0s autopkgtest [15:49:48]: starting date and time: 2025-03-15 15:49:48+0000 0s autopkgtest [15:49:48]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [15:49:48]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.7iu6zedb/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:glibc --apt-upgrade python-pysam --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- lxd -r lxd-armhf-10.145.243.171 lxd-armhf-10.145.243.171:autopkgtest/ubuntu/plucky/armhf 22s autopkgtest [15:50:10]: testbed dpkg architecture: armhf 24s autopkgtest [15:50:12]: testbed apt version: 2.9.33 28s autopkgtest [15:50:16]: @@@@@@@@@@@@@@@@@@@@ test bed setup 30s autopkgtest [15:50:18]: testbed release detected to be: None 38s autopkgtest [15:50:26]: updating testbed package index (apt update) 40s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 41s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 41s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 41s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 42s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 42s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 42s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 42s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [114 kB] 42s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1832 B] 42s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 42s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [312 kB] 43s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [11.1 kB] 43s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 43s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [240 B] 43s Get:15 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 43s Get:16 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 67s Get:17 http://ftpmaster.internal/ubuntu plucky/main Sources [1394 kB] 68s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 70s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 70s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 70s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 87s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 89s Fetched 41.0 MB in 48s (850 kB/s) 90s Reading package lists... 100s autopkgtest [15:51:28]: upgrading testbed (apt dist-upgrade and autopurge) 104s Reading package lists... 105s Building dependency tree... 105s Reading state information... 105s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 105s Starting 2 pkgProblemResolver with broken count: 0 105s Done 106s Entering ResolveByKeep 106s 106s Calculating upgrade... 107s The following packages will be upgraded: 107s libc-bin libc6 locales pinentry-curses python3-jinja2 sos strace 107s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 107s Need to get 8683 kB of archives. 107s After this operation, 23.6 kB of additional disk space will be used. 107s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 110s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 111s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 116s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 117s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf pinentry-curses armhf 1.3.1-2ubuntu3 [40.6 kB] 117s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 117s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 118s Preconfiguring packages ... 118s Fetched 8683 kB in 10s (850 kB/s) 118s (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 ... 64655 files and directories currently installed.) 118s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 118s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 118s Setting up libc6:armhf (2.41-1ubuntu2) ... 119s (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 ... 64655 files and directories currently installed.) 119s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 119s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 119s Setting up libc-bin (2.41-1ubuntu2) ... 119s (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 ... 64655 files and directories currently installed.) 119s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 119s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 119s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 119s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 119s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_armhf.deb ... 119s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 119s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 119s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 119s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 120s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 120s Setting up sos (4.9.0-5) ... 121s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 121s Setting up locales (2.41-1ubuntu2) ... 121s Generating locales (this might take a while)... 123s en_US.UTF-8... done 123s Generation complete. 123s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 123s Setting up strace (6.13+ds-1ubuntu1) ... 123s Processing triggers for man-db (2.13.0-1) ... 124s Processing triggers for systemd (257.3-1ubuntu3) ... 127s Reading package lists... 127s Building dependency tree... 127s Reading state information... 128s Starting pkgProblemResolver with broken count: 0 128s Starting 2 pkgProblemResolver with broken count: 0 128s Done 128s Solving dependencies... 129s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 131s autopkgtest [15:51:59]: rebooting testbed after setup commands that affected boot 172s autopkgtest [15:52:40]: testbed running kernel: Linux 6.8.0-52-generic #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 18:10:51 UTC 2 197s autopkgtest [15:53:05]: @@@@@@@@@@@@@@@@@@@@ apt-source python-pysam 212s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-pysam 0.23.0+ds-1build1 (dsc) [2436 B] 212s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-pysam 0.23.0+ds-1build1 (tar) [1519 kB] 212s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-pysam 0.23.0+ds-1build1 (diff) [10.7 kB] 212s gpgv: Signature made Tue Mar 4 19:20:47 2025 UTC 212s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 212s gpgv: Can't check signature: No public key 212s dpkg-source: warning: cannot verify inline signature for ./python-pysam_0.23.0+ds-1build1.dsc: no acceptable signature found 213s autopkgtest [15:53:21]: testing package python-pysam version 0.23.0+ds-1build1 215s autopkgtest [15:53:23]: build not needed 218s autopkgtest [15:53:26]: test command1: preparing testbed 220s Reading package lists... 220s Building dependency tree... 220s Reading state information... 221s Starting pkgProblemResolver with broken count: 0 222s Starting 2 pkgProblemResolver with broken count: 0 222s Done 224s The following NEW packages will be installed: 224s autoconf automake autopoint autotools-dev bcftools build-essential 224s comerr-dev cpp cpp-14 cpp-14-arm-linux-gnueabihf cpp-arm-linux-gnueabihf 224s cython3 debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism 224s dwz g++ g++-14 g++-14-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc gcc-14 224s gcc-14-arm-linux-gnueabihf gcc-arm-linux-gnueabihf gettext intltool-debian 224s krb5-multidev libarchive-zip-perl libasan8 libbrotli-dev libbz2-dev 224s libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libcurl4-gnutls-dev 224s libdebhelper-perl libdeflate-dev libdeflate0 libdw1t64 libevent-2.1-7t64 224s libexpat1-dev libfile-stripnondeterminism-perl libgcc-14-dev libgmp-dev 224s libgmpxx4ldbl libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev 224s libgomp1 libgssrpc4t64 libhts-dev libhts3t64 libhtscodecs2 libidn2-dev 224s libisl23 libjs-jquery libjs-sphinxdoc libjs-underscore libkadm5clnt-mit12 224s libkadm5srv-mit12 libkdb5-10t64 libkrb5-dev libldap-dev liblzma-dev libmpc3 224s libnghttp2-dev libp11-kit-dev libpkgconf3 libpsl-dev libpython3-all-dev 224s libpython3-dev libpython3.13 libpython3.13-dev librtmp-dev libssh2-1-dev 224s libssl-dev libstdc++-14-dev libtasn1-6-dev libtool libubsan1 libunbound8 224s libzstd-dev linux-libc-dev m4 nettle-dev pkgconf pkgconf-bin po-debconf 224s python3-all python3-all-dev python3-dev python3-iniconfig python3-pluggy 224s python3-pysam python3-pytest python3.13-dev rpcsvc-proto samtools tabix 224s zlib1g-dev 224s 0 upgraded, 103 newly installed, 0 to remove and 0 not upgraded. 224s Need to get 82.0 MB of archives. 224s After this operation, 272 MB of additional disk space will be used. 224s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf m4 armhf 1.4.19-7 [238 kB] 225s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf autoconf all 2.72-3ubuntu1 [383 kB] 225s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf autotools-dev all 20220109.1 [44.9 kB] 225s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf automake all 1:1.17-3ubuntu1 [572 kB] 226s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf autopoint all 0.23.1-1 [619 kB] 226s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.23-1 [38.5 kB] 227s Get:7 http://ftpmaster.internal/ubuntu plucky/universe armhf libhtscodecs2 armhf 1.6.1-2 [67.5 kB] 227s Get:8 http://ftpmaster.internal/ubuntu plucky/universe armhf libhts3t64 armhf 1.21+ds-1 [399 kB] 227s Get:9 http://ftpmaster.internal/ubuntu plucky/universe armhf bcftools armhf 1.21-1 [747 kB] 228s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-dev-bin armhf 2.41-1ubuntu2 [23.0 kB] 228s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf linux-libc-dev armhf 6.14.0-10.10 [1683 kB] 229s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libcrypt-dev armhf 1:4.4.38-1 [120 kB] 229s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf rpcsvc-proto armhf 1.4.2-0ubuntu7 [62.2 kB] 230s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6-dev armhf 2.41-1ubuntu2 [1396 kB] 231s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf libisl23 armhf 0.27-1 [546 kB] 231s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf libmpc3 armhf 1.3.1-1build2 [47.1 kB] 231s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-14-arm-linux-gnueabihf armhf 14.2.0-17ubuntu3 [9220 kB] 241s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-14 armhf 14.2.0-17ubuntu3 [1030 B] 241s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [5578 B] 241s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf cpp armhf 4:14.2.0-1ubuntu1 [22.4 kB] 241s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libcc1-0 armhf 15-20250222-0ubuntu1 [38.9 kB] 241s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 15-20250222-0ubuntu1 [128 kB] 242s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf libasan8 armhf 15-20250222-0ubuntu1 [2955 kB] 245s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf libubsan1 armhf 15-20250222-0ubuntu1 [1191 kB] 246s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf libgcc-14-dev armhf 14.2.0-17ubuntu3 [897 kB] 247s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14-arm-linux-gnueabihf armhf 14.2.0-17ubuntu3 [18.0 MB] 265s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14 armhf 14.2.0-17ubuntu3 [506 kB] 266s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [1218 B] 266s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf gcc armhf 4:14.2.0-1ubuntu1 [5004 B] 266s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf libstdc++-14-dev armhf 14.2.0-17ubuntu3 [2573 kB] 269s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf g++-14-arm-linux-gnueabihf armhf 14.2.0-17ubuntu3 [10.5 MB] 280s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf g++-14 armhf 14.2.0-17ubuntu3 [21.8 kB] 280s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf g++-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [966 B] 280s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf g++ armhf 4:14.2.0-1ubuntu1 [1084 B] 280s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf build-essential armhf 12.10ubuntu1 [4928 B] 280s Get:36 http://ftpmaster.internal/ubuntu plucky/universe armhf cython3 armhf 3.0.11+dfsg-2ubuntu2 [2469 kB] 283s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libdebhelper-perl all 13.24.1ubuntu2 [95.4 kB] 283s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libtool all 2.5.4-4 [168 kB] 283s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf dh-autoreconf all 20 [16.1 kB] 283s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf libarchive-zip-perl all 1.68-1 [90.2 kB] 283s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf libfile-stripnondeterminism-perl all 1.14.1-2 [20.3 kB] 283s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf dh-strip-nondeterminism all 1.14.1-2 [5064 B] 283s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf libdw1t64 armhf 0.192-4 [243 kB] 283s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf debugedit armhf 1:5.1-2 [46.7 kB] 283s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf dwz armhf 0.15-1build6 [116 kB] 284s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf gettext armhf 0.23.1-1 [1053 kB] 285s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf intltool-debian all 0.35.0+20060710.6 [23.2 kB] 285s Get:48 http://ftpmaster.internal/ubuntu plucky/main armhf po-debconf all 1.0.21+nmu1 [233 kB] 285s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf debhelper all 13.24.1ubuntu2 [895 kB] 286s Get:50 http://ftpmaster.internal/ubuntu plucky/universe armhf dh-python all 6.20250308 [118 kB] 286s Get:51 http://ftpmaster.internal/ubuntu plucky/main armhf comerr-dev armhf 2.1-1.47.2-1ubuntu1 [44.1 kB] 286s Get:52 http://ftpmaster.internal/ubuntu plucky/main armhf libgssrpc4t64 armhf 1.21.3-4ubuntu2 [51.5 kB] 286s Get:53 http://ftpmaster.internal/ubuntu plucky/main armhf libkadm5clnt-mit12 armhf 1.21.3-4ubuntu2 [35.7 kB] 286s Get:54 http://ftpmaster.internal/ubuntu plucky/main armhf libkdb5-10t64 armhf 1.21.3-4ubuntu2 [35.2 kB] 286s Get:55 http://ftpmaster.internal/ubuntu plucky/main armhf libkadm5srv-mit12 armhf 1.21.3-4ubuntu2 [46.3 kB] 287s Get:56 http://ftpmaster.internal/ubuntu plucky/main armhf krb5-multidev armhf 1.21.3-4ubuntu2 [125 kB] 287s Get:57 http://ftpmaster.internal/ubuntu plucky/main armhf libbrotli-dev armhf 1.1.0-2build4 [336 kB] 287s Get:58 http://ftpmaster.internal/ubuntu plucky/main armhf libbz2-dev armhf 1.0.8-6 [30.9 kB] 287s Get:59 http://ftpmaster.internal/ubuntu plucky/main armhf libevent-2.1-7t64 armhf 2.1.12-stable-10 [127 kB] 287s Get:60 http://ftpmaster.internal/ubuntu plucky/main armhf libunbound8 armhf 1.22.0-1ubuntu1 [423 kB] 288s Get:61 http://ftpmaster.internal/ubuntu plucky/main armhf libgnutls-dane0t64 armhf 3.8.9-2ubuntu2 [34.9 kB] 288s Get:62 http://ftpmaster.internal/ubuntu plucky/main armhf libgnutls-openssl27t64 armhf 3.8.9-2ubuntu2 [34.8 kB] 288s Get:63 http://ftpmaster.internal/ubuntu plucky/main armhf libidn2-dev armhf 2.3.7-2build2 [115 kB] 288s Get:64 http://ftpmaster.internal/ubuntu plucky/main armhf libp11-kit-dev armhf 0.25.5-2ubuntu3 [23.5 kB] 288s Get:65 http://ftpmaster.internal/ubuntu plucky/main armhf libtasn1-6-dev armhf 4.20.0-2 [86.5 kB] 288s Get:66 http://ftpmaster.internal/ubuntu plucky/main armhf libgmpxx4ldbl armhf 2:6.3.0+dfsg-3ubuntu1 [9152 B] 288s Get:67 http://ftpmaster.internal/ubuntu plucky/main armhf libgmp-dev armhf 2:6.3.0+dfsg-3ubuntu1 [290 kB] 288s Get:68 http://ftpmaster.internal/ubuntu plucky/main armhf nettle-dev armhf 3.10.1-1 [1173 kB] 289s Get:69 http://ftpmaster.internal/ubuntu plucky/main armhf libgnutls28-dev armhf 3.8.9-2ubuntu2 [1023 kB] 290s Get:70 http://ftpmaster.internal/ubuntu plucky/main armhf libkrb5-dev armhf 1.21.3-4ubuntu2 [11.9 kB] 290s Get:71 http://ftpmaster.internal/ubuntu plucky/main armhf libldap-dev armhf 2.6.9+dfsg-1~exp2ubuntu1 [289 kB] 291s Get:72 http://ftpmaster.internal/ubuntu plucky/main armhf libpkgconf3 armhf 1.8.1-4 [26.6 kB] 291s Get:73 http://ftpmaster.internal/ubuntu plucky/main armhf pkgconf-bin armhf 1.8.1-4 [21.2 kB] 291s Get:74 http://ftpmaster.internal/ubuntu plucky/main armhf pkgconf armhf 1.8.1-4 [16.8 kB] 291s Get:75 http://ftpmaster.internal/ubuntu plucky/main armhf libnghttp2-dev armhf 1.64.0-1 [106 kB] 291s Get:76 http://ftpmaster.internal/ubuntu plucky/main armhf libpsl-dev armhf 0.21.2-1.1build1 [75.6 kB] 291s Get:77 http://ftpmaster.internal/ubuntu plucky/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1ubuntu1 [880 kB] 292s Get:78 http://ftpmaster.internal/ubuntu plucky/main armhf librtmp-dev armhf 2.4+20151223.gitfa8646d.1-2build7 [62.9 kB] 292s Get:79 http://ftpmaster.internal/ubuntu plucky/main armhf libssl-dev armhf 3.4.1-1ubuntu1 [2381 kB] 294s Get:80 http://ftpmaster.internal/ubuntu plucky/main armhf libssh2-1-dev armhf 1.11.1-1 [270 kB] 295s Get:81 http://ftpmaster.internal/ubuntu plucky/main armhf libzstd-dev armhf 1.5.6+dfsg-2 [332 kB] 295s Get:82 http://ftpmaster.internal/ubuntu plucky/main armhf libcurl4-gnutls-dev armhf 8.12.1-3ubuntu1 [457 kB] 296s Get:83 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate-dev armhf 1.23-1 [45.0 kB] 296s Get:84 http://ftpmaster.internal/ubuntu plucky/main armhf libexpat1-dev armhf 2.6.4-1 [121 kB] 296s Get:85 http://ftpmaster.internal/ubuntu plucky/main armhf liblzma-dev armhf 5.6.4-1 [166 kB] 296s Get:86 http://ftpmaster.internal/ubuntu plucky/universe armhf libhts-dev armhf 1.21+ds-1 [1786 kB] 298s Get:87 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 298s Get:88 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 298s Get:89 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-sphinxdoc all 8.1.3-4 [30.9 kB] 298s Get:90 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13 armhf 3.13.2-2 [2079 kB] 301s Get:91 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13-dev armhf 3.13.2-2 [4265 kB] 305s Get:92 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3-dev armhf 3.13.2-2 [10.7 kB] 305s Get:93 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3-all-dev armhf 3.13.2-2 [910 B] 305s Get:94 http://ftpmaster.internal/ubuntu plucky/main armhf python3-all armhf 3.13.2-2 [886 B] 305s Get:95 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-dev armhf 3.13.2-2 [509 kB] 306s Get:96 http://ftpmaster.internal/ubuntu plucky/main armhf python3-dev armhf 3.13.2-2 [26.7 kB] 306s Get:97 http://ftpmaster.internal/ubuntu plucky/main armhf python3-all-dev armhf 3.13.2-2 [912 B] 306s Get:98 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-iniconfig all 1.1.1-2 [6024 B] 306s Get:99 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pluggy all 1.5.0-1 [21.0 kB] 306s Get:100 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pysam armhf 0.23.0+ds-1build1 [3569 kB] 310s Get:101 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pytest all 8.3.5-1 [252 kB] 310s Get:102 http://ftpmaster.internal/ubuntu plucky/universe armhf samtools armhf 1.21-1 [619 kB] 311s Get:103 http://ftpmaster.internal/ubuntu plucky/universe armhf tabix armhf 1.21+ds-1 [433 kB] 312s Fetched 82.0 MB in 1min 27s (938 kB/s) 312s Selecting previously unselected package m4. 312s (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 ... 64655 files and directories currently installed.) 312s Preparing to unpack .../000-m4_1.4.19-7_armhf.deb ... 312s Unpacking m4 (1.4.19-7) ... 312s Selecting previously unselected package autoconf. 312s Preparing to unpack .../001-autoconf_2.72-3ubuntu1_all.deb ... 312s Unpacking autoconf (2.72-3ubuntu1) ... 312s Selecting previously unselected package autotools-dev. 312s Preparing to unpack .../002-autotools-dev_20220109.1_all.deb ... 312s Unpacking autotools-dev (20220109.1) ... 312s Selecting previously unselected package automake. 312s Preparing to unpack .../003-automake_1%3a1.17-3ubuntu1_all.deb ... 312s Unpacking automake (1:1.17-3ubuntu1) ... 312s Selecting previously unselected package autopoint. 312s Preparing to unpack .../004-autopoint_0.23.1-1_all.deb ... 312s Unpacking autopoint (0.23.1-1) ... 312s Selecting previously unselected package libdeflate0:armhf. 312s Preparing to unpack .../005-libdeflate0_1.23-1_armhf.deb ... 312s Unpacking libdeflate0:armhf (1.23-1) ... 312s Selecting previously unselected package libhtscodecs2:armhf. 312s Preparing to unpack .../006-libhtscodecs2_1.6.1-2_armhf.deb ... 312s Unpacking libhtscodecs2:armhf (1.6.1-2) ... 312s Selecting previously unselected package libhts3t64:armhf. 312s Preparing to unpack .../007-libhts3t64_1.21+ds-1_armhf.deb ... 312s Unpacking libhts3t64:armhf (1.21+ds-1) ... 312s Selecting previously unselected package bcftools. 312s Preparing to unpack .../008-bcftools_1.21-1_armhf.deb ... 312s Unpacking bcftools (1.21-1) ... 312s Selecting previously unselected package libc-dev-bin. 312s Preparing to unpack .../009-libc-dev-bin_2.41-1ubuntu2_armhf.deb ... 312s Unpacking libc-dev-bin (2.41-1ubuntu2) ... 312s Selecting previously unselected package linux-libc-dev:armhf. 312s Preparing to unpack .../010-linux-libc-dev_6.14.0-10.10_armhf.deb ... 312s Unpacking linux-libc-dev:armhf (6.14.0-10.10) ... 312s Selecting previously unselected package libcrypt-dev:armhf. 312s Preparing to unpack .../011-libcrypt-dev_1%3a4.4.38-1_armhf.deb ... 312s Unpacking libcrypt-dev:armhf (1:4.4.38-1) ... 312s Selecting previously unselected package rpcsvc-proto. 312s Preparing to unpack .../012-rpcsvc-proto_1.4.2-0ubuntu7_armhf.deb ... 312s Unpacking rpcsvc-proto (1.4.2-0ubuntu7) ... 313s Selecting previously unselected package libc6-dev:armhf. 313s Preparing to unpack .../013-libc6-dev_2.41-1ubuntu2_armhf.deb ... 313s Unpacking libc6-dev:armhf (2.41-1ubuntu2) ... 313s Selecting previously unselected package libisl23:armhf. 313s Preparing to unpack .../014-libisl23_0.27-1_armhf.deb ... 313s Unpacking libisl23:armhf (0.27-1) ... 313s Selecting previously unselected package libmpc3:armhf. 313s Preparing to unpack .../015-libmpc3_1.3.1-1build2_armhf.deb ... 313s Unpacking libmpc3:armhf (1.3.1-1build2) ... 313s Selecting previously unselected package cpp-14-arm-linux-gnueabihf. 313s Preparing to unpack .../016-cpp-14-arm-linux-gnueabihf_14.2.0-17ubuntu3_armhf.deb ... 313s Unpacking cpp-14-arm-linux-gnueabihf (14.2.0-17ubuntu3) ... 313s Selecting previously unselected package cpp-14. 313s Preparing to unpack .../017-cpp-14_14.2.0-17ubuntu3_armhf.deb ... 313s Unpacking cpp-14 (14.2.0-17ubuntu3) ... 313s Selecting previously unselected package cpp-arm-linux-gnueabihf. 313s Preparing to unpack .../018-cpp-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 313s Unpacking cpp-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 313s Selecting previously unselected package cpp. 313s Preparing to unpack .../019-cpp_4%3a14.2.0-1ubuntu1_armhf.deb ... 313s Unpacking cpp (4:14.2.0-1ubuntu1) ... 313s Selecting previously unselected package libcc1-0:armhf. 313s Preparing to unpack .../020-libcc1-0_15-20250222-0ubuntu1_armhf.deb ... 313s Unpacking libcc1-0:armhf (15-20250222-0ubuntu1) ... 313s Selecting previously unselected package libgomp1:armhf. 313s Preparing to unpack .../021-libgomp1_15-20250222-0ubuntu1_armhf.deb ... 313s Unpacking libgomp1:armhf (15-20250222-0ubuntu1) ... 313s Selecting previously unselected package libasan8:armhf. 313s Preparing to unpack .../022-libasan8_15-20250222-0ubuntu1_armhf.deb ... 313s Unpacking libasan8:armhf (15-20250222-0ubuntu1) ... 313s Selecting previously unselected package libubsan1:armhf. 313s Preparing to unpack .../023-libubsan1_15-20250222-0ubuntu1_armhf.deb ... 313s Unpacking libubsan1:armhf (15-20250222-0ubuntu1) ... 313s Selecting previously unselected package libgcc-14-dev:armhf. 313s Preparing to unpack .../024-libgcc-14-dev_14.2.0-17ubuntu3_armhf.deb ... 313s Unpacking libgcc-14-dev:armhf (14.2.0-17ubuntu3) ... 313s Selecting previously unselected package gcc-14-arm-linux-gnueabihf. 313s Preparing to unpack .../025-gcc-14-arm-linux-gnueabihf_14.2.0-17ubuntu3_armhf.deb ... 313s Unpacking gcc-14-arm-linux-gnueabihf (14.2.0-17ubuntu3) ... 314s Selecting previously unselected package gcc-14. 314s Preparing to unpack .../026-gcc-14_14.2.0-17ubuntu3_armhf.deb ... 314s Unpacking gcc-14 (14.2.0-17ubuntu3) ... 314s Selecting previously unselected package gcc-arm-linux-gnueabihf. 314s Preparing to unpack .../027-gcc-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 314s Unpacking gcc-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 314s Selecting previously unselected package gcc. 314s Preparing to unpack .../028-gcc_4%3a14.2.0-1ubuntu1_armhf.deb ... 314s Unpacking gcc (4:14.2.0-1ubuntu1) ... 314s Selecting previously unselected package libstdc++-14-dev:armhf. 314s Preparing to unpack .../029-libstdc++-14-dev_14.2.0-17ubuntu3_armhf.deb ... 314s Unpacking libstdc++-14-dev:armhf (14.2.0-17ubuntu3) ... 314s Selecting previously unselected package g++-14-arm-linux-gnueabihf. 314s Preparing to unpack .../030-g++-14-arm-linux-gnueabihf_14.2.0-17ubuntu3_armhf.deb ... 314s Unpacking g++-14-arm-linux-gnueabihf (14.2.0-17ubuntu3) ... 314s Selecting previously unselected package g++-14. 314s Preparing to unpack .../031-g++-14_14.2.0-17ubuntu3_armhf.deb ... 314s Unpacking g++-14 (14.2.0-17ubuntu3) ... 314s Selecting previously unselected package g++-arm-linux-gnueabihf. 314s Preparing to unpack .../032-g++-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 314s Unpacking g++-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 314s Selecting previously unselected package g++. 314s Preparing to unpack .../033-g++_4%3a14.2.0-1ubuntu1_armhf.deb ... 314s Unpacking g++ (4:14.2.0-1ubuntu1) ... 314s Selecting previously unselected package build-essential. 314s Preparing to unpack .../034-build-essential_12.10ubuntu1_armhf.deb ... 314s Unpacking build-essential (12.10ubuntu1) ... 314s Selecting previously unselected package cython3. 314s Preparing to unpack .../035-cython3_3.0.11+dfsg-2ubuntu2_armhf.deb ... 314s Unpacking cython3 (3.0.11+dfsg-2ubuntu2) ... 315s Selecting previously unselected package libdebhelper-perl. 315s Preparing to unpack .../036-libdebhelper-perl_13.24.1ubuntu2_all.deb ... 315s Unpacking libdebhelper-perl (13.24.1ubuntu2) ... 315s Selecting previously unselected package libtool. 315s Preparing to unpack .../037-libtool_2.5.4-4_all.deb ... 315s Unpacking libtool (2.5.4-4) ... 315s Selecting previously unselected package dh-autoreconf. 315s Preparing to unpack .../038-dh-autoreconf_20_all.deb ... 315s Unpacking dh-autoreconf (20) ... 315s Selecting previously unselected package libarchive-zip-perl. 315s Preparing to unpack .../039-libarchive-zip-perl_1.68-1_all.deb ... 315s Unpacking libarchive-zip-perl (1.68-1) ... 315s Selecting previously unselected package libfile-stripnondeterminism-perl. 315s Preparing to unpack .../040-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... 315s Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... 315s Selecting previously unselected package dh-strip-nondeterminism. 315s Preparing to unpack .../041-dh-strip-nondeterminism_1.14.1-2_all.deb ... 315s Unpacking dh-strip-nondeterminism (1.14.1-2) ... 315s Selecting previously unselected package libdw1t64:armhf. 315s Preparing to unpack .../042-libdw1t64_0.192-4_armhf.deb ... 315s Unpacking libdw1t64:armhf (0.192-4) ... 315s Selecting previously unselected package debugedit. 315s Preparing to unpack .../043-debugedit_1%3a5.1-2_armhf.deb ... 315s Unpacking debugedit (1:5.1-2) ... 315s Selecting previously unselected package dwz. 315s Preparing to unpack .../044-dwz_0.15-1build6_armhf.deb ... 315s Unpacking dwz (0.15-1build6) ... 315s Selecting previously unselected package gettext. 315s Preparing to unpack .../045-gettext_0.23.1-1_armhf.deb ... 315s Unpacking gettext (0.23.1-1) ... 315s Selecting previously unselected package intltool-debian. 315s Preparing to unpack .../046-intltool-debian_0.35.0+20060710.6_all.deb ... 315s Unpacking intltool-debian (0.35.0+20060710.6) ... 315s Selecting previously unselected package po-debconf. 315s Preparing to unpack .../047-po-debconf_1.0.21+nmu1_all.deb ... 315s Unpacking po-debconf (1.0.21+nmu1) ... 315s Selecting previously unselected package debhelper. 315s Preparing to unpack .../048-debhelper_13.24.1ubuntu2_all.deb ... 315s Unpacking debhelper (13.24.1ubuntu2) ... 315s Selecting previously unselected package dh-python. 315s Preparing to unpack .../049-dh-python_6.20250308_all.deb ... 315s Unpacking dh-python (6.20250308) ... 315s Selecting previously unselected package comerr-dev:armhf. 315s Preparing to unpack .../050-comerr-dev_2.1-1.47.2-1ubuntu1_armhf.deb ... 315s Unpacking comerr-dev:armhf (2.1-1.47.2-1ubuntu1) ... 315s Selecting previously unselected package libgssrpc4t64:armhf. 315s Preparing to unpack .../051-libgssrpc4t64_1.21.3-4ubuntu2_armhf.deb ... 315s Unpacking libgssrpc4t64:armhf (1.21.3-4ubuntu2) ... 315s Selecting previously unselected package libkadm5clnt-mit12:armhf. 315s Preparing to unpack .../052-libkadm5clnt-mit12_1.21.3-4ubuntu2_armhf.deb ... 315s Unpacking libkadm5clnt-mit12:armhf (1.21.3-4ubuntu2) ... 315s Selecting previously unselected package libkdb5-10t64:armhf. 315s Preparing to unpack .../053-libkdb5-10t64_1.21.3-4ubuntu2_armhf.deb ... 315s Unpacking libkdb5-10t64:armhf (1.21.3-4ubuntu2) ... 315s Selecting previously unselected package libkadm5srv-mit12:armhf. 315s Preparing to unpack .../054-libkadm5srv-mit12_1.21.3-4ubuntu2_armhf.deb ... 315s Unpacking libkadm5srv-mit12:armhf (1.21.3-4ubuntu2) ... 315s Selecting previously unselected package krb5-multidev:armhf. 315s Preparing to unpack .../055-krb5-multidev_1.21.3-4ubuntu2_armhf.deb ... 315s Unpacking krb5-multidev:armhf (1.21.3-4ubuntu2) ... 316s Selecting previously unselected package libbrotli-dev:armhf. 316s Preparing to unpack .../056-libbrotli-dev_1.1.0-2build4_armhf.deb ... 316s Unpacking libbrotli-dev:armhf (1.1.0-2build4) ... 316s Selecting previously unselected package libbz2-dev:armhf. 316s Preparing to unpack .../057-libbz2-dev_1.0.8-6_armhf.deb ... 316s Unpacking libbz2-dev:armhf (1.0.8-6) ... 316s Selecting previously unselected package libevent-2.1-7t64:armhf. 316s Preparing to unpack .../058-libevent-2.1-7t64_2.1.12-stable-10_armhf.deb ... 316s Unpacking libevent-2.1-7t64:armhf (2.1.12-stable-10) ... 316s Selecting previously unselected package libunbound8:armhf. 316s Preparing to unpack .../059-libunbound8_1.22.0-1ubuntu1_armhf.deb ... 316s Unpacking libunbound8:armhf (1.22.0-1ubuntu1) ... 316s Selecting previously unselected package libgnutls-dane0t64:armhf. 316s Preparing to unpack .../060-libgnutls-dane0t64_3.8.9-2ubuntu2_armhf.deb ... 316s Unpacking libgnutls-dane0t64:armhf (3.8.9-2ubuntu2) ... 316s Selecting previously unselected package libgnutls-openssl27t64:armhf. 316s Preparing to unpack .../061-libgnutls-openssl27t64_3.8.9-2ubuntu2_armhf.deb ... 316s Unpacking libgnutls-openssl27t64:armhf (3.8.9-2ubuntu2) ... 316s Selecting previously unselected package libidn2-dev:armhf. 316s Preparing to unpack .../062-libidn2-dev_2.3.7-2build2_armhf.deb ... 316s Unpacking libidn2-dev:armhf (2.3.7-2build2) ... 316s Selecting previously unselected package libp11-kit-dev:armhf. 316s Preparing to unpack .../063-libp11-kit-dev_0.25.5-2ubuntu3_armhf.deb ... 316s Unpacking libp11-kit-dev:armhf (0.25.5-2ubuntu3) ... 316s Selecting previously unselected package libtasn1-6-dev:armhf. 316s Preparing to unpack .../064-libtasn1-6-dev_4.20.0-2_armhf.deb ... 316s Unpacking libtasn1-6-dev:armhf (4.20.0-2) ... 316s Selecting previously unselected package libgmpxx4ldbl:armhf. 316s Preparing to unpack .../065-libgmpxx4ldbl_2%3a6.3.0+dfsg-3ubuntu1_armhf.deb ... 316s Unpacking libgmpxx4ldbl:armhf (2:6.3.0+dfsg-3ubuntu1) ... 316s Selecting previously unselected package libgmp-dev:armhf. 316s Preparing to unpack .../066-libgmp-dev_2%3a6.3.0+dfsg-3ubuntu1_armhf.deb ... 316s Unpacking libgmp-dev:armhf (2:6.3.0+dfsg-3ubuntu1) ... 316s Selecting previously unselected package nettle-dev:armhf. 316s Preparing to unpack .../067-nettle-dev_3.10.1-1_armhf.deb ... 316s Unpacking nettle-dev:armhf (3.10.1-1) ... 316s Selecting previously unselected package libgnutls28-dev:armhf. 316s Preparing to unpack .../068-libgnutls28-dev_3.8.9-2ubuntu2_armhf.deb ... 316s Unpacking libgnutls28-dev:armhf (3.8.9-2ubuntu2) ... 316s Selecting previously unselected package libkrb5-dev:armhf. 316s Preparing to unpack .../069-libkrb5-dev_1.21.3-4ubuntu2_armhf.deb ... 316s Unpacking libkrb5-dev:armhf (1.21.3-4ubuntu2) ... 316s Selecting previously unselected package libldap-dev:armhf. 316s Preparing to unpack .../070-libldap-dev_2.6.9+dfsg-1~exp2ubuntu1_armhf.deb ... 316s Unpacking libldap-dev:armhf (2.6.9+dfsg-1~exp2ubuntu1) ... 316s Selecting previously unselected package libpkgconf3:armhf. 316s Preparing to unpack .../071-libpkgconf3_1.8.1-4_armhf.deb ... 316s Unpacking libpkgconf3:armhf (1.8.1-4) ... 316s Selecting previously unselected package pkgconf-bin. 316s Preparing to unpack .../072-pkgconf-bin_1.8.1-4_armhf.deb ... 316s Unpacking pkgconf-bin (1.8.1-4) ... 316s Selecting previously unselected package pkgconf:armhf. 316s Preparing to unpack .../073-pkgconf_1.8.1-4_armhf.deb ... 316s Unpacking pkgconf:armhf (1.8.1-4) ... 316s Selecting previously unselected package libnghttp2-dev:armhf. 316s Preparing to unpack .../074-libnghttp2-dev_1.64.0-1_armhf.deb ... 316s Unpacking libnghttp2-dev:armhf (1.64.0-1) ... 316s Selecting previously unselected package libpsl-dev:armhf. 316s Preparing to unpack .../075-libpsl-dev_0.21.2-1.1build1_armhf.deb ... 316s Unpacking libpsl-dev:armhf (0.21.2-1.1build1) ... 316s Selecting previously unselected package zlib1g-dev:armhf. 316s Preparing to unpack .../076-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_armhf.deb ... 316s Unpacking zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 316s Selecting previously unselected package librtmp-dev:armhf. 316s Preparing to unpack .../077-librtmp-dev_2.4+20151223.gitfa8646d.1-2build7_armhf.deb ... 316s Unpacking librtmp-dev:armhf (2.4+20151223.gitfa8646d.1-2build7) ... 316s Selecting previously unselected package libssl-dev:armhf. 316s Preparing to unpack .../078-libssl-dev_3.4.1-1ubuntu1_armhf.deb ... 316s Unpacking libssl-dev:armhf (3.4.1-1ubuntu1) ... 317s Selecting previously unselected package libssh2-1-dev:armhf. 317s Preparing to unpack .../079-libssh2-1-dev_1.11.1-1_armhf.deb ... 317s Unpacking libssh2-1-dev:armhf (1.11.1-1) ... 317s Selecting previously unselected package libzstd-dev:armhf. 317s Preparing to unpack .../080-libzstd-dev_1.5.6+dfsg-2_armhf.deb ... 317s Unpacking libzstd-dev:armhf (1.5.6+dfsg-2) ... 317s Selecting previously unselected package libcurl4-gnutls-dev:armhf. 317s Preparing to unpack .../081-libcurl4-gnutls-dev_8.12.1-3ubuntu1_armhf.deb ... 317s Unpacking libcurl4-gnutls-dev:armhf (8.12.1-3ubuntu1) ... 317s Selecting previously unselected package libdeflate-dev:armhf. 317s Preparing to unpack .../082-libdeflate-dev_1.23-1_armhf.deb ... 317s Unpacking libdeflate-dev:armhf (1.23-1) ... 317s Selecting previously unselected package libexpat1-dev:armhf. 317s Preparing to unpack .../083-libexpat1-dev_2.6.4-1_armhf.deb ... 317s Unpacking libexpat1-dev:armhf (2.6.4-1) ... 317s Selecting previously unselected package liblzma-dev:armhf. 317s Preparing to unpack .../084-liblzma-dev_5.6.4-1_armhf.deb ... 317s Unpacking liblzma-dev:armhf (5.6.4-1) ... 317s Selecting previously unselected package libhts-dev:armhf. 317s Preparing to unpack .../085-libhts-dev_1.21+ds-1_armhf.deb ... 317s Unpacking libhts-dev:armhf (1.21+ds-1) ... 317s Selecting previously unselected package libjs-jquery. 317s Preparing to unpack .../086-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 317s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 317s Selecting previously unselected package libjs-underscore. 317s Preparing to unpack .../087-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 317s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 317s Selecting previously unselected package libjs-sphinxdoc. 317s Preparing to unpack .../088-libjs-sphinxdoc_8.1.3-4_all.deb ... 317s Unpacking libjs-sphinxdoc (8.1.3-4) ... 317s Selecting previously unselected package libpython3.13:armhf. 317s Preparing to unpack .../089-libpython3.13_3.13.2-2_armhf.deb ... 317s Unpacking libpython3.13:armhf (3.13.2-2) ... 317s Selecting previously unselected package libpython3.13-dev:armhf. 317s Preparing to unpack .../090-libpython3.13-dev_3.13.2-2_armhf.deb ... 317s Unpacking libpython3.13-dev:armhf (3.13.2-2) ... 317s Selecting previously unselected package libpython3-dev:armhf. 317s Preparing to unpack .../091-libpython3-dev_3.13.2-2_armhf.deb ... 317s Unpacking libpython3-dev:armhf (3.13.2-2) ... 317s Selecting previously unselected package libpython3-all-dev:armhf. 317s Preparing to unpack .../092-libpython3-all-dev_3.13.2-2_armhf.deb ... 317s Unpacking libpython3-all-dev:armhf (3.13.2-2) ... 317s Selecting previously unselected package python3-all. 317s Preparing to unpack .../093-python3-all_3.13.2-2_armhf.deb ... 317s Unpacking python3-all (3.13.2-2) ... 317s Selecting previously unselected package python3.13-dev. 317s Preparing to unpack .../094-python3.13-dev_3.13.2-2_armhf.deb ... 317s Unpacking python3.13-dev (3.13.2-2) ... 317s Selecting previously unselected package python3-dev. 317s Preparing to unpack .../095-python3-dev_3.13.2-2_armhf.deb ... 317s Unpacking python3-dev (3.13.2-2) ... 317s Selecting previously unselected package python3-all-dev. 317s Preparing to unpack .../096-python3-all-dev_3.13.2-2_armhf.deb ... 317s Unpacking python3-all-dev (3.13.2-2) ... 318s Selecting previously unselected package python3-iniconfig. 318s Preparing to unpack .../097-python3-iniconfig_1.1.1-2_all.deb ... 318s Unpacking python3-iniconfig (1.1.1-2) ... 318s Selecting previously unselected package python3-pluggy. 318s Preparing to unpack .../098-python3-pluggy_1.5.0-1_all.deb ... 318s Unpacking python3-pluggy (1.5.0-1) ... 318s Selecting previously unselected package python3-pysam. 318s Preparing to unpack .../099-python3-pysam_0.23.0+ds-1build1_armhf.deb ... 318s Unpacking python3-pysam (0.23.0+ds-1build1) ... 318s Selecting previously unselected package python3-pytest. 318s Preparing to unpack .../100-python3-pytest_8.3.5-1_all.deb ... 318s Unpacking python3-pytest (8.3.5-1) ... 318s Selecting previously unselected package samtools. 318s Preparing to unpack .../101-samtools_1.21-1_armhf.deb ... 318s Unpacking samtools (1.21-1) ... 318s Selecting previously unselected package tabix. 318s Preparing to unpack .../102-tabix_1.21+ds-1_armhf.deb ... 318s Unpacking tabix (1.21+ds-1) ... 318s Setting up libpython3.13:armhf (3.13.2-2) ... 318s Setting up libhtscodecs2:armhf (1.6.1-2) ... 318s Setting up dh-python (6.20250308) ... 318s Setting up libgnutls-openssl27t64:armhf (3.8.9-2ubuntu2) ... 318s Setting up python3-iniconfig (1.1.1-2) ... 318s Setting up libzstd-dev:armhf (1.5.6+dfsg-2) ... 318s Setting up libarchive-zip-perl (1.68-1) ... 318s Setting up libdebhelper-perl (13.24.1ubuntu2) ... 318s Setting up libdeflate0:armhf (1.23-1) ... 318s Setting up linux-libc-dev:armhf (6.14.0-10.10) ... 318s Setting up m4 (1.4.19-7) ... 318s Setting up libevent-2.1-7t64:armhf (2.1.12-stable-10) ... 318s Setting up python3-all (3.13.2-2) ... 318s Setting up libgomp1:armhf (15-20250222-0ubuntu1) ... 318s Setting up libpsl-dev:armhf (0.21.2-1.1build1) ... 318s Setting up libdw1t64:armhf (0.192-4) ... 318s Setting up autotools-dev (20220109.1) ... 318s Setting up libunbound8:armhf (1.22.0-1ubuntu1) ... 318s Setting up libpkgconf3:armhf (1.8.1-4) ... 318s Setting up libgmpxx4ldbl:armhf (2:6.3.0+dfsg-3ubuntu1) ... 318s Setting up rpcsvc-proto (1.4.2-0ubuntu7) ... 318s Setting up libgnutls-dane0t64:armhf (3.8.9-2ubuntu2) ... 318s Setting up libgssrpc4t64:armhf (1.21.3-4ubuntu2) ... 318s Setting up libldap-dev:armhf (2.6.9+dfsg-1~exp2ubuntu1) ... 318s Setting up libssl-dev:armhf (3.4.1-1ubuntu1) ... 318s Setting up libmpc3:armhf (1.3.1-1build2) ... 318s Setting up cython3 (3.0.11+dfsg-2ubuntu2) ... 319s Setting up autopoint (0.23.1-1) ... 319s Setting up pkgconf-bin (1.8.1-4) ... 319s Setting up libidn2-dev:armhf (2.3.7-2build2) ... 319s Setting up autoconf (2.72-3ubuntu1) ... 319s Setting up python3-pluggy (1.5.0-1) ... 319s Setting up liblzma-dev:armhf (5.6.4-1) ... 319s Setting up libubsan1:armhf (15-20250222-0ubuntu1) ... 319s Setting up dwz (0.15-1build6) ... 319s Setting up libcrypt-dev:armhf (1:4.4.38-1) ... 319s Setting up libasan8:armhf (15-20250222-0ubuntu1) ... 319s Setting up debugedit (1:5.1-2) ... 319s Setting up libhts3t64:armhf (1.21+ds-1) ... 319s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 319s Setting up libgcc-14-dev:armhf (14.2.0-17ubuntu3) ... 319s Setting up libisl23:armhf (0.27-1) ... 319s Setting up libc-dev-bin (2.41-1ubuntu2) ... 319s Setting up libtasn1-6-dev:armhf (4.20.0-2) ... 319s Setting up libdeflate-dev:armhf (1.23-1) ... 319s Setting up tabix (1.21+ds-1) ... 319s Setting up libcc1-0:armhf (15-20250222-0ubuntu1) ... 319s Setting up libbrotli-dev:armhf (1.1.0-2build4) ... 319s Setting up libp11-kit-dev:armhf (0.25.5-2ubuntu3) ... 319s Setting up cpp-14-arm-linux-gnueabihf (14.2.0-17ubuntu3) ... 319s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 319s Setting up libkadm5clnt-mit12:armhf (1.21.3-4ubuntu2) ... 319s Setting up automake (1:1.17-3ubuntu1) ... 319s update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode 319s Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... 319s Setting up gettext (0.23.1-1) ... 319s Setting up python3-pysam (0.23.0+ds-1build1) ... 320s Setting up libgmp-dev:armhf (2:6.3.0+dfsg-3ubuntu1) ... 320s Setting up nettle-dev:armhf (3.10.1-1) ... 320s Setting up libkdb5-10t64:armhf (1.21.3-4ubuntu2) ... 320s Setting up python3-pytest (8.3.5-1) ... 320s Setting up bcftools (1.21-1) ... 320s Setting up gcc-14-arm-linux-gnueabihf (14.2.0-17ubuntu3) ... 320s Setting up pkgconf:armhf (1.8.1-4) ... 320s Setting up samtools (1.21-1) ... 320s Setting up intltool-debian (0.35.0+20060710.6) ... 320s Setting up libjs-sphinxdoc (8.1.3-4) ... 320s Setting up cpp-14 (14.2.0-17ubuntu3) ... 320s Setting up dh-strip-nondeterminism (1.14.1-2) ... 320s Setting up libkadm5srv-mit12:armhf (1.21.3-4ubuntu2) ... 320s Setting up libc6-dev:armhf (2.41-1ubuntu2) ... 320s Setting up libstdc++-14-dev:armhf (14.2.0-17ubuntu3) ... 320s Setting up cpp-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 320s Setting up libbz2-dev:armhf (1.0.8-6) ... 320s Setting up gcc-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 320s Setting up libgnutls28-dev:armhf (3.8.9-2ubuntu2) ... 320s Setting up libnghttp2-dev:armhf (1.64.0-1) ... 320s Setting up g++-14-arm-linux-gnueabihf (14.2.0-17ubuntu3) ... 320s Setting up po-debconf (1.0.21+nmu1) ... 320s Setting up gcc-14 (14.2.0-17ubuntu3) ... 320s Setting up libexpat1-dev:armhf (2.6.4-1) ... 320s Setting up comerr-dev:armhf (2.1-1.47.2-1ubuntu1) ... 320s Setting up zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 320s Setting up cpp (4:14.2.0-1ubuntu1) ... 320s Setting up g++-14 (14.2.0-17ubuntu3) ... 320s Setting up krb5-multidev:armhf (1.21.3-4ubuntu2) ... 320s Setting up g++-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 320s Setting up libtool (2.5.4-4) ... 320s Setting up gcc (4:14.2.0-1ubuntu1) ... 320s Setting up dh-autoreconf (20) ... 320s Setting up libkrb5-dev:armhf (1.21.3-4ubuntu2) ... 320s Setting up libpython3.13-dev:armhf (3.13.2-2) ... 320s Setting up librtmp-dev:armhf (2.4+20151223.gitfa8646d.1-2build7) ... 320s Setting up libssh2-1-dev:armhf (1.11.1-1) ... 320s Setting up g++ (4:14.2.0-1ubuntu1) ... 320s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 320s Setting up build-essential (12.10ubuntu1) ... 320s Setting up libpython3-dev:armhf (3.13.2-2) ... 320s Setting up python3.13-dev (3.13.2-2) ... 320s Setting up debhelper (13.24.1ubuntu2) ... 320s Setting up libcurl4-gnutls-dev:armhf (8.12.1-3ubuntu1) ... 320s Setting up libpython3-all-dev:armhf (3.13.2-2) ... 320s Setting up python3-dev (3.13.2-2) ... 320s Setting up python3-all-dev (3.13.2-2) ... 320s Setting up libhts-dev:armhf (1.21+ds-1) ... 320s Processing triggers for install-info (7.1.1-1) ... 320s Processing triggers for libc-bin (2.41-1ubuntu2) ... 320s Processing triggers for man-db (2.13.0-1) ... 331s autopkgtest [15:55:19]: test command1: export HOME=$PWD && make -C tests/pysam_data && make -C tests/cbcf_data && pytest-3 331s autopkgtest [15:55:19]: test command1: [----------------------- 333s make: Entering directory '/tmp/autopkgtest.IyFJtf/build.i0v/src/tests/pysam_data' 333s samtools faidx ex1.fa 333s samtools view --no-PG -bo ex1.bam -t ex1.fa.fai ex1.sam.gz 333s samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz 333s [mpileup] 1 samples in 1 input files 333s gunzip < ex1.sam.gz > ex1.sam 333s samtools index ex1.bam 333s samtools view --no-PG -h ex1.bam | gzip > ex2.sam.gz 333s gunzip < ex2.sam.gz > ex2.sam 333s samtools view --no-PG -bo ex2.bam ex2.sam 333s samtools index ex2.bam 333s samtools calmd --no-PG --output-fmt BAM ex2.bam ex1.fa > with_md.sam.gz 333s [bam_fillmd1] different NM for read 'EAS139_11:7:46:695:738': 3 -> 8 333s [bam_fillmd1] different NM for read 'EAS218_4:1:48:9:409': 0 -> 5 333s [bam_fillmd1] different NM for read 'B7_591:7:200:192:373': 0 -> 5 333s [bam_fillmd1] different NM for read 'EAS56_65:1:163:846:223': 0 -> 5 333s [bam_fillmd1] different NM for read 'EAS114_30:7:283:799:560': 0 -> 5 333s [bam_fillmd1] different NM for read 'B7_595:4:84:802:737': 0 -> 4 333s [bam_fillmd1] different NM for read 'EAS51_66:5:308:400:602': 0 -> 3 333s [bam_fillmd1] different NM for read 'EAS54_81:2:285:367:932': 0 -> 3 333s [bam_fillmd1] different NM for read 'EAS114_39:1:70:147:84': 0 -> 3 333s [bam_fillmd1] different NM for read 'EAS56_53:1:124:243:35': 2 -> 5 333s [bam_fillmd1] different NM for read 'EAS1_103:2:226:302:758': 2 -> 3 333s [bam_fillmd1] different NM for read 'EAS114_28:6:175:705:982': 1 -> 0 333s [bam_fillmd1] different NM for read 'EAS51_64:4:179:389:585': 7 -> 8 333s [bam_fillmd1] different NM for read 'B7_589:1:122:337:968': 3 -> 2 333s [bam_fillmd1] different NM for read 'B7_610:4:15:805:420': 4 -> 5 333s gunzip < with_md.sam.gz > with_md.sam 333s samtools view --no-PG -bo with_md.bam with_md.sam 333s samtools index with_md.bam 333s samtools view --no-PG -bu -o uncompressed.bam ex2.sam 333s samtools view --no-PG -bo MM-chebi.bam MM-chebi.sam 333s [bam_fillmd1] different NM for read 'B7_591:2:279:124:41': 2 -> 4 333s [bam_fillmd1] different NM for read 'EAS112_32:8:89:254:332': 0 -> 1 333s [bam_fillmd1] different NM for read 'B7_597:7:103:731:697': 0 -> 2 333s [bam_fillmd1] different NM for read 'EAS139_11:2:71:83:58': 0 -> 2 333s [bam_fillmd1] different NM for read 'EAS192_3:4:63:5:870': 0 -> 2 333s [bam_fillmd1] different NM for read 'EAS139_19:2:29:1822:1881': 0 -> 2 333s [bam_fillmd1] different NM for read 'EAS188_7:3:15:568:42': 2 -> 1 333s [bam_fillmd1] different NM for read 'EAS1_95:4:176:971:874': 0 -> 1 333s [bam_fillmd1] different NM for read 'EAS1_99:1:34:649:318': 3 -> 4 333s [bam_fillmd1] different NM for read 'EAS54_65:4:61:346:384': 3 -> 4 333s [bam_fillmd1] different NM for read 'B7_597:6:20:592:496': 0 -> 1 333s [bam_fillmd1] different NM for read 'B7_597:4:38:999:463': 2 -> 1 333s [bam_fillmd1] different NM for read 'EAS114_28:5:23:944:377': 0 -> 3 333s [bam_fillmd1] different NM for read 'EAS219_1:3:90:219:528': 0 -> 3 333s [bam_fillmd1] different NM for read 'EAS1_108:5:89:942:84': 0 -> 4 333s [bam_fillmd1] different NM for read 'EAS1_108:6:159:493:275': 0 -> 5 333s [bam_fillmd1] different NM for read 'EAS139_11:1:81:1019:558': 0 -> 5 333s [bam_fillmd1] different NM for read 'EAS51_62:7:162:195:761': 0 -> 4 333s [bam_fillmd1] different NM for read 'B7_597:3:115:646:430': 0 -> 4 333s [bam_fillmd1] different NM for read 'EAS114_30:6:243:209:110': 0 -> 4 333s [bam_fillmd1] different NM for read 'EAS1_108:2:266:994:429': 0 -> 4 333s [bam_fillmd1] different NM for read 'EAS114_30:5:32:461:154': 0 -> 4 333s [bam_fillmd1] different NM for read 'EAS114_39:6:7:492:1088': 0 -> 4 333s [bam_fillmd1] different NM for read 'EAS1_95:6:174:650:125': 0 -> 4 333s [bam_fillmd1] different NM for read 'EAS56_59:6:89:457:591': 1 -> 5 333s [bam_fillmd1] different NM for read 'EAS114_39:2:38:670:564': 0 -> 4 333s [bam_fillmd1] different NM for read 'EAS188_7:4:92:693:228': 1 -> 6 333s [bam_fillmd1] different NM for read 'EAS218_1:4:61:1369:440': 0 -> 4 333s [bam_fillmd1] different NM for read 'EAS114_26:4:123:1001:580': 0 -> 4 333s [bam_fillmd1] different NM for read 'EAS114_39:4:10:1312:1558': 0 -> 4 333s [bam_fillmd1] different NM for read 'EAS220_1:8:45:178:1321': 0 -> 4 333s [bam_fillmd1] different NM for read 'EAS56_59:5:125:137:58': 0 -> 4 333s [bam_fillmd1] different NM for read 'EAS192_3:3:285:349:797': 1 -> 5 333s [bam_fillmd1] different NM for read 'EAS114_45:5:56:1757:1319': 0 -> 4 333s [bam_fillmd1] different NM for read 'B7_591:3:291:404:199': 0 -> 4 333s [bam_fillmd1] different NM for read 'EAS54_65:7:159:253:353': 0 -> 4 333s [bam_fillmd1] different NM for read 'EAS56_57:1:122:38:103': 0 -> 4 333s [bam_fillmd1] different NM for read 'EAS188_4:5:103:870:105': 0 -> 4 333s [bam_fillmd1] different NM for read 'EAS1_105:8:24:718:322': 3 -> 7 333s [bam_fillmd1] different NM for read 'EAS51_64:6:118:41:489': 0 -> 4 333s [bam_fillmd1] different NM for read 'EAS56_61:3:165:665:220': 0 -> 4 333s [bam_fillmd1] different NM for read 'EAS114_30:6:238:803:383': 0 -> 4 333s [bam_fillmd1] different NM for read 'EAS1_105:3:232:364:583': 0 -> 3 333s [bam_fillmd1] different NM for read 'B7_595:2:29:729:70': 3 -> 4 333s [bam_fillmd1] different NM for read 'EAS114_30:6:220:809:850': 4 -> 6 333s [bam_fillmd1] different NM for read 'EAS54_65:2:264:157:150': 3 -> 5 333s [bam_fillmd1] different NM for read 'B7_595:8:26:242:35': 2 -> 1 333s [bam_fillmd1] different NM for read 'B7_610:7:34:144:868': 4 -> 5 333s [bam_fillmd1] different NM for read 'B7_597:8:147:360:141': 1 -> 2 333s [bam_fillmd1] different NM for read 'EAS139_19:2:82:154:1333': 0 -> 4 333s [bam_fillmd1] different NM for read 'EAS56_63:3:41:468:459': 0 -> 3 333s [bam_fillmd1] different NM for read 'EAS1_97:4:274:287:423': 0 -> 1 333s [bam_fillmd1] different NM for read 'EAS114_30:2:303:428:326': 0 -> 1 333s [bam_fillmd1] different NM for read 'EAS54_71:8:105:854:975': 0 -> 3 333s [W::bam_hdr_read] EOF marker is absent. The input is probably truncated 333s samtools view --no-PG -bo MM-double.bam MM-double.sam 333s samtools view --no-PG -bo MM-explicit.bam MM-explicit.sam 333s samtools view --no-PG -bo MM-multi.bam MM-multi.sam 333s samtools view --no-PG -bo MM-orient.bam MM-orient.sam 333s samtools view --no-PG -bo ex10.bam ex10.sam 333s samtools view --no-PG -bo ex3.bam ex3.sam 333s samtools view --no-PG -bo ex4.bam ex4.sam 333s samtools view --no-PG -bo ex5.bam ex5.sam 333s samtools view --no-PG -bo ex6.bam ex6.sam 333s samtools view --no-PG -bo ex8.bam ex8.sam 333s samtools view --no-PG -bo ex9_fail.bam ex9_fail.sam 333s samtools view --no-PG -bo ex9_nofail.bam ex9_nofail.sam 333s samtools view --no-PG -bo ex_spliced.bam ex_spliced.sam 333s samtools view --no-PG -bo example_aligned_pairs.bam example_aligned_pairs.sam 333s samtools view --no-PG -bo example_btag.bam example_btag.sam 333s samtools view --no-PG -bo example_dash_in_chr.bam example_dash_in_chr.sam 333s samtools view --no-PG -bo example_empty_header.bam example_empty_header.sam 333s samtools view --no-PG -bo example_empty_with_header.bam example_empty_with_header.sam 333s samtools view --no-PG -bo example_reverse_complement.bam example_reverse_complement.sam 333s touch tmp.list 333s samtools view --no-PG -bo example_unmapped_reads_no_sq.bam -t tmp.list example_unmapped_reads_no_sq.sam 333s rm -f tmp.list 333s samtools view --no-PG -bo issue100.bam issue100.sam 333s samtools view --no-PG -bo rg_with_tab.bam rg_with_tab.sam 333s samtools view --no-PG -bo softclip.bam softclip.sam 333s samtools view --no-PG -bo tag_bug.bam tag_bug.sam 333s samtools view --no-PG -bo test_mapped_unmapped.bam test_mapped_unmapped.sam 333s samtools view --no-PG -bo test_query_position.bam test_query_position.sam 333s samtools view --no-PG -bo test_unaligned.bam test_unaligned.sam 333s samtools index MM-chebi.bam 334s samtools index MM-double.bam 334s samtools index MM-explicit.bam 334s samtools index MM-multi.bam 334s samtools index MM-orient.bam 334s samtools index ex10.bam 334s samtools index ex3.bam 334s samtools index ex4.bam 334s samtools index ex5.bam 334s samtools index ex6.bam 334s samtools index ex8.bam 334s samtools index ex9_fail.bam 334s samtools index ex9_nofail.bam 334s samtools index ex_spliced.bam 334s samtools index example_aligned_pairs.bam 334s samtools index example_btag.bam 334s samtools index example_dash_in_chr.bam 334s samtools index example_empty_header.bam 334s samtools index example_empty_with_header.bam 334s samtools index example_reverse_complement.bam 334s samtools index example_unmapped_reads_no_sq.bam 334s samtools index issue100.bam 334s samtools index rg_with_tab.bam 334s samtools index softclip.bam 334s samtools index tag_bug.bam 334s samtools index test_mapped_unmapped.bam 334s samtools index test_query_position.bam 334s samtools index test_unaligned.bam 334s samtools view --no-PG -Co ex1.cram -T ex1.fa ex1.sam 334s samtools view --no-PG -Co ex2.cram -T ex1.fa ex2.sam 334s samtools view --no-PG -Co ex3.cram -T ex1.fa ex3.sam 334s samtools index ex1.cram 334s samtools index ex2.cram 334s samtools index ex3.cram 334s cp ex1.bam example_bai.bam 334s samtools index example_bai.bam 334s mv example_bai.bam.bai example_bai.bai 334s dd if=ex2.bam of=ex2_truncated.bam bs=$((`wc -c < ex2.bam`-512)) count=1 334s (bgzip -d < ex2.bam; printf '\37\0\0\0\1\0\0\0') | bgzip > ex2_corrupt.bam 334s 1+0 records in 334s 1+0 records out 334s 122288 bytes (122 kB, 119 KiB) copied, 0.000195362 s, 626 MB/s 334s grep "^@" ex2.sam | samtools view --no-PG -bo empty.bam - 334s samtools index empty.bam 334s cp ex1.bam explicit_index.bam 334s cp ex1.cram explicit_index.cram 334s gzip < faidx_empty_seq.fq > faidx_empty_seq.fq.gz 334s bgzip < ex1.fa > ex1.fa.gz 334s samtools faidx ex1.fa.gz 334s cp ex1.bam ex1_csi.bam 334s samtools index -c ex1_csi.bam 334s touch all.stamp 334s rm with_md.sam 334s make: Leaving directory '/tmp/autopkgtest.IyFJtf/build.i0v/src/tests/pysam_data' 334s make: Entering directory '/tmp/autopkgtest.IyFJtf/build.i0v/src/tests/cbcf_data' 334s bgzip < example_vcf40.vcf > example_vcf40.vcf.gz 334s tabix -f -p vcf example_vcf40.vcf.gz # create tbi index 334s bcftools index -f example_vcf40.vcf.gz # create csi index 334s bgzip < example_vcf42.vcf > example_vcf42.vcf.gz 334s tabix -f -p vcf example_vcf42.vcf.gz # create tbi index 334s bcftools index -f example_vcf42.vcf.gz # create csi index 334s bgzip < example_vcf42_only_header.vcf > example_vcf42_only_header.vcf.gz 334s tabix -f -p vcf example_vcf42_only_header.vcf.gz # create tbi index 334s bcftools index -f example_vcf42_only_header.vcf.gz # create csi index 334s bgzip < example_vcf42_withcontigs.vcf > example_vcf42_withcontigs.vcf.gz 334s tabix -f -p vcf example_vcf42_withcontigs.vcf.gz # create tbi index 334s bcftools index -f example_vcf42_withcontigs.vcf.gz # create csi index 334s bgzip < example_vcf43.vcf > example_vcf43.vcf.gz 334s tabix -f -p vcf example_vcf43.vcf.gz # create tbi index 334s bcftools index -f example_vcf43.vcf.gz # create csi index 334s bgzip < example_vcf43_with_utf8.vcf > example_vcf43_with_utf8.vcf.gz 334s tabix -f -p vcf example_vcf43_with_utf8.vcf.gz # create tbi index 334s bcftools index -f example_vcf43_with_utf8.vcf.gz # create csi index 334s bgzip < gnomad.vcf > gnomad.vcf.gz 334s tabix -f -p vcf gnomad.vcf.gz # create tbi index 334s bcftools index -f gnomad.vcf.gz # create csi index 334s bgzip < gnomad_fixed.vcf > gnomad_fixed.vcf.gz 334s tabix -f -p vcf gnomad_fixed.vcf.gz # create tbi index 334s bcftools index -f gnomad_fixed.vcf.gz # create csi index 334s bgzip < missing_genotypes.vcf > missing_genotypes.vcf.gz 334s tabix -f -p vcf missing_genotypes.vcf.gz # create tbi index 334s bcftools index -f missing_genotypes.vcf.gz # create csi index 334s bcftools view -O b example_vcf40.vcf.gz -o example_vcf40.bcf 334s bcftools index -f example_vcf40.bcf 334s bcftools view -O b example_vcf42.vcf.gz -o example_vcf42.bcf 334s bcftools index -f example_vcf42.bcf 334s bcftools view -O b example_vcf42_only_header.vcf.gz -o example_vcf42_only_header.bcf 334s bcftools index -f example_vcf42_only_header.bcf 334s bcftools view -O b example_vcf42_withcontigs.vcf.gz -o example_vcf42_withcontigs.bcf 334s bcftools index -f example_vcf42_withcontigs.bcf 334s bcftools view -O b example_vcf43.vcf.gz -o example_vcf43.bcf 334s bcftools index -f example_vcf43.bcf 334s bcftools view -O b example_vcf43_with_utf8.vcf.gz -o example_vcf43_with_utf8.bcf 334s bcftools index -f example_vcf43_with_utf8.bcf 334s bcftools view -O b gnomad.vcf.gz -o gnomad.bcf 334s bcftools index -f gnomad.bcf 334s [W::bcf_hdr_check_sanity] PL should be declared as Number=G 334s bcftools view -O b gnomad_fixed.vcf.gz -o gnomad_fixed.bcf 334s bcftools index -f gnomad_fixed.bcf 334s [W::bcf_hdr_check_sanity] PL should be declared as Number=G 334s bcftools view -O b missing_genotypes.vcf.gz -o missing_genotypes.bcf 334s bcftools index -f missing_genotypes.bcf 334s touch all.stamp 334s make: Leaving directory '/tmp/autopkgtest.IyFJtf/build.i0v/src/tests/cbcf_data' 334s ============================= test session starts ============================== 334s platform linux -- Python 3.13.2, pytest-8.3.5, pluggy-1.5.0 -- /usr/bin/python3 334s cachedir: .pytest_cache 334s rootdir: /tmp/autopkgtest.IyFJtf/build.i0v/src 334s configfile: setup.cfg 334s testpaths: pysam, tests 334s plugins: typeguard-4.4.2 335s collecting ... collected 960 items / 1 skipped 335s 335s tests/AlignedSegment_test.py::TestAlignedSegment::testBlocks PASSED 335s tests/AlignedSegment_test.py::TestAlignedSegment::testCompare PASSED 335s tests/AlignedSegment_test.py::TestAlignedSegment::testEmpty PASSED 335s tests/AlignedSegment_test.py::TestAlignedSegment::testFullReferencePositions PASSED 335s tests/AlignedSegment_test.py::TestAlignedSegment::testHashing PASSED 335s tests/AlignedSegment_test.py::TestAlignedSegment::testLargeRead PASSED 335s tests/AlignedSegment_test.py::TestAlignedSegment::testNoSequence PASSED 335s tests/AlignedSegment_test.py::TestAlignedSegment::testPositions PASSED 335s tests/AlignedSegment_test.py::TestAlignedSegment::testSettingTagInEmptyRead PASSED 335s tests/AlignedSegment_test.py::TestAlignedSegment::testStrOfEmptyRead PASSED 335s tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate PASSED 335s tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate2 PASSED 335s tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateQual PASSED 335s tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateTlen PASSED 335s tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_mapped_reads_are_updated PASSED 335s tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_unmapped_reads_ignore_length PASSED 335s tests/AlignedSegment_test.py::TestAlignedSegment::test_equivalence_matches_only_and_with_seq PASSED 335s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs PASSED 335s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_1character_md PASSED 335s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_bad_type_md PASSED 335s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_hard_clipping PASSED 335s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_lowercase_md PASSED 335s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_match_mismatch PASSED 335s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding PASSED 335s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding_via_cigarstring PASSED 335s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding_with_seq PASSED 335s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip PASSED 335s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip_reference PASSED 335s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_soft_clipping PASSED 335s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_uppercase_md PASSED 335s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_with_malformed_MD_tag PASSED 335s tests/AlignedSegment_test.py::TestAlignedSegment::test_header_accessible PASSED 335s tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_query_length PASSED 335s tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_read_length PASSED 335s tests/AlignedSegment_test.py::TestAlignedSegment::test_query_length_is_limited PASSED 335s tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_asterisk PASSED 335s tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_chromosome PASSED 335s tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_none PASSED 335s tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_not_be_set_to_unknown_chromosome PASSED 335s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_chromosome PASSED 335s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing PASSED 335s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing_without_header PASSED 335s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_without_header PASSED 335s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_not_be_set_to_unknown_chromosome PASSED 335s tests/AlignedSegment_test.py::TestTidMapping::test_unmapped_tid_is_asterisk_in_output PASSED 335s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_asterisk PASSED 335s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_chromosome PASSED 335s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_none PASSED 335s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_not_be_set_to_unknown_chromosome PASSED 335s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_chromosome PASSED 335s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_equal PASSED 335s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing PASSED 335s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing_without_header PASSED 335s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_without_header PASSED 335s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_not_be_set_to_unknown_chromosome PASSED 335s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_unmapped_tid_is_asterisk_in_output PASSED 335s tests/AlignedSegment_test.py::TestCigar::testCigar PASSED 335s tests/AlignedSegment_test.py::TestCigar::testCigarString PASSED 335s tests/AlignedSegment_test.py::TestCigarStats::testStats PASSED 335s tests/AlignedSegment_test.py::TestAlignedPairs::testReferenceBases PASSED 335s tests/AlignedSegment_test.py::TestBaseModifications::testChebi PASSED 335s tests/AlignedSegment_test.py::TestBaseModifications::testDouble PASSED 335s tests/AlignedSegment_test.py::TestBaseModifications::testExplicit PASSED 335s tests/AlignedSegment_test.py::TestBaseModifications::testMulti PASSED 335s tests/AlignedSegment_test.py::TestBaseModifications::testOrient PASSED 335s tests/AlignedSegment_test.py::TestTags::testAddTags PASSED 335s tests/AlignedSegment_test.py::TestTags::testAddTagsType PASSED 335s tests/AlignedSegment_test.py::TestTags::testArrayTags PASSED 335s tests/AlignedSegment_test.py::TestTags::testEmptyTag PASSED 335s tests/AlignedSegment_test.py::TestTags::testLongTags PASSED 335s tests/AlignedSegment_test.py::TestTags::testMDTagComplex PASSED 335s tests/AlignedSegment_test.py::TestTags::testMDTagDeletions PASSED 335s tests/AlignedSegment_test.py::TestTags::testMDTagInsertions PASSED 335s tests/AlignedSegment_test.py::TestTags::testMDTagMatchOnly PASSED 335s tests/AlignedSegment_test.py::TestTags::testMDTagRefSkipping PASSED 335s tests/AlignedSegment_test.py::TestTags::testMDTagSoftClipping PASSED 335s tests/AlignedSegment_test.py::TestTags::testMissingTag PASSED 335s tests/AlignedSegment_test.py::TestTags::testNegativeIntegers PASSED 335s tests/AlignedSegment_test.py::TestTags::testNegativeIntegersWrittenToFile PASSED 335s tests/AlignedSegment_test.py::TestTags::testSetTag PASSED 335s tests/AlignedSegment_test.py::TestTags::testTagParsing PASSED 335s tests/AlignedSegment_test.py::TestTags::testTagsUpdatingFloat PASSED 335s tests/AlignedSegment_test.py::TestCopy::testCopy PASSED 335s tests/AlignedSegment_test.py::TestCopy::testDeepCopy PASSED 335s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_array_tag_invalid_typecode PASSED 335s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_array_tag_invalid_value_type PASSED 335s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_invalid_value_type PASSED 335s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_A PASSED 335s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_C PASSED 335s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_H PASSED 335s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_I PASSED 335s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_S PASSED 335s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_a PASSED 335s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_automated_type_detection PASSED 335s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_c PASSED 335s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_d PASSED 335s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_f PASSED 335s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_i PASSED 335s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_s PASSED 335s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_array_tag_invalid_typecode PASSED 335s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_array_tag_invalid_value_type PASSED 335s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_invalid_value_type PASSED 335s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_A PASSED 335s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_C PASSED 335s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_H PASSED 335s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_I PASSED 335s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_S PASSED 335s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_a PASSED 335s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_automated_type_detection PASSED 335s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_c PASSED 335s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_d PASSED 335s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_f PASSED 335s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_i PASSED 335s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_s PASSED 335s tests/AlignedSegment_test.py::TestEnums::test_cigar_enums_are_defined PASSED 335s tests/AlignedSegment_test.py::TestEnums::test_sam_flags_are_defined PASSED 335s tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_constructed_without_header PASSED 335s tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_written_to_file PASSED 335s tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_id_can_be_set PASSED 335s tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_name_is_not_available PASSED 335s tests/AlignedSegment_test.py::TestForwardStrandValues::test_qualities_are_complemented PASSED 335s tests/AlignedSegment_test.py::TestForwardStrandValues::test_sequence_is_complemented PASSED 335s tests/AlignedSegment_test.py::TestExportImport::test_dict_export PASSED 335s tests/AlignedSegment_test.py::TestExportImport::test_string_export PASSED 335s tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_with_tags PASSED 335s tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_without_tags PASSED 335s tests/AlignedSegment_test.py::TestExportImport::test_to_string_without_alignment_file PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_dict PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_header PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references_without_text PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_text PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_access_works PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_contains_works PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_get_works PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_keys_works PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_len_works PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_setting_raises_error PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_values_works PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_header_content_is_as_expected PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_name_mapping PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_text_access_works PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works PASSED[E::cram_index_load] Could not retrieve index file for '/tmp/autopkgtest.IyFJtf/build.i0v/src/tests/tmp/pysamtests_tmp_check_read_write_l1ugn9o3' 335s [W::sanitise_SQ_lines] Header @SQ length mismatch for ref chr1, 2147483647 vs 1575 335s [E::cram_index_load] Could not retrieve index file for '/tmp/autopkgtest.IyFJtf/build.i0v/src/tests/tmp/pysamtests_tmp_check_read_write_zhgmbl8m' 335s 335s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_contains_works PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_get_works PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_keys_works PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_len_works PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_setting_raises_error PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_values_works PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_name_mapping PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_text_access_works PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_contains_works PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_get_works PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_keys_works PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_len_works PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_setting_raises_error PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_values_works PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_name_mapping PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_text_access_works PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM PASSED 335s tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM PASSED 335s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_all_stepper PASSED 335s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_ignore_overlaps PASSED 335s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper PASSED 335s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_base_quality_threshold PASSED 336s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_ignore_orphans PASSED 336s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_mapping_quality_threshold PASSED 336s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_redo_baq PASSED 336s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_all_stepper PASSED 336s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_ignore_overlaps PASSED 336s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper PASSED 336s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_base_quality_threshold PASSED 336s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_ignore_orphans PASSED 336s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_mapping_quality_threshold PASSED 336s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_redo_baq PASSED 336s tests/AlignmentFilePileup_test.py::TestPileupQueryPosition::testPileup PASSED 336s tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope SKIPPED 336s tests/AlignmentFilePileup_test.py::TestPileupObjects::testPileupColumn PASSED 336s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testInverse PASSED 336s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateAll PASSED 336s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIteratePerContig PASSED 336s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateRanges PASSED 336s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateTruncate PASSED 336s tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testAccessOnClosedIterator PASSED 336s tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStart PASSED 336s tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStr PASSED 336s tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testTruncate PASSED 336s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_depths_are_equal PASSED 336s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_mapping_qualities_are_equal PASSED 336s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_with_reference_are_equal PASSED 336s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_without_reference_are_equal PASSED 336s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_are_equal PASSED 337s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_from_pileups_are_equal PASSED 337s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARQueryLength PASSED 337s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigar PASSED 337s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigarstring PASSED 337s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARflag PASSED 337s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmapq PASSED 337s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmpos PASSED 337s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmrnm PASSED 337s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARpos PASSED 337s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqname PASSED 337s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqqual PASSED 337s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqual PASSED 337s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARquery PASSED 337s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARrname PASSED 337s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARseq PASSED 337s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testOpt PASSED 337s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPairedBools PASSED 337s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPresentOptionalFields PASSED 337s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testTags PASSED 337s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARQueryLength PASSED 337s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigar PASSED 337s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigarstring PASSED 337s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARflag PASSED 337s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmapq PASSED 337s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmpos PASSED 337s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmrnm PASSED 337s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARpos PASSED 337s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqname PASSED 337s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqqual PASSED 337s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqual PASSED 337s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARquery PASSED 337s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARrname PASSED 337s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARseq PASSED 337s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testOpt PASSED 337s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPairedBools PASSED 337s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPresentOptionalFields PASSED 337s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testTags PASSED 337s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARQueryLength PASSED 337s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigar PASSED 338s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigarstring PASSED 338s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARflag PASSED 338s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmapq PASSED 339s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmpos PASSED 339s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmrnm PASSED 339s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARpos PASSED 339s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqname PASSED 340s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqqual PASSED 340s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqual PASSED 340s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARquery PASSED 341s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARrname PASSED 341s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARseq PASSED 341s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testOpt PASSED 342s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPairedBools PASSED 342s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPresentOptionalFields PASSED 342s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testTags PASSED 342s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARQueryLength PASSED 342s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigar PASSED 342s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigarstring PASSED 342s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARflag PASSED 342s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmapq PASSED 342s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmpos PASSED 342s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmrnm PASSED 342s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARpos PASSED 342s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqname PASSED 342s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqqual PASSED 342s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqual PASSED 342s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARquery PASSED 342s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARrname PASSED 342s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARseq PASSED 342s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testOpt PASSED 342s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPairedBools PASSED 342s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPresentOptionalFields PASSED 342s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testTags PASSED 343s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARQueryLength PASSED 343s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigar PASSED 343s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigarstring PASSED 343s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARflag PASSED 344s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmapq PASSED 344s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmpos PASSED 344s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmrnm PASSED 345s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARpos PASSED 345s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqname PASSED 345s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqqual PASSED 346s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqual PASSED 346s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARquery PASSED 346s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARrname PASSED 347s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARseq PASSED 347s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testOpt PASSED 347s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPairedBools PASSED 348s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPresentOptionalFields PASSED 348s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testTags PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARQueryLength PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigar PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigarstring PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARflag PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmapq PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmpos PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmrnm PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARpos PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqname PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqqual PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqual PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARquery PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARrname PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARseq PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testOpt PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPairedBools PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPresentOptionalFields PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testTags PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARQueryLength PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigar PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigarstring PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARflag PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmapq PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmpos PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmrnm PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARpos PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqname PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqqual PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqual PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARquery PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARrname PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARseq PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testOpt PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPairedBools PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPresentOptionalFields PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testTags PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARQueryLength PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigar PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigarstring PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARflag PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmapq PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmpos PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmrnm PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARpos PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqname PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqqual PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqual PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARquery PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARrname PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARseq PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testOpt PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPairedBools PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPresentOptionalFields PASSED 348s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testTags PASSED 348s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARQueryLength PASSED 348s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigar PASSED 348s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigarstring PASSED 348s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARflag PASSED 348s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmapq PASSED 348s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmpos PASSED 348s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmrnm PASSED 348s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARpos PASSED 348s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqname PASSED 348s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqqual PASSED 348s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqual PASSED 348s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARquery PASSED 348s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARrname PASSED 348s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARseq PASSED 348s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testOpt PASSED 348s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPairedBools PASSED 348s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPresentOptionalFields PASSED 348s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testTags PASSED 348s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARQueryLength PASSED 348s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigar PASSED 348s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigarstring PASSED 348s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARflag PASSED 348s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmapq PASSED 348s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmpos PASSED 348s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmrnm PASSED 348s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARpos PASSED 348s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqname PASSED 348s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqqual PASSED 348s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqual PASSED 348s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARquery PASSED 348s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARrname PASSED 348s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARseq PASSED 348s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testOpt PASSED 348s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPairedBools PASSED 348s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPresentOptionalFields PASSED 348s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testTags PASSED 348s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARQueryLength PASSED 349s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigar PASSED 349s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigarstring PASSED 349s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARflag PASSED 349s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmapq PASSED 350s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmpos PASSED 350s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmrnm PASSED 350s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARpos PASSED 351s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqname PASSED 351s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqqual PASSED 352s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqual PASSED 352s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARquery PASSED 352s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARrname PASSED 353s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARseq PASSED 353s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testOpt PASSED 353s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPairedBools PASSED 354s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPresentOptionalFields PASSED 354s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testTags PASSED 354s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARQueryLength PASSED 354s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigar PASSED 355s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigarstring PASSED 355s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARflag PASSED 355s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmapq PASSED 356s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmpos PASSED 356s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmrnm PASSED 356s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARpos PASSED 357s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqname PASSED 357s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqqual PASSED 357s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqual PASSED 358s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARquery PASSED 358s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARrname PASSED 358s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARseq PASSED 359s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testOpt PASSED 359s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPairedBools PASSED 359s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPresentOptionalFields PASSED 359s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testTags PASSED 359s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARQueryLength PASSED 359s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigar PASSED 359s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigarstring PASSED 359s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARflag PASSED 360s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmapq PASSED 360s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmpos PASSED 360s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmrnm PASSED 360s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARpos PASSED 360s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqname PASSED 360s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqqual PASSED 360s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqual PASSED 360s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARquery PASSED 360s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARrname PASSED 360s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARseq PASSED 360s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testOpt PASSED 360s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPairedBools PASSED 360s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPresentOptionalFields PASSED 360s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testRaises PASSED 360s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testTags PASSED 360s tests/AlignmentFile_test.py::TestIO::testBAM2BAM PASSED 360s tests/AlignmentFile_test.py::TestIO::testBAM2SAM PASSED 360s tests/AlignmentFile_test.py::TestIO::testBAMWithCSIIndex PASSED 360s tests/AlignmentFile_test.py::TestIO::testBAMWithShortBAI PASSED 360s tests/AlignmentFile_test.py::TestIO::testBAMWithoutAlignedSegments PASSED 360s tests/AlignmentFile_test.py::TestIO::testCRAM2BAM PASSED 361s tests/AlignmentFile_test.py::TestIO::testCRAM2CRAM PASSED 361s tests/AlignmentFile_test.py::TestIO::testCRAM2SAM PASSED 361s tests/AlignmentFile_test.py::TestIO::testEmptyBAM PASSED 361s tests/AlignmentFile_test.py::TestIO::testEmptyWithHeaderBAM PASSED 361s tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFile PASSED 361s tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject PASSED 361s tests/AlignmentFile_test.py::TestIO::testHead PASSED 361s tests/AlignmentFile_test.py::TestIO::testOpenFromFilename PASSED 361s tests/AlignmentFile_test.py::TestIO::testReadBamWithoutTargetNames PASSED 361s tests/AlignmentFile_test.py::TestIO::testReadSamWithoutTargetNames PASSED 361s tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex PASSED 361s tests/AlignmentFile_test.py::TestIO::testSAM2BAM PASSED 362s tests/AlignmentFile_test.py::TestIO::testSAM2CRAM PASSED 362s tests/AlignmentFile_test.py::TestIO::testSAM2SAM PASSED 362s tests/AlignmentFile_test.py::TestIO::testSAM2SAMWithoutHeader PASSED 363s tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile PASSED 363s tests/AlignmentFile_test.py::TestIO::test_accessing_attributes_in_closed_file_raises_errors PASSED 363s tests/AlignmentFile_test.py::TestIO::test_fail_read_sam_without_header PASSED 363s tests/AlignmentFile_test.py::TestIO::test_fail_when_reading_unformatted_files PASSED 363s tests/AlignmentFile_test.py::TestIO::test_fetch_by_tid PASSED 363s tests/AlignmentFile_test.py::TestIO::test_header_available_after_closing_file [E::hts_open_format] Failed to open file "missing_directory/new_file.bam" : No such file or directory 363s PASSED 363s tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_with_header_without_header_check PASSED 363s tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_without_header_with_refs PASSED 363s tests/AlignmentFile_test.py::TestIO::test_reference_name_available_after_closing_file PASSED 363s tests/AlignmentFile_test.py::TestIO::test_write_bam_to_unknown_path_fails PASSED 363s tests/AlignmentFile_test.py::TestAutoDetect::testBAM PASSED 363s tests/AlignmentFile_test.py::TestAutoDetect::testCRAM PASSED 363s tests/AlignmentFile_test.py::TestAutoDetect::testSAM PASSED 363s tests/AlignmentFile_test.py::TestIteratorRowBAM::testIteratePerContig PASSED 363s tests/AlignmentFile_test.py::TestIteratorRowBAM::testIterateRanges PASSED 363s tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate PASSED 365s tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIteratePerContig PASSED 376s tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIterateRanges PASSED 377s tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIteratePerContig PASSED 388s tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIterateRanges PASSED 388s tests/AlignmentFile_test.py::TestFloatTagBug::testFloatTagBug PASSED 388s tests/AlignmentFile_test.py::TestLargeFieldBug::testLargeFileBug PASSED 388s tests/AlignmentFile_test.py::TestClipping::testClipping PASSED 388s tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_bam_with_until_eof_reads_unmapped_reads PASSED 388s tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_sam_with_until_eof_reads_unmapped_reads [E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory 388s [E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory 388s [E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory 388s [E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory 388s PASSED 388s tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads PASSED 388s tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads_by_contig PASSED 388s tests/AlignmentFile_test.py::TestContextManager::testManager PASSED 388s tests/AlignmentFile_test.py::TestMultiThread::testSingleThreadEqualsMultithread PASSED 388s tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED 388s tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED 388s tests/AlignmentFile_test.py::TestExceptions::testBadContig PASSED 388s tests/AlignmentFile_test.py::TestExceptions::testMeaninglessCrap PASSED 388s tests/AlignmentFile_test.py::TestExceptions::testMissingFile PASSED 388s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangNewFormat PASSED 388s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeNewFormat PASSED 388s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeOldFormat PASSED 388s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeNewFormat PASSED 388s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeOldFormat PASSED 388s tests/AlignmentFile_test.py::TestExceptions::testZeroToZero PASSED 388s tests/AlignmentFile_test.py::TestWrongFormat::testOpenBamAsSam PASSED 388s tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsBam PASSED 388s tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsSam PASSED 388s tests/AlignmentFile_test.py::TestWrongFormat::testOpenSamAsBam PASSED 388s tests/AlignmentFile_test.py::TestRegionParsing::test_dash_in_chr PASSED 388s tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile PASSED 388s tests/AlignmentFile_test.py::TestDeNovoConstruction::test_pass_if_reads_binary_equal PASSED 388s tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader PASSED 388s tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_in_header PASSED 388s tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_with_null_bytes_in_header PASSED 388s tests/AlignmentFile_test.py::TestMismatchingHeader::testMismatchingHeader PASSED 389s tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader PASSED 389s tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2 PASSED 389s tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator [W::bam_hdr_read] EOF marker is absent. The input is probably truncated 389s [E::bgzf_read_block] Failed to read BGZF block data at offset 105176 expected 17578 bytes; hread returned 17094 389s [E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes 389s PASSED 389s tests/AlignmentFile_test.py::TestCorruptBAM::testCorruptBamIterator PASSED 389s tests/AlignmentFile_test.py::TestBTagSam::testReadTags PASSED 389s tests/AlignmentFile_test.py::TestBTagSam::testReadWriteTags PASSED 389s tests/AlignmentFile_test.py::TestBTagBam::testReadTags PASSED 389s tests/AlignmentFile_test.py::TestBTagBam::testReadWriteTags PASSED 389s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetch PASSED 389s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchUntilEOF PASSED 389s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionFalseTrue PASSED 389s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueFalse PASSED 389s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueTrue PASSED 389s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetch PASSED 390s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchUntilEOF PASSED 390s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionFalseTrue PASSED 391s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueFalse PASSED 392s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueTrue PASSED 393s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetch PASSED 393s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchUntilEOF PASSED 394s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionFalseTrue PASSED 395s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueFalse PASSED 396s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueTrue PASSED 396s tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetch PASSED 396s tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetchAll PASSED 396s tests/AlignmentFile_test.py::TestRemoteFileHTTP::testView PASSED 396s tests/AlignmentFile_test.py::TestLargeOptValues::testBAM PASSED 396s tests/AlignmentFile_test.py::TestLargeOptValues::testSAM PASSED 396s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_counts_as_expected PASSED 396s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_nofilter PASSED 396s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_quality_filter PASSED 396s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_all PASSED 396s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_callback PASSED 396s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_with_coordinates_works PASSED 396s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_without_coordinates_fails PASSED 397s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_wrong_coordinates_fails PASSED 397s tests/AlignmentFile_test.py::TestCountCoverage::test_counting_the_same_region_works PASSED 397s tests/AlignmentFile_test.py::TestFindIntrons::test_all PASSED 397s tests/AlignmentFile_test.py::TestFindIntrons::test_first PASSED 397s tests/AlignmentFile_test.py::TestFindIntrons::test_total PASSED 397s tests/AlignmentFile_test.py::TestLogging::testFail1 PASSED 397s tests/AlignmentFile_test.py::TestLogging::testNoFail1 PASSED 397s tests/AlignmentFile_test.py::TestLogging::testNoFail2 PASSED 397s tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testCount PASSED 397s tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testIndexStats PASSED 398s tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testMate PASSED 398s tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct PASSED 398s tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct_per_chromosome PASSED 398s tests/AlignmentFile_test.py::TestSamtoolsProxy::testIndex [E::hts_open_format] Failed to open file "missing_file" : No such file or directory 398s PASSED 398s tests/AlignmentFile_test.py::TestSamtoolsProxy::testSort PASSED 398s tests/AlignmentFile_test.py::TestSamtoolsProxy::testView [E::hts_open_format] Failed to open file "missing_file" : No such file or directory 399s PASSED 399s tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED 399s tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM PASSED[W::hts_idx_load3] The index file is older than the data file: /tmp/autopkgtest.IyFJtf/build.i0v/src/tests/pysam_data/ex1.bam.bai 399s 399s tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexCRAM PASSED 399s tests/AlignmentFile_test.py::TestExplicitIndex::testRemoteExplicitIndexBAM PASSED 399s tests/AlignmentFile_test.py::TestVerbosity::testVerbosity PASSED 399s tests/AlignmentFile_test.py::TestSanityCheckingBAM::test_empty_read_gives_value_error PASSED 399s tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_bam PASSED 399s tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_cram SKIPPED 399s tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_sam PASSED 399s tests/StreamFiledescriptors_test.py::StreamTest::test_samtools_processing SKIPPED 399s tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing PASSED 399s tests/VariantFile_test.py::TestMissingGenotypes::testVCF PASSED 399s tests/VariantFile_test.py::TestMissingGenotypes::testVCFGZ PASSED 399s tests/VariantFile_test.py::TestMissingSamples::testVCF PASSED 399s tests/VariantFile_test.py::TestMissingSamples::testVCFGZ [W::bcf_hdr_check_sanity] PL should be declared as Number=G 399s [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 399s [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) 399s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 399s [E::hts_open_format] Failed to open file "missing_file.vcf" : No such file or directory 399s [E::hts_open_format] Failed to open file "missing_file.vcf.gz" : No such file or directory 399s PASSED 399s tests/VariantFile_test.py::TestMissingSamplesFixed::testVCF PASSED 399s tests/VariantFile_test.py::TestMissingSamplesFixed::testVCFGZ PASSED 399s tests/VariantFile_test.py::TestOpening::testDetectBCF PASSED 399s tests/VariantFile_test.py::TestOpening::testDetectVCF PASSED 399s tests/VariantFile_test.py::TestOpening::testDetectVCFGZ PASSED 399s tests/VariantFile_test.py::TestOpening::testEmptyFileVCF PASSED 399s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFFromPath PASSED 399s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZOnlyHeader PASSED 399s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithIndex PASSED 399s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithoutIndex PASSED 399s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFOnlyHeader PASSED 399s tests/VariantFile_test.py::TestOpening::testMissingFile PASSED 399s tests/VariantFile_test.py::TestOpening::testMissingFileVCFGZ PASSED 399s tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_csi_index PASSED 399s tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_prebuilt_csi PASSED 399s tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_tbi_index_will_produce_csi PASSED 399s tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_csi_index PASSED 399s tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_tbi_index PASSED 399s tests/VariantFile_test.py::TestHeader::testIterator PASSED 399s tests/VariantFile_test.py::TestHeader::testStr PASSED 399s tests/VariantFile_test.py::TestParsing::testAlleles PASSED 399s tests/VariantFile_test.py::TestParsing::testAllelesVariantTypes PASSED 399s tests/VariantFile_test.py::TestParsing::testAlt PASSED 399s tests/VariantFile_test.py::TestParsing::testChrom PASSED 399s tests/VariantFile_test.py::TestParsing::testChromFromPath PASSED 399s tests/VariantFile_test.py::TestParsing::testFilter PASSED 399s tests/VariantFile_test.py::TestParsing::testFormat PASSED 399s tests/VariantFile_test.py::TestParsing::testId PASSED 399s tests/VariantFile_test.py::TestParsing::testInfo PASSED 399s tests/VariantFile_test.py::TestParsing::testPos PASSED 399s tests/VariantFile_test.py::TestParsing::testQual PASSED 399s tests/VariantFile_test.py::TestParsing::testRef PASSED 399s tests/VariantFile_test.py::TestParsing::testSampleAlleleIndices PASSED 399s tests/VariantFile_test.py::TestParsing::testSampleAlleles PASSED 399s tests/VariantFile_test.py::TestParsing::testSampleFormats PASSED 399s tests/VariantFile_test.py::TestParsing::testStart PASSED 399s tests/VariantFile_test.py::TestParsing::testStop PASSED 399s tests/VariantFile_test.py::TestIndexFilename::testOpen PASSED 399s tests/VariantFile_test.py::TestConstructionVCFWithContigs::testBase PASSED 399s tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionFromCopy PASSED 399s tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithLines PASSED 399s tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithRecords PASSED 399s tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testBase PASSED 399s tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionFromCopy PASSED 399s tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithLines PASSED 399s tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithRecords PASSED 399s tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testBase PASSED 399s tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionFromCopy PASSED 399s tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithLines PASSED 399s tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithRecords PASSED 399s tests/VariantFile_test.py::TestSettingRecordValues::testBase PASSED[W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 399s 399s tests/VariantFile_test.py::TestSettingRecordValues::testGenotype (0, 0) 399s PASSED 399s tests/VariantFile_test.py::TestSettingRecordValues::testSetQual PASSED 399s tests/VariantFile_test.py::TestMultiThreading::testNoMultiThreadingWithIgnoreTruncation PASSED 399s tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 399s PASSED[E::idx_find_and_load] Could not retrieve index file for '/tmp/autopkgtest.IyFJtf/build.i0v/src/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithreadResult_o3jrm6vi.bcf' 399s 399s tests/VariantFile_test.py::TestSubsetting::testSubsetting PASSED 399s 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.) 399s [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) 399s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 399s [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 399s [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) 399s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 399s PASSED 399s tests/VariantFile_test.py::TestUnicode::test_record_with_unicode PASSED 399s tests/VariantRecord_test.py::test_ascii_annotation_can_be_added PASSED 399s tests/VariantRecord_test.py::test_ascii_annotation_with_variable_length_can_be_added PASSED 399s tests/VariantRecord_test.py::test_unicode_annotation_can_be_added PASSED 399s tests/VariantRecord_test.py::test_set_sample_alleles PASSED 399s tests/VariantRecord_test.py::test_repeated_new_record PASSED 399s tests/compile_test.py::test_bam SKIPPED (no pyximport) 399s tests/compile_test.py::test_gtf SKIPPED (no pyximport) 399s tests/faidx_test.py::TestFastaFile::testFetch PASSED 399s tests/faidx_test.py::TestFastaFile::testFetchErrors PASSED 399s tests/faidx_test.py::TestFastaFile::testLength PASSED 399s tests/faidx_test.py::TestFastaFile::testOutOfRangeAccess PASSED 399s tests/faidx_test.py::TestFastaFile::testSequenceLengths PASSED 399s tests/faidx_test.py::TestFastaFile::test_fetch_with_region_and_contig_raises_exception PASSED 399s tests/faidx_test.py::TestFastaFile::test_fetch_with_region_is_equivalent PASSED 399s tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED 399s tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_index_succeeds PASSED 399s tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_without_index_succeeds PASSED 399s tests/faidx_test.py::TestFastaFilePathIndex::test_raise_exception_if_index_is_missing PASSED 399s tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED 399s tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_index_succeeds PASSED 399s tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_without_index_succeeds PASSED 399s tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_raise_exception_if_index_is_missing PASSED 399s tests/faidx_test.py::TestFastxFileFastq::testCounts PASSED 400s tests/faidx_test.py::TestFastxFileFastq::testManager PASSED 400s tests/faidx_test.py::TestFastxFileFastq::testMissingFile PASSED 400s tests/faidx_test.py::TestFastxFileFastq::testSequence PASSED 400s tests/faidx_test.py::TestFastqFileFastq::testCounts PASSED 400s tests/faidx_test.py::TestFastqFileFastq::testManager PASSED 400s tests/faidx_test.py::TestFastqFileFastq::testMissingFile PASSED 400s tests/faidx_test.py::TestFastqFileFastq::testSequence PASSED 400s tests/faidx_test.py::TestFastxFileFasta::testCounts PASSED 400s tests/faidx_test.py::TestFastxFileFasta::testManager PASSED 400s tests/faidx_test.py::TestFastxFileFasta::testMissingFile PASSED 400s tests/faidx_test.py::TestFastxFileFasta::testSequence PASSED 400s tests/faidx_test.py::TestFastxFileFastqStream::testCounts PASSED 400s tests/faidx_test.py::TestFastxFileFastqStream::testManager PASSED 400s tests/faidx_test.py::TestFastxFileFastqStream::testMissingFile PASSED 400s tests/faidx_test.py::TestFastxFileFastqStream::testSequence PASSED 400s tests/faidx_test.py::TestFastxFileWithEmptySequence::testIteration PASSED 400s tests/faidx_test.py::TestRemoteFileFTP::testFTPView PASSED 400s tests/faidx_test.py::TestRemoteFileFTP::test_sequence_lengths_are_available PASSED 400s tests/faidx_test.py::TestFastqRecord::test_fastx_record_can_be_created_from_scratch PASSED 400s tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_None PASSED 400s tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_modified PASSED 400s tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_name_is_None PASSED 400s tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_quality_is_wrong_length PASSED 400s tests/faidx_test.py::TestFastqRecord::test_fastx_record_name_can_be_modified PASSED 400s tests/faidx_test.py::TestFastqRecord::test_fastx_record_quality_can_be_modified PASSED 400s tests/faidx_test.py::TestFastqRecord::test_fastx_record_sequence_can_be_modified PASSED 400s tests/faidx_test.py::TestFastqProxy::test_fastq_proxy_instantiation_raises_error PASSED 400s tests/linking_test.py::TestLinking::test_package_can_be_installed SKIPPED 400s tests/linking_test.py::TestLinkWithRpath::test_package_can_be_installed SKIPPED 400s tests/linking_test.py::TestLinkWithRpath::test_package_tests_pass SKIPPED 400s tests/linking_test.py::TestLinkWithoutRpath::test_package_can_be_installed SKIPPED 400s tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_fail_on_import SKIPPED 400s tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_pass_if_ld_library_path_set SKIPPED 401s tests/samtools_test.py::SamtoolsTest::testStatements PASSED 401s tests/samtools_test.py::SamtoolsTest::testUsage SKIPPED (skipping us...) 401s tests/samtools_test.py::EmptyIndexTest::testEmptyIndex PASSED 401s tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraArg PASSED 401s tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraFlag PASSED 401s tests/samtools_test.py::TestReturnType::testReturnValueData PASSED 401s tests/samtools_test.py::TestReturnType::testReturnValueString PASSED 401s tests/samtools_test.py::StdoutTest::testDoubleCalling PASSED 401s tests/samtools_test.py::StdoutTest::testSaveStdout PASSED 401s tests/samtools_test.py::StdoutTest::testWithRedirectedStdout PASSED 401s tests/samtools_test.py::StdoutTest::testWithoutRedirectedStdout PASSED 402s tests/samtools_test.py::PysamTest::testStatements PASSED 402s tests/samtools_test.py::PysamTest::testUsage SKIPPED (skipping usage...) 402s tests/tabix_test.py::TestIndexing::test_indexing_to_custom_location_works PASSED 402s tests/tabix_test.py::TestIndexing::test_indexing_with_explict_columns_works PASSED 402s tests/tabix_test.py::TestIndexing::test_indexing_with_lineskipping_works PASSED 402s tests/tabix_test.py::TestIndexing::test_indexing_with_preset_works PASSED 402s tests/tabix_test.py::TestCompression::testCompression PASSED 402s tests/tabix_test.py::TestCompression::testIndexPresetCompressed PASSED 402s tests/tabix_test.py::TestCompression::testIndexPresetUncompressed PASSED 402s tests/tabix_test.py::TestCompressionSam::testCompression PASSED 402s tests/tabix_test.py::TestCompressionSam::testIndexPresetCompressed PASSED 402s tests/tabix_test.py::TestCompressionSam::testIndexPresetUncompressed PASSED 402s tests/tabix_test.py::TestCompressionBed::testCompression PASSED 402s tests/tabix_test.py::TestCompressionBed::testIndexPresetCompressed PASSED 402s tests/tabix_test.py::TestCompressionBed::testIndexPresetUncompressed PASSED 402s tests/tabix_test.py::TestCompressionVCF::testCompression PASSED 402s tests/tabix_test.py::TestCompressionVCF::testIndexPresetCompressed PASSED 402s tests/tabix_test.py::TestCompressionVCF::testIndexPresetUncompressed PASSED 402s tests/tabix_test.py::TestGZFile::testAll PASSED 402s tests/tabix_test.py::TestIterationWithoutComments::testAll PASSED 402s tests/tabix_test.py::TestIterationWithoutComments::testGetContigs PASSED 402s tests/tabix_test.py::TestIterationWithoutComments::testHeader PASSED 402s tests/tabix_test.py::TestIterationWithoutComments::testInvalidIntervals PASSED 402s tests/tabix_test.py::TestIterationWithoutComments::testPerContig PASSED 402s tests/tabix_test.py::TestIterationWithoutComments::testPerContig2 PASSED 402s tests/tabix_test.py::TestIterationWithoutComments::testPerContigFromStart PASSED 402s tests/tabix_test.py::TestIterationWithoutComments::testPerContigToEnd PASSED 402s tests/tabix_test.py::TestIterationWithoutComments::testPerInterval PASSED 402s tests/tabix_test.py::TestIterationWithoutComments::testRegionStrings PASSED 403s tests/tabix_test.py::TestIterationWithoutComments::testReopening PASSED 403s tests/tabix_test.py::TestIterationWithComments::testAll PASSED 403s tests/tabix_test.py::TestIterationWithComments::testGetContigs PASSED 403s tests/tabix_test.py::TestIterationWithComments::testHeader PASSED 403s tests/tabix_test.py::TestIterationWithComments::testInvalidIntervals PASSED 403s tests/tabix_test.py::TestIterationWithComments::testPerContig PASSED 403s tests/tabix_test.py::TestIterationWithComments::testPerContig2 PASSED 403s tests/tabix_test.py::TestIterationWithComments::testPerContigFromStart PASSED 403s tests/tabix_test.py::TestIterationWithComments::testPerContigToEnd PASSED 403s tests/tabix_test.py::TestIterationWithComments::testPerInterval PASSED 403s tests/tabix_test.py::TestIterationWithComments::testRegionStrings PASSED 403s tests/tabix_test.py::TestIterationWithComments::testReopening PASSED 403s tests/tabix_test.py::TestIterators::testClosedFile PASSED 403s tests/tabix_test.py::TestIterators::testClosedFileIteration PASSED 403s tests/tabix_test.py::TestIterators::testIteration PASSED 403s tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFile PASSED 403s tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFileIteration PASSED 403s tests/tabix_test.py::TestIteratorsGenericCompressed::testIteration PASSED 403s tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFile PASSED 403s tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFileIteration PASSED 403s tests/tabix_test.py::TestIteratorsFileCompressed::testIteration PASSED 403s tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFile PASSED 403s tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFileIteration PASSED 403s tests/tabix_test.py::TestIteratorsFileUncompressed::testIteration PASSED 403s tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooFewFields PASSED 403s tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooManyFields PASSED 403s tests/tabix_test.py::TestBed::testRead PASSED 403s tests/tabix_test.py::TestBed::testWrite PASSED 403s tests/tabix_test.py::TestUnicode::testFromTabix PASSED 403s tests/tabix_test.py::TestUnicode::testFromVCF PASSED 403s tests/tabix_test.py::TestVCFFromTabix::testRead PASSED 403s tests/tabix_test.py::TestVCFFromTabix::testWrite PASSED 403s tests/tabix_test.py::TestVCFFromVCF::testConnecting PASSED 403s tests/tabix_test.py::TestVCFFromVCF::testParsing PASSED 403s tests/tabix_test.py::VCFFromTabixTest_10::testRead PASSED 403s tests/tabix_test.py::VCFFromTabixTest_10::testWrite PASSED 403s tests/tabix_test.py::VCFFromVCFTest_10::testConnecting PASSED 404s tests/tabix_test.py::VCFFromVCFTest_10::testParsing PASSED 404s tests/tabix_test.py::VCFFromTabixTest_11::testRead PASSED 404s tests/tabix_test.py::VCFFromTabixTest_11::testWrite PASSED 404s tests/tabix_test.py::VCFFromVCFTest_11::testConnecting PASSED 404s tests/tabix_test.py::VCFFromVCFTest_11::testParsing PASSED 404s tests/tabix_test.py::VCFFromTabixTest_12::testRead PASSED 404s tests/tabix_test.py::VCFFromTabixTest_12::testWrite PASSED 404s tests/tabix_test.py::VCFFromVCFTest_12::testConnecting PASSED 404s tests/tabix_test.py::VCFFromVCFTest_12::testParsing PASSED 404s tests/tabix_test.py::VCFFromTabixTest_13::testRead PASSED 404s tests/tabix_test.py::VCFFromTabixTest_13::testWrite PASSED 404s tests/tabix_test.py::VCFFromVCFTest_13::testConnecting PASSED 404s tests/tabix_test.py::VCFFromVCFTest_13::testParsing PASSED 405s tests/tabix_test.py::VCFFromTabixTest_15::testRead PASSED 405s tests/tabix_test.py::VCFFromTabixTest_15::testWrite PASSED 405s tests/tabix_test.py::VCFFromVCFTest_15::testConnecting PASSED 405s tests/tabix_test.py::VCFFromVCFTest_15::testParsing PASSED 405s tests/tabix_test.py::VCFFromTabixTest_16::testRead PASSED 405s tests/tabix_test.py::VCFFromTabixTest_16::testWrite PASSED 405s tests/tabix_test.py::VCFFromVCFTest_16::testConnecting PASSED 405s tests/tabix_test.py::VCFFromVCFTest_16::testParsing PASSED 405s tests/tabix_test.py::VCFFromTabixTest_18::testRead PASSED 405s tests/tabix_test.py::VCFFromTabixTest_18::testWrite PASSED 405s tests/tabix_test.py::VCFFromVCFTest_18::testConnecting PASSED 406s tests/tabix_test.py::VCFFromVCFTest_18::testParsing PASSED 406s tests/tabix_test.py::VCFFromTabixTest_2::testRead PASSED 406s tests/tabix_test.py::VCFFromTabixTest_2::testWrite PASSED 406s tests/tabix_test.py::VCFFromVCFTest_2::testConnecting PASSED 406s tests/tabix_test.py::VCFFromVCFTest_2::testParsing PASSED 406s tests/tabix_test.py::VCFFromTabixTest_20::testRead PASSED 406s tests/tabix_test.py::VCFFromTabixTest_20::testWrite PASSED 406s tests/tabix_test.py::VCFFromVCFTest_20::testConnecting PASSED 406s tests/tabix_test.py::VCFFromVCFTest_20::testParsing PASSED 406s tests/tabix_test.py::VCFFromTabixTest_21::testRead PASSED 406s tests/tabix_test.py::VCFFromTabixTest_21::testWrite PASSED 406s tests/tabix_test.py::VCFFromVCFTest_21::testConnecting PASSED 406s tests/tabix_test.py::VCFFromVCFTest_21::testParsing PASSED 406s tests/tabix_test.py::VCFFromTabixTest_22::testRead PASSED 406s tests/tabix_test.py::VCFFromTabixTest_22::testWrite PASSED 406s tests/tabix_test.py::VCFFromVCFTest_22::testConnecting PASSED 407s tests/tabix_test.py::VCFFromVCFTest_22::testParsing PASSED 407s tests/tabix_test.py::VCFFromTabixTest_23::testRead PASSED 407s tests/tabix_test.py::VCFFromTabixTest_23::testWrite PASSED 407s tests/tabix_test.py::VCFFromVCFTest_23::testConnecting PASSED 407s tests/tabix_test.py::VCFFromVCFTest_23::testParsing PASSED 407s tests/tabix_test.py::VCFFromTabixTest_24::testRead PASSED 407s tests/tabix_test.py::VCFFromTabixTest_24::testWrite PASSED 407s tests/tabix_test.py::VCFFromVCFTest_24::testConnecting PASSED 407s tests/tabix_test.py::VCFFromVCFTest_24::testParsing PASSED 407s tests/tabix_test.py::VCFFromTabixTest_3::testRead PASSED 407s tests/tabix_test.py::VCFFromTabixTest_3::testWrite PASSED 407s tests/tabix_test.py::VCFFromVCFTest_3::testConnecting PASSED 407s tests/tabix_test.py::VCFFromVCFTest_3::testParsing PASSED 408s tests/tabix_test.py::VCFFromTabixTest_4::testRead PASSED 408s tests/tabix_test.py::VCFFromTabixTest_4::testWrite PASSED 408s tests/tabix_test.py::VCFFromVCFTest_4::testConnecting PASSED 408s tests/tabix_test.py::VCFFromVCFTest_4::testParsing PASSED 408s tests/tabix_test.py::VCFFromTabixTest_5::testRead PASSED 408s tests/tabix_test.py::VCFFromTabixTest_5::testWrite PASSED 408s tests/tabix_test.py::VCFFromVCFTest_5::testConnecting PASSED 408s tests/tabix_test.py::VCFFromVCFTest_5::testParsing PASSED 408s tests/tabix_test.py::VCFFromTabixTest_6::testRead PASSED 409s tests/tabix_test.py::VCFFromTabixTest_6::testWrite PASSED 409s tests/tabix_test.py::VCFFromVCFTest_6::testConnecting PASSED 409s tests/tabix_test.py::VCFFromVCFTest_6::testParsing PASSED 409s tests/tabix_test.py::VCFFromTabixTest_7::testRead PASSED 409s tests/tabix_test.py::VCFFromTabixTest_7::testWrite PASSED 409s tests/tabix_test.py::VCFFromVCFTest_7::testConnecting PASSED 410s tests/tabix_test.py::VCFFromVCFTest_7::testParsing PASSED 410s tests/tabix_test.py::VCFFromTabixTest_8::testRead PASSED 410s tests/tabix_test.py::VCFFromTabixTest_8::testWrite PASSED 410s tests/tabix_test.py::VCFFromVCFTest_8::testConnecting PASSED 410s tests/tabix_test.py::VCFFromVCFTest_8::testParsing PASSED 410s tests/tabix_test.py::VCFFromTabixTest_9::testRead PASSED 410s tests/tabix_test.py::VCFFromTabixTest_9::testWrite PASSED 410s tests/tabix_test.py::VCFFromVCFTest_9::testConnecting PASSED 410s tests/tabix_test.py::VCFFromVCFTest_9::testParsing PASSED 410s tests/tabix_test.py::VCFFromTabixTest_issue85::testRead PASSED 410s tests/tabix_test.py::VCFFromTabixTest_issue85::testWrite PASSED 410s tests/tabix_test.py::VCFFromVCFTest_issue85::testConnecting PASSED 410s tests/tabix_test.py::VCFFromVCFTest_issue85::testParsing PASSED 410s tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testRead PASSED 410s tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testWrite PASSED 410s tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testConnecting PASSED[W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 410s [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) 410s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 410s 410s tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testParsing PASSED 410s tests/tabix_test.py::TestVCFFromVariantFile::testConnecting PASSED 410s tests/tabix_test.py::TestVCFFromVariantFile::testParsing PASSED 410s tests/tabix_test.py::TestVCFFromVariantFile_10::testConnecting PASSED 410s tests/tabix_test.py::TestVCFFromVariantFile_10::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 410s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:676148 is not defined in the header, assuming Type=String 410s PASSED 410s tests/tabix_test.py::TestVCFFromVariantFile_11::testConnecting PASSED 410s tests/tabix_test.py::TestVCFFromVariantFile_11::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 410s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:669442 is not defined in the header, assuming Type=String 410s PASSED 411s tests/tabix_test.py::TestVCFFromVariantFile_12::testConnecting PASSED 411s tests/tabix_test.py::TestVCFFromVariantFile_12::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String 411s [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String 411s [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String 411s [W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String 411s [W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String 411s [W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String 411s [W::vcf_parse_format_dict2] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String 411s [W::vcf_parse_format_dict2] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String 411s [W::vcf_parse_format_dict2] FORMAT 'GQ' at chr1:1281168 is not defined in the header, assuming Type=String 411s [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) 411s PASSED 411s tests/tabix_test.py::TestVCFFromVariantFile_13::testConnecting PASSED 411s tests/tabix_test.py::TestVCFFromVariantFile_13::testParsing [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::bcf_hrec_check] Invalid tag name: "1000g" 411s [W::bcf_hrec_check] Invalid tag name: "GT:GL:GQ:NR" 411s [W::bcf_hdr_check_sanity] GL should be declared as Number=G 411s [W::bcf_hrec_check] Invalid tag name: "1000g" 411s [W::bcf_hrec_check] Invalid tag name: "GT:GL:GQ:NR" 411s [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse_info] INFO 'MMLQ' is not defined in the header, assuming Type=String 411s [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr17_gl000205_random' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr18' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr19' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr20' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr21' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr22' is not defined in the header. (Quick workaround: index the file with tabix.) 411s PASSED 411s tests/tabix_test.py::TestVCFFromVariantFile_15::testConnecting [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chrUn_gl000214' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chrUn_gl000220' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chrUn_gl000225' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chrX' is not defined in the header. (Quick workaround: index the file with tabix.) 411s PASSED 411s tests/tabix_test.py::TestVCFFromVariantFile_15::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:439104 is not defined in the header, assuming Type=String 411s PASSED 411s tests/tabix_test.py::TestVCFFromVariantFile_16::testConnecting PASSED 411s tests/tabix_test.py::TestVCFFromVariantFile_16::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String 411s PASSED 411s tests/tabix_test.py::TestVCFFromVariantFile_18::testConnecting PASSED 411s 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.) 411s [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String 411s [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String 411s [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String 411s [W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String 411s [W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String 411s [W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String 411s [W::vcf_parse_format_dict2] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String 411s [W::vcf_parse_format_dict2] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String 411s [W::vcf_parse_format_dict2] FORMAT 'GQ' at chr1:1281168 is not defined in the header, assuming Type=String 411s [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) 411s PASSED 411s tests/tabix_test.py::TestVCFFromVariantFile_2::testConnecting PASSED 411s tests/tabix_test.py::TestVCFFromVariantFile_2::testParsing [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 411s [W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String 411s PASSED 411s tests/tabix_test.py::TestVCFFromVariantFile_20::testConnecting [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 411s PASSED 411s tests/tabix_test.py::TestVCFFromVariantFile_20::testParsing [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 411s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 411s PASSED 411s tests/tabix_test.py::TestVCFFromVariantFile_21::testConnecting [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 411s PASSED 411s tests/tabix_test.py::TestVCFFromVariantFile_21::testParsing [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 411s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 411s PASSED 411s tests/tabix_test.py::TestVCFFromVariantFile_22::testConnecting PASSED 412s 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.) 412s [W::vcf_parse_info] INFO 'refseq.name' is not defined in the header, assuming Type=String 412s [W::vcf_parse_info] INFO 'refseq.positionType' is not defined in the header, assuming Type=String 412s [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) 412s PASSED 412s tests/tabix_test.py::TestVCFFromVariantFile_23::testConnecting PASSED 412s tests/tabix_test.py::TestVCFFromVariantFile_23::testParsing [W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String 412s PASSED 412s tests/tabix_test.py::TestVCFFromVariantFile_24::testConnecting [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: 412s #CHROM POS ID REF ALT QUAL FILTER INFO 412s 412s PASSED 412s tests/tabix_test.py::TestVCFFromVariantFile_24::testParsing PASSED 412s tests/tabix_test.py::TestVCFFromVariantFile_3::testConnecting PASSED 412s tests/tabix_test.py::TestVCFFromVariantFile_3::testParsing [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) 412s PASSED 412s tests/tabix_test.py::TestVCFFromVariantFile_4::testConnecting PASSED 412s tests/tabix_test.py::TestVCFFromVariantFile_4::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 412s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:249843 is not defined in the header, assuming Type=String 413s PASSED 413s tests/tabix_test.py::TestVCFFromVariantFile_5::testConnecting PASSED 413s 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.) 413s PASSED 413s tests/tabix_test.py::TestVCFFromVariantFile_6::testConnecting PASSED 413s 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.) 413s [W::vcf_parse_info] INFO 'CallSetAC' is not defined in the header, assuming Type=String 413s [W::vcf_parse_info] INFO 'CallSetAC2' is not defined in the header, assuming Type=String 413s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:669442 is not defined in the header, assuming Type=String 413s PASSED 413s tests/tabix_test.py::TestVCFFromVariantFile_7::testConnecting PASSED 413s 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.) 413s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:249843 is not defined in the header, assuming Type=String 414s PASSED 414s tests/tabix_test.py::TestVCFFromVariantFile_8::testConnecting PASSED 414s 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.) 414s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:676148 is not defined in the header, assuming Type=String 414s PASSED 414s tests/tabix_test.py::TestVCFFromVariantFile_9::testConnecting PASSED 414s tests/tabix_test.py::TestVCFFromVariantFile_9::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) 414s [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String 414s [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String 414s [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String 414s [W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String 414s [W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String 414s [W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String 414s [W::vcf_parse_format_dict2] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String 414s [W::vcf_parse_format_dict2] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String 414s [W::vcf_parse_format_dict2] FORMAT 'GQ' at chr1:1281168 is not defined in the header, assuming Type=String 414s [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) 414s [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) 414s [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) 414s PASSED 414s tests/tabix_test.py::TestVCFFromVariantFile_issue85::testConnecting PASSED 414s tests/tabix_test.py::TestVCFFromVariantFile_issue85::testParsing PASSED 414s tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testConnecting PASSED 414s tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testParsing PASSED 414s tests/tabix_test.py::TestIndexArgument::testFetchAll PASSED 414s tests/tabix_test.py::TestIndexArgument::testLoadIndexWithoutTbiExtension [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) 414s [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) 414s [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) 414s [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) 414s [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) 414s [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) 414s [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) 414s [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) 414s [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) 414s [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) 414s [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) 414s [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) 414s [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) 414s [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) 414s [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) 414s [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) 414s [E::bcf_hdr_parse] Could not parse the header, sample line not found 414s PASSED 414s tests/tabix_test.py::TestBackwardsCompatibility::testBED PASSED 414s tests/tabix_test.py::TestBackwardsCompatibility::testBED0v23 PASSED 414s tests/tabix_test.py::TestBackwardsCompatibility::testBED0v26 PASSED 414s tests/tabix_test.py::TestBackwardsCompatibility::testEmpty PASSED 414s tests/tabix_test.py::TestBackwardsCompatibility::testVCF PASSED 414s tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v23 PASSED 414s tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v26 PASSED 414s tests/tabix_test.py::TestMultipleIterators::testDisjointIterators PASSED 414s tests/tabix_test.py::TestMultipleIterators::testDoubleFetch PASSED 414s tests/tabix_test.py::TestMultipleIterators::testJoinedIterators PASSED 414s tests/tabix_test.py::TestMultipleIterators::testScope PASSED 414s tests/tabix_test.py::TestContextManager::testManager PASSED 414s tests/tabix_test.py::TestMultithreadTabixFile::testMultithreadEqualsSinglethread PASSED 414s tests/tabixproxies_test.py::TestBED::testAssignmentToTargetList PASSED 414s tests/tabixproxies_test.py::TestParser::testAssignmentToTargetList PASSED 414s tests/tabixproxies_test.py::TestParser::testCopy PASSED 414s tests/tabixproxies_test.py::TestParser::testIteratorCompressed PASSED 414s tests/tabixproxies_test.py::TestParser::testIteratorUncompressed PASSED 414s tests/tabixproxies_test.py::TestParser::testRead PASSED 414s tests/tabixproxies_test.py::TestParser::testUnset PASSED 414s tests/tabixproxies_test.py::TestParser::testWrite PASSED 414s tests/tabixproxies_test.py::TestGTF::testAssignmentToTargetList PASSED 414s tests/tabixproxies_test.py::TestGTF::testCopy PASSED 414s tests/tabixproxies_test.py::TestGTF::testIteratorCompressed PASSED 414s tests/tabixproxies_test.py::TestGTF::testIteratorUncompressed PASSED 414s tests/tabixproxies_test.py::TestGTF::testRead PASSED 414s tests/tabixproxies_test.py::TestGTF::testUnset PASSED 414s tests/tabixproxies_test.py::TestGTF::testWrite PASSED 414s tests/tabixproxies_test.py::TestGTF::test_added_attribute_is_output PASSED 414s tests/tabixproxies_test.py::TestGTF::test_asdict_can_be_modified PASSED 414s tests/tabixproxies_test.py::TestGTF::test_asdict_contains_attributes PASSED 414s tests/tabixproxies_test.py::TestGTF::test_setAttribute_makes_changes PASSED 414s tests/tabixproxies_test.py::TestGTF::test_setting_end_is_one_based PASSED 414s tests/tabixproxies_test.py::TestGTF::test_setting_feature_to_none_produces_dot PASSED 414s tests/tabixproxies_test.py::TestGTF::test_setting_fields PASSED 414s tests/tabixproxies_test.py::TestGTF::test_setting_frame_to_none_produces_dot PASSED 414s tests/tabixproxies_test.py::TestGTF::test_setting_score_to_none_produces_dot PASSED 414s tests/tabixproxies_test.py::TestGTF::test_setting_source_to_none_produces_dot PASSED 414s tests/tabixproxies_test.py::TestGTF::test_setting_start_is_one_based PASSED 414s tests/tabixproxies_test.py::TestGTF::test_setting_strand_to_none_produces_dot PASSED 414s tests/tabixproxies_test.py::TestGFF3::testAssignmentToTargetList PASSED 414s tests/tabixproxies_test.py::TestGFF3::testCopy PASSED 414s tests/tabixproxies_test.py::TestGFF3::testIteratorCompressed PASSED 414s tests/tabixproxies_test.py::TestGFF3::testIteratorUncompressed PASSED 414s tests/tabixproxies_test.py::TestGFF3::testRead PASSED 414s tests/tabixproxies_test.py::TestGFF3::testUnset PASSED 414s tests/tabixproxies_test.py::TestGFF3::testWrite PASSED 414s tests/tabixproxies_test.py::TestGFF3::test_added_attribute_is_output PASSED 414s tests/tabixproxies_test.py::TestGFF3::test_asdict_can_be_modified PASSED 414s tests/tabixproxies_test.py::TestGFF3::test_asdict_contains_attributes PASSED 414s tests/tabixproxies_test.py::TestGFF3::test_setAttribute_makes_changes PASSED 414s tests/tabixproxies_test.py::TestGFF3::test_setting_end_is_one_based PASSED 414s tests/tabixproxies_test.py::TestGFF3::test_setting_feature_to_none_produces_dot PASSED 414s tests/tabixproxies_test.py::TestGFF3::test_setting_fields PASSED 414s tests/tabixproxies_test.py::TestGFF3::test_setting_frame_to_none_produces_dot PASSED 414s tests/tabixproxies_test.py::TestGFF3::test_setting_score_to_none_produces_dot PASSED 414s tests/tabixproxies_test.py::TestGFF3::test_setting_source_to_none_produces_dot PASSED 414s tests/tabixproxies_test.py::TestGFF3::test_setting_start_is_one_based PASSED 414s tests/tabixproxies_test.py::TestGFF3::test_setting_strand_to_none_produces_dot PASSED 414s tests/test_samtools_python.py::test_idxstats_parse_split_lines PASSED 414s tests/test_samtools_python.py::test_bedcov_split_lines PASSED 414s tests/test_samtools_python.py::test_idxstats_parse PASSED 414s tests/test_samtools_python.py::test_bedcov PASSED 414s 414s ================== 947 passed, 14 skipped in 79.89s (0:01:19) ================== 415s autopkgtest [15:56:43]: test command1: -----------------------] 419s autopkgtest [15:56:47]: test command1: - - - - - - - - - - results - - - - - - - - - - 419s command1 PASS 422s autopkgtest [15:56:50]: test autodep8-python3: preparing testbed 445s autopkgtest [15:57:13]: testbed dpkg architecture: armhf 447s autopkgtest [15:57:15]: testbed apt version: 2.9.33 451s autopkgtest [15:57:19]: @@@@@@@@@@@@@@@@@@@@ test bed setup 456s autopkgtest [15:57:24]: testbed release detected to be: plucky 464s autopkgtest [15:57:32]: updating testbed package index (apt update) 466s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 466s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 467s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 467s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 467s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 467s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 468s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 468s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [114 kB] 468s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1832 B] 468s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 468s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [312 kB] 468s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [11.1 kB] 468s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 468s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [240 B] 468s Get:15 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 468s Get:16 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 490s Get:17 http://ftpmaster.internal/ubuntu plucky/main Sources [1394 kB] 491s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 493s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 493s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 493s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 510s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 511s Fetched 41.0 MB in 45s (906 kB/s) 512s Reading package lists... 518s autopkgtest [15:58:26]: upgrading testbed (apt dist-upgrade and autopurge) 520s Reading package lists... 520s Building dependency tree... 520s Reading state information... 521s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 521s Starting 2 pkgProblemResolver with broken count: 0 521s Done 521s Entering ResolveByKeep 523s 523s Calculating upgrade... 523s The following packages will be upgraded: 523s libc-bin libc6 locales pinentry-curses python3-jinja2 sos strace 523s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 523s Need to get 8683 kB of archives. 523s After this operation, 23.6 kB of additional disk space will be used. 523s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 527s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 528s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 535s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 536s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf pinentry-curses armhf 1.3.1-2ubuntu3 [40.6 kB] 536s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 536s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 537s Preconfiguring packages ... 537s Fetched 8683 kB in 14s (624 kB/s) 537s (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 ... 64655 files and directories currently installed.) 537s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 537s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 537s Setting up libc6:armhf (2.41-1ubuntu2) ... 538s (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 ... 64655 files and directories currently installed.) 538s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 538s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 538s Setting up libc-bin (2.41-1ubuntu2) ... 538s (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 ... 64655 files and directories currently installed.) 538s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 538s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 538s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 538s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 538s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_armhf.deb ... 538s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 538s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 538s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 538s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 539s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 539s Setting up sos (4.9.0-5) ... 539s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 539s Setting up locales (2.41-1ubuntu2) ... 540s Generating locales (this might take a while)... 542s en_US.UTF-8... done 542s Generation complete. 542s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 542s Setting up strace (6.13+ds-1ubuntu1) ... 542s Processing triggers for man-db (2.13.0-1) ... 543s Processing triggers for systemd (257.3-1ubuntu3) ... 546s Reading package lists... 546s Building dependency tree... 546s Reading state information... 546s Starting pkgProblemResolver with broken count: 0 547s Starting 2 pkgProblemResolver with broken count: 0 547s Done 547s Solving dependencies... 547s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 549s autopkgtest [15:58:57]: rebooting testbed after setup commands that affected boot 615s Reading package lists... 616s Building dependency tree... 616s Reading state information... 616s Starting pkgProblemResolver with broken count: 0 616s Starting 2 pkgProblemResolver with broken count: 0 616s Done 617s The following NEW packages will be installed: 617s libdeflate0 libhts3t64 libhtscodecs2 python3-all python3-pysam 617s 0 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. 617s Need to get 4075 kB of archives. 617s After this operation, 35.6 MB of additional disk space will be used. 617s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.23-1 [38.5 kB] 617s Get:2 http://ftpmaster.internal/ubuntu plucky/universe armhf libhtscodecs2 armhf 1.6.1-2 [67.5 kB] 617s Get:3 http://ftpmaster.internal/ubuntu plucky/universe armhf libhts3t64 armhf 1.21+ds-1 [399 kB] 618s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf python3-all armhf 3.13.2-2 [886 B] 618s Get:5 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pysam armhf 0.23.0+ds-1build1 [3569 kB] 622s Fetched 4075 kB in 5s (835 kB/s) 622s Selecting previously unselected package libdeflate0:armhf. 622s (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 ... 64655 files and directories currently installed.) 622s Preparing to unpack .../libdeflate0_1.23-1_armhf.deb ... 622s Unpacking libdeflate0:armhf (1.23-1) ... 622s Selecting previously unselected package libhtscodecs2:armhf. 622s Preparing to unpack .../libhtscodecs2_1.6.1-2_armhf.deb ... 622s Unpacking libhtscodecs2:armhf (1.6.1-2) ... 622s Selecting previously unselected package libhts3t64:armhf. 622s Preparing to unpack .../libhts3t64_1.21+ds-1_armhf.deb ... 622s Unpacking libhts3t64:armhf (1.21+ds-1) ... 622s Selecting previously unselected package python3-all. 622s Preparing to unpack .../python3-all_3.13.2-2_armhf.deb ... 622s Unpacking python3-all (3.13.2-2) ... 623s Selecting previously unselected package python3-pysam. 623s Preparing to unpack .../python3-pysam_0.23.0+ds-1build1_armhf.deb ... 623s Unpacking python3-pysam (0.23.0+ds-1build1) ... 623s Setting up libhtscodecs2:armhf (1.6.1-2) ... 623s Setting up libdeflate0:armhf (1.23-1) ... 623s Setting up python3-all (3.13.2-2) ... 623s Setting up libhts3t64:armhf (1.21+ds-1) ... 623s Setting up python3-pysam (0.23.0+ds-1build1) ... 623s Processing triggers for man-db (2.13.0-1) ... 623s Processing triggers for libc-bin (2.41-1ubuntu2) ... 639s autopkgtest [16:00:27]: 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 639s autopkgtest [16:00:27]: test autodep8-python3: [----------------------- 642s Testing with python3.13: 642s 642s autopkgtest [16:00:30]: test autodep8-python3: -----------------------] 646s autodep8-python3 PASS (superficial) 646s autopkgtest [16:00:34]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 650s autopkgtest [16:00:38]: @@@@@@@@@@@@@@@@@@@@ summary 650s command1 PASS 650s autodep8-python3 PASS (superficial)