0s autopkgtest [18:10:30]: starting date and time: 2024-03-25 18:10:30+0000 0s autopkgtest [18:10:30]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [18:10:30]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.t6nf704_/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed --apt-upgrade python-pysam --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python-pysam/0.22.0+ds-1build1 curl/8.5.0-2ubuntu8 gnutls28/3.8.3-1.1ubuntu2 htslib/1.19+ds-1.1build2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-ppc64el-20.secgroup --name adt-noble-ppc64el-python-pysam-20240325-181029-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 215s autopkgtest [18:14:03]: testbed dpkg architecture: ppc64el 215s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 215s autopkgtest [18:14:04]: testbed apt version: 2.7.12 215s autopkgtest [18:14:04]: @@@@@@@@@@@@@@@@@@@@ test bed setup 215s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [7608 B] 215s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [498 kB] 216s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.0 kB] 216s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3989 kB] 217s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [702 kB] 218s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 218s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 218s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 218s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4271 kB] 219s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 219s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [61.7 kB] 219s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 222s Fetched 9715 kB in 5s (1961 kB/s) 222s Reading package lists... 225s Reading package lists... 225s Building dependency tree... 225s Reading state information... 225s Calculating upgrade... 225s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 225s Reading package lists... 225s Building dependency tree... 225s Reading state information... 226s 0 upgraded, 0 newly installed, 0 to remove and 246 not upgraded. 226s sh: Attempting to set up Debian/Ubuntu apt sources automatically 226s sh: Distribution appears to be Ubuntu 227s Reading package lists... 228s Building dependency tree... 228s Reading state information... 228s eatmydata is already the newest version (131-1). 228s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 228s Reading package lists... 228s Building dependency tree... 228s Reading state information... 228s dbus is already the newest version (1.14.10-4ubuntu1). 228s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 228s Reading package lists... 228s Building dependency tree... 228s Reading state information... 229s rng-tools-debian is already the newest version (2.4). 229s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 229s Reading package lists... 229s Building dependency tree... 229s Reading state information... 229s The following packages will be REMOVED: 229s cloud-init* python3-configobj* python3-debconf* 229s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 229s After this operation, 3256 kB disk space will be freed. 229s (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 ... 70156 files and directories currently installed.) 229s Removing cloud-init (24.1.2-0ubuntu1) ... 230s Removing python3-configobj (5.0.8-3) ... 230s Removing python3-debconf (1.5.86) ... 230s Processing triggers for man-db (2.12.0-3) ... 231s (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 ... 69767 files and directories currently installed.) 231s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 232s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 232s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 232s invoke-rc.d: policy-rc.d denied execution of try-restart. 232s Reading package lists... 232s Building dependency tree... 232s Reading state information... 232s linux-generic is already the newest version (6.8.0-11.11+1). 232s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 233s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 233s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 233s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 236s Reading package lists... 236s Reading package lists... 236s Building dependency tree... 236s Reading state information... 236s Calculating upgrade... 237s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 237s Reading package lists... 237s Building dependency tree... 237s Reading state information... 237s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 237s autopkgtest [18:14:27]: rebooting testbed after setup commands that affected boot 408s autopkgtest [18:17:13]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 410s autopkgtest [18:17:20]: @@@@@@@@@@@@@@@@@@@@ apt-source python-pysam 416s Get:1 http://ftpmaster.internal/ubuntu noble/universe python-pysam 0.22.0+ds-1 (dsc) [2446 B] 416s Get:2 http://ftpmaster.internal/ubuntu noble/universe python-pysam 0.22.0+ds-1 (tar) [1497 kB] 416s Get:3 http://ftpmaster.internal/ubuntu noble/universe python-pysam 0.22.0+ds-1 (diff) [10.2 kB] 416s gpgv: Signature made Wed Nov 8 09:41:49 2023 UTC 416s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 416s gpgv: issuer "tille@debian.org" 416s gpgv: Can't check signature: No public key 416s dpkg-source: warning: cannot verify inline signature for ./python-pysam_0.22.0+ds-1.dsc: no acceptable signature found 416s autopkgtest [18:17:26]: testing package python-pysam version 0.22.0+ds-1 417s autopkgtest [18:17:27]: build not needed 430s autopkgtest [18:17:40]: test command1: preparing testbed 435s Reading package lists... 435s Building dependency tree... 435s Reading state information... 435s Starting pkgProblemResolver with broken count: 0 435s Starting 2 pkgProblemResolver with broken count: 0 435s Done 435s The following additional packages will be installed: 435s autoconf automake autopoint autotools-dev bcftools build-essential cpp 435s cpp-13 cpp-13-powerpc64le-linux-gnu cpp-powerpc64le-linux-gnu cython3 435s debhelper debugedit dh-autoreconf dh-exec dh-python dh-strip-nondeterminism 435s dwz g++ g++-13 g++-13-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc 435s gcc-13 gcc-13-powerpc64le-linux-gnu gcc-powerpc64le-linux-gnu gettext 435s intltool-debian libarchive-zip-perl libasan8 libatomic1 libc-dev-bin 435s libc6-dev libcc1-0 libcrypt-dev libcurl4-gnutls-dev libdebhelper-perl 435s libdeflate-dev libdeflate0 libdw1 libexpat1-dev 435s libfile-stripnondeterminism-perl libgcc-13-dev libgomp1 libhts-dev libhts3 435s libhtscodecs2 libisl23 libitm1 libjs-jquery libjs-sphinxdoc libjs-underscore 435s liblsan0 liblzma-dev libmpc3 libpython3-all-dev libpython3-dev libpython3.12 435s libpython3.12-dev libquadmath0 libstdc++-13-dev libsub-override-perl libtool 435s libtsan2 libubsan1 linux-libc-dev m4 po-debconf python3-all python3-all-dev 435s python3-dev python3-iniconfig python3-packaging python3-pluggy python3-pysam 435s python3-pytest python3.12-dev rpcsvc-proto samtools tabix zlib1g-dev 435s Suggested packages: 435s autoconf-archive gnu-standards autoconf-doc python3-numpy python3-matplotlib 435s texlive-latex-recommended cpp-doc gcc-13-locales cpp-13-doc cython-doc 435s dh-make flit python3-build python3-installer python3-wheel gcc-13-doc 436s gcc-multilib manpages-dev flex bison gdb gcc-doc gdb-powerpc64le-linux-gnu 436s gettext-doc libasprintf-dev libgettextpo-dev glibc-doc libcurl4-doc 436s libgnutls28-dev libidn-dev libkrb5-dev libldap2-dev librtmp-dev 436s libssh2-1-dev pkg-config liblzma-doc libstdc++-13-doc libtool-doc gfortran 436s | fortran95-compiler gcj-jdk m4-doc libmail-box-perl cwltool 436s Recommended packages: 436s manpages manpages-dev libc-devtools libarchive-cpio-perl javascript-common 436s libltdl-dev libmail-sendmail-perl 436s The following NEW packages will be installed: 436s autoconf automake autopkgtest-satdep autopoint autotools-dev bcftools 436s build-essential cpp cpp-13 cpp-13-powerpc64le-linux-gnu 436s cpp-powerpc64le-linux-gnu cython3 debhelper debugedit dh-autoreconf dh-exec 436s dh-python dh-strip-nondeterminism dwz g++ g++-13 436s g++-13-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc gcc-13 436s gcc-13-powerpc64le-linux-gnu gcc-powerpc64le-linux-gnu gettext 436s intltool-debian libarchive-zip-perl libasan8 libatomic1 libc-dev-bin 436s libc6-dev libcc1-0 libcrypt-dev libcurl4-gnutls-dev libdebhelper-perl 436s libdeflate-dev libdeflate0 libdw1 libexpat1-dev 436s libfile-stripnondeterminism-perl libgcc-13-dev libgomp1 libhts-dev libhts3 436s libhtscodecs2 libisl23 libitm1 libjs-jquery libjs-sphinxdoc libjs-underscore 436s liblsan0 liblzma-dev libmpc3 libpython3-all-dev libpython3-dev libpython3.12 436s libpython3.12-dev libquadmath0 libstdc++-13-dev libsub-override-perl libtool 436s libtsan2 libubsan1 linux-libc-dev m4 po-debconf python3-all python3-all-dev 436s python3-dev python3-iniconfig python3-packaging python3-pluggy python3-pysam 436s python3-pytest python3.12-dev rpcsvc-proto samtools tabix zlib1g-dev 436s 0 upgraded, 82 newly installed, 0 to remove and 0 not upgraded. 436s Need to get 99.9 MB/99.9 MB of archives. 436s After this operation, 411 MB of additional disk space will be used. 436s Get:1 /tmp/autopkgtest.wqFkeX/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [824 B] 436s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el m4 ppc64el 1.4.19-4 [275 kB] 436s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el autoconf all 2.71-3 [339 kB] 437s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el autotools-dev all 20220109.1 [44.9 kB] 437s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el automake all 1:1.16.5-1.3ubuntu1 [558 kB] 437s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el autopoint all 0.21-14ubuntu1 [422 kB] 438s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 438s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 438s Get:9 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB] 438s Get:10 http://ftpmaster.internal/ubuntu noble/universe ppc64el bcftools ppc64el 1.19-1 [976 kB] 439s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el libc-dev-bin ppc64el 2.39-0ubuntu6 [21.3 kB] 439s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el linux-libc-dev ppc64el 6.8.0-11.11 [1585 kB] 440s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el libcrypt-dev ppc64el 1:4.4.36-4 [167 kB] 440s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el rpcsvc-proto ppc64el 1.4.2-0ubuntu6 [82.3 kB] 440s Get:15 http://ftpmaster.internal/ubuntu noble/main ppc64el libc6-dev ppc64el 2.39-0ubuntu6 [2102 kB] 444s Get:16 http://ftpmaster.internal/ubuntu noble/main ppc64el libisl23 ppc64el 0.26-3 [864 kB] 444s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el libmpc3 ppc64el 1.3.1-1 [61.2 kB] 444s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el cpp-13-powerpc64le-linux-gnu ppc64el 13.2.0-17ubuntu2 [10.7 MB] 453s Get:19 http://ftpmaster.internal/ubuntu noble/main ppc64el cpp-13 ppc64el 13.2.0-17ubuntu2 [1038 B] 453s Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el cpp-powerpc64le-linux-gnu ppc64el 4:13.2.0-7ubuntu1 [5330 B] 453s Get:21 http://ftpmaster.internal/ubuntu noble/main ppc64el cpp ppc64el 4:13.2.0-7ubuntu1 [22.5 kB] 453s Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el libcc1-0 ppc64el 14-20240303-1ubuntu1 [48.1 kB] 453s Get:23 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240303-1ubuntu1 [161 kB] 453s Get:24 http://ftpmaster.internal/ubuntu noble/main ppc64el libitm1 ppc64el 14-20240303-1ubuntu1 [32.4 kB] 453s Get:25 http://ftpmaster.internal/ubuntu noble/main ppc64el libatomic1 ppc64el 14-20240303-1ubuntu1 [10.7 kB] 453s Get:26 http://ftpmaster.internal/ubuntu noble/main ppc64el libasan8 ppc64el 14-20240303-1ubuntu1 [2973 kB] 456s Get:27 http://ftpmaster.internal/ubuntu noble/main ppc64el liblsan0 ppc64el 14-20240303-1ubuntu1 [1325 kB] 457s Get:28 http://ftpmaster.internal/ubuntu noble/main ppc64el libtsan2 ppc64el 14-20240303-1ubuntu1 [2734 kB] 460s Get:29 http://ftpmaster.internal/ubuntu noble/main ppc64el libubsan1 ppc64el 14-20240303-1ubuntu1 [1194 kB] 460s Get:30 http://ftpmaster.internal/ubuntu noble/main ppc64el libquadmath0 ppc64el 14-20240303-1ubuntu1 [158 kB] 460s Get:31 http://ftpmaster.internal/ubuntu noble/main ppc64el libgcc-13-dev ppc64el 13.2.0-17ubuntu2 [1581 kB] 462s Get:32 http://ftpmaster.internal/ubuntu noble/main ppc64el gcc-13-powerpc64le-linux-gnu ppc64el 13.2.0-17ubuntu2 [20.6 MB] 478s Get:33 http://ftpmaster.internal/ubuntu noble/main ppc64el gcc-13 ppc64el 13.2.0-17ubuntu2 [477 kB] 478s Get:34 http://ftpmaster.internal/ubuntu noble/main ppc64el gcc-powerpc64le-linux-gnu ppc64el 4:13.2.0-7ubuntu1 [1224 B] 478s Get:35 http://ftpmaster.internal/ubuntu noble/main ppc64el gcc ppc64el 4:13.2.0-7ubuntu1 [5022 B] 478s Get:36 http://ftpmaster.internal/ubuntu noble/main ppc64el libstdc++-13-dev ppc64el 13.2.0-17ubuntu2 [2445 kB] 480s Get:37 http://ftpmaster.internal/ubuntu noble/main ppc64el g++-13-powerpc64le-linux-gnu ppc64el 13.2.0-17ubuntu2 [12.2 MB] 488s Get:38 http://ftpmaster.internal/ubuntu noble/main ppc64el g++-13 ppc64el 13.2.0-17ubuntu2 [14.5 kB] 488s Get:39 http://ftpmaster.internal/ubuntu noble/main ppc64el g++-powerpc64le-linux-gnu ppc64el 4:13.2.0-7ubuntu1 [968 B] 488s Get:40 http://ftpmaster.internal/ubuntu noble/main ppc64el g++ ppc64el 4:13.2.0-7ubuntu1 [1086 B] 488s Get:41 http://ftpmaster.internal/ubuntu noble/main ppc64el build-essential ppc64el 12.10ubuntu1 [4936 B] 488s Get:42 http://ftpmaster.internal/ubuntu noble/universe ppc64el cython3 ppc64el 3.0.8-1ubuntu1 [7218 kB] 493s Get:43 http://ftpmaster.internal/ubuntu noble/main ppc64el libdebhelper-perl all 13.14.1ubuntu1 [89.5 kB] 493s Get:44 http://ftpmaster.internal/ubuntu noble/main ppc64el libtool all 2.4.7-7 [166 kB] 493s Get:45 http://ftpmaster.internal/ubuntu noble/main ppc64el dh-autoreconf all 20 [16.1 kB] 493s Get:46 http://ftpmaster.internal/ubuntu noble/main ppc64el libarchive-zip-perl all 1.68-1 [90.2 kB] 493s Get:47 http://ftpmaster.internal/ubuntu noble/main ppc64el libsub-override-perl all 0.10-1 [10.0 kB] 493s Get:48 http://ftpmaster.internal/ubuntu noble/main ppc64el libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] 493s Get:49 http://ftpmaster.internal/ubuntu noble/main ppc64el dh-strip-nondeterminism all 1.13.1-1 [5362 B] 493s Get:50 http://ftpmaster.internal/ubuntu noble/main ppc64el libdw1 ppc64el 0.190-1 [294 kB] 494s Get:51 http://ftpmaster.internal/ubuntu noble/main ppc64el debugedit ppc64el 1:5.0-5 [51.1 kB] 494s Get:52 http://ftpmaster.internal/ubuntu noble/main ppc64el dwz ppc64el 0.15-1 [139 kB] 494s Get:53 http://ftpmaster.internal/ubuntu noble/main ppc64el gettext ppc64el 0.21-14ubuntu1 [979 kB] 496s Get:54 http://ftpmaster.internal/ubuntu noble/main ppc64el intltool-debian all 0.35.0+20060710.6 [23.2 kB] 496s Get:55 http://ftpmaster.internal/ubuntu noble/main ppc64el po-debconf all 1.0.21+nmu1 [233 kB] 496s Get:56 http://ftpmaster.internal/ubuntu noble/main ppc64el debhelper all 13.14.1ubuntu1 [869 kB] 496s Get:57 http://ftpmaster.internal/ubuntu noble/universe ppc64el dh-python all 6.20231223ubuntu2 [111 kB] 496s Get:58 http://ftpmaster.internal/ubuntu noble/main ppc64el libcurl4-gnutls-dev ppc64el 8.5.0-2ubuntu2 [530 kB] 496s Get:59 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate-dev ppc64el 1.19-1 [69.7 kB] 496s Get:60 http://ftpmaster.internal/ubuntu noble/main ppc64el libexpat1-dev ppc64el 2.6.0-1 [152 kB] 496s Get:61 http://ftpmaster.internal/ubuntu noble/main ppc64el liblzma-dev ppc64el 5.4.5-0.3 [243 kB] 497s Get:62 http://ftpmaster.internal/ubuntu noble/main ppc64el zlib1g-dev ppc64el 1:1.3.dfsg-3ubuntu1 [902 kB] 497s Get:63 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts-dev ppc64el 1.18+ds-1 [6252 kB] 504s Get:64 http://ftpmaster.internal/ubuntu noble/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 505s Get:65 http://ftpmaster.internal/ubuntu noble/main ppc64el libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 505s Get:66 http://ftpmaster.internal/ubuntu noble/main ppc64el libjs-sphinxdoc all 7.2.6-4 [149 kB] 505s Get:67 http://ftpmaster.internal/ubuntu noble/main ppc64el libpython3.12 ppc64el 3.12.2-1 [2575 kB] 507s Get:68 http://ftpmaster.internal/ubuntu noble/main ppc64el libpython3.12-dev ppc64el 3.12.2-1 [6012 kB] 512s Get:69 http://ftpmaster.internal/ubuntu noble/main ppc64el libpython3-dev ppc64el 3.12.1-0ubuntu2 [10.0 kB] 512s Get:70 http://ftpmaster.internal/ubuntu noble/main ppc64el libpython3-all-dev ppc64el 3.12.1-0ubuntu2 [912 B] 512s Get:71 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-all ppc64el 3.12.1-0ubuntu2 [904 B] 512s Get:72 http://ftpmaster.internal/ubuntu noble/main ppc64el python3.12-dev ppc64el 3.12.2-1 [505 kB] 512s Get:73 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-dev ppc64el 3.12.1-0ubuntu2 [26.7 kB] 512s Get:74 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-all-dev ppc64el 3.12.1-0ubuntu2 [908 B] 512s Get:75 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-iniconfig all 1.1.1-2 [6024 B] 512s Get:76 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-packaging all 23.2-1 [40.6 kB] 512s Get:77 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pluggy all 1.4.0-1 [20.4 kB] 512s Get:78 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pysam ppc64el 0.22.0+ds-1 [5037 kB] 516s Get:79 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pytest all 7.4.4-1 [305 kB] 516s Get:80 http://ftpmaster.internal/ubuntu noble/universe ppc64el samtools ppc64el 1.19.2-1 [669 kB] 517s Get:81 http://ftpmaster.internal/ubuntu noble/universe ppc64el tabix ppc64el 1.18+ds-1 [692 kB] 518s Get:82 http://ftpmaster.internal/ubuntu noble/main ppc64el dh-exec ppc64el 0.29 [26.7 kB] 518s Fetched 99.9 MB in 1min 22s (1218 kB/s) 518s Selecting previously unselected package m4. 518s (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 ... 69712 files and directories currently installed.) 518s Preparing to unpack .../00-m4_1.4.19-4_ppc64el.deb ... 518s Unpacking m4 (1.4.19-4) ... 518s Selecting previously unselected package autoconf. 518s Preparing to unpack .../01-autoconf_2.71-3_all.deb ... 518s Unpacking autoconf (2.71-3) ... 518s Selecting previously unselected package autotools-dev. 518s Preparing to unpack .../02-autotools-dev_20220109.1_all.deb ... 518s Unpacking autotools-dev (20220109.1) ... 518s Selecting previously unselected package automake. 518s Preparing to unpack .../03-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 518s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 518s Selecting previously unselected package autopoint. 518s Preparing to unpack .../04-autopoint_0.21-14ubuntu1_all.deb ... 518s Unpacking autopoint (0.21-14ubuntu1) ... 518s Selecting previously unselected package libdeflate0:ppc64el. 518s Preparing to unpack .../05-libdeflate0_1.19-1_ppc64el.deb ... 518s Unpacking libdeflate0:ppc64el (1.19-1) ... 518s Selecting previously unselected package libhtscodecs2:ppc64el. 518s Preparing to unpack .../06-libhtscodecs2_1.6.0-1_ppc64el.deb ... 518s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 518s Selecting previously unselected package libhts3:ppc64el. 518s Preparing to unpack .../07-libhts3_1.18+ds-1_ppc64el.deb ... 518s Unpacking libhts3:ppc64el (1.18+ds-1) ... 518s Selecting previously unselected package bcftools. 518s Preparing to unpack .../08-bcftools_1.19-1_ppc64el.deb ... 518s Unpacking bcftools (1.19-1) ... 518s Selecting previously unselected package libc-dev-bin. 518s Preparing to unpack .../09-libc-dev-bin_2.39-0ubuntu6_ppc64el.deb ... 518s Unpacking libc-dev-bin (2.39-0ubuntu6) ... 518s Selecting previously unselected package linux-libc-dev:ppc64el. 518s Preparing to unpack .../10-linux-libc-dev_6.8.0-11.11_ppc64el.deb ... 518s Unpacking linux-libc-dev:ppc64el (6.8.0-11.11) ... 519s Selecting previously unselected package libcrypt-dev:ppc64el. 519s Preparing to unpack .../11-libcrypt-dev_1%3a4.4.36-4_ppc64el.deb ... 519s Unpacking libcrypt-dev:ppc64el (1:4.4.36-4) ... 519s Selecting previously unselected package rpcsvc-proto. 519s Preparing to unpack .../12-rpcsvc-proto_1.4.2-0ubuntu6_ppc64el.deb ... 519s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 519s Selecting previously unselected package libc6-dev:ppc64el. 519s Preparing to unpack .../13-libc6-dev_2.39-0ubuntu6_ppc64el.deb ... 519s Unpacking libc6-dev:ppc64el (2.39-0ubuntu6) ... 519s Selecting previously unselected package libisl23:ppc64el. 519s Preparing to unpack .../14-libisl23_0.26-3_ppc64el.deb ... 519s Unpacking libisl23:ppc64el (0.26-3) ... 519s Selecting previously unselected package libmpc3:ppc64el. 519s Preparing to unpack .../15-libmpc3_1.3.1-1_ppc64el.deb ... 519s Unpacking libmpc3:ppc64el (1.3.1-1) ... 519s Selecting previously unselected package cpp-13-powerpc64le-linux-gnu. 519s Preparing to unpack .../16-cpp-13-powerpc64le-linux-gnu_13.2.0-17ubuntu2_ppc64el.deb ... 519s Unpacking cpp-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 519s Selecting previously unselected package cpp-13. 519s Preparing to unpack .../17-cpp-13_13.2.0-17ubuntu2_ppc64el.deb ... 519s Unpacking cpp-13 (13.2.0-17ubuntu2) ... 519s Selecting previously unselected package cpp-powerpc64le-linux-gnu. 519s Preparing to unpack .../18-cpp-powerpc64le-linux-gnu_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 519s Unpacking cpp-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 519s Selecting previously unselected package cpp. 519s Preparing to unpack .../19-cpp_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 519s Unpacking cpp (4:13.2.0-7ubuntu1) ... 519s Selecting previously unselected package libcc1-0:ppc64el. 519s Preparing to unpack .../20-libcc1-0_14-20240303-1ubuntu1_ppc64el.deb ... 519s Unpacking libcc1-0:ppc64el (14-20240303-1ubuntu1) ... 519s Selecting previously unselected package libgomp1:ppc64el. 519s Preparing to unpack .../21-libgomp1_14-20240303-1ubuntu1_ppc64el.deb ... 519s Unpacking libgomp1:ppc64el (14-20240303-1ubuntu1) ... 519s Selecting previously unselected package libitm1:ppc64el. 519s Preparing to unpack .../22-libitm1_14-20240303-1ubuntu1_ppc64el.deb ... 519s Unpacking libitm1:ppc64el (14-20240303-1ubuntu1) ... 519s Selecting previously unselected package libatomic1:ppc64el. 519s Preparing to unpack .../23-libatomic1_14-20240303-1ubuntu1_ppc64el.deb ... 519s Unpacking libatomic1:ppc64el (14-20240303-1ubuntu1) ... 519s Selecting previously unselected package libasan8:ppc64el. 519s Preparing to unpack .../24-libasan8_14-20240303-1ubuntu1_ppc64el.deb ... 519s Unpacking libasan8:ppc64el (14-20240303-1ubuntu1) ... 519s Selecting previously unselected package liblsan0:ppc64el. 519s Preparing to unpack .../25-liblsan0_14-20240303-1ubuntu1_ppc64el.deb ... 519s Unpacking liblsan0:ppc64el (14-20240303-1ubuntu1) ... 519s Selecting previously unselected package libtsan2:ppc64el. 519s Preparing to unpack .../26-libtsan2_14-20240303-1ubuntu1_ppc64el.deb ... 519s Unpacking libtsan2:ppc64el (14-20240303-1ubuntu1) ... 519s Selecting previously unselected package libubsan1:ppc64el. 519s Preparing to unpack .../27-libubsan1_14-20240303-1ubuntu1_ppc64el.deb ... 519s Unpacking libubsan1:ppc64el (14-20240303-1ubuntu1) ... 520s Selecting previously unselected package libquadmath0:ppc64el. 520s Preparing to unpack .../28-libquadmath0_14-20240303-1ubuntu1_ppc64el.deb ... 520s Unpacking libquadmath0:ppc64el (14-20240303-1ubuntu1) ... 520s Selecting previously unselected package libgcc-13-dev:ppc64el. 520s Preparing to unpack .../29-libgcc-13-dev_13.2.0-17ubuntu2_ppc64el.deb ... 520s Unpacking libgcc-13-dev:ppc64el (13.2.0-17ubuntu2) ... 520s Selecting previously unselected package gcc-13-powerpc64le-linux-gnu. 520s Preparing to unpack .../30-gcc-13-powerpc64le-linux-gnu_13.2.0-17ubuntu2_ppc64el.deb ... 520s Unpacking gcc-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 520s Selecting previously unselected package gcc-13. 520s Preparing to unpack .../31-gcc-13_13.2.0-17ubuntu2_ppc64el.deb ... 520s Unpacking gcc-13 (13.2.0-17ubuntu2) ... 520s Selecting previously unselected package gcc-powerpc64le-linux-gnu. 520s Preparing to unpack .../32-gcc-powerpc64le-linux-gnu_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 520s Unpacking gcc-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 520s Selecting previously unselected package gcc. 520s Preparing to unpack .../33-gcc_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 520s Unpacking gcc (4:13.2.0-7ubuntu1) ... 520s Selecting previously unselected package libstdc++-13-dev:ppc64el. 520s Preparing to unpack .../34-libstdc++-13-dev_13.2.0-17ubuntu2_ppc64el.deb ... 520s Unpacking libstdc++-13-dev:ppc64el (13.2.0-17ubuntu2) ... 520s Selecting previously unselected package g++-13-powerpc64le-linux-gnu. 520s Preparing to unpack .../35-g++-13-powerpc64le-linux-gnu_13.2.0-17ubuntu2_ppc64el.deb ... 520s Unpacking g++-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 521s Selecting previously unselected package g++-13. 521s Preparing to unpack .../36-g++-13_13.2.0-17ubuntu2_ppc64el.deb ... 521s Unpacking g++-13 (13.2.0-17ubuntu2) ... 521s Selecting previously unselected package g++-powerpc64le-linux-gnu. 521s Preparing to unpack .../37-g++-powerpc64le-linux-gnu_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 521s Unpacking g++-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 521s Selecting previously unselected package g++. 521s Preparing to unpack .../38-g++_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 521s Unpacking g++ (4:13.2.0-7ubuntu1) ... 521s Selecting previously unselected package build-essential. 521s Preparing to unpack .../39-build-essential_12.10ubuntu1_ppc64el.deb ... 521s Unpacking build-essential (12.10ubuntu1) ... 521s Selecting previously unselected package cython3. 521s Preparing to unpack .../40-cython3_3.0.8-1ubuntu1_ppc64el.deb ... 521s Unpacking cython3 (3.0.8-1ubuntu1) ... 521s Selecting previously unselected package libdebhelper-perl. 521s Preparing to unpack .../41-libdebhelper-perl_13.14.1ubuntu1_all.deb ... 521s Unpacking libdebhelper-perl (13.14.1ubuntu1) ... 521s Selecting previously unselected package libtool. 521s Preparing to unpack .../42-libtool_2.4.7-7_all.deb ... 521s Unpacking libtool (2.4.7-7) ... 521s Selecting previously unselected package dh-autoreconf. 521s Preparing to unpack .../43-dh-autoreconf_20_all.deb ... 521s Unpacking dh-autoreconf (20) ... 521s Selecting previously unselected package libarchive-zip-perl. 521s Preparing to unpack .../44-libarchive-zip-perl_1.68-1_all.deb ... 521s Unpacking libarchive-zip-perl (1.68-1) ... 521s Selecting previously unselected package libsub-override-perl. 521s Preparing to unpack .../45-libsub-override-perl_0.10-1_all.deb ... 521s Unpacking libsub-override-perl (0.10-1) ... 521s Selecting previously unselected package libfile-stripnondeterminism-perl. 521s Preparing to unpack .../46-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... 521s Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... 521s Selecting previously unselected package dh-strip-nondeterminism. 521s Preparing to unpack .../47-dh-strip-nondeterminism_1.13.1-1_all.deb ... 521s Unpacking dh-strip-nondeterminism (1.13.1-1) ... 521s Selecting previously unselected package libdw1:ppc64el. 521s Preparing to unpack .../48-libdw1_0.190-1_ppc64el.deb ... 521s Unpacking libdw1:ppc64el (0.190-1) ... 521s Selecting previously unselected package debugedit. 521s Preparing to unpack .../49-debugedit_1%3a5.0-5_ppc64el.deb ... 521s Unpacking debugedit (1:5.0-5) ... 521s Selecting previously unselected package dwz. 521s Preparing to unpack .../50-dwz_0.15-1_ppc64el.deb ... 521s Unpacking dwz (0.15-1) ... 521s Selecting previously unselected package gettext. 521s Preparing to unpack .../51-gettext_0.21-14ubuntu1_ppc64el.deb ... 521s Unpacking gettext (0.21-14ubuntu1) ... 521s Selecting previously unselected package intltool-debian. 521s Preparing to unpack .../52-intltool-debian_0.35.0+20060710.6_all.deb ... 521s Unpacking intltool-debian (0.35.0+20060710.6) ... 521s Selecting previously unselected package po-debconf. 521s Preparing to unpack .../53-po-debconf_1.0.21+nmu1_all.deb ... 521s Unpacking po-debconf (1.0.21+nmu1) ... 521s Selecting previously unselected package debhelper. 521s Preparing to unpack .../54-debhelper_13.14.1ubuntu1_all.deb ... 521s Unpacking debhelper (13.14.1ubuntu1) ... 522s Selecting previously unselected package dh-python. 522s Preparing to unpack .../55-dh-python_6.20231223ubuntu2_all.deb ... 522s Unpacking dh-python (6.20231223ubuntu2) ... 522s Selecting previously unselected package libcurl4-gnutls-dev:ppc64el. 522s Preparing to unpack .../56-libcurl4-gnutls-dev_8.5.0-2ubuntu2_ppc64el.deb ... 522s Unpacking libcurl4-gnutls-dev:ppc64el (8.5.0-2ubuntu2) ... 522s Selecting previously unselected package libdeflate-dev:ppc64el. 522s Preparing to unpack .../57-libdeflate-dev_1.19-1_ppc64el.deb ... 522s Unpacking libdeflate-dev:ppc64el (1.19-1) ... 522s Selecting previously unselected package libexpat1-dev:ppc64el. 522s Preparing to unpack .../58-libexpat1-dev_2.6.0-1_ppc64el.deb ... 522s Unpacking libexpat1-dev:ppc64el (2.6.0-1) ... 522s Selecting previously unselected package liblzma-dev:ppc64el. 522s Preparing to unpack .../59-liblzma-dev_5.4.5-0.3_ppc64el.deb ... 522s Unpacking liblzma-dev:ppc64el (5.4.5-0.3) ... 522s Selecting previously unselected package zlib1g-dev:ppc64el. 522s Preparing to unpack .../60-zlib1g-dev_1%3a1.3.dfsg-3ubuntu1_ppc64el.deb ... 522s Unpacking zlib1g-dev:ppc64el (1:1.3.dfsg-3ubuntu1) ... 522s Selecting previously unselected package libhts-dev:ppc64el. 522s Preparing to unpack .../61-libhts-dev_1.18+ds-1_ppc64el.deb ... 522s Unpacking libhts-dev:ppc64el (1.18+ds-1) ... 522s Selecting previously unselected package libjs-jquery. 522s Preparing to unpack .../62-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 522s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 522s Selecting previously unselected package libjs-underscore. 522s Preparing to unpack .../63-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 522s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 522s Selecting previously unselected package libjs-sphinxdoc. 522s Preparing to unpack .../64-libjs-sphinxdoc_7.2.6-4_all.deb ... 522s Unpacking libjs-sphinxdoc (7.2.6-4) ... 522s Selecting previously unselected package libpython3.12:ppc64el. 522s Preparing to unpack .../65-libpython3.12_3.12.2-1_ppc64el.deb ... 522s Unpacking libpython3.12:ppc64el (3.12.2-1) ... 522s Selecting previously unselected package libpython3.12-dev:ppc64el. 522s Preparing to unpack .../66-libpython3.12-dev_3.12.2-1_ppc64el.deb ... 522s Unpacking libpython3.12-dev:ppc64el (3.12.2-1) ... 522s Selecting previously unselected package libpython3-dev:ppc64el. 522s Preparing to unpack .../67-libpython3-dev_3.12.1-0ubuntu2_ppc64el.deb ... 522s Unpacking libpython3-dev:ppc64el (3.12.1-0ubuntu2) ... 522s Selecting previously unselected package libpython3-all-dev:ppc64el. 522s Preparing to unpack .../68-libpython3-all-dev_3.12.1-0ubuntu2_ppc64el.deb ... 522s Unpacking libpython3-all-dev:ppc64el (3.12.1-0ubuntu2) ... 522s Selecting previously unselected package python3-all. 522s Preparing to unpack .../69-python3-all_3.12.1-0ubuntu2_ppc64el.deb ... 522s Unpacking python3-all (3.12.1-0ubuntu2) ... 522s Selecting previously unselected package python3.12-dev. 522s Preparing to unpack .../70-python3.12-dev_3.12.2-1_ppc64el.deb ... 522s Unpacking python3.12-dev (3.12.2-1) ... 522s Selecting previously unselected package python3-dev. 522s Preparing to unpack .../71-python3-dev_3.12.1-0ubuntu2_ppc64el.deb ... 522s Unpacking python3-dev (3.12.1-0ubuntu2) ... 522s Selecting previously unselected package python3-all-dev. 522s Preparing to unpack .../72-python3-all-dev_3.12.1-0ubuntu2_ppc64el.deb ... 522s Unpacking python3-all-dev (3.12.1-0ubuntu2) ... 522s Selecting previously unselected package python3-iniconfig. 522s Preparing to unpack .../73-python3-iniconfig_1.1.1-2_all.deb ... 522s Unpacking python3-iniconfig (1.1.1-2) ... 522s Selecting previously unselected package python3-packaging. 522s Preparing to unpack .../74-python3-packaging_23.2-1_all.deb ... 522s Unpacking python3-packaging (23.2-1) ... 522s Selecting previously unselected package python3-pluggy. 522s Preparing to unpack .../75-python3-pluggy_1.4.0-1_all.deb ... 522s Unpacking python3-pluggy (1.4.0-1) ... 522s Selecting previously unselected package python3-pysam. 522s Preparing to unpack .../76-python3-pysam_0.22.0+ds-1_ppc64el.deb ... 522s Unpacking python3-pysam (0.22.0+ds-1) ... 523s Selecting previously unselected package python3-pytest. 523s Preparing to unpack .../77-python3-pytest_7.4.4-1_all.deb ... 523s Unpacking python3-pytest (7.4.4-1) ... 523s Selecting previously unselected package samtools. 523s Preparing to unpack .../78-samtools_1.19.2-1_ppc64el.deb ... 523s Unpacking samtools (1.19.2-1) ... 523s Selecting previously unselected package tabix. 523s Preparing to unpack .../79-tabix_1.18+ds-1_ppc64el.deb ... 523s Unpacking tabix (1.18+ds-1) ... 523s Selecting previously unselected package dh-exec. 523s Preparing to unpack .../80-dh-exec_0.29_ppc64el.deb ... 523s Unpacking dh-exec (0.29) ... 523s Selecting previously unselected package autopkgtest-satdep. 523s Preparing to unpack .../81-1-autopkgtest-satdep.deb ... 523s Unpacking autopkgtest-satdep (0) ... 523s Setting up libhtscodecs2:ppc64el (1.6.0-1) ... 523s Setting up dh-python (6.20231223ubuntu2) ... 523s Setting up python3-iniconfig (1.1.1-2) ... 523s Setting up libdw1:ppc64el (0.190-1) ... 523s Setting up libarchive-zip-perl (1.68-1) ... 523s Setting up libdebhelper-perl (13.14.1ubuntu1) ... 523s Setting up libdeflate0:ppc64el (1.19-1) ... 523s Setting up linux-libc-dev:ppc64el (6.8.0-11.11) ... 523s Setting up m4 (1.4.19-4) ... 523s Setting up python3-all (3.12.1-0ubuntu2) ... 523s Setting up libgomp1:ppc64el (14-20240303-1ubuntu1) ... 523s Setting up libcurl4-gnutls-dev:ppc64el (8.5.0-2ubuntu2) ... 523s Setting up autotools-dev (20220109.1) ... 523s Setting up python3-packaging (23.2-1) ... 523s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 523s Setting up libquadmath0:ppc64el (14-20240303-1ubuntu1) ... 523s Setting up libmpc3:ppc64el (1.3.1-1) ... 523s Setting up libatomic1:ppc64el (14-20240303-1ubuntu1) ... 523s Setting up cython3 (3.0.8-1ubuntu1) ... 524s Setting up autopoint (0.21-14ubuntu1) ... 524s Setting up autoconf (2.71-3) ... 524s Setting up python3-pluggy (1.4.0-1) ... 524s Setting up liblzma-dev:ppc64el (5.4.5-0.3) ... 524s Setting up libubsan1:ppc64el (14-20240303-1ubuntu1) ... 524s Setting up dwz (0.15-1) ... 524s Setting up libcrypt-dev:ppc64el (1:4.4.36-4) ... 524s Setting up libasan8:ppc64el (14-20240303-1ubuntu1) ... 524s Setting up debugedit (1:5.0-5) ... 524s Setting up libsub-override-perl (0.10-1) ... 524s Setting up libtsan2:ppc64el (14-20240303-1ubuntu1) ... 524s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 524s Setting up libisl23:ppc64el (0.26-3) ... 524s Setting up libc-dev-bin (2.39-0ubuntu6) ... 525s Setting up cpp-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 525s Setting up libdeflate-dev:ppc64el (1.19-1) ... 525s Setting up tabix (1.18+ds-1) ... 525s Setting up libpython3.12:ppc64el (3.12.2-1) ... 525s Setting up libcc1-0:ppc64el (14-20240303-1ubuntu1) ... 525s Setting up liblsan0:ppc64el (14-20240303-1ubuntu1) ... 525s Setting up libitm1:ppc64el (14-20240303-1ubuntu1) ... 525s Setting up cpp-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 525s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 525s Setting up automake (1:1.16.5-1.3ubuntu1) ... 525s update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode 525s Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... 525s Setting up libhts3:ppc64el (1.18+ds-1) ... 525s Setting up gettext (0.21-14ubuntu1) ... 525s Setting up python3-pysam (0.22.0+ds-1) ... 525s Setting up cpp-13 (13.2.0-17ubuntu2) ... 525s Setting up python3-pytest (7.4.4-1) ... 525s Setting up bcftools (1.19-1) ... 525s Setting up samtools (1.19.2-1) ... 525s Setting up intltool-debian (0.35.0+20060710.6) ... 525s Setting up libjs-sphinxdoc (7.2.6-4) ... 525s Setting up dh-strip-nondeterminism (1.13.1-1) ... 525s Setting up libgcc-13-dev:ppc64el (13.2.0-17ubuntu2) ... 525s Setting up cpp (4:13.2.0-7ubuntu1) ... 525s Setting up libc6-dev:ppc64el (2.39-0ubuntu6) ... 525s Setting up libstdc++-13-dev:ppc64el (13.2.0-17ubuntu2) ... 525s Setting up po-debconf (1.0.21+nmu1) ... 525s Setting up libexpat1-dev:ppc64el (2.6.0-1) ... 525s Setting up gcc-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 525s Setting up gcc-13 (13.2.0-17ubuntu2) ... 525s Setting up zlib1g-dev:ppc64el (1:1.3.dfsg-3ubuntu1) ... 525s Setting up libtool (2.4.7-7) ... 525s Setting up libhts-dev:ppc64el (1.18+ds-1) ... 525s Setting up libpython3.12-dev:ppc64el (3.12.2-1) ... 525s Setting up g++-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 525s Setting up dh-autoreconf (20) ... 525s Setting up gcc-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 525s Setting up python3.12-dev (3.12.2-1) ... 525s Setting up g++-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 525s Setting up g++-13 (13.2.0-17ubuntu2) ... 525s Setting up libpython3-dev:ppc64el (3.12.1-0ubuntu2) ... 525s Setting up debhelper (13.14.1ubuntu1) ... 525s Setting up dh-exec (0.29) ... 525s Setting up gcc (4:13.2.0-7ubuntu1) ... 525s Setting up libpython3-all-dev:ppc64el (3.12.1-0ubuntu2) ... 525s Setting up python3-dev (3.12.1-0ubuntu2) ... 525s Setting up g++ (4:13.2.0-7ubuntu1) ... 525s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 525s Setting up build-essential (12.10ubuntu1) ... 525s Setting up python3-all-dev (3.12.1-0ubuntu2) ... 525s Setting up autopkgtest-satdep (0) ... 525s Processing triggers for man-db (2.12.0-3) ... 526s Processing triggers for install-info (7.1-3) ... 526s Processing triggers for libc-bin (2.39-0ubuntu6) ... 530s (Reading database ... 75272 files and directories currently installed.) 530s Removing autopkgtest-satdep (0) ... 531s autopkgtest [18:19:21]: test command1: export HOME=$PWD && make -C tests/pysam_data && make -C tests/cbcf_data && pytest-3 531s autopkgtest [18:19:21]: test command1: [----------------------- 531s make: Entering directory '/tmp/autopkgtest.wqFkeX/build.BHm/src/tests/pysam_data' 531s samtools faidx ex1.fa 531s samtools view --no-PG -bo ex1.bam -t ex1.fa.fai ex1.sam.gz 531s samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz 531s [mpileup] 1 samples in 1 input files 531s gunzip < ex1.sam.gz > ex1.sam 531s samtools index ex1.bam 531s samtools view --no-PG -h ex1.bam | gzip > ex2.sam.gz 531s gunzip < ex2.sam.gz > ex2.sam 531s samtools view --no-PG -bo ex2.bam ex2.sam 531s samtools index ex2.bam 531s samtools calmd --no-PG --output-fmt BAM ex2.bam ex1.fa > with_md.sam.gz 531s [bam_fillmd1] different NM for read 'EAS139_11:7:46:695:738': 3 -> 8 531s [bam_fillmd1] different NM for read 'EAS218_4:1:48:9:409': 0 -> 5 531s [bam_fillmd1] different NM for read 'B7_591:7:200:192:373': 0 -> 5 531s [bam_fillmd1] different NM for read 'EAS56_65:1:163:846:223': 0 -> 5 531s [bam_fillmd1] different NM for read 'EAS114_30:7:283:799:560': 0 -> 5 531s [bam_fillmd1] different NM for read 'B7_595:4:84:802:737': 0 -> 4 531s [bam_fillmd1] different NM for read 'EAS51_66:5:308:400:602': 0 -> 3 531s [bam_fillmd1] different NM for read 'EAS54_81:2:285:367:932': 0 -> 3 531s [bam_fillmd1] different NM for read 'EAS114_39:1:70:147:84': 0 -> 3 531s [bam_fillmd1] different NM for read 'EAS56_53:1:124:243:35': 2 -> 5 531s [bam_fillmd1] different NM for read 'EAS1_103:2:226:302:758': 2 -> 3 531s [bam_fillmd1] different NM for read 'EAS114_28:6:175:705:982': 1 -> 0 531s [bam_fillmd1] different NM for read 'EAS51_64:4:179:389:585': 7 -> 8 531s [bam_fillmd1] different NM for read 'B7_589:1:122:337:968': 3 -> 2 531s [bam_fillmd1] different NM for read 'B7_610:4:15:805:420': 4 -> 5 531s [bam_fillmd1] different NM for read 'B7_591:2:279:124:41': 2 -> 4 531s [bam_fillmd1] different NM for read 'EAS112_32:8:89:254:332': 0 -> 1 531s [bam_fillmd1] different NM for read 'B7_597:7:103:731:697': 0 -> 2 531s [bam_fillmd1] different NM for read 'EAS139_11:2:71:83:58': 0 -> 2 531s [bam_fillmd1] different NM for read 'EAS192_3:4:63:5:870': 0 -> 2 531s [bam_fillmd1] different NM for read 'EAS139_19:2:29:1822:1881': 0 -> 2 531s [bam_fillmd1] different NM for read 'EAS188_7:3:15:568:42': 2 -> 1 531s [bam_fillmd1] different NM for read 'EAS1_95:4:176:971:874': 0 -> 1 531s [bam_fillmd1] different NM for read 'EAS1_99:1:34:649:318': 3 -> 4 531s [bam_fillmd1] different NM for read 'EAS54_65:4:61:346:384': 3 -> 4 531s [bam_fillmd1] different NM for read 'B7_597:6:20:592:496': 0 -> 1 531s [bam_fillmd1] different NM for read 'B7_597:4:38:999:463': 2 -> 1 531s [bam_fillmd1] different NM for read 'EAS114_28:5:23:944:377': 0 -> 3 531s [bam_fillmd1] different NM for read 'EAS219_1:3:90:219:528': 0 -> 3 531s [bam_fillmd1] different NM for read 'EAS1_108:5:89:942:84': 0 -> 4 531s [bam_fillmd1] different NM for read 'EAS1_108:6:159:493:275': 0 -> 5 531s [bam_fillmd1] different NM for read 'EAS139_11:1:81:1019:558': 0 -> 5 531s [bam_fillmd1] different NM for read 'EAS51_62:7:162:195:761': 0 -> 4 531s [bam_fillmd1] different NM for read 'B7_597:3:115:646:430': 0 -> 4 531s [bam_fillmd1] different NM for read 'EAS114_30:6:243:209:110': 0 -> 4 531s [bam_fillmd1] different NM for read 'EAS1_108:2:266:994:429': 0 -> 4 531s [bam_fillmd1] different NM for read 'EAS114_30:5:32:461:154': 0 -> 4 531s [bam_fillmd1] different NM for read 'EAS114_39:6:7:492:1088': 0 -> 4 531s [bam_fillmd1] different NM for read 'EAS1_95:6:174:650:125': 0 -> 4 531s [bam_fillmd1] different NM for read 'EAS56_59:6:89:457:591': 1 -> 5 531s [bam_fillmd1] different NM for read 'EAS114_39:2:38:670:564': 0 -> 4 531s [bam_fillmd1] different NM for read 'EAS188_7:4:92:693:228': 1 -> 6 531s [bam_fillmd1] different NM for read 'EAS218_1:4:61:1369:440': 0 -> 4 531s [bam_fillmd1] different NM for read 'EAS114_26:4:123:1001:580': 0 -> 4 531s [bam_fillmd1] different NM for read 'EAS114_39:4:10:1312:1558': 0 -> 4 531s [bam_fillmd1] different NM for read 'EAS220_1:8:45:178:1321': 0 -> 4 531s [bam_fillmd1] different NM for read 'EAS56_59:5:125:137:58': 0 -> 4 531s [bam_fillmd1] different NM for read 'EAS192_3:3:285:349:797': 1 -> 5 531s [bam_fillmd1] different NM for read 'EAS114_45:5:56:1757:1319': 0 -> 4 531s [bam_fillmd1] different NM for read 'B7_591:3:291:404:199': 0 -> 4 531s [bam_fillmd1] different NM for read 'EAS54_65:7:159:253:353': 0 -> 4 531s [bam_fillmd1] different NM for read 'EAS56_57:1:122:38:103': 0 -> 4 531s [bam_fillmd1] different NM for read 'EAS188_4:5:103:870:105': 0 -> 4 531s [bam_fillmd1] different NM for read 'EAS1_105:8:24:718:322': 3 -> 7 531s [bam_fillmd1] different NM for read 'EAS51_64:6:118:41:489': 0 -> 4 531s [bam_fillmd1] different NM for read 'EAS56_61:3:165:665:220': 0 -> 4 531s [bam_fillmd1] different NM for read 'EAS114_30:6:238:803:383': 0 -> 4 531s [bam_fillmd1] different NM for read 'EAS1_105:3:232:364:583': 0 -> 3 531s [bam_fillmd1] different NM for read 'B7_595:2:29:729:70': 3 -> 4 531s [bam_fillmd1] different NM for read 'EAS114_30:6:220:809:850': 4 -> 6 531s [bam_fillmd1] different NM for read 'EAS54_65:2:264:157:150': 3 -> 5 531s [bam_fillmd1] different NM for read 'B7_595:8:26:242:35': 2 -> 1 531s [bam_fillmd1] different NM for read 'B7_610:7:34:144:868': 4 -> 5 531s [bam_fillmd1] different NM for read 'B7_597:8:147:360:141': 1 -> 2 531s [bam_fillmd1] different NM for read 'EAS139_19:2:82:154:1333': 0 -> 4 531s [bam_fillmd1] different NM for read 'EAS56_63:3:41:468:459': 0 -> 3 531s [bam_fillmd1] different NM for read 'EAS1_97:4:274:287:423': 0 -> 1 531s [bam_fillmd1] different NM for read 'EAS114_30:2:303:428:326': 0 -> 1 531s [bam_fillmd1] different NM for read 'EAS54_71:8:105:854:975': 0 -> 3 531s gunzip < with_md.sam.gz > with_md.sam 531s [W::bam_hdr_read] samtools view --no-PG -bo with_md.bam with_md.sam 531s EOF marker is absent. The input is probably truncated 531s samtools index with_md.bam 531s samtools view --no-PG -bu -o uncompressed.bam ex2.sam 531s samtools view --no-PG -bo MM-chebi.bam MM-chebi.sam 531s samtools view --no-PG -bo MM-double.bam MM-double.sam 531s samtools view --no-PG -bo MM-multi.bam MM-multi.sam 531s samtools view --no-PG -bo MM-orient.bam MM-orient.sam 531s samtools view --no-PG -bo ex10.bam ex10.sam 531s samtools view --no-PG -bo ex3.bam ex3.sam 531s samtools view --no-PG -bo ex4.bam ex4.sam 531s samtools view --no-PG -bo ex5.bam ex5.sam 531s samtools view --no-PG -bo ex6.bam ex6.sam 531s samtools view --no-PG -bo ex8.bam ex8.sam 531s samtools view --no-PG -bo ex9_fail.bam ex9_fail.sam 531s samtools view --no-PG -bo ex9_nofail.bam ex9_nofail.sam 531s samtools view --no-PG -bo ex_spliced.bam ex_spliced.sam 531s samtools view --no-PG -bo example_aligned_pairs.bam example_aligned_pairs.sam 531s samtools view --no-PG -bo example_btag.bam example_btag.sam 531s samtools view --no-PG -bo example_dash_in_chr.bam example_dash_in_chr.sam 531s samtools view --no-PG -bo example_empty_header.bam example_empty_header.sam 531s samtools view --no-PG -bo example_empty_with_header.bam example_empty_with_header.sam 531s samtools view --no-PG -bo example_reverse_complement.bam example_reverse_complement.sam 531s touch tmp.list 531s samtools view --no-PG -bo example_unmapped_reads_no_sq.bam -t tmp.list example_unmapped_reads_no_sq.sam 531s rm -f tmp.list 531s samtools view --no-PG -bo issue100.bam issue100.sam 531s samtools view --no-PG -bo rg_with_tab.bam rg_with_tab.sam 531s samtools view --no-PG -bo softclip.bam softclip.sam 531s samtools view --no-PG -bo tag_bug.bam tag_bug.sam 531s samtools view --no-PG -bo test_mapped_unmapped.bam test_mapped_unmapped.sam 531s samtools view --no-PG -bo test_query_position.bam test_query_position.sam 531s samtools view --no-PG -bo test_unaligned.bam test_unaligned.sam 531s samtools index MM-chebi.bam 531s samtools index MM-double.bam 531s samtools index MM-multi.bam 531s samtools index MM-orient.bam 532s samtools index ex10.bam 532s samtools index ex3.bam 532s samtools index ex4.bam 532s samtools index ex5.bam 532s samtools index ex6.bam 532s samtools index ex8.bam 532s samtools index ex9_fail.bam 532s samtools index ex9_nofail.bam 532s samtools index ex_spliced.bam 532s samtools index example_aligned_pairs.bam 532s samtools index example_btag.bam 532s samtools index example_dash_in_chr.bam 532s samtools index example_empty_header.bam 532s samtools index example_empty_with_header.bam 532s samtools index example_reverse_complement.bam 532s samtools index example_unmapped_reads_no_sq.bam 532s samtools index issue100.bam 532s samtools index rg_with_tab.bam 532s samtools index softclip.bam 532s samtools index tag_bug.bam 532s samtools index test_mapped_unmapped.bam 532s samtools index test_query_position.bam 532s samtools index test_unaligned.bam 532s samtools view --no-PG -Co ex1.cram -T ex1.fa ex1.sam 532s samtools view --no-PG -Co ex2.cram -T ex1.fa ex2.sam 532s samtools view --no-PG -Co ex3.cram -T ex1.fa ex3.sam 532s samtools index ex1.cram 532s samtools index ex2.cram 532s samtools index ex3.cram 532s cp ex1.bam example_bai.bam 532s samtools index example_bai.bam 532s mv example_bai.bam.bai example_bai.bai 532s dd if=ex2.bam of=ex2_truncated.bam bs=$((`wc -c < ex2.bam`-512)) count=1 532s (bgzip -d < ex2.bam; printf '\37\0\0\0\1\0\0\0') | bgzip > ex2_corrupt.bam 532s 1+0 records in 532s 1+0 records out 532s 122288 bytes (122 kB, 119 KiB) copied, 8.56e-05 s, 1.4 GB/s 532s grep "^@" ex2.sam | samtools view --no-PG -bo empty.bam - 532s samtools index empty.bam 532s cp ex1.bam explicit_index.bam 532s cp ex1.cram explicit_index.cram 532s gzip < faidx_empty_seq.fq > faidx_empty_seq.fq.gz 532s bgzip < ex1.fa > ex1.fa.gz 532s samtools faidx ex1.fa.gz 532s cp ex1.bam ex1_csi.bam 532s samtools index -c ex1_csi.bam 532s touch all.stamp 532s rm with_md.sam 532s make: Leaving directory '/tmp/autopkgtest.wqFkeX/build.BHm/src/tests/pysam_data' 532s make: Entering directory '/tmp/autopkgtest.wqFkeX/build.BHm/src/tests/cbcf_data' 532s bgzip < example_vcf40.vcf > example_vcf40.vcf.gz 532s tabix -p vcf example_vcf40.vcf.gz # create tbi index 532s bcftools index example_vcf40.vcf.gz # create csi index 532s bgzip < example_vcf42.vcf > example_vcf42.vcf.gz 532s tabix -p vcf example_vcf42.vcf.gz # create tbi index 532s bcftools index example_vcf42.vcf.gz # create csi index 532s bgzip < example_vcf42_only_header.vcf > example_vcf42_only_header.vcf.gz 532s tabix -p vcf example_vcf42_only_header.vcf.gz # create tbi index 532s bcftools index example_vcf42_only_header.vcf.gz # create csi index 532s bgzip < example_vcf42_withcontigs.vcf > example_vcf42_withcontigs.vcf.gz 532s tabix -p vcf example_vcf42_withcontigs.vcf.gz # create tbi index 532s bcftools index example_vcf42_withcontigs.vcf.gz # create csi index 532s bgzip < example_vcf43.vcf > example_vcf43.vcf.gz 532s tabix -p vcf example_vcf43.vcf.gz # create tbi index 532s bcftools index example_vcf43.vcf.gz # create csi index 532s bgzip < example_vcf43_with_utf8.vcf > example_vcf43_with_utf8.vcf.gz 532s tabix -p vcf example_vcf43_with_utf8.vcf.gz # create tbi index 532s bcftools index example_vcf43_with_utf8.vcf.gz # create csi index 532s bgzip < gnomad.vcf > gnomad.vcf.gz 532s tabix -p vcf gnomad.vcf.gz # create tbi index 532s bcftools index gnomad.vcf.gz # create csi index 532s bgzip < gnomad_fixed.vcf > gnomad_fixed.vcf.gz 532s tabix -p vcf gnomad_fixed.vcf.gz # create tbi index 532s bcftools index gnomad_fixed.vcf.gz # create csi index 532s bgzip < missing_genotypes.vcf > missing_genotypes.vcf.gz 532s tabix -p vcf missing_genotypes.vcf.gz # create tbi index 532s bcftools index missing_genotypes.vcf.gz # create csi index 532s bcftools view -O b example_vcf40.vcf.gz -o example_vcf40.bcf 532s bcftools index example_vcf40.bcf 532s bcftools view -O b example_vcf42.vcf.gz -o example_vcf42.bcf 532s bcftools index example_vcf42.bcf 532s bcftools view -O b example_vcf42_only_header.vcf.gz -o example_vcf42_only_header.bcf 532s bcftools index example_vcf42_only_header.bcf 532s bcftools view -O b example_vcf42_withcontigs.vcf.gz -o example_vcf42_withcontigs.bcf 532s bcftools index example_vcf42_withcontigs.bcf 532s bcftools view -O b example_vcf43.vcf.gz -o example_vcf43.bcf 532s bcftools index example_vcf43.bcf 532s bcftools view -O b example_vcf43_with_utf8.vcf.gz -o example_vcf43_with_utf8.bcf 532s bcftools index example_vcf43_with_utf8.bcf 532s bcftools view -O b gnomad.vcf.gz -o gnomad.bcf 532s bcftools index gnomad.bcf 532s bcftools view -O b gnomad_fixed.vcf.gz -o gnomad_fixed.bcf 532s [W::bcf_hdr_check_sanity] PL should be declared as Number=G 532s bcftools index gnomad_fixed.bcf 532s [W::bcf_hdr_check_sanity] PL should be declared as Number=G 532s bcftools view -O b missing_genotypes.vcf.gz -o missing_genotypes.bcf 532s bcftools index missing_genotypes.bcf 532s touch all.stamp 532s make: Leaving directory '/tmp/autopkgtest.wqFkeX/build.BHm/src/tests/cbcf_data' 532s ============================= test session starts ============================== 532s platform linux -- Python 3.12.2, pytest-7.4.4, pluggy-1.4.0 -- /usr/bin/python3 532s cachedir: .pytest_cache 532s rootdir: /tmp/autopkgtest.wqFkeX/build.BHm/src 532s configfile: setup.cfg 532s testpaths: pysam, tests 534s collecting ... collected 951 items 534s 534s tests/AlignedSegment_test.py::TestAlignedSegment::testBlocks [E::cram_index_load] Could not retrieve index file for '/tmp/autopkgtest.wqFkeX/build.BHm/src/tests/tmp/pysamtests_tmp_check_read_write_2ia6jvf5' 534s PASSED 534s tests/AlignedSegment_test.py::TestAlignedSegment::testCompare PASSED 534s tests/AlignedSegment_test.py::TestAlignedSegment::testEmpty PASSED 534s tests/AlignedSegment_test.py::TestAlignedSegment::testFullReferencePositions PASSED 534s tests/AlignedSegment_test.py::TestAlignedSegment::testHashing PASSED 534s tests/AlignedSegment_test.py::TestAlignedSegment::testLargeRead PASSED 534s tests/AlignedSegment_test.py::TestAlignedSegment::testNoSequence PASSED 534s tests/AlignedSegment_test.py::TestAlignedSegment::testPositions PASSED 534s tests/AlignedSegment_test.py::TestAlignedSegment::testSettingTagInEmptyRead PASSED 534s tests/AlignedSegment_test.py::TestAlignedSegment::testStrOfEmptyRead PASSED 534s tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate PASSED 534s tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate2 PASSED 534s tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateQual PASSED 534s tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateTlen PASSED 534s tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_mapped_reads_are_updated PASSED 534s tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_unmapped_reads_ignore_length PASSED 534s tests/AlignedSegment_test.py::TestAlignedSegment::test_equivalence_matches_only_and_with_seq PASSED 534s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs PASSED 534s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_1character_md PASSED 534s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_bad_type_md PASSED 534s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_hard_clipping PASSED 534s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_lowercase_md PASSED 534s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_match_mismatch PASSED 534s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding PASSED 534s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding_with_seq PASSED 534s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip PASSED 534s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip_reference PASSED 534s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_soft_clipping PASSED 534s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_uppercase_md PASSED 534s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_with_malformed_MD_tag PASSED 534s tests/AlignedSegment_test.py::TestAlignedSegment::test_header_accessible PASSED 534s tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_query_length PASSED 534s tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_read_length PASSED 534s tests/AlignedSegment_test.py::TestAlignedSegment::test_query_length_is_limited PASSED 534s tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_asterisk PASSED 534s tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_chromosome PASSED 534s tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_none PASSED 534s tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_not_be_set_to_unknown_chromosome PASSED 534s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_chromosome PASSED 534s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing PASSED 534s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing_without_header PASSED 534s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_without_header PASSED 534s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_not_be_set_to_unknown_chromosome PASSED 534s tests/AlignedSegment_test.py::TestTidMapping::test_unmapped_tid_is_asterisk_in_output PASSED 534s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_asterisk PASSED 534s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_chromosome PASSED 534s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_none PASSED 534s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_not_be_set_to_unknown_chromosome PASSED 534s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_chromosome PASSED 534s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_equal PASSED 534s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing PASSED 534s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing_without_header PASSED 534s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_without_header PASSED 534s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_not_be_set_to_unknown_chromosome PASSED 534s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_unmapped_tid_is_asterisk_in_output PASSED 534s tests/AlignedSegment_test.py::TestCigar::testCigar PASSED 534s tests/AlignedSegment_test.py::TestCigar::testCigarString PASSED 534s tests/AlignedSegment_test.py::TestCigarStats::testStats PASSED 534s tests/AlignedSegment_test.py::TestAlignedPairs::testReferenceBases PASSED 534s tests/AlignedSegment_test.py::TestBaseModifications::testChebi PASSED 534s tests/AlignedSegment_test.py::TestBaseModifications::testDouble PASSED 534s tests/AlignedSegment_test.py::TestBaseModifications::testMulti PASSED 534s tests/AlignedSegment_test.py::TestBaseModifications::testOrient PASSED 534s tests/AlignedSegment_test.py::TestTags::testAddTags PASSED 534s tests/AlignedSegment_test.py::TestTags::testAddTagsType PASSED 534s tests/AlignedSegment_test.py::TestTags::testArrayTags PASSED 534s tests/AlignedSegment_test.py::TestTags::testEmptyTag PASSED 534s tests/AlignedSegment_test.py::TestTags::testLongTags PASSED 534s tests/AlignedSegment_test.py::TestTags::testMDTagComplex PASSED 534s tests/AlignedSegment_test.py::TestTags::testMDTagDeletions PASSED 534s tests/AlignedSegment_test.py::TestTags::testMDTagInsertions PASSED 534s tests/AlignedSegment_test.py::TestTags::testMDTagMatchOnly PASSED 534s tests/AlignedSegment_test.py::TestTags::testMDTagRefSkipping PASSED 534s tests/AlignedSegment_test.py::TestTags::testMDTagSoftClipping PASSED 534s tests/AlignedSegment_test.py::TestTags::testMissingTag PASSED 534s tests/AlignedSegment_test.py::TestTags::testNegativeIntegers PASSED 534s tests/AlignedSegment_test.py::TestTags::testNegativeIntegersWrittenToFile PASSED 534s tests/AlignedSegment_test.py::TestTags::testSetTag PASSED 534s tests/AlignedSegment_test.py::TestTags::testTagParsing PASSED 534s tests/AlignedSegment_test.py::TestTags::testTagsUpdatingFloat PASSED 534s tests/AlignedSegment_test.py::TestCopy::testCopy PASSED 534s tests/AlignedSegment_test.py::TestCopy::testDeepCopy PASSED 534s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_A PASSED 534s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_C PASSED 534s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_H PASSED 534s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_I PASSED 534s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_S PASSED 534s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_a PASSED 534s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_automated_type_detection PASSED 534s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_c PASSED 534s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_d PASSED 534s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_f PASSED 534s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_i PASSED 534s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_s PASSED 534s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_A PASSED 534s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_C PASSED 534s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_H PASSED 534s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_I PASSED 534s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_S PASSED 534s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_a PASSED 534s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_automated_type_detection PASSED 534s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_c PASSED 534s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_d PASSED 534s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_f PASSED 534s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_i PASSED 534s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_s PASSED 534s tests/AlignedSegment_test.py::TestEnums::test_cigar_enums_are_defined PASSED 534s tests/AlignedSegment_test.py::TestEnums::test_sam_flags_are_defined PASSED 534s tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_constructed_without_header PASSED 534s tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_written_to_file PASSED 534s tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_id_can_be_set PASSED 534s tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_name_is_not_available PASSED 534s tests/AlignedSegment_test.py::TestForwardStrandValues::test_qualities_are_complemented PASSED 534s tests/AlignedSegment_test.py::TestForwardStrandValues::test_sequence_is_complemented PASSED 534s tests/AlignedSegment_test.py::TestExportImport::test_dict_export PASSED 534s tests/AlignedSegment_test.py::TestExportImport::test_string_export PASSED 534s tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_with_tags PASSED 534s tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_without_tags PASSED 534s tests/AlignedSegment_test.py::TestExportImport::test_to_string_without_alignment_file PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_dict PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_header PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references_without_text PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_text PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_access_works PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_contains_works PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_get_works PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_keys_works PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_len_works PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_setting_raises_error PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_values_works PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_header_content_is_as_expected PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_name_mapping PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_text_access_works PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_contains_works PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_get_works PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_keys_works PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_len_works PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_setting_raises_error PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_values_works PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_name_mapping PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_text_access_works PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_contains_works PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_get_works PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_keys_works PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_len_works PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_setting_raises_error PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_values_works PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_name_mapping PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_text_access_works PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM /tmp/autopkgtest.wqFkeX/build.BHm/src/tests/tmp/pysamtests_tmp_check_read_write_kbv0hmng 534s PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM /tmp/autopkgtest.wqFkeX/build.BHm/src/tests/tmp/pysamtests_tmp_check_read_write_2ia6jvf5 534s PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /tmp/autopkgtest.wqFkeX/build.BHm/src/tests/tmp/pysamtests_tmp_check_read_write_ut75syle 534s PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM /tmp/autopkgtest.wqFkeX/build.BHm/src/tests/tmp/pysamtests_tmp_check_read_write__i2xxd9y 534s PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM /tmp/autopkgtest.wqFkeX/build.BHm/src/tests/tmp/pysamtests_tmp_check_read_write_z_qltuqd 534s PASSED 534s tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM /tmp/autopkgtest.wqFkeX/build.BHm/src/tests/tmp/pysamtests_tmp_check_read_write_pjstign2 534s PASSED 534s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_all_stepper PASSED 534s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_ignore_overlaps PASSED 534s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper PASSED 534s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_base_quality_threshold PASSED 534s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_ignore_orphans PASSED 534s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_mapping_quality_threshold PASSED 534s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_redo_baq PASSED 534s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_all_stepper PASSED 534s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_ignore_overlaps PASSED 534s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper [W::sanitise_SQ_lines] Header @SQ length mismatch for ref chr1, 2147483647 vs 1575 534s [E::cram_index_load] Could not retrieve index file for '/tmp/autopkgtest.wqFkeX/build.BHm/src/tests/tmp/pysamtests_tmp_check_read_write_z_qltuqd' 534s PASSED 534s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_base_quality_threshold PASSED 534s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_ignore_orphans PASSED 534s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_mapping_quality_threshold PASSED 534s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_redo_baq PASSED 534s tests/AlignmentFilePileup_test.py::TestPileupQueryPosition::testPileup PASSED 534s tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope SKIPPED 534s tests/AlignmentFilePileup_test.py::TestPileupObjects::testPileupColumn PASSED 534s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testInverse PASSED 534s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateAll PASSED 534s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIteratePerContig PASSED 534s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateRanges PASSED 534s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateTruncate PASSED 534s tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testAccessOnClosedIterator PASSED 534s tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStart PASSED 534s tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStr PASSED 534s tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testTruncate PASSED 534s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_depths_are_equal PASSED 534s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_mapping_qualities_are_equal PASSED 534s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_with_reference_are_equal PASSED 535s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_without_reference_are_equal PASSED 535s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_are_equal PASSED 535s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_from_pileups_are_equal PASSED 535s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARQueryLength PASSED 535s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigar PASSED 535s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigarstring PASSED 535s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARflag PASSED 535s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmapq PASSED 535s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmpos PASSED 535s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmrnm PASSED 535s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARpos PASSED 535s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqname PASSED 535s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqqual PASSED 535s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqual PASSED 535s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARquery PASSED 535s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARrname PASSED 535s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARseq PASSED 535s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testOpt PASSED 535s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPairedBools PASSED 535s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPresentOptionalFields PASSED 535s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testTags PASSED 535s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARQueryLength PASSED 535s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigar PASSED 535s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigarstring PASSED 535s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARflag PASSED 535s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmapq PASSED 535s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmpos PASSED 535s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmrnm PASSED 535s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARpos PASSED 535s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqname PASSED 535s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqqual PASSED 535s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqual PASSED 535s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARquery PASSED 535s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARrname PASSED 535s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARseq PASSED 535s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testOpt PASSED 535s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPairedBools PASSED 535s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPresentOptionalFields PASSED 535s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testTags PASSED 535s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARQueryLength PASSED 536s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigar PASSED 536s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigarstring PASSED 537s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARflag PASSED 538s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmapq PASSED 538s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmpos PASSED 539s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmrnm PASSED 539s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARpos PASSED 540s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqname PASSED 540s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqqual PASSED 541s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqual PASSED 541s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARquery PASSED 542s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARrname PASSED 542s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARseq PASSED 543s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testOpt PASSED 544s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPairedBools PASSED 544s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPresentOptionalFields PASSED 545s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testTags PASSED 545s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARQueryLength PASSED 545s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigar PASSED 545s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigarstring PASSED 545s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARflag PASSED 545s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmapq PASSED 545s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmpos PASSED 545s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmrnm PASSED 545s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARpos PASSED 545s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqname PASSED 545s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqqual PASSED 545s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqual PASSED 545s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARquery PASSED 545s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARrname PASSED 545s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARseq PASSED 545s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testOpt PASSED 545s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPairedBools PASSED 545s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPresentOptionalFields PASSED 545s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testTags PASSED 545s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARQueryLength PASSED 546s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigar PASSED 546s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigarstring PASSED 548s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARflag PASSED 550s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmapq PASSED 550s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmpos PASSED 550s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmrnm PASSED 550s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARpos PASSED 550s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqname PASSED 550s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqqual PASSED 551s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqual PASSED 551s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARquery PASSED 552s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARrname PASSED 552s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARseq PASSED 553s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testOpt PASSED 554s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPairedBools PASSED 554s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPresentOptionalFields PASSED 555s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testTags PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARQueryLength PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigar PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigarstring PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARflag PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmapq PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmpos PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmrnm PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARpos PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqname PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqqual PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqual PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARquery PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARrname PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARseq PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testOpt PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPairedBools PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPresentOptionalFields PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testTags PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARQueryLength PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigar PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigarstring PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARflag PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmapq PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmpos PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmrnm PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARpos PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqname PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqqual PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqual PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARquery PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARrname PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARseq PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testOpt PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPairedBools PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPresentOptionalFields PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testTags PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARQueryLength PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigar PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigarstring PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARflag PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmapq PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmpos PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmrnm PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARpos PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqname PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqqual PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqual PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARquery PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARrname PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARseq PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testOpt PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPairedBools PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPresentOptionalFields PASSED 555s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testTags PASSED 555s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARQueryLength PASSED 555s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigar PASSED 555s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigarstring PASSED 555s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARflag PASSED 555s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmapq PASSED 555s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmpos PASSED 555s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmrnm PASSED 555s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARpos PASSED 555s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqname PASSED 555s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqqual PASSED 555s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqual PASSED 555s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARquery PASSED 555s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARrname PASSED 555s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARseq PASSED 555s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testOpt PASSED 555s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPairedBools PASSED 555s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPresentOptionalFields PASSED 555s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testTags PASSED 555s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARQueryLength PASSED 555s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigar PASSED 555s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigarstring PASSED 555s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARflag PASSED 555s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmapq PASSED 555s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmpos PASSED 555s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmrnm PASSED 555s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARpos PASSED 555s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqname PASSED 555s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqqual PASSED 555s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqual PASSED 555s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARquery PASSED 555s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARrname PASSED 555s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARseq PASSED 555s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testOpt PASSED 555s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPairedBools PASSED 555s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPresentOptionalFields PASSED 555s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testTags PASSED 555s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARQueryLength PASSED 556s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigar PASSED 556s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigarstring PASSED 557s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARflag PASSED 557s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmapq PASSED 558s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmpos PASSED 558s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmrnm PASSED 559s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARpos PASSED 559s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqname PASSED 560s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqqual PASSED 560s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqual PASSED 561s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARquery PASSED 562s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARrname PASSED 562s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARseq PASSED 563s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testOpt PASSED 565s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPairedBools PASSED 565s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPresentOptionalFields PASSED 565s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testTags PASSED 565s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARQueryLength PASSED 565s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigar PASSED 565s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigarstring PASSED 566s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARflag PASSED 566s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmapq PASSED 567s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmpos PASSED 568s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmrnm PASSED 569s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARpos PASSED 569s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqname PASSED 569s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqqual PASSED 570s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqual PASSED 570s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARquery PASSED 571s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARrname PASSED 571s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARseq PASSED 572s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testOpt PASSED 572s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPairedBools PASSED 573s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPresentOptionalFields PASSED 573s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testTags PASSED 573s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARQueryLength PASSED 573s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigar PASSED 573s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigarstring PASSED 573s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARflag PASSED 573s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmapq PASSED 573s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmpos PASSED 573s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmrnm PASSED 573s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARpos PASSED 573s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqname PASSED 573s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqqual PASSED 573s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqual PASSED 573s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARquery PASSED 573s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARrname PASSED 573s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARseq PASSED 573s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testOpt PASSED 573s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPairedBools PASSED 573s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPresentOptionalFields PASSED 573s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testRaises PASSED 573s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testTags PASSED 573s tests/AlignmentFile_test.py::TestIO::testBAM2BAM PASSED 574s tests/AlignmentFile_test.py::TestIO::testBAM2SAM PASSED 574s tests/AlignmentFile_test.py::TestIO::testBAMWithCSIIndex PASSED 574s tests/AlignmentFile_test.py::TestIO::testBAMWithShortBAI PASSED 574s tests/AlignmentFile_test.py::TestIO::testBAMWithoutAlignedSegments PASSED 574s tests/AlignmentFile_test.py::TestIO::testCRAM2BAM PASSED 576s tests/AlignmentFile_test.py::TestIO::testCRAM2CRAM PASSED 576s tests/AlignmentFile_test.py::TestIO::testCRAM2SAM PASSED 576s tests/AlignmentFile_test.py::TestIO::testEmptyBAM PASSED 576s tests/AlignmentFile_test.py::TestIO::testEmptyWithHeaderBAM PASSED 576s tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFile PASSED 576s tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject PASSED 576s tests/AlignmentFile_test.py::TestIO::testHead PASSED 576s tests/AlignmentFile_test.py::TestIO::testOpenFromFilename PASSED 576s tests/AlignmentFile_test.py::TestIO::testReadBamWithoutTargetNames PASSED 576s tests/AlignmentFile_test.py::TestIO::testReadSamWithoutTargetNames PASSED 576s tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex PASSED 576s tests/AlignmentFile_test.py::TestIO::testSAM2BAM PASSED 577s tests/AlignmentFile_test.py::TestIO::testSAM2CRAM PASSED 578s tests/AlignmentFile_test.py::TestIO::testSAM2SAM PASSED 578s tests/AlignmentFile_test.py::TestIO::testSAM2SAMWithoutHeader PASSED 578s tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile PASSED 578s tests/AlignmentFile_test.py::TestIO::test_accessing_attributes_in_closed_file_raises_errors PASSED 578s tests/AlignmentFile_test.py::TestIO::test_fail_read_sam_without_header PASSED 578s tests/AlignmentFile_test.py::TestIO::test_fail_when_reading_unformatted_files PASSED 578s tests/AlignmentFile_test.py::TestIO::test_fetch_by_tid PASSED 578s tests/AlignmentFile_test.py::TestIO::test_header_available_after_closing_file PASSED 578s tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_with_header_without_header_check PASSED 578s tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_without_header_with_refs PASSED 578s tests/AlignmentFile_test.py::TestIO::test_reference_name_available_after_closing_file PASSED 578s tests/AlignmentFile_test.py::TestIO::test_write_bam_to_unknown_path_fails PASSED 578s tests/AlignmentFile_test.py::TestAutoDetect::testBAM PASSED 578s tests/AlignmentFile_test.py::TestAutoDetect::testCRAM [E::hts_open_format] Failed to open file "missing_directory/new_file.bam" : No such file or directory 579s PASSED 579s tests/AlignmentFile_test.py::TestAutoDetect::testSAM PASSED 579s tests/AlignmentFile_test.py::TestIteratorRowBAM::testIteratePerContig PASSED 579s tests/AlignmentFile_test.py::TestIteratorRowBAM::testIterateRanges PASSED 579s tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate PASSED 581s tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIteratePerContig PASSED 604s tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIterateRanges PASSED 604s tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIteratePerContig PASSED 619s tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIterateRanges PASSED 619s tests/AlignmentFile_test.py::TestFloatTagBug::testFloatTagBug PASSED 619s tests/AlignmentFile_test.py::TestLargeFieldBug::testLargeFileBug PASSED 619s tests/AlignmentFile_test.py::TestClipping::testClipping PASSED 619s tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_bam_with_until_eof_reads_unmapped_reads PASSED 619s tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_sam_with_until_eof_reads_unmapped_reads PASSED 619s tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads PASSED 619s tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads_by_contig PASSED 619s tests/AlignmentFile_test.py::TestContextManager::testManager PASSED 619s tests/AlignmentFile_test.py::TestMultiThread::testSingleThreadEqualsMultithread PASSED 619s tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED 619s tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED 619s tests/AlignmentFile_test.py::TestExceptions::testBadContig PASSED 619s tests/AlignmentFile_test.py::TestExceptions::testMeaninglessCrap PASSED 619s tests/AlignmentFile_test.py::TestExceptions::testMissingFile PASSED 619s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangNewFormat PASSED 619s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeNewFormat PASSED 619s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeOldFormat PASSED[E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory 619s [E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory 619s [E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory 619s [E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory 619s 619s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeNewFormat PASSED 619s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeOldFormat PASSED 619s tests/AlignmentFile_test.py::TestExceptions::testZeroToZero PASSED 619s tests/AlignmentFile_test.py::TestWrongFormat::testOpenBamAsSam PASSED 619s tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsBam PASSED 619s tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsSam PASSED 619s tests/AlignmentFile_test.py::TestWrongFormat::testOpenSamAsBam PASSED 619s tests/AlignmentFile_test.py::TestRegionParsing::test_dash_in_chr PASSED 619s tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile PASSED 619s tests/AlignmentFile_test.py::TestDeNovoConstruction::test_pass_if_reads_binary_equal PASSED 619s tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader PASSED 619s tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_in_header PASSED 619s tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_with_null_bytes_in_header PASSED 619s tests/AlignmentFile_test.py::TestMismatchingHeader::testMismatchingHeader PASSED 619s tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader PASSED 619s tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2 PASSED 619s tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator [W::bam_hdr_read] EOF marker is absent. The input is probably truncated 619s [E::bgzf_read_block] PASSED 619s tests/AlignmentFile_test.py::TestCorruptBAM::testCorruptBamIterator Failed to read BGZF block data at offset 105176 expected 17578 bytes; hread returned 17094 619s [E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes 619s PASSED 619s tests/AlignmentFile_test.py::TestBTagSam::testReadTags PASSED 619s tests/AlignmentFile_test.py::TestBTagSam::testReadWriteTags PASSED 619s tests/AlignmentFile_test.py::TestBTagBam::testReadTags PASSED 619s tests/AlignmentFile_test.py::TestBTagBam::testReadWriteTags PASSED 619s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetch PASSED 619s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchUntilEOF PASSED 619s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionFalseTrue PASSED 619s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueFalse PASSED 619s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueTrue PASSED 620s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetch PASSED 621s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchUntilEOF PASSED 622s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionFalseTrue PASSED 624s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueFalse PASSED 624s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueTrue PASSED 625s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetch PASSED 626s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchUntilEOF PASSED 627s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionFalseTrue PASSED 628s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueFalse PASSED 630s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueTrue PASSED 630s tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetch PASSED 630s tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetchAll PASSED 631s tests/AlignmentFile_test.py::TestRemoteFileHTTP::testView PASSED 631s tests/AlignmentFile_test.py::TestLargeOptValues::testBAM PASSED 631s tests/AlignmentFile_test.py::TestLargeOptValues::testSAM PASSED 631s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_counts_as_expected PASSED 631s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_nofilter PASSED 631s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_quality_filter PASSED 631s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_all PASSED 631s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_callback PASSED 631s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_with_coordinates_works PASSED 631s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_without_coordinates_fails PASSED 631s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_wrong_coordinates_fails PASSED 631s tests/AlignmentFile_test.py::TestCountCoverage::test_counting_the_same_region_works PASSED 631s tests/AlignmentFile_test.py::TestFindIntrons::test_all PASSED 631s tests/AlignmentFile_test.py::TestFindIntrons::test_first PASSED 631s tests/AlignmentFile_test.py::TestFindIntrons::test_total PASSED 631s tests/AlignmentFile_test.py::TestLogging::testFail1 PASSED 631s tests/AlignmentFile_test.py::TestLogging::testNoFail1 PASSED 631s tests/AlignmentFile_test.py::TestLogging::testNoFail2 PASSED 632s tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testCount PASSED 632s tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testIndexStats PASSED 635s tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testMate PASSED[E::hts_open_format] Failed to open file "missing_file" : No such file or directory 635s tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct PASSED 635s tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct_per_chromosome PASSED 635s tests/AlignmentFile_test.py::TestSamtoolsProxy::testIndex PASSED 635s tests/AlignmentFile_test.py::TestSamtoolsProxy::testSort PASSED 635s tests/AlignmentFile_test.py::TestSamtoolsProxy::testView PASSED 635s tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED 635s tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM PASSED 635s tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexCRAM PASSED 635s tests/AlignmentFile_test.py::TestExplicitIndex::testRemoteExplicitIndexBAM 635s [E::hts_open_format] Failed to open file "missing_file" : No such file or directory 635s [W::hts_idx_load3] The index file is older than the data file: /tmp/autopkgtest.wqFkeX/build.BHm/src/tests/pysam_data/ex1.bam.bai 635s PASSED 635s tests/AlignmentFile_test.py::TestVerbosity::testVerbosity PASSED 635s tests/AlignmentFile_test.py::TestSanityCheckingBAM::test_empty_read_gives_value_error PASSED 635s tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_bam PASSED 635s tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_cram SKIPPED 635s tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_sam PASSED 635s tests/StreamFiledescriptors_test.py::StreamTest::test_samtools_processing SKIPPED 635s tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing PASSED 635s tests/VariantFile_test.py::TestMissingGenotypes::testVCF PASSED 635s tests/VariantFile_test.py::TestMissingGenotypes::testVCFGZ PASSED 635s tests/VariantFile_test.py::TestMissingSamples::testVCF PASSED 635s tests/VariantFile_test.py::TestMissingSamples::testVCFGZ PASSED 635s tests/VariantFile_test.py::TestMissingSamplesFixed::testVCF [W::bcf_hdr_check_sanity] PASSEDPL should be declared as Number=G 635s 635s tests/VariantFile_test.py::TestMissingSamplesFixed::testVCFGZ PASSED 635s tests/VariantFile_test.py::TestOpening::testDetectBCF PASSED 635s tests/VariantFile_test.py::TestOpening::testDetectVCF [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 635s [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) 635s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 635s PASSED 635s tests/VariantFile_test.py::TestOpening::testDetectVCFGZ PASSED 635s tests/VariantFile_test.py::TestOpening::testEmptyFileVCF PASSED 635s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFFromPath PASSED 635s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZOnlyHeader PASSED 635s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithIndex PASSED 635s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithoutIndex PASSED 635s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFOnlyHeader PASSED 635s tests/VariantFile_test.py::TestOpening::testMissingFile [E::hts_open_format] PASSED 635s tests/VariantFile_test.py::TestOpening::testMissingFileVCFGZ PASSED 635s tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_csi_index Failed to open file "missing_file.vcf" : No such file or directory 635s [E::hts_open_format] Failed to open file "missing_file.vcf.gz" : No such file or directory 635s PASSED 635s tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_prebuilt_csi PASSED 635s tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_tbi_index_will_produce_csi PASSED 635s tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_csi_index PASSED 635s tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_tbi_index PASSED 635s tests/VariantFile_test.py::TestHeader::testIterator PASSED 635s tests/VariantFile_test.py::TestHeader::testStr PASSED 635s tests/VariantFile_test.py::TestParsing::testAlleles PASSED 635s tests/VariantFile_test.py::TestParsing::testAllelesVariantTypes PASSED 635s tests/VariantFile_test.py::TestParsing::testAlt PASSED 635s tests/VariantFile_test.py::TestParsing::testChrom PASSED 635s tests/VariantFile_test.py::TestParsing::testChromFromPath PASSED 635s tests/VariantFile_test.py::TestParsing::testFilter PASSED 635s tests/VariantFile_test.py::TestParsing::testFormat PASSED 635s tests/VariantFile_test.py::TestParsing::testId PASSED 635s tests/VariantFile_test.py::TestParsing::testInfo PASSED 635s tests/VariantFile_test.py::TestParsing::testPos PASSED 635s tests/VariantFile_test.py::TestParsing::testQual PASSED 635s tests/VariantFile_test.py::TestParsing::testRef PASSED 635s tests/VariantFile_test.py::TestParsing::testSampleAlleleIndices PASSED 635s tests/VariantFile_test.py::TestParsing::testSampleAlleles PASSED 635s tests/VariantFile_test.py::TestParsing::testSampleFormats PASSED 635s tests/VariantFile_test.py::TestParsing::testStart PASSED 635s tests/VariantFile_test.py::TestParsing::testStop PASSED 635s tests/VariantFile_test.py::TestIndexFilename::testOpen PASSED 635s tests/VariantFile_test.py::TestConstructionVCFWithContigs::testBase PASSED 635s tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionFromCopy PASSED 635s tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithLines PASSED 635s tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithRecords PASSED 635s tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testBase PASSED 635s tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionFromCopy PASSED 635s tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithLines PASSED 635s tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithRecords PASSED 635s tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testBase PASSED 635s tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionFromCopy PASSED 635s tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithLines PASSED 635s tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithRecords PASSED 635s tests/VariantFile_test.py::TestSettingRecordValues::testBase PASSED 635s tests/VariantFile_test.py::TestSettingRecordValues::testGenotype [W::vcf_parse] (0, 0) 635s PASSEDContig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 635s 635s tests/VariantFile_test.py::TestSettingRecordValues::testSetQual [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 635s PASSED 635s tests/VariantFile_test.py::TestMultiThreading::testNoMultiThreadingWithIgnoreTruncation PASSED 635s tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult [E::idx_find_and_load] Could not retrieve index file for '/tmp/autopkgtest.wqFkeX/build.BHm/src/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithreadResult_xytymbzy.bcf' 635s PASSED 635s tests/VariantFile_test.py::TestSubsetting::testSubsetting PASSED 635s tests/VariantFile_test.py::TestVCFVersions::test_all_records_can_be_fetched [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 635s [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) 635s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 635s [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 635s [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) 635s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 635s PASSED 635s tests/VariantFile_test.py::TestUnicode::test_record_with_unicode PASSED 635s tests/VariantRecord_test.py::test_ascii_annotation_can_be_added PASSED 635s tests/VariantRecord_test.py::test_ascii_annotation_with_variable_length_can_be_added PASSED 635s tests/VariantRecord_test.py::test_unicode_annotation_can_be_added PASSED 635s tests/VariantRecord_test.py::test_set_sample_alleles PASSED 635s tests/compile_test.py::test_bam SKIPPED (no pyximport) 635s tests/compile_test.py::test_gtf SKIPPED (no pyximport) 635s tests/faidx_test.py::TestFastaFile::testFetch PASSED 635s tests/faidx_test.py::TestFastaFile::testFetchErrors PASSED 635s tests/faidx_test.py::TestFastaFile::testLength PASSED 635s tests/faidx_test.py::TestFastaFile::testOutOfRangeAccess PASSED 635s tests/faidx_test.py::TestFastaFile::testSequenceLengths PASSED 635s tests/faidx_test.py::TestFastaFile::test_fetch_with_region_and_contig_raises_exception PASSED 635s tests/faidx_test.py::TestFastaFile::test_fetch_with_region_is_equivalent PASSED 635s tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED 635s tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_index_succeeds PASSED 635s tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_without_index_succeeds PASSED 635s tests/faidx_test.py::TestFastaFilePathIndex::test_raise_exception_if_index_is_missing PASSED 635s tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED 635s tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_index_succeeds PASSED 635s tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_without_index_succeeds PASSED 635s tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_raise_exception_if_index_is_missing PASSED 635s tests/faidx_test.py::TestFastxFileFastq::testCounts PASSED 635s tests/faidx_test.py::TestFastxFileFastq::testManager PASSED 635s tests/faidx_test.py::TestFastxFileFastq::testMissingFile PASSED 635s tests/faidx_test.py::TestFastxFileFastq::testSequence PASSED 635s tests/faidx_test.py::TestFastqFileFastq::testCounts PASSED 635s tests/faidx_test.py::TestFastqFileFastq::testManager PASSED 635s tests/faidx_test.py::TestFastqFileFastq::testMissingFile PASSED 635s tests/faidx_test.py::TestFastqFileFastq::testSequence PASSED 635s tests/faidx_test.py::TestFastxFileFasta::testCounts PASSED 635s tests/faidx_test.py::TestFastxFileFasta::testManager PASSED 635s tests/faidx_test.py::TestFastxFileFasta::testMissingFile PASSED 635s tests/faidx_test.py::TestFastxFileFasta::testSequence PASSED 635s tests/faidx_test.py::TestFastxFileFastqStream::testCounts PASSED 635s tests/faidx_test.py::TestFastxFileFastqStream::testManager PASSED 635s tests/faidx_test.py::TestFastxFileFastqStream::testMissingFile PASSED 635s tests/faidx_test.py::TestFastxFileFastqStream::testSequence PASSED 635s tests/faidx_test.py::TestFastxFileWithEmptySequence::testIteration PASSED 636s tests/faidx_test.py::TestRemoteFileFTP::testFTPView PASSED 639s tests/faidx_test.py::TestRemoteFileFTP::test_sequence_lengths_are_available PASSED 639s tests/faidx_test.py::TestFastqRecord::test_fastx_record_can_be_created_from_scratch PASSED 639s tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_None PASSED 639s tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_modified PASSED 639s tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_name_is_None PASSED 639s tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_quality_is_wrong_length PASSED 639s tests/faidx_test.py::TestFastqRecord::test_fastx_record_name_can_be_modified PASSED 639s tests/faidx_test.py::TestFastqRecord::test_fastx_record_quality_can_be_modified PASSED 639s tests/faidx_test.py::TestFastqRecord::test_fastx_record_sequence_can_be_modified PASSED 639s tests/faidx_test.py::TestFastqProxy::test_fastq_proxy_instantiation_raises_error PASSED 639s tests/linking_test.py::TestLinking::test_package_can_be_installed SKIPPED 639s tests/linking_test.py::TestLinkWithRpath::test_package_can_be_installed SKIPPED 639s tests/linking_test.py::TestLinkWithRpath::test_package_tests_pass SKIPPED 639s tests/linking_test.py::TestLinkWithoutRpath::test_package_can_be_installed SKIPPED 639s tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_fail_on_import SKIPPED 639s tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_pass_if_ld_library_path_set SKIPPED 639s tests/samtools_test.py::SamtoolsTest::testStatements PASSED 639s tests/samtools_test.py::SamtoolsTest::testUsage SKIPPED (skipping us...) 639s tests/samtools_test.py::EmptyIndexTest::testEmptyIndex PASSED 639s tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraArg PASSED 639s tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraFlag PASSED 639s tests/samtools_test.py::TestReturnType::testReturnValueData PASSED 639s tests/samtools_test.py::TestReturnType::testReturnValueString PASSED 639s tests/samtools_test.py::StdoutTest::testDoubleCalling PASSED 639s tests/samtools_test.py::StdoutTest::testSaveStdout PASSED 639s tests/samtools_test.py::StdoutTest::testWithRedirectedStdout PASSED 639s tests/samtools_test.py::StdoutTest::testWithoutRedirectedStdout PASSED 640s tests/samtools_test.py::PysamTest::testStatements PASSED 640s tests/samtools_test.py::PysamTest::testUsage SKIPPED (skipping usage...) 640s tests/tabix_test.py::TestIndexing::test_indexing_to_custom_location_works PASSED 640s tests/tabix_test.py::TestIndexing::test_indexing_with_explict_columns_works PASSED 640s tests/tabix_test.py::TestIndexing::test_indexing_with_lineskipping_works PASSED 640s tests/tabix_test.py::TestIndexing::test_indexing_with_preset_works PASSED 640s tests/tabix_test.py::TestCompression::testCompression PASSED 640s tests/tabix_test.py::TestCompression::testIndexPresetCompressed PASSED 640s tests/tabix_test.py::TestCompression::testIndexPresetUncompressed PASSED 640s tests/tabix_test.py::TestCompressionSam::testCompression PASSED 640s tests/tabix_test.py::TestCompressionSam::testIndexPresetCompressed PASSED 640s tests/tabix_test.py::TestCompressionSam::testIndexPresetUncompressed PASSED 640s tests/tabix_test.py::TestCompressionBed::testCompression PASSED 640s tests/tabix_test.py::TestCompressionBed::testIndexPresetCompressed PASSED 640s tests/tabix_test.py::TestCompressionBed::testIndexPresetUncompressed PASSED 640s tests/tabix_test.py::TestCompressionVCF::testCompression PASSED 640s tests/tabix_test.py::TestCompressionVCF::testIndexPresetCompressed PASSED 640s tests/tabix_test.py::TestCompressionVCF::testIndexPresetUncompressed PASSED 640s tests/tabix_test.py::TestGZFile::testAll PASSED 640s tests/tabix_test.py::TestIterationWithoutComments::testAll PASSED 640s tests/tabix_test.py::TestIterationWithoutComments::testGetContigs PASSED 640s tests/tabix_test.py::TestIterationWithoutComments::testHeader PASSED 640s tests/tabix_test.py::TestIterationWithoutComments::testInvalidIntervals PASSED 640s tests/tabix_test.py::TestIterationWithoutComments::testPerContig PASSED 640s tests/tabix_test.py::TestIterationWithoutComments::testPerContig2 PASSED 640s tests/tabix_test.py::TestIterationWithoutComments::testPerContigFromStart PASSED 641s tests/tabix_test.py::TestIterationWithoutComments::testPerContigToEnd PASSED 641s tests/tabix_test.py::TestIterationWithoutComments::testPerInterval PASSED 641s tests/tabix_test.py::TestIterationWithoutComments::testRegionStrings PASSED 641s tests/tabix_test.py::TestIterationWithoutComments::testReopening PASSED 641s tests/tabix_test.py::TestIterationWithComments::testAll PASSED 641s tests/tabix_test.py::TestIterationWithComments::testGetContigs PASSED 641s tests/tabix_test.py::TestIterationWithComments::testHeader PASSED 641s tests/tabix_test.py::TestIterationWithComments::testInvalidIntervals PASSED 641s tests/tabix_test.py::TestIterationWithComments::testPerContig PASSED 641s tests/tabix_test.py::TestIterationWithComments::testPerContig2 PASSED 641s tests/tabix_test.py::TestIterationWithComments::testPerContigFromStart PASSED 641s tests/tabix_test.py::TestIterationWithComments::testPerContigToEnd PASSED 641s tests/tabix_test.py::TestIterationWithComments::testPerInterval PASSED 641s tests/tabix_test.py::TestIterationWithComments::testRegionStrings PASSED 642s tests/tabix_test.py::TestIterationWithComments::testReopening PASSED 642s tests/tabix_test.py::TestIterators::testClosedFile PASSED 642s tests/tabix_test.py::TestIterators::testClosedFileIteration PASSED 642s tests/tabix_test.py::TestIterators::testIteration PASSED 642s tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFile PASSED 642s tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFileIteration PASSED 642s tests/tabix_test.py::TestIteratorsGenericCompressed::testIteration PASSED 642s tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFile PASSED 642s tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFileIteration PASSED 642s tests/tabix_test.py::TestIteratorsFileCompressed::testIteration PASSED 642s tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFile PASSED 642s tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFileIteration PASSED 642s tests/tabix_test.py::TestIteratorsFileUncompressed::testIteration PASSED 642s tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooFewFields PASSED 642s tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooManyFields PASSED 642s tests/tabix_test.py::TestBed::testRead PASSED 642s tests/tabix_test.py::TestBed::testWrite PASSED 642s tests/tabix_test.py::TestUnicode::testFromTabix PASSED 642s tests/tabix_test.py::TestUnicode::testFromVCF PASSED 642s tests/tabix_test.py::TestVCFFromTabix::testRead PASSED 642s tests/tabix_test.py::TestVCFFromTabix::testWrite PASSED 642s tests/tabix_test.py::TestVCFFromVCF::testConnecting PASSED 642s tests/tabix_test.py::TestVCFFromVCF::testParsing PASSED 642s tests/tabix_test.py::VCFFromTabixTest_13::testRead PASSED 642s tests/tabix_test.py::VCFFromTabixTest_13::testWrite PASSED 642s tests/tabix_test.py::VCFFromVCFTest_13::testConnecting PASSED 642s tests/tabix_test.py::VCFFromVCFTest_13::testParsing PASSED 642s tests/tabix_test.py::VCFFromTabixTest_11::testRead PASSED 642s tests/tabix_test.py::VCFFromTabixTest_11::testWrite PASSED 642s tests/tabix_test.py::VCFFromVCFTest_11::testConnecting PASSED 643s tests/tabix_test.py::VCFFromVCFTest_11::testParsing PASSED 643s tests/tabix_test.py::VCFFromTabixTest_9::testRead PASSED 643s tests/tabix_test.py::VCFFromTabixTest_9::testWrite PASSED 643s tests/tabix_test.py::VCFFromVCFTest_9::testConnecting PASSED 643s tests/tabix_test.py::VCFFromVCFTest_9::testParsing PASSED 643s tests/tabix_test.py::VCFFromTabixTest_24::testRead PASSED 643s tests/tabix_test.py::VCFFromTabixTest_24::testWrite PASSED 643s tests/tabix_test.py::VCFFromVCFTest_24::testConnecting PASSED 643s tests/tabix_test.py::VCFFromVCFTest_24::testParsing PASSED 643s tests/tabix_test.py::VCFFromTabixTest_16::testRead PASSED 643s tests/tabix_test.py::VCFFromTabixTest_16::testWrite PASSED 643s tests/tabix_test.py::VCFFromVCFTest_16::testConnecting PASSED 643s tests/tabix_test.py::VCFFromVCFTest_16::testParsing PASSED 643s tests/tabix_test.py::VCFFromTabixTest_12::testRead PASSED 643s tests/tabix_test.py::VCFFromTabixTest_12::testWrite PASSED 643s tests/tabix_test.py::VCFFromVCFTest_12::testConnecting PASSED 643s tests/tabix_test.py::VCFFromVCFTest_12::testParsing PASSED 644s tests/tabix_test.py::VCFFromTabixTest_4::testRead PASSED 644s tests/tabix_test.py::VCFFromTabixTest_4::testWrite PASSED 644s tests/tabix_test.py::VCFFromVCFTest_4::testConnecting PASSED 644s tests/tabix_test.py::VCFFromVCFTest_4::testParsing PASSED 644s tests/tabix_test.py::VCFFromTabixTest_6::testRead PASSED 645s tests/tabix_test.py::VCFFromTabixTest_6::testWrite PASSED 645s tests/tabix_test.py::VCFFromVCFTest_6::testConnecting PASSED 645s tests/tabix_test.py::VCFFromVCFTest_6::testParsing PASSED 646s tests/tabix_test.py::VCFFromTabixTest_22::testRead PASSED 646s tests/tabix_test.py::VCFFromTabixTest_22::testWrite PASSED 646s tests/tabix_test.py::VCFFromVCFTest_22::testConnecting PASSED 647s tests/tabix_test.py::VCFFromVCFTest_22::testParsing PASSED 647s tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testRead PASSED 647s tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testWrite PASSED 647s tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testConnecting PASSED 647s tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testParsing PASSED 647s tests/tabix_test.py::VCFFromTabixTest_8::testRead PASSED 647s tests/tabix_test.py::VCFFromTabixTest_8::testWrite PASSED 647s tests/tabix_test.py::VCFFromVCFTest_8::testConnecting PASSED 648s tests/tabix_test.py::VCFFromVCFTest_8::testParsing PASSED 648s tests/tabix_test.py::VCFFromTabixTest_10::testRead PASSED 648s tests/tabix_test.py::VCFFromTabixTest_10::testWrite PASSED 648s tests/tabix_test.py::VCFFromVCFTest_10::testConnecting PASSED 648s tests/tabix_test.py::VCFFromVCFTest_10::testParsing PASSED 648s tests/tabix_test.py::VCFFromTabixTest_20::testRead PASSED 648s tests/tabix_test.py::VCFFromTabixTest_20::testWrite PASSED 648s tests/tabix_test.py::VCFFromVCFTest_20::testConnecting PASSED 648s tests/tabix_test.py::VCFFromVCFTest_20::testParsing PASSED 648s tests/tabix_test.py::VCFFromTabixTest_2::testRead PASSED 648s tests/tabix_test.py::VCFFromTabixTest_2::testWrite PASSED 648s tests/tabix_test.py::VCFFromVCFTest_2::testConnecting PASSED 648s tests/tabix_test.py::VCFFromVCFTest_2::testParsing PASSED 648s tests/tabix_test.py::VCFFromTabixTest_15::testRead PASSED 649s tests/tabix_test.py::VCFFromTabixTest_15::testWrite PASSED 649s tests/tabix_test.py::VCFFromVCFTest_15::testConnecting PASSED 649s tests/tabix_test.py::VCFFromVCFTest_15::testParsing PASSED 649s tests/tabix_test.py::VCFFromTabixTest_5::testRead PASSED 649s tests/tabix_test.py::VCFFromTabixTest_5::testWrite PASSED 650s tests/tabix_test.py::VCFFromVCFTest_5::testConnecting PASSED 650s tests/tabix_test.py::VCFFromVCFTest_5::testParsing PASSED 650s tests/tabix_test.py::VCFFromTabixTest_23::testRead PASSED 650s tests/tabix_test.py::VCFFromTabixTest_23::testWrite PASSED 650s tests/tabix_test.py::VCFFromVCFTest_23::testConnecting PASSED 650s tests/tabix_test.py::VCFFromVCFTest_23::testParsing PASSED 650s tests/tabix_test.py::VCFFromTabixTest_7::testRead PASSED 652s tests/tabix_test.py::VCFFromTabixTest_7::testWrite PASSED[W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 652s 652s tests/tabix_test.py::VCFFromVCFTest_7::testConnecting PASSED 652s tests/tabix_test.py::VCFFromVCFTest_7::testParsing PASSED 652s tests/tabix_test.py::VCFFromTabixTest_18::testRead PASSED 652s tests/tabix_test.py::VCFFromTabixTest_18::testWrite PASSED 652s tests/tabix_test.py::VCFFromVCFTest_18::testConnecting PASSED 652s tests/tabix_test.py::VCFFromVCFTest_18::testParsing PASSED 652s tests/tabix_test.py::VCFFromTabixTest_3::testRead PASSED 652s tests/tabix_test.py::VCFFromTabixTest_3::testWrite PASSED 652s tests/tabix_test.py::VCFFromVCFTest_3::testConnecting PASSED 652s tests/tabix_test.py::VCFFromVCFTest_3::testParsing PASSED 652s tests/tabix_test.py::VCFFromTabixTest_21::testRead PASSED 652s tests/tabix_test.py::VCFFromTabixTest_21::testWrite PASSED 652s tests/tabix_test.py::VCFFromVCFTest_21::testConnecting PASSED 652s tests/tabix_test.py::VCFFromVCFTest_21::testParsing PASSED 652s tests/tabix_test.py::VCFFromTabixTest_issue85::testRead PASSED 652s tests/tabix_test.py::VCFFromTabixTest_issue85::testWrite PASSED 652s tests/tabix_test.py::VCFFromVCFTest_issue85::testConnecting PASSED 652s tests/tabix_test.py::VCFFromVCFTest_issue85::testParsing PASSED 652s tests/tabix_test.py::TestVCFFromVariantFile::testConnecting PASSED 652s tests/tabix_test.py::TestVCFFromVariantFile::testParsing PASSED 652s tests/tabix_test.py::TestVCFFromVariantFile_13::testConnecting PASSED 652s tests/tabix_test.py::TestVCFFromVariantFile_13::testParsing PASSED 652s tests/tabix_test.py::TestVCFFromVariantFile_11::testConnecting PASSED 652s tests/tabix_test.py::TestVCFFromVariantFile_11::testParsing PASSED 652s tests/tabix_test.py::TestVCFFromVariantFile_9::testConnecting PASSED 652s tests/tabix_test.py::TestVCFFromVariantFile_9::testParsing PASSED 652s tests/tabix_test.py::TestVCFFromVariantFile_24::testConnecting PASSED 652s tests/tabix_test.py::TestVCFFromVariantFile_24::testParsing PASSED 652s tests/tabix_test.py::TestVCFFromVariantFile_16::testConnecting PASSED 652s tests/tabix_test.py::TestVCFFromVariantFile_16::testParsing PASSED 652s tests/tabix_test.py::TestVCFFromVariantFile_12::testConnecting PASSED 652s tests/tabix_test.py::TestVCFFromVariantFile_12::testParsing PASSED 652s tests/tabix_test.py::TestVCFFromVariantFile_4::testConnecting PASSED 652s tests/tabix_test.py::TestVCFFromVariantFile_4::testParsing [W::bcf_hrec_check] Invalid tag name: "1000g" 652s [W::bcf_hrec_check] Invalid tag name: "GT:GL:GQ:NR" 652s [W::bcf_hdr_check_sanity] GL should be declared as Number=G 652s [W::bcf_hrec_check] Invalid tag name: "1000g" 652s [W::bcf_hrec_check] Invalid tag name: "GT:GL:GQ:NR" 652s [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse_info] INFO 'MMLQ' is not defined in the header, assuming Type=String 652s [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr17_gl000205_random' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr18' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr19' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr20' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr21' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr22' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chrUn_gl000214' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chrUn_gl000220' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chrUn_gl000225' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chrX' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse_format] FORMAT 'GT' at 20:669442 is not defined in the header, assuming Type=String 652s [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String 652s [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String 652s [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String 652s [W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String 652s [W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String 652s [W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String 652s [W::vcf_parse_format] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String 652s [W::vcf_parse_format] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String 652s [W::vcf_parse_format] FORMAT 'GQ' at chr1:1281168 is not defined in the header, assuming Type=String 652s [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: 652s #CHROM POS ID REF ALT QUAL FILTER INFO 652s 652s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String 652s [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String 652s [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String 652s [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String 652s [W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String 652s [W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String 652s [W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String 652s [W::vcf_parse_format] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String 652s [W::vcf_parse_format] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String 652s [W::vcf_parse_format] FORMAT 'GQ' at chr1:1281168 is not defined in the header, assuming Type=String 652s [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 652s [W::vcf_parse_format] FORMAT 'GT' at 20:249843 is not defined in the header, assuming Type=String 653s PASSED 653s tests/tabix_test.py::TestVCFFromVariantFile_6::testConnecting PASSED 653s 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.) 653s [W::vcf_parse_info] INFO 'CallSetAC' is not defined in the header, assuming Type=String 653s [W::vcf_parse_info] INFO 'CallSetAC2' is not defined in the header, assuming Type=String 653s [W::vcf_parse_format] FORMAT 'GT' at 20:669442 is not defined in the header, assuming Type=String 653s PASSED 653s tests/tabix_test.py::TestVCFFromVariantFile_22::testConnecting PASSED 653s 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.) 653s [W::vcf_parse_info] INFO 'refseq.name' is not defined in the header, assuming Type=String 653s [W::vcf_parse_info] INFO 'refseq.positionType' is not defined in the header, assuming Type=String 654s [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) 655s PASSED 655s tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testConnecting PASSED 655s tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testParsing PASSED 655s tests/tabix_test.py::TestVCFFromVariantFile_8::testConnecting PASSED 655s 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.) 655s [W::vcf_parse_format] FORMAT 'GT' at 20:676148 is not defined in the header, assuming Type=String 655s PASSED[W::vcf_parse] 655s tests/tabix_test.py::TestVCFFromVariantFile_10::testConnecting PASSED 655s tests/tabix_test.py::TestVCFFromVariantFile_10::testParsing PASSED 655s tests/tabix_test.py::TestVCFFromVariantFile_20::testConnecting PASSED 655s tests/tabix_test.py::TestVCFFromVariantFile_20::testParsing PASSED 655s tests/tabix_test.py::TestVCFFromVariantFile_2::testConnecting PASSED 655s tests/tabix_test.py::TestVCFFromVariantFile_2::testParsing PASSED 655s tests/tabix_test.py::TestVCFFromVariantFile_15::testConnecting PASSED 655s tests/tabix_test.py::TestVCFFromVariantFile_15::testParsing Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 655s [W::vcf_parse_format] FORMAT 'GT' at 20:676148 is not defined in the header, assuming Type=String 655s [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 655s [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 655s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 655s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 655s [W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String 655s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 655s [W::vcf_parse_format] FORMAT 'GT' at 20:439104 is not defined in the header, assuming Type=String 656s PASSED 656s tests/tabix_test.py::TestVCFFromVariantFile_5::testConnecting PASSED 656s 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.) 656s PASSED 656s tests/tabix_test.py::TestVCFFromVariantFile_23::testConnecting PASSED 656s tests/tabix_test.py::TestVCFFromVariantFile_23::testParsing [W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String 656s PASSED 656s tests/tabix_test.py::TestVCFFromVariantFile_7::testConnecting PASSED 656s 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.) 656s [W::vcf_parse_format] FORMAT 'GT' at 20:249843 is not defined in the header, assuming Type=String 657s PASSED 657s tests/tabix_test.py::TestVCFFromVariantFile_18::testConnecting PASSED 657s 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.) 657s [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String 657s [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String 657s [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String 657s [W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String 657s [W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String 657s [W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String 657s [W::vcf_parse_format] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String 657s [W::vcf_parse_format] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String 657s [W::vcf_parse_format] FORMAT 'GQ' at chr1:1281168 is not defined in the header, assuming Type=String 657s [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) 657s [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) 657s [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) 657s [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) 657s [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) 657s [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) 657s [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) 657s [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) 657s [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) 657s [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) 657s [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) 657s [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) 657s PASSED 657s tests/tabix_test.py::TestVCFFromVariantFile_3::testConnecting PASSED 657s tests/tabix_test.py::TestVCFFromVariantFile_3::testParsing [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) 657s [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) 657s [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) 657s [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) 657s [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) 657s [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) 657s [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) 657s [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) 657s PASSED 657s tests/tabix_test.py::TestVCFFromVariantFile_21::testConnecting PASSED 657s tests/tabix_test.py::TestVCFFromVariantFile_21::testParsing [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 657s [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 657s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 657s PASSED 657s tests/tabix_test.py::TestVCFFromVariantFile_issue85::testConnecting [E::bcf_hdr_parse] Could not parse the header, sample line not found 657s PASSED 657s tests/tabix_test.py::TestVCFFromVariantFile_issue85::testParsing PASSED 657s tests/tabix_test.py::TestIndexArgument::testFetchAll PASSED 657s tests/tabix_test.py::TestIndexArgument::testLoadIndexWithoutTbiExtension PASSED 657s tests/tabix_test.py::TestBackwardsCompatibility::testBED PASSED 657s tests/tabix_test.py::TestBackwardsCompatibility::testBED0v23 PASSED 657s tests/tabix_test.py::TestBackwardsCompatibility::testBED0v26 PASSED 657s tests/tabix_test.py::TestBackwardsCompatibility::testEmpty PASSED 657s tests/tabix_test.py::TestBackwardsCompatibility::testVCF PASSED 657s tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v23 PASSED 657s tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v26 PASSED 657s tests/tabix_test.py::TestMultipleIterators::testDisjointIterators PASSED 657s tests/tabix_test.py::TestMultipleIterators::testDoubleFetch PASSED 657s tests/tabix_test.py::TestMultipleIterators::testJoinedIterators PASSED 657s tests/tabix_test.py::TestMultipleIterators::testScope PASSED 657s tests/tabix_test.py::TestContextManager::testManager PASSED 657s tests/tabix_test.py::TestMultithreadTabixFile::testMultithreadEqualsSinglethread PASSED 657s tests/tabixproxies_test.py::TestBED::testAssignmentToTargetList PASSED 657s tests/tabixproxies_test.py::TestParser::testAssignmentToTargetList PASSED 657s tests/tabixproxies_test.py::TestParser::testCopy PASSED 657s tests/tabixproxies_test.py::TestParser::testIteratorCompressed PASSED 657s tests/tabixproxies_test.py::TestParser::testIteratorUncompressed PASSED 657s tests/tabixproxies_test.py::TestParser::testRead PASSED 657s tests/tabixproxies_test.py::TestParser::testUnset PASSED 657s tests/tabixproxies_test.py::TestParser::testWrite PASSED 657s tests/tabixproxies_test.py::TestGTF::testAssignmentToTargetList PASSED 657s tests/tabixproxies_test.py::TestGTF::testCopy PASSED 657s tests/tabixproxies_test.py::TestGTF::testIteratorCompressed PASSED 657s tests/tabixproxies_test.py::TestGTF::testIteratorUncompressed PASSED 657s tests/tabixproxies_test.py::TestGTF::testRead PASSED 657s tests/tabixproxies_test.py::TestGTF::testUnset PASSED 657s tests/tabixproxies_test.py::TestGTF::testWrite PASSED 657s tests/tabixproxies_test.py::TestGTF::test_added_attribute_is_output PASSED 657s tests/tabixproxies_test.py::TestGTF::test_asdict_can_be_modified PASSED 657s tests/tabixproxies_test.py::TestGTF::test_asdict_contains_attributes PASSED 657s tests/tabixproxies_test.py::TestGTF::test_setAttribute_makes_changes PASSED 657s tests/tabixproxies_test.py::TestGTF::test_setting_end_is_one_based PASSED 657s tests/tabixproxies_test.py::TestGTF::test_setting_feature_to_none_produces_dot PASSED 657s tests/tabixproxies_test.py::TestGTF::test_setting_fields PASSED 657s tests/tabixproxies_test.py::TestGTF::test_setting_frame_to_none_produces_dot PASSED 657s tests/tabixproxies_test.py::TestGTF::test_setting_score_to_none_produces_dot PASSED 657s tests/tabixproxies_test.py::TestGTF::test_setting_source_to_none_produces_dot PASSED 657s tests/tabixproxies_test.py::TestGTF::test_setting_start_is_one_based PASSED 657s tests/tabixproxies_test.py::TestGTF::test_setting_strand_to_none_produces_dot PASSED 657s tests/tabixproxies_test.py::TestGFF3::testAssignmentToTargetList PASSED 657s tests/tabixproxies_test.py::TestGFF3::testCopy PASSED 657s tests/tabixproxies_test.py::TestGFF3::testIteratorCompressed PASSED 657s tests/tabixproxies_test.py::TestGFF3::testIteratorUncompressed PASSED 657s tests/tabixproxies_test.py::TestGFF3::testRead PASSED 657s tests/tabixproxies_test.py::TestGFF3::testUnset PASSED 657s tests/tabixproxies_test.py::TestGFF3::testWrite PASSED 657s tests/tabixproxies_test.py::TestGFF3::test_added_attribute_is_output PASSED 657s tests/tabixproxies_test.py::TestGFF3::test_asdict_can_be_modified PASSED 657s tests/tabixproxies_test.py::TestGFF3::test_asdict_contains_attributes PASSED 657s tests/tabixproxies_test.py::TestGFF3::test_setAttribute_makes_changes PASSED 657s tests/tabixproxies_test.py::TestGFF3::test_setting_end_is_one_based PASSED 657s tests/tabixproxies_test.py::TestGFF3::test_setting_feature_to_none_produces_dot PASSED 657s tests/tabixproxies_test.py::TestGFF3::test_setting_fields PASSED 657s tests/tabixproxies_test.py::TestGFF3::test_setting_frame_to_none_produces_dot PASSED 657s tests/tabixproxies_test.py::TestGFF3::test_setting_score_to_none_produces_dot PASSED 657s tests/tabixproxies_test.py::TestGFF3::test_setting_source_to_none_produces_dot PASSED 657s tests/tabixproxies_test.py::TestGFF3::test_setting_start_is_one_based PASSED 657s tests/tabixproxies_test.py::TestGFF3::test_setting_strand_to_none_produces_dot PASSED 657s tests/test_samtools_python.py::test_idxstats_parse_split_lines PASSED 657s tests/test_samtools_python.py::test_bedcov_split_lines PASSED 657s tests/test_samtools_python.py::test_idxstats_parse PASSED 658s tests/test_samtools_python.py::test_bedcov PASSED 658s 658s =============================== warnings summary =============================== 658s tests/samtools_test.py::SamtoolsTest::testStatements 658s tests/samtools_test.py::PysamTest::testStatements 658s /tmp/autopkgtest.wqFkeX/build.BHm/src/tests/samtools_test.py:144: UserWarning: versions of pysam.samtools and samtools differ: 1.18 != 1.19.2 658s warnings.warn( 658s 658s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 658s =========== 938 passed, 13 skipped, 2 warnings in 125.42s (0:02:05) ============ 658s autopkgtest [18:21:28]: test command1: -----------------------] 658s command1 PASS 658s autopkgtest [18:21:28]: test command1: - - - - - - - - - - results - - - - - - - - - - 659s autopkgtest [18:21:29]: test autodep8-python3: preparing testbed 1067s autopkgtest [18:28:17]: testbed dpkg architecture: ppc64el 1068s autopkgtest [18:28:18]: testbed apt version: 2.7.12 1068s autopkgtest [18:28:18]: @@@@@@@@@@@@@@@@@@@@ test bed setup 1069s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 1069s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [7608 B] 1069s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [498 kB] 1070s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.0 kB] 1070s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3989 kB] 1071s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [702 kB] 1071s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 1071s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 1071s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 1071s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4271 kB] 1071s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 1072s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [61.7 kB] 1072s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 1075s Fetched 9715 kB in 4s (2498 kB/s) 1076s Reading package lists... 1077s Reading package lists... 1077s Building dependency tree... 1077s Reading state information... 1077s Calculating upgrade... 1078s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1078s Reading package lists... 1078s Building dependency tree... 1078s Reading state information... 1078s 0 upgraded, 0 newly installed, 0 to remove and 246 not upgraded. 1079s sh: Attempting to set up Debian/Ubuntu apt sources automatically 1079s sh: Distribution appears to be Ubuntu 1080s Reading package lists... 1080s Building dependency tree... 1080s Reading state information... 1080s eatmydata is already the newest version (131-1). 1080s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1080s Reading package lists... 1080s Building dependency tree... 1080s Reading state information... 1081s dbus is already the newest version (1.14.10-4ubuntu1). 1081s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1081s Reading package lists... 1081s Building dependency tree... 1081s Reading state information... 1081s rng-tools-debian is already the newest version (2.4). 1081s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1081s Reading package lists... 1081s Building dependency tree... 1081s Reading state information... 1081s The following packages will be REMOVED: 1081s cloud-init* python3-configobj* python3-debconf* 1082s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 1082s After this operation, 3256 kB disk space will be freed. 1082s (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 ... 70156 files and directories currently installed.) 1082s Removing cloud-init (24.1.2-0ubuntu1) ... 1082s Removing python3-configobj (5.0.8-3) ... 1082s Removing python3-debconf (1.5.86) ... 1083s Processing triggers for man-db (2.12.0-3) ... 1083s (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 ... 69767 files and directories currently installed.) 1083s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 1084s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 1084s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 1084s invoke-rc.d: policy-rc.d denied execution of try-restart. 1084s Reading package lists... 1084s Building dependency tree... 1084s Reading state information... 1084s linux-generic is already the newest version (6.8.0-11.11+1). 1084s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1085s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 1085s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 1085s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 1088s Reading package lists... 1088s Reading package lists... 1088s Building dependency tree... 1088s Reading state information... 1088s Calculating upgrade... 1088s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1088s Reading package lists... 1088s Building dependency tree... 1088s Reading state information... 1088s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1089s autopkgtest [18:28:39]: rebooting testbed after setup commands that affected boot 1140s Reading package lists... 1140s Building dependency tree... 1140s Reading state information... 1140s Starting pkgProblemResolver with broken count: 0 1140s Starting 2 pkgProblemResolver with broken count: 0 1140s Done 1140s The following additional packages will be installed: 1140s libdeflate0 libhts3 libhtscodecs2 python3-all python3-pysam 1140s The following NEW packages will be installed: 1140s autopkgtest-satdep libdeflate0 libhts3 libhtscodecs2 python3-all 1140s python3-pysam 1140s 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. 1140s Need to get 5762 kB/5762 kB of archives. 1140s After this operation, 47.4 MB of additional disk space will be used. 1140s Get:1 /tmp/autopkgtest.wqFkeX/2-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [716 B] 1140s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 1141s Get:3 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 1141s Get:4 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB] 1141s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-all ppc64el 3.12.1-0ubuntu2 [904 B] 1141s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pysam ppc64el 0.22.0+ds-1 [5037 kB] 1142s Fetched 5762 kB in 1s (3888 kB/s) 1142s Selecting previously unselected package libdeflate0:ppc64el. 1142s (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 ... 69712 files and directories currently installed.) 1142s Preparing to unpack .../0-libdeflate0_1.19-1_ppc64el.deb ... 1142s Unpacking libdeflate0:ppc64el (1.19-1) ... 1142s Selecting previously unselected package libhtscodecs2:ppc64el. 1142s Preparing to unpack .../1-libhtscodecs2_1.6.0-1_ppc64el.deb ... 1142s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 1142s Selecting previously unselected package libhts3:ppc64el. 1142s Preparing to unpack .../2-libhts3_1.18+ds-1_ppc64el.deb ... 1142s Unpacking libhts3:ppc64el (1.18+ds-1) ... 1142s Selecting previously unselected package python3-all. 1142s Preparing to unpack .../3-python3-all_3.12.1-0ubuntu2_ppc64el.deb ... 1142s Unpacking python3-all (3.12.1-0ubuntu2) ... 1142s Selecting previously unselected package python3-pysam. 1142s Preparing to unpack .../4-python3-pysam_0.22.0+ds-1_ppc64el.deb ... 1142s Unpacking python3-pysam (0.22.0+ds-1) ... 1143s Selecting previously unselected package autopkgtest-satdep. 1143s Preparing to unpack .../5-2-autopkgtest-satdep.deb ... 1143s Unpacking autopkgtest-satdep (0) ... 1143s Setting up libhtscodecs2:ppc64el (1.6.0-1) ... 1143s Setting up libdeflate0:ppc64el (1.19-1) ... 1143s Setting up python3-all (3.12.1-0ubuntu2) ... 1143s Setting up libhts3:ppc64el (1.18+ds-1) ... 1143s Setting up python3-pysam (0.22.0+ds-1) ... 1143s Setting up autopkgtest-satdep (0) ... 1143s Processing triggers for man-db (2.12.0-3) ... 1143s Processing triggers for libc-bin (2.39-0ubuntu6) ... 1145s (Reading database ... 70115 files and directories currently installed.) 1145s Removing autopkgtest-satdep (0) ... 1153s autopkgtest [18:29:43]: 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 1153s autopkgtest [18:29:43]: test autodep8-python3: [----------------------- 1153s Testing with python3.12: 1153s 1154s autopkgtest [18:29:44]: test autodep8-python3: -----------------------] 1154s autopkgtest [18:29:44]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 1154s autodep8-python3 PASS (superficial) 1155s autopkgtest [18:29:45]: @@@@@@@@@@@@@@@@@@@@ summary 1155s command1 PASS 1155s autodep8-python3 PASS (superficial) 1175s Creating nova instance adt-noble-ppc64el-python-pysam-20240325-181029-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240325.img (UUID ce50e202-ac12-4562-879d-419903f0141e)... 1175s Creating nova instance adt-noble-ppc64el-python-pysam-20240325-181029-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240325.img (UUID ce50e202-ac12-4562-879d-419903f0141e)...