0s autopkgtest [14:55:53]: starting date and time: 2025-03-15 14:55:53+0000 0s autopkgtest [14:55:53]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [14:55:53]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.cp9ap44y/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade python-pysam --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-10.secgroup --name adt-plucky-arm64-python-pysam-20250315-145552-juju-7f2275-prod-proposed-migration-environment-2-81ab0726-c1ea-420a-b070-080c3234808f --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 158s autopkgtest [14:58:31]: testbed dpkg architecture: arm64 158s autopkgtest [14:58:31]: testbed apt version: 2.9.33 158s autopkgtest [14:58:31]: @@@@@@@@@@@@@@@@@@@@ test bed setup 158s autopkgtest [14:58:31]: testbed release detected to be: None 159s autopkgtest [14:58:32]: updating testbed package index (apt update) 160s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 160s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 160s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 160s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 160s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 160s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 160s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 161s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [78.2 kB] 161s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1976 B] 161s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 161s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [346 kB] 162s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [15.8 kB] 162s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 162s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [572 B] 162s Fetched 1094 kB in 2s (475 kB/s) 163s Reading package lists... 164s Reading package lists... 164s Building dependency tree... 164s Reading state information... 164s Calculating upgrade... 165s Calculating upgrade... 166s The following packages will be upgraded: 166s python3-jinja2 strace 166s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 166s Need to get 608 kB of archives. 166s After this operation, 11.3 kB of additional disk space will be used. 166s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 167s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 168s Fetched 608 kB in 1s (444 kB/s) 168s (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 ... 117701 files and directories currently installed.) 168s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 168s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 168s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 168s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 168s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 169s Setting up strace (6.13+ds-1ubuntu1) ... 169s Processing triggers for man-db (2.13.0-1) ... 170s Reading package lists... 170s Building dependency tree... 170s Reading state information... 171s Solving dependencies... 171s The following packages will be REMOVED: 171s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 171s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 171s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 171s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 171s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 171s After this operation, 267 MB disk space will be freed. 172s (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 ... 117701 files and directories currently installed.) 172s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 172s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 172s Removing libpython3.12t64:arm64 (3.12.9-1) ... 172s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 172s Removing libnsl2:arm64 (1.3.0-3build3) ... 172s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 172s Removing libunwind8:arm64 (1.6.2-3.1) ... 172s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 172s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 174s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 175s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 175s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 175s /etc/kernel/postrm.d/initramfs-tools: 175s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 175s /etc/kernel/postrm.d/zz-flash-kernel: 175s flash-kernel: Kernel 6.11.0-8-generic has been removed. 175s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 175s /etc/kernel/postrm.d/zz-update-grub: 175s Sourcing file `/etc/default/grub' 175s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 175s Generating grub configuration file ... 175s Found linux image: /boot/vmlinuz-6.14.0-10-generic 175s Found initrd image: /boot/initrd.img-6.14.0-10-generic 176s Warning: os-prober will not be executed to detect other bootable partitions. 176s Systems on them will not be added to the GRUB boot configuration. 176s Check GRUB_DISABLE_OS_PROBER documentation entry. 176s Adding boot menu entry for UEFI Firmware Settings ... 176s done 176s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 176s Processing triggers for libc-bin (2.41-1ubuntu1) ... 176s (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 ... 81650 files and directories currently installed.) 176s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 176s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 176s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 176s autopkgtest [14:58:49]: upgrading testbed (apt dist-upgrade and autopurge) 176s Reading package lists... 177s Building dependency tree... 177s Reading state information... 177s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 177s Starting 2 pkgProblemResolver with broken count: 0 177s Done 178s Entering ResolveByKeep 179s 179s Calculating upgrade... 179s The following packages will be upgraded: 179s libc-bin libc-dev-bin libc6 libc6-dev locales 179s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 179s Need to get 9530 kB of archives. 179s After this operation, 0 B of additional disk space will be used. 179s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 183s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 183s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 190s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 191s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 200s Preconfiguring packages ... 200s Fetched 9530 kB in 21s (460 kB/s) 200s (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 ... 81647 files and directories currently installed.) 200s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 200s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 201s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 201s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 201s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 201s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 201s Setting up libc6:arm64 (2.41-1ubuntu2) ... 201s (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 ... 81647 files and directories currently installed.) 201s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 201s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 201s Setting up libc-bin (2.41-1ubuntu2) ... 202s (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 ... 81647 files and directories currently installed.) 202s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 202s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 202s Setting up locales (2.41-1ubuntu2) ... 202s Generating locales (this might take a while)... 205s en_US.UTF-8... done 205s Generation complete. 205s Setting up libc-dev-bin (2.41-1ubuntu2) ... 205s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 205s Processing triggers for man-db (2.13.0-1) ... 206s Processing triggers for systemd (257.3-1ubuntu3) ... 207s Reading package lists... 207s Building dependency tree... 207s Reading state information... 208s Starting pkgProblemResolver with broken count: 0 208s Starting 2 pkgProblemResolver with broken count: 0 208s Done 208s Solving dependencies... 209s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 209s autopkgtest [14:59:22]: rebooting testbed after setup commands that affected boot 232s autopkgtest [14:59:45]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 235s autopkgtest [14:59:48]: @@@@@@@@@@@@@@@@@@@@ apt-source python-pysam 241s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-pysam 0.23.0+ds-1build1 (dsc) [2436 B] 241s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-pysam 0.23.0+ds-1build1 (tar) [1519 kB] 241s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-pysam 0.23.0+ds-1build1 (diff) [10.7 kB] 241s gpgv: Signature made Tue Mar 4 19:20:47 2025 UTC 241s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 241s gpgv: Can't check signature: No public key 241s dpkg-source: warning: cannot verify inline signature for ./python-pysam_0.23.0+ds-1build1.dsc: no acceptable signature found 242s autopkgtest [14:59:55]: testing package python-pysam version 0.23.0+ds-1build1 242s autopkgtest [14:59:55]: build not needed 243s autopkgtest [14:59:56]: test command1: preparing testbed 244s Reading package lists... 244s Building dependency tree... 244s Reading state information... 244s Starting pkgProblemResolver with broken count: 0 244s Starting 2 pkgProblemResolver with broken count: 0 244s Done 245s The following NEW packages will be installed: 245s autoconf automake autopoint autotools-dev bcftools build-essential 245s comerr-dev cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu cython3 245s debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz g++ 245s g++-14 g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14 245s gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext intltool-debian 245s krb5-multidev libarchive-zip-perl libasan8 libbrotli-dev libbz2-dev libcc1-0 245s libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 245s libevent-2.1-7t64 libexpat1-dev libfile-stripnondeterminism-perl 245s libgcc-14-dev libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 245s libgnutls-openssl27t64 libgnutls28-dev libgomp1 libgssrpc4t64 libhts-dev 245s libhts3t64 libhtscodecs2 libhwasan0 libidn2-dev libisl23 libitm1 245s libjs-jquery libjs-sphinxdoc libjs-underscore libkadm5clnt-mit12 245s libkadm5srv-mit12 libkdb5-10t64 libkrb5-dev libldap-dev liblsan0 liblzma-dev 245s libmpc3 libnghttp2-dev libp11-kit-dev libpkgconf3 libpsl-dev 245s libpython3-all-dev libpython3-dev libpython3.13-dev librtmp-dev 245s libssh2-1-dev libssl-dev libstdc++-14-dev libtasn1-6-dev libtool libtsan2 245s libubsan1 libunbound8 libzstd-dev m4 nettle-dev pkgconf pkgconf-bin 245s po-debconf python3-all python3-all-dev python3-dev python3-iniconfig 245s python3-packaging python3-pluggy python3-pysam python3-pytest python3.13-dev 245s samtools tabix zlib1g-dev 246s 0 upgraded, 101 newly installed, 0 to remove and 0 not upgraded. 246s Need to get 96.7 MB of archives. 246s After this operation, 363 MB of additional disk space will be used. 246s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 m4 arm64 1.4.19-7 [244 kB] 246s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 autoconf all 2.72-3ubuntu1 [383 kB] 247s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 autotools-dev all 20220109.1 [44.9 kB] 247s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 automake all 1:1.17-3ubuntu1 [572 kB] 248s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 autopoint all 0.23.1-1 [619 kB] 250s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 250s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.1-2 [82.7 kB] 250s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts3t64 arm64 1.21+ds-1 [441 kB] 251s Get:9 http://ftpmaster.internal/ubuntu plucky/universe arm64 bcftools arm64 1.21-1 [804 kB] 253s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libisl23 arm64 0.27-1 [676 kB] 254s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB] 254s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [10.6 MB] 276s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14 arm64 14.2.0-17ubuntu3 [1028 B] 276s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [5558 B] 276s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp arm64 4:14.2.0-1ubuntu1 [22.4 kB] 276s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libcc1-0 arm64 15-20250222-0ubuntu1 [44.2 kB] 276s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB] 276s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 15-20250222-0ubuntu1 [28.0 kB] 276s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 15-20250222-0ubuntu1 [2924 kB] 282s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 15-20250222-0ubuntu1 [1319 kB] 284s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 15-20250222-0ubuntu1 [2694 kB] 289s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 15-20250222-0ubuntu1 [1178 kB] 291s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 15-20250222-0ubuntu1 [1642 kB] 294s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-17ubuntu3 [2593 kB] 299s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [20.9 MB] 336s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14 arm64 14.2.0-17ubuntu3 [526 kB] 337s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1200 B] 337s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc arm64 4:14.2.0-1ubuntu1 [4998 B] 337s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-17ubuntu3 [2499 kB] 342s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [12.1 MB] 363s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14 arm64 14.2.0-17ubuntu3 [21.8 kB] 363s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [956 B] 363s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 g++ arm64 4:14.2.0-1ubuntu1 [1080 B] 363s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 363s Get:35 http://ftpmaster.internal/ubuntu plucky/universe arm64 cython3 arm64 3.0.11+dfsg-2ubuntu2 [2436 kB] 367s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libdebhelper-perl all 13.24.1ubuntu2 [95.4 kB] 367s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libtool all 2.5.4-4 [168 kB] 367s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 dh-autoreconf all 20 [16.1 kB] 368s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] 368s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [20.3 kB] 368s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 dh-strip-nondeterminism all 1.14.1-2 [5064 B] 368s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 debugedit arm64 1:5.1-2 [46.1 kB] 368s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 dwz arm64 0.15-1build6 [113 kB] 368s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 gettext arm64 0.23.1-1 [998 kB] 370s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 370s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] 371s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 debhelper all 13.24.1ubuntu2 [895 kB] 373s Get:48 http://ftpmaster.internal/ubuntu plucky/universe arm64 dh-python all 6.20250308 [118 kB] 373s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 comerr-dev arm64 2.1-1.47.2-1ubuntu1 [45.1 kB] 373s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 libgssrpc4t64 arm64 1.21.3-4ubuntu2 [58.5 kB] 373s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 libkadm5clnt-mit12 arm64 1.21.3-4ubuntu2 [40.3 kB] 373s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 libkdb5-10t64 arm64 1.21.3-4ubuntu2 [40.9 kB] 373s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 libkadm5srv-mit12 arm64 1.21.3-4ubuntu2 [53.8 kB] 373s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 krb5-multidev arm64 1.21.3-4ubuntu2 [125 kB] 374s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 libbrotli-dev arm64 1.1.0-2build4 [359 kB] 374s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 libbz2-dev arm64 1.0.8-6 [36.1 kB] 374s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10 [140 kB] 375s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 libunbound8 arm64 1.22.0-1ubuntu1 [437 kB] 375s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 libgnutls-dane0t64 arm64 3.8.9-2ubuntu2 [24.4 kB] 375s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 libgnutls-openssl27t64 arm64 3.8.9-2ubuntu2 [24.4 kB] 375s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 libidn2-dev arm64 2.3.7-2build2 [120 kB] 376s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 libp11-kit-dev arm64 0.25.5-2ubuntu3 [23.5 kB] 376s Get:63 http://ftpmaster.internal/ubuntu plucky/main arm64 libtasn1-6-dev arm64 4.20.0-2 [91.1 kB] 376s Get:64 http://ftpmaster.internal/ubuntu plucky/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-3ubuntu1 [10.1 kB] 376s Get:65 http://ftpmaster.internal/ubuntu plucky/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-3ubuntu1 [335 kB] 377s Get:66 http://ftpmaster.internal/ubuntu plucky/main arm64 nettle-dev arm64 3.10.1-1 [1190 kB] 379s Get:67 http://ftpmaster.internal/ubuntu plucky/main arm64 libgnutls28-dev arm64 3.8.9-2ubuntu2 [1143 kB] 381s Get:68 http://ftpmaster.internal/ubuntu plucky/main arm64 libkrb5-dev arm64 1.21.3-4ubuntu2 [11.9 kB] 381s Get:69 http://ftpmaster.internal/ubuntu plucky/main arm64 libldap-dev arm64 2.6.9+dfsg-1~exp2ubuntu1 [318 kB] 382s Get:70 http://ftpmaster.internal/ubuntu plucky/main arm64 libpkgconf3 arm64 1.8.1-4 [31.4 kB] 382s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 pkgconf-bin arm64 1.8.1-4 [20.9 kB] 382s Get:72 http://ftpmaster.internal/ubuntu plucky/main arm64 pkgconf arm64 1.8.1-4 [16.7 kB] 382s Get:73 http://ftpmaster.internal/ubuntu plucky/main arm64 libnghttp2-dev arm64 1.64.0-1 [120 kB] 382s Get:74 http://ftpmaster.internal/ubuntu plucky/main arm64 libpsl-dev arm64 0.21.2-1.1build1 [77.2 kB] 382s Get:75 http://ftpmaster.internal/ubuntu plucky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB] 384s Get:76 http://ftpmaster.internal/ubuntu plucky/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-2build7 [69.4 kB] 384s Get:77 http://ftpmaster.internal/ubuntu plucky/main arm64 libssl-dev arm64 3.4.1-1ubuntu1 [3287 kB] 390s Get:78 http://ftpmaster.internal/ubuntu plucky/main arm64 libssh2-1-dev arm64 1.11.1-1 [286 kB] 391s Get:79 http://ftpmaster.internal/ubuntu plucky/main arm64 libzstd-dev arm64 1.5.6+dfsg-2 [353 kB] 391s Get:80 http://ftpmaster.internal/ubuntu plucky/main arm64 libcurl4-gnutls-dev arm64 8.12.1-3ubuntu1 [502 kB] 392s Get:81 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate-dev arm64 1.23-1 [53.7 kB] 392s Get:82 http://ftpmaster.internal/ubuntu plucky/main arm64 libexpat1-dev arm64 2.6.4-1 [129 kB] 393s Get:83 http://ftpmaster.internal/ubuntu plucky/main arm64 liblzma-dev arm64 5.6.4-1 [180 kB] 393s Get:84 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts-dev arm64 1.21+ds-1 [6019 kB] 403s Get:85 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 404s Get:86 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 404s Get:87 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-sphinxdoc all 8.1.3-4 [30.9 kB] 404s Get:88 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-dev arm64 3.13.2-2 [5399 kB] 414s Get:89 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3-dev arm64 3.13.2-2 [10.7 kB] 414s Get:90 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3-all-dev arm64 3.13.2-2 [910 B] 414s Get:91 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.13.2-2 [886 B] 414s Get:92 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-dev arm64 3.13.2-2 [509 kB] 415s Get:93 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dev arm64 3.13.2-2 [26.7 kB] 415s Get:94 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all-dev arm64 3.13.2-2 [914 B] 415s Get:95 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 415s Get:96 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.2-1 [51.5 kB] 415s Get:97 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 415s Get:98 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pysam arm64 0.23.0+ds-1build1 [3621 kB] 422s Get:99 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.5-1 [252 kB] 422s Get:100 http://ftpmaster.internal/ubuntu plucky/universe arm64 samtools arm64 1.21-1 [609 kB] 423s Get:101 http://ftpmaster.internal/ubuntu plucky/universe arm64 tabix arm64 1.21+ds-1 [527 kB] 425s Fetched 96.7 MB in 2min 58s (542 kB/s) 425s Selecting previously unselected package m4. 425s (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 ... 81647 files and directories currently installed.) 425s Preparing to unpack .../000-m4_1.4.19-7_arm64.deb ... 425s Unpacking m4 (1.4.19-7) ... 425s Selecting previously unselected package autoconf. 425s Preparing to unpack .../001-autoconf_2.72-3ubuntu1_all.deb ... 425s Unpacking autoconf (2.72-3ubuntu1) ... 425s Selecting previously unselected package autotools-dev. 425s Preparing to unpack .../002-autotools-dev_20220109.1_all.deb ... 425s Unpacking autotools-dev (20220109.1) ... 425s Selecting previously unselected package automake. 425s Preparing to unpack .../003-automake_1%3a1.17-3ubuntu1_all.deb ... 425s Unpacking automake (1:1.17-3ubuntu1) ... 426s Selecting previously unselected package autopoint. 426s Preparing to unpack .../004-autopoint_0.23.1-1_all.deb ... 426s Unpacking autopoint (0.23.1-1) ... 426s Selecting previously unselected package libdeflate0:arm64. 426s Preparing to unpack .../005-libdeflate0_1.23-1_arm64.deb ... 426s Unpacking libdeflate0:arm64 (1.23-1) ... 426s Selecting previously unselected package libhtscodecs2:arm64. 426s Preparing to unpack .../006-libhtscodecs2_1.6.1-2_arm64.deb ... 426s Unpacking libhtscodecs2:arm64 (1.6.1-2) ... 426s Selecting previously unselected package libhts3t64:arm64. 426s Preparing to unpack .../007-libhts3t64_1.21+ds-1_arm64.deb ... 426s Unpacking libhts3t64:arm64 (1.21+ds-1) ... 426s Selecting previously unselected package bcftools. 426s Preparing to unpack .../008-bcftools_1.21-1_arm64.deb ... 426s Unpacking bcftools (1.21-1) ... 426s Selecting previously unselected package libisl23:arm64. 426s Preparing to unpack .../009-libisl23_0.27-1_arm64.deb ... 426s Unpacking libisl23:arm64 (0.27-1) ... 426s Selecting previously unselected package libmpc3:arm64. 426s Preparing to unpack .../010-libmpc3_1.3.1-1build2_arm64.deb ... 426s Unpacking libmpc3:arm64 (1.3.1-1build2) ... 426s Selecting previously unselected package cpp-14-aarch64-linux-gnu. 426s Preparing to unpack .../011-cpp-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ... 426s Unpacking cpp-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 426s Selecting previously unselected package cpp-14. 426s Preparing to unpack .../012-cpp-14_14.2.0-17ubuntu3_arm64.deb ... 426s Unpacking cpp-14 (14.2.0-17ubuntu3) ... 426s Selecting previously unselected package cpp-aarch64-linux-gnu. 426s Preparing to unpack .../013-cpp-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 426s Unpacking cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 426s Selecting previously unselected package cpp. 426s Preparing to unpack .../014-cpp_4%3a14.2.0-1ubuntu1_arm64.deb ... 426s Unpacking cpp (4:14.2.0-1ubuntu1) ... 426s Selecting previously unselected package libcc1-0:arm64. 426s Preparing to unpack .../015-libcc1-0_15-20250222-0ubuntu1_arm64.deb ... 426s Unpacking libcc1-0:arm64 (15-20250222-0ubuntu1) ... 426s Selecting previously unselected package libgomp1:arm64. 427s Preparing to unpack .../016-libgomp1_15-20250222-0ubuntu1_arm64.deb ... 427s Unpacking libgomp1:arm64 (15-20250222-0ubuntu1) ... 427s Selecting previously unselected package libitm1:arm64. 427s Preparing to unpack .../017-libitm1_15-20250222-0ubuntu1_arm64.deb ... 427s Unpacking libitm1:arm64 (15-20250222-0ubuntu1) ... 427s Selecting previously unselected package libasan8:arm64. 427s Preparing to unpack .../018-libasan8_15-20250222-0ubuntu1_arm64.deb ... 427s Unpacking libasan8:arm64 (15-20250222-0ubuntu1) ... 427s Selecting previously unselected package liblsan0:arm64. 427s Preparing to unpack .../019-liblsan0_15-20250222-0ubuntu1_arm64.deb ... 427s Unpacking liblsan0:arm64 (15-20250222-0ubuntu1) ... 427s Selecting previously unselected package libtsan2:arm64. 427s Preparing to unpack .../020-libtsan2_15-20250222-0ubuntu1_arm64.deb ... 427s Unpacking libtsan2:arm64 (15-20250222-0ubuntu1) ... 427s Selecting previously unselected package libubsan1:arm64. 427s Preparing to unpack .../021-libubsan1_15-20250222-0ubuntu1_arm64.deb ... 427s Unpacking libubsan1:arm64 (15-20250222-0ubuntu1) ... 427s Selecting previously unselected package libhwasan0:arm64. 427s Preparing to unpack .../022-libhwasan0_15-20250222-0ubuntu1_arm64.deb ... 427s Unpacking libhwasan0:arm64 (15-20250222-0ubuntu1) ... 427s Selecting previously unselected package libgcc-14-dev:arm64. 427s Preparing to unpack .../023-libgcc-14-dev_14.2.0-17ubuntu3_arm64.deb ... 427s Unpacking libgcc-14-dev:arm64 (14.2.0-17ubuntu3) ... 427s Selecting previously unselected package gcc-14-aarch64-linux-gnu. 427s Preparing to unpack .../024-gcc-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ... 427s Unpacking gcc-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 428s Selecting previously unselected package gcc-14. 428s Preparing to unpack .../025-gcc-14_14.2.0-17ubuntu3_arm64.deb ... 428s Unpacking gcc-14 (14.2.0-17ubuntu3) ... 428s Selecting previously unselected package gcc-aarch64-linux-gnu. 428s Preparing to unpack .../026-gcc-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 428s Unpacking gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 428s Selecting previously unselected package gcc. 428s Preparing to unpack .../027-gcc_4%3a14.2.0-1ubuntu1_arm64.deb ... 428s Unpacking gcc (4:14.2.0-1ubuntu1) ... 428s Selecting previously unselected package libstdc++-14-dev:arm64. 428s Preparing to unpack .../028-libstdc++-14-dev_14.2.0-17ubuntu3_arm64.deb ... 428s Unpacking libstdc++-14-dev:arm64 (14.2.0-17ubuntu3) ... 428s Selecting previously unselected package g++-14-aarch64-linux-gnu. 428s Preparing to unpack .../029-g++-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ... 428s Unpacking g++-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 429s Selecting previously unselected package g++-14. 429s Preparing to unpack .../030-g++-14_14.2.0-17ubuntu3_arm64.deb ... 429s Unpacking g++-14 (14.2.0-17ubuntu3) ... 429s Selecting previously unselected package g++-aarch64-linux-gnu. 429s Preparing to unpack .../031-g++-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 429s Unpacking g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 429s Selecting previously unselected package g++. 429s Preparing to unpack .../032-g++_4%3a14.2.0-1ubuntu1_arm64.deb ... 429s Unpacking g++ (4:14.2.0-1ubuntu1) ... 429s Selecting previously unselected package build-essential. 429s Preparing to unpack .../033-build-essential_12.10ubuntu1_arm64.deb ... 429s Unpacking build-essential (12.10ubuntu1) ... 429s Selecting previously unselected package cython3. 429s Preparing to unpack .../034-cython3_3.0.11+dfsg-2ubuntu2_arm64.deb ... 429s Unpacking cython3 (3.0.11+dfsg-2ubuntu2) ... 429s Selecting previously unselected package libdebhelper-perl. 429s Preparing to unpack .../035-libdebhelper-perl_13.24.1ubuntu2_all.deb ... 429s Unpacking libdebhelper-perl (13.24.1ubuntu2) ... 429s Selecting previously unselected package libtool. 429s Preparing to unpack .../036-libtool_2.5.4-4_all.deb ... 429s Unpacking libtool (2.5.4-4) ... 429s Selecting previously unselected package dh-autoreconf. 429s Preparing to unpack .../037-dh-autoreconf_20_all.deb ... 429s Unpacking dh-autoreconf (20) ... 429s Selecting previously unselected package libarchive-zip-perl. 429s Preparing to unpack .../038-libarchive-zip-perl_1.68-1_all.deb ... 429s Unpacking libarchive-zip-perl (1.68-1) ... 429s Selecting previously unselected package libfile-stripnondeterminism-perl. 429s Preparing to unpack .../039-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... 429s Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... 429s Selecting previously unselected package dh-strip-nondeterminism. 429s Preparing to unpack .../040-dh-strip-nondeterminism_1.14.1-2_all.deb ... 429s Unpacking dh-strip-nondeterminism (1.14.1-2) ... 429s Selecting previously unselected package debugedit. 429s Preparing to unpack .../041-debugedit_1%3a5.1-2_arm64.deb ... 429s Unpacking debugedit (1:5.1-2) ... 429s Selecting previously unselected package dwz. 429s Preparing to unpack .../042-dwz_0.15-1build6_arm64.deb ... 429s Unpacking dwz (0.15-1build6) ... 429s Selecting previously unselected package gettext. 429s Preparing to unpack .../043-gettext_0.23.1-1_arm64.deb ... 429s Unpacking gettext (0.23.1-1) ... 430s Selecting previously unselected package intltool-debian. 430s Preparing to unpack .../044-intltool-debian_0.35.0+20060710.6_all.deb ... 430s Unpacking intltool-debian (0.35.0+20060710.6) ... 430s Selecting previously unselected package po-debconf. 430s Preparing to unpack .../045-po-debconf_1.0.21+nmu1_all.deb ... 430s Unpacking po-debconf (1.0.21+nmu1) ... 430s Selecting previously unselected package debhelper. 430s Preparing to unpack .../046-debhelper_13.24.1ubuntu2_all.deb ... 430s Unpacking debhelper (13.24.1ubuntu2) ... 430s Selecting previously unselected package dh-python. 430s Preparing to unpack .../047-dh-python_6.20250308_all.deb ... 430s Unpacking dh-python (6.20250308) ... 430s Selecting previously unselected package comerr-dev:arm64. 430s Preparing to unpack .../048-comerr-dev_2.1-1.47.2-1ubuntu1_arm64.deb ... 430s Unpacking comerr-dev:arm64 (2.1-1.47.2-1ubuntu1) ... 430s Selecting previously unselected package libgssrpc4t64:arm64. 430s Preparing to unpack .../049-libgssrpc4t64_1.21.3-4ubuntu2_arm64.deb ... 430s Unpacking libgssrpc4t64:arm64 (1.21.3-4ubuntu2) ... 430s Selecting previously unselected package libkadm5clnt-mit12:arm64. 430s Preparing to unpack .../050-libkadm5clnt-mit12_1.21.3-4ubuntu2_arm64.deb ... 430s Unpacking libkadm5clnt-mit12:arm64 (1.21.3-4ubuntu2) ... 430s Selecting previously unselected package libkdb5-10t64:arm64. 430s Preparing to unpack .../051-libkdb5-10t64_1.21.3-4ubuntu2_arm64.deb ... 430s Unpacking libkdb5-10t64:arm64 (1.21.3-4ubuntu2) ... 430s Selecting previously unselected package libkadm5srv-mit12:arm64. 430s Preparing to unpack .../052-libkadm5srv-mit12_1.21.3-4ubuntu2_arm64.deb ... 430s Unpacking libkadm5srv-mit12:arm64 (1.21.3-4ubuntu2) ... 430s Selecting previously unselected package krb5-multidev:arm64. 430s Preparing to unpack .../053-krb5-multidev_1.21.3-4ubuntu2_arm64.deb ... 430s Unpacking krb5-multidev:arm64 (1.21.3-4ubuntu2) ... 430s Selecting previously unselected package libbrotli-dev:arm64. 430s Preparing to unpack .../054-libbrotli-dev_1.1.0-2build4_arm64.deb ... 430s Unpacking libbrotli-dev:arm64 (1.1.0-2build4) ... 430s Selecting previously unselected package libbz2-dev:arm64. 430s Preparing to unpack .../055-libbz2-dev_1.0.8-6_arm64.deb ... 430s Unpacking libbz2-dev:arm64 (1.0.8-6) ... 430s Selecting previously unselected package libevent-2.1-7t64:arm64. 430s Preparing to unpack .../056-libevent-2.1-7t64_2.1.12-stable-10_arm64.deb ... 430s Unpacking libevent-2.1-7t64:arm64 (2.1.12-stable-10) ... 430s Selecting previously unselected package libunbound8:arm64. 430s Preparing to unpack .../057-libunbound8_1.22.0-1ubuntu1_arm64.deb ... 430s Unpacking libunbound8:arm64 (1.22.0-1ubuntu1) ... 430s Selecting previously unselected package libgnutls-dane0t64:arm64. 431s Preparing to unpack .../058-libgnutls-dane0t64_3.8.9-2ubuntu2_arm64.deb ... 431s Unpacking libgnutls-dane0t64:arm64 (3.8.9-2ubuntu2) ... 431s Selecting previously unselected package libgnutls-openssl27t64:arm64. 431s Preparing to unpack .../059-libgnutls-openssl27t64_3.8.9-2ubuntu2_arm64.deb ... 431s Unpacking libgnutls-openssl27t64:arm64 (3.8.9-2ubuntu2) ... 431s Selecting previously unselected package libidn2-dev:arm64. 431s Preparing to unpack .../060-libidn2-dev_2.3.7-2build2_arm64.deb ... 431s Unpacking libidn2-dev:arm64 (2.3.7-2build2) ... 431s Selecting previously unselected package libp11-kit-dev:arm64. 431s Preparing to unpack .../061-libp11-kit-dev_0.25.5-2ubuntu3_arm64.deb ... 431s Unpacking libp11-kit-dev:arm64 (0.25.5-2ubuntu3) ... 431s Selecting previously unselected package libtasn1-6-dev:arm64. 431s Preparing to unpack .../062-libtasn1-6-dev_4.20.0-2_arm64.deb ... 431s Unpacking libtasn1-6-dev:arm64 (4.20.0-2) ... 431s Selecting previously unselected package libgmpxx4ldbl:arm64. 431s Preparing to unpack .../063-libgmpxx4ldbl_2%3a6.3.0+dfsg-3ubuntu1_arm64.deb ... 431s Unpacking libgmpxx4ldbl:arm64 (2:6.3.0+dfsg-3ubuntu1) ... 431s Selecting previously unselected package libgmp-dev:arm64. 431s Preparing to unpack .../064-libgmp-dev_2%3a6.3.0+dfsg-3ubuntu1_arm64.deb ... 431s Unpacking libgmp-dev:arm64 (2:6.3.0+dfsg-3ubuntu1) ... 431s Selecting previously unselected package nettle-dev:arm64. 431s Preparing to unpack .../065-nettle-dev_3.10.1-1_arm64.deb ... 431s Unpacking nettle-dev:arm64 (3.10.1-1) ... 431s Selecting previously unselected package libgnutls28-dev:arm64. 431s Preparing to unpack .../066-libgnutls28-dev_3.8.9-2ubuntu2_arm64.deb ... 431s Unpacking libgnutls28-dev:arm64 (3.8.9-2ubuntu2) ... 431s Selecting previously unselected package libkrb5-dev:arm64. 431s Preparing to unpack .../067-libkrb5-dev_1.21.3-4ubuntu2_arm64.deb ... 431s Unpacking libkrb5-dev:arm64 (1.21.3-4ubuntu2) ... 431s Selecting previously unselected package libldap-dev:arm64. 431s Preparing to unpack .../068-libldap-dev_2.6.9+dfsg-1~exp2ubuntu1_arm64.deb ... 431s Unpacking libldap-dev:arm64 (2.6.9+dfsg-1~exp2ubuntu1) ... 431s Selecting previously unselected package libpkgconf3:arm64. 431s Preparing to unpack .../069-libpkgconf3_1.8.1-4_arm64.deb ... 431s Unpacking libpkgconf3:arm64 (1.8.1-4) ... 431s Selecting previously unselected package pkgconf-bin. 431s Preparing to unpack .../070-pkgconf-bin_1.8.1-4_arm64.deb ... 431s Unpacking pkgconf-bin (1.8.1-4) ... 431s Selecting previously unselected package pkgconf:arm64. 431s Preparing to unpack .../071-pkgconf_1.8.1-4_arm64.deb ... 431s Unpacking pkgconf:arm64 (1.8.1-4) ... 431s Selecting previously unselected package libnghttp2-dev:arm64. 431s Preparing to unpack .../072-libnghttp2-dev_1.64.0-1_arm64.deb ... 431s Unpacking libnghttp2-dev:arm64 (1.64.0-1) ... 431s Selecting previously unselected package libpsl-dev:arm64. 431s Preparing to unpack .../073-libpsl-dev_0.21.2-1.1build1_arm64.deb ... 431s Unpacking libpsl-dev:arm64 (0.21.2-1.1build1) ... 432s Selecting previously unselected package zlib1g-dev:arm64. 432s Preparing to unpack .../074-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_arm64.deb ... 432s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 432s Selecting previously unselected package librtmp-dev:arm64. 432s Preparing to unpack .../075-librtmp-dev_2.4+20151223.gitfa8646d.1-2build7_arm64.deb ... 432s Unpacking librtmp-dev:arm64 (2.4+20151223.gitfa8646d.1-2build7) ... 432s Selecting previously unselected package libssl-dev:arm64. 432s Preparing to unpack .../076-libssl-dev_3.4.1-1ubuntu1_arm64.deb ... 432s Unpacking libssl-dev:arm64 (3.4.1-1ubuntu1) ... 432s Selecting previously unselected package libssh2-1-dev:arm64. 432s Preparing to unpack .../077-libssh2-1-dev_1.11.1-1_arm64.deb ... 432s Unpacking libssh2-1-dev:arm64 (1.11.1-1) ... 432s Selecting previously unselected package libzstd-dev:arm64. 432s Preparing to unpack .../078-libzstd-dev_1.5.6+dfsg-2_arm64.deb ... 432s Unpacking libzstd-dev:arm64 (1.5.6+dfsg-2) ... 432s Selecting previously unselected package libcurl4-gnutls-dev:arm64. 432s Preparing to unpack .../079-libcurl4-gnutls-dev_8.12.1-3ubuntu1_arm64.deb ... 432s Unpacking libcurl4-gnutls-dev:arm64 (8.12.1-3ubuntu1) ... 432s Selecting previously unselected package libdeflate-dev:arm64. 432s Preparing to unpack .../080-libdeflate-dev_1.23-1_arm64.deb ... 432s Unpacking libdeflate-dev:arm64 (1.23-1) ... 432s Selecting previously unselected package libexpat1-dev:arm64. 432s Preparing to unpack .../081-libexpat1-dev_2.6.4-1_arm64.deb ... 432s Unpacking libexpat1-dev:arm64 (2.6.4-1) ... 432s Selecting previously unselected package liblzma-dev:arm64. 432s Preparing to unpack .../082-liblzma-dev_5.6.4-1_arm64.deb ... 432s Unpacking liblzma-dev:arm64 (5.6.4-1) ... 432s Selecting previously unselected package libhts-dev:arm64. 432s Preparing to unpack .../083-libhts-dev_1.21+ds-1_arm64.deb ... 432s Unpacking libhts-dev:arm64 (1.21+ds-1) ... 432s Selecting previously unselected package libjs-jquery. 432s Preparing to unpack .../084-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 432s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 432s Selecting previously unselected package libjs-underscore. 433s Preparing to unpack .../085-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 433s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 433s Selecting previously unselected package libjs-sphinxdoc. 433s Preparing to unpack .../086-libjs-sphinxdoc_8.1.3-4_all.deb ... 433s Unpacking libjs-sphinxdoc (8.1.3-4) ... 433s Selecting previously unselected package libpython3.13-dev:arm64. 433s Preparing to unpack .../087-libpython3.13-dev_3.13.2-2_arm64.deb ... 433s Unpacking libpython3.13-dev:arm64 (3.13.2-2) ... 433s Selecting previously unselected package libpython3-dev:arm64. 433s Preparing to unpack .../088-libpython3-dev_3.13.2-2_arm64.deb ... 433s Unpacking libpython3-dev:arm64 (3.13.2-2) ... 433s Selecting previously unselected package libpython3-all-dev:arm64. 433s Preparing to unpack .../089-libpython3-all-dev_3.13.2-2_arm64.deb ... 433s Unpacking libpython3-all-dev:arm64 (3.13.2-2) ... 433s Selecting previously unselected package python3-all. 433s Preparing to unpack .../090-python3-all_3.13.2-2_arm64.deb ... 433s Unpacking python3-all (3.13.2-2) ... 433s Selecting previously unselected package python3.13-dev. 433s Preparing to unpack .../091-python3.13-dev_3.13.2-2_arm64.deb ... 433s Unpacking python3.13-dev (3.13.2-2) ... 433s Selecting previously unselected package python3-dev. 433s Preparing to unpack .../092-python3-dev_3.13.2-2_arm64.deb ... 433s Unpacking python3-dev (3.13.2-2) ... 433s Selecting previously unselected package python3-all-dev. 433s Preparing to unpack .../093-python3-all-dev_3.13.2-2_arm64.deb ... 433s Unpacking python3-all-dev (3.13.2-2) ... 433s Selecting previously unselected package python3-iniconfig. 433s Preparing to unpack .../094-python3-iniconfig_1.1.1-2_all.deb ... 433s Unpacking python3-iniconfig (1.1.1-2) ... 433s Selecting previously unselected package python3-packaging. 433s Preparing to unpack .../095-python3-packaging_24.2-1_all.deb ... 433s Unpacking python3-packaging (24.2-1) ... 433s Selecting previously unselected package python3-pluggy. 433s Preparing to unpack .../096-python3-pluggy_1.5.0-1_all.deb ... 433s Unpacking python3-pluggy (1.5.0-1) ... 433s Selecting previously unselected package python3-pysam. 433s Preparing to unpack .../097-python3-pysam_0.23.0+ds-1build1_arm64.deb ... 433s Unpacking python3-pysam (0.23.0+ds-1build1) ... 434s Selecting previously unselected package python3-pytest. 434s Preparing to unpack .../098-python3-pytest_8.3.5-1_all.deb ... 434s Unpacking python3-pytest (8.3.5-1) ... 434s Selecting previously unselected package samtools. 434s Preparing to unpack .../099-samtools_1.21-1_arm64.deb ... 434s Unpacking samtools (1.21-1) ... 434s Selecting previously unselected package tabix. 434s Preparing to unpack .../100-tabix_1.21+ds-1_arm64.deb ... 434s Unpacking tabix (1.21+ds-1) ... 434s Setting up libhtscodecs2:arm64 (1.6.1-2) ... 434s Setting up dh-python (6.20250308) ... 434s Setting up libgnutls-openssl27t64:arm64 (3.8.9-2ubuntu2) ... 434s Setting up python3-iniconfig (1.1.1-2) ... 434s Setting up libzstd-dev:arm64 (1.5.6+dfsg-2) ... 434s Setting up libarchive-zip-perl (1.68-1) ... 434s Setting up libdebhelper-perl (13.24.1ubuntu2) ... 434s Setting up libdeflate0:arm64 (1.23-1) ... 434s Setting up m4 (1.4.19-7) ... 434s Setting up libevent-2.1-7t64:arm64 (2.1.12-stable-10) ... 434s Setting up python3-all (3.13.2-2) ... 434s Setting up libgomp1:arm64 (15-20250222-0ubuntu1) ... 434s Setting up libpsl-dev:arm64 (0.21.2-1.1build1) ... 434s Setting up autotools-dev (20220109.1) ... 434s Setting up python3-packaging (24.2-1) ... 435s Setting up libunbound8:arm64 (1.22.0-1ubuntu1) ... 435s Setting up libpkgconf3:arm64 (1.8.1-4) ... 435s Setting up libgmpxx4ldbl:arm64 (2:6.3.0+dfsg-3ubuntu1) ... 435s Setting up libexpat1-dev:arm64 (2.6.4-1) ... 435s Setting up libgnutls-dane0t64:arm64 (3.8.9-2ubuntu2) ... 435s Setting up libgssrpc4t64:arm64 (1.21.3-4ubuntu2) ... 435s Setting up libldap-dev:arm64 (2.6.9+dfsg-1~exp2ubuntu1) ... 435s Setting up comerr-dev:arm64 (2.1-1.47.2-1ubuntu1) ... 435s Setting up libssl-dev:arm64 (3.4.1-1ubuntu1) ... 435s Setting up libmpc3:arm64 (1.3.1-1build2) ... 435s Setting up cython3 (3.0.11+dfsg-2ubuntu2) ... 436s Setting up autopoint (0.23.1-1) ... 436s Setting up pkgconf-bin (1.8.1-4) ... 436s Setting up libidn2-dev:arm64 (2.3.7-2build2) ... 436s Setting up autoconf (2.72-3ubuntu1) ... 436s Setting up python3-pluggy (1.5.0-1) ... 436s Setting up liblzma-dev:arm64 (5.6.4-1) ... 436s Setting up libubsan1:arm64 (15-20250222-0ubuntu1) ... 436s Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 436s Setting up dwz (0.15-1build6) ... 436s Setting up libhwasan0:arm64 (15-20250222-0ubuntu1) ... 436s Setting up libasan8:arm64 (15-20250222-0ubuntu1) ... 436s Setting up debugedit (1:5.1-2) ... 436s Setting up libhts3t64:arm64 (1.21+ds-1) ... 436s Setting up libtsan2:arm64 (15-20250222-0ubuntu1) ... 436s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 436s Setting up libisl23:arm64 (0.27-1) ... 436s Setting up libtasn1-6-dev:arm64 (4.20.0-2) ... 436s Setting up libdeflate-dev:arm64 (1.23-1) ... 436s Setting up tabix (1.21+ds-1) ... 436s Setting up libcc1-0:arm64 (15-20250222-0ubuntu1) ... 436s Setting up libbrotli-dev:arm64 (1.1.0-2build4) ... 436s Setting up liblsan0:arm64 (15-20250222-0ubuntu1) ... 436s Setting up libp11-kit-dev:arm64 (0.25.5-2ubuntu3) ... 436s Setting up libitm1:arm64 (15-20250222-0ubuntu1) ... 436s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 436s Setting up libkadm5clnt-mit12:arm64 (1.21.3-4ubuntu2) ... 436s Setting up libbz2-dev:arm64 (1.0.8-6) ... 436s Setting up automake (1:1.17-3ubuntu1) ... 436s update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode 436s Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... 436s Setting up gettext (0.23.1-1) ... 436s Setting up python3-pysam (0.23.0+ds-1build1) ... 436s Setting up libgmp-dev:arm64 (2:6.3.0+dfsg-3ubuntu1) ... 436s Setting up nettle-dev:arm64 (3.10.1-1) ... 436s Setting up libkdb5-10t64:arm64 (1.21.3-4ubuntu2) ... 436s Setting up python3-pytest (8.3.5-1) ... 437s Setting up bcftools (1.21-1) ... 437s Setting up pkgconf:arm64 (1.8.1-4) ... 437s Setting up samtools (1.21-1) ... 437s Setting up intltool-debian (0.35.0+20060710.6) ... 437s Setting up libpython3.13-dev:arm64 (3.13.2-2) ... 437s Setting up libssh2-1-dev:arm64 (1.11.1-1) ... 437s Setting up libjs-sphinxdoc (8.1.3-4) ... 437s Setting up dh-strip-nondeterminism (1.14.1-2) ... 437s Setting up cpp-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 437s Setting up libkadm5srv-mit12:arm64 (1.21.3-4ubuntu2) ... 437s Setting up libgcc-14-dev:arm64 (14.2.0-17ubuntu3) ... 437s Setting up libstdc++-14-dev:arm64 (14.2.0-17ubuntu3) ... 437s Setting up krb5-multidev:arm64 (1.21.3-4ubuntu2) ... 437s Setting up libgnutls28-dev:arm64 (3.8.9-2ubuntu2) ... 437s Setting up libnghttp2-dev:arm64 (1.64.0-1) ... 437s Setting up libpython3-dev:arm64 (3.13.2-2) ... 437s Setting up python3.13-dev (3.13.2-2) ... 437s Setting up po-debconf (1.0.21+nmu1) ... 437s Setting up libkrb5-dev:arm64 (1.21.3-4ubuntu2) ... 437s Setting up cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 437s Setting up libpython3-all-dev:arm64 (3.13.2-2) ... 437s Setting up python3-dev (3.13.2-2) ... 437s Setting up librtmp-dev:arm64 (2.4+20151223.gitfa8646d.1-2build7) ... 437s Setting up cpp-14 (14.2.0-17ubuntu3) ... 437s Setting up cpp (4:14.2.0-1ubuntu1) ... 437s Setting up gcc-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 437s Setting up python3-all-dev (3.13.2-2) ... 437s Setting up gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 437s Setting up g++-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 437s Setting up libcurl4-gnutls-dev:arm64 (8.12.1-3ubuntu1) ... 437s Setting up gcc-14 (14.2.0-17ubuntu3) ... 437s Setting up g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 437s Setting up g++-14 (14.2.0-17ubuntu3) ... 437s Setting up libtool (2.5.4-4) ... 437s Setting up libhts-dev:arm64 (1.21+ds-1) ... 437s Setting up gcc (4:14.2.0-1ubuntu1) ... 437s Setting up dh-autoreconf (20) ... 437s Setting up g++ (4:14.2.0-1ubuntu1) ... 437s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 437s Setting up build-essential (12.10ubuntu1) ... 437s Setting up debhelper (13.24.1ubuntu2) ... 437s Processing triggers for install-info (7.1.1-1) ... 437s Processing triggers for libc-bin (2.41-1ubuntu2) ... 437s Processing triggers for man-db (2.13.0-1) ... 441s autopkgtest [15:03:14]: test command1: export HOME=$PWD && make -C tests/pysam_data && make -C tests/cbcf_data && pytest-3 441s autopkgtest [15:03:14]: test command1: [----------------------- 441s make: Entering directory '/tmp/autopkgtest.kIxNq9/build.HXX/src/tests/pysam_data' 441s samtools faidx ex1.fa 441s samtools view --no-PG -bo ex1.bam -t ex1.fa.fai ex1.sam.gz 441s samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz 441s [mpileup] 1 samples in 1 input files 441s gunzip < ex1.sam.gz > ex1.sam 441s samtools index ex1.bam 441s samtools view --no-PG -h ex1.bam | gzip > ex2.sam.gz 441s gunzip < ex2.sam.gz > ex2.sam 441s samtools view --no-PG -bo ex2.bam ex2.sam 441s samtools index ex2.bam 441s [bam_fillmd1] different NM for read 'EAS139_11:7:46:695:738': 3 -> 8 441s [bam_fillmd1] different NM for read 'EAS218_4:1:48:9:409': 0 -> 5 441s [bam_fillmd1] different NM for read 'B7_591:7:200:192:373': 0 -> 5 441s samtools calmd --no-PG --output-fmt BAM ex2.bam ex1.fa > with_md.sam.gz 441s [bam_fillmd1] different NM for read 'EAS56_65:1:163:846:223': 0 -> 5 441s [bam_fillmd1] different NM for read 'EAS114_30:7:283:799:560': 0 -> 5 441s [bam_fillmd1] different NM for read 'B7_595:4:84:802:737': 0 -> 4 441s [bam_fillmd1] different NM for read 'EAS51_66:5:308:400:602': 0 -> 3 441s [bam_fillmd1] different NM for read 'EAS54_81:2:285:367:932': 0 -> 3 441s [bam_fillmd1] different NM for read 'EAS114_39:1:70:147:84': 0 -> 3 441s [bam_fillmd1] different NM for read 'EAS56_53:1:124:243:35': 2 -> 5 441s [bam_fillmd1] different NM for read 'EAS1_103:2:226:302:758': 2 -> 3 441s [bam_fillmd1] different NM for read 'EAS114_28:6:175:705:982': 1 -> 0 441s [bam_fillmd1] different NM for read 'EAS51_64:4:179:389:585': 7 -> 8 441s [bam_fillmd1] different NM for read 'B7_589:1:122:337:968': 3 -> 2 441s [bam_fillmd1] different NM for read 'B7_610:4:15:805:420': 4 -> 5 441s [bam_fillmd1] different NM for read 'B7_591:2:279:124:41': 2 -> 4 441s [bam_fillmd1] different NM for read 'EAS112_32:8:89:254:332': 0 -> 1 441s [bam_fillmd1] different NM for read 'B7_597:7:103:731:697': 0 -> 2 441s [bam_fillmd1] different NM for read 'EAS139_11:2:71:83:58': 0 -> 2 441s [bam_fillmd1] different NM for read 'EAS192_3:4:63:5:870': 0 -> 2 441s [bam_fillmd1] different NM for read 'EAS139_19:2:29:1822:1881': 0 -> 2 441s [bam_fillmd1] different NM for read 'EAS188_7:3:15:568:42': 2 -> 1 441s [bam_fillmd1] different NM for read 'EAS1_95:4:176:971:874': 0 -> 1 441s [bam_fillmd1] different NM for read 'EAS1_99:1:34:649:318': 3 -> 4 441s [bam_fillmd1] different NM for read 'EAS54_65:4:61:346:384': 3 -> 4 441s [bam_fillmd1] different NM for read 'B7_597:6:20:592:496': 0 -> 1 441s [bam_fillmd1] different NM for read 'B7_597:4:38:999:463': 2 -> 1 441s [bam_fillmd1] different NM for read 'EAS114_28:5:23:944:377': 0 -> 3 441s [bam_fillmd1] different NM for read 'EAS219_1:3:90:219:528': 0 -> 3 441s [bam_fillmd1] different NM for read 'EAS1_108:5:89:942:84': 0 -> 4 441s [bam_fillmd1] different NM for read 'EAS1_108:6:159:493:275': 0 -> 5 441s [bam_fillmd1] different NM for read 'EAS139_11:1:81:1019:558': 0 -> 5 441s [bam_fillmd1] different NM for read 'EAS51_62:7:162:195:761': 0 -> 4 441s [bam_fillmd1] different NM for read 'B7_597:3:115:646:430': 0 -> 4 441s [bam_fillmd1] different NM for read 'EAS114_30:6:243:209:110': 0 -> 4 441s [bam_fillmd1] different NM for read 'EAS1_108:2:266:994:429': 0 -> 4 441s [bam_fillmd1] different NM for read 'EAS114_30:5:32:461:154': 0 -> 4 441s [bam_fillmd1] different NM for read 'EAS114_39:6:7:492:1088': 0 -> 4 441s [bam_fillmd1] different NM for read 'EAS1_95:6:174:650:125': 0 -> 4 441s [bam_fillmd1] different NM for read 'EAS56_59:6:89:457:591': 1 -> 5 441s [bam_fillmd1] different NM for read 'EAS114_39:2:38:670:564': 0 -> 4 441s [bam_fillmd1] different NM for read 'EAS188_7:4:92:693:228': 1 -> 6 441s [bam_fillmd1] different NM for read 'EAS218_1:4:61:1369:440': 0 -> 4 441s [bam_fillmd1] different NM for read 'EAS114_26:4:123:1001:580': 0 -> 4 441s [bam_fillmd1] different NM for read 'EAS114_39:4:10:1312:1558': 0 -> 4 441s [bam_fillmd1] different NM for read 'EAS220_1:8:45:178:1321': 0 -> 4 441s [bam_fillmd1] different NM for read 'EAS56_59:5:125:137:58': 0 -> 4 441s [bam_fillmd1] different NM for read 'EAS192_3:3:285:349:797': 1 -> 5 441s [bam_fillmd1] different NM for read 'EAS114_45:5:56:1757:1319': 0 -> 4 441s [bam_fillmd1] different NM for read 'B7_591:3:291:404:199': 0 -> 4 441s [bam_fillmd1] different NM for read 'EAS54_65:7:159:253:353': 0 -> 4 441s [bam_fillmd1] different NM for read 'EAS56_57:1:122:38:103': 0 -> 4 441s [bam_fillmd1] different NM for read 'EAS188_4:5:103:870:105': 0 -> 4 441s [bam_fillmd1] different NM for read 'EAS1_105:8:24:718:322': 3 -> 7 441s [bam_fillmd1] different NM for read 'EAS51_64:6:118:41:489': 0 -> 4 441s [bam_fillmd1] different NM for read 'EAS56_61:3:165:665:220': 0 -> 4 441s [bam_fillmd1] different NM for read 'EAS114_30:6:238:803:383': 0 -> 4 441s [bam_fillmd1] different NM for read 'EAS1_105:3:232:364:583': 0 -> 3 441s [bam_fillmd1] different NM for read 'B7_595:2:29:729:70': 3 -> 4 441s [bam_fillmd1] different NM for read 'EAS114_30:6:220:809:850': 4 -> 6 441s [bam_fillmd1] different NM for read 'EAS54_65:2:264:157:150': 3 -> 5 441s [bam_fillmd1] different NM for read 'B7_595:8:26:242:35': 2 -> 1 441s [bam_fillmd1] different NM for read 'B7_610:7:34:144:868': 4 -> 5 441s [bam_fillmd1] different NM for read 'B7_597:8:147:360:141': 1 -> 2 441s [bam_fillmd1] different NM for read 'EAS139_19:2:82:154:1333': 0 -> 4 441s [bam_fillmd1] different NM for read 'EAS56_63:3:41:468:459': 0 -> 3 441s [bam_fillmd1] different NM for read 'EAS1_97:4:274:287:423': 0 -> 1 441s [bam_fillmd1] different NM for read 'EAS114_30:2:303:428:326': 0 -> 1 441s [bam_fillmd1] different NM for read 'EAS54_71:8:105:854:975': 0 -> 3 441s gunzip < with_md.sam.gz > with_md.sam 441s [W::bam_hdr_read] EOF marker is absent. The input is probably truncated 441s samtools view --no-PG -bo with_md.bam with_md.sam 441s samtools index with_md.bam 441s samtools view --no-PG -bu -o uncompressed.bam ex2.sam 441s samtools view --no-PG -bo MM-chebi.bam MM-chebi.sam 441s samtools view --no-PG -bo MM-double.bam MM-double.sam 441s samtools view --no-PG -bo MM-explicit.bam MM-explicit.sam 441s samtools view --no-PG -bo MM-multi.bam MM-multi.sam 441s samtools view --no-PG -bo MM-orient.bam MM-orient.sam 441s samtools view --no-PG -bo ex10.bam ex10.sam 441s samtools view --no-PG -bo ex3.bam ex3.sam 441s samtools view --no-PG -bo ex4.bam ex4.sam 441s samtools view --no-PG -bo ex5.bam ex5.sam 441s samtools view --no-PG -bo ex6.bam ex6.sam 441s samtools view --no-PG -bo ex8.bam ex8.sam 441s samtools view --no-PG -bo ex9_fail.bam ex9_fail.sam 441s samtools view --no-PG -bo ex9_nofail.bam ex9_nofail.sam 441s samtools view --no-PG -bo ex_spliced.bam ex_spliced.sam 441s samtools view --no-PG -bo example_aligned_pairs.bam example_aligned_pairs.sam 441s samtools view --no-PG -bo example_btag.bam example_btag.sam 441s samtools view --no-PG -bo example_dash_in_chr.bam example_dash_in_chr.sam 441s samtools view --no-PG -bo example_empty_header.bam example_empty_header.sam 441s samtools view --no-PG -bo example_empty_with_header.bam example_empty_with_header.sam 441s samtools view --no-PG -bo example_reverse_complement.bam example_reverse_complement.sam 441s touch tmp.list 441s samtools view --no-PG -bo example_unmapped_reads_no_sq.bam -t tmp.list example_unmapped_reads_no_sq.sam 441s rm -f tmp.list 441s samtools view --no-PG -bo issue100.bam issue100.sam 441s samtools view --no-PG -bo rg_with_tab.bam rg_with_tab.sam 441s samtools view --no-PG -bo softclip.bam softclip.sam 441s samtools view --no-PG -bo tag_bug.bam tag_bug.sam 441s samtools view --no-PG -bo test_mapped_unmapped.bam test_mapped_unmapped.sam 441s samtools view --no-PG -bo test_query_position.bam test_query_position.sam 441s samtools view --no-PG -bo test_unaligned.bam test_unaligned.sam 441s samtools index MM-chebi.bam 441s samtools index MM-double.bam 441s samtools index MM-explicit.bam 441s samtools index MM-multi.bam 441s samtools index MM-orient.bam 441s samtools index ex10.bam 441s samtools index ex3.bam 441s samtools index ex4.bam 441s samtools index ex5.bam 441s samtools index ex6.bam 441s samtools index ex8.bam 441s samtools index ex9_fail.bam 441s samtools index ex9_nofail.bam 441s samtools index ex_spliced.bam 441s samtools index example_aligned_pairs.bam 441s samtools index example_btag.bam 441s samtools index example_dash_in_chr.bam 441s samtools index example_empty_header.bam 441s samtools index example_empty_with_header.bam 441s samtools index example_reverse_complement.bam 441s samtools index example_unmapped_reads_no_sq.bam 441s samtools index issue100.bam 441s samtools index rg_with_tab.bam 441s samtools index softclip.bam 441s samtools index tag_bug.bam 441s samtools index test_mapped_unmapped.bam 441s samtools index test_query_position.bam 441s samtools index test_unaligned.bam 441s samtools view --no-PG -Co ex1.cram -T ex1.fa ex1.sam 441s samtools view --no-PG -Co ex2.cram -T ex1.fa ex2.sam 442s samtools view --no-PG -Co ex3.cram -T ex1.fa ex3.sam 442s samtools index ex1.cram 442s samtools index ex2.cram 442s samtools index ex3.cram 442s cp ex1.bam example_bai.bam 442s samtools index example_bai.bam 442s mv example_bai.bam.bai example_bai.bai 442s dd if=ex2.bam of=ex2_truncated.bam bs=$((`wc -c < ex2.bam`-512)) count=1 442s 1+0 records in 442s 1+0 records out 442s 122288 bytes (122 kB, 119 KiB) copied, 0.000315151 s, 388 MB/s 442s (bgzip -d < ex2.bam; printf '\37\0\0\0\1\0\0\0') | bgzip > ex2_corrupt.bam 442s grep "^@" ex2.sam | samtools view --no-PG -bo empty.bam - 442s samtools index empty.bam 442s cp ex1.bam explicit_index.bam 442s cp ex1.cram explicit_index.cram 442s gzip < faidx_empty_seq.fq > faidx_empty_seq.fq.gz 442s bgzip < ex1.fa > ex1.fa.gz 442s samtools faidx ex1.fa.gz 442s cp ex1.bam ex1_csi.bam 442s samtools index -c ex1_csi.bam 442s touch all.stamp 442s rm with_md.sam 442s make: Leaving directory '/tmp/autopkgtest.kIxNq9/build.HXX/src/tests/pysam_data' 442s make: Entering directory '/tmp/autopkgtest.kIxNq9/build.HXX/src/tests/cbcf_data' 442s bgzip < example_vcf40.vcf > example_vcf40.vcf.gz 442s tabix -f -p vcf example_vcf40.vcf.gz # create tbi index 442s bcftools index -f example_vcf40.vcf.gz # create csi index 442s bgzip < example_vcf42.vcf > example_vcf42.vcf.gz 442s tabix -f -p vcf example_vcf42.vcf.gz # create tbi index 442s bcftools index -f example_vcf42.vcf.gz # create csi index 442s bgzip < example_vcf42_only_header.vcf > example_vcf42_only_header.vcf.gz 442s tabix -f -p vcf example_vcf42_only_header.vcf.gz # create tbi index 442s bcftools index -f example_vcf42_only_header.vcf.gz # create csi index 442s bgzip < example_vcf42_withcontigs.vcf > example_vcf42_withcontigs.vcf.gz 442s tabix -f -p vcf example_vcf42_withcontigs.vcf.gz # create tbi index 442s bcftools index -f example_vcf42_withcontigs.vcf.gz # create csi index 442s bgzip < example_vcf43.vcf > example_vcf43.vcf.gz 442s tabix -f -p vcf example_vcf43.vcf.gz # create tbi index 442s bcftools index -f example_vcf43.vcf.gz # create csi index 442s bgzip < example_vcf43_with_utf8.vcf > example_vcf43_with_utf8.vcf.gz 442s tabix -f -p vcf example_vcf43_with_utf8.vcf.gz # create tbi index 442s bcftools index -f example_vcf43_with_utf8.vcf.gz # create csi index 442s bgzip < gnomad.vcf > gnomad.vcf.gz 442s tabix -f -p vcf gnomad.vcf.gz # create tbi index 442s bcftools index -f gnomad.vcf.gz # create csi index 442s bgzip < gnomad_fixed.vcf > gnomad_fixed.vcf.gz 442s tabix -f -p vcf gnomad_fixed.vcf.gz # create tbi index 442s bcftools index -f gnomad_fixed.vcf.gz # create csi index 442s bgzip < missing_genotypes.vcf > missing_genotypes.vcf.gz 442s tabix -f -p vcf missing_genotypes.vcf.gz # create tbi index 442s bcftools index -f missing_genotypes.vcf.gz # create csi index 442s bcftools view -O b example_vcf40.vcf.gz -o example_vcf40.bcf 442s bcftools index -f example_vcf40.bcf 442s bcftools view -O b example_vcf42.vcf.gz -o example_vcf42.bcf 442s bcftools index -f example_vcf42.bcf 442s bcftools view -O b example_vcf42_only_header.vcf.gz -o example_vcf42_only_header.bcf 442s bcftools index -f example_vcf42_only_header.bcf 442s bcftools view -O b example_vcf42_withcontigs.vcf.gz -o example_vcf42_withcontigs.bcf 442s bcftools index -f example_vcf42_withcontigs.bcf 442s bcftools view -O b example_vcf43.vcf.gz -o example_vcf43.bcf 442s bcftools index -f example_vcf43.bcf 442s bcftools view -O b example_vcf43_with_utf8.vcf.gz -o example_vcf43_with_utf8.bcf 442s bcftools index -f example_vcf43_with_utf8.bcf 442s bcftools view -O b gnomad.vcf.gz -o gnomad.bcf 442s bcftools index -f gnomad.bcf 442s bcftools view -O b gnomad_fixed.vcf.gz -o gnomad_fixed.bcf 442s [W::bcf_hdr_check_sanity] PL should be declared as Number=G 442s [W::bcf_hdr_check_sanity] PL should be declared as Number=G 442s bcftools index -f gnomad_fixed.bcf 442s bcftools view -O b missing_genotypes.vcf.gz -o missing_genotypes.bcf 442s bcftools index -f missing_genotypes.bcf 442s touch all.stamp 442s make: Leaving directory '/tmp/autopkgtest.kIxNq9/build.HXX/src/tests/cbcf_data' 442s ============================= test session starts ============================== 442s platform linux -- Python 3.13.2, pytest-8.3.5, pluggy-1.5.0 -- /usr/bin/python3 442s cachedir: .pytest_cache 442s rootdir: /tmp/autopkgtest.kIxNq9/build.HXX/src 442s configfile: setup.cfg 442s testpaths: pysam, tests 442s plugins: typeguard-4.4.2 443s collecting ... collected 960 items / 1 skipped 443s 443s tests/AlignedSegment_test.py::TestAlignedSegment::testBlocks PASSED 443s tests/AlignedSegment_test.py::TestAlignedSegment::testCompare PASSED 443s tests/AlignedSegment_test.py::TestAlignedSegment::testEmpty PASSED 443s tests/AlignedSegment_test.py::TestAlignedSegment::testFullReferencePositions PASSED 443s tests/AlignedSegment_test.py::TestAlignedSegment::testHashing PASSED 443s tests/AlignedSegment_test.py::TestAlignedSegment::testLargeRead PASSED 443s tests/AlignedSegment_test.py::TestAlignedSegment::testNoSequence PASSED 443s tests/AlignedSegment_test.py::TestAlignedSegment::testPositions PASSED 443s tests/AlignedSegment_test.py::TestAlignedSegment::testSettingTagInEmptyRead PASSED 443s tests/AlignedSegment_test.py::TestAlignedSegment::testStrOfEmptyRead PASSED 443s tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate PASSED 443s tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate2 PASSED 443s tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateQual PASSED 443s tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateTlen PASSED 443s tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_mapped_reads_are_updated PASSED 443s tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_unmapped_reads_ignore_length PASSED 443s tests/AlignedSegment_test.py::TestAlignedSegment::test_equivalence_matches_only_and_with_seq PASSED 443s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs PASSED 443s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_1character_md PASSED 443s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_bad_type_md PASSED 443s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_hard_clipping PASSED 443s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_lowercase_md PASSED 443s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_match_mismatch PASSED 443s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding PASSED 443s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding_via_cigarstring PASSED 443s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding_with_seq PASSED 443s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip PASSED 443s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip_reference PASSED 443s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_soft_clipping PASSED 443s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_uppercase_md PASSED 443s tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_with_malformed_MD_tag PASSED 443s tests/AlignedSegment_test.py::TestAlignedSegment::test_header_accessible PASSED 443s tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_query_length PASSED 443s tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_read_length PASSED 443s tests/AlignedSegment_test.py::TestAlignedSegment::test_query_length_is_limited PASSED 443s tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_asterisk PASSED 443s tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_chromosome PASSED 443s tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_none PASSED 443s tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_not_be_set_to_unknown_chromosome PASSED 443s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_chromosome PASSED 443s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing PASSED 443s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing_without_header PASSED 443s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_without_header PASSED 443s tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_not_be_set_to_unknown_chromosome PASSED 443s tests/AlignedSegment_test.py::TestTidMapping::test_unmapped_tid_is_asterisk_in_output PASSED 443s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_asterisk PASSED 443s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_chromosome PASSED 443s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_none PASSED 443s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_not_be_set_to_unknown_chromosome PASSED 443s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_chromosome PASSED 443s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_equal PASSED 443s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing PASSED 443s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing_without_header PASSED 443s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_without_header PASSED 443s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_not_be_set_to_unknown_chromosome PASSED 443s tests/AlignedSegment_test.py::TestNextTidMapping::test_next_unmapped_tid_is_asterisk_in_output PASSED 443s tests/AlignedSegment_test.py::TestCigar::testCigar PASSED 443s tests/AlignedSegment_test.py::TestCigar::testCigarString PASSED 443s tests/AlignedSegment_test.py::TestCigarStats::testStats PASSED 443s tests/AlignedSegment_test.py::TestAlignedPairs::testReferenceBases PASSED 443s tests/AlignedSegment_test.py::TestBaseModifications::testChebi PASSED 443s tests/AlignedSegment_test.py::TestBaseModifications::testDouble PASSED 443s tests/AlignedSegment_test.py::TestBaseModifications::testExplicit PASSED 443s tests/AlignedSegment_test.py::TestBaseModifications::testMulti PASSED 443s tests/AlignedSegment_test.py::TestBaseModifications::testOrient PASSED 443s tests/AlignedSegment_test.py::TestTags::testAddTags PASSED 443s tests/AlignedSegment_test.py::TestTags::testAddTagsType PASSED 443s tests/AlignedSegment_test.py::TestTags::testArrayTags PASSED 443s tests/AlignedSegment_test.py::TestTags::testEmptyTag PASSED 443s tests/AlignedSegment_test.py::TestTags::testLongTags PASSED 443s tests/AlignedSegment_test.py::TestTags::testMDTagComplex PASSED 443s tests/AlignedSegment_test.py::TestTags::testMDTagDeletions PASSED 443s tests/AlignedSegment_test.py::TestTags::testMDTagInsertions PASSED 443s tests/AlignedSegment_test.py::TestTags::testMDTagMatchOnly PASSED 443s tests/AlignedSegment_test.py::TestTags::testMDTagRefSkipping PASSED 443s tests/AlignedSegment_test.py::TestTags::testMDTagSoftClipping PASSED 443s tests/AlignedSegment_test.py::TestTags::testMissingTag PASSED 443s tests/AlignedSegment_test.py::TestTags::testNegativeIntegers PASSED 443s tests/AlignedSegment_test.py::TestTags::testNegativeIntegersWrittenToFile PASSED 443s tests/AlignedSegment_test.py::TestTags::testSetTag PASSED 443s tests/AlignedSegment_test.py::TestTags::testTagParsing PASSED 443s tests/AlignedSegment_test.py::TestTags::testTagsUpdatingFloat PASSED 443s tests/AlignedSegment_test.py::TestCopy::testCopy PASSED 443s tests/AlignedSegment_test.py::TestCopy::testDeepCopy PASSED 443s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_array_tag_invalid_typecode PASSED 443s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_array_tag_invalid_value_type PASSED 443s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_invalid_value_type PASSED 443s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_A PASSED 443s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_C PASSED 443s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_H PASSED 443s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_I PASSED 443s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_S PASSED 443s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_a PASSED 443s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_automated_type_detection PASSED 443s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_c PASSED 443s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_d PASSED 443s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_f PASSED 443s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_i PASSED 443s tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_s PASSED 443s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_array_tag_invalid_typecode PASSED 443s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_array_tag_invalid_value_type PASSED 443s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_invalid_value_type PASSED 443s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_A PASSED 443s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_C PASSED 443s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_H PASSED 443s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_I PASSED 443s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_S PASSED 443s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_a PASSED 443s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_automated_type_detection PASSED 443s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_c PASSED 443s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_d PASSED 443s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_f PASSED 443s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_i PASSED 443s tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_s PASSED 443s tests/AlignedSegment_test.py::TestEnums::test_cigar_enums_are_defined PASSED 443s tests/AlignedSegment_test.py::TestEnums::test_sam_flags_are_defined PASSED 443s tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_constructed_without_header PASSED 443s tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_written_to_file PASSED 443s tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_id_can_be_set PASSED 443s tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_name_is_not_available PASSED 443s tests/AlignedSegment_test.py::TestForwardStrandValues::test_qualities_are_complemented PASSED 443s tests/AlignedSegment_test.py::TestForwardStrandValues::test_sequence_is_complemented PASSED 443s tests/AlignedSegment_test.py::TestExportImport::test_dict_export PASSED 443s tests/AlignedSegment_test.py::TestExportImport::test_string_export PASSED 443s tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_with_tags PASSED 443s tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_without_tags PASSED 443s tests/AlignedSegment_test.py::TestExportImport::test_to_string_without_alignment_file PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_dict PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_header PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references_without_text PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_text PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_access_works PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_contains_works PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_get_works PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_keys_works PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_len_works PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_setting_raises_error PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_values_works PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_header_content_is_as_expected PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_name_mapping PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_text_access_works PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_contains_works PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_get_works PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_keys_works PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_len_works PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_setting_raises_error PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_values_works PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_name_mapping PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_text_access_works PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_contains_works PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_get_works PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_keys_works PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_len_works PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_setting_raises_error PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_values_works PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_name_mapping PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_text_access_works PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM [E::cram_index_load] Could not retrieve index file for '/tmp/autopkgtest.kIxNq9/build.HXX/src/tests/tmp/pysamtests_tmp_check_read_write_eo4arjc7' 443s PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM [W::sanitise_SQ_lines] Header @SQ length mismatch for ref chr1, 2147483647 vs 1575 443s [E::cram_index_load] Could not retrieve index file for '/tmp/autopkgtest.kIxNq9/build.HXX/src/tests/tmp/pysamtests_tmp_check_read_write_w3ncvf1x' 443s PASSED 443s tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM PASSED 443s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_all_stepper PASSED 443s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_ignore_overlaps PASSED 443s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper PASSED 444s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_base_quality_threshold PASSED 444s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_ignore_orphans PASSED 444s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_mapping_quality_threshold PASSED 444s tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_redo_baq PASSED 444s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_all_stepper PASSED 444s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_ignore_overlaps PASSED 444s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper PASSED 444s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_base_quality_threshold PASSED 444s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_ignore_orphans PASSED 444s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_mapping_quality_threshold PASSED 444s tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_redo_baq PASSED 444s tests/AlignmentFilePileup_test.py::TestPileupQueryPosition::testPileup PASSED 444s tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope SKIPPED 444s tests/AlignmentFilePileup_test.py::TestPileupObjects::testPileupColumn PASSED 444s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testInverse PASSED 444s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateAll PASSED 444s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIteratePerContig PASSED 444s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateRanges PASSED 444s tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateTruncate PASSED 444s tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testAccessOnClosedIterator PASSED 444s tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStart PASSED 444s tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStr PASSED 444s tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testTruncate PASSED 444s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_depths_are_equal PASSED 444s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_mapping_qualities_are_equal PASSED 444s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_with_reference_are_equal PASSED 444s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_without_reference_are_equal PASSED 444s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_are_equal PASSED 444s tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_from_pileups_are_equal PASSED 444s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARQueryLength PASSED 444s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigar PASSED 444s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigarstring PASSED 444s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARflag PASSED 444s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmapq PASSED 444s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmpos PASSED 444s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmrnm PASSED 444s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARpos PASSED 444s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqname PASSED 444s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqqual PASSED 444s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqual PASSED 444s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARquery PASSED 444s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARrname PASSED 444s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARseq PASSED 444s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testOpt PASSED 444s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPairedBools PASSED 444s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPresentOptionalFields PASSED 444s tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testTags PASSED 444s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARQueryLength PASSED 444s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigar PASSED 444s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigarstring PASSED 444s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARflag PASSED 444s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmapq PASSED 444s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmpos PASSED 444s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmrnm PASSED 444s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARpos PASSED 444s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqname PASSED 444s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqqual PASSED 444s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqual PASSED 444s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARquery PASSED 444s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARrname PASSED 444s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARseq PASSED 444s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testOpt PASSED 444s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPairedBools PASSED 444s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPresentOptionalFields PASSED 444s tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testTags PASSED 445s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARQueryLength PASSED 445s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigar PASSED 446s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigarstring PASSED 446s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARflag PASSED 446s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmapq PASSED 447s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmpos PASSED 447s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmrnm PASSED 447s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARpos PASSED 447s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqname PASSED 448s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqqual PASSED 448s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqual PASSED 448s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARquery PASSED 449s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARrname PASSED 449s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARseq PASSED 449s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testOpt PASSED 450s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPairedBools PASSED 450s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPresentOptionalFields PASSED 450s tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testTags PASSED 450s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARQueryLength PASSED 450s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigar PASSED 450s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigarstring PASSED 450s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARflag PASSED 451s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmapq PASSED 451s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmpos PASSED 451s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmrnm PASSED 451s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARpos PASSED 451s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqname PASSED 451s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqqual PASSED 451s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqual PASSED 451s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARquery PASSED 451s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARrname PASSED 451s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARseq PASSED 451s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testOpt PASSED 451s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPairedBools PASSED 451s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPresentOptionalFields PASSED 451s tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testTags PASSED 451s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARQueryLength PASSED 451s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigar PASSED 451s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigarstring PASSED 452s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARflag PASSED 452s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmapq PASSED 452s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmpos PASSED 453s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmrnm PASSED 453s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARpos PASSED 453s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqname PASSED 454s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqqual PASSED 454s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqual PASSED 454s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARquery PASSED 454s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARrname PASSED 455s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARseq PASSED 455s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testOpt PASSED 455s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPairedBools PASSED 456s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPresentOptionalFields PASSED 456s tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testTags PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARQueryLength PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigar PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigarstring PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARflag PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmapq PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmpos PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmrnm PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARpos PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqname PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqqual PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqual PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARquery PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARrname PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARseq PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testOpt PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPairedBools PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPresentOptionalFields PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testTags PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARQueryLength PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigar PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigarstring PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARflag PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmapq PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmpos PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmrnm PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARpos PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqname PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqqual PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqual PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARquery PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARrname PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARseq PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testOpt PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPairedBools PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPresentOptionalFields PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFile::testTags PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARQueryLength PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigar PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigarstring PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARflag PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmapq PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmpos PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmrnm PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARpos PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqname PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqqual PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqual PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARquery PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARrname PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARseq PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testOpt PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPairedBools PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPresentOptionalFields PASSED 456s tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testTags PASSED 456s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARQueryLength PASSED 456s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigar PASSED 456s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigarstring PASSED 456s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARflag PASSED 456s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmapq PASSED 456s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmpos PASSED 456s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmrnm PASSED 456s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARpos PASSED 456s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqname PASSED 456s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqqual PASSED 456s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqual PASSED 456s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARquery PASSED 456s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARrname PASSED 456s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARseq PASSED 456s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testOpt PASSED 456s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPairedBools PASSED 456s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPresentOptionalFields PASSED 456s tests/AlignmentFile_test.py::BasicTestSAMFromFile::testTags PASSED 456s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARQueryLength PASSED 456s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigar PASSED 456s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigarstring PASSED 456s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARflag PASSED 456s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmapq PASSED 456s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmpos PASSED 456s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmrnm PASSED 456s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARpos PASSED 456s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqname PASSED 456s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqqual PASSED 456s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqual PASSED 456s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARquery PASSED 456s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARrname PASSED 456s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARseq PASSED 456s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testOpt PASSED 456s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPairedBools PASSED 456s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPresentOptionalFields PASSED 456s tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testTags PASSED 456s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARQueryLength PASSED 457s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigar PASSED 457s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigarstring PASSED 457s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARflag PASSED 458s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmapq PASSED 458s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmpos PASSED 458s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmrnm PASSED 459s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARpos PASSED 459s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqname PASSED 459s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqqual PASSED 459s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqual PASSED 460s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARquery PASSED 460s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARrname PASSED 460s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARseq PASSED 461s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testOpt PASSED 461s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPairedBools PASSED 461s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPresentOptionalFields PASSED 462s tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testTags PASSED 462s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARQueryLength PASSED 462s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigar PASSED 462s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigarstring PASSED 463s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARflag PASSED 463s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmapq PASSED 463s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmpos PASSED 464s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmrnm PASSED 464s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARpos PASSED 464s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqname PASSED 465s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqqual PASSED 465s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqual PASSED 465s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARquery PASSED 466s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARrname PASSED 466s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARseq PASSED 466s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testOpt PASSED 466s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPairedBools PASSED 467s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPresentOptionalFields PASSED 467s tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testTags PASSED 467s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARQueryLength PASSED 467s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigar PASSED 467s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigarstring PASSED 467s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARflag PASSED 467s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmapq PASSED 467s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmpos PASSED 467s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmrnm PASSED 467s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARpos PASSED 467s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqname PASSED 467s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqqual PASSED 467s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqual PASSED 467s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARquery PASSED 467s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARrname PASSED 467s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARseq PASSED 467s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testOpt PASSED 467s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPairedBools PASSED 467s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPresentOptionalFields PASSED 467s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testRaises PASSED 467s tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testTags PASSED 467s tests/AlignmentFile_test.py::TestIO::testBAM2BAM PASSED 467s tests/AlignmentFile_test.py::TestIO::testBAM2SAM PASSED 467s tests/AlignmentFile_test.py::TestIO::testBAMWithCSIIndex PASSED 467s tests/AlignmentFile_test.py::TestIO::testBAMWithShortBAI PASSED 467s tests/AlignmentFile_test.py::TestIO::testBAMWithoutAlignedSegments PASSED 468s tests/AlignmentFile_test.py::TestIO::testCRAM2BAM PASSED 469s tests/AlignmentFile_test.py::TestIO::testCRAM2CRAM PASSED 469s tests/AlignmentFile_test.py::TestIO::testCRAM2SAM PASSED 469s tests/AlignmentFile_test.py::TestIO::testEmptyBAM PASSED 469s tests/AlignmentFile_test.py::TestIO::testEmptyWithHeaderBAM PASSED 469s tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFile PASSED 469s tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject PASSED 469s tests/AlignmentFile_test.py::TestIO::testHead PASSED 469s tests/AlignmentFile_test.py::TestIO::testOpenFromFilename PASSED 469s tests/AlignmentFile_test.py::TestIO::testReadBamWithoutTargetNames PASSED 469s tests/AlignmentFile_test.py::TestIO::testReadSamWithoutTargetNames PASSED 469s tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex PASSED 469s tests/AlignmentFile_test.py::TestIO::testSAM2BAM PASSED 470s tests/AlignmentFile_test.py::TestIO::testSAM2CRAM PASSED 470s tests/AlignmentFile_test.py::TestIO::testSAM2SAM PASSED 470s tests/AlignmentFile_test.py::TestIO::testSAM2SAMWithoutHeader PASSED 470s tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile PASSED 470s tests/AlignmentFile_test.py::TestIO::test_accessing_attributes_in_closed_file_raises_errors PASSED 470s tests/AlignmentFile_test.py::TestIO::test_fail_read_sam_without_header PASSED 470s tests/AlignmentFile_test.py::TestIO::test_fail_when_reading_unformatted_files PASSED 470s tests/AlignmentFile_test.py::TestIO::test_fetch_by_tid PASSED 470s tests/AlignmentFile_test.py::TestIO::test_header_available_after_closing_file PASSED 470s tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_with_header_without_header_check PASSED 470s tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_without_header_with_refs PASSED 470s tests/AlignmentFile_test.py::TestIO::test_reference_name_available_after_closing_file PASSED 470s tests/AlignmentFile_test.py::TestIO::test_write_bam_to_unknown_path_fails PASSED 470s tests/AlignmentFile_test.py::TestAutoDetect::testBAM PASSED 470s tests/AlignmentFile_test.py::TestAutoDetect::testCRAM [E::hts_open_format] Failed to open file "missing_directory/new_file.bam" : No such file or directory 471s PASSED 471s tests/AlignmentFile_test.py::TestAutoDetect::testSAM PASSED 471s tests/AlignmentFile_test.py::TestIteratorRowBAM::testIteratePerContig PASSED 471s tests/AlignmentFile_test.py::TestIteratorRowBAM::testIterateRanges PASSED 471s tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate PASSED 472s tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIteratePerContig PASSED 484s tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIterateRanges PASSED 485s tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIteratePerContig PASSED 496s tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIterateRanges PASSED 496s tests/AlignmentFile_test.py::TestFloatTagBug::testFloatTagBug PASSED 496s tests/AlignmentFile_test.py::TestLargeFieldBug::testLargeFileBug PASSED 496s tests/AlignmentFile_test.py::TestClipping::testClipping PASSED 496s tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_bam_with_until_eof_reads_unmapped_reads PASSED 496s 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 496s [E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory 496s [E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory 496s [E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory 496s PASSED 496s tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads PASSED 496s tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads_by_contig PASSED 496s tests/AlignmentFile_test.py::TestContextManager::testManager PASSED 496s tests/AlignmentFile_test.py::TestMultiThread::testSingleThreadEqualsMultithread PASSED 496s tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED 496s tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED 496s tests/AlignmentFile_test.py::TestExceptions::testBadContig PASSED 496s tests/AlignmentFile_test.py::TestExceptions::testMeaninglessCrap PASSED 496s tests/AlignmentFile_test.py::TestExceptions::testMissingFile PASSED 496s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangNewFormat PASSED 496s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeNewFormat PASSED 496s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeOldFormat PASSED 496s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeNewFormat PASSED 496s tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeOldFormat PASSED 496s tests/AlignmentFile_test.py::TestExceptions::testZeroToZero PASSED 496s tests/AlignmentFile_test.py::TestWrongFormat::testOpenBamAsSam PASSED 496s tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsBam PASSED 496s tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsSam PASSED 496s tests/AlignmentFile_test.py::TestWrongFormat::testOpenSamAsBam PASSED 496s tests/AlignmentFile_test.py::TestRegionParsing::test_dash_in_chr PASSED 496s tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile PASSED 496s tests/AlignmentFile_test.py::TestDeNovoConstruction::test_pass_if_reads_binary_equal PASSED 496s tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader PASSED 496s tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_in_header PASSED 496s tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_with_null_bytes_in_header PASSED 496s tests/AlignmentFile_test.py::TestMismatchingHeader::testMismatchingHeader PASSED 496s tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader PASSED 496s tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2 PASSED 496s tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator [W::bam_hdr_read] EOF marker is absent. The input is probably truncated 496s [E::bgzf_read_block] Failed to read BGZF block data at offset 105176 expected 17578 bytes; hread returned 17094 496s [E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes 496s PASSED 496s tests/AlignmentFile_test.py::TestCorruptBAM::testCorruptBamIterator PASSED 497s tests/AlignmentFile_test.py::TestBTagSam::testReadTags PASSED 497s tests/AlignmentFile_test.py::TestBTagSam::testReadWriteTags PASSED 497s tests/AlignmentFile_test.py::TestBTagBam::testReadTags PASSED 497s tests/AlignmentFile_test.py::TestBTagBam::testReadWriteTags PASSED 497s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetch PASSED 497s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchUntilEOF PASSED 497s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionFalseTrue PASSED 497s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueFalse PASSED 497s tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueTrue PASSED 497s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetch PASSED 498s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchUntilEOF PASSED 499s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionFalseTrue PASSED 499s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueFalse PASSED 500s tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueTrue PASSED 501s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetch PASSED 501s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchUntilEOF PASSED 502s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionFalseTrue PASSED 503s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueFalse PASSED 504s tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueTrue PASSED 504s tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetch PASSED 504s tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetchAll PASSED 504s tests/AlignmentFile_test.py::TestRemoteFileHTTP::testView PASSED 504s tests/AlignmentFile_test.py::TestLargeOptValues::testBAM PASSED 504s tests/AlignmentFile_test.py::TestLargeOptValues::testSAM PASSED 504s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_counts_as_expected PASSED 504s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_nofilter PASSED 505s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_quality_filter PASSED 505s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_all PASSED 505s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_callback PASSED 505s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_with_coordinates_works PASSED 505s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_without_coordinates_fails PASSED 505s tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_wrong_coordinates_fails PASSED 505s tests/AlignmentFile_test.py::TestCountCoverage::test_counting_the_same_region_works PASSED 505s tests/AlignmentFile_test.py::TestFindIntrons::test_all PASSED 505s tests/AlignmentFile_test.py::TestFindIntrons::test_first PASSED 505s tests/AlignmentFile_test.py::TestFindIntrons::test_total PASSED 505s tests/AlignmentFile_test.py::TestLogging::testFail1 PASSED 505s tests/AlignmentFile_test.py::TestLogging::testNoFail1 PASSED 505s tests/AlignmentFile_test.py::TestLogging::testNoFail2 PASSED 505s tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testCount PASSED 505s tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testIndexStats PASSED 506s tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testMate PASSED 506s tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct PASSED 506s tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct_per_chromosome PASSED 506s tests/AlignmentFile_test.py::TestSamtoolsProxy::testIndex PASSED 506s tests/AlignmentFile_test.py::TestSamtoolsProxy::testSort PASSED[E::hts_open_format] Failed to open file "missing_file" : No such file or directory 506s 506s tests/AlignmentFile_test.py::TestSamtoolsProxy::testView PASSED 506s tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex [E::hts_open_format] Failed to open file "missing_file" : No such file or directory 506s PASSED 506s tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM PASSED 506s tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexCRAM PASSED 506s tests/AlignmentFile_test.py::TestExplicitIndex::testRemoteExplicitIndexBAM [W::hts_idx_load3] The index file is older than the data file: /tmp/autopkgtest.kIxNq9/build.HXX/src/tests/pysam_data/ex1.bam.bai 506s PASSED 506s tests/AlignmentFile_test.py::TestVerbosity::testVerbosity PASSED 506s tests/AlignmentFile_test.py::TestSanityCheckingBAM::test_empty_read_gives_value_error PASSED 507s tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_bam PASSED 507s tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_cram SKIPPED 507s tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_sam PASSED 507s tests/StreamFiledescriptors_test.py::StreamTest::test_samtools_processing SKIPPED 507s tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing PASSED 507s tests/VariantFile_test.py::TestMissingGenotypes::testVCF PASSED 507s tests/VariantFile_test.py::TestMissingGenotypes::testVCFGZ PASSED 507s tests/VariantFile_test.py::TestMissingSamples::testVCF PASSED 507s tests/VariantFile_test.py::TestMissingSamples::testVCFGZ PASSED 507s tests/VariantFile_test.py::TestMissingSamplesFixed::testVCF PASSED 507s tests/VariantFile_test.py::TestMissingSamplesFixed::testVCFGZ [W::bcf_hdr_check_sanity] PL should be declared as Number=G 507s PASSED 507s tests/VariantFile_test.py::TestOpening::testDetectBCF PASSED 507s tests/VariantFile_test.py::TestOpening::testDetectVCF PASSED 507s tests/VariantFile_test.py::TestOpening::testDetectVCFGZ PASSED 507s tests/VariantFile_test.py::TestOpening::testEmptyFileVCF PASSED 507s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFFromPath PASSED 507s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZOnlyHeader PASSED 507s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithIndex PASSED 507s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithoutIndex PASSED 507s tests/VariantFile_test.py::TestOpening::testEmptyFileVCFOnlyHeader PASSED 507s tests/VariantFile_test.py::TestOpening::testMissingFile PASSED 507s tests/VariantFile_test.py::TestOpening::testMissingFileVCFGZ PASSED 507s tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_csi_index PASSED 507s tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_prebuilt_csi PASSED 507s tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_tbi_index_will_produce_csi [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 507s [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) 507s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 507s [E::hts_open_format] Failed to open file "missing_file.vcf" : No such file or directory 507s [E::hts_open_format] Failed to open file "missing_file.vcf.gz" : No such file or directory 507s PASSED 507s tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_csi_index PASSED 507s tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_tbi_index PASSED 507s tests/VariantFile_test.py::TestHeader::testIterator PASSED 507s tests/VariantFile_test.py::TestHeader::testStr PASSED 507s tests/VariantFile_test.py::TestParsing::testAlleles PASSED 507s tests/VariantFile_test.py::TestParsing::testAllelesVariantTypes PASSED 507s tests/VariantFile_test.py::TestParsing::testAlt PASSED 507s tests/VariantFile_test.py::TestParsing::testChrom PASSED 507s tests/VariantFile_test.py::TestParsing::testChromFromPath PASSED 507s tests/VariantFile_test.py::TestParsing::testFilter PASSED 507s tests/VariantFile_test.py::TestParsing::testFormat PASSED 507s tests/VariantFile_test.py::TestParsing::testId PASSED 507s tests/VariantFile_test.py::TestParsing::testInfo PASSED 507s tests/VariantFile_test.py::TestParsing::testPos PASSED 507s tests/VariantFile_test.py::TestParsing::testQual PASSED 507s tests/VariantFile_test.py::TestParsing::testRef PASSED 507s tests/VariantFile_test.py::TestParsing::testSampleAlleleIndices PASSED 507s tests/VariantFile_test.py::TestParsing::testSampleAlleles PASSED 507s tests/VariantFile_test.py::TestParsing::testSampleFormats PASSED 507s tests/VariantFile_test.py::TestParsing::testStart PASSED 507s tests/VariantFile_test.py::TestParsing::testStop PASSED 507s tests/VariantFile_test.py::TestIndexFilename::testOpen PASSED 507s tests/VariantFile_test.py::TestConstructionVCFWithContigs::testBase PASSED 507s tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionFromCopy PASSED 507s tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithLines PASSED 507s tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithRecords PASSED 507s tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testBase PASSED 507s tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionFromCopy PASSED 507s tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithLines PASSED 507s tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithRecords PASSED 507s tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testBase PASSED 507s tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionFromCopy PASSED 507s tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithLines PASSED 507s tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithRecords PASSED 507s tests/VariantFile_test.py::TestSettingRecordValues::testBase PASSED 507s tests/VariantFile_test.py::TestSettingRecordValues::testGenotype (0, 0) 507s PASSED[W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 507s [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 507s 507s tests/VariantFile_test.py::TestSettingRecordValues::testSetQual PASSED 507s tests/VariantFile_test.py::TestMultiThreading::testNoMultiThreadingWithIgnoreTruncation PASSED 507s tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult [E::idx_find_and_load] Could not retrieve index file for '/tmp/autopkgtest.kIxNq9/build.HXX/src/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithreadResult_5_k41i2y.bcf' 507s PASSED 507s tests/VariantFile_test.py::TestSubsetting::testSubsetting PASSED 507s 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.) 507s [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) 507s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 507s [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 507s [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) 507s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 507s PASSED 507s tests/VariantFile_test.py::TestUnicode::test_record_with_unicode PASSED 507s tests/VariantRecord_test.py::test_ascii_annotation_can_be_added PASSED 507s tests/VariantRecord_test.py::test_ascii_annotation_with_variable_length_can_be_added PASSED 507s tests/VariantRecord_test.py::test_unicode_annotation_can_be_added PASSED 507s tests/VariantRecord_test.py::test_set_sample_alleles PASSED 507s tests/VariantRecord_test.py::test_repeated_new_record PASSED 507s tests/compile_test.py::test_bam SKIPPED (no pyximport) 507s tests/compile_test.py::test_gtf SKIPPED (no pyximport) 507s tests/faidx_test.py::TestFastaFile::testFetch PASSED 507s tests/faidx_test.py::TestFastaFile::testFetchErrors PASSED 507s tests/faidx_test.py::TestFastaFile::testLength PASSED 507s tests/faidx_test.py::TestFastaFile::testOutOfRangeAccess PASSED 507s tests/faidx_test.py::TestFastaFile::testSequenceLengths PASSED 507s tests/faidx_test.py::TestFastaFile::test_fetch_with_region_and_contig_raises_exception PASSED 507s tests/faidx_test.py::TestFastaFile::test_fetch_with_region_is_equivalent PASSED 507s tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED 507s tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_index_succeeds PASSED 507s tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_without_index_succeeds PASSED 507s tests/faidx_test.py::TestFastaFilePathIndex::test_raise_exception_if_index_is_missing PASSED 507s tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED 507s tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_index_succeeds PASSED 507s tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_without_index_succeeds PASSED 507s tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_raise_exception_if_index_is_missing PASSED 507s tests/faidx_test.py::TestFastxFileFastq::testCounts PASSED 507s tests/faidx_test.py::TestFastxFileFastq::testManager PASSED 507s tests/faidx_test.py::TestFastxFileFastq::testMissingFile PASSED 507s tests/faidx_test.py::TestFastxFileFastq::testSequence PASSED 507s tests/faidx_test.py::TestFastqFileFastq::testCounts PASSED 507s tests/faidx_test.py::TestFastqFileFastq::testManager PASSED 507s tests/faidx_test.py::TestFastqFileFastq::testMissingFile PASSED 507s tests/faidx_test.py::TestFastqFileFastq::testSequence PASSED 507s tests/faidx_test.py::TestFastxFileFasta::testCounts PASSED 507s tests/faidx_test.py::TestFastxFileFasta::testManager PASSED 507s tests/faidx_test.py::TestFastxFileFasta::testMissingFile PASSED 507s tests/faidx_test.py::TestFastxFileFasta::testSequence PASSED 507s tests/faidx_test.py::TestFastxFileFastqStream::testCounts PASSED 507s tests/faidx_test.py::TestFastxFileFastqStream::testManager PASSED 507s tests/faidx_test.py::TestFastxFileFastqStream::testMissingFile PASSED 507s tests/faidx_test.py::TestFastxFileFastqStream::testSequence PASSED 507s tests/faidx_test.py::TestFastxFileWithEmptySequence::testIteration PASSED 508s tests/faidx_test.py::TestRemoteFileFTP::testFTPView PASSED 508s tests/faidx_test.py::TestRemoteFileFTP::test_sequence_lengths_are_available PASSED 508s tests/faidx_test.py::TestFastqRecord::test_fastx_record_can_be_created_from_scratch PASSED 508s tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_None PASSED 508s tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_modified PASSED 508s tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_name_is_None PASSED 508s tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_quality_is_wrong_length PASSED 508s tests/faidx_test.py::TestFastqRecord::test_fastx_record_name_can_be_modified PASSED 508s tests/faidx_test.py::TestFastqRecord::test_fastx_record_quality_can_be_modified PASSED 508s tests/faidx_test.py::TestFastqRecord::test_fastx_record_sequence_can_be_modified PASSED 508s tests/faidx_test.py::TestFastqProxy::test_fastq_proxy_instantiation_raises_error PASSED 508s tests/linking_test.py::TestLinking::test_package_can_be_installed SKIPPED 508s tests/linking_test.py::TestLinkWithRpath::test_package_can_be_installed SKIPPED 508s tests/linking_test.py::TestLinkWithRpath::test_package_tests_pass SKIPPED 508s tests/linking_test.py::TestLinkWithoutRpath::test_package_can_be_installed SKIPPED 508s tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_fail_on_import SKIPPED 508s tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_pass_if_ld_library_path_set SKIPPED 509s tests/samtools_test.py::SamtoolsTest::testStatements PASSED 509s tests/samtools_test.py::SamtoolsTest::testUsage SKIPPED (skipping us...) 509s tests/samtools_test.py::EmptyIndexTest::testEmptyIndex PASSED 509s tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraArg PASSED 509s tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraFlag PASSED 509s tests/samtools_test.py::TestReturnType::testReturnValueData PASSED 509s tests/samtools_test.py::TestReturnType::testReturnValueString PASSED 509s tests/samtools_test.py::StdoutTest::testDoubleCalling PASSED 509s tests/samtools_test.py::StdoutTest::testSaveStdout PASSED 509s tests/samtools_test.py::StdoutTest::testWithRedirectedStdout PASSED 509s tests/samtools_test.py::StdoutTest::testWithoutRedirectedStdout PASSED 509s tests/samtools_test.py::PysamTest::testStatements PASSED 509s tests/samtools_test.py::PysamTest::testUsage SKIPPED (skipping usage...) 510s tests/tabix_test.py::TestIndexing::test_indexing_to_custom_location_works PASSED 510s tests/tabix_test.py::TestIndexing::test_indexing_with_explict_columns_works PASSED 510s tests/tabix_test.py::TestIndexing::test_indexing_with_lineskipping_works PASSED 510s tests/tabix_test.py::TestIndexing::test_indexing_with_preset_works PASSED 510s tests/tabix_test.py::TestCompression::testCompression PASSED 510s tests/tabix_test.py::TestCompression::testIndexPresetCompressed PASSED 510s tests/tabix_test.py::TestCompression::testIndexPresetUncompressed PASSED 510s tests/tabix_test.py::TestCompressionSam::testCompression PASSED 510s tests/tabix_test.py::TestCompressionSam::testIndexPresetCompressed PASSED 510s tests/tabix_test.py::TestCompressionSam::testIndexPresetUncompressed PASSED 510s tests/tabix_test.py::TestCompressionBed::testCompression PASSED 510s tests/tabix_test.py::TestCompressionBed::testIndexPresetCompressed PASSED 510s tests/tabix_test.py::TestCompressionBed::testIndexPresetUncompressed PASSED 510s tests/tabix_test.py::TestCompressionVCF::testCompression PASSED 510s tests/tabix_test.py::TestCompressionVCF::testIndexPresetCompressed PASSED 510s tests/tabix_test.py::TestCompressionVCF::testIndexPresetUncompressed PASSED 510s tests/tabix_test.py::TestGZFile::testAll PASSED 510s tests/tabix_test.py::TestIterationWithoutComments::testAll PASSED 510s tests/tabix_test.py::TestIterationWithoutComments::testGetContigs PASSED 510s tests/tabix_test.py::TestIterationWithoutComments::testHeader PASSED 510s tests/tabix_test.py::TestIterationWithoutComments::testInvalidIntervals PASSED 510s tests/tabix_test.py::TestIterationWithoutComments::testPerContig PASSED 510s tests/tabix_test.py::TestIterationWithoutComments::testPerContig2 PASSED 510s tests/tabix_test.py::TestIterationWithoutComments::testPerContigFromStart PASSED 510s tests/tabix_test.py::TestIterationWithoutComments::testPerContigToEnd PASSED 510s tests/tabix_test.py::TestIterationWithoutComments::testPerInterval PASSED 510s tests/tabix_test.py::TestIterationWithoutComments::testRegionStrings PASSED 510s tests/tabix_test.py::TestIterationWithoutComments::testReopening PASSED 510s tests/tabix_test.py::TestIterationWithComments::testAll PASSED 510s tests/tabix_test.py::TestIterationWithComments::testGetContigs PASSED 510s tests/tabix_test.py::TestIterationWithComments::testHeader PASSED 510s tests/tabix_test.py::TestIterationWithComments::testInvalidIntervals PASSED 510s tests/tabix_test.py::TestIterationWithComments::testPerContig PASSED 510s tests/tabix_test.py::TestIterationWithComments::testPerContig2 PASSED 510s tests/tabix_test.py::TestIterationWithComments::testPerContigFromStart PASSED 510s tests/tabix_test.py::TestIterationWithComments::testPerContigToEnd PASSED 511s tests/tabix_test.py::TestIterationWithComments::testPerInterval PASSED 511s tests/tabix_test.py::TestIterationWithComments::testRegionStrings PASSED 511s tests/tabix_test.py::TestIterationWithComments::testReopening PASSED 511s tests/tabix_test.py::TestIterators::testClosedFile PASSED 511s tests/tabix_test.py::TestIterators::testClosedFileIteration PASSED 511s tests/tabix_test.py::TestIterators::testIteration PASSED 511s tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFile PASSED 511s tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFileIteration PASSED 511s tests/tabix_test.py::TestIteratorsGenericCompressed::testIteration PASSED 511s tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFile PASSED 511s tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFileIteration PASSED 511s tests/tabix_test.py::TestIteratorsFileCompressed::testIteration PASSED 511s tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFile PASSED 511s tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFileIteration PASSED 511s tests/tabix_test.py::TestIteratorsFileUncompressed::testIteration PASSED 511s tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooFewFields PASSED 511s tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooManyFields PASSED 511s tests/tabix_test.py::TestBed::testRead PASSED 511s tests/tabix_test.py::TestBed::testWrite PASSED 511s tests/tabix_test.py::TestUnicode::testFromTabix PASSED 511s tests/tabix_test.py::TestUnicode::testFromVCF PASSED 511s tests/tabix_test.py::TestVCFFromTabix::testRead PASSED 511s tests/tabix_test.py::TestVCFFromTabix::testWrite PASSED 511s tests/tabix_test.py::TestVCFFromVCF::testConnecting PASSED 511s tests/tabix_test.py::TestVCFFromVCF::testParsing PASSED 511s tests/tabix_test.py::VCFFromTabixTest_22::testRead PASSED 511s tests/tabix_test.py::VCFFromTabixTest_22::testWrite PASSED 511s tests/tabix_test.py::VCFFromVCFTest_22::testConnecting PASSED 512s tests/tabix_test.py::VCFFromVCFTest_22::testParsing PASSED 512s tests/tabix_test.py::VCFFromTabixTest_8::testRead PASSED 512s tests/tabix_test.py::VCFFromTabixTest_8::testWrite PASSED 512s tests/tabix_test.py::VCFFromVCFTest_8::testConnecting PASSED 512s tests/tabix_test.py::VCFFromVCFTest_8::testParsing PASSED 512s tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testRead PASSED 512s tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testWrite PASSED 512s tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testConnecting PASSED 512s tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testParsing PASSED 512s tests/tabix_test.py::VCFFromTabixTest_7::testRead PASSED 513s tests/tabix_test.py::VCFFromTabixTest_7::testWrite PASSED 513s tests/tabix_test.py::VCFFromVCFTest_7::testConnecting PASSED 513s tests/tabix_test.py::VCFFromVCFTest_7::testParsing PASSED 513s tests/tabix_test.py::VCFFromTabixTest_13::testRead PASSED 513s tests/tabix_test.py::VCFFromTabixTest_13::testWrite PASSED 513s tests/tabix_test.py::VCFFromVCFTest_13::testConnecting PASSED 513s tests/tabix_test.py::VCFFromVCFTest_13::testParsing PASSED 513s tests/tabix_test.py::VCFFromTabixTest_6::testRead PASSED 513s tests/tabix_test.py::VCFFromTabixTest_6::testWrite PASSED 513s tests/tabix_test.py::VCFFromVCFTest_6::testConnecting PASSED 514s tests/tabix_test.py::VCFFromVCFTest_6::testParsing PASSED 514s tests/tabix_test.py::VCFFromTabixTest_11::testRead PASSED 514s tests/tabix_test.py::VCFFromTabixTest_11::testWrite PASSED 514s tests/tabix_test.py::VCFFromVCFTest_11::testConnecting PASSED 514s tests/tabix_test.py::VCFFromVCFTest_11::testParsing PASSED 514s tests/tabix_test.py::VCFFromTabixTest_18::testRead PASSED 514s tests/tabix_test.py::VCFFromTabixTest_18::testWrite PASSED 514s tests/tabix_test.py::VCFFromVCFTest_18::testConnecting PASSED 514s tests/tabix_test.py::VCFFromVCFTest_18::testParsing PASSED 514s tests/tabix_test.py::VCFFromTabixTest_issue85::testRead PASSED 515s tests/tabix_test.py::VCFFromTabixTest_issue85::testWrite PASSED 515s tests/tabix_test.py::VCFFromVCFTest_issue85::testConnecting PASSED 515s tests/tabix_test.py::VCFFromVCFTest_issue85::testParsing PASSED 515s tests/tabix_test.py::VCFFromTabixTest_3::testRead PASSED 515s tests/tabix_test.py::VCFFromTabixTest_3::testWrite PASSED 515s tests/tabix_test.py::VCFFromVCFTest_3::testConnecting PASSED 515s tests/tabix_test.py::VCFFromVCFTest_3::testParsing PASSED 515s tests/tabix_test.py::VCFFromTabixTest_16::testRead PASSED 515s tests/tabix_test.py::VCFFromTabixTest_16::testWrite PASSED 515s tests/tabix_test.py::VCFFromVCFTest_16::testConnecting PASSED 515s tests/tabix_test.py::VCFFromVCFTest_16::testParsing PASSED 515s tests/tabix_test.py::VCFFromTabixTest_21::testRead PASSED 515s tests/tabix_test.py::VCFFromTabixTest_21::testWrite PASSED 515s tests/tabix_test.py::VCFFromVCFTest_21::testConnecting PASSED 515s tests/tabix_test.py::VCFFromVCFTest_21::testParsing PASSED 515s tests/tabix_test.py::VCFFromTabixTest_9::testRead PASSED 515s tests/tabix_test.py::VCFFromTabixTest_9::testWrite PASSED 515s tests/tabix_test.py::VCFFromVCFTest_9::testConnecting PASSED 515s tests/tabix_test.py::VCFFromVCFTest_9::testParsing PASSED 515s tests/tabix_test.py::VCFFromTabixTest_24::testRead PASSED 515s tests/tabix_test.py::VCFFromTabixTest_24::testWrite PASSED 515s tests/tabix_test.py::VCFFromVCFTest_24::testConnecting PASSED 515s tests/tabix_test.py::VCFFromVCFTest_24::testParsing PASSED 515s tests/tabix_test.py::VCFFromTabixTest_23::testRead PASSED 515s tests/tabix_test.py::VCFFromTabixTest_23::testWrite PASSED 515s tests/tabix_test.py::VCFFromVCFTest_23::testConnecting PASSED 515s tests/tabix_test.py::VCFFromVCFTest_23::testParsing PASSED 515s tests/tabix_test.py::VCFFromTabixTest_15::testRead PASSED 516s tests/tabix_test.py::VCFFromTabixTest_15::testWrite PASSED 516s tests/tabix_test.py::VCFFromVCFTest_15::testConnecting PASSED 516s tests/tabix_test.py::VCFFromVCFTest_15::testParsing PASSED 516s tests/tabix_test.py::VCFFromTabixTest_4::testRead PASSED 516s tests/tabix_test.py::VCFFromTabixTest_4::testWrite PASSED 516s tests/tabix_test.py::VCFFromVCFTest_4::testConnecting PASSED 517s tests/tabix_test.py::VCFFromVCFTest_4::testParsing PASSED 517s tests/tabix_test.py::VCFFromTabixTest_5::testRead PASSED 517s tests/tabix_test.py::VCFFromTabixTest_5::testWrite PASSED 517s tests/tabix_test.py::VCFFromVCFTest_5::testConnecting PASSED 517s tests/tabix_test.py::VCFFromVCFTest_5::testParsing PASSED 517s tests/tabix_test.py::VCFFromTabixTest_20::testRead PASSED 517s tests/tabix_test.py::VCFFromTabixTest_20::testWrite PASSED 517s tests/tabix_test.py::VCFFromVCFTest_20::testConnecting PASSED 517s tests/tabix_test.py::VCFFromVCFTest_20::testParsing PASSED 517s tests/tabix_test.py::VCFFromTabixTest_12::testRead PASSED 517s tests/tabix_test.py::VCFFromTabixTest_12::testWrite PASSED 517s tests/tabix_test.py::VCFFromVCFTest_12::testConnecting PASSED 517s tests/tabix_test.py::VCFFromVCFTest_12::testParsing PASSED 517s tests/tabix_test.py::VCFFromTabixTest_2::testRead PASSED 517s tests/tabix_test.py::VCFFromTabixTest_2::testWrite PASSED 517s tests/tabix_test.py::VCFFromVCFTest_2::testConnecting PASSED 517s tests/tabix_test.py::VCFFromVCFTest_2::testParsing PASSED 517s tests/tabix_test.py::VCFFromTabixTest_10::testRead PASSED 517s tests/tabix_test.py::VCFFromTabixTest_10::testWrite PASSED 517s tests/tabix_test.py::VCFFromVCFTest_10::testConnecting PASSED 517s tests/tabix_test.py::VCFFromVCFTest_10::testParsing PASSED 517s tests/tabix_test.py::TestVCFFromVariantFile::testConnecting PASSED 517s tests/tabix_test.py::TestVCFFromVariantFile::testParsing [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) 517s [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) 517s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 517s PASSED 517s tests/tabix_test.py::TestVCFFromVariantFile_22::testConnecting PASSED 517s 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.) 517s [W::vcf_parse_info] INFO 'refseq.name' is not defined in the header, assuming Type=String 517s [W::vcf_parse_info] INFO 'refseq.positionType' is not defined in the header, assuming Type=String 518s [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) 518s PASSED 518s tests/tabix_test.py::TestVCFFromVariantFile_8::testConnecting PASSED 518s 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.) 518s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:676148 is not defined in the header, assuming Type=String 518s PASSED 518s tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testConnecting PASSED 518s tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testParsing PASSED 518s tests/tabix_test.py::TestVCFFromVariantFile_7::testConnecting PASSED 518s 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.) 518s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:249843 is not defined in the header, assuming Type=String 519s PASSED 519s tests/tabix_test.py::TestVCFFromVariantFile_13::testConnecting PASSED 519s tests/tabix_test.py::TestVCFFromVariantFile_13::testParsing [W::bcf_hrec_check] Invalid tag name: "1000g" 519s [W::bcf_hrec_check] Invalid tag name: "GT:GL:GQ:NR" 519s [W::bcf_hdr_check_sanity] GL should be declared as Number=G 519s [W::bcf_hrec_check] Invalid tag name: "1000g" 519s [W::bcf_hrec_check] Invalid tag name: "GT:GL:GQ:NR" 519s [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) 519s [W::vcf_parse_info] INFO 'MMLQ' is not defined in the header, assuming Type=String 519s [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) 519s [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) 519s [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) 519s [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) 519s [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) 519s [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) 519s [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) 519s [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) 519s [W::vcf_parse] Contig 'chr17_gl000205_random' is not defined in the header. (Quick workaround: index the file with tabix.) 519s [W::vcf_parse] Contig 'chr18' is not defined in the header. (Quick workaround: index the file with tabix.) 519s [W::vcf_parse] Contig 'chr19' is not defined in the header. (Quick workaround: index the file with tabix.) 519s [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) 519s [W::vcf_parse] Contig 'chr20' is not defined in the header. (Quick workaround: index the file with tabix.) 519s [W::vcf_parse] Contig 'chr21' is not defined in the header. (Quick workaround: index the file with tabix.) 519s [W::vcf_parse] Contig 'chr22' is not defined in the header. (Quick workaround: index the file with tabix.) 519s [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) 519s [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) 519s [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) 519s [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) 519s [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) 519s [W::vcf_parse] PASSED 519s tests/tabix_test.py::TestVCFFromVariantFile_6::testConnecting Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) 519s [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) 519s [W::vcf_parse] Contig 'chrUn_gl000214' is not defined in the header. (Quick workaround: index the file with tabix.) 519s [W::vcf_parse] Contig 'chrUn_gl000220' is not defined in the header. (Quick workaround: index the file with tabix.) 519s [W::vcf_parse] Contig 'chrUn_gl000225' is not defined in the header. (Quick workaround: index the file with tabix.) 519s [W::vcf_parse] Contig 'chrX' is not defined in the header. (Quick workaround: index the file with tabix.) 519s PASSED 519s 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.) 519s [W::vcf_parse_info] INFO 'CallSetAC' is not defined in the header, assuming Type=String 519s [W::vcf_parse_info] INFO 'CallSetAC2' is not defined in the header, assuming Type=String 519s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:669442 is not defined in the header, assuming Type=String 519s PASSED 519s tests/tabix_test.py::TestVCFFromVariantFile_11::testConnecting PASSED 519s 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.) 519s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:669442 is not defined in the header, assuming Type=String 520s PASSED 520s tests/tabix_test.py::TestVCFFromVariantFile_18::testConnecting PASSED 520s 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.) 520s [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String 520s [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String 520s [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String 520s [W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String 520s [W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String 520s [W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String 520s [W::vcf_parse_format_dict2] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String 520s [W::vcf_parse_format_dict2] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String 520s [W::vcf_parse_format_dict2] FORMAT 'GQ' at chr1:1281168 is not defined in the header, assuming Type=String 520s [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [E::bcf_hdr_parse] Could not parse the header, sample line not found 520s PASSED 520s tests/tabix_test.py::TestVCFFromVariantFile_issue85::testConnecting PASSED 520s tests/tabix_test.py::TestVCFFromVariantFile_issue85::testParsing PASSED 520s tests/tabix_test.py::TestVCFFromVariantFile_3::testConnecting PASSED 520s 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.) 520s PASSED 520s tests/tabix_test.py::TestVCFFromVariantFile_16::testConnecting PASSED 520s 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.) 520s [W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String 520s PASSED 520s tests/tabix_test.py::TestVCFFromVariantFile_21::testConnecting PASSED 520s tests/tabix_test.py::TestVCFFromVariantFile_21::testParsing [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 520s PASSED[W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 520s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 520s 520s tests/tabix_test.py::TestVCFFromVariantFile_9::testConnecting PASSED 520s 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.) 520s [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String 520s [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String 520s [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String 520s [W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String 520s [W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String 520s [W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String 520s [W::vcf_parse_format_dict2] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String 520s [W::vcf_parse_format_dict2] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String 520s [W::vcf_parse_format_dict2] FORMAT 'GQ' at chr1:1281168 is not defined in the header, assuming Type=String 520s [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) 520s [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: 520s #CHROM POS ID REF ALT QUAL FILTER INFO 520s 520s PASSED 520s tests/tabix_test.py::TestVCFFromVariantFile_24::testConnecting PASSED 520s tests/tabix_test.py::TestVCFFromVariantFile_24::testParsing PASSED 520s tests/tabix_test.py::TestVCFFromVariantFile_23::testConnecting PASSED 520s tests/tabix_test.py::TestVCFFromVariantFile_23::testParsing [W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String 520s PASSED 520s tests/tabix_test.py::TestVCFFromVariantFile_15::testConnecting PASSED 520s 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.) 520s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:439104 is not defined in the header, assuming Type=String 521s PASSED 521s tests/tabix_test.py::TestVCFFromVariantFile_4::testConnecting PASSED 521s 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.) 521s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:249843 is not defined in the header, assuming Type=String 521s PASSED 521s tests/tabix_test.py::TestVCFFromVariantFile_5::testConnecting PASSED 521s 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.) 521s PASSED 521s tests/tabix_test.py::TestVCFFromVariantFile_20::testConnecting [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 521s PASSED 521s tests/tabix_test.py::TestVCFFromVariantFile_20::testParsing [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 521s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 521s PASSED 521s tests/tabix_test.py::TestVCFFromVariantFile_12::testConnecting PASSED 521s 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.) 521s [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String 521s [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String 521s [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String 521s [W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String 521s [W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String 521s [W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String 521s [W::vcf_parse_format_dict2] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String 521s [W::vcf_parse_format_dict2] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String 521s [W::vcf_parse_format_dict2] FORMAT 'GQ' at chr1:1281168 is not defined in the header, assuming Type=String 521s [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) 521s [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) 521s [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) 521s [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) 521s [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) 521s [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) 521s [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) 521s [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) 521s [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) 521s [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) 521s [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) 521s [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) 521s [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) 521s [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) 521s [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) 521s [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) 521s [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) 521s PASSED 521s tests/tabix_test.py::TestVCFFromVariantFile_2::testConnecting PASSED 521s tests/tabix_test.py::TestVCFFromVariantFile_2::testParsing [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) 521s [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) 521s PASSED 521s tests/tabix_test.py::TestVCFFromVariantFile_10::testConnecting PASSED 521s 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.) 521s [W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String 521s [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 521s [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:676148 is not defined in the header, assuming Type=String 521s PASSED 521s tests/tabix_test.py::TestIndexArgument::testFetchAll PASSED 521s tests/tabix_test.py::TestIndexArgument::testLoadIndexWithoutTbiExtension PASSED 521s tests/tabix_test.py::TestBackwardsCompatibility::testBED PASSED 521s tests/tabix_test.py::TestBackwardsCompatibility::testBED0v23 PASSED 521s tests/tabix_test.py::TestBackwardsCompatibility::testBED0v26 PASSED 521s tests/tabix_test.py::TestBackwardsCompatibility::testEmpty PASSED 521s tests/tabix_test.py::TestBackwardsCompatibility::testVCF PASSED 521s tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v23 PASSED 521s tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v26 PASSED 521s tests/tabix_test.py::TestMultipleIterators::testDisjointIterators PASSED 521s tests/tabix_test.py::TestMultipleIterators::testDoubleFetch PASSED 521s tests/tabix_test.py::TestMultipleIterators::testJoinedIterators PASSED 521s tests/tabix_test.py::TestMultipleIterators::testScope PASSED 521s tests/tabix_test.py::TestContextManager::testManager PASSED 521s tests/tabix_test.py::TestMultithreadTabixFile::testMultithreadEqualsSinglethread PASSED 521s tests/tabixproxies_test.py::TestBED::testAssignmentToTargetList PASSED 521s tests/tabixproxies_test.py::TestParser::testAssignmentToTargetList PASSED 521s tests/tabixproxies_test.py::TestParser::testCopy PASSED 521s tests/tabixproxies_test.py::TestParser::testIteratorCompressed PASSED 521s tests/tabixproxies_test.py::TestParser::testIteratorUncompressed PASSED 521s tests/tabixproxies_test.py::TestParser::testRead PASSED 522s tests/tabixproxies_test.py::TestParser::testUnset PASSED 522s tests/tabixproxies_test.py::TestParser::testWrite PASSED 522s tests/tabixproxies_test.py::TestGTF::testAssignmentToTargetList PASSED 522s tests/tabixproxies_test.py::TestGTF::testCopy PASSED 522s tests/tabixproxies_test.py::TestGTF::testIteratorCompressed PASSED 522s tests/tabixproxies_test.py::TestGTF::testIteratorUncompressed PASSED 522s tests/tabixproxies_test.py::TestGTF::testRead PASSED 522s tests/tabixproxies_test.py::TestGTF::testUnset PASSED 522s tests/tabixproxies_test.py::TestGTF::testWrite PASSED 522s tests/tabixproxies_test.py::TestGTF::test_added_attribute_is_output PASSED 522s tests/tabixproxies_test.py::TestGTF::test_asdict_can_be_modified PASSED 522s tests/tabixproxies_test.py::TestGTF::test_asdict_contains_attributes PASSED 522s tests/tabixproxies_test.py::TestGTF::test_setAttribute_makes_changes PASSED 522s tests/tabixproxies_test.py::TestGTF::test_setting_end_is_one_based PASSED 522s tests/tabixproxies_test.py::TestGTF::test_setting_feature_to_none_produces_dot PASSED 522s tests/tabixproxies_test.py::TestGTF::test_setting_fields PASSED 522s tests/tabixproxies_test.py::TestGTF::test_setting_frame_to_none_produces_dot PASSED 522s tests/tabixproxies_test.py::TestGTF::test_setting_score_to_none_produces_dot PASSED 522s tests/tabixproxies_test.py::TestGTF::test_setting_source_to_none_produces_dot PASSED 522s tests/tabixproxies_test.py::TestGTF::test_setting_start_is_one_based PASSED 522s tests/tabixproxies_test.py::TestGTF::test_setting_strand_to_none_produces_dot PASSED 522s tests/tabixproxies_test.py::TestGFF3::testAssignmentToTargetList PASSED 522s tests/tabixproxies_test.py::TestGFF3::testCopy PASSED 522s tests/tabixproxies_test.py::TestGFF3::testIteratorCompressed PASSED 522s tests/tabixproxies_test.py::TestGFF3::testIteratorUncompressed PASSED 522s tests/tabixproxies_test.py::TestGFF3::testRead PASSED 522s tests/tabixproxies_test.py::TestGFF3::testUnset PASSED 522s tests/tabixproxies_test.py::TestGFF3::testWrite PASSED 522s tests/tabixproxies_test.py::TestGFF3::test_added_attribute_is_output PASSED 522s tests/tabixproxies_test.py::TestGFF3::test_asdict_can_be_modified PASSED 522s tests/tabixproxies_test.py::TestGFF3::test_asdict_contains_attributes PASSED 522s tests/tabixproxies_test.py::TestGFF3::test_setAttribute_makes_changes PASSED 522s tests/tabixproxies_test.py::TestGFF3::test_setting_end_is_one_based PASSED 522s tests/tabixproxies_test.py::TestGFF3::test_setting_feature_to_none_produces_dot PASSED 522s tests/tabixproxies_test.py::TestGFF3::test_setting_fields PASSED 522s tests/tabixproxies_test.py::TestGFF3::test_setting_frame_to_none_produces_dot PASSED 522s tests/tabixproxies_test.py::TestGFF3::test_setting_score_to_none_produces_dot PASSED 522s tests/tabixproxies_test.py::TestGFF3::test_setting_source_to_none_produces_dot PASSED 522s tests/tabixproxies_test.py::TestGFF3::test_setting_start_is_one_based PASSED 522s tests/tabixproxies_test.py::TestGFF3::test_setting_strand_to_none_produces_dot PASSED 522s tests/test_samtools_python.py::test_idxstats_parse_split_lines PASSED 522s tests/test_samtools_python.py::test_bedcov_split_lines PASSED 522s tests/test_samtools_python.py::test_idxstats_parse PASSED 522s tests/test_samtools_python.py::test_bedcov PASSED 522s 522s ================== 947 passed, 14 skipped in 79.40s (0:01:19) ================== 522s autopkgtest [15:04:35]: test command1: -----------------------] 523s command1 PASS 523s autopkgtest [15:04:36]: test command1: - - - - - - - - - - results - - - - - - - - - - 523s autopkgtest [15:04:36]: test autodep8-python3: preparing testbed 695s autopkgtest [15:07:28]: testbed dpkg architecture: arm64 695s autopkgtest [15:07:28]: testbed apt version: 2.9.33 696s autopkgtest [15:07:29]: @@@@@@@@@@@@@@@@@@@@ test bed setup 696s autopkgtest [15:07:29]: testbed release detected to be: plucky 697s autopkgtest [15:07:30]: updating testbed package index (apt update) 697s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 697s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 697s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 697s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 698s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 698s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 698s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 698s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [78.2 kB] 698s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1976 B] 698s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 698s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [346 kB] 699s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [15.8 kB] 699s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 699s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [572 B] 699s Fetched 1094 kB in 2s (592 kB/s) 700s Reading package lists... 701s Reading package lists... 701s Building dependency tree... 701s Reading state information... 702s Calculating upgrade... 702s Calculating upgrade... 703s The following packages will be upgraded: 703s python3-jinja2 strace 703s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 703s Need to get 608 kB of archives. 703s After this operation, 11.3 kB of additional disk space will be used. 703s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 704s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 704s Fetched 608 kB in 1s (558 kB/s) 705s (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 ... 117701 files and directories currently installed.) 705s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 705s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 705s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 705s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 705s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 705s Setting up strace (6.13+ds-1ubuntu1) ... 705s Processing triggers for man-db (2.13.0-1) ... 706s Reading package lists... 707s Building dependency tree... 707s Reading state information... 707s Solving dependencies... 708s The following packages will be REMOVED: 708s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 708s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 708s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 708s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 708s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 708s After this operation, 267 MB disk space will be freed. 708s (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 ... 117701 files and directories currently installed.) 708s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 708s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 708s Removing libpython3.12t64:arm64 (3.12.9-1) ... 708s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 708s Removing libnsl2:arm64 (1.3.0-3build3) ... 708s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 709s Removing libunwind8:arm64 (1.6.2-3.1) ... 709s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 709s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 711s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 712s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 712s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 712s /etc/kernel/postrm.d/initramfs-tools: 712s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 712s /etc/kernel/postrm.d/zz-flash-kernel: 712s flash-kernel: Kernel 6.11.0-8-generic has been removed. 712s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 712s /etc/kernel/postrm.d/zz-update-grub: 712s Sourcing file `/etc/default/grub' 712s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 712s Generating grub configuration file ... 713s Found linux image: /boot/vmlinuz-6.14.0-10-generic 713s Found initrd image: /boot/initrd.img-6.14.0-10-generic 713s Warning: os-prober will not be executed to detect other bootable partitions. 713s Systems on them will not be added to the GRUB boot configuration. 713s Check GRUB_DISABLE_OS_PROBER documentation entry. 713s Adding boot menu entry for UEFI Firmware Settings ... 713s done 713s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 714s Processing triggers for libc-bin (2.41-1ubuntu1) ... 714s (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 ... 81650 files and directories currently installed.) 714s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 714s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 714s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 714s autopkgtest [15:07:47]: upgrading testbed (apt dist-upgrade and autopurge) 715s Reading package lists... 715s Building dependency tree... 715s Reading state information... 715s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 716s Starting 2 pkgProblemResolver with broken count: 0 716s Done 716s Entering ResolveByKeep 717s 717s Calculating upgrade... 717s The following packages will be upgraded: 717s libc-bin libc-dev-bin libc6 libc6-dev locales 718s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 718s Need to get 9530 kB of archives. 718s After this operation, 0 B of additional disk space will be used. 718s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 720s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 720s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 723s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 723s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 728s Preconfiguring packages ... 728s Fetched 9530 kB in 10s (947 kB/s) 728s (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 ... 81647 files and directories currently installed.) 728s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 728s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 728s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 728s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 728s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 729s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 729s Setting up libc6:arm64 (2.41-1ubuntu2) ... 729s (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 ... 81647 files and directories currently installed.) 729s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 729s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 729s Setting up libc-bin (2.41-1ubuntu2) ... 729s (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 ... 81647 files and directories currently installed.) 729s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 729s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 730s Setting up locales (2.41-1ubuntu2) ... 730s Generating locales (this might take a while)... 733s en_US.UTF-8... done 733s Generation complete. 733s Setting up libc-dev-bin (2.41-1ubuntu2) ... 733s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 733s Processing triggers for man-db (2.13.0-1) ... 734s Processing triggers for systemd (257.3-1ubuntu3) ... 734s Reading package lists... 735s Building dependency tree... 735s Reading state information... 735s Starting pkgProblemResolver with broken count: 0 735s Starting 2 pkgProblemResolver with broken count: 0 735s Done 736s Solving dependencies... 736s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 737s autopkgtest [15:08:10]: rebooting testbed after setup commands that affected boot 759s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 769s Reading package lists... 769s Building dependency tree... 769s Reading state information... 769s Starting pkgProblemResolver with broken count: 0 769s Starting 2 pkgProblemResolver with broken count: 0 769s Done 770s The following NEW packages will be installed: 770s libdeflate0 libhts3t64 libhtscodecs2 python3-all python3-pysam 770s 0 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. 770s Need to get 4193 kB of archives. 770s After this operation, 37.7 MB of additional disk space will be used. 770s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 771s Get:2 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.1-2 [82.7 kB] 771s Get:3 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts3t64 arm64 1.21+ds-1 [441 kB] 771s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.13.2-2 [886 B] 771s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pysam arm64 0.23.0+ds-1build1 [3621 kB] 776s Fetched 4193 kB in 5s (765 kB/s) 776s Selecting previously unselected package libdeflate0:arm64. 777s (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 ... 81647 files and directories currently installed.) 777s Preparing to unpack .../libdeflate0_1.23-1_arm64.deb ... 777s Unpacking libdeflate0:arm64 (1.23-1) ... 777s Selecting previously unselected package libhtscodecs2:arm64. 777s Preparing to unpack .../libhtscodecs2_1.6.1-2_arm64.deb ... 777s Unpacking libhtscodecs2:arm64 (1.6.1-2) ... 777s Selecting previously unselected package libhts3t64:arm64. 777s Preparing to unpack .../libhts3t64_1.21+ds-1_arm64.deb ... 777s Unpacking libhts3t64:arm64 (1.21+ds-1) ... 777s Selecting previously unselected package python3-all. 777s Preparing to unpack .../python3-all_3.13.2-2_arm64.deb ... 777s Unpacking python3-all (3.13.2-2) ... 777s Selecting previously unselected package python3-pysam. 777s Preparing to unpack .../python3-pysam_0.23.0+ds-1build1_arm64.deb ... 777s Unpacking python3-pysam (0.23.0+ds-1build1) ... 777s Setting up libhtscodecs2:arm64 (1.6.1-2) ... 777s Setting up libdeflate0:arm64 (1.23-1) ... 777s Setting up python3-all (3.13.2-2) ... 777s Setting up libhts3t64:arm64 (1.21+ds-1) ... 777s Setting up python3-pysam (0.23.0+ds-1build1) ... 777s Processing triggers for man-db (2.13.0-1) ... 778s Processing triggers for libc-bin (2.41-1ubuntu2) ... 782s autopkgtest [15:08:55]: 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 782s autopkgtest [15:08:55]: test autodep8-python3: [----------------------- 783s Testing with python3.13: 783s 783s autopkgtest [15:08:56]: test autodep8-python3: -----------------------] 784s autopkgtest [15:08:57]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 784s autodep8-python3 PASS (superficial) 784s autopkgtest [15:08:57]: @@@@@@@@@@@@@@@@@@@@ summary 784s command1 PASS 784s autodep8-python3 PASS (superficial) 803s nova [W] Using flock in prodstack6-arm64 803s Creating nova instance adt-plucky-arm64-python-pysam-20250315-145552-juju-7f2275-prod-proposed-migration-environment-2-81ab0726-c1ea-420a-b070-080c3234808f from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 803s nova [W] Timed out waiting for 12d23dfd-bd60-4549-8272-b78e85dca9e8 to get deleted. 803s nova [W] Using flock in prodstack6-arm64 803s Creating nova instance adt-plucky-arm64-python-pysam-20250315-145552-juju-7f2275-prod-proposed-migration-environment-2-81ab0726-c1ea-420a-b070-080c3234808f from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 803s nova [W] Timed out waiting for 06081dfc-82f3-41be-bb41-0c2b14317d5b to get deleted.