=G 285s PASSED 285s tests/tabix_test.py::TestVCFFromVariantFile_23::testParsing [W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String 285s PASSED 285s tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testConnecting PASSED 285s tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testParsing PASSED 285s tests/tabix_test.py::TestVCFFromVariantFile_3::testConnecting PASSED 285s 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.) 285s PASSED 285s tests/tabix_test.py::TestVCFFromVariantFile_2::testConnecting PASSED 285s 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.) 285s [W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String 285s PASSED 285s tests/tabix_test.py::TestVCFFromVariantFile_15::testConnecting PASSED 285s 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.) 285s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:439104 is not defined in the header, assuming Type=String 286s PASSED 286s tests/tabix_test.py::TestVCFFromVariantFile_7::testConnecting PASSED 286s 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.) 286s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:249843 is not defined in the header, assuming Type=String 286s PASSED 286s tests/tabix_test.py::TestVCFFromVariantFile_10::testConnecting PASSED 286s 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.) 286s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:676148 is not defined in the header, assuming Type=String 286s PASSED 286s tests/tabix_test.py::TestVCFFromVariantFile_12::testConnecting PASSED 286s 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.) 286s [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String 286s [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String 286s [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String 286s [W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String 286s [W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String 286s [W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String 286s [W::vcf_parse_format_dict2] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String 286s [W::vcf_parse_format_dict2] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String 286s [W::vcf_parse_format_dict2] FORMAT 'GQ' at chr1:1281168 is not defined in the header, assuming Type=String 286s [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) 286s [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) 286s [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) 286s [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) 286s [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) 286s [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) 286s [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) 287s PASSED 287s tests/tabix_test.py::TestVCFFromVariantFile_4::testConnecting PASSED 287s 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.) 287s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:249843 is not defined in the header, assuming Type=String 287s PASSED 287s tests/tabix_test.py::TestVCFFromVariantFile_13::testConnecting [W::bcf_hrec_check] Invalid tag name: "1000g" 287s [W::bcf_hrec_check] Invalid tag name: "GT:GL:GQ:NR" 287s PASSED 287s tests/tabix_test.py::TestVCFFromVariantFile_13::testParsing [W::bcf_hrec_check] Invalid tag name: "1000g" 287s [W::bcf_hrec_check] Invalid tag name: "GT:GL:GQ:NR" 287s [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse_info] INFO 'MMLQ' is not defined in the header, assuming Type=String 287s [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr17_gl000205_random' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr18' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr19' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr20' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr21' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr22' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chrUn_gl000214' is not defined in the header. (Quick workaround: index the file with tabix.) 287s PASSED 287s tests/tabix_test.py::TestVCFFromVariantFile_18::testConnecting [W::vcf_parse] Contig 'chrUn_gl000220' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chrUn_gl000225' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chrX' is not defined in the header. (Quick workaround: index the file with tabix.) 287s PASSED 287s 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.) 287s [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String 287s [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String 287s [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String 287s [W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String 287s [W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String 287s [W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String 287s [W::vcf_parse_format_dict2] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String 287s [W::vcf_parse_format_dict2] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String 287s [W::vcf_parse_format_dict2] FORMAT 'GQ' at chr1:1281168 is not defined in the header, assuming Type=String 287s [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) 287s [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) 287s PASSED 287s tests/tabix_test.py::TestVCFFromVariantFile_22::testConnecting PASSED 287s 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.) 287s [W::vcf_parse_info] INFO 'refseq.name' is not defined in the header, assuming Type=String 287s [W::vcf_parse_info] INFO 'refseq.positionType' is not defined in the header, assuming Type=String 288s [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) 289s PASSED 289s tests/tabix_test.py::TestVCFFromVariantFile_16::testConnecting PASSED 289s 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.) 289s [W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String 289s PASSED 289s tests/tabix_test.py::TestVCFFromVariantFile_9::testConnecting PASSED 289s 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.) 289s [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String 289s [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String 289s [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String 289s [W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String 289s [W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String 289s [W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String 289s [W::vcf_parse_format_dict2] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String 289s [W::vcf_parse_format_dict2] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String 289s [W::vcf_parse_format_dict2] FORMAT 'GQ' at chr1:1281168 is not defined in the header, assuming Type=String 289s [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) 289s [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) 289s [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) 289s [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) 289s [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) 289s [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) 289s [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) 289s [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) 289s [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) 289s [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) 289s [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) 289s PASSED 289s tests/tabix_test.py::TestVCFFromVariantFile_5::testConnecting [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) 289s [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) 289s [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) 289s [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) 289s [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) 289s [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) 289s [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) 289s [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) 289s PASSED 289s 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.) 289s PASSED 289s tests/tabix_test.py::TestVCFFromVariantFile_24::testConnecting [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: 289s #CHROM POS ID REF ALT QUAL FILTER INFO 289s 289s PASSED 289s tests/tabix_test.py::TestVCFFromVariantFile_24::testParsing PASSED 289s tests/tabix_test.py::TestVCFFromVariantFile_20::testConnecting [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 289s PASSED 289s tests/tabix_test.py::TestVCFFromVariantFile_20::testParsing [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 289s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 289s PASSED 289s tests/tabix_test.py::TestVCFFromVariantFile_6::testConnecting PASSED 289s 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.) 289s [W::vcf_parse_info] INFO 'CallSetAC' is not defined in the header, assuming Type=String 289s [W::vcf_parse_info] INFO 'CallSetAC2' is not defined in the header, assuming Type=String 289s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:669442 is not defined in the header, assuming Type=String 290s PASSED 290s tests/tabix_test.py::TestIndexArgument::testFetchAll PASSED 290s tests/tabix_test.py::TestIndexArgument::testLoadIndexWithoutTbiExtension PASSED 290s tests/tabix_test.py::TestBackwardsCompatibility::testBED PASSED 290s tests/tabix_test.py::TestBackwardsCompatibility::testBED0v23 PASSED 290s tests/tabix_test.py::TestBackwardsCompatibility::testBED0v26 PASSED 290s tests/tabix_test.py::TestBackwardsCompatibility::testEmpty PASSED 290s tests/tabix_test.py::TestBackwardsCompatibility::testVCF PASSED 290s tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v23 PASSED 290s tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v26 PASSED 290s tests/tabix_test.py::TestMultipleIterators::testDisjointIterators PASSED 290s tests/tabix_test.py::TestMultipleIterators::testDoubleFetch PASSED 290s tests/tabix_test.py::TestMultipleIterators::testJoinedIterators PASSED 290s tests/tabix_test.py::TestMultipleIterators::testScope PASSED 290s tests/tabix_test.py::TestContextManager::testManager PASSED 290s tests/tabix_test.py::TestMultithreadTabixFile::testMultithreadEqualsSinglethread PASSED 290s tests/tabixproxies_test.py::TestBED::testAssignmentToTargetList PASSED 290s tests/tabixproxies_test.py::TestParser::testAssignmentToTargetList PASSED 290s tests/tabixproxies_test.py::TestParser::testCopy PASSED 290s tests/tabixproxies_test.py::TestParser::testIteratorCompressed PASSED 290s tests/tabixproxies_test.py::TestParser::testIteratorUncompressed PASSED 290s tests/tabixproxies_test.py::TestParser::testRead PASSED 290s tests/tabixproxies_test.py::TestParser::testUnset PASSED 290s tests/tabixproxies_test.py::TestParser::testWrite PASSED 290s tests/tabixproxies_test.py::TestGTF::testAssignmentToTargetList PASSED 290s tests/tabixproxies_test.py::TestGTF::testCopy PASSED 290s tests/tabixproxies_test.py::TestGTF::testIteratorCompressed PASSED 290s tests/tabixproxies_test.py::TestGTF::testIteratorUncompressed PASSED 290s tests/tabixproxies_test.py::TestGTF::testRead PASSED 290s tests/tabixproxies_test.py::TestGTF::testUnset PASSED 290s tests/tabixproxies_test.py::TestGTF::testWrite PASSED 290s tests/tabixproxies_test.py::TestGTF::test_added_attribute_is_output PASSED 290s tests/tabixproxies_test.py::TestGTF::test_asdict_can_be_modified PASSED 290s tests/tabixproxies_test.py::TestGTF::test_asdict_contains_attributes PASSED 290s tests/tabixproxies_test.py::TestGTF::test_setAttribute_makes_changes PASSED 290s tests/tabixproxies_test.py::TestGTF::test_setting_end_is_one_based PASSED 290s tests/tabixproxies_test.py::TestGTF::test_setting_feature_to_none_produces_dot PASSED 290s tests/tabixproxies_test.py::TestGTF::test_setting_fields PASSED 290s tests/tabixproxies_test.py::TestGTF::test_setting_frame_to_none_produces_dot PASSED 290s tests/tabixproxies_test.py::TestGTF::test_setting_score_to_none_produces_dot PASSED 290s tests/tabixproxies_test.py::TestGTF::test_setting_source_to_none_produces_dot PASSED 290s tests/tabixproxies_test.py::TestGTF::test_setting_start_is_one_based PASSED 290s tests/tabixproxies_test.py::TestGTF::test_setting_strand_to_none_produces_dot PASSED 290s tests/tabixproxies_test.py::TestGFF3::testAssignmentToTargetList PASSED 290s tests/tabixproxies_test.py::TestGFF3::testCopy PASSED 290s tests/tabixproxies_test.py::TestGFF3::testIteratorCompressed PASSED 290s tests/tabixproxies_test.py::TestGFF3::testIteratorUncompressed PASSED 290s tests/tabixproxies_test.py::TestGFF3::testRead PASSED 290s tests/tabixproxies_test.py::TestGFF3::testUnset PASSED 290s tests/tabixproxies_test.py::TestGFF3::testWrite PASSED 290s tests/tabixproxies_test.py::TestGFF3::test_added_attribute_is_output PASSED 290s tests/tabixproxies_test.py::TestGFF3::test_asdict_can_be_modified PASSED 290s tests/tabixproxies_test.py::TestGFF3::test_asdict_contains_attributes PASSED 290s tests/tabixproxies_test.py::TestGFF3::test_setAttribute_makes_changes PASSED 290s tests/tabixproxies_test.py::TestGFF3::test_setting_end_is_one_based PASSED 290s tests/tabixproxies_test.py::TestGFF3::test_setting_feature_to_none_produces_dot PASSED 290s tests/tabixproxies_test.py::TestGFF3::test_setting_fields PASSED 290s tests/tabixproxies_test.py::TestGFF3::test_setting_frame_to_none_produces_dot PASSED 290s tests/tabixproxies_test.py::TestGFF3::test_setting_score_to_none_produces_dot PASSED 290s tests/tabixproxies_test.py::TestGFF3::test_setting_source_to_none_produces_dot PASSED 290s tests/tabixproxies_test.py::TestGFF3::test_setting_start_is_one_based PASSED 290s tests/tabixproxies_test.py::TestGFF3::test_setting_strand_to_none_produces_dot PASSED 290s tests/test_samtools_python.py::test_idxstats_parse_split_lines PASSED 290s tests/test_samtools_python.py::test_bedcov_split_lines PASSED 290s tests/test_samtools_python.py::test_idxstats_parse PASSED 290s tests/test_samtools_python.py::test_bedcov PASSED 290s 290s =============================== warnings summary =============================== 290s tests/samtools_test.py::SamtoolsTest::testStatements 290s tests/samtools_test.py::PysamTest::testStatements 290s /tmp/autopkgtest.TIYAUm/build.Rhj/src/tests/samtools_test.py:137: UserWarning: versions of pysam.samtools and samtools differ: 1.18 != 1.20 290s warnings.warn( 290s 290s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 290s =========== 938 passed, 13 skipped, 2 warnings in 113.26s (0:01:53) ============ 291s autopkgtest [07:47:31]: test command1: -----------------------] 291s command1 PASS 291s autopkgtest [07:47:31]: test command1: - - - - - - - - - - results - - - - - - - - - - 292s autopkgtest [07:47:32]: test autodep8-python3: preparing testbed 392s autopkgtest [07:49:12]: testbed dpkg architecture: ppc64el 392s autopkgtest [07:49:12]: testbed apt version: 2.9.8 392s autopkgtest [07:49:12]: @@@@@@@@@@@@@@@@@@@@ test bed setup 393s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 393s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [31.2 kB] 393s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [177 kB] 394s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 394s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [2268 kB] 396s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [213 kB] 396s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [1576 kB] 396s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [37.8 kB] 396s Fetched 4384 kB in 4s (1119 kB/s) 397s Reading package lists... 399s Reading package lists... 399s Building dependency tree... 399s Reading state information... 399s Calculating upgrade... 400s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 400s Reading package lists... 400s Building dependency tree... 400s Reading state information... 400s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 400s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 401s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 401s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 401s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 402s Reading package lists... 402s Reading package lists... 402s Building dependency tree... 402s Reading state information... 402s Calculating upgrade... 402s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 402s Reading package lists... 402s Building dependency tree... 402s Reading state information... 403s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 407s Reading package lists... 407s Building dependency tree... 407s Reading state information... 407s Starting pkgProblemResolver with broken count: 0 407s Starting 2 pkgProblemResolver with broken count: 0 407s Done 407s The following additional packages will be installed: 407s libdeflate0 libhts3t64 libhtscodecs2 python3-all python3-pysam 408s The following NEW packages will be installed: 408s autopkgtest-satdep libdeflate0 libhts3t64 libhtscodecs2 python3-all 408s python3-pysam 408s 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. 408s Need to get 4566 kB/4566 kB of archives. 408s After this operation, 39.2 MB of additional disk space will be used. 408s Get:1 /tmp/autopkgtest.TIYAUm/2-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [716 B] 408s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdeflate0 ppc64el 1.21-1 [63.3 kB] 408s Get:3 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1build1 [110 kB] 408s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el libhts3t64 ppc64el 1.20+ds-2 [574 kB] 408s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-all ppc64el 3.12.6-0ubuntu1 [888 B] 408s Get:6 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pysam ppc64el 0.22.1+ds-2 [3818 kB] 410s Fetched 4566 kB in 2s (2524 kB/s) 410s Selecting previously unselected package libdeflate0:ppc64el. 410s (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 ... 73549 files and directories currently installed.) 410s Preparing to unpack .../0-libdeflate0_1.21-1_ppc64el.deb ... 410s Unpacking libdeflate0:ppc64el (1.21-1) ... 410s Selecting previously unselected package libhtscodecs2:ppc64el. 410s Preparing to unpack .../1-libhtscodecs2_1.6.0-1build1_ppc64el.deb ... 410s Unpacking libhtscodecs2:ppc64el (1.6.0-1build1) ... 410s Selecting previously unselected package libhts3t64:ppc64el. 410s Preparing to unpack .../2-libhts3t64_1.20+ds-2_ppc64el.deb ... 410s Unpacking libhts3t64:ppc64el (1.20+ds-2) ... 410s Selecting previously unselected package python3-all. 410s Preparing to unpack .../3-python3-all_3.12.6-0ubuntu1_ppc64el.deb ... 410s Unpacking python3-all (3.12.6-0ubuntu1) ... 410s Selecting previously unselected package python3-pysam. 410s Preparing to unpack .../4-python3-pysam_0.22.1+ds-2_ppc64el.deb ... 410s Unpacking python3-pysam (0.22.1+ds-2) ... 410s Selecting previously unselected package autopkgtest-satdep. 410s Preparing to unpack .../5-2-autopkgtest-satdep.deb ... 410s Unpacking autopkgtest-satdep (0) ... 410s Setting up libhtscodecs2:ppc64el (1.6.0-1build1) ... 410s Setting up libdeflate0:ppc64el (1.21-1) ... 410s Setting up python3-all (3.12.6-0ubuntu1) ... 410s Setting up libhts3t64:ppc64el (1.20+ds-2) ... 410s Setting up python3-pysam (0.22.1+ds-2) ... 410s Setting up autopkgtest-satdep (0) ... 410s Processing triggers for man-db (2.12.1-3) ... 411s Processing triggers for libc-bin (2.40-1ubuntu3) ... 413s (Reading database ... 73935 files and directories currently installed.) 413s Removing autopkgtest-satdep (0) ... 419s autopkgtest [07:49:39]: 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 419s autopkgtest [07:49:39]: test autodep8-python3: [----------------------- 420s Testing with python3.12: 420s 420s autopkgtest [07:49:40]: test autodep8-python3: -----------------------] 420s autodep8-python3 PASS (superficial) 420s autopkgtest [07:49:40]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 421s autopkgtest [07:49:41]: @@@@@@@@@@@@@@@@@@@@ summary 421s command1 PASS 421s autodep8-python3 PASS (superficial) 426s nova [W] Using flock in prodstack6-ppc64el 426s Creating nova instance adt-plucky-ppc64el-python-pysam-20241103-074240-juju-7f2275-prod-proposed-migration-environment-14-ba3a0410-7bb9-4a9a-ac5f-32af078039a1 from image adt/ubuntu-plucky-ppc64el-server-20241103.img (UUID 8938751d-c60c-4749-8c34-7df179962ea5)... 426s nova [W] Using flock in prodstack6-ppc64el 426s Creating nova instance adt-plucky-ppc64el-python-pysam-20241103-074240-juju-7f2275-prod-proposed-migration-environment-14-ba3a0410-7bb9-4a9a-ac5f-32af078039a1 from image adt/ubuntu-plucky-ppc64el-server-20241103.img (UUID 8938751d-c60c-4749-8c34-7df179962ea5)...