0s autopkgtest [17:15:55]: starting date and time: 2024-03-16 17:15:55+0000 0s autopkgtest [17:15:55]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [17:15:55]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.3hen3_88/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:htslib,src:curl,src:gnutls28,src:libpsl,src:nettle,src:openssl --apt-upgrade vcftools --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=htslib/1.19+ds-1.1build2 curl/8.5.0-2ubuntu7 gnutls28/3.8.3-1.1ubuntu2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-7.secgroup --name adt-noble-arm64-vcftools-20240316-171555-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-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,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 110s autopkgtest [17:17:45]: testbed dpkg architecture: arm64 111s autopkgtest [17:17:46]: testbed apt version: 2.7.12 111s autopkgtest [17:17:46]: @@@@@@@@@@@@@@@@@@@@ test bed setup 111s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 112s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 112s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 112s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB] 112s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3673 kB] 112s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB] 112s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 112s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 112s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 112s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [3994 kB] 112s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 112s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.6 kB] 112s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 114s Fetched 9063 kB in 2s (4271 kB/s) 114s Reading package lists... 117s Reading package lists... 118s Building dependency tree... 118s Reading state information... 118s Calculating upgrade... 119s The following packages will be REMOVED: 119s libssl3 119s The following NEW packages will be installed: 119s libssl3t64 119s The following packages have been kept back: 119s curl 119s The following packages will be upgraded: 119s openssl ubuntu-minimal ubuntu-standard 119s 3 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 119s Need to get 2775 kB of archives. 119s After this operation, 72.7 kB of additional disk space will be used. 119s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 120s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 120s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.536 [10.7 kB] 120s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.536 [10.7 kB] 120s Fetched 2775 kB in 1s (4034 kB/s) 120s (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 ... 74758 files and directories currently installed.) 120s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 120s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 121s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 121s wget depends on libssl3 (>= 3.0.0). 121s u-boot-tools depends on libssl3 (>= 3.0.0). 121s tnftp depends on libssl3 (>= 3.0.0). 121s tcpdump depends on libssl3 (>= 3.0.0). 121s systemd-resolved depends on libssl3 (>= 3.0.0). 121s systemd depends on libssl3 (>= 3.0.0). 121s sudo depends on libssl3 (>= 3.0.0). 121s sbsigntool depends on libssl3 (>= 3.0.0). 121s rsync depends on libssl3 (>= 3.0.0). 121s python3-cryptography depends on libssl3 (>= 3.0.0). 121s openssh-server depends on libssl3 (>= 3.0.10). 121s openssh-client depends on libssl3 (>= 3.0.10). 121s mtd-utils depends on libssl3 (>= 3.0.0). 121s mokutil depends on libssl3 (>= 3.0.0). 121s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 121s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 121s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 121s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 121s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 121s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 121s libnvme1 depends on libssl3 (>= 3.0.0). 121s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 121s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 121s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 121s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 121s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 121s kmod depends on libssl3 (>= 3.0.0). 121s dhcpcd-base depends on libssl3 (>= 3.0.0). 121s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 121s 121s (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 ... 74758 files and directories currently installed.) 121s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 121s Selecting previously unselected package libssl3t64:arm64. 121s (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 ... 74747 files and directories currently installed.) 121s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 121s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 121s Preparing to unpack .../ubuntu-minimal_1.536_arm64.deb ... 121s Unpacking ubuntu-minimal (1.536) over (1.535) ... 121s Preparing to unpack .../ubuntu-standard_1.536_arm64.deb ... 121s Unpacking ubuntu-standard (1.536) over (1.535) ... 121s Setting up ubuntu-minimal (1.536) ... 121s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 121s Setting up ubuntu-standard (1.536) ... 121s Setting up openssl (3.0.13-0ubuntu1) ... 121s Processing triggers for man-db (2.12.0-3) ... 122s Processing triggers for libc-bin (2.39-0ubuntu2) ... 122s Reading package lists... 122s Building dependency tree... 122s Reading state information... 124s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 124s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 124s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 124s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 125s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 126s Reading package lists... 127s Reading package lists... 127s Building dependency tree... 127s Reading state information... 128s Calculating upgrade... 128s The following packages have been kept back: 128s curl 128s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 128s Reading package lists... 128s Building dependency tree... 128s Reading state information... 129s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 132s autopkgtest [17:18:07]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 133s autopkgtest [17:18:08]: @@@@@@@@@@@@@@@@@@@@ apt-source vcftools 134s Get:1 http://ftpmaster.internal/ubuntu noble/universe vcftools 0.1.16-3 (dsc) [2071 B] 134s Get:2 http://ftpmaster.internal/ubuntu noble/universe vcftools 0.1.16-3 (tar) [245 kB] 134s Get:3 http://ftpmaster.internal/ubuntu noble/universe vcftools 0.1.16-3 (diff) [14.0 kB] 135s gpgv: Signature made Thu Oct 7 06:07:18 2021 UTC 135s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 135s gpgv: issuer "tille@debian.org" 135s gpgv: Can't check signature: No public key 135s dpkg-source: warning: cannot verify inline signature for ./vcftools_0.1.16-3.dsc: no acceptable signature found 135s autopkgtest [17:18:10]: testing package vcftools version 0.1.16-3 135s autopkgtest [17:18:10]: build not needed 136s autopkgtest [17:18:11]: test run-unit-test: preparing testbed 137s Reading package lists... 137s Building dependency tree... 137s Reading state information... 138s Starting pkgProblemResolver with broken count: 0 138s Starting 2 pkgProblemResolver with broken count: 0 138s Done 138s The following additional packages will be installed: 138s libalgorithm-diff-perl libcapture-tiny-perl libclass-data-inheritable-perl 138s libdeflate0 libdevel-stacktrace-perl libexception-class-perl libhtscodecs2 138s libsub-uplevel-perl libtest-deep-perl libtest-differences-perl 138s libtest-exception-perl libtest-most-perl libtest-warn-perl libtext-diff-perl 138s tabix vcftools 139s Recommended packages: 139s libalgorithm-diff-xs-perl 139s The following NEW packages will be installed: 139s autopkgtest-satdep libalgorithm-diff-perl libcapture-tiny-perl 139s libclass-data-inheritable-perl libdeflate0 libdevel-stacktrace-perl 139s libexception-class-perl libhtscodecs2 libsub-uplevel-perl libtest-deep-perl 139s libtest-differences-perl libtest-exception-perl libtest-most-perl 139s libtest-warn-perl libtext-diff-perl tabix vcftools 139s 0 upgraded, 17 newly installed, 0 to remove and 1 not upgraded. 139s Need to get 1280 kB/1281 kB of archives. 139s After this operation, 4801 kB of additional disk space will be used. 139s Get:1 /tmp/autopkgtest.lsGDB0/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [724 B] 139s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libalgorithm-diff-perl all 1.201-1 [41.8 kB] 139s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libcapture-tiny-perl all 0.48-2 [20.2 kB] 139s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libclass-data-inheritable-perl all 0.08-3 [8084 B] 139s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 139s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libdevel-stacktrace-perl all 2.0500-1 [22.1 kB] 139s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libexception-class-perl all 1.45-1 [28.6 kB] 139s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 139s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 libsub-uplevel-perl all 0.2800-3 [11.6 kB] 139s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 libtest-deep-perl all 1.204-1 [47.1 kB] 139s Get:11 http://ftpmaster.internal/ubuntu noble/universe arm64 libtext-diff-perl all 1.45-2 [25.6 kB] 139s Get:12 http://ftpmaster.internal/ubuntu noble/universe arm64 libtest-differences-perl all 0.71-1 [15.8 kB] 139s Get:13 http://ftpmaster.internal/ubuntu noble/universe arm64 libtest-exception-perl all 0.43-3 [13.4 kB] 139s Get:14 http://ftpmaster.internal/ubuntu noble/universe arm64 libtest-warn-perl all 0.37-2 [12.6 kB] 139s Get:15 http://ftpmaster.internal/ubuntu noble/universe arm64 libtest-most-perl all 0.38-1 [21.5 kB] 139s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 tabix arm64 1.19+ds-1.1build2 [515 kB] 139s Get:17 http://ftpmaster.internal/ubuntu noble/universe arm64 vcftools arm64 0.1.16-3 [375 kB] 140s Fetched 1280 kB in 1s (1964 kB/s) 140s Selecting previously unselected package libalgorithm-diff-perl. 140s (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 ... 74760 files and directories currently installed.) 140s Preparing to unpack .../00-libalgorithm-diff-perl_1.201-1_all.deb ... 140s Unpacking libalgorithm-diff-perl (1.201-1) ... 140s Selecting previously unselected package libcapture-tiny-perl. 140s Preparing to unpack .../01-libcapture-tiny-perl_0.48-2_all.deb ... 140s Unpacking libcapture-tiny-perl (0.48-2) ... 140s Selecting previously unselected package libclass-data-inheritable-perl. 140s Preparing to unpack .../02-libclass-data-inheritable-perl_0.08-3_all.deb ... 140s Unpacking libclass-data-inheritable-perl (0.08-3) ... 140s Selecting previously unselected package libdeflate0:arm64. 140s Preparing to unpack .../03-libdeflate0_1.19-1_arm64.deb ... 140s Unpacking libdeflate0:arm64 (1.19-1) ... 140s Selecting previously unselected package libdevel-stacktrace-perl. 140s Preparing to unpack .../04-libdevel-stacktrace-perl_2.0500-1_all.deb ... 140s Unpacking libdevel-stacktrace-perl (2.0500-1) ... 140s Selecting previously unselected package libexception-class-perl. 140s Preparing to unpack .../05-libexception-class-perl_1.45-1_all.deb ... 140s Unpacking libexception-class-perl (1.45-1) ... 140s Selecting previously unselected package libhtscodecs2:arm64. 140s Preparing to unpack .../06-libhtscodecs2_1.6.0-1_arm64.deb ... 140s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 140s Selecting previously unselected package libsub-uplevel-perl. 140s Preparing to unpack .../07-libsub-uplevel-perl_0.2800-3_all.deb ... 140s Unpacking libsub-uplevel-perl (0.2800-3) ... 140s Selecting previously unselected package libtest-deep-perl. 140s Preparing to unpack .../08-libtest-deep-perl_1.204-1_all.deb ... 140s Unpacking libtest-deep-perl (1.204-1) ... 140s Selecting previously unselected package libtext-diff-perl. 140s Preparing to unpack .../09-libtext-diff-perl_1.45-2_all.deb ... 140s Unpacking libtext-diff-perl (1.45-2) ... 140s Selecting previously unselected package libtest-differences-perl. 140s Preparing to unpack .../10-libtest-differences-perl_0.71-1_all.deb ... 140s Unpacking libtest-differences-perl (0.71-1) ... 140s Selecting previously unselected package libtest-exception-perl. 140s Preparing to unpack .../11-libtest-exception-perl_0.43-3_all.deb ... 140s Unpacking libtest-exception-perl (0.43-3) ... 140s Selecting previously unselected package libtest-warn-perl. 140s Preparing to unpack .../12-libtest-warn-perl_0.37-2_all.deb ... 140s Unpacking libtest-warn-perl (0.37-2) ... 140s Selecting previously unselected package libtest-most-perl. 140s Preparing to unpack .../13-libtest-most-perl_0.38-1_all.deb ... 140s Unpacking libtest-most-perl (0.38-1) ... 140s Selecting previously unselected package tabix. 140s Preparing to unpack .../14-tabix_1.19+ds-1.1build2_arm64.deb ... 140s Unpacking tabix (1.19+ds-1.1build2) ... 140s Selecting previously unselected package vcftools. 140s Preparing to unpack .../15-vcftools_0.1.16-3_arm64.deb ... 140s Unpacking vcftools (0.1.16-3) ... 140s Selecting previously unselected package autopkgtest-satdep. 140s Preparing to unpack .../16-1-autopkgtest-satdep.deb ... 140s Unpacking autopkgtest-satdep (0) ... 140s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 140s Setting up vcftools (0.1.16-3) ... 140s Setting up libtest-deep-perl (1.204-1) ... 140s Setting up libalgorithm-diff-perl (1.201-1) ... 140s Setting up libdeflate0:arm64 (1.19-1) ... 140s Setting up libclass-data-inheritable-perl (0.08-3) ... 140s Setting up libtext-diff-perl (1.45-2) ... 140s Setting up libcapture-tiny-perl (0.48-2) ... 140s Setting up libsub-uplevel-perl (0.2800-3) ... 140s Setting up libdevel-stacktrace-perl (2.0500-1) ... 140s Setting up tabix (1.19+ds-1.1build2) ... 140s Setting up libtest-warn-perl (0.37-2) ... 140s Setting up libtest-differences-perl (0.71-1) ... 140s Setting up libexception-class-perl (1.45-1) ... 140s Setting up libtest-exception-perl (0.43-3) ... 140s Setting up libtest-most-perl (0.38-1) ... 140s Setting up autopkgtest-satdep (0) ... 140s Processing triggers for man-db (2.12.0-3) ... 141s Processing triggers for libc-bin (2.39-0ubuntu2) ... 144s (Reading database ... 75040 files and directories currently installed.) 144s Removing autopkgtest-satdep (0) ... 145s autopkgtest [17:18:20]: test run-unit-test: [----------------------- 145s FaSlice.pm 145s Vcf.pm 145s VcfStats.pm 145s fill-aa 145s fill-an-ac 145s fill-fs 145s fill-ref-md5 145s test.t 145s vcf-annotate 145s vcf-compare 145s vcf-concat 145s vcf-consensus 145s vcf-contrast 145s vcf-convert 145s vcf-fix-newlines 145s vcf-fix-ploidy 145s vcf-indel-stats 145s vcf-isec 145s vcf-merge 145s vcf-phased-join 145s vcf-query 145s vcf-shuffle-cols 145s vcf-sort 145s vcf-stats 145s vcf-subset 145s vcf-to-tab 145s vcf-tstv 145s vcf-validator 145s vcftools 145s 1..68 145s ok 1 - Is bgzip OK? .. cat /tmp/autopkgtest.lsGDB0/autopkgtest_tmp/testsuite/../testdata/merge-test-a.vcf | bgzip -c > /tmp/autopkgtest.lsGDB0/autopkgtest_tmp/testsuite/../testdata/merge-test-a.vcf.gz 145s ok 2 - Is tabix OK? .. tabix /tmp/autopkgtest.lsGDB0/autopkgtest_tmp/testsuite/../testdata/merge-test-a.vcf.gz 145s ok 3 - Testing validator .. perl -I/tmp/autopkgtest.lsGDB0/autopkgtest_tmp/testsuite -MVcf -e validate /tmp/autopkgtest.lsGDB0/autopkgtest_tmp/testsuite/../testdata/valid-3.3.vcf 145s ok 4 - Testing validator .. perl -I/tmp/autopkgtest.lsGDB0/autopkgtest_tmp/testsuite -MVcf -e validate /tmp/autopkgtest.lsGDB0/autopkgtest_tmp/testsuite/../testdata/valid-4.0.vcf 145s ok 5 - Testing validator .. perl -I/tmp/autopkgtest.lsGDB0/autopkgtest_tmp/testsuite -MVcf -e validate /tmp/autopkgtest.lsGDB0/autopkgtest_tmp/testsuite/../testdata/valid-4.1.vcf 145s ok 6 - Testing validator .. perl -I/tmp/autopkgtest.lsGDB0/autopkgtest_tmp/testsuite -MVcf -e validate /tmp/autopkgtest.lsGDB0/autopkgtest_tmp/testsuite/../testdata/floats.vcf 145s ok 7 - Testing formatting followed by validation .. perl -I/tmp/autopkgtest.lsGDB0/autopkgtest_tmp/testsuite -MVcf -e validate 2>&1 145s ok 8 - Testing formatting followed by validation .. perl -I/tmp/autopkgtest.lsGDB0/autopkgtest_tmp/testsuite -MVcf -e validate 2>&1 145s ok 9 - Testing formatting followed by validation .. perl -I/tmp/autopkgtest.lsGDB0/autopkgtest_tmp/testsuite -MVcf -e validate 2>&1 145s ok 10 - Testing next_data_array 145s ok 11 - Testing next_data_array 145s ok 12 - Testing next_data_array 145s ok 13 - Testing next_data_array 145s ok 14 - Testing add_columns with genotypes full, 4.0. 145s ok 15 - Testing add_columns with genotypes brief, 4.0. 145s ok 16 - Testing add_columns brief, 4.0. 145s ok 17 - Testing add_columns no gtypes, 4.0. 146s 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 146s 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 146s ok 20 - Testing vcf-shuffle-cols .. perl -I../. -MVcf /usr/bin/vcf-shuffle-cols -t cmp-test-a.vcf shuffle-test.vcf 146s 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 146s ok 22 - Testing fill-an-ac .. perl -I../. -MVcf /usr/bin/fill-an-ac concat-a.vcf 146s ok 23 - Testing fill-an-ac .. perl -I../. -MVcf /usr/bin/vcf-indel-stats -e indel-stats.tab < indel-stats.vcf 146s Looks as fasta file snippet, the sequence 1 starts at position 1 146s Looks as fasta file snippet, the sequence 2 starts at position 1 146s ok 24 - Testing vcf-consensus .. perl -I../. -MVcf /usr/bin/vcf-consensus consensus.vcf.gz < consensus.fa 146s Looks as fasta file snippet, the sequence 1 starts at position 1 146s Looks as fasta file snippet, the sequence 2 starts at position 1 146s ok 25 - Testing vcf-consensus .. perl -I../. -MVcf /usr/bin/vcf-consensus -s NA001 consensus.vcf.gz < consensus.fa 146s 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' 146s ok 27 - Testing API event_type(A,C) .. s 1 C 146s ok 28 - Testing API event_type(A,ACGT) .. i 3 CGT 146s ok 29 - Testing API event_type(ACGT,A) .. i -3 CGT 146s ok 30 - Testing API event_type(ACGT,ACT) .. i -1 G 146s ok 31 - Testing API event_type(ACGT,AAA) .. o 3 AAA 146s ok 32 - Testing API event_type(A,.) .. r 0 A 146s ok 33 - Testing API event_type(A,) .. u 0 146s ok 34 - Testing API event_type(ACG,AGC) .. s 2 AGC 146s ok 35 - Testing API event_type(A,.A) .. b 146s ok 36 - Testing API event_type(A,A.) .. b 146s ok 37 - Testing get_tag_index(GT:GL:PL,'GT',':') 146s ok 38 - Testing get_tag_index(GT:GL:PL,'GL',':') 146s ok 39 - Testing get_tag_index(GT:GL:PL,'PL',':') 146s ok 40 - Testing get_tag_index(GT:GL:PL,0,':') 146s ok 41 - Testing get_tag_index(GT:GL:PL,1,':') 146s ok 42 - Testing get_tag_index(GT:GL:PL,2,':') 146s ok 43 - Testing get_tag_index(GT:GL:PL,'XX',0,':') 146s ok 44 - Testing get_tag_index(GT:GL:PL,'XX',1,':') 146s ok 45 - Testing get_tag_index(GT:GL:PL,'XX',2,':') 146s ok 46 - Testing get_tag_index(GT:GL:PL,'XX',4,':') 146s ok 47 - Testing decode_genotype('C',['G','T'],'0/1/2|1/0|1|2') 146s ok 48 - Testing decode_genotype('C',['G','T'],'2|1') 146s ok 49 - Testing decode_genotype('C',['G','T'],'2') 146s ok 50 - Testing get_info_field(NS=2;HM;AF=0.333;AFA=T;DB,'NS') 146s ok 51 - Testing get_info_field(NS=2;HM;AF=0.333;AFA=T;DB,'AF') 146s ok 52 - Testing get_info_field(NS=2;HM;AF=0.333;AFA=T;DB,'AFA') 146s ok 53 - Testing get_info_field(NS=2;HM;AF=0.333;AFA=T;DB,'HM') 146s ok 54 - Testing get_info_field(NS=2;HM;AF=0.333;AFA=T;DB,'DB') 146s ok 55 - Testing get_info_field(NS=2;HM;AF=0.333;AFA=T;DB,'DBX') 146s ok 56 - Testing get_info_field('DB','DB') 146s ok 57 - Testing get_info_field('XDB','DB') 146s ok 58 - Testing split_gt('0/1') 146s ok 59 - Testing split_gt('0') 146s ok 60 - Testing normalize_alleles(TTGGTAT,TTGGTATCTAGTGGTAT,TGGTATCTAGTGGTAT) 146s ok 61 - Testing normalize_alleles(TT,TCTAGTGGTAAT,TCT) 146s ok 62 - Testing normalize_alleles(TGGGGGG,TGGGGGGG) 146s ok 63 - Testing normalize_alleles(CAAAAAA,CAAAAA) 146s ok 64 - Testing normalize_alleles(CA,CT) 146s ok 65 - Testing normalize_alleles_pos(GAACCCACA,GA) 146s ok 66 - Testing normalize_alleles_pos(CAGTAAAA,CAGAAAA) 146s ok 67 - Testing normalize_alleles_pos(CAGTAAA,CAGAAAA) 146s ok 68 - Testing normalize_alleles_pos(GA,GACC) 146s PASS 146s autopkgtest [17:18:21]: test run-unit-test: -----------------------] 147s run-unit-test PASS 147s autopkgtest [17:18:22]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 147s autopkgtest [17:18:22]: @@@@@@@@@@@@@@@@@@@@ summary 147s run-unit-test PASS 165s Creating nova instance adt-noble-arm64-vcftools-20240316-171555-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240314.img (UUID 7faf5f09-d335-4346-a441-4eab2f9c04fe)...