1s autopkgtest [00:42:37]: starting date and time: 2024-11-04 00:42:37+0000 1s autopkgtest [00:42:37]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 1s autopkgtest [00:42:37]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.zfxu5mym/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:htslib --apt-upgrade python-pysam --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=htslib/1.20+ds-2 -- lxd -r lxd-armhf-10.145.243.142 lxd-armhf-10.145.243.142:autopkgtest/ubuntu/plucky/armhf 56s autopkgtest [00:43:32]: testbed dpkg architecture: armhf 58s autopkgtest [00:43:34]: testbed apt version: 2.9.8 58s autopkgtest [00:43:34]: @@@@@@@@@@@@@@@@@@@@ test bed setup 66s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 66s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [31.2 kB] 66s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 66s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [177 kB] 67s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [2268 kB] 67s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [209 kB] 67s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [1640 kB] 67s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [23.9 kB] 67s Fetched 4430 kB in 1s (3606 kB/s) 67s Reading package lists... 84s tee: /proc/self/fd/2: Permission denied 106s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 106s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 106s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 106s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 108s Reading package lists... 108s Reading package lists... 109s Building dependency tree... 109s Reading state information... 110s Calculating upgrade... 111s The following packages were automatically installed and are no longer required: 111s libperl5.38t64 perl-modules-5.38 111s Use 'apt autoremove' to remove them. 112s The following NEW packages will be installed: 112s libperl5.40 perl-modules-5.40 112s The following packages will be upgraded: 112s base-files distro-info-data fwupd gcc-14-base info install-info iproute2 112s libatomic1 libblockdev-crypto3 libblockdev-fs3 libblockdev-loop3 112s libblockdev-mdraid3 libblockdev-nvme3 libblockdev-part3 libblockdev-swap3 112s libblockdev-utils3 libblockdev3 libdb5.3t64 libdw1t64 libelf1t64 libevdev2 112s libftdi1-2 libfwupd2 libgcc-s1 libinih1 libkeyutils1 liblocale-gettext-perl 112s libpipeline1 libsgutils2-1.46-2 libstdc++6 libtext-charwidth-perl 112s libtext-iconv-perl motd-news-config nano perl perl-base python3-configobj 112s python3-json-pointer python3-lazr.uri python3-zipp sg3-utils sg3-utils-udev 112s vim-common vim-tiny xxd 112s 45 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 112s Need to get 19.6 MB of archives. 112s After this operation, 42.8 MB of additional disk space will be used. 112s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf motd-news-config all 13.5ubuntu2 [5274 B] 112s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf base-files armhf 13.5ubuntu2 [68.6 kB] 112s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf perl-modules-5.40 all 5.40.0-6 [3214 kB] 112s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libperl5.40 armhf 5.40.0-6 [4140 kB] 112s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf perl armhf 5.40.0-6 [262 kB] 112s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf perl-base armhf 5.40.0-6 [1674 kB] 112s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf liblocale-gettext-perl armhf 1.07-7build1 [15.0 kB] 112s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf libtext-iconv-perl armhf 1.7-8build4 [12.8 kB] 112s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf libtext-charwidth-perl armhf 0.04-11build4 [9128 B] 112s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libdb5.3t64 armhf 5.3.28+dfsg2-9 [655 kB] 112s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libatomic1 armhf 14.2.0-7ubuntu1 [7842 B] 112s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14-base armhf 14.2.0-7ubuntu1 [51.2 kB] 112s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libstdc++6 armhf 14.2.0-7ubuntu1 [711 kB] 112s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf libgcc-s1 armhf 14.2.0-7ubuntu1 [40.8 kB] 112s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf install-info armhf 7.1.1-1 [61.4 kB] 112s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf distro-info-data all 0.63 [6588 B] 112s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libdw1t64 armhf 0.192-4 [243 kB] 112s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf libelf1t64 armhf 0.192-4 [50.2 kB] 112s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf iproute2 armhf 6.10.0-2ubuntu1 [1082 kB] 112s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libkeyutils1 armhf 1.6.3-4ubuntu2 [8712 B] 112s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf vim-tiny armhf 2:9.1.0777-1ubuntu1 [693 kB] 112s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf vim-common all 2:9.1.0777-1ubuntu1 [394 kB] 112s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf xxd armhf 2:9.1.0777-1ubuntu1 [66.8 kB] 112s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf info armhf 7.1.1-1 [126 kB] 112s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf libevdev2 armhf 1.13.3+dfsg-1 [29.7 kB] 112s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf libpipeline1 armhf 1.5.8-1 [26.9 kB] 112s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf nano armhf 8.2-1 [276 kB] 112s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf libfwupd2 armhf 1.9.26-2 [125 kB] 112s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf fwupd armhf 1.9.26-2 [4404 kB] 113s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-utils3 armhf 3.2.0-2 [17.4 kB] 113s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-crypto3 armhf 3.2.0-2 [22.3 kB] 113s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-fs3 armhf 3.2.0-2 [34.3 kB] 113s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-loop3 armhf 3.2.0-2 [6552 B] 113s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-mdraid3 armhf 3.2.0-2 [13.4 kB] 113s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-nvme3 armhf 3.2.0-2 [17.6 kB] 113s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-part3 armhf 3.2.0-2 [16.5 kB] 113s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-swap3 armhf 3.2.0-2 [8942 B] 113s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev3 armhf 3.2.0-2 [44.2 kB] 113s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf libftdi1-2 armhf 1.5-7 [25.7 kB] 113s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf libinih1 armhf 58-1ubuntu1 [6750 B] 113s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf libsgutils2-1.46-2 armhf 1.46-3ubuntu5 [82.5 kB] 113s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf python3-configobj all 5.0.9-1 [33.9 kB] 113s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf python3-json-pointer all 2.4-2 [8396 B] 113s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf python3-lazr.uri all 1.0.6-4 [13.6 kB] 113s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf python3-zipp all 3.20.2-1 [10.1 kB] 113s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf sg3-utils armhf 1.46-3ubuntu5 [816 kB] 113s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf sg3-utils-udev all 1.46-3ubuntu5 [5916 B] 113s Preconfiguring packages ... 113s Fetched 19.6 MB in 1s (14.2 MB/s) 113s (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 ... 59386 files and directories currently installed.) 113s Preparing to unpack .../motd-news-config_13.5ubuntu2_all.deb ... 113s Unpacking motd-news-config (13.5ubuntu2) over (13.3ubuntu6) ... 114s Preparing to unpack .../base-files_13.5ubuntu2_armhf.deb ... 114s Unpacking base-files (13.5ubuntu2) over (13.3ubuntu6) ... 114s Setting up base-files (13.5ubuntu2) ... 114s Installing new version of config file /etc/issue ... 114s Installing new version of config file /etc/issue.net ... 114s Installing new version of config file /etc/lsb-release ... 115s motd-news.service is a disabled or a static unit not running, not starting it. 115s (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 ... 59386 files and directories currently installed.) 115s Preparing to unpack .../perl_5.40.0-6_armhf.deb ... 115s Unpacking perl (5.40.0-6) over (5.38.2-5) ... 115s Selecting previously unselected package perl-modules-5.40. 115s Preparing to unpack .../perl-modules-5.40_5.40.0-6_all.deb ... 115s Unpacking perl-modules-5.40 (5.40.0-6) ... 115s Selecting previously unselected package libperl5.40:armhf. 115s Preparing to unpack .../libperl5.40_5.40.0-6_armhf.deb ... 115s Unpacking libperl5.40:armhf (5.40.0-6) ... 115s Preparing to unpack .../perl-base_5.40.0-6_armhf.deb ... 115s Unpacking perl-base (5.40.0-6) over (5.38.2-5) ... 116s Setting up perl-base (5.40.0-6) ... 116s (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 ... 61462 files and directories currently installed.) 116s Preparing to unpack .../liblocale-gettext-perl_1.07-7build1_armhf.deb ... 116s Unpacking liblocale-gettext-perl (1.07-7build1) over (1.07-7) ... 116s Preparing to unpack .../libtext-iconv-perl_1.7-8build4_armhf.deb ... 116s Unpacking libtext-iconv-perl:armhf (1.7-8build4) over (1.7-8build3) ... 116s Preparing to unpack .../libtext-charwidth-perl_0.04-11build4_armhf.deb ... 116s Unpacking libtext-charwidth-perl:armhf (0.04-11build4) over (0.04-11build3) ... 116s Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-9_armhf.deb ... 116s Unpacking libdb5.3t64:armhf (5.3.28+dfsg2-9) over (5.3.28+dfsg2-7) ... 116s Setting up libdb5.3t64:armhf (5.3.28+dfsg2-9) ... 116s (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 ... 61462 files and directories currently installed.) 116s Preparing to unpack .../libatomic1_14.2.0-7ubuntu1_armhf.deb ... 116s Unpacking libatomic1:armhf (14.2.0-7ubuntu1) over (14.2.0-4ubuntu2) ... 116s Preparing to unpack .../gcc-14-base_14.2.0-7ubuntu1_armhf.deb ... 116s Unpacking gcc-14-base:armhf (14.2.0-7ubuntu1) over (14.2.0-4ubuntu2) ... 116s Setting up gcc-14-base:armhf (14.2.0-7ubuntu1) ... 116s (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 ... 61462 files and directories currently installed.) 116s Preparing to unpack .../libstdc++6_14.2.0-7ubuntu1_armhf.deb ... 116s Unpacking libstdc++6:armhf (14.2.0-7ubuntu1) over (14.2.0-4ubuntu2) ... 116s Setting up libstdc++6:armhf (14.2.0-7ubuntu1) ... 116s (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 ... 61462 files and directories currently installed.) 116s Preparing to unpack .../libgcc-s1_14.2.0-7ubuntu1_armhf.deb ... 116s Unpacking libgcc-s1:armhf (14.2.0-7ubuntu1) over (14.2.0-4ubuntu2) ... 116s Setting up libgcc-s1:armhf (14.2.0-7ubuntu1) ... 116s (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 ... 61462 files and directories currently installed.) 116s Preparing to unpack .../install-info_7.1.1-1_armhf.deb ... 116s Unpacking install-info (7.1.1-1) over (7.1-3build2) ... 116s Setting up install-info (7.1.1-1) ... 117s (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 ... 61462 files and directories currently installed.) 117s Preparing to unpack .../00-distro-info-data_0.63_all.deb ... 117s Unpacking distro-info-data (0.63) over (0.62) ... 117s Preparing to unpack .../01-libdw1t64_0.192-4_armhf.deb ... 117s Unpacking libdw1t64:armhf (0.192-4) over (0.191-2) ... 117s Preparing to unpack .../02-libelf1t64_0.192-4_armhf.deb ... 117s Unpacking libelf1t64:armhf (0.192-4) over (0.191-2) ... 117s Preparing to unpack .../03-iproute2_6.10.0-2ubuntu1_armhf.deb ... 117s Unpacking iproute2 (6.10.0-2ubuntu1) over (6.10.0-2) ... 117s Preparing to unpack .../04-libkeyutils1_1.6.3-4ubuntu2_armhf.deb ... 117s Unpacking libkeyutils1:armhf (1.6.3-4ubuntu2) over (1.6.3-3build1) ... 118s Preparing to unpack .../05-vim-tiny_2%3a9.1.0777-1ubuntu1_armhf.deb ... 118s Unpacking vim-tiny (2:9.1.0777-1ubuntu1) over (2:9.1.0496-1ubuntu6) ... 118s Preparing to unpack .../06-vim-common_2%3a9.1.0777-1ubuntu1_all.deb ... 118s Unpacking vim-common (2:9.1.0777-1ubuntu1) over (2:9.1.0496-1ubuntu6) ... 118s Preparing to unpack .../07-xxd_2%3a9.1.0777-1ubuntu1_armhf.deb ... 118s Unpacking xxd (2:9.1.0777-1ubuntu1) over (2:9.1.0496-1ubuntu6) ... 118s Preparing to unpack .../08-info_7.1.1-1_armhf.deb ... 118s Unpacking info (7.1.1-1) over (7.1-3build2) ... 118s Preparing to unpack .../09-libevdev2_1.13.3+dfsg-1_armhf.deb ... 118s Unpacking libevdev2:armhf (1.13.3+dfsg-1) over (1.13.2+dfsg-1) ... 118s Preparing to unpack .../10-libpipeline1_1.5.8-1_armhf.deb ... 118s Unpacking libpipeline1:armhf (1.5.8-1) over (1.5.7-2) ... 118s Preparing to unpack .../11-nano_8.2-1_armhf.deb ... 118s Unpacking nano (8.2-1) over (8.1-1) ... 118s Preparing to unpack .../12-libfwupd2_1.9.26-2_armhf.deb ... 118s Unpacking libfwupd2:armhf (1.9.26-2) over (1.9.24-1) ... 118s Preparing to unpack .../13-fwupd_1.9.26-2_armhf.deb ... 118s Unpacking fwupd (1.9.26-2) over (1.9.24-1) ... 118s Preparing to unpack .../14-libblockdev-utils3_3.2.0-2_armhf.deb ... 118s Unpacking libblockdev-utils3:armhf (3.2.0-2) over (3.1.1-2) ... 118s Preparing to unpack .../15-libblockdev-crypto3_3.2.0-2_armhf.deb ... 118s Unpacking libblockdev-crypto3:armhf (3.2.0-2) over (3.1.1-2) ... 118s Preparing to unpack .../16-libblockdev-fs3_3.2.0-2_armhf.deb ... 118s Unpacking libblockdev-fs3:armhf (3.2.0-2) over (3.1.1-2) ... 118s Preparing to unpack .../17-libblockdev-loop3_3.2.0-2_armhf.deb ... 118s Unpacking libblockdev-loop3:armhf (3.2.0-2) over (3.1.1-2) ... 118s Preparing to unpack .../18-libblockdev-mdraid3_3.2.0-2_armhf.deb ... 118s Unpacking libblockdev-mdraid3:armhf (3.2.0-2) over (3.1.1-2) ... 119s Preparing to unpack .../19-libblockdev-nvme3_3.2.0-2_armhf.deb ... 119s Unpacking libblockdev-nvme3:armhf (3.2.0-2) over (3.1.1-2) ... 119s Preparing to unpack .../20-libblockdev-part3_3.2.0-2_armhf.deb ... 119s Unpacking libblockdev-part3:armhf (3.2.0-2) over (3.1.1-2) ... 119s Preparing to unpack .../21-libblockdev-swap3_3.2.0-2_armhf.deb ... 119s Unpacking libblockdev-swap3:armhf (3.2.0-2) over (3.1.1-2) ... 119s Preparing to unpack .../22-libblockdev3_3.2.0-2_armhf.deb ... 119s Unpacking libblockdev3:armhf (3.2.0-2) over (3.1.1-2) ... 119s Preparing to unpack .../23-libftdi1-2_1.5-7_armhf.deb ... 119s Unpacking libftdi1-2:armhf (1.5-7) over (1.5-6build5) ... 119s Preparing to unpack .../24-libinih1_58-1ubuntu1_armhf.deb ... 119s Unpacking libinih1:armhf (58-1ubuntu1) over (55-1ubuntu2) ... 119s Preparing to unpack .../25-libsgutils2-1.46-2_1.46-3ubuntu5_armhf.deb ... 119s Unpacking libsgutils2-1.46-2:armhf (1.46-3ubuntu5) over (1.46-3ubuntu4) ... 119s Preparing to unpack .../26-python3-configobj_5.0.9-1_all.deb ... 119s Unpacking python3-configobj (5.0.9-1) over (5.0.8-3) ... 119s Preparing to unpack .../27-python3-json-pointer_2.4-2_all.deb ... 119s Unpacking python3-json-pointer (2.4-2) over (2.0-0ubuntu1) ... 119s Preparing to unpack .../28-python3-lazr.uri_1.0.6-4_all.deb ... 119s Unpacking python3-lazr.uri (1.0.6-4) over (1.0.6-3) ... 119s Preparing to unpack .../29-python3-zipp_3.20.2-1_all.deb ... 120s Unpacking python3-zipp (3.20.2-1) over (3.20.0-1) ... 120s Preparing to unpack .../30-sg3-utils_1.46-3ubuntu5_armhf.deb ... 120s Unpacking sg3-utils (1.46-3ubuntu5) over (1.46-3ubuntu4) ... 120s Preparing to unpack .../31-sg3-utils-udev_1.46-3ubuntu5_all.deb ... 120s Unpacking sg3-utils-udev (1.46-3ubuntu5) over (1.46-3ubuntu4) ... 120s Setting up libpipeline1:armhf (1.5.8-1) ... 120s Setting up motd-news-config (13.5ubuntu2) ... 120s Setting up libtext-iconv-perl:armhf (1.7-8build4) ... 120s Setting up libtext-charwidth-perl:armhf (0.04-11build4) ... 120s Setting up libkeyutils1:armhf (1.6.3-4ubuntu2) ... 120s Setting up distro-info-data (0.63) ... 120s Setting up libinih1:armhf (58-1ubuntu1) ... 120s Setting up libfwupd2:armhf (1.9.26-2) ... 120s Setting up libsgutils2-1.46-2:armhf (1.46-3ubuntu5) ... 120s Setting up python3-lazr.uri (1.0.6-4) ... 120s Setting up python3-zipp (3.20.2-1) ... 120s Setting up xxd (2:9.1.0777-1ubuntu1) ... 120s Setting up libelf1t64:armhf (0.192-4) ... 120s Setting up libdw1t64:armhf (0.192-4) ... 120s Setting up libftdi1-2:armhf (1.5-7) ... 120s Setting up python3-configobj (5.0.9-1) ... 120s Setting up vim-common (2:9.1.0777-1ubuntu1) ... 120s Installing new version of config file /etc/vim/vimrc ... 120s Setting up libblockdev-utils3:armhf (3.2.0-2) ... 120s Setting up libatomic1:armhf (14.2.0-7ubuntu1) ... 120s Setting up libblockdev-nvme3:armhf (3.2.0-2) ... 120s Setting up nano (8.2-1) ... 120s Setting up libblockdev-fs3:armhf (3.2.0-2) ... 120s Setting up perl-modules-5.40 (5.40.0-6) ... 120s Setting up python3-json-pointer (2.4-2) ... 121s Setting up libevdev2:armhf (1.13.3+dfsg-1) ... 121s Setting up fwupd (1.9.26-2) ... 121s fwupd-offline-update.service is a disabled or a static unit not running, not starting it. 121s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 121s fwupd.service is a disabled or a static unit not running, not starting it. 121s Setting up info (7.1.1-1) ... 121s Setting up liblocale-gettext-perl (1.07-7build1) ... 121s Setting up sg3-utils (1.46-3ubuntu5) ... 121s Setting up libblockdev-mdraid3:armhf (3.2.0-2) ... 121s Setting up libblockdev-crypto3:armhf (3.2.0-2) ... 121s Setting up libblockdev-swap3:armhf (3.2.0-2) ... 121s Setting up iproute2 (6.10.0-2ubuntu1) ... 122s Setting up libblockdev-loop3:armhf (3.2.0-2) ... 122s Setting up vim-tiny (2:9.1.0777-1ubuntu1) ... 122s Setting up libblockdev3:armhf (3.2.0-2) ... 122s Installing new version of config file /etc/libblockdev/3/conf.d/00-default.cfg ... 122s Setting up libblockdev-part3:armhf (3.2.0-2) ... 122s Setting up sg3-utils-udev (1.46-3ubuntu5) ... 122s update-initramfs: deferring update (trigger activated) 122s Setting up libperl5.40:armhf (5.40.0-6) ... 122s Setting up perl (5.40.0-6) ... 122s Processing triggers for dbus (1.14.10-4ubuntu5) ... 122s Processing triggers for install-info (7.1.1-1) ... 122s Processing triggers for initramfs-tools (0.142ubuntu34) ... 122s Processing triggers for libc-bin (2.40-1ubuntu3) ... 122s Processing triggers for man-db (2.12.1-3) ... 124s Processing triggers for plymouth-theme-ubuntu-text (24.004.60-1ubuntu10) ... 124s update-initramfs: deferring update (trigger activated) 124s Processing triggers for initramfs-tools (0.142ubuntu34) ... 124s Reading package lists... 124s Building dependency tree... 124s Reading state information... 125s The following packages will be REMOVED: 125s libperl5.38t64* perl-modules-5.38* 125s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 125s After this operation, 41.6 MB disk space will be freed. 126s (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 ... 61462 files and directories currently installed.) 126s Removing libperl5.38t64:armhf (5.38.2-5) ... 126s Removing perl-modules-5.38 (5.38.2-5) ... 126s Processing triggers for man-db (2.12.1-3) ... 126s Processing triggers for libc-bin (2.40-1ubuntu3) ... 128s autopkgtest [00:44:44]: rebooting testbed after setup commands that affected boot 194s autopkgtest [00:45:50]: testbed running kernel: Linux 6.8.0-47-generic #47~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Oct 2 16:39:14 UTC 2 220s autopkgtest [00:46:16]: @@@@@@@@@@@@@@@@@@@@ apt-source python-pysam 234s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-pysam 0.22.1+ds-2 (dsc) [2563 B] 234s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-pysam 0.22.1+ds-2 (tar) [1447 kB] 234s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-pysam 0.22.1+ds-2 (diff) [10.7 kB] 234s gpgv: Signature made Wed May 29 11:37:25 2024 UTC 234s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 234s gpgv: issuer "emollier@debian.org" 234s gpgv: Can't check signature: No public key 234s dpkg-source: warning: cannot verify inline signature for ./python-pysam_0.22.1+ds-2.dsc: no acceptable signature found 234s autopkgtest [00:46:30]: testing package python-pysam version 0.22.1+ds-2 236s autopkgtest [00:46:32]: build not needed 239s autopkgtest [00:46:35]: test command1: preparing testbed 249s Reading package lists... 249s Building dependency tree... 249s Reading state information... 249s Starting pkgProblemResolver with broken count: 0 250s Starting 2 pkgProblemResolver with broken count: 0 250s Done 250s The following additional packages will be installed: 250s autoconf automake autopoint autotools-dev bcftools build-essential cpp 250s cpp-14 cpp-14-arm-linux-gnueabihf cpp-arm-linux-gnueabihf cython3 debhelper 250s debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz g++ g++-14 250s g++-14-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc gcc-14 250s gcc-14-arm-linux-gnueabihf gcc-arm-linux-gnueabihf gettext intltool-debian 250s libarchive-zip-perl libasan8 libbrotli-dev libbz2-dev libc-dev-bin libc6-dev 250s libcc1-0 libcrypt-dev libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev 250s libdeflate0 libevent-2.1-7t64 libexpat1-dev libfile-stripnondeterminism-perl 250s libgcc-14-dev libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 250s libgnutls-openssl27t64 libgnutls28-dev libgomp1 libhts-dev libhts3t64 250s libhtscodecs2 libidn2-dev libisl23 libjs-jquery libjs-sphinxdoc 251s libjs-underscore liblzma-dev libmpc3 libnghttp2-dev libp11-kit-dev 251s libpkgconf3 libpsl-dev libpython3-all-dev libpython3-dev libpython3.12-dev 251s libpython3.12t64 librtmp-dev libssh2-1-dev libssl-dev libstdc++-14-dev 251s libtasn1-6-dev libtool libubsan1 libunbound8 libzstd-dev linux-libc-dev m4 251s nettle-dev pkgconf pkgconf-bin po-debconf python3-all python3-all-dev 251s python3-dev python3-iniconfig python3-packaging python3-pluggy python3-pysam 251s python3-pytest python3.12-dev rpcsvc-proto samtools tabix zlib1g-dev 251s Suggested packages: 251s autoconf-archive gnu-standards autoconf-doc python3-numpy 251s texlive-latex-recommended cpp-doc gcc-14-locales cpp-14-doc cython-doc 251s dh-make flit python3-build python3-installer python3-wheel gcc-14-doc 251s gcc-multilib manpages-dev flex bison gdb gcc-doc gdb-arm-linux-gnueabihf 251s gettext-doc libasprintf-dev libgettextpo-dev libc-devtools glibc-doc 251s libcurl4-doc libidn-dev libkrb5-dev libldap2-dev gmp-doc libgmp10-doc 251s libmpfr-dev dns-root-data gnutls-bin gnutls-doc liblzma-doc libnghttp2-doc 251s p11-kit-doc libssl-doc libstdc++-14-doc libtool-doc gfortran 251s | fortran95-compiler gcj-jdk m4-doc libmail-box-perl cwltool 251s Recommended packages: 251s python3-gffutils python3-matplotlib bzip2-doc manpages manpages-dev 251s libarchive-cpio-perl javascript-common libtasn1-doc libltdl-dev 251s libmail-sendmail-perl 251s The following NEW packages will be installed: 251s autoconf automake autopkgtest-satdep autopoint autotools-dev bcftools 251s build-essential cpp cpp-14 cpp-14-arm-linux-gnueabihf 251s cpp-arm-linux-gnueabihf cython3 debhelper debugedit dh-autoreconf dh-python 251s dh-strip-nondeterminism dwz g++ g++-14 g++-14-arm-linux-gnueabihf 251s g++-arm-linux-gnueabihf gcc gcc-14 gcc-14-arm-linux-gnueabihf 251s gcc-arm-linux-gnueabihf gettext intltool-debian libarchive-zip-perl libasan8 251s libbrotli-dev libbz2-dev libc-dev-bin libc6-dev libcc1-0 libcrypt-dev 251s libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 251s libevent-2.1-7t64 libexpat1-dev libfile-stripnondeterminism-perl 251s libgcc-14-dev libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 251s libgnutls-openssl27t64 libgnutls28-dev libgomp1 libhts-dev libhts3t64 251s libhtscodecs2 libidn2-dev libisl23 libjs-jquery libjs-sphinxdoc 251s libjs-underscore liblzma-dev libmpc3 libnghttp2-dev libp11-kit-dev 251s libpkgconf3 libpsl-dev libpython3-all-dev libpython3-dev libpython3.12-dev 251s libpython3.12t64 librtmp-dev libssh2-1-dev libssl-dev libstdc++-14-dev 251s libtasn1-6-dev libtool libubsan1 libunbound8 libzstd-dev linux-libc-dev m4 251s nettle-dev pkgconf pkgconf-bin po-debconf python3-all python3-all-dev 251s python3-dev python3-iniconfig python3-packaging python3-pluggy python3-pysam 251s python3-pytest python3.12-dev rpcsvc-proto samtools tabix zlib1g-dev 251s 0 upgraded, 96 newly installed, 0 to remove and 0 not upgraded. 251s Need to get 80.6 MB/80.6 MB of archives. 251s After this operation, 263 MB of additional disk space will be used. 251s Get:1 /tmp/autopkgtest.OEVu7F/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [816 B] 251s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf m4 armhf 1.4.19-4build1 [235 kB] 251s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf autoconf all 2.72-3 [382 kB] 251s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf autotools-dev all 20220109.1 [44.9 kB] 251s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf automake all 1:1.16.5-1.3ubuntu1 [558 kB] 251s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf autopoint all 0.22.5-2 [616 kB] 251s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.21-1 [38.8 kB] 251s Get:8 http://ftpmaster.internal/ubuntu plucky/universe armhf libhtscodecs2 armhf 1.6.0-1build1 [65.8 kB] 251s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf libhts3t64 armhf 1.20+ds-2 [394 kB] 251s Get:10 http://ftpmaster.internal/ubuntu plucky/universe armhf bcftools armhf 1.20-2 [726 kB] 251s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libc-dev-bin armhf 2.40-1ubuntu3 [19.2 kB] 251s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf linux-libc-dev armhf 6.11.0-8.8 [1628 kB] 251s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libcrypt-dev armhf 1:4.4.36-4build1 [120 kB] 251s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf rpcsvc-proto armhf 1.4.2-0ubuntu7 [62.2 kB] 251s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf libc6-dev armhf 2.40-1ubuntu3 [1370 kB] 251s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf libisl23 armhf 0.27-1 [546 kB] 251s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libmpc3 armhf 1.3.1-1build2 [47.1 kB] 251s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-14-arm-linux-gnueabihf armhf 14.2.0-7ubuntu1 [9219 kB] 252s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-14 armhf 14.2.0-7ubuntu1 [1030 B] 252s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-arm-linux-gnueabihf armhf 4:14.1.0-2ubuntu1 [5464 B] 252s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf cpp armhf 4:14.1.0-2ubuntu1 [22.4 kB] 252s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf libcc1-0 armhf 14.2.0-7ubuntu1 [43.3 kB] 252s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 14.2.0-7ubuntu1 [125 kB] 252s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf libasan8 armhf 14.2.0-7ubuntu1 [2901 kB] 252s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf libubsan1 armhf 14.2.0-7ubuntu1 [1150 kB] 252s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf libgcc-14-dev armhf 14.2.0-7ubuntu1 [897 kB] 252s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14-arm-linux-gnueabihf armhf 14.2.0-7ubuntu1 [18.0 MB] 252s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14 armhf 14.2.0-7ubuntu1 [495 kB] 252s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-arm-linux-gnueabihf armhf 4:14.1.0-2ubuntu1 [1222 B] 252s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf gcc armhf 4:14.1.0-2ubuntu1 [5002 B] 252s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf libstdc++-14-dev armhf 14.2.0-7ubuntu1 [2567 kB] 252s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf g++-14-arm-linux-gnueabihf armhf 14.2.0-7ubuntu1 [10.5 MB] 253s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf g++-14 armhf 14.2.0-7ubuntu1 [19.8 kB] 253s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf g++-arm-linux-gnueabihf armhf 4:14.1.0-2ubuntu1 [968 B] 253s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf g++ armhf 4:14.1.0-2ubuntu1 [1084 B] 253s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf build-essential armhf 12.10ubuntu1 [4928 B] 253s Get:37 http://ftpmaster.internal/ubuntu plucky/universe armhf cython3 armhf 3.0.11+dfsg-1ubuntu1 [2391 kB] 253s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libdebhelper-perl all 13.20ubuntu1 [94.2 kB] 253s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf libtool all 2.4.7-7build1 [166 kB] 253s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf dh-autoreconf all 20 [16.1 kB] 253s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf libarchive-zip-perl all 1.68-1 [90.2 kB] 253s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] 253s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf dh-strip-nondeterminism all 1.14.0-1 [5058 B] 253s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf debugedit armhf 1:5.1-1 [46.5 kB] 253s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf dwz armhf 0.15-1build6 [116 kB] 253s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf gettext armhf 0.22.5-2 [995 kB] 253s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf intltool-debian all 0.35.0+20060710.6 [23.2 kB] 253s Get:48 http://ftpmaster.internal/ubuntu plucky/main armhf po-debconf all 1.0.21+nmu1 [233 kB] 253s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf debhelper all 13.20ubuntu1 [893 kB] 253s Get:50 http://ftpmaster.internal/ubuntu plucky/universe armhf dh-python all 6.20240824 [112 kB] 253s Get:51 http://ftpmaster.internal/ubuntu plucky/main armhf libbrotli-dev armhf 1.1.0-2build2 [337 kB] 253s Get:52 http://ftpmaster.internal/ubuntu plucky/main armhf libbz2-dev armhf 1.0.8-6 [30.9 kB] 253s Get:53 http://ftpmaster.internal/ubuntu plucky/main armhf libevent-2.1-7t64 armhf 2.1.12-stable-10 [127 kB] 253s Get:54 http://ftpmaster.internal/ubuntu plucky/main armhf libunbound8 armhf 1.20.0-1ubuntu2.1 [416 kB] 253s Get:55 http://ftpmaster.internal/ubuntu plucky/main armhf libgnutls-dane0t64 armhf 3.8.6-2ubuntu1 [33.8 kB] 253s Get:56 http://ftpmaster.internal/ubuntu plucky/main armhf libgnutls-openssl27t64 armhf 3.8.6-2ubuntu1 [33.6 kB] 253s Get:57 http://ftpmaster.internal/ubuntu plucky/main armhf libidn2-dev armhf 2.3.7-2build2 [115 kB] 253s Get:58 http://ftpmaster.internal/ubuntu plucky/main armhf libp11-kit-dev armhf 0.25.5-2ubuntu1 [22.7 kB] 253s Get:59 http://ftpmaster.internal/ubuntu plucky/main armhf libtasn1-6-dev armhf 4.19.0-3build1 [86.0 kB] 253s Get:60 http://ftpmaster.internal/ubuntu plucky/main armhf libgmpxx4ldbl armhf 2:6.3.0+dfsg-2ubuntu7 [9124 B] 253s Get:61 http://ftpmaster.internal/ubuntu plucky/main armhf libgmp-dev armhf 2:6.3.0+dfsg-2ubuntu7 [290 kB] 253s Get:62 http://ftpmaster.internal/ubuntu plucky/main armhf nettle-dev armhf 3.10-1 [1173 kB] 253s Get:63 http://ftpmaster.internal/ubuntu plucky/main armhf libgnutls28-dev armhf 3.8.6-2ubuntu1 [1017 kB] 253s Get:64 http://ftpmaster.internal/ubuntu plucky/main armhf libpkgconf3 armhf 1.8.1-3ubuntu1 [26.6 kB] 253s Get:65 http://ftpmaster.internal/ubuntu plucky/main armhf pkgconf-bin armhf 1.8.1-3ubuntu1 [21.2 kB] 253s Get:66 http://ftpmaster.internal/ubuntu plucky/main armhf pkgconf armhf 1.8.1-3ubuntu1 [16.8 kB] 253s Get:67 http://ftpmaster.internal/ubuntu plucky/main armhf libnghttp2-dev armhf 1.62.1-2 [107 kB] 253s Get:68 http://ftpmaster.internal/ubuntu plucky/main armhf libpsl-dev armhf 0.21.2-1.1build1 [75.6 kB] 253s Get:69 http://ftpmaster.internal/ubuntu plucky/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1ubuntu1 [880 kB] 253s Get:70 http://ftpmaster.internal/ubuntu plucky/main armhf librtmp-dev armhf 2.4+20151223.gitfa8646d.1-2build7 [62.9 kB] 253s Get:71 http://ftpmaster.internal/ubuntu plucky/main armhf libssl-dev armhf 3.3.1-2ubuntu2 [2335 kB] 253s Get:72 http://ftpmaster.internal/ubuntu plucky/main armhf libssh2-1-dev armhf 1.11.0-7 [248 kB] 253s Get:73 http://ftpmaster.internal/ubuntu plucky/main armhf libzstd-dev armhf 1.5.6+dfsg-1 [331 kB] 253s Get:74 http://ftpmaster.internal/ubuntu plucky/main armhf libcurl4-gnutls-dev armhf 8.9.1-2ubuntu2 [443 kB] 253s Get:75 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate-dev armhf 1.21-1 [45.0 kB] 253s Get:76 http://ftpmaster.internal/ubuntu plucky/main armhf libexpat1-dev armhf 2.6.2-2 [121 kB] 253s Get:77 http://ftpmaster.internal/ubuntu plucky/main armhf liblzma-dev armhf 5.6.2-2 [166 kB] 253s Get:78 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf libhts-dev armhf 1.20+ds-2 [1752 kB] 253s Get:79 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 253s Get:80 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 253s Get:81 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-sphinxdoc all 7.4.7-3 [157 kB] 253s Get:82 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.12t64 armhf 3.12.7-1 [2076 kB] 253s Get:83 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.12-dev armhf 3.12.7-1 [4344 kB] 254s Get:84 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3-dev armhf 3.12.6-0ubuntu1 [10.2 kB] 254s Get:85 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3-all-dev armhf 3.12.6-0ubuntu1 [914 B] 254s Get:86 http://ftpmaster.internal/ubuntu plucky/main armhf python3-all armhf 3.12.6-0ubuntu1 [886 B] 254s Get:87 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12-dev armhf 3.12.7-1 [504 kB] 254s Get:88 http://ftpmaster.internal/ubuntu plucky/main armhf python3-dev armhf 3.12.6-0ubuntu1 [26.7 kB] 254s Get:89 http://ftpmaster.internal/ubuntu plucky/main armhf python3-all-dev armhf 3.12.6-0ubuntu1 [908 B] 254s Get:90 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-iniconfig all 1.1.1-2 [6024 B] 254s Get:91 http://ftpmaster.internal/ubuntu plucky/main armhf python3-packaging all 24.1-1 [41.4 kB] 254s Get:92 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pluggy all 1.5.0-1 [21.0 kB] 254s Get:93 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pysam armhf 0.22.1+ds-2 [3383 kB] 254s Get:94 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pytest all 8.3.2-1 [251 kB] 254s Get:95 http://ftpmaster.internal/ubuntu plucky/universe armhf samtools armhf 1.20-3 [607 kB] 254s Get:96 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf tabix armhf 1.20+ds-2 [429 kB] 254s Fetched 80.6 MB in 3s (25.7 MB/s) 254s Selecting previously unselected package m4. 254s (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 ... 59532 files and directories currently installed.) 255s Preparing to unpack .../00-m4_1.4.19-4build1_armhf.deb ... 255s Unpacking m4 (1.4.19-4build1) ... 255s Selecting previously unselected package autoconf. 255s Preparing to unpack .../01-autoconf_2.72-3_all.deb ... 255s Unpacking autoconf (2.72-3) ... 255s Selecting previously unselected package autotools-dev. 255s Preparing to unpack .../02-autotools-dev_20220109.1_all.deb ... 255s Unpacking autotools-dev (20220109.1) ... 255s Selecting previously unselected package automake. 255s Preparing to unpack .../03-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 255s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 255s Selecting previously unselected package autopoint. 255s Preparing to unpack .../04-autopoint_0.22.5-2_all.deb ... 255s Unpacking autopoint (0.22.5-2) ... 255s Selecting previously unselected package libdeflate0:armhf. 255s Preparing to unpack .../05-libdeflate0_1.21-1_armhf.deb ... 255s Unpacking libdeflate0:armhf (1.21-1) ... 255s Selecting previously unselected package libhtscodecs2:armhf. 255s Preparing to unpack .../06-libhtscodecs2_1.6.0-1build1_armhf.deb ... 255s Unpacking libhtscodecs2:armhf (1.6.0-1build1) ... 255s Selecting previously unselected package libhts3t64:armhf. 255s Preparing to unpack .../07-libhts3t64_1.20+ds-2_armhf.deb ... 255s Unpacking libhts3t64:armhf (1.20+ds-2) ... 255s Selecting previously unselected package bcftools. 255s Preparing to unpack .../08-bcftools_1.20-2_armhf.deb ... 255s Unpacking bcftools (1.20-2) ... 255s Selecting previously unselected package libc-dev-bin. 255s Preparing to unpack .../09-libc-dev-bin_2.40-1ubuntu3_armhf.deb ... 255s Unpacking libc-dev-bin (2.40-1ubuntu3) ... 255s Selecting previously unselected package linux-libc-dev:armhf. 255s Preparing to unpack .../10-linux-libc-dev_6.11.0-8.8_armhf.deb ... 255s Unpacking linux-libc-dev:armhf (6.11.0-8.8) ... 255s Selecting previously unselected package libcrypt-dev:armhf. 255s Preparing to unpack .../11-libcrypt-dev_1%3a4.4.36-4build1_armhf.deb ... 255s Unpacking libcrypt-dev:armhf (1:4.4.36-4build1) ... 255s Selecting previously unselected package rpcsvc-proto. 255s Preparing to unpack .../12-rpcsvc-proto_1.4.2-0ubuntu7_armhf.deb ... 255s Unpacking rpcsvc-proto (1.4.2-0ubuntu7) ... 255s Selecting previously unselected package libc6-dev:armhf. 255s Preparing to unpack .../13-libc6-dev_2.40-1ubuntu3_armhf.deb ... 255s Unpacking libc6-dev:armhf (2.40-1ubuntu3) ... 255s Selecting previously unselected package libisl23:armhf. 255s Preparing to unpack .../14-libisl23_0.27-1_armhf.deb ... 255s Unpacking libisl23:armhf (0.27-1) ... 256s Selecting previously unselected package libmpc3:armhf. 256s Preparing to unpack .../15-libmpc3_1.3.1-1build2_armhf.deb ... 256s Unpacking libmpc3:armhf (1.3.1-1build2) ... 256s Selecting previously unselected package cpp-14-arm-linux-gnueabihf. 256s Preparing to unpack .../16-cpp-14-arm-linux-gnueabihf_14.2.0-7ubuntu1_armhf.deb ... 256s Unpacking cpp-14-arm-linux-gnueabihf (14.2.0-7ubuntu1) ... 256s Selecting previously unselected package cpp-14. 256s Preparing to unpack .../17-cpp-14_14.2.0-7ubuntu1_armhf.deb ... 256s Unpacking cpp-14 (14.2.0-7ubuntu1) ... 256s Selecting previously unselected package cpp-arm-linux-gnueabihf. 256s Preparing to unpack .../18-cpp-arm-linux-gnueabihf_4%3a14.1.0-2ubuntu1_armhf.deb ... 256s Unpacking cpp-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 256s Selecting previously unselected package cpp. 256s Preparing to unpack .../19-cpp_4%3a14.1.0-2ubuntu1_armhf.deb ... 256s Unpacking cpp (4:14.1.0-2ubuntu1) ... 256s Selecting previously unselected package libcc1-0:armhf. 256s Preparing to unpack .../20-libcc1-0_14.2.0-7ubuntu1_armhf.deb ... 256s Unpacking libcc1-0:armhf (14.2.0-7ubuntu1) ... 256s Selecting previously unselected package libgomp1:armhf. 256s Preparing to unpack .../21-libgomp1_14.2.0-7ubuntu1_armhf.deb ... 256s Unpacking libgomp1:armhf (14.2.0-7ubuntu1) ... 256s Selecting previously unselected package libasan8:armhf. 256s Preparing to unpack .../22-libasan8_14.2.0-7ubuntu1_armhf.deb ... 256s Unpacking libasan8:armhf (14.2.0-7ubuntu1) ... 256s Selecting previously unselected package libubsan1:armhf. 256s Preparing to unpack .../23-libubsan1_14.2.0-7ubuntu1_armhf.deb ... 256s Unpacking libubsan1:armhf (14.2.0-7ubuntu1) ... 256s Selecting previously unselected package libgcc-14-dev:armhf. 256s Preparing to unpack .../24-libgcc-14-dev_14.2.0-7ubuntu1_armhf.deb ... 256s Unpacking libgcc-14-dev:armhf (14.2.0-7ubuntu1) ... 256s Selecting previously unselected package gcc-14-arm-linux-gnueabihf. 256s Preparing to unpack .../25-gcc-14-arm-linux-gnueabihf_14.2.0-7ubuntu1_armhf.deb ... 256s Unpacking gcc-14-arm-linux-gnueabihf (14.2.0-7ubuntu1) ... 257s Selecting previously unselected package gcc-14. 257s Preparing to unpack .../26-gcc-14_14.2.0-7ubuntu1_armhf.deb ... 257s Unpacking gcc-14 (14.2.0-7ubuntu1) ... 257s Selecting previously unselected package gcc-arm-linux-gnueabihf. 257s Preparing to unpack .../27-gcc-arm-linux-gnueabihf_4%3a14.1.0-2ubuntu1_armhf.deb ... 257s Unpacking gcc-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 257s Selecting previously unselected package gcc. 257s Preparing to unpack .../28-gcc_4%3a14.1.0-2ubuntu1_armhf.deb ... 257s Unpacking gcc (4:14.1.0-2ubuntu1) ... 257s Selecting previously unselected package libstdc++-14-dev:armhf. 257s Preparing to unpack .../29-libstdc++-14-dev_14.2.0-7ubuntu1_armhf.deb ... 257s Unpacking libstdc++-14-dev:armhf (14.2.0-7ubuntu1) ... 257s Selecting previously unselected package g++-14-arm-linux-gnueabihf. 257s Preparing to unpack .../30-g++-14-arm-linux-gnueabihf_14.2.0-7ubuntu1_armhf.deb ... 257s Unpacking g++-14-arm-linux-gnueabihf (14.2.0-7ubuntu1) ... 257s Selecting previously unselected package g++-14. 257s Preparing to unpack .../31-g++-14_14.2.0-7ubuntu1_armhf.deb ... 257s Unpacking g++-14 (14.2.0-7ubuntu1) ... 257s Selecting previously unselected package g++-arm-linux-gnueabihf. 257s Preparing to unpack .../32-g++-arm-linux-gnueabihf_4%3a14.1.0-2ubuntu1_armhf.deb ... 257s Unpacking g++-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 258s Selecting previously unselected package g++. 258s Preparing to unpack .../33-g++_4%3a14.1.0-2ubuntu1_armhf.deb ... 258s Unpacking g++ (4:14.1.0-2ubuntu1) ... 258s Selecting previously unselected package build-essential. 258s Preparing to unpack .../34-build-essential_12.10ubuntu1_armhf.deb ... 258s Unpacking build-essential (12.10ubuntu1) ... 258s Selecting previously unselected package cython3. 258s Preparing to unpack .../35-cython3_3.0.11+dfsg-1ubuntu1_armhf.deb ... 258s Unpacking cython3 (3.0.11+dfsg-1ubuntu1) ... 258s Selecting previously unselected package libdebhelper-perl. 258s Preparing to unpack .../36-libdebhelper-perl_13.20ubuntu1_all.deb ... 258s Unpacking libdebhelper-perl (13.20ubuntu1) ... 258s Selecting previously unselected package libtool. 258s Preparing to unpack .../37-libtool_2.4.7-7build1_all.deb ... 258s Unpacking libtool (2.4.7-7build1) ... 258s Selecting previously unselected package dh-autoreconf. 258s Preparing to unpack .../38-dh-autoreconf_20_all.deb ... 258s Unpacking dh-autoreconf (20) ... 258s Selecting previously unselected package libarchive-zip-perl. 258s Preparing to unpack .../39-libarchive-zip-perl_1.68-1_all.deb ... 258s Unpacking libarchive-zip-perl (1.68-1) ... 258s Selecting previously unselected package libfile-stripnondeterminism-perl. 258s Preparing to unpack .../40-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... 258s Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... 258s Selecting previously unselected package dh-strip-nondeterminism. 258s Preparing to unpack .../41-dh-strip-nondeterminism_1.14.0-1_all.deb ... 258s Unpacking dh-strip-nondeterminism (1.14.0-1) ... 258s Selecting previously unselected package debugedit. 258s Preparing to unpack .../42-debugedit_1%3a5.1-1_armhf.deb ... 258s Unpacking debugedit (1:5.1-1) ... 258s Selecting previously unselected package dwz. 258s Preparing to unpack .../43-dwz_0.15-1build6_armhf.deb ... 258s Unpacking dwz (0.15-1build6) ... 258s Selecting previously unselected package gettext. 258s Preparing to unpack .../44-gettext_0.22.5-2_armhf.deb ... 258s Unpacking gettext (0.22.5-2) ... 258s Selecting previously unselected package intltool-debian. 258s Preparing to unpack .../45-intltool-debian_0.35.0+20060710.6_all.deb ... 258s Unpacking intltool-debian (0.35.0+20060710.6) ... 258s Selecting previously unselected package po-debconf. 258s Preparing to unpack .../46-po-debconf_1.0.21+nmu1_all.deb ... 258s Unpacking po-debconf (1.0.21+nmu1) ... 258s Selecting previously unselected package debhelper. 258s Preparing to unpack .../47-debhelper_13.20ubuntu1_all.deb ... 258s Unpacking debhelper (13.20ubuntu1) ... 258s Selecting previously unselected package dh-python. 258s Preparing to unpack .../48-dh-python_6.20240824_all.deb ... 258s Unpacking dh-python (6.20240824) ... 258s Selecting previously unselected package libbrotli-dev:armhf. 258s Preparing to unpack .../49-libbrotli-dev_1.1.0-2build2_armhf.deb ... 258s Unpacking libbrotli-dev:armhf (1.1.0-2build2) ... 258s Selecting previously unselected package libbz2-dev:armhf. 258s Preparing to unpack .../50-libbz2-dev_1.0.8-6_armhf.deb ... 258s Unpacking libbz2-dev:armhf (1.0.8-6) ... 258s Selecting previously unselected package libevent-2.1-7t64:armhf. 258s Preparing to unpack .../51-libevent-2.1-7t64_2.1.12-stable-10_armhf.deb ... 258s Unpacking libevent-2.1-7t64:armhf (2.1.12-stable-10) ... 259s Selecting previously unselected package libunbound8:armhf. 259s Preparing to unpack .../52-libunbound8_1.20.0-1ubuntu2.1_armhf.deb ... 259s Unpacking libunbound8:armhf (1.20.0-1ubuntu2.1) ... 259s Selecting previously unselected package libgnutls-dane0t64:armhf. 259s Preparing to unpack .../53-libgnutls-dane0t64_3.8.6-2ubuntu1_armhf.deb ... 259s Unpacking libgnutls-dane0t64:armhf (3.8.6-2ubuntu1) ... 259s Selecting previously unselected package libgnutls-openssl27t64:armhf. 259s Preparing to unpack .../54-libgnutls-openssl27t64_3.8.6-2ubuntu1_armhf.deb ... 259s Unpacking libgnutls-openssl27t64:armhf (3.8.6-2ubuntu1) ... 259s Selecting previously unselected package libidn2-dev:armhf. 259s Preparing to unpack .../55-libidn2-dev_2.3.7-2build2_armhf.deb ... 259s Unpacking libidn2-dev:armhf (2.3.7-2build2) ... 259s Selecting previously unselected package libp11-kit-dev:armhf. 259s Preparing to unpack .../56-libp11-kit-dev_0.25.5-2ubuntu1_armhf.deb ... 259s Unpacking libp11-kit-dev:armhf (0.25.5-2ubuntu1) ... 259s Selecting previously unselected package libtasn1-6-dev:armhf. 259s Preparing to unpack .../57-libtasn1-6-dev_4.19.0-3build1_armhf.deb ... 259s Unpacking libtasn1-6-dev:armhf (4.19.0-3build1) ... 259s Selecting previously unselected package libgmpxx4ldbl:armhf. 259s Preparing to unpack .../58-libgmpxx4ldbl_2%3a6.3.0+dfsg-2ubuntu7_armhf.deb ... 259s Unpacking libgmpxx4ldbl:armhf (2:6.3.0+dfsg-2ubuntu7) ... 259s Selecting previously unselected package libgmp-dev:armhf. 259s Preparing to unpack .../59-libgmp-dev_2%3a6.3.0+dfsg-2ubuntu7_armhf.deb ... 259s Unpacking libgmp-dev:armhf (2:6.3.0+dfsg-2ubuntu7) ... 259s Selecting previously unselected package nettle-dev:armhf. 259s Preparing to unpack .../60-nettle-dev_3.10-1_armhf.deb ... 259s Unpacking nettle-dev:armhf (3.10-1) ... 259s Selecting previously unselected package libgnutls28-dev:armhf. 259s Preparing to unpack .../61-libgnutls28-dev_3.8.6-2ubuntu1_armhf.deb ... 259s Unpacking libgnutls28-dev:armhf (3.8.6-2ubuntu1) ... 259s Selecting previously unselected package libpkgconf3:armhf. 259s Preparing to unpack .../62-libpkgconf3_1.8.1-3ubuntu1_armhf.deb ... 259s Unpacking libpkgconf3:armhf (1.8.1-3ubuntu1) ... 259s Selecting previously unselected package pkgconf-bin. 259s Preparing to unpack .../63-pkgconf-bin_1.8.1-3ubuntu1_armhf.deb ... 259s Unpacking pkgconf-bin (1.8.1-3ubuntu1) ... 259s Selecting previously unselected package pkgconf:armhf. 259s Preparing to unpack .../64-pkgconf_1.8.1-3ubuntu1_armhf.deb ... 259s Unpacking pkgconf:armhf (1.8.1-3ubuntu1) ... 259s Selecting previously unselected package libnghttp2-dev:armhf. 259s Preparing to unpack .../65-libnghttp2-dev_1.62.1-2_armhf.deb ... 259s Unpacking libnghttp2-dev:armhf (1.62.1-2) ... 259s Selecting previously unselected package libpsl-dev:armhf. 259s Preparing to unpack .../66-libpsl-dev_0.21.2-1.1build1_armhf.deb ... 259s Unpacking libpsl-dev:armhf (0.21.2-1.1build1) ... 259s Selecting previously unselected package zlib1g-dev:armhf. 259s Preparing to unpack .../67-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_armhf.deb ... 259s Unpacking zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 259s Selecting previously unselected package librtmp-dev:armhf. 259s Preparing to unpack .../68-librtmp-dev_2.4+20151223.gitfa8646d.1-2build7_armhf.deb ... 259s Unpacking librtmp-dev:armhf (2.4+20151223.gitfa8646d.1-2build7) ... 259s Selecting previously unselected package libssl-dev:armhf. 259s Preparing to unpack .../69-libssl-dev_3.3.1-2ubuntu2_armhf.deb ... 259s Unpacking libssl-dev:armhf (3.3.1-2ubuntu2) ... 259s Selecting previously unselected package libssh2-1-dev:armhf. 259s Preparing to unpack .../70-libssh2-1-dev_1.11.0-7_armhf.deb ... 259s Unpacking libssh2-1-dev:armhf (1.11.0-7) ... 260s Selecting previously unselected package libzstd-dev:armhf. 260s Preparing to unpack .../71-libzstd-dev_1.5.6+dfsg-1_armhf.deb ... 260s Unpacking libzstd-dev:armhf (1.5.6+dfsg-1) ... 260s Selecting previously unselected package libcurl4-gnutls-dev:armhf. 260s Preparing to unpack .../72-libcurl4-gnutls-dev_8.9.1-2ubuntu2_armhf.deb ... 260s Unpacking libcurl4-gnutls-dev:armhf (8.9.1-2ubuntu2) ... 260s Selecting previously unselected package libdeflate-dev:armhf. 260s Preparing to unpack .../73-libdeflate-dev_1.21-1_armhf.deb ... 260s Unpacking libdeflate-dev:armhf (1.21-1) ... 260s Selecting previously unselected package libexpat1-dev:armhf. 260s Preparing to unpack .../74-libexpat1-dev_2.6.2-2_armhf.deb ... 260s Unpacking libexpat1-dev:armhf (2.6.2-2) ... 260s Selecting previously unselected package liblzma-dev:armhf. 260s Preparing to unpack .../75-liblzma-dev_5.6.2-2_armhf.deb ... 260s Unpacking liblzma-dev:armhf (5.6.2-2) ... 260s Selecting previously unselected package libhts-dev:armhf. 260s Preparing to unpack .../76-libhts-dev_1.20+ds-2_armhf.deb ... 260s Unpacking libhts-dev:armhf (1.20+ds-2) ... 260s Selecting previously unselected package libjs-jquery. 260s Preparing to unpack .../77-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 260s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 260s Selecting previously unselected package libjs-underscore. 260s Preparing to unpack .../78-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 260s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 260s Selecting previously unselected package libjs-sphinxdoc. 260s Preparing to unpack .../79-libjs-sphinxdoc_7.4.7-3_all.deb ... 260s Unpacking libjs-sphinxdoc (7.4.7-3) ... 260s Selecting previously unselected package libpython3.12t64:armhf. 260s Preparing to unpack .../80-libpython3.12t64_3.12.7-1_armhf.deb ... 260s Unpacking libpython3.12t64:armhf (3.12.7-1) ... 260s Selecting previously unselected package libpython3.12-dev:armhf. 260s Preparing to unpack .../81-libpython3.12-dev_3.12.7-1_armhf.deb ... 260s Unpacking libpython3.12-dev:armhf (3.12.7-1) ... 260s Selecting previously unselected package libpython3-dev:armhf. 260s Preparing to unpack .../82-libpython3-dev_3.12.6-0ubuntu1_armhf.deb ... 260s Unpacking libpython3-dev:armhf (3.12.6-0ubuntu1) ... 260s Selecting previously unselected package libpython3-all-dev:armhf. 260s Preparing to unpack .../83-libpython3-all-dev_3.12.6-0ubuntu1_armhf.deb ... 260s Unpacking libpython3-all-dev:armhf (3.12.6-0ubuntu1) ... 260s Selecting previously unselected package python3-all. 260s Preparing to unpack .../84-python3-all_3.12.6-0ubuntu1_armhf.deb ... 260s Unpacking python3-all (3.12.6-0ubuntu1) ... 260s Selecting previously unselected package python3.12-dev. 260s Preparing to unpack .../85-python3.12-dev_3.12.7-1_armhf.deb ... 260s Unpacking python3.12-dev (3.12.7-1) ... 261s Selecting previously unselected package python3-dev. 261s Preparing to unpack .../86-python3-dev_3.12.6-0ubuntu1_armhf.deb ... 261s Unpacking python3-dev (3.12.6-0ubuntu1) ... 261s Selecting previously unselected package python3-all-dev. 261s Preparing to unpack .../87-python3-all-dev_3.12.6-0ubuntu1_armhf.deb ... 261s Unpacking python3-all-dev (3.12.6-0ubuntu1) ... 261s Selecting previously unselected package python3-iniconfig. 261s Preparing to unpack .../88-python3-iniconfig_1.1.1-2_all.deb ... 261s Unpacking python3-iniconfig (1.1.1-2) ... 261s Selecting previously unselected package python3-packaging. 261s Preparing to unpack .../89-python3-packaging_24.1-1_all.deb ... 261s Unpacking python3-packaging (24.1-1) ... 261s Selecting previously unselected package python3-pluggy. 261s Preparing to unpack .../90-python3-pluggy_1.5.0-1_all.deb ... 261s Unpacking python3-pluggy (1.5.0-1) ... 261s Selecting previously unselected package python3-pysam. 261s Preparing to unpack .../91-python3-pysam_0.22.1+ds-2_armhf.deb ... 261s Unpacking python3-pysam (0.22.1+ds-2) ... 261s Selecting previously unselected package python3-pytest. 261s Preparing to unpack .../92-python3-pytest_8.3.2-1_all.deb ... 261s Unpacking python3-pytest (8.3.2-1) ... 261s Selecting previously unselected package samtools. 261s Preparing to unpack .../93-samtools_1.20-3_armhf.deb ... 261s Unpacking samtools (1.20-3) ... 261s Selecting previously unselected package tabix. 261s Preparing to unpack .../94-tabix_1.20+ds-2_armhf.deb ... 261s Unpacking tabix (1.20+ds-2) ... 261s Selecting previously unselected package autopkgtest-satdep. 262s Preparing to unpack .../95-1-autopkgtest-satdep.deb ... 262s Unpacking autopkgtest-satdep (0) ... 262s Setting up libhtscodecs2:armhf (1.6.0-1build1) ... 262s Setting up dh-python (6.20240824) ... 262s Setting up libgnutls-openssl27t64:armhf (3.8.6-2ubuntu1) ... 262s Setting up python3-iniconfig (1.1.1-2) ... 262s Setting up libzstd-dev:armhf (1.5.6+dfsg-1) ... 262s Setting up libarchive-zip-perl (1.68-1) ... 262s Setting up libdebhelper-perl (13.20ubuntu1) ... 262s Setting up libdeflate0:armhf (1.21-1) ... 262s Setting up linux-libc-dev:armhf (6.11.0-8.8) ... 262s Setting up m4 (1.4.19-4build1) ... 262s Setting up libevent-2.1-7t64:armhf (2.1.12-stable-10) ... 262s Setting up python3-all (3.12.6-0ubuntu1) ... 262s Setting up libgomp1:armhf (14.2.0-7ubuntu1) ... 262s Setting up libpsl-dev:armhf (0.21.2-1.1build1) ... 262s Setting up libpython3.12t64:armhf (3.12.7-1) ... 262s Setting up autotools-dev (20220109.1) ... 262s Setting up python3-packaging (24.1-1) ... 262s Setting up libunbound8:armhf (1.20.0-1ubuntu2.1) ... 262s Setting up libpkgconf3:armhf (1.8.1-3ubuntu1) ... 262s Setting up libgmpxx4ldbl:armhf (2:6.3.0+dfsg-2ubuntu7) ... 262s Setting up rpcsvc-proto (1.4.2-0ubuntu7) ... 262s Setting up libgnutls-dane0t64:armhf (3.8.6-2ubuntu1) ... 262s Setting up libssl-dev:armhf (3.3.1-2ubuntu2) ... 262s Setting up libmpc3:armhf (1.3.1-1build2) ... 262s Setting up cython3 (3.0.11+dfsg-1ubuntu1) ... 263s Setting up autopoint (0.22.5-2) ... 263s Setting up pkgconf-bin (1.8.1-3ubuntu1) ... 263s Setting up libidn2-dev:armhf (2.3.7-2build2) ... 263s Setting up autoconf (2.72-3) ... 263s Setting up python3-pluggy (1.5.0-1) ... 263s Setting up liblzma-dev:armhf (5.6.2-2) ... 263s Setting up libubsan1:armhf (14.2.0-7ubuntu1) ... 263s Setting up dwz (0.15-1build6) ... 263s Setting up libcrypt-dev:armhf (1:4.4.36-4build1) ... 263s Setting up libasan8:armhf (14.2.0-7ubuntu1) ... 263s Setting up debugedit (1:5.1-1) ... 263s Setting up libhts3t64:armhf (1.20+ds-2) ... 263s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 263s Setting up libgcc-14-dev:armhf (14.2.0-7ubuntu1) ... 263s Setting up libisl23:armhf (0.27-1) ... 263s Setting up libc-dev-bin (2.40-1ubuntu3) ... 263s Setting up libtasn1-6-dev:armhf (4.19.0-3build1) ... 263s Setting up libdeflate-dev:armhf (1.21-1) ... 263s Setting up tabix (1.20+ds-2) ... 263s Setting up libcc1-0:armhf (14.2.0-7ubuntu1) ... 263s Setting up libbrotli-dev:armhf (1.1.0-2build2) ... 263s Setting up libp11-kit-dev:armhf (0.25.5-2ubuntu1) ... 263s Setting up cpp-14-arm-linux-gnueabihf (14.2.0-7ubuntu1) ... 263s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 263s Setting up automake (1:1.16.5-1.3ubuntu1) ... 263s update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode 263s Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... 263s Setting up gettext (0.22.5-2) ... 263s Setting up python3-pysam (0.22.1+ds-2) ... 263s Setting up libgmp-dev:armhf (2:6.3.0+dfsg-2ubuntu7) ... 263s Setting up nettle-dev:armhf (3.10-1) ... 263s Setting up python3-pytest (8.3.2-1) ... 264s Setting up bcftools (1.20-2) ... 264s Setting up gcc-14-arm-linux-gnueabihf (14.2.0-7ubuntu1) ... 264s Setting up pkgconf:armhf (1.8.1-3ubuntu1) ... 264s Setting up samtools (1.20-3) ... 264s Setting up intltool-debian (0.35.0+20060710.6) ... 264s Setting up libjs-sphinxdoc (7.4.7-3) ... 264s Setting up cpp-14 (14.2.0-7ubuntu1) ... 264s Setting up dh-strip-nondeterminism (1.14.0-1) ... 264s Setting up libc6-dev:armhf (2.40-1ubuntu3) ... 264s Setting up libstdc++-14-dev:armhf (14.2.0-7ubuntu1) ... 264s Setting up cpp-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 264s Setting up libbz2-dev:armhf (1.0.8-6) ... 264s Setting up gcc-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 264s Setting up libgnutls28-dev:armhf (3.8.6-2ubuntu1) ... 264s Setting up libnghttp2-dev:armhf (1.62.1-2) ... 264s Setting up g++-14-arm-linux-gnueabihf (14.2.0-7ubuntu1) ... 264s Setting up po-debconf (1.0.21+nmu1) ... 264s Setting up gcc-14 (14.2.0-7ubuntu1) ... 264s Setting up libexpat1-dev:armhf (2.6.2-2) ... 264s Setting up zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 264s Setting up cpp (4:14.1.0-2ubuntu1) ... 264s Setting up g++-14 (14.2.0-7ubuntu1) ... 264s Setting up g++-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 264s Setting up libtool (2.4.7-7build1) ... 264s Setting up libpython3.12-dev:armhf (3.12.7-1) ... 264s Setting up gcc (4:14.1.0-2ubuntu1) ... 264s Setting up dh-autoreconf (20) ... 264s Setting up librtmp-dev:armhf (2.4+20151223.gitfa8646d.1-2build7) ... 264s Setting up python3.12-dev (3.12.7-1) ... 264s Setting up libssh2-1-dev:armhf (1.11.0-7) ... 264s Setting up g++ (4:14.1.0-2ubuntu1) ... 264s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 264s Setting up build-essential (12.10ubuntu1) ... 264s Setting up libpython3-dev:armhf (3.12.6-0ubuntu1) ... 264s Setting up debhelper (13.20ubuntu1) ... 264s Setting up libcurl4-gnutls-dev:armhf (8.9.1-2ubuntu2) ... 264s Setting up libpython3-all-dev:armhf (3.12.6-0ubuntu1) ... 264s Setting up python3-dev (3.12.6-0ubuntu1) ... 264s Setting up python3-all-dev (3.12.6-0ubuntu1) ... 264s Setting up libhts-dev:armhf (1.20+ds-2) ... 264s Setting up autopkgtest-satdep (0) ... 264s Processing triggers for man-db (2.12.1-3) ... 265s Processing triggers for install-info (7.1.1-1) ... 265s Processing triggers for libc-bin (2.40-1ubuntu3) ... 282s (Reading database ... 65740 files and directories currently installed.) 282s Removing autopkgtest-satdep (0) ... 290s autopkgtest [00:47:26]: test command1: export HOME=$PWD && make -C tests/pysam_data && make -C tests/cbcf_data && pytest-3 290s autopkgtest [00:47:26]: test command1: [----------------------- 292s make: Entering directory '/tmp/autopkgtest.OEVu7F/build.w8D/src/tests/pysam_data' 292s samtools faidx ex1.fa 292s samtools view --no-PG -bo ex1.bam -t ex1.fa.fai ex1.sam.gz 292s samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz 292s [mpileup] 1 samples in 1 input files 292s gunzip < ex1.sam.gz > ex1.sam 292s samtools index ex1.bam 292s samtools view --no-PG -h ex1.bam | gzip > ex2.sam.gz 292s gunzip < ex2.sam.gz > ex2.sam 292s samtools view --no-PG -bo ex2.bam ex2.sam 292s samtools index ex2.bam 292s samtools calmd --no-PG --output-fmt BAM ex2.bam ex1.fa > with_md.sam.gz 292s [bam_fillmd1] different NM for read 'EAS139_11:7:46:695:738': 3 -> 8 292s [bam_fillmd1] different NM for read 'EAS218_4:1:48:9:409': 0 -> 5 292s [bam_fillmd1] different NM for read 'B7_591:7:200:192:373': 0 -> 5 292s [bam_fillmd1] different NM for read 'EAS56_65:1:163:846:223': 0 -> 5 292s [bam_fillmd1] different NM for read 'EAS114_30:7:283:799:560': 0 -> 5 292s [bam_fillmd1] different NM for read 'B7_595:4:84:802:737': 0 -> 4 292s [bam_fillmd1] different NM for read 'EAS51_66:5:308:400:602': 0 -> 3 292s [bam_fillmd1] different NM for read 'EAS54_81:2:285:367:932': 0 -> 3 292s [bam_fillmd1] different NM for read 'EAS114_39:1:70:147:84': 0 -> 3 292s [bam_fillmd1] different NM for read 'EAS56_53:1:124:243:35': 2 -> 5 292s [bam_fillmd1] different NM for read 'EAS1_103:2:226:302:758': 2 -> 3 292s [bam_fillmd1] different NM for read 'EAS114_28:6:175:705:982': 1 -> 0 292s [bam_fillmd1] different NM for read 'EAS51_64:4:179:389:585': 7 -> 8 292s [bam_fillmd1] different NM for read 'B7_589:1:122:337:968': 3 -> 2 292s [bam_fillmd1] different NM for read 'B7_610:4:15:805:420': 4 -> 5 292s [bam_fillmd1] different NM for read 'B7_591:2:279:124:41': 2 -> 4 292s [bam_fillmd1] different NM for read 'EAS112_32:8:89:254:332': 0 -> 1 292s [bam_fillmd1] different NM for read 'B7_597:7:103:731:697': 0 -> 2 292s [bam_fillmd1] different NM for read 'EAS139_11:2:71:83:58': 0 -> 2 292s [bam_fillmd1] different NM for read 'EAS192_3:4:63:5:870': 0 -> 2 292s [bam_fillmd1] different NM for read 'EAS139_19:2:29:1822:1881': 0 -> 2 292s [bam_fillmd1] different NM for read 'EAS188_7:3:15:568:42': 2 -> 1 292s [bam_fillmd1] different NM for read 'EAS1_95:4:176:971:874': 0 -> 1 292s [bam_fillmd1] different NM for read 'EAS1_99:1:34:649:318': 3 -> 4 292s [bam_fillmd1] different NM for read 'EAS54_65:4:61:346:384': 3 -> 4 292s [bam_fillmd1] different NM for read 'B7_597:6:20:592:496': 0 -> 1 292s [bam_fillmd1] different NM for read 'B7_597:4:38:999:463': 2 -> 1 292s [bam_fillmd1] different NM for read 'EAS114_28:5:23:944:377': 0 -> 3 292s [bam_fillmd1] different NM for read 'EAS219_1:3:90:219:528': 0 -> 3 292s [bam_fillmd1] different NM for read 'EAS1_108:5:89:942:84': 0 -> 4 292s [bam_fillmd1] different NM for read 'EAS1_108:6:159:493:275': 0 -> 5 292s [bam_fillmd1] different NM for read 'EAS139_11:1:81:1019:558': 0 -> 5 292s [bam_fillmd1] different NM for read 'EAS51_62:7:162:195:761': 0 -> 4 292s [bam_fillmd1] different NM for read 'B7_597:3:115:646:430': 0 -> 4 292s [bam_fillmd1] different NM for read 'EAS114_30:6:243:209:110': 0 -> 4 292s [bam_fillmd1] different NM for read 'EAS1_108:2:266:994:429': 0 -> 4 292s [bam_fillmd1] different NM for read 'EAS114_30:5:32:461:154': 0 -> 4 292s [bam_fillmd1] different NM for read 'EAS114_39:6:7:492:1088': 0 -> 4 292s [bam_fillmd1] different NM for read 'EAS1_95:6:174:650:125': 0 -> 4 292s [bam_fillmd1] different NM for read 'EAS56_59:6:89:457:591': 1 -> 5 292s [bam_fillmd1] different NM for read 'EAS114_39:2:38:670:564': 0 -> 4 292s [bam_fillmd1] different NM for read 'EAS188_7:4:92:693:228': 1 -> 6 292s [bam_fillmd1] different NM for read 'EAS218_1:4:61:1369:440': 0 -> 4 292s [bam_fillmd1] different NM for read 'EAS114_26:4:123:1001:580': 0 -> 4 292s [bam_fillmd1] different NM for read 'EAS114_39:4:10:1312:1558': 0 -> 4 292s [bam_fillmd1] different NM for read 'EAS220_1:8:45:178:1321': 0 -> 4 292s [bam_fillmd1] different NM for read 'EAS56_59:5:125:137:58': 0 -> 4 292s [bam_fillmd1] different NM for read 'EAS192_3:3:285:349:797': 1 -> 5 292s [bam_fillmd1] different NM for read 'EAS114_45:5:56:1757:1319': 0 -> 4 292s [bam_fillmd1] different NM for read 'B7_591:3:291:404:199': 0 -> 4 292s [bam_fillmd1] different NM for read 'EAS54_65:7:159:253:353': 0 -> 4 292s [bam_fillmd1] different NM for read 'EAS56_57:1:122:38:103': 0 -> 4 292s [bam_fillmd1] different NM for read 'EAS188_4:5:103:870:105': 0 -> 4 292s [bam_fillmd1] different NM for read 'EAS1_105:8:24:718:322': 3 -> 7 292s [bam_fillmd1] different NM for read 'EAS51_64:6:118:41:489': 0 -> 4 292s [bam_fillmd1] different NM for read 'EAS56_61:3:165:665:220': 0 -> 4 292s [bam_fillmd1] different NM for read 'EAS114_30:6:238:803:383': 0 -> 4 292s [bam_fillmd1] different NM for read 'EAS1_105:3:232:364:583': 0 -> 3 292s [bam_fillmd1] different NM for read 'B7_595:2:29:729:70': 3 -> 4 292s [bam_fillmd1] different NM for read 'EAS114_30:6:220:809:850': 4 -> 6 292s [bam_fillmd1] different NM for read 'EAS54_65:2:264:157:150': 3 -> 5 292s [bam_fillmd1] different NM for read 'B7_595:8:26:242:35': 2 -> 1 292s [bam_fillmd1] different NM for read 'B7_610:7:34:144:868': 4 -> 5 292s [bam_fillmd1] different NM for read 'B7_597:8:147:360:141': 1 -> 2 292s [bam_fillmd1] different NM for read 'EAS139_19:2:82:154:1333': 0 -> 4 292s [bam_fillmd1] different NM for read 'EAS56_63:3:41:468:459': 0 -> 3 292s [bam_fillmd1] different NM for read 'EAS1_97:4:274:287:423': 0 -> 1 292s [bam_fillmd1] different NM for read 'EAS114_30:2:303:428:326': 0 -> 1 292s [bam_fillmd1] different NM for read 'EAS54_71:8:105:854:975': 0 -> 3 292s gunzip < with_md.sam.gz > with_md.sam 292s samtools view --no-PG -bo with_md.bam with_md.sam 292s samtools index with_md.bam 292s samtools view --no-PG -bu -o uncompressed.bam ex2.sam 292s [W::bam_hdr_read] EOF marker is absent. The input is probably truncated 292s samtools view --no-PG -bo MM-chebi.bam MM-chebi.sam 292s samtools view --no-PG -bo MM-double.bam MM-double.sam 292s samtools view --no-PG -bo MM-multi.bam MM-multi.sam 292s samtools view --no-PG -bo MM-orient.bam MM-orient.sam 292s samtools view --no-PG -bo ex10.bam ex10.sam 292s samtools view --no-PG -bo ex3.bam ex3.sam 292s samtools view --no-PG -bo ex4.bam ex4.sam 292s samtools view --no-PG -bo ex5.bam ex5.sam 292s samtools view --no-PG -bo ex6.bam ex6.sam 292s samtools view --no-PG -bo ex8.bam ex8.sam 292s samtools view --no-PG -bo ex9_fail.bam ex9_fail.sam 292s samtools view --no-PG -bo ex9_nofail.bam ex9_nofail.sam 292s samtools view --no-PG -bo ex_spliced.bam ex_spliced.sam 292s samtools view --no-PG -bo example_aligned_pairs.bam example_aligned_pairs.sam 292s samtools view --no-PG -bo example_btag.bam example_btag.sam 292s samtools view --no-PG -bo example_dash_in_chr.bam example_dash_in_chr.sam 292s samtools view --no-PG -bo example_empty_header.bam example_empty_header.sam 292s samtools view --no-PG -bo example_empty_with_header.bam example_empty_with_header.sam 292s samtools view --no-PG -bo example_reverse_complement.bam example_reverse_complement.sam 292s touch tmp.list 292s samtools view --no-PG -bo example_unmapped_reads_no_sq.bam -t tmp.list example_unmapped_reads_no_sq.sam 292s rm -f tmp.list 292s samtools view --no-PG -bo issue100.bam issue100.sam 292s samtools view --no-PG -bo rg_with_tab.bam rg_with_tab.sam 292s samtools view --no-PG -bo softclip.bam softclip.sam 292s samtools view --no-PG -bo tag_bug.bam tag_bug.sam 292s samtools view --no-PG -bo test_mapped_unmapped.bam test_mapped_unmapped.sam 292s samtools view --no-PG -bo test_query_position.bam test_query_position.sam 292s samtools view --no-PG -bo test_unaligned.bam test_unaligned.sam 292s samtools index MM-chebi.bam 292s samtools index MM-double.bam 292s samtools index MM-multi.bam 292s samtools index MM-orient.bam 292s samtools index ex10.bam 292s samtools index ex3.bam 292s samtools index ex4.bam 292s samtools index ex5.bam 292s samtools index ex6.bam 292s samtools index ex8.bam 292s samtools index ex9_fail.bam 292s samtools index ex9_nofail.bam 292s samtools index ex_spliced.bam 292s samtools index example_aligned_pairs.bam 292s samtools index example_btag.bam 292s samtools index example_dash_in_chr.bam 292s samtools index example_empty_header.bam 292s samtools index example_empty_with_header.bam 292s samtools index example_reverse_complement.bam 292s samtools index example_unmapped_reads_no_sq.bam 292s samtools index issue100.bam 292s samtools index rg_with_tab.bam 292s samtools index softclip.bam 292s samtools index tag_bug.bam 292s samtools index test_mapped_unmapped.bam 292s samtools index test_query_position.bam 292s samtools index test_unaligned.bam 292s samtools view --no-PG -Co ex1.cram -T ex1.fa ex1.sam 292s samtools view --no-PG -Co ex2.cram -T ex1.fa ex2.sam 292s samtools view --no-PG -Co ex3.cram -T ex1.fa ex3.sam 292s samtools index ex1.cram 292s samtools index ex2.cram 292s samtools index ex3.cram 292s cp ex1.bam example_bai.bam 292s samtools index example_bai.bam 292s mv example_bai.bam.bai example_bai.bai 292s dd if=ex2.bam of=ex2_truncated.bam bs=$((`wc -c < ex2.bam`-512)) count=1 292s 1+0 records in 292s 1+0 records out 292s 122288 bytes (122 kB, 119 KiB) copied, 0.000274681 s, 445 MB/s 292s (bgzip -d < ex2.bam; printf '\37\0\0\0\1\0\0\0') | bgzip > ex2_corrupt.bam 292s grep "^@" ex2.sam | samtools view --no-PG -bo empty.bam - 292s samtools index empty.bam 292s cp ex1.bam explicit_index.bam 292s cp ex1.cram explicit_index.cram 292s gzip < faidx_empty_seq.fq > faidx_empty_seq.fq.gz 292s bgzip < ex1.fa > ex1.fa.gz 292s samtools faidx ex1.fa.gz 292s cp ex1.bam ex1_csi.bam 292s samtools index -c ex1_csi.bam 292s touch all.stamp 292s rm with_md.sam 292s make: Leaving directory '/tmp/autopkgtest.OEVu7F/build.w8D/src/tests/pysam_data' 292s make: Entering directory '/tmp/autopkgtest.OEVu7F/build.w8D/src/tests/cbcf_data' 292s bgzip < example_vcf40.vcf > example_vcf40.vcf.gz 292s tabix -p vcf example_vcf40.vcf.gz # create tbi index 292s bcftools index example_vcf40.vcf.gz # create csi index 292s bgzip < example_vcf42.vcf > example_vcf42.vcf.gz 292s tabix -p vcf example_vcf42.vcf.gz # create tbi index 292s bcftools index example_vcf42.vcf.gz # create csi index 292s bgzip < example_vcf42_only_header.vcf > example_vcf42_only_header.vcf.gz 293s tabix -p vcf example_vcf42_only_header.vcf.gz # create tbi index 293s bcftools index example_vcf42_only_header.vcf.gz # create csi index 293s bgzip < example_vcf42_withcontigs.vcf > example_vcf42_withcontigs.vcf.gz 293s tabix -p vcf example_vcf42_withcontigs.vcf.gz # create tbi index 293s bcftools index example_vcf42_withcontigs.vcf.gz # create csi index 293s bgzip < example_vcf43.vcf > example_vcf43.vcf.gz 293s tabix -p vcf example_vcf43.vcf.gz # create tbi index 293s bcftools index example_vcf43.vcf.gz # create csi index 293s bgzip < example_vcf43_with_utf8.vcf > example_vcf43_with_utf8.vcf.gz 293s tabix -p vcf example_vcf43_with_utf8.vcf.gz # create tbi index 293s bcftools index example_vcf43_with_utf8.vcf.gz # create csi index 293s bgzip < gnomad.vcf > gnomad.vcf.gz 293s tabix -p vcf gnomad.vcf.gz # create tbi index 293s bcftools index gnomad.vcf.gz # create csi index 293s bgzip < gnomad_fixed.vcf > gnomad_fixed.vcf.gz 293s tabix -p vcf gnomad_fixed.vcf.gz # create tbi index 293s bcftools index gnomad_fixed.vcf.gz # create csi index 293s bgzip < missing_genotypes.vcf > missing_genotypes.vcf.gz 293s tabix -p vcf missing_genotypes.vcf.gz # create tbi index 293s bcftools index missing_genotypes.vcf.gz # create csi index 293s bcftools view -O b example_vcf40.vcf.gz -o example_vcf40.bcf 293s bcftools index example_vcf40.bcf 293s bcftools view -O b example_vcf42.vcf.gz -o example_vcf42.bcf 293s bcftools index example_vcf42.bcf 293s bcftools view -O b example_vcf42_only_header.vcf.gz -o example_vcf42_only_header.bcf 293s bcftools index example_vcf42_only_header.bcf 293s bcftools view -O b example_vcf42_withcontigs.vcf.gz -o example_vcf42_withcontigs.bcf 293s bcftools index example_vcf42_withcontigs.bcf 293s bcftools view -O b example_vcf43.vcf.gz -o example_vcf43.bcf 293s bcftools index example_vcf43.bcf 293s bcftools view -O b example_vcf43_with_utf8.vcf.gz -o example_vcf43_with_utf8.bcf 293s bcftools index example_vcf43_with_utf8.bcf 293s bcftools view -O b gnomad.vcf.gz -o gnomad.bcf 293s bcftools index gnomad.bcf 293s bcftools view -O b gnomad_fixed.vcf.gz -o gnomad_fixed.bcf 293s [W::bcf_hdr_check_sanity] PL should be declared as Number=G 293s bcftools index gnomad_fixed.bcf 293s [W::bcf_hdr_check_sanity] PL should be declared as Number=G 293s bcftools view -O b missing_genotypes.vcf.gz -o missing_genotypes.bcf 293s bcftools index missing_genotypes.bcf 293s touch all.stamp 293s make: Leaving directory '/tmp/autopkgtest.OEVu7F/build.w8D/src/tests/cbcf_data' 293s ============================= test session starts ============================== 293s platform linux -- Python 3.12.7, pytest-8.3.2, pluggy-1.5.0 -- /usr/bin/python3 293s cachedir: .pytest_cache 293s rootdir: /tmp/autopkgtest.OEVu7F/build.w8D/src 293s configfile: setup.cfg 293s testpaths: pysam, tests 293s plugins: typeguard-4.3.0 294s collecting ... collected 951 items 294s 294s tests/AlignedSegment_test.py::TestAlignedSegment::testBlocks PASSED 294s tests/AlignedSegment_test.py::TestAlignedSegment::testCompare PASSED 294s tests/AlignedSegment_test.py::TestAlignedSegment::testEmpty PASSED 294s tests/AlignedSegment_test.py::TestAlignedSegment::testFullReferencePositions PASSED 294s tests/AlignedSegment_test.py::TestAlignedSegment::testHashing PASSED 294s tests/AlignedSegment_test.py::TestAlignedSegment::testLargeRead PASSED 294s tests/AlignedSegment_test.py::TestAlignedSegment::testNoSequence PASSED 294s tests/AlignedSegment_test.py::TestAlignedSegment::testPositions PASSED 294s tests/AlignedSegment_test.py::TestAlignedSegment::testSettingTagInEmptyRead PASSED 294s tests/AlignedSegment_test.py::TestAlignedSegment::testStrOfEmptyRead PASSED 294s tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate PASSED 294s tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate2 PASSED 294s tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateQual PASSED 294s tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateTlen PASSED 294s tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_mapped_reads_are_updated PASSED 294s tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_unmapped_reads_ignore_length PASSED 294s tests/AlignedSegment_test.py::TestAlignedSegment::test_equivalence_matches_only_and_with_seq PASSED 294s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs PASSED 294s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_1character_md PASSED 294s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_bad_type_md PASSED 294s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_hard_clipping PASSED 294s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_lowercase_md PASSED 294s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_match_mismatch PASSED 294s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding PASSED 294s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding_with_seq PASSED 294s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip PASSED 294s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip_reference PASSED 294s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_soft_clipping PASSED 294s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_uppercase_md PASSED 294s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_with_malformed_MD_tag PASSED 294s tests/AlignedSegment_test.py::TestAlignedSegment::test_header_accessible PASSED 294s tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_query_length PASSED 294s tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_read_length PASSED 294s tests/AlignedSegment_test.py::TestAlignedSegment::test_query_length_is_limited PASSED 294s tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_asterisk PASSED 294s tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_chromosome PASSED 294s tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_none PASSED 294s tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_not_be_set_to_unknown_chromosome PASSED 294s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_chromosome PASSED 294s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing PASSED 294s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing_without_header PASSED 294s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_without_header PASSED 294s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_not_be_set_to_unknown_chromosome PASSED 294s tests/AlignedSegment_test.py::TestTidMapping::test_unmapped_tid_is_asterisk_in_output PASSED 294s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_asterisk PASSED 294s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_chromosome PASSED 294s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_none PASSED 294s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_not_be_set_to_unknown_chromosome PASSED 294s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_chromosome PASSED 294s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_equal PASSED 294s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing PASSED 294s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing_without_header PASSED 294s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_without_header PASSED 294s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_not_be_set_to_unknown_chromosome PASSED 294s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_unmapped_tid_is_asterisk_in_output PASSED 294s tests/AlignedSegment_test.py::TestCigar::testCigar PASSED 294s tests/AlignedSegment_test.py::TestCigar::testCigarString PASSED 294s tests/AlignedSegment_test.py::TestCigarStats::testStats PASSED 294s tests/AlignedSegment_test.py::TestAlignedPairs::testReferenceBases PASSED 294s tests/AlignedSegment_test.py::TestBaseModifications::testChebi PASSED 294s tests/AlignedSegment_test.py::TestBaseModifications::testDouble PASSED 294s tests/AlignedSegment_test.py::TestBaseModifications::testMulti PASSED 294s tests/AlignedSegment_test.py::TestBaseModifications::testOrient PASSED 294s tests/AlignedSegment_test.py::TestTags::testAddTags PASSED 294s tests/AlignedSegment_test.py::TestTags::testAddTagsType PASSED 294s tests/AlignedSegment_test.py::TestTags::testArrayTags PASSED 294s tests/AlignedSegment_test.py::TestTags::testEmptyTag PASSED 294s tests/AlignedSegment_test.py::TestTags::testLongTags PASSED 294s tests/AlignedSegment_test.py::TestTags::testMDTagComplex PASSED 294s tests/AlignedSegment_test.py::TestTags::testMDTagDeletions PASSED 294s tests/AlignedSegment_test.py::TestTags::testMDTagInsertions PASSED 294s tests/AlignedSegment_test.py::TestTags::testMDTagMatchOnly PASSED 294s tests/AlignedSegment_test.py::TestTags::testMDTagRefSkipping PASSED 294s tests/AlignedSegment_test.py::TestTags::testMDTagSoftClipping PASSED 294s tests/AlignedSegment_test.py::TestTags::testMissingTag PASSED 294s tests/AlignedSegment_test.py::TestTags::testNegativeIntegers PASSED 294s tests/AlignedSegment_test.py::TestTags::testNegativeIntegersWrittenToFile PASSED 294s tests/AlignedSegment_test.py::TestTags::testSetTag PASSED 294s tests/AlignedSegment_test.py::TestTags::testTagParsing PASSED 294s tests/AlignedSegment_test.py::TestTags::testTagsUpdatingFloat PASSED 294s tests/AlignedSegment_test.py::TestCopy::testCopy PASSED 294s tests/AlignedSegment_test.py::TestCopy::testDeepCopy PASSED 294s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_A PASSED 294s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_C PASSED 294s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_H PASSED 294s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_I PASSED 294s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_S PASSED 294s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_a PASSED 294s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_automated_type_detection PASSED 294s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_c PASSED 294s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_d PASSED 294s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_f PASSED 294s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_i PASSED 294s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_s PASSED 294s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_A PASSED 294s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_C PASSED 294s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_H PASSED 294s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_I PASSED 294s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_S PASSED 294s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_a PASSED 294s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_automated_type_detection PASSED 294s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_c PASSED 294s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_d PASSED 294s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_f PASSED 294s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_i PASSED 294s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_s PASSED 294s tests/AlignedSegment_test.py::TestEnums::test_cigar_enums_are_defined PASSED 294s tests/AlignedSegment_test.py::TestEnums::test_sam_flags_are_defined PASSED 294s tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_constructed_without_header PASSED 294s tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_written_to_file PASSED 294s tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_id_can_be_set PASSED 294s tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_name_is_not_available PASSED 294s tests/AlignedSegment_test.py::TestForwardStrandValues::test_qualities_are_complemented PASSED 294s tests/AlignedSegment_test.py::TestForwardStrandValues::test_sequence_is_complemented PASSED 294s tests/AlignedSegment_test.py::TestExportImport::test_dict_export PASSED 294s tests/AlignedSegment_test.py::TestExportImport::test_string_export PASSED 294s tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_with_tags PASSED 294s tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_without_tags PASSED 294s tests/AlignedSegment_test.py::TestExportImport::test_to_string_without_alignment_file PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_dict PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_header PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references_without_text PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_text PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_access_works PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_contains_works PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_get_works PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_keys_works PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_len_works PASSED[E::cram_index_load] Could not retrieve index file for '/tmp/autopkgtest.OEVu7F/build.w8D/src/tests/tmp/pysamtests_tmp_check_read_write_d3bqp7tn' 294s [W::sanitise_SQ_lines] Header @SQ length mismatch for ref chr1, 2147483647 vs 1575 294s [E::cram_index_load] Could not retrieve index file for '/tmp/autopkgtest.OEVu7F/build.w8D/src/tests/tmp/pysamtests_tmp_check_read_write_9rkb3ziw' 294s 294s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_setting_raises_error PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_values_works PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_header_content_is_as_expected PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_name_mapping PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_text_access_works PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_contains_works PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_get_works PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_keys_works PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_len_works PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_setting_raises_error PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_values_works PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_name_mapping PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_text_access_works PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_contains_works PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_get_works PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_keys_works PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_len_works PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_setting_raises_error PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_values_works PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_name_mapping PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_text_access_works PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM /tmp/autopkgtest.OEVu7F/build.w8D/src/tests/tmp/pysamtests_tmp_check_read_write_jy3z17cu 294s PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM /tmp/autopkgtest.OEVu7F/build.w8D/src/tests/tmp/pysamtests_tmp_check_read_write_d3bqp7tn 294s PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /tmp/autopkgtest.OEVu7F/build.w8D/src/tests/tmp/pysamtests_tmp_check_read_write_vddnkzmv 294s PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM /tmp/autopkgtest.OEVu7F/build.w8D/src/tests/tmp/pysamtests_tmp_check_read_write_j5efk_br 294s PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM /tmp/autopkgtest.OEVu7F/build.w8D/src/tests/tmp/pysamtests_tmp_check_read_write_9rkb3ziw 294s PASSED 294s tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM /tmp/autopkgtest.OEVu7F/build.w8D/src/tests/tmp/pysamtests_tmp_check_read_write_kjq6jxvy 294s PASSED 294s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_all_stepper PASSED 294s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_ignore_overlaps PASSED 294s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper PASSED 294s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_base_quality_threshold PASSED 294s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_ignore_orphans PASSED 294s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_mapping_quality_threshold PASSED 295s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_redo_baq PASSED 295s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_all_stepper PASSED 295s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_ignore_overlaps PASSED 295s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper PASSED 295s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_base_quality_threshold PASSED 295s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_ignore_orphans PASSED 295s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_mapping_quality_threshold PASSED 295s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_redo_baq PASSED 295s tests/AlignmentFilePileup_test.py::TestPileupQueryPosition::testPileup PASSED 295s tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope SKIPPED 295s tests/AlignmentFilePileup_test.py::TestPileupObjects::testPileupColumn PASSED 295s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testInverse PASSED 295s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateAll PASSED 295s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIteratePerContig PASSED 295s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateRanges PASSED 295s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateTruncate PASSED 295s tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testAccessOnClosedIterator PASSED 295s tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStart PASSED 295s tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStr PASSED 295s tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testTruncate PASSED 295s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_depths_are_equal PASSED 295s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_mapping_qualities_are_equal PASSED 295s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_with_reference_are_equal PASSED 295s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_without_reference_are_equal PASSED 295s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_are_equal PASSED 295s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_from_pileups_are_equal PASSED 295s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARQueryLength PASSED 295s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigar PASSED 295s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigarstring PASSED 295s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARflag PASSED 295s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmapq PASSED 295s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmpos PASSED 295s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmrnm PASSED 295s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARpos PASSED 295s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqname PASSED 295s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqqual PASSED 295s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqual PASSED 295s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARquery PASSED 295s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARrname PASSED 295s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARseq PASSED 295s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testOpt PASSED 295s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPairedBools PASSED 295s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPresentOptionalFields PASSED 295s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testTags PASSED 295s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARQueryLength PASSED 295s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigar PASSED 295s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigarstring PASSED 295s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARflag PASSED 295s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmapq PASSED 295s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmpos PASSED 295s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmrnm PASSED 295s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARpos PASSED 295s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqname PASSED 295s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqqual PASSED 295s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqual PASSED 295s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARquery PASSED 296s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARrname PASSED 296s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARseq PASSED 296s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testOpt PASSED 296s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPairedBools PASSED 296s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPresentOptionalFields PASSED 296s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testTags PASSED 296s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARQueryLength PASSED 296s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigar PASSED 297s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigarstring PASSED 297s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARflag PASSED 298s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmapq PASSED 298s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmpos PASSED 298s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmrnm PASSED 299s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARpos PASSED 299s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqname PASSED 299s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqqual PASSED 300s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqual PASSED 300s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARquery PASSED 300s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARrname PASSED 301s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARseq PASSED 301s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testOpt PASSED 301s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPairedBools PASSED 302s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPresentOptionalFields PASSED 302s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testTags PASSED 302s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARQueryLength PASSED 302s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigar PASSED 302s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigarstring PASSED 302s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARflag PASSED 302s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmapq PASSED 302s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmpos PASSED 302s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmrnm PASSED 302s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARpos PASSED 302s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqname PASSED 302s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqqual PASSED 302s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqual PASSED 302s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARquery PASSED 302s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARrname PASSED 302s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARseq PASSED 302s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testOpt PASSED 302s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPairedBools PASSED 302s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPresentOptionalFields PASSED 302s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testTags PASSED 303s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARQueryLength PASSED 303s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigar PASSED 303s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigarstring PASSED 304s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARflag PASSED 304s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmapq PASSED 304s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmpos PASSED 305s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmrnm PASSED 305s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARpos PASSED 305s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqname PASSED 306s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqqual PASSED 306s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqual PASSED 307s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARquery PASSED 307s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARrname PASSED 307s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARseq PASSED 308s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testOpt PASSED 308s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPairedBools PASSED 308s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPresentOptionalFields PASSED 309s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testTags PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARQueryLength PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigar PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigarstring PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARflag PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmapq PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmpos PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmrnm PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARpos PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqname PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqqual PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqual PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARquery PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARrname PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARseq PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testOpt PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPairedBools PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPresentOptionalFields PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testTags PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARQueryLength PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigar PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigarstring PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARflag PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmapq PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmpos PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmrnm PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARpos PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqname PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqqual PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqual PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARquery PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARrname PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARseq PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testOpt PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPairedBools PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPresentOptionalFields PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testTags PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARQueryLength PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigar PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigarstring PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARflag PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmapq PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmpos PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmrnm PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARpos PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqname PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqqual PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqual PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARquery PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARrname PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARseq PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testOpt PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPairedBools PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPresentOptionalFields PASSED 309s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testTags PASSED 309s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARQueryLength PASSED 309s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigar PASSED 309s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigarstring PASSED 309s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARflag PASSED 309s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmapq PASSED 309s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmpos PASSED 309s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmrnm PASSED 309s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARpos PASSED 309s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqname PASSED 309s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqqual PASSED 309s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqual PASSED 309s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARquery PASSED 309s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARrname PASSED 309s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARseq PASSED 309s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testOpt PASSED 309s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPairedBools PASSED 309s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPresentOptionalFields PASSED 309s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testTags PASSED 309s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARQueryLength PASSED 309s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigar PASSED 309s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigarstring PASSED 309s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARflag PASSED 309s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmapq PASSED 309s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmpos PASSED 309s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmrnm PASSED 309s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARpos PASSED 309s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqname PASSED 309s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqqual PASSED 309s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqual PASSED 309s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARquery PASSED 309s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARrname PASSED 309s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARseq PASSED 309s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testOpt PASSED 309s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPairedBools PASSED 309s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPresentOptionalFields PASSED 309s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testTags PASSED 309s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARQueryLength PASSED 310s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigar PASSED 310s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigarstring PASSED 310s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARflag PASSED 311s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmapq PASSED 311s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmpos PASSED 311s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmrnm PASSED 312s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARpos PASSED 312s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqname PASSED 313s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqqual PASSED 313s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqual PASSED 313s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARquery PASSED 314s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARrname PASSED 314s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARseq PASSED 314s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testOpt PASSED 315s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPairedBools PASSED 315s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPresentOptionalFields PASSED 316s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testTags PASSED 316s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARQueryLength PASSED 316s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigar PASSED 317s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigarstring PASSED 317s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARflag PASSED 318s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmapq PASSED 318s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmpos PASSED 318s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmrnm PASSED 319s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARpos PASSED 319s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqname PASSED 319s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqqual PASSED 320s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqual PASSED 320s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARquery PASSED 321s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARrname PASSED 321s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARseq PASSED 321s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testOpt PASSED 322s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPairedBools PASSED 322s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPresentOptionalFields PASSED 322s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testTags PASSED 322s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARQueryLength PASSED 322s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigar PASSED 322s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigarstring PASSED 322s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARflag PASSED 322s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmapq PASSED 322s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmpos PASSED 322s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmrnm PASSED 322s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARpos PASSED 322s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqname PASSED 322s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqqual PASSED 322s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqual PASSED 322s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARquery PASSED 322s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARrname PASSED 322s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARseq PASSED 322s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testOpt PASSED 322s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPairedBools PASSED 322s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPresentOptionalFields PASSED 322s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testRaises PASSED 322s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testTags PASSED 322s tests/AlignmentFile_test.py::TestIO::testBAM2BAM PASSED 323s tests/AlignmentFile_test.py::TestIO::testBAM2SAM PASSED 323s tests/AlignmentFile_test.py::TestIO::testBAMWithCSIIndex PASSED 323s tests/AlignmentFile_test.py::TestIO::testBAMWithShortBAI PASSED 323s tests/AlignmentFile_test.py::TestIO::testBAMWithoutAlignedSegments PASSED 323s tests/AlignmentFile_test.py::TestIO::testCRAM2BAM PASSED 324s tests/AlignmentFile_test.py::TestIO::testCRAM2CRAM PASSED 325s tests/AlignmentFile_test.py::TestIO::testCRAM2SAM PASSED 325s tests/AlignmentFile_test.py::TestIO::testEmptyBAM PASSED 325s tests/AlignmentFile_test.py::TestIO::testEmptyWithHeaderBAM PASSED 325s tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFile PASSED 325s tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject PASSED 325s tests/AlignmentFile_test.py::TestIO::testHead PASSED 325s tests/AlignmentFile_test.py::TestIO::testOpenFromFilename PASSED 325s tests/AlignmentFile_test.py::TestIO::testReadBamWithoutTargetNames PASSED 325s tests/AlignmentFile_test.py::TestIO::testReadSamWithoutTargetNames PASSED 325s tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex PASSED 325s tests/AlignmentFile_test.py::TestIO::testSAM2BAM PASSED 325s tests/AlignmentFile_test.py::TestIO::testSAM2CRAM PASSED 326s tests/AlignmentFile_test.py::TestIO::testSAM2SAM PASSED 326s tests/AlignmentFile_test.py::TestIO::testSAM2SAMWithoutHeader PASSED 326s tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile PASSED 326s tests/AlignmentFile_test.py::TestIO::test_accessing_attributes_in_closed_file_raises_errors PASSED 326s tests/AlignmentFile_test.py::TestIO::test_fail_read_sam_without_header PASSED 326s tests/AlignmentFile_test.py::TestIO::test_fail_when_reading_unformatted_files PASSED 326s tests/AlignmentFile_test.py::TestIO::test_fetch_by_tid PASSED 326s 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 326s PASSED 326s tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_with_header_without_header_check PASSED 326s tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_without_header_with_refs PASSED 326s tests/AlignmentFile_test.py::TestIO::test_reference_name_available_after_closing_file PASSED 326s tests/AlignmentFile_test.py::TestIO::test_write_bam_to_unknown_path_fails PASSED 326s tests/AlignmentFile_test.py::TestAutoDetect::testBAM PASSED 326s tests/AlignmentFile_test.py::TestAutoDetect::testCRAM PASSED 326s tests/AlignmentFile_test.py::TestAutoDetect::testSAM PASSED 327s tests/AlignmentFile_test.py::TestIteratorRowBAM::testIteratePerContig PASSED 327s tests/AlignmentFile_test.py::TestIteratorRowBAM::testIterateRanges PASSED 327s tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate PASSED 328s tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIteratePerContig PASSED 342s tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIterateRanges PASSED 343s tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIteratePerContig PASSED 357s tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIterateRanges PASSED 357s tests/AlignmentFile_test.py::TestFloatTagBug::testFloatTagBug PASSED 357s tests/AlignmentFile_test.py::TestLargeFieldBug::testLargeFileBug PASSED 357s tests/AlignmentFile_test.py::TestClipping::testClipping PASSED 357s tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_bam_with_until_eof_reads_unmapped_reads PASSED 357s 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 357s [E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory 357s [E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory 357s [E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory 357s PASSED 357s tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads PASSED 357s tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads_by_contig PASSED 357s tests/AlignmentFile_test.py::TestContextManager::testManager PASSED 357s tests/AlignmentFile_test.py::TestMultiThread::testSingleThreadEqualsMultithread PASSED 357s tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED 357s tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED 357s tests/AlignmentFile_test.py::TestExceptions::testBadContig PASSED 357s tests/AlignmentFile_test.py::TestExceptions::testMeaninglessCrap PASSED 357s tests/AlignmentFile_test.py::TestExceptions::testMissingFile PASSED 357s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangNewFormat PASSED 357s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeNewFormat PASSED 357s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeOldFormat PASSED 357s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeNewFormat PASSED 357s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeOldFormat PASSED 357s tests/AlignmentFile_test.py::TestExceptions::testZeroToZero PASSED 357s tests/AlignmentFile_test.py::TestWrongFormat::testOpenBamAsSam PASSED 357s tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsBam PASSED 357s tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsSam PASSED 357s tests/AlignmentFile_test.py::TestWrongFormat::testOpenSamAsBam PASSED 357s tests/AlignmentFile_test.py::TestRegionParsing::test_dash_in_chr PASSED 357s tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile PASSED 357s tests/AlignmentFile_test.py::TestDeNovoConstruction::test_pass_if_reads_binary_equal PASSED 357s tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader PASSED 357s tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_in_header PASSED 357s tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_with_null_bytes_in_header PASSED[W::bam_hdr_read] EOF marker is absent. The input is probably truncated 357s [E::bgzf_read_block] Failed to read BGZF block data at offset 105176 expected 17578 bytes; hread returned 17094 357s [E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes 357s 357s tests/AlignmentFile_test.py::TestMismatchingHeader::testMismatchingHeader PASSED 357s tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader PASSED 357s tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2 PASSED 357s tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator PASSED 357s tests/AlignmentFile_test.py::TestCorruptBAM::testCorruptBamIterator PASSED 357s tests/AlignmentFile_test.py::TestBTagSam::testReadTags PASSED 357s tests/AlignmentFile_test.py::TestBTagSam::testReadWriteTags PASSED 357s tests/AlignmentFile_test.py::TestBTagBam::testReadTags PASSED 357s tests/AlignmentFile_test.py::TestBTagBam::testReadWriteTags PASSED 357s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetch PASSED 357s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchUntilEOF PASSED 357s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionFalseTrue PASSED 357s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueFalse PASSED 357s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueTrue PASSED 357s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetch PASSED 358s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchUntilEOF PASSED 359s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionFalseTrue PASSED 360s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueFalse PASSED 361s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueTrue PASSED 362s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetch PASSED 362s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchUntilEOF PASSED 363s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionFalseTrue PASSED 364s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueFalse PASSED 365s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueTrue PASSED 365s tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetch PASSED 365s tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetchAll PASSED 366s tests/AlignmentFile_test.py::TestRemoteFileHTTP::testView PASSED 366s tests/AlignmentFile_test.py::TestLargeOptValues::testBAM PASSED 366s tests/AlignmentFile_test.py::TestLargeOptValues::testSAM PASSED 366s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_counts_as_expected PASSED 366s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_nofilter PASSED 366s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_quality_filter PASSED 366s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_all PASSED 366s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_callback PASSED 366s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_with_coordinates_works PASSED 366s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_without_coordinates_fails PASSED 367s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_wrong_coordinates_fails PASSED 367s tests/AlignmentFile_test.py::TestCountCoverage::test_counting_the_same_region_works PASSED 367s tests/AlignmentFile_test.py::TestFindIntrons::test_all PASSED 367s tests/AlignmentFile_test.py::TestFindIntrons::test_first PASSED 367s tests/AlignmentFile_test.py::TestFindIntrons::test_total PASSED 367s tests/AlignmentFile_test.py::TestLogging::testFail1 PASSED 367s tests/AlignmentFile_test.py::TestLogging::testNoFail1 PASSED 367s tests/AlignmentFile_test.py::TestLogging::testNoFail2 PASSED 367s tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testCount PASSED 367s tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testIndexStats PASSED 369s tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testMate PASSED 369s tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct PASSED 369s tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct_per_chromosome PASSED 369s tests/AlignmentFile_test.py::TestSamtoolsProxy::testIndex PASSED 369s tests/AlignmentFile_test.py::TestSamtoolsProxy::testSort [E::hts_open_format] Failed to open file "missing_file" : No such file or directory 369s PASSED 369s tests/AlignmentFile_test.py::TestSamtoolsProxy::testView [E::hts_open_format] Failed to open file "missing_file" : No such file or directory 369s PASSED 370s tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED 370s tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM PASSED 370s tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexCRAM PASSED 370s tests/AlignmentFile_test.py::TestExplicitIndex::testRemoteExplicitIndexBAM PASSED 370s tests/AlignmentFile_test.py::TestVerbosity::testVerbosity PASSED 370s tests/AlignmentFile_test.py::TestSanityCheckingBAM::test_empty_read_gives_value_error PASSED 370s tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_bam PASSED 370s tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_cram SKIPPED 370s tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_sam PASSED 370s tests/StreamFiledescriptors_test.py::StreamTest::test_samtools_processing SKIPPED 370s tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing PASSED 370s tests/VariantFile_test.py::TestMissingGenotypes::testVCF PASSED 370s tests/VariantFile_test.py::TestMissingGenotypes::testVCFGZ PASSED 370s tests/VariantFile_test.py::TestMissingSamples::testVCF PASSED 370s tests/VariantFile_test.py::TestMissingSamples::testVCFGZ [W::bcf_hdr_check_sanity] PL should be declared as Number=G 370s [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 370s [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) 370s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 370s PASSED 370s tests/VariantFile_test.py::TestMissingSamplesFixed::testVCF PASSED 370s tests/VariantFile_test.py::TestMissingSamplesFixed::testVCFGZ PASSED 370s tests/VariantFile_test.py::TestOpening::testDetectBCF PASSED 370s tests/VariantFile_test.py::TestOpening::testDetectVCF PASSED 370s tests/VariantFile_test.py::TestOpening::testDetectVCFGZ PASSED 370s tests/VariantFile_test.py::TestOpening::testEmptyFileVCF PASSED 370s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFFromPath PASSED 370s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZOnlyHeader PASSED 370s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithIndex PASSED 370s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithoutIndex PASSED 370s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFOnlyHeader PASSED 370s tests/VariantFile_test.py::TestOpening::testMissingFile PASSED[E::hts_open_format] Failed to open file "missing_file.vcf" : No such file or directory 370s 370s tests/VariantFile_test.py::TestOpening::testMissingFileVCFGZ [E::hts_open_format] Failed to open file "missing_file.vcf.gz" : No such file or directory 370s PASSED 370s tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_csi_index PASSED 370s tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_prebuilt_csi PASSED 370s tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_tbi_index_will_produce_csi PASSED 370s tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_csi_index PASSED 370s tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_tbi_index PASSED 370s tests/VariantFile_test.py::TestHeader::testIterator PASSED 370s tests/VariantFile_test.py::TestHeader::testStr PASSED 370s tests/VariantFile_test.py::TestParsing::testAlleles PASSED 370s tests/VariantFile_test.py::TestParsing::testAllelesVariantTypes PASSED 370s tests/VariantFile_test.py::TestParsing::testAlt PASSED 370s tests/VariantFile_test.py::TestParsing::testChrom PASSED 370s tests/VariantFile_test.py::TestParsing::testChromFromPath PASSED 370s tests/VariantFile_test.py::TestParsing::testFilter PASSED 370s tests/VariantFile_test.py::TestParsing::testFormat PASSED 370s tests/VariantFile_test.py::TestParsing::testId PASSED 370s tests/VariantFile_test.py::TestParsing::testInfo PASSED 370s tests/VariantFile_test.py::TestParsing::testPos PASSED 370s tests/VariantFile_test.py::TestParsing::testQual PASSED 370s tests/VariantFile_test.py::TestParsing::testRef PASSED 370s tests/VariantFile_test.py::TestParsing::testSampleAlleleIndices PASSED 370s tests/VariantFile_test.py::TestParsing::testSampleAlleles PASSED 370s tests/VariantFile_test.py::TestParsing::testSampleFormats PASSED 370s tests/VariantFile_test.py::TestParsing::testStart PASSED 370s tests/VariantFile_test.py::TestParsing::testStop PASSED 370s tests/VariantFile_test.py::TestIndexFilename::testOpen PASSED 370s tests/VariantFile_test.py::TestConstructionVCFWithContigs::testBase PASSED 370s tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionFromCopy PASSED 370s tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithLines PASSED 370s tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithRecords PASSED 370s tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testBase PASSED 370s tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionFromCopy PASSED 370s tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithLines PASSED 370s tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithRecords PASSED 370s tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testBase PASSED 370s tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionFromCopy PASSED 370s tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithLines PASSED 370s tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithRecords PASSED 370s tests/VariantFile_test.py::TestSettingRecordValues::testBase PASSED 370s tests/VariantFile_test.py::TestSettingRecordValues::testGenotype [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 370s (0, 0) 370s PASSED 370s tests/VariantFile_test.py::TestSettingRecordValues::testSetQual [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 370s PASSED 370s tests/VariantFile_test.py::TestMultiThreading::testNoMultiThreadingWithIgnoreTruncation PASSED 370s tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult [E::idx_find_and_load] Could not retrieve index file for '/tmp/autopkgtest.OEVu7F/build.w8D/src/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithreadResult_8w5l2wzc.bcf' 370s PASSED 370s tests/VariantFile_test.py::TestSubsetting::testSubsetting PASSED 370s 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.) 370s [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) 370s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 370s [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 370s [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) 370s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 370s PASSED 370s tests/VariantFile_test.py::TestUnicode::test_record_with_unicode PASSED 370s tests/VariantRecord_test.py::test_ascii_annotation_can_be_added PASSED 370s tests/VariantRecord_test.py::test_ascii_annotation_with_variable_length_can_be_added PASSED 370s tests/VariantRecord_test.py::test_unicode_annotation_can_be_added PASSED 370s tests/VariantRecord_test.py::test_set_sample_alleles PASSED 370s tests/compile_test.py::test_bam SKIPPED (no pyximport) 370s tests/compile_test.py::test_gtf SKIPPED (no pyximport) 370s tests/faidx_test.py::TestFastaFile::testFetch PASSED 370s tests/faidx_test.py::TestFastaFile::testFetchErrors PASSED 370s tests/faidx_test.py::TestFastaFile::testLength PASSED 370s tests/faidx_test.py::TestFastaFile::testOutOfRangeAccess PASSED 370s tests/faidx_test.py::TestFastaFile::testSequenceLengths PASSED 370s tests/faidx_test.py::TestFastaFile::test_fetch_with_region_and_contig_raises_exception PASSED 370s tests/faidx_test.py::TestFastaFile::test_fetch_with_region_is_equivalent PASSED 370s tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED 370s tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_index_succeeds PASSED 370s tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_without_index_succeeds PASSED 370s tests/faidx_test.py::TestFastaFilePathIndex::test_raise_exception_if_index_is_missing PASSED 370s tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED 370s tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_index_succeeds PASSED 370s tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_without_index_succeeds PASSED 370s tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_raise_exception_if_index_is_missing PASSED 370s tests/faidx_test.py::TestFastxFileFastq::testCounts PASSED 370s tests/faidx_test.py::TestFastxFileFastq::testManager PASSED 370s tests/faidx_test.py::TestFastxFileFastq::testMissingFile PASSED 370s tests/faidx_test.py::TestFastxFileFastq::testSequence PASSED 370s tests/faidx_test.py::TestFastqFileFastq::testCounts PASSED 370s tests/faidx_test.py::TestFastqFileFastq::testManager PASSED 370s tests/faidx_test.py::TestFastqFileFastq::testMissingFile PASSED 370s tests/faidx_test.py::TestFastqFileFastq::testSequence PASSED 370s tests/faidx_test.py::TestFastxFileFasta::testCounts PASSED 370s tests/faidx_test.py::TestFastxFileFasta::testManager PASSED 370s tests/faidx_test.py::TestFastxFileFasta::testMissingFile PASSED 370s tests/faidx_test.py::TestFastxFileFasta::testSequence PASSED 370s tests/faidx_test.py::TestFastxFileFastqStream::testCounts PASSED 370s tests/faidx_test.py::TestFastxFileFastqStream::testManager PASSED 370s tests/faidx_test.py::TestFastxFileFastqStream::testMissingFile PASSED 370s tests/faidx_test.py::TestFastxFileFastqStream::testSequence PASSED 370s tests/faidx_test.py::TestFastxFileWithEmptySequence::testIteration PASSED 371s tests/faidx_test.py::TestRemoteFileFTP::testFTPView PASSED 371s tests/faidx_test.py::TestRemoteFileFTP::test_sequence_lengths_are_available PASSED 371s tests/faidx_test.py::TestFastqRecord::test_fastx_record_can_be_created_from_scratch PASSED 371s tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_None PASSED 371s tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_modified PASSED 371s tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_name_is_None PASSED 371s tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_quality_is_wrong_length PASSED 371s tests/faidx_test.py::TestFastqRecord::test_fastx_record_name_can_be_modified PASSED 371s tests/faidx_test.py::TestFastqRecord::test_fastx_record_quality_can_be_modified PASSED 371s tests/faidx_test.py::TestFastqRecord::test_fastx_record_sequence_can_be_modified PASSED 371s tests/faidx_test.py::TestFastqProxy::test_fastq_proxy_instantiation_raises_error PASSED 371s tests/linking_test.py::TestLinking::test_package_can_be_installed SKIPPED 371s tests/linking_test.py::TestLinkWithRpath::test_package_can_be_installed SKIPPED 371s tests/linking_test.py::TestLinkWithRpath::test_package_tests_pass SKIPPED 371s tests/linking_test.py::TestLinkWithoutRpath::test_package_can_be_installed SKIPPED 371s tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_fail_on_import SKIPPED 371s tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_pass_if_ld_library_path_set SKIPPED 372s tests/samtools_test.py::SamtoolsTest::testStatements PASSED 372s tests/samtools_test.py::SamtoolsTest::testUsage SKIPPED (skipping us...) 372s tests/samtools_test.py::EmptyIndexTest::testEmptyIndex PASSED 372s tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraArg PASSED 372s tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraFlag PASSED 372s tests/samtools_test.py::TestReturnType::testReturnValueData PASSED 372s tests/samtools_test.py::TestReturnType::testReturnValueString PASSED 372s tests/samtools_test.py::StdoutTest::testDoubleCalling PASSED 372s tests/samtools_test.py::StdoutTest::testSaveStdout PASSED 372s tests/samtools_test.py::StdoutTest::testWithRedirectedStdout PASSED 372s tests/samtools_test.py::StdoutTest::testWithoutRedirectedStdout PASSED 373s tests/samtools_test.py::PysamTest::testStatements PASSED 373s tests/samtools_test.py::PysamTest::testUsage SKIPPED (skipping usage...) 373s tests/tabix_test.py::TestIndexing::test_indexing_to_custom_location_works PASSED 373s tests/tabix_test.py::TestIndexing::test_indexing_with_explict_columns_works PASSED 373s tests/tabix_test.py::TestIndexing::test_indexing_with_lineskipping_works PASSED 373s tests/tabix_test.py::TestIndexing::test_indexing_with_preset_works PASSED 373s tests/tabix_test.py::TestCompression::testCompression PASSED 373s tests/tabix_test.py::TestCompression::testIndexPresetCompressed PASSED 373s tests/tabix_test.py::TestCompression::testIndexPresetUncompressed PASSED 373s tests/tabix_test.py::TestCompressionSam::testCompression PASSED 373s tests/tabix_test.py::TestCompressionSam::testIndexPresetCompressed PASSED 373s tests/tabix_test.py::TestCompressionSam::testIndexPresetUncompressed PASSED 373s tests/tabix_test.py::TestCompressionBed::testCompression PASSED 373s tests/tabix_test.py::TestCompressionBed::testIndexPresetCompressed PASSED 373s tests/tabix_test.py::TestCompressionBed::testIndexPresetUncompressed PASSED 373s tests/tabix_test.py::TestCompressionVCF::testCompression PASSED 373s tests/tabix_test.py::TestCompressionVCF::testIndexPresetCompressed PASSED 373s tests/tabix_test.py::TestCompressionVCF::testIndexPresetUncompressed PASSED 373s tests/tabix_test.py::TestGZFile::testAll PASSED 373s tests/tabix_test.py::TestIterationWithoutComments::testAll PASSED 373s tests/tabix_test.py::TestIterationWithoutComments::testGetContigs PASSED 373s tests/tabix_test.py::TestIterationWithoutComments::testHeader PASSED 373s tests/tabix_test.py::TestIterationWithoutComments::testInvalidIntervals PASSED 373s tests/tabix_test.py::TestIterationWithoutComments::testPerContig PASSED 373s tests/tabix_test.py::TestIterationWithoutComments::testPerContig2 PASSED 374s tests/tabix_test.py::TestIterationWithoutComments::testPerContigFromStart PASSED 374s tests/tabix_test.py::TestIterationWithoutComments::testPerContigToEnd PASSED 374s tests/tabix_test.py::TestIterationWithoutComments::testPerInterval PASSED 374s tests/tabix_test.py::TestIterationWithoutComments::testRegionStrings PASSED 374s tests/tabix_test.py::TestIterationWithoutComments::testReopening PASSED 374s tests/tabix_test.py::TestIterationWithComments::testAll PASSED 374s tests/tabix_test.py::TestIterationWithComments::testGetContigs PASSED 374s tests/tabix_test.py::TestIterationWithComments::testHeader PASSED 374s tests/tabix_test.py::TestIterationWithComments::testInvalidIntervals PASSED 374s tests/tabix_test.py::TestIterationWithComments::testPerContig PASSED 374s tests/tabix_test.py::TestIterationWithComments::testPerContig2 PASSED 374s tests/tabix_test.py::TestIterationWithComments::testPerContigFromStart PASSED 374s tests/tabix_test.py::TestIterationWithComments::testPerContigToEnd PASSED 374s tests/tabix_test.py::TestIterationWithComments::testPerInterval PASSED 374s tests/tabix_test.py::TestIterationWithComments::testRegionStrings PASSED 375s tests/tabix_test.py::TestIterationWithComments::testReopening PASSED 375s tests/tabix_test.py::TestIterators::testClosedFile PASSED 375s tests/tabix_test.py::TestIterators::testClosedFileIteration PASSED 375s tests/tabix_test.py::TestIterators::testIteration PASSED 375s tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFile PASSED 375s tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFileIteration PASSED 375s tests/tabix_test.py::TestIteratorsGenericCompressed::testIteration PASSED 375s tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFile PASSED 375s tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFileIteration PASSED 375s tests/tabix_test.py::TestIteratorsFileCompressed::testIteration PASSED 375s tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFile PASSED 375s tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFileIteration PASSED 375s tests/tabix_test.py::TestIteratorsFileUncompressed::testIteration PASSED 375s tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooFewFields PASSED 375s tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooManyFields PASSED 375s tests/tabix_test.py::TestBed::testRead PASSED 375s tests/tabix_test.py::TestBed::testWrite PASSED 375s tests/tabix_test.py::TestUnicode::testFromTabix PASSED 375s tests/tabix_test.py::TestUnicode::testFromVCF PASSED 375s tests/tabix_test.py::TestVCFFromTabix::testRead PASSED 375s tests/tabix_test.py::TestVCFFromTabix::testWrite PASSED 375s tests/tabix_test.py::TestVCFFromVCF::testConnecting PASSED 375s tests/tabix_test.py::TestVCFFromVCF::testParsing PASSED 375s tests/tabix_test.py::VCFFromTabixTest_10::testRead PASSED 375s tests/tabix_test.py::VCFFromTabixTest_10::testWrite PASSED 375s tests/tabix_test.py::VCFFromVCFTest_10::testConnecting PASSED 375s tests/tabix_test.py::VCFFromVCFTest_10::testParsing PASSED 375s tests/tabix_test.py::VCFFromTabixTest_11::testRead PASSED 375s tests/tabix_test.py::VCFFromTabixTest_11::testWrite PASSED 375s tests/tabix_test.py::VCFFromVCFTest_11::testConnecting PASSED 376s tests/tabix_test.py::VCFFromVCFTest_11::testParsing PASSED 376s tests/tabix_test.py::VCFFromTabixTest_12::testRead PASSED 376s tests/tabix_test.py::VCFFromTabixTest_12::testWrite PASSED 376s tests/tabix_test.py::VCFFromVCFTest_12::testConnecting PASSED 376s tests/tabix_test.py::VCFFromVCFTest_12::testParsing PASSED 376s tests/tabix_test.py::VCFFromTabixTest_13::testRead PASSED 376s tests/tabix_test.py::VCFFromTabixTest_13::testWrite PASSED 376s tests/tabix_test.py::VCFFromVCFTest_13::testConnecting PASSED 376s tests/tabix_test.py::VCFFromVCFTest_13::testParsing PASSED 376s tests/tabix_test.py::VCFFromTabixTest_15::testRead PASSED 376s tests/tabix_test.py::VCFFromTabixTest_15::testWrite PASSED 376s tests/tabix_test.py::VCFFromVCFTest_15::testConnecting PASSED 377s tests/tabix_test.py::VCFFromVCFTest_15::testParsing PASSED 377s tests/tabix_test.py::VCFFromTabixTest_16::testRead PASSED 377s tests/tabix_test.py::VCFFromTabixTest_16::testWrite PASSED 377s tests/tabix_test.py::VCFFromVCFTest_16::testConnecting PASSED 377s tests/tabix_test.py::VCFFromVCFTest_16::testParsing PASSED 377s tests/tabix_test.py::VCFFromTabixTest_18::testRead PASSED 377s tests/tabix_test.py::VCFFromTabixTest_18::testWrite PASSED 377s tests/tabix_test.py::VCFFromVCFTest_18::testConnecting PASSED 377s tests/tabix_test.py::VCFFromVCFTest_18::testParsing PASSED 377s tests/tabix_test.py::VCFFromTabixTest_2::testRead PASSED 377s tests/tabix_test.py::VCFFromTabixTest_2::testWrite PASSED 377s tests/tabix_test.py::VCFFromVCFTest_2::testConnecting PASSED 377s tests/tabix_test.py::VCFFromVCFTest_2::testParsing PASSED 377s tests/tabix_test.py::VCFFromTabixTest_20::testRead PASSED 377s tests/tabix_test.py::VCFFromTabixTest_20::testWrite PASSED 377s tests/tabix_test.py::VCFFromVCFTest_20::testConnecting PASSED 377s tests/tabix_test.py::VCFFromVCFTest_20::testParsing PASSED 377s tests/tabix_test.py::VCFFromTabixTest_21::testRead PASSED 378s tests/tabix_test.py::VCFFromTabixTest_21::testWrite PASSED 378s tests/tabix_test.py::VCFFromVCFTest_21::testConnecting PASSED 378s tests/tabix_test.py::VCFFromVCFTest_21::testParsing PASSED 378s tests/tabix_test.py::VCFFromTabixTest_22::testRead PASSED 378s tests/tabix_test.py::VCFFromTabixTest_22::testWrite PASSED 378s tests/tabix_test.py::VCFFromVCFTest_22::testConnecting PASSED 379s tests/tabix_test.py::VCFFromVCFTest_22::testParsing PASSED 379s tests/tabix_test.py::VCFFromTabixTest_23::testRead PASSED 379s tests/tabix_test.py::VCFFromTabixTest_23::testWrite PASSED 379s tests/tabix_test.py::VCFFromVCFTest_23::testConnecting PASSED 379s tests/tabix_test.py::VCFFromVCFTest_23::testParsing PASSED 379s tests/tabix_test.py::VCFFromTabixTest_24::testRead PASSED 379s tests/tabix_test.py::VCFFromTabixTest_24::testWrite PASSED 379s tests/tabix_test.py::VCFFromVCFTest_24::testConnecting PASSED 379s tests/tabix_test.py::VCFFromVCFTest_24::testParsing PASSED 379s tests/tabix_test.py::VCFFromTabixTest_3::testRead PASSED 379s tests/tabix_test.py::VCFFromTabixTest_3::testWrite PASSED 379s tests/tabix_test.py::VCFFromVCFTest_3::testConnecting PASSED 379s tests/tabix_test.py::VCFFromVCFTest_3::testParsing PASSED 379s tests/tabix_test.py::VCFFromTabixTest_4::testRead PASSED 380s tests/tabix_test.py::VCFFromTabixTest_4::testWrite PASSED 380s tests/tabix_test.py::VCFFromVCFTest_4::testConnecting PASSED 380s tests/tabix_test.py::VCFFromVCFTest_4::testParsing PASSED 380s tests/tabix_test.py::VCFFromTabixTest_5::testRead PASSED 380s tests/tabix_test.py::VCFFromTabixTest_5::testWrite PASSED 380s tests/tabix_test.py::VCFFromVCFTest_5::testConnecting PASSED 380s tests/tabix_test.py::VCFFromVCFTest_5::testParsing PASSED 380s tests/tabix_test.py::VCFFromTabixTest_6::testRead PASSED 380s tests/tabix_test.py::VCFFromTabixTest_6::testWrite PASSED 380s tests/tabix_test.py::VCFFromVCFTest_6::testConnecting PASSED 381s tests/tabix_test.py::VCFFromVCFTest_6::testParsing PASSED 381s tests/tabix_test.py::VCFFromTabixTest_7::testRead PASSED 381s tests/tabix_test.py::VCFFromTabixTest_7::testWrite PASSED 381s tests/tabix_test.py::VCFFromVCFTest_7::testConnecting PASSED 382s tests/tabix_test.py::VCFFromVCFTest_7::testParsing PASSED 382s tests/tabix_test.py::VCFFromTabixTest_8::testRead PASSED 382s tests/tabix_test.py::VCFFromTabixTest_8::testWrite PASSED 382s tests/tabix_test.py::VCFFromVCFTest_8::testConnecting PASSED 382s tests/tabix_test.py::VCFFromVCFTest_8::testParsing PASSED 382s tests/tabix_test.py::VCFFromTabixTest_9::testRead PASSED 382s tests/tabix_test.py::VCFFromTabixTest_9::testWrite PASSED 382s tests/tabix_test.py::VCFFromVCFTest_9::testConnecting PASSED 382s tests/tabix_test.py::VCFFromVCFTest_9::testParsing PASSED 382s tests/tabix_test.py::VCFFromTabixTest_issue85::testRead PASSED 382s tests/tabix_test.py::VCFFromTabixTest_issue85::testWrite PASSED 382s tests/tabix_test.py::VCFFromVCFTest_issue85::testConnecting PASSED 382s tests/tabix_test.py::VCFFromVCFTest_issue85::testParsing PASSED 382s tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testRead PASSED 382s tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testWrite PASSED 382s tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testConnecting PASSED 382s tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testParsing PASSED 382s tests/tabix_test.py::TestVCFFromVariantFile::testConnecting PASSED 382s tests/tabix_test.py::TestVCFFromVariantFile::testParsing [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 382s [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) 382s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 382s PASSED 382s tests/tabix_test.py::TestVCFFromVariantFile_10::testConnecting PASSED 382s 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.) 382s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:676148 is not defined in the header, assuming Type=String 382s PASSED 382s tests/tabix_test.py::TestVCFFromVariantFile_11::testConnecting PASSED 382s 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.) 382s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:669442 is not defined in the header, assuming Type=String 383s PASSED 383s tests/tabix_test.py::TestVCFFromVariantFile_12::testConnecting PASSED 383s 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.) 383s [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String 383s [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String 383s [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String 383s [W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String 383s [W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String 383s [W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String 383s [W::vcf_parse_format_dict2] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String 383s [W::vcf_parse_format_dict2] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String 383s [W::vcf_parse_format_dict2] FORMAT 'GQ' at chr1:1281168 is not defined in the header, assuming Type=String 383s [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) 383s PASSED 383s tests/tabix_test.py::TestVCFFromVariantFile_13::testConnecting PASSED 383s tests/tabix_test.py::TestVCFFromVariantFile_13::testParsing [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::bcf_hrec_check] Invalid tag name: "1000g" 383s [W::bcf_hrec_check] Invalid tag name: "GT:GL:GQ:NR" 383s [W::bcf_hdr_check_sanity] GL should be declared as Number=G 383s [W::bcf_hrec_check] Invalid tag name: "1000g" 383s [W::bcf_hrec_check] Invalid tag name: "GT:GL:GQ:NR" 383s [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse_info] INFO 'MMLQ' is not defined in the header, assuming Type=String 383s [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr17_gl000205_random' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr18' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr19' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr20' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr21' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr22' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chrUn_gl000214' is not defined in the header. (Quick workaround: index the file with tabix.) 383s PASSED 383s tests/tabix_test.py::TestVCFFromVariantFile_15::testConnecting [W::vcf_parse] Contig 'chrUn_gl000220' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chrUn_gl000225' is not defined in the header. (Quick workaround: index the file with tabix.) 383s [W::vcf_parse] Contig 'chrX' is not defined in the header. (Quick workaround: index the file with tabix.) 383s PASSED 383s 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.) 383s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:439104 is not defined in the header, assuming Type=String 384s PASSED 384s tests/tabix_test.py::TestVCFFromVariantFile_16::testConnecting PASSED 384s 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.) 384s [W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String 384s PASSED 384s tests/tabix_test.py::TestVCFFromVariantFile_18::testConnecting PASSED 384s 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.) 384s [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String 384s [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String 384s [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String 384s [W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String 384s [W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String 384s [W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String 384s [W::vcf_parse_format_dict2] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String 384s [W::vcf_parse_format_dict2] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String 384s [W::vcf_parse_format_dict2] FORMAT 'GQ' at chr1:1281168 is not defined in the header, assuming Type=String 384s [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) 384s [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) 384s [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) 384s [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) 384s [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) 384s [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) 384s PASSED 384s tests/tabix_test.py::TestVCFFromVariantFile_2::testConnecting PASSED 384s tests/tabix_test.py::TestVCFFromVariantFile_2::testParsing [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) 384s [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) 384s [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) 384s [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) 384s [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) 384s [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) 384s [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) 384s [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) 384s [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) 384s [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) 384s [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) 384s [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) 384s [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) 384s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 384s [W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String 384s PASSED 384s tests/tabix_test.py::TestVCFFromVariantFile_20::testConnecting [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 384s PASSED 384s tests/tabix_test.py::TestVCFFromVariantFile_20::testParsing [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 384s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 384s PASSED 384s tests/tabix_test.py::TestVCFFromVariantFile_21::testConnecting [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 384s PASSED 384s tests/tabix_test.py::TestVCFFromVariantFile_21::testParsing [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 384s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 384s PASSED 384s tests/tabix_test.py::TestVCFFromVariantFile_22::testConnecting PASSED 384s 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.) 384s [W::vcf_parse_info] INFO 'refseq.name' is not defined in the header, assuming Type=String 384s [W::vcf_parse_info] INFO 'refseq.positionType' is not defined in the header, assuming Type=String 385s [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) 385s PASSED 385s tests/tabix_test.py::TestVCFFromVariantFile_23::testConnecting PASSED 385s tests/tabix_test.py::TestVCFFromVariantFile_23::testParsing [W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String 385s PASSED 385s 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: 385s #CHROM POS ID REF ALT QUAL FILTER INFO 385s 385s PASSED 385s tests/tabix_test.py::TestVCFFromVariantFile_24::testParsing PASSED 385s tests/tabix_test.py::TestVCFFromVariantFile_3::testConnecting PASSED 385s 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.) 385s PASSED 385s tests/tabix_test.py::TestVCFFromVariantFile_4::testConnecting PASSED 385s 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.) 385s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:249843 is not defined in the header, assuming Type=String 385s PASSED 385s tests/tabix_test.py::TestVCFFromVariantFile_5::testConnecting PASSED 385s 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.) 385s PASSED 386s tests/tabix_test.py::TestVCFFromVariantFile_6::testConnecting PASSED 386s 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.) 386s [W::vcf_parse_info] INFO 'CallSetAC' is not defined in the header, assuming Type=String 386s [W::vcf_parse_info] INFO 'CallSetAC2' is not defined in the header, assuming Type=String 386s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:669442 is not defined in the header, assuming Type=String 386s PASSED 386s tests/tabix_test.py::TestVCFFromVariantFile_7::testConnecting PASSED 386s 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.) 386s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:249843 is not defined in the header, assuming Type=String 386s PASSED 386s tests/tabix_test.py::TestVCFFromVariantFile_8::testConnecting PASSED 386s 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.) 386s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:676148 is not defined in the header, assuming Type=String 387s PASSED 387s tests/tabix_test.py::TestVCFFromVariantFile_9::testConnecting PASSED 387s 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.) 387s [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String 387s [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String 387s [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String 387s [W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String 387s [W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String 387s [W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String 387s [W::vcf_parse_format_dict2] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String 387s [W::vcf_parse_format_dict2] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String 387s [W::vcf_parse_format_dict2] FORMAT 'GQ' at chr1:1281168 is not defined in the header, assuming Type=String 387s [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) 387s [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) 387s [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) 387s [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) 387s PASSED 387s tests/tabix_test.py::TestVCFFromVariantFile_issue85::testConnecting PASSED 387s tests/tabix_test.py::TestVCFFromVariantFile_issue85::testParsing PASSED 387s tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testConnecting PASSED 387s tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testParsing [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) 387s [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) 387s [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) 387s [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) 387s [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) 387s [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) 387s [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) 387s [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) 387s [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) 387s [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) 387s [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) 387s [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) 387s [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) 387s [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) 387s [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) 387s [E::bcf_hdr_parse] Could not parse the header, sample line not found 387s PASSED 387s tests/tabix_test.py::TestIndexArgument::testFetchAll PASSED 387s tests/tabix_test.py::TestIndexArgument::testLoadIndexWithoutTbiExtension PASSED 387s tests/tabix_test.py::TestBackwardsCompatibility::testBED PASSED 387s tests/tabix_test.py::TestBackwardsCompatibility::testBED0v23 PASSED 387s tests/tabix_test.py::TestBackwardsCompatibility::testBED0v26 PASSED 387s tests/tabix_test.py::TestBackwardsCompatibility::testEmpty PASSED 387s tests/tabix_test.py::TestBackwardsCompatibility::testVCF PASSED 387s tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v23 PASSED 387s tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v26 PASSED 387s tests/tabix_test.py::TestMultipleIterators::testDisjointIterators PASSED 387s tests/tabix_test.py::TestMultipleIterators::testDoubleFetch PASSED 387s tests/tabix_test.py::TestMultipleIterators::testJoinedIterators PASSED 387s tests/tabix_test.py::TestMultipleIterators::testScope PASSED 387s tests/tabix_test.py::TestContextManager::testManager PASSED 387s tests/tabix_test.py::TestMultithreadTabixFile::testMultithreadEqualsSinglethread PASSED 387s tests/tabixproxies_test.py::TestBED::testAssignmentToTargetList PASSED 387s tests/tabixproxies_test.py::TestParser::testAssignmentToTargetList PASSED 387s tests/tabixproxies_test.py::TestParser::testCopy PASSED 387s tests/tabixproxies_test.py::TestParser::testIteratorCompressed PASSED 387s tests/tabixproxies_test.py::TestParser::testIteratorUncompressed PASSED 387s tests/tabixproxies_test.py::TestParser::testRead PASSED 387s tests/tabixproxies_test.py::TestParser::testUnset PASSED 387s tests/tabixproxies_test.py::TestParser::testWrite PASSED 387s tests/tabixproxies_test.py::TestGTF::testAssignmentToTargetList PASSED 387s tests/tabixproxies_test.py::TestGTF::testCopy PASSED 387s tests/tabixproxies_test.py::TestGTF::testIteratorCompressed PASSED 387s tests/tabixproxies_test.py::TestGTF::testIteratorUncompressed PASSED 387s tests/tabixproxies_test.py::TestGTF::testRead PASSED 387s tests/tabixproxies_test.py::TestGTF::testUnset PASSED 387s tests/tabixproxies_test.py::TestGTF::testWrite PASSED 387s tests/tabixproxies_test.py::TestGTF::test_added_attribute_is_output PASSED 387s tests/tabixproxies_test.py::TestGTF::test_asdict_can_be_modified PASSED 387s tests/tabixproxies_test.py::TestGTF::test_asdict_contains_attributes PASSED 387s tests/tabixproxies_test.py::TestGTF::test_setAttribute_makes_changes PASSED 387s tests/tabixproxies_test.py::TestGTF::test_setting_end_is_one_based PASSED 387s tests/tabixproxies_test.py::TestGTF::test_setting_feature_to_none_produces_dot PASSED 387s tests/tabixproxies_test.py::TestGTF::test_setting_fields PASSED 387s tests/tabixproxies_test.py::TestGTF::test_setting_frame_to_none_produces_dot PASSED 387s tests/tabixproxies_test.py::TestGTF::test_setting_score_to_none_produces_dot PASSED 387s tests/tabixproxies_test.py::TestGTF::test_setting_source_to_none_produces_dot PASSED 387s tests/tabixproxies_test.py::TestGTF::test_setting_start_is_one_based PASSED 387s tests/tabixproxies_test.py::TestGTF::test_setting_strand_to_none_produces_dot PASSED 387s tests/tabixproxies_test.py::TestGFF3::testAssignmentToTargetList PASSED 387s tests/tabixproxies_test.py::TestGFF3::testCopy PASSED 387s tests/tabixproxies_test.py::TestGFF3::testIteratorCompressed PASSED 387s tests/tabixproxies_test.py::TestGFF3::testIteratorUncompressed PASSED 387s tests/tabixproxies_test.py::TestGFF3::testRead PASSED 387s tests/tabixproxies_test.py::TestGFF3::testUnset PASSED 387s tests/tabixproxies_test.py::TestGFF3::testWrite PASSED 387s tests/tabixproxies_test.py::TestGFF3::test_added_attribute_is_output PASSED 387s tests/tabixproxies_test.py::TestGFF3::test_asdict_can_be_modified PASSED 387s tests/tabixproxies_test.py::TestGFF3::test_asdict_contains_attributes PASSED 387s tests/tabixproxies_test.py::TestGFF3::test_setAttribute_makes_changes PASSED 387s tests/tabixproxies_test.py::TestGFF3::test_setting_end_is_one_based PASSED 387s tests/tabixproxies_test.py::TestGFF3::test_setting_feature_to_none_produces_dot PASSED 387s tests/tabixproxies_test.py::TestGFF3::test_setting_fields PASSED 387s tests/tabixproxies_test.py::TestGFF3::test_setting_frame_to_none_produces_dot PASSED 387s tests/tabixproxies_test.py::TestGFF3::test_setting_score_to_none_produces_dot PASSED 387s tests/tabixproxies_test.py::TestGFF3::test_setting_source_to_none_produces_dot PASSED 387s tests/tabixproxies_test.py::TestGFF3::test_setting_start_is_one_based PASSED 387s tests/tabixproxies_test.py::TestGFF3::test_setting_strand_to_none_produces_dot PASSED 387s tests/test_samtools_python.py::test_idxstats_parse_split_lines PASSED 387s tests/test_samtools_python.py::test_bedcov_split_lines PASSED 387s tests/test_samtools_python.py::test_idxstats_parse PASSED 387s tests/test_samtools_python.py::test_bedcov PASSED 387s 387s =============================== warnings summary =============================== 387s tests/samtools_test.py::SamtoolsTest::testStatements 387s tests/samtools_test.py::PysamTest::testStatements 387s /tmp/autopkgtest.OEVu7F/build.w8D/src/tests/samtools_test.py:137: UserWarning: versions of pysam.samtools and samtools differ: 1.18 != 1.20 387s warnings.warn( 387s 387s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 387s ============ 938 passed, 13 skipped, 2 warnings in 94.10s (0:01:34) ============ 388s autopkgtest [00:49:04]: test command1: -----------------------] 392s autopkgtest [00:49:08]: test command1: - - - - - - - - - - results - - - - - - - - - - 392s command1 PASS 395s autopkgtest [00:49:11]: test autodep8-python3: preparing testbed 449s autopkgtest [00:50:05]: testbed dpkg architecture: armhf 451s autopkgtest [00:50:07]: testbed apt version: 2.9.8 451s autopkgtest [00:50:07]: @@@@@@@@@@@@@@@@@@@@ test bed setup 459s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 459s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [177 kB] 459s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [31.2 kB] 459s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [2268 kB] 460s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 460s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [209 kB] 460s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [1640 kB] 460s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [23.9 kB] 460s Fetched 4430 kB in 1s (3397 kB/s) 460s Reading package lists... 475s tee: /proc/self/fd/2: Permission denied 497s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 497s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 497s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 497s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 499s Reading package lists... 499s Reading package lists... 500s Building dependency tree... 500s Reading state information... 501s Calculating upgrade... 502s The following packages were automatically installed and are no longer required: 502s libperl5.38t64 perl-modules-5.38 502s Use 'apt autoremove' to remove them. 502s The following NEW packages will be installed: 502s libperl5.40 perl-modules-5.40 502s The following packages will be upgraded: 502s base-files distro-info-data fwupd gcc-14-base info install-info iproute2 502s libatomic1 libblockdev-crypto3 libblockdev-fs3 libblockdev-loop3 502s libblockdev-mdraid3 libblockdev-nvme3 libblockdev-part3 libblockdev-swap3 502s libblockdev-utils3 libblockdev3 libdb5.3t64 libdw1t64 libelf1t64 libevdev2 502s libftdi1-2 libfwupd2 libgcc-s1 libinih1 libkeyutils1 liblocale-gettext-perl 502s libpipeline1 libsgutils2-1.46-2 libstdc++6 libtext-charwidth-perl 502s libtext-iconv-perl motd-news-config nano perl perl-base python3-configobj 502s python3-json-pointer python3-lazr.uri python3-zipp sg3-utils sg3-utils-udev 502s vim-common vim-tiny xxd 503s 45 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 503s Need to get 19.6 MB of archives. 503s After this operation, 42.8 MB of additional disk space will be used. 503s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf motd-news-config all 13.5ubuntu2 [5274 B] 503s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf base-files armhf 13.5ubuntu2 [68.6 kB] 503s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf perl-modules-5.40 all 5.40.0-6 [3214 kB] 503s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libperl5.40 armhf 5.40.0-6 [4140 kB] 503s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf perl armhf 5.40.0-6 [262 kB] 503s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf perl-base armhf 5.40.0-6 [1674 kB] 503s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf liblocale-gettext-perl armhf 1.07-7build1 [15.0 kB] 503s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf libtext-iconv-perl armhf 1.7-8build4 [12.8 kB] 503s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf libtext-charwidth-perl armhf 0.04-11build4 [9128 B] 503s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libdb5.3t64 armhf 5.3.28+dfsg2-9 [655 kB] 503s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libatomic1 armhf 14.2.0-7ubuntu1 [7842 B] 503s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14-base armhf 14.2.0-7ubuntu1 [51.2 kB] 503s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libstdc++6 armhf 14.2.0-7ubuntu1 [711 kB] 503s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf libgcc-s1 armhf 14.2.0-7ubuntu1 [40.8 kB] 503s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf install-info armhf 7.1.1-1 [61.4 kB] 503s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf distro-info-data all 0.63 [6588 B] 503s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libdw1t64 armhf 0.192-4 [243 kB] 503s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf libelf1t64 armhf 0.192-4 [50.2 kB] 503s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf iproute2 armhf 6.10.0-2ubuntu1 [1082 kB] 503s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libkeyutils1 armhf 1.6.3-4ubuntu2 [8712 B] 503s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf vim-tiny armhf 2:9.1.0777-1ubuntu1 [693 kB] 503s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf vim-common all 2:9.1.0777-1ubuntu1 [394 kB] 503s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf xxd armhf 2:9.1.0777-1ubuntu1 [66.8 kB] 503s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf info armhf 7.1.1-1 [126 kB] 503s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf libevdev2 armhf 1.13.3+dfsg-1 [29.7 kB] 503s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf libpipeline1 armhf 1.5.8-1 [26.9 kB] 503s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf nano armhf 8.2-1 [276 kB] 503s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf libfwupd2 armhf 1.9.26-2 [125 kB] 503s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf fwupd armhf 1.9.26-2 [4404 kB] 504s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-utils3 armhf 3.2.0-2 [17.4 kB] 504s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-crypto3 armhf 3.2.0-2 [22.3 kB] 504s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-fs3 armhf 3.2.0-2 [34.3 kB] 504s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-loop3 armhf 3.2.0-2 [6552 B] 504s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-mdraid3 armhf 3.2.0-2 [13.4 kB] 504s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-nvme3 armhf 3.2.0-2 [17.6 kB] 504s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-part3 armhf 3.2.0-2 [16.5 kB] 504s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-swap3 armhf 3.2.0-2 [8942 B] 504s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev3 armhf 3.2.0-2 [44.2 kB] 504s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf libftdi1-2 armhf 1.5-7 [25.7 kB] 504s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf libinih1 armhf 58-1ubuntu1 [6750 B] 504s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf libsgutils2-1.46-2 armhf 1.46-3ubuntu5 [82.5 kB] 504s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf python3-configobj all 5.0.9-1 [33.9 kB] 504s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf python3-json-pointer all 2.4-2 [8396 B] 504s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf python3-lazr.uri all 1.0.6-4 [13.6 kB] 504s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf python3-zipp all 3.20.2-1 [10.1 kB] 504s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf sg3-utils armhf 1.46-3ubuntu5 [816 kB] 504s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf sg3-utils-udev all 1.46-3ubuntu5 [5916 B] 504s Preconfiguring packages ... 504s Fetched 19.6 MB in 1s (14.4 MB/s) 505s (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 ... 59386 files and directories currently installed.) 505s Preparing to unpack .../motd-news-config_13.5ubuntu2_all.deb ... 505s Unpacking motd-news-config (13.5ubuntu2) over (13.3ubuntu6) ... 505s Preparing to unpack .../base-files_13.5ubuntu2_armhf.deb ... 505s Unpacking base-files (13.5ubuntu2) over (13.3ubuntu6) ... 505s Setting up base-files (13.5ubuntu2) ... 505s Installing new version of config file /etc/issue ... 505s Installing new version of config file /etc/issue.net ... 505s Installing new version of config file /etc/lsb-release ... 506s motd-news.service is a disabled or a static unit not running, not starting it. 506s (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 ... 59386 files and directories currently installed.) 506s Preparing to unpack .../perl_5.40.0-6_armhf.deb ... 506s Unpacking perl (5.40.0-6) over (5.38.2-5) ... 506s Selecting previously unselected package perl-modules-5.40. 506s Preparing to unpack .../perl-modules-5.40_5.40.0-6_all.deb ... 506s Unpacking perl-modules-5.40 (5.40.0-6) ... 506s Selecting previously unselected package libperl5.40:armhf. 506s Preparing to unpack .../libperl5.40_5.40.0-6_armhf.deb ... 506s Unpacking libperl5.40:armhf (5.40.0-6) ... 507s Preparing to unpack .../perl-base_5.40.0-6_armhf.deb ... 507s Unpacking perl-base (5.40.0-6) over (5.38.2-5) ... 507s Setting up perl-base (5.40.0-6) ... 507s (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 ... 61462 files and directories currently installed.) 507s Preparing to unpack .../liblocale-gettext-perl_1.07-7build1_armhf.deb ... 507s Unpacking liblocale-gettext-perl (1.07-7build1) over (1.07-7) ... 507s Preparing to unpack .../libtext-iconv-perl_1.7-8build4_armhf.deb ... 507s Unpacking libtext-iconv-perl:armhf (1.7-8build4) over (1.7-8build3) ... 507s Preparing to unpack .../libtext-charwidth-perl_0.04-11build4_armhf.deb ... 507s Unpacking libtext-charwidth-perl:armhf (0.04-11build4) over (0.04-11build3) ... 507s Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-9_armhf.deb ... 507s Unpacking libdb5.3t64:armhf (5.3.28+dfsg2-9) over (5.3.28+dfsg2-7) ... 507s Setting up libdb5.3t64:armhf (5.3.28+dfsg2-9) ... 507s (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 ... 61462 files and directories currently installed.) 507s Preparing to unpack .../libatomic1_14.2.0-7ubuntu1_armhf.deb ... 507s Unpacking libatomic1:armhf (14.2.0-7ubuntu1) over (14.2.0-4ubuntu2) ... 507s Preparing to unpack .../gcc-14-base_14.2.0-7ubuntu1_armhf.deb ... 507s Unpacking gcc-14-base:armhf (14.2.0-7ubuntu1) over (14.2.0-4ubuntu2) ... 507s Setting up gcc-14-base:armhf (14.2.0-7ubuntu1) ... 508s (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 ... 61462 files and directories currently installed.) 508s Preparing to unpack .../libstdc++6_14.2.0-7ubuntu1_armhf.deb ... 508s Unpacking libstdc++6:armhf (14.2.0-7ubuntu1) over (14.2.0-4ubuntu2) ... 508s Setting up libstdc++6:armhf (14.2.0-7ubuntu1) ... 508s (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 ... 61462 files and directories currently installed.) 508s Preparing to unpack .../libgcc-s1_14.2.0-7ubuntu1_armhf.deb ... 508s Unpacking libgcc-s1:armhf (14.2.0-7ubuntu1) over (14.2.0-4ubuntu2) ... 508s Setting up libgcc-s1:armhf (14.2.0-7ubuntu1) ... 508s (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 ... 61462 files and directories currently installed.) 508s Preparing to unpack .../install-info_7.1.1-1_armhf.deb ... 508s Unpacking install-info (7.1.1-1) over (7.1-3build2) ... 508s Setting up install-info (7.1.1-1) ... 508s (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 ... 61462 files and directories currently installed.) 508s Preparing to unpack .../00-distro-info-data_0.63_all.deb ... 508s Unpacking distro-info-data (0.63) over (0.62) ... 508s Preparing to unpack .../01-libdw1t64_0.192-4_armhf.deb ... 508s Unpacking libdw1t64:armhf (0.192-4) over (0.191-2) ... 508s Preparing to unpack .../02-libelf1t64_0.192-4_armhf.deb ... 508s Unpacking libelf1t64:armhf (0.192-4) over (0.191-2) ... 508s Preparing to unpack .../03-iproute2_6.10.0-2ubuntu1_armhf.deb ... 509s Unpacking iproute2 (6.10.0-2ubuntu1) over (6.10.0-2) ... 509s Preparing to unpack .../04-libkeyutils1_1.6.3-4ubuntu2_armhf.deb ... 509s Unpacking libkeyutils1:armhf (1.6.3-4ubuntu2) over (1.6.3-3build1) ... 509s Preparing to unpack .../05-vim-tiny_2%3a9.1.0777-1ubuntu1_armhf.deb ... 509s Unpacking vim-tiny (2:9.1.0777-1ubuntu1) over (2:9.1.0496-1ubuntu6) ... 509s Preparing to unpack .../06-vim-common_2%3a9.1.0777-1ubuntu1_all.deb ... 509s Unpacking vim-common (2:9.1.0777-1ubuntu1) over (2:9.1.0496-1ubuntu6) ... 509s Preparing to unpack .../07-xxd_2%3a9.1.0777-1ubuntu1_armhf.deb ... 509s Unpacking xxd (2:9.1.0777-1ubuntu1) over (2:9.1.0496-1ubuntu6) ... 509s Preparing to unpack .../08-info_7.1.1-1_armhf.deb ... 509s Unpacking info (7.1.1-1) over (7.1-3build2) ... 509s Preparing to unpack .../09-libevdev2_1.13.3+dfsg-1_armhf.deb ... 509s Unpacking libevdev2:armhf (1.13.3+dfsg-1) over (1.13.2+dfsg-1) ... 509s Preparing to unpack .../10-libpipeline1_1.5.8-1_armhf.deb ... 509s Unpacking libpipeline1:armhf (1.5.8-1) over (1.5.7-2) ... 509s Preparing to unpack .../11-nano_8.2-1_armhf.deb ... 509s Unpacking nano (8.2-1) over (8.1-1) ... 509s Preparing to unpack .../12-libfwupd2_1.9.26-2_armhf.deb ... 509s Unpacking libfwupd2:armhf (1.9.26-2) over (1.9.24-1) ... 509s Preparing to unpack .../13-fwupd_1.9.26-2_armhf.deb ... 510s Unpacking fwupd (1.9.26-2) over (1.9.24-1) ... 510s Preparing to unpack .../14-libblockdev-utils3_3.2.0-2_armhf.deb ... 510s Unpacking libblockdev-utils3:armhf (3.2.0-2) over (3.1.1-2) ... 510s Preparing to unpack .../15-libblockdev-crypto3_3.2.0-2_armhf.deb ... 510s Unpacking libblockdev-crypto3:armhf (3.2.0-2) over (3.1.1-2) ... 510s Preparing to unpack .../16-libblockdev-fs3_3.2.0-2_armhf.deb ... 510s Unpacking libblockdev-fs3:armhf (3.2.0-2) over (3.1.1-2) ... 510s Preparing to unpack .../17-libblockdev-loop3_3.2.0-2_armhf.deb ... 510s Unpacking libblockdev-loop3:armhf (3.2.0-2) over (3.1.1-2) ... 510s Preparing to unpack .../18-libblockdev-mdraid3_3.2.0-2_armhf.deb ... 510s Unpacking libblockdev-mdraid3:armhf (3.2.0-2) over (3.1.1-2) ... 510s Preparing to unpack .../19-libblockdev-nvme3_3.2.0-2_armhf.deb ... 510s Unpacking libblockdev-nvme3:armhf (3.2.0-2) over (3.1.1-2) ... 510s Preparing to unpack .../20-libblockdev-part3_3.2.0-2_armhf.deb ... 510s Unpacking libblockdev-part3:armhf (3.2.0-2) over (3.1.1-2) ... 510s Preparing to unpack .../21-libblockdev-swap3_3.2.0-2_armhf.deb ... 510s Unpacking libblockdev-swap3:armhf (3.2.0-2) over (3.1.1-2) ... 510s Preparing to unpack .../22-libblockdev3_3.2.0-2_armhf.deb ... 510s Unpacking libblockdev3:armhf (3.2.0-2) over (3.1.1-2) ... 510s Preparing to unpack .../23-libftdi1-2_1.5-7_armhf.deb ... 510s Unpacking libftdi1-2:armhf (1.5-7) over (1.5-6build5) ... 510s Preparing to unpack .../24-libinih1_58-1ubuntu1_armhf.deb ... 510s Unpacking libinih1:armhf (58-1ubuntu1) over (55-1ubuntu2) ... 510s Preparing to unpack .../25-libsgutils2-1.46-2_1.46-3ubuntu5_armhf.deb ... 510s Unpacking libsgutils2-1.46-2:armhf (1.46-3ubuntu5) over (1.46-3ubuntu4) ... 510s Preparing to unpack .../26-python3-configobj_5.0.9-1_all.deb ... 510s Unpacking python3-configobj (5.0.9-1) over (5.0.8-3) ... 511s Preparing to unpack .../27-python3-json-pointer_2.4-2_all.deb ... 511s Unpacking python3-json-pointer (2.4-2) over (2.0-0ubuntu1) ... 511s Preparing to unpack .../28-python3-lazr.uri_1.0.6-4_all.deb ... 511s Unpacking python3-lazr.uri (1.0.6-4) over (1.0.6-3) ... 511s Preparing to unpack .../29-python3-zipp_3.20.2-1_all.deb ... 511s Unpacking python3-zipp (3.20.2-1) over (3.20.0-1) ... 511s Preparing to unpack .../30-sg3-utils_1.46-3ubuntu5_armhf.deb ... 511s Unpacking sg3-utils (1.46-3ubuntu5) over (1.46-3ubuntu4) ... 511s Preparing to unpack .../31-sg3-utils-udev_1.46-3ubuntu5_all.deb ... 511s Unpacking sg3-utils-udev (1.46-3ubuntu5) over (1.46-3ubuntu4) ... 511s Setting up libpipeline1:armhf (1.5.8-1) ... 511s Setting up motd-news-config (13.5ubuntu2) ... 511s Setting up libtext-iconv-perl:armhf (1.7-8build4) ... 511s Setting up libtext-charwidth-perl:armhf (0.04-11build4) ... 511s Setting up libkeyutils1:armhf (1.6.3-4ubuntu2) ... 511s Setting up distro-info-data (0.63) ... 511s Setting up libinih1:armhf (58-1ubuntu1) ... 511s Setting up libfwupd2:armhf (1.9.26-2) ... 511s Setting up libsgutils2-1.46-2:armhf (1.46-3ubuntu5) ... 511s Setting up python3-lazr.uri (1.0.6-4) ... 511s Setting up python3-zipp (3.20.2-1) ... 512s Setting up xxd (2:9.1.0777-1ubuntu1) ... 512s Setting up libelf1t64:armhf (0.192-4) ... 512s Setting up libdw1t64:armhf (0.192-4) ... 512s Setting up libftdi1-2:armhf (1.5-7) ... 512s Setting up python3-configobj (5.0.9-1) ... 512s Setting up vim-common (2:9.1.0777-1ubuntu1) ... 512s Installing new version of config file /etc/vim/vimrc ... 512s Setting up libblockdev-utils3:armhf (3.2.0-2) ... 512s Setting up libatomic1:armhf (14.2.0-7ubuntu1) ... 512s Setting up libblockdev-nvme3:armhf (3.2.0-2) ... 512s Setting up nano (8.2-1) ... 512s Setting up libblockdev-fs3:armhf (3.2.0-2) ... 512s Setting up perl-modules-5.40 (5.40.0-6) ... 512s Setting up python3-json-pointer (2.4-2) ... 512s Setting up libevdev2:armhf (1.13.3+dfsg-1) ... 512s Setting up fwupd (1.9.26-2) ... 513s fwupd-offline-update.service is a disabled or a static unit not running, not starting it. 513s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 513s fwupd.service is a disabled or a static unit not running, not starting it. 513s Setting up info (7.1.1-1) ... 513s Setting up liblocale-gettext-perl (1.07-7build1) ... 513s Setting up sg3-utils (1.46-3ubuntu5) ... 513s Setting up libblockdev-mdraid3:armhf (3.2.0-2) ... 513s Setting up libblockdev-crypto3:armhf (3.2.0-2) ... 513s Setting up libblockdev-swap3:armhf (3.2.0-2) ... 513s Setting up iproute2 (6.10.0-2ubuntu1) ... 513s Setting up libblockdev-loop3:armhf (3.2.0-2) ... 513s Setting up vim-tiny (2:9.1.0777-1ubuntu1) ... 513s Setting up libblockdev3:armhf (3.2.0-2) ... 513s Installing new version of config file /etc/libblockdev/3/conf.d/00-default.cfg ... 513s Setting up libblockdev-part3:armhf (3.2.0-2) ... 513s Setting up sg3-utils-udev (1.46-3ubuntu5) ... 513s update-initramfs: deferring update (trigger activated) 513s Setting up libperl5.40:armhf (5.40.0-6) ... 513s Setting up perl (5.40.0-6) ... 513s Processing triggers for dbus (1.14.10-4ubuntu5) ... 513s Processing triggers for install-info (7.1.1-1) ... 513s Processing triggers for initramfs-tools (0.142ubuntu34) ... 513s Processing triggers for libc-bin (2.40-1ubuntu3) ... 514s Processing triggers for man-db (2.12.1-3) ... 515s Processing triggers for plymouth-theme-ubuntu-text (24.004.60-1ubuntu10) ... 515s update-initramfs: deferring update (trigger activated) 515s Processing triggers for initramfs-tools (0.142ubuntu34) ... 516s Reading package lists... 516s Building dependency tree... 516s Reading state information... 517s The following packages will be REMOVED: 517s libperl5.38t64* perl-modules-5.38* 517s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 517s After this operation, 41.6 MB disk space will be freed. 517s (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 ... 61462 files and directories currently installed.) 518s Removing libperl5.38t64:armhf (5.38.2-5) ... 518s Removing perl-modules-5.38 (5.38.2-5) ... 518s Processing triggers for man-db (2.12.1-3) ... 518s Processing triggers for libc-bin (2.40-1ubuntu3) ... 520s autopkgtest [00:51:16]: rebooting testbed after setup commands that affected boot 622s Reading package lists... 622s Building dependency tree... 622s Reading state information... 623s Starting pkgProblemResolver with broken count: 0 623s Starting 2 pkgProblemResolver with broken count: 0 623s Done 625s The following additional packages will be installed: 625s libdeflate0 libhts3t64 libhtscodecs2 python3-all python3-pysam 625s The following NEW packages will be installed: 625s autopkgtest-satdep libdeflate0 libhts3t64 libhtscodecs2 python3-all 625s python3-pysam 625s 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. 625s Need to get 3882 kB/3883 kB of archives. 625s After this operation, 33.9 MB of additional disk space will be used. 625s Get:1 /tmp/autopkgtest.OEVu7F/2-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [720 B] 625s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.21-1 [38.8 kB] 626s Get:3 http://ftpmaster.internal/ubuntu plucky/universe armhf libhtscodecs2 armhf 1.6.0-1build1 [65.8 kB] 626s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf libhts3t64 armhf 1.20+ds-2 [394 kB] 626s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3-all armhf 3.12.6-0ubuntu1 [886 B] 626s Get:6 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pysam armhf 0.22.1+ds-2 [3383 kB] 627s Fetched 3882 kB in 1s (4740 kB/s) 627s Selecting previously unselected package libdeflate0:armhf. 627s (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 ... 59532 files and directories currently installed.) 627s Preparing to unpack .../0-libdeflate0_1.21-1_armhf.deb ... 627s Unpacking libdeflate0:armhf (1.21-1) ... 627s Selecting previously unselected package libhtscodecs2:armhf. 627s Preparing to unpack .../1-libhtscodecs2_1.6.0-1build1_armhf.deb ... 627s Unpacking libhtscodecs2:armhf (1.6.0-1build1) ... 627s Selecting previously unselected package libhts3t64:armhf. 627s Preparing to unpack .../2-libhts3t64_1.20+ds-2_armhf.deb ... 627s Unpacking libhts3t64:armhf (1.20+ds-2) ... 627s Selecting previously unselected package python3-all. 627s Preparing to unpack .../3-python3-all_3.12.6-0ubuntu1_armhf.deb ... 627s Unpacking python3-all (3.12.6-0ubuntu1) ... 627s Selecting previously unselected package python3-pysam. 627s Preparing to unpack .../4-python3-pysam_0.22.1+ds-2_armhf.deb ... 627s Unpacking python3-pysam (0.22.1+ds-2) ... 627s Selecting previously unselected package autopkgtest-satdep. 627s Preparing to unpack .../5-2-autopkgtest-satdep.deb ... 627s Unpacking autopkgtest-satdep (0) ... 627s Setting up libhtscodecs2:armhf (1.6.0-1build1) ... 627s Setting up libdeflate0:armhf (1.21-1) ... 627s Setting up python3-all (3.12.6-0ubuntu1) ... 627s Setting up libhts3t64:armhf (1.20+ds-2) ... 627s Setting up python3-pysam (0.22.1+ds-2) ... 627s Setting up autopkgtest-satdep (0) ... 627s Processing triggers for man-db (2.12.1-3) ... 628s Processing triggers for libc-bin (2.40-1ubuntu3) ... 640s (Reading database ... 59918 files and directories currently installed.) 640s Removing autopkgtest-satdep (0) ... 651s autopkgtest [00:53:27]: 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 651s autopkgtest [00:53:27]: test autodep8-python3: [----------------------- 653s Testing with python3.12: 653s 654s autopkgtest [00:53:30]: test autodep8-python3: -----------------------] 658s autopkgtest [00:53:34]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 658s autodep8-python3 PASS (superficial) 661s autopkgtest [00:53:37]: @@@@@@@@@@@@@@@@@@@@ summary 661s command1 PASS 661s autodep8-python3 PASS (superficial)