0s autopkgtest [15:57:16]: starting date and time: 2025-03-15 15:57:16+0000 0s autopkgtest [15:57:16]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [15:57:16]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.dwp80byp/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:glibc --apt-upgrade vcftools --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- lxd -r lxd-armhf-10.145.243.227 lxd-armhf-10.145.243.227:autopkgtest/ubuntu/plucky/armhf 20s autopkgtest [15:57:36]: testbed dpkg architecture: armhf 22s autopkgtest [15:57:38]: testbed apt version: 2.9.33 26s autopkgtest [15:57:42]: @@@@@@@@@@@@@@@@@@@@ test bed setup 28s autopkgtest [15:57:44]: testbed release detected to be: None 35s autopkgtest [15:57:51]: updating testbed package index (apt update) 37s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 38s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 38s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 38s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 38s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 38s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 38s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 39s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [114 kB] 39s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1832 B] 39s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 39s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [312 kB] 39s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [11.1 kB] 39s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 39s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [240 B] 39s Get:15 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 61s Get:16 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 62s Get:17 http://ftpmaster.internal/ubuntu plucky/main Sources [1394 kB] 63s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 65s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 65s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 65s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 81s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 83s Fetched 41.0 MB in 45s (903 kB/s) 85s Reading package lists... 90s autopkgtest [15:58:46]: upgrading testbed (apt dist-upgrade and autopurge) 92s Reading package lists... 92s Building dependency tree... 92s Reading state information... 93s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 93s Starting 2 pkgProblemResolver with broken count: 0 93s Done 94s Entering ResolveByKeep 94s 94s Calculating upgrade... 95s The following packages will be upgraded: 95s libc-bin libc6 locales pinentry-curses python3-jinja2 sos strace 95s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 95s Need to get 8683 kB of archives. 95s After this operation, 23.6 kB of additional disk space will be used. 95s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 100s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 100s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 106s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 107s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf pinentry-curses armhf 1.3.1-2ubuntu3 [40.6 kB] 107s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 107s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 108s Preconfiguring packages ... 109s Fetched 8683 kB in 13s (672 kB/s) 109s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 64655 files and directories currently installed.) 109s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 109s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 109s Setting up libc6:armhf (2.41-1ubuntu2) ... 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 ... 64655 files and directories currently installed.) 110s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 110s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 110s Setting up libc-bin (2.41-1ubuntu2) ... 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 ... 64655 files and directories currently installed.) 110s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 110s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 111s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 111s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 111s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_armhf.deb ... 111s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 111s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 111s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 111s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 111s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 111s Setting up sos (4.9.0-5) ... 112s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 112s Setting up locales (2.41-1ubuntu2) ... 113s Generating locales (this might take a while)... 115s en_US.UTF-8... done 115s Generation complete. 115s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 115s Setting up strace (6.13+ds-1ubuntu1) ... 115s Processing triggers for man-db (2.13.0-1) ... 116s 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 120s Starting 2 pkgProblemResolver with broken count: 0 120s Done 120s Solving dependencies... 120s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 122s autopkgtest [15:59:18]: rebooting testbed after setup commands that affected boot 163s autopkgtest [15:59:59]: testbed running kernel: Linux 6.8.0-52-generic #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 18:10:51 UTC 2 188s autopkgtest [16:00:24]: @@@@@@@@@@@@@@@@@@@@ apt-source vcftools 199s Get:1 http://ftpmaster.internal/ubuntu plucky/universe vcftools 0.1.16-3 (dsc) [2071 B] 199s Get:2 http://ftpmaster.internal/ubuntu plucky/universe vcftools 0.1.16-3 (tar) [245 kB] 199s Get:3 http://ftpmaster.internal/ubuntu plucky/universe vcftools 0.1.16-3 (diff) [14.0 kB] 199s gpgv: Signature made Thu Oct 7 06:07:18 2021 UTC 199s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 199s gpgv: issuer "tille@debian.org" 199s gpgv: Can't check signature: No public key 199s dpkg-source: warning: cannot verify inline signature for ./vcftools_0.1.16-3.dsc: no acceptable signature found 199s autopkgtest [16:00:35]: testing package vcftools version 0.1.16-3 201s autopkgtest [16:00:37]: build not needed 203s autopkgtest [16:00:39]: test run-unit-test: preparing testbed 205s Reading package lists... 206s Building dependency tree... 206s Reading state information... 207s Starting pkgProblemResolver with broken count: 0 207s Starting 2 pkgProblemResolver with broken count: 0 207s Done 209s The following NEW packages will be installed: 209s libalgorithm-diff-perl libcapture-tiny-perl libclass-data-inheritable-perl 209s libdeflate0 libdevel-stacktrace-perl libexception-class-perl libhtscodecs2 209s libsub-uplevel-perl libtest-deep-perl libtest-differences-perl 209s libtest-exception-perl libtest-most-perl libtest-warn-perl libtext-diff-perl 209s tabix vcftools 209s 0 upgraded, 16 newly installed, 0 to remove and 0 not upgraded. 209s Need to get 1236 kB of archives. 209s After this operation, 4008 kB of additional disk space will be used. 209s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf libalgorithm-diff-perl all 1.201-1 [41.8 kB] 210s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libcapture-tiny-perl all 0.50-1 [20.7 kB] 210s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf libclass-data-inheritable-perl all 0.10-1 [8038 B] 210s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.23-1 [38.5 kB] 210s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf libdevel-stacktrace-perl all 2.0500-1 [22.1 kB] 210s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf libexception-class-perl all 1.45-1 [28.6 kB] 210s Get:7 http://ftpmaster.internal/ubuntu plucky/universe armhf libhtscodecs2 armhf 1.6.1-2 [67.5 kB] 210s Get:8 http://ftpmaster.internal/ubuntu plucky/universe armhf libsub-uplevel-perl all 0.2800-3 [11.6 kB] 210s Get:9 http://ftpmaster.internal/ubuntu plucky/universe armhf libtest-deep-perl all 1.204-1 [47.1 kB] 210s Get:10 http://ftpmaster.internal/ubuntu plucky/universe armhf libtext-diff-perl all 1.45-2 [25.6 kB] 210s Get:11 http://ftpmaster.internal/ubuntu plucky/universe armhf libtest-differences-perl all 0.71-1 [15.8 kB] 210s Get:12 http://ftpmaster.internal/ubuntu plucky/universe armhf libtest-exception-perl all 0.43-3 [13.4 kB] 210s Get:13 http://ftpmaster.internal/ubuntu plucky/universe armhf libtest-warn-perl all 0.37-2 [12.6 kB] 210s Get:14 http://ftpmaster.internal/ubuntu plucky/universe armhf libtest-most-perl all 0.38-1 [21.5 kB] 210s Get:15 http://ftpmaster.internal/ubuntu plucky/universe armhf tabix armhf 1.21+ds-1 [433 kB] 210s Get:16 http://ftpmaster.internal/ubuntu plucky/universe armhf vcftools armhf 0.1.16-3 [428 kB] 211s Fetched 1236 kB in 2s (736 kB/s) 211s Selecting previously unselected package libalgorithm-diff-perl. 211s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 64655 files and directories currently installed.) 211s Preparing to unpack .../00-libalgorithm-diff-perl_1.201-1_all.deb ... 211s Unpacking libalgorithm-diff-perl (1.201-1) ... 211s Selecting previously unselected package libcapture-tiny-perl. 212s Preparing to unpack .../01-libcapture-tiny-perl_0.50-1_all.deb ... 212s Unpacking libcapture-tiny-perl (0.50-1) ... 212s Selecting previously unselected package libclass-data-inheritable-perl. 212s Preparing to unpack .../02-libclass-data-inheritable-perl_0.10-1_all.deb ... 212s Unpacking libclass-data-inheritable-perl (0.10-1) ... 212s Selecting previously unselected package libdeflate0:armhf. 212s Preparing to unpack .../03-libdeflate0_1.23-1_armhf.deb ... 212s Unpacking libdeflate0:armhf (1.23-1) ... 212s Selecting previously unselected package libdevel-stacktrace-perl. 212s Preparing to unpack .../04-libdevel-stacktrace-perl_2.0500-1_all.deb ... 212s Unpacking libdevel-stacktrace-perl (2.0500-1) ... 212s Selecting previously unselected package libexception-class-perl. 212s Preparing to unpack .../05-libexception-class-perl_1.45-1_all.deb ... 212s Unpacking libexception-class-perl (1.45-1) ... 212s Selecting previously unselected package libhtscodecs2:armhf. 212s Preparing to unpack .../06-libhtscodecs2_1.6.1-2_armhf.deb ... 212s Unpacking libhtscodecs2:armhf (1.6.1-2) ... 212s Selecting previously unselected package libsub-uplevel-perl. 212s Preparing to unpack .../07-libsub-uplevel-perl_0.2800-3_all.deb ... 212s Unpacking libsub-uplevel-perl (0.2800-3) ... 212s Selecting previously unselected package libtest-deep-perl. 212s Preparing to unpack .../08-libtest-deep-perl_1.204-1_all.deb ... 212s Unpacking libtest-deep-perl (1.204-1) ... 212s Selecting previously unselected package libtext-diff-perl. 212s Preparing to unpack .../09-libtext-diff-perl_1.45-2_all.deb ... 212s Unpacking libtext-diff-perl (1.45-2) ... 212s Selecting previously unselected package libtest-differences-perl. 212s Preparing to unpack .../10-libtest-differences-perl_0.71-1_all.deb ... 212s Unpacking libtest-differences-perl (0.71-1) ... 212s Selecting previously unselected package libtest-exception-perl. 212s Preparing to unpack .../11-libtest-exception-perl_0.43-3_all.deb ... 212s Unpacking libtest-exception-perl (0.43-3) ... 212s Selecting previously unselected package libtest-warn-perl. 212s Preparing to unpack .../12-libtest-warn-perl_0.37-2_all.deb ... 212s Unpacking libtest-warn-perl (0.37-2) ... 212s Selecting previously unselected package libtest-most-perl. 212s Preparing to unpack .../13-libtest-most-perl_0.38-1_all.deb ... 212s Unpacking libtest-most-perl (0.38-1) ... 212s Selecting previously unselected package tabix. 212s Preparing to unpack .../14-tabix_1.21+ds-1_armhf.deb ... 212s Unpacking tabix (1.21+ds-1) ... 212s Selecting previously unselected package vcftools. 212s Preparing to unpack .../15-vcftools_0.1.16-3_armhf.deb ... 212s Unpacking vcftools (0.1.16-3) ... 212s Setting up libhtscodecs2:armhf (1.6.1-2) ... 212s Setting up vcftools (0.1.16-3) ... 212s Setting up libtest-deep-perl (1.204-1) ... 212s Setting up libalgorithm-diff-perl (1.201-1) ... 212s Setting up libdeflate0:armhf (1.23-1) ... 212s Setting up libclass-data-inheritable-perl (0.10-1) ... 212s Setting up libtext-diff-perl (1.45-2) ... 212s Setting up libcapture-tiny-perl (0.50-1) ... 212s Setting up libsub-uplevel-perl (0.2800-3) ... 212s Setting up libdevel-stacktrace-perl (2.0500-1) ... 212s Setting up tabix (1.21+ds-1) ... 212s Setting up libtest-warn-perl (0.37-2) ... 212s Setting up libtest-differences-perl (0.71-1) ... 212s Setting up libexception-class-perl (1.45-1) ... 212s Setting up libtest-exception-perl (0.43-3) ... 212s Setting up libtest-most-perl (0.38-1) ... 212s Processing triggers for man-db (2.13.0-1) ... 213s Processing triggers for libc-bin (2.41-1ubuntu2) ... 221s autopkgtest [16:00:57]: test run-unit-test: [----------------------- 223s FaSlice.pm 223s Vcf.pm 223s VcfStats.pm 223s fill-aa 223s fill-an-ac 223s fill-fs 223s fill-ref-md5 223s test.t 223s vcf-annotate 223s vcf-compare 223s vcf-concat 223s vcf-consensus 223s vcf-contrast 223s vcf-convert 223s vcf-fix-newlines 223s vcf-fix-ploidy 223s vcf-indel-stats 223s vcf-isec 223s vcf-merge 223s vcf-phased-join 223s vcf-query 223s vcf-shuffle-cols 223s vcf-sort 223s vcf-stats 223s vcf-subset 223s vcf-to-tab 223s vcf-tstv 223s vcf-validator 223s vcftools 223s 1..68 223s ok 1 - Is bgzip OK? .. cat /tmp/autopkgtest.irGshQ/autopkgtest_tmp/testsuite/../testdata/merge-test-a.vcf | bgzip -c > /tmp/autopkgtest.irGshQ/autopkgtest_tmp/testsuite/../testdata/merge-test-a.vcf.gz 223s ok 2 - Is tabix OK? .. tabix /tmp/autopkgtest.irGshQ/autopkgtest_tmp/testsuite/../testdata/merge-test-a.vcf.gz 223s ok 3 - Testing validator .. perl -I/tmp/autopkgtest.irGshQ/autopkgtest_tmp/testsuite -MVcf -e validate /tmp/autopkgtest.irGshQ/autopkgtest_tmp/testsuite/../testdata/valid-3.3.vcf 223s ok 4 - Testing validator .. perl -I/tmp/autopkgtest.irGshQ/autopkgtest_tmp/testsuite -MVcf -e validate /tmp/autopkgtest.irGshQ/autopkgtest_tmp/testsuite/../testdata/valid-4.0.vcf 224s ok 5 - Testing validator .. perl -I/tmp/autopkgtest.irGshQ/autopkgtest_tmp/testsuite -MVcf -e validate /tmp/autopkgtest.irGshQ/autopkgtest_tmp/testsuite/../testdata/valid-4.1.vcf 224s ok 6 - Testing validator .. perl -I/tmp/autopkgtest.irGshQ/autopkgtest_tmp/testsuite -MVcf -e validate /tmp/autopkgtest.irGshQ/autopkgtest_tmp/testsuite/../testdata/floats.vcf 224s ok 7 - Testing formatting followed by validation .. perl -I/tmp/autopkgtest.irGshQ/autopkgtest_tmp/testsuite -MVcf -e validate 2>&1 224s ok 8 - Testing formatting followed by validation .. perl -I/tmp/autopkgtest.irGshQ/autopkgtest_tmp/testsuite -MVcf -e validate 2>&1 224s ok 9 - Testing formatting followed by validation .. perl -I/tmp/autopkgtest.irGshQ/autopkgtest_tmp/testsuite -MVcf -e validate 2>&1 224s ok 10 - Testing next_data_array 224s ok 11 - Testing next_data_array 224s ok 12 - Testing next_data_array 224s ok 13 - Testing next_data_array 224s ok 14 - Testing add_columns with genotypes full, 4.0. 224s ok 15 - Testing add_columns with genotypes brief, 4.0. 224s ok 16 - Testing add_columns brief, 4.0. 224s ok 17 - Testing add_columns no gtypes, 4.0. 224s 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 224s 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 224s ok 20 - Testing vcf-shuffle-cols .. perl -I../. -MVcf /usr/bin/vcf-shuffle-cols -t cmp-test-a.vcf shuffle-test.vcf 224s 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 224s ok 22 - Testing fill-an-ac .. perl -I../. -MVcf /usr/bin/fill-an-ac concat-a.vcf 224s ok 23 - Testing fill-an-ac .. perl -I../. -MVcf /usr/bin/vcf-indel-stats -e indel-stats.tab < indel-stats.vcf 224s Looks as fasta file snippet, the sequence 1 starts at position 1 224s Looks as fasta file snippet, the sequence 2 starts at position 1 224s ok 24 - Testing vcf-consensus .. perl -I../. -MVcf /usr/bin/vcf-consensus consensus.vcf.gz < consensus.fa 224s Looks as fasta file snippet, the sequence 1 starts at position 1 224s Looks as fasta file snippet, the sequence 2 starts at position 1 224s ok 25 - Testing vcf-consensus .. perl -I../. -MVcf /usr/bin/vcf-consensus -s NA001 consensus.vcf.gz < consensus.fa 224s 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' 224s ok 27 - Testing API event_type(A,C) .. s 1 C 224s ok 28 - Testing API event_type(A,ACGT) .. i 3 CGT 224s ok 29 - Testing API event_type(ACGT,A) .. i -3 CGT 224s ok 30 - Testing API event_type(ACGT,ACT) .. i -1 G 224s ok 31 - Testing API event_type(ACGT,AAA) .. o 3 AAA 224s ok 32 - Testing API event_type(A,.) .. r 0 A 224s ok 33 - Testing API event_type(A,) .. u 0 224s ok 34 - Testing API event_type(ACG,AGC) .. s 2 AGC 224s ok 35 - Testing API event_type(A,.A) .. b 224s ok 36 - Testing API event_type(A,A.) .. b 224s ok 37 - Testing get_tag_index(GT:GL:PL,'GT',':') 224s ok 38 - Testing get_tag_index(GT:GL:PL,'GL',':') 224s ok 39 - Testing get_tag_index(GT:GL:PL,'PL',':') 224s ok 40 - Testing get_tag_index(GT:GL:PL,0,':') 224s ok 41 - Testing get_tag_index(GT:GL:PL,1,':') 224s ok 42 - Testing get_tag_index(GT:GL:PL,2,':') 224s ok 43 - Testing get_tag_index(GT:GL:PL,'XX',0,':') 224s ok 44 - Testing get_tag_index(GT:GL:PL,'XX',1,':') 224s ok 45 - Testing get_tag_index(GT:GL:PL,'XX',2,':') 224s ok 46 - Testing get_tag_index(GT:GL:PL,'XX',4,':') 224s ok 47 - Testing decode_genotype('C',['G','T'],'0/1/2|1/0|1|2') 224s ok 48 - Testing decode_genotype('C',['G','T'],'2|1') 224s ok 49 - Testing decode_genotype('C',['G','T'],'2') 224s ok 50 - Testing get_info_field(NS=2;HM;AF=0.333;AFA=T;DB,'NS') 224s ok 51 - Testing get_info_field(NS=2;HM;AF=0.333;AFA=T;DB,'AF') 224s ok 52 - Testing get_info_field(NS=2;HM;AF=0.333;AFA=T;DB,'AFA') 224s ok 53 - Testing get_info_field(NS=2;HM;AF=0.333;AFA=T;DB,'HM') 224s ok 54 - Testing get_info_field(NS=2;HM;AF=0.333;AFA=T;DB,'DB') 224s ok 55 - Testing get_info_field(NS=2;HM;AF=0.333;AFA=T;DB,'DBX') 224s ok 56 - Testing get_info_field('DB','DB') 224s ok 57 - Testing get_info_field('XDB','DB') 224s ok 58 - Testing split_gt('0/1') 224s ok 59 - Testing split_gt('0') 224s ok 60 - Testing normalize_alleles(TTGGTAT,TTGGTATCTAGTGGTAT,TGGTATCTAGTGGTAT) 224s ok 61 - Testing normalize_alleles(TT,TCTAGTGGTAAT,TCT) 224s ok 62 - Testing normalize_alleles(TGGGGGG,TGGGGGGG) 224s ok 63 - Testing normalize_alleles(CAAAAAA,CAAAAA) 225s ok 64 - Testing normalize_alleles(CA,CT) 225s ok 65 - Testing normalize_alleles_pos(GAACCCACA,GA) 225s ok 66 - Testing normalize_alleles_pos(CAGTAAAA,CAGAAAA) 225s ok 67 - Testing normalize_alleles_pos(CAGTAAA,CAGAAAA) 225s ok 68 - Testing normalize_alleles_pos(GA,GACC) 225s PASS 225s autopkgtest [16:01:01]: test run-unit-test: -----------------------] 229s run-unit-test PASS 229s autopkgtest [16:01:05]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 233s autopkgtest [16:01:09]: @@@@@@@@@@@@@@@@@@@@ summary 233s run-unit-test PASS