0s autopkgtest [19:40:13]: starting date and time: 2025-03-15 19:40:13+0000 0s autopkgtest [19:40:13]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [19:40:13]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.eu9qbio1/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade vcftools --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-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-s390x-10.secgroup --name adt-plucky-s390x-vcftools-20250315-194013-juju-7f2275-prod-proposed-migration-environment-2-93b07177-800a-4369-921d-eafd33ad8612 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-s390x -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/ 105s autopkgtest [19:41:58]: testbed dpkg architecture: s390x 105s autopkgtest [19:41:58]: testbed apt version: 2.9.33 105s autopkgtest [19:41:58]: @@@@@@@@@@@@@@@@@@@@ test bed setup 105s autopkgtest [19:41:58]: testbed release detected to be: None 106s autopkgtest [19:41:59]: updating testbed package index (apt update) 106s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 107s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 107s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 107s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 107s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [369 kB] 107s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.5 kB] 107s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [45.1 kB] 107s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [77.3 kB] 107s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1824 B] 107s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 107s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [314 kB] 107s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [13.3 kB] 107s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3532 B] 107s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [240 B] 107s Fetched 965 kB in 1s (997 kB/s) 108s Reading package lists... 109s Reading package lists... 109s Building dependency tree... 109s Reading state information... 109s Calculating upgrade... 109s Calculating upgrade... 109s The following packages were automatically installed and are no longer required: 109s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 109s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 109s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 109s linux-tools-6.11.0-8-generic 109s Use 'sudo apt autoremove' to remove them. 109s The following packages will be upgraded: 109s pinentry-curses python3-jinja2 strace 109s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 109s Need to get 652 kB of archives. 109s After this operation, 27.6 kB of additional disk space will be used. 109s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB] 110s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pinentry-curses s390x 1.3.1-2ubuntu3 [42.9 kB] 110s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 110s Fetched 652 kB in 1s (924 kB/s) 110s (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 ... 81428 files and directories currently installed.) 110s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ... 110s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 110s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_s390x.deb ... 110s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 110s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 110s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 110s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 110s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 110s Setting up strace (6.13+ds-1ubuntu1) ... 110s Processing triggers for man-db (2.13.0-1) ... 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s Solving dependencies... 111s The following packages will be REMOVED: 111s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 111s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 111s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 111s linux-tools-6.11.0-8-generic* 111s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded. 111s After this operation, 167 MB disk space will be freed. 111s (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 ... 81428 files and directories currently installed.) 111s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 111s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 111s Removing libpython3.12t64:s390x (3.12.9-1) ... 111s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 111s Removing libnsl2:s390x (1.3.0-3build3) ... 111s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 111s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 111s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 112s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 112s Processing triggers for libc-bin (2.41-1ubuntu1) ... 112s (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 ... 56328 files and directories currently installed.) 112s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 112s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 113s autopkgtest [19:42:06]: upgrading testbed (apt dist-upgrade and autopurge) 113s Reading package lists... 113s Building dependency tree... 113s Reading state information... 113s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 113s Starting 2 pkgProblemResolver with broken count: 0 113s Done 113s Entering ResolveByKeep 113s 113s Calculating upgrade... 113s The following packages will be upgraded: 113s libc-bin libc-dev-bin libc6 libc6-dev locales 114s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 114s Need to get 9512 kB of archives. 114s After this operation, 8192 B of additional disk space will be used. 114s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB] 114s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB] 114s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB] 115s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB] 115s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB] 115s Preconfiguring packages ... 115s Fetched 9512 kB in 2s (6279 kB/s) 115s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 56326 files and directories currently installed.) 115s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ... 115s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 115s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ... 115s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 115s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ... 115s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 116s Setting up libc6:s390x (2.41-1ubuntu2) ... 116s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 56326 files and directories currently installed.) 116s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ... 116s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 116s Setting up libc-bin (2.41-1ubuntu2) ... 116s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 56326 files and directories currently installed.) 116s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 116s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 116s Setting up locales (2.41-1ubuntu2) ... 116s Generating locales (this might take a while)... 117s en_US.UTF-8... done 117s Generation complete. 117s Setting up libc-dev-bin (2.41-1ubuntu2) ... 117s Setting up libc6-dev:s390x (2.41-1ubuntu2) ... 117s Processing triggers for man-db (2.13.0-1) ... 118s Processing triggers for systemd (257.3-1ubuntu3) ... 119s Reading package lists... 119s Building dependency tree... 119s Reading state information... 119s Starting pkgProblemResolver with broken count: 0 119s Starting 2 pkgProblemResolver with broken count: 0 119s Done 119s Solving dependencies... 119s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 119s autopkgtest [19:42:12]: rebooting testbed after setup commands that affected boot 138s autopkgtest [19:42:31]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025 140s autopkgtest [19:42:33]: @@@@@@@@@@@@@@@@@@@@ apt-source vcftools 142s Get:1 http://ftpmaster.internal/ubuntu plucky/universe vcftools 0.1.16-3 (dsc) [2071 B] 142s Get:2 http://ftpmaster.internal/ubuntu plucky/universe vcftools 0.1.16-3 (tar) [245 kB] 142s Get:3 http://ftpmaster.internal/ubuntu plucky/universe vcftools 0.1.16-3 (diff) [14.0 kB] 142s gpgv: Signature made Thu Oct 7 06:07:18 2021 UTC 142s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 142s gpgv: issuer "tille@debian.org" 142s gpgv: Can't check signature: No public key 142s dpkg-source: warning: cannot verify inline signature for ./vcftools_0.1.16-3.dsc: no acceptable signature found 142s autopkgtest [19:42:35]: testing package vcftools version 0.1.16-3 142s autopkgtest [19:42:35]: build not needed 143s autopkgtest [19:42:36]: test run-unit-test: preparing testbed 143s Reading package lists... 143s Building dependency tree... 143s Reading state information... 143s Starting pkgProblemResolver with broken count: 0 143s Starting 2 pkgProblemResolver with broken count: 0 143s Done 144s The following NEW packages will be installed: 144s libalgorithm-diff-perl libcapture-tiny-perl libclass-data-inheritable-perl 144s libdeflate0 libdevel-stacktrace-perl libexception-class-perl libhtscodecs2 144s libsub-uplevel-perl libtest-deep-perl libtest-differences-perl 144s libtest-exception-perl libtest-most-perl libtest-warn-perl libtext-diff-perl 144s tabix vcftools 144s 0 upgraded, 16 newly installed, 0 to remove and 0 not upgraded. 144s Need to get 1333 kB of archives. 144s After this operation, 5229 kB of additional disk space will be used. 144s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libalgorithm-diff-perl all 1.201-1 [41.8 kB] 144s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libcapture-tiny-perl all 0.50-1 [20.7 kB] 144s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x libclass-data-inheritable-perl all 0.10-1 [8038 B] 144s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate0 s390x 1.23-1 [46.1 kB] 144s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x libdevel-stacktrace-perl all 2.0500-1 [22.1 kB] 144s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x libexception-class-perl all 1.45-1 [28.6 kB] 144s Get:7 http://ftpmaster.internal/ubuntu plucky/universe s390x libhtscodecs2 s390x 1.6.1-2 [91.0 kB] 144s Get:8 http://ftpmaster.internal/ubuntu plucky/universe s390x libsub-uplevel-perl all 0.2800-3 [11.6 kB] 144s Get:9 http://ftpmaster.internal/ubuntu plucky/universe s390x libtest-deep-perl all 1.204-1 [47.1 kB] 144s Get:10 http://ftpmaster.internal/ubuntu plucky/universe s390x libtext-diff-perl all 1.45-2 [25.6 kB] 144s Get:11 http://ftpmaster.internal/ubuntu plucky/universe s390x libtest-differences-perl all 0.71-1 [15.8 kB] 144s Get:12 http://ftpmaster.internal/ubuntu plucky/universe s390x libtest-exception-perl all 0.43-3 [13.4 kB] 144s Get:13 http://ftpmaster.internal/ubuntu plucky/universe s390x libtest-warn-perl all 0.37-2 [12.6 kB] 144s Get:14 http://ftpmaster.internal/ubuntu plucky/universe s390x libtest-most-perl all 0.38-1 [21.5 kB] 144s Get:15 http://ftpmaster.internal/ubuntu plucky/universe s390x tabix s390x 1.21+ds-1 [546 kB] 144s Get:16 http://ftpmaster.internal/ubuntu plucky/universe s390x vcftools s390x 0.1.16-3 [381 kB] 145s Fetched 1333 kB in 1s (1748 kB/s) 145s Selecting previously unselected package libalgorithm-diff-perl. 145s (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 ... 56326 files and directories currently installed.) 145s Preparing to unpack .../00-libalgorithm-diff-perl_1.201-1_all.deb ... 145s Unpacking libalgorithm-diff-perl (1.201-1) ... 145s Selecting previously unselected package libcapture-tiny-perl. 145s Preparing to unpack .../01-libcapture-tiny-perl_0.50-1_all.deb ... 145s Unpacking libcapture-tiny-perl (0.50-1) ... 145s Selecting previously unselected package libclass-data-inheritable-perl. 145s Preparing to unpack .../02-libclass-data-inheritable-perl_0.10-1_all.deb ... 145s Unpacking libclass-data-inheritable-perl (0.10-1) ... 145s Selecting previously unselected package libdeflate0:s390x. 145s Preparing to unpack .../03-libdeflate0_1.23-1_s390x.deb ... 145s Unpacking libdeflate0:s390x (1.23-1) ... 145s Selecting previously unselected package libdevel-stacktrace-perl. 145s Preparing to unpack .../04-libdevel-stacktrace-perl_2.0500-1_all.deb ... 145s Unpacking libdevel-stacktrace-perl (2.0500-1) ... 145s Selecting previously unselected package libexception-class-perl. 145s Preparing to unpack .../05-libexception-class-perl_1.45-1_all.deb ... 145s Unpacking libexception-class-perl (1.45-1) ... 145s Selecting previously unselected package libhtscodecs2:s390x. 145s Preparing to unpack .../06-libhtscodecs2_1.6.1-2_s390x.deb ... 145s Unpacking libhtscodecs2:s390x (1.6.1-2) ... 145s Selecting previously unselected package libsub-uplevel-perl. 145s Preparing to unpack .../07-libsub-uplevel-perl_0.2800-3_all.deb ... 145s Unpacking libsub-uplevel-perl (0.2800-3) ... 145s Selecting previously unselected package libtest-deep-perl. 145s Preparing to unpack .../08-libtest-deep-perl_1.204-1_all.deb ... 145s Unpacking libtest-deep-perl (1.204-1) ... 145s Selecting previously unselected package libtext-diff-perl. 145s Preparing to unpack .../09-libtext-diff-perl_1.45-2_all.deb ... 145s Unpacking libtext-diff-perl (1.45-2) ... 145s Selecting previously unselected package libtest-differences-perl. 145s Preparing to unpack .../10-libtest-differences-perl_0.71-1_all.deb ... 145s Unpacking libtest-differences-perl (0.71-1) ... 145s Selecting previously unselected package libtest-exception-perl. 145s Preparing to unpack .../11-libtest-exception-perl_0.43-3_all.deb ... 145s Unpacking libtest-exception-perl (0.43-3) ... 145s Selecting previously unselected package libtest-warn-perl. 145s Preparing to unpack .../12-libtest-warn-perl_0.37-2_all.deb ... 145s Unpacking libtest-warn-perl (0.37-2) ... 145s Selecting previously unselected package libtest-most-perl. 145s Preparing to unpack .../13-libtest-most-perl_0.38-1_all.deb ... 145s Unpacking libtest-most-perl (0.38-1) ... 145s Selecting previously unselected package tabix. 145s Preparing to unpack .../14-tabix_1.21+ds-1_s390x.deb ... 145s Unpacking tabix (1.21+ds-1) ... 145s Selecting previously unselected package vcftools. 145s Preparing to unpack .../15-vcftools_0.1.16-3_s390x.deb ... 145s Unpacking vcftools (0.1.16-3) ... 145s Setting up libhtscodecs2:s390x (1.6.1-2) ... 145s Setting up vcftools (0.1.16-3) ... 145s Setting up libtest-deep-perl (1.204-1) ... 145s Setting up libalgorithm-diff-perl (1.201-1) ... 145s Setting up libdeflate0:s390x (1.23-1) ... 145s Setting up libclass-data-inheritable-perl (0.10-1) ... 145s Setting up libtext-diff-perl (1.45-2) ... 145s Setting up libcapture-tiny-perl (0.50-1) ... 145s Setting up libsub-uplevel-perl (0.2800-3) ... 145s Setting up libdevel-stacktrace-perl (2.0500-1) ... 145s Setting up tabix (1.21+ds-1) ... 145s Setting up libtest-warn-perl (0.37-2) ... 145s Setting up libtest-differences-perl (0.71-1) ... 145s Setting up libexception-class-perl (1.45-1) ... 145s Setting up libtest-exception-perl (0.43-3) ... 145s Setting up libtest-most-perl (0.38-1) ... 145s Processing triggers for man-db (2.13.0-1) ... 145s Processing triggers for libc-bin (2.41-1ubuntu2) ... 146s autopkgtest [19:42:39]: test run-unit-test: [----------------------- 146s FaSlice.pm 146s Vcf.pm 146s VcfStats.pm 146s fill-aa 146s fill-an-ac 146s fill-fs 146s fill-ref-md5 146s test.t 146s vcf-annotate 146s vcf-compare 146s vcf-concat 146s vcf-consensus 146s vcf-contrast 146s vcf-convert 146s vcf-fix-newlines 146s vcf-fix-ploidy 146s vcf-indel-stats 146s vcf-isec 146s vcf-merge 146s vcf-phased-join 146s vcf-query 146s vcf-shuffle-cols 146s vcf-sort 146s vcf-stats 146s vcf-subset 146s vcf-to-tab 146s vcf-tstv 146s vcf-validator 146s vcftools 146s 1..68 146s ok 1 - Is bgzip OK? .. cat /tmp/autopkgtest.ifgyvr/autopkgtest_tmp/testsuite/../testdata/merge-test-a.vcf | bgzip -c > /tmp/autopkgtest.ifgyvr/autopkgtest_tmp/testsuite/../testdata/merge-test-a.vcf.gz 146s ok 2 - Is tabix OK? .. tabix /tmp/autopkgtest.ifgyvr/autopkgtest_tmp/testsuite/../testdata/merge-test-a.vcf.gz 146s ok 3 - Testing validator .. perl -I/tmp/autopkgtest.ifgyvr/autopkgtest_tmp/testsuite -MVcf -e validate /tmp/autopkgtest.ifgyvr/autopkgtest_tmp/testsuite/../testdata/valid-3.3.vcf 147s ok 4 - Testing validator .. perl -I/tmp/autopkgtest.ifgyvr/autopkgtest_tmp/testsuite -MVcf -e validate /tmp/autopkgtest.ifgyvr/autopkgtest_tmp/testsuite/../testdata/valid-4.0.vcf 147s ok 5 - Testing validator .. perl -I/tmp/autopkgtest.ifgyvr/autopkgtest_tmp/testsuite -MVcf -e validate /tmp/autopkgtest.ifgyvr/autopkgtest_tmp/testsuite/../testdata/valid-4.1.vcf 147s ok 6 - Testing validator .. perl -I/tmp/autopkgtest.ifgyvr/autopkgtest_tmp/testsuite -MVcf -e validate /tmp/autopkgtest.ifgyvr/autopkgtest_tmp/testsuite/../testdata/floats.vcf 147s ok 7 - Testing formatting followed by validation .. perl -I/tmp/autopkgtest.ifgyvr/autopkgtest_tmp/testsuite -MVcf -e validate 2>&1 147s ok 8 - Testing formatting followed by validation .. perl -I/tmp/autopkgtest.ifgyvr/autopkgtest_tmp/testsuite -MVcf -e validate 2>&1 147s ok 9 - Testing formatting followed by validation .. perl -I/tmp/autopkgtest.ifgyvr/autopkgtest_tmp/testsuite -MVcf -e validate 2>&1 147s ok 10 - Testing next_data_array 147s ok 11 - Testing next_data_array 147s ok 12 - Testing next_data_array 147s ok 13 - Testing next_data_array 147s ok 14 - Testing add_columns with genotypes full, 4.0. 147s ok 15 - Testing add_columns with genotypes brief, 4.0. 147s ok 16 - Testing add_columns brief, 4.0. 147s ok 17 - Testing add_columns no gtypes, 4.0. 147s ok 18 - Testing vcf-isec .. perl -I../. -MVcf /usr/bin/vcf-isec -f -n +2 merge-test-a.vcf.gz merge-test-b.vcf.gz merge-test-c.vcf.gz 147s ok 19 - Testing vcf-query .. perl -I../. -MVcf /usr/bin/vcf-query -f '%CHROM:%POS\tref=%REF\talt=%ALT\tqual=%QUAL\t%INFO/DP[\t%SAMPLE=%GT]\n' cmp-test-a.vcf 147s ok 20 - Testing vcf-shuffle-cols .. perl -I../. -MVcf /usr/bin/vcf-shuffle-cols -t cmp-test-a.vcf shuffle-test.vcf 147s ok 21 - Testing vcf-concat .. perl -I../. -MVcf /usr/bin/vcf-concat -s 3 concat-a.vcf.gz concat-b.vcf.gz concat-c.vcf.gz 147s ok 22 - Testing fill-an-ac .. perl -I../. -MVcf /usr/bin/fill-an-ac concat-a.vcf 147s ok 23 - Testing fill-an-ac .. perl -I../. -MVcf /usr/bin/vcf-indel-stats -e indel-stats.tab < indel-stats.vcf 147s Looks as fasta file snippet, the sequence 1 starts at position 1 147s Looks as fasta file snippet, the sequence 2 starts at position 1 147s ok 24 - Testing vcf-consensus .. perl -I../. -MVcf /usr/bin/vcf-consensus consensus.vcf.gz < consensus.fa 147s Looks as fasta file snippet, the sequence 1 starts at position 1 147s Looks as fasta file snippet, the sequence 2 starts at position 1 147s ok 25 - Testing vcf-consensus .. perl -I../. -MVcf /usr/bin/vcf-consensus -s NA001 consensus.vcf.gz < consensus.fa 147s ok 26 - Testing vcf-fix-ploidy .. cat fix-ploidy.vcf | perl -I../. -MVcf /usr/bin/vcf-fix-ploidy -s fix-ploidy.samples -p fix-ploidy.txt 2>/dev/null | vcf-query -f '%POS[\t%SAMPLE %GTR %PL]\n' 147s ok 27 - Testing API event_type(A,C) .. s 1 C 147s ok 28 - Testing API event_type(A,ACGT) .. i 3 CGT 147s ok 29 - Testing API event_type(ACGT,A) .. i -3 CGT 147s ok 30 - Testing API event_type(ACGT,ACT) .. i -1 G 147s ok 31 - Testing API event_type(ACGT,AAA) .. o 3 AAA 147s ok 32 - Testing API event_type(A,.) .. r 0 A 147s ok 33 - Testing API event_type(A,) .. u 0 147s ok 34 - Testing API event_type(ACG,AGC) .. s 2 AGC 147s ok 35 - Testing API event_type(A,.A) .. b 147s ok 36 - Testing API event_type(A,A.) .. b 147s ok 37 - Testing get_tag_index(GT:GL:PL,'GT',':') 147s ok 38 - Testing get_tag_index(GT:GL:PL,'GL',':') 147s ok 39 - Testing get_tag_index(GT:GL:PL,'PL',':') 147s ok 40 - Testing get_tag_index(GT:GL:PL,0,':') 147s ok 41 - Testing get_tag_index(GT:GL:PL,1,':') 147s ok 42 - Testing get_tag_index(GT:GL:PL,2,':') 147s ok 43 - Testing get_tag_index(GT:GL:PL,'XX',0,':') 147s ok 44 - Testing get_tag_index(GT:GL:PL,'XX',1,':') 147s ok 45 - Testing get_tag_index(GT:GL:PL,'XX',2,':') 147s ok 46 - Testing get_tag_index(GT:GL:PL,'XX',4,':') 147s ok 47 - Testing decode_genotype('C',['G','T'],'0/1/2|1/0|1|2') 147s ok 48 - Testing decode_genotype('C',['G','T'],'2|1') 147s ok 49 - Testing decode_genotype('C',['G','T'],'2') 147s ok 50 - Testing get_info_field(NS=2;HM;AF=0.333;AFA=T;DB,'NS') 147s ok 51 - Testing get_info_field(NS=2;HM;AF=0.333;AFA=T;DB,'AF') 147s ok 52 - Testing get_info_field(NS=2;HM;AF=0.333;AFA=T;DB,'AFA') 147s ok 53 - Testing get_info_field(NS=2;HM;AF=0.333;AFA=T;DB,'HM') 147s ok 54 - Testing get_info_field(NS=2;HM;AF=0.333;AFA=T;DB,'DB') 147s ok 55 - Testing get_info_field(NS=2;HM;AF=0.333;AFA=T;DB,'DBX') 147s ok 56 - Testing get_info_field('DB','DB') 147s ok 57 - Testing get_info_field('XDB','DB') 147s ok 58 - Testing split_gt('0/1') 147s ok 59 - Testing split_gt('0') 147s ok 60 - Testing normalize_alleles(TTGGTAT,TTGGTATCTAGTGGTAT,TGGTATCTAGTGGTAT) 147s ok 61 - Testing normalize_alleles(TT,TCTAGTGGTAAT,TCT) 147s ok 62 - Testing normalize_alleles(TGGGGGG,TGGGGGGG) 147s ok 63 - Testing normalize_alleles(CAAAAAA,CAAAAA) 147s ok 64 - Testing normalize_alleles(CA,CT) 147s ok 65 - Testing normalize_alleles_pos(GAACCCACA,GA) 147s ok 66 - Testing normalize_alleles_pos(CAGTAAAA,CAGAAAA) 147s ok 67 - Testing normalize_alleles_pos(CAGTAAA,CAGAAAA) 147s ok 68 - Testing normalize_alleles_pos(GA,GACC) 147s PASS 147s autopkgtest [19:42:40]: test run-unit-test: -----------------------] 148s run-unit-test PASS 148s autopkgtest [19:42:41]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 148s autopkgtest [19:42:41]: @@@@@@@@@@@@@@@@@@@@ summary 148s run-unit-test PASS 166s nova [W] Using flock in prodstack6-s390x 166s flock: timeout while waiting to get lock 166s Creating nova instance adt-plucky-s390x-vcftools-20250315-194013-juju-7f2275-prod-proposed-migration-environment-2-93b07177-800a-4369-921d-eafd33ad8612 from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 166s nova [W] Timed out waiting for aafc7dfb-2da0-44b0-9190-1655d56b0d2b to get deleted.