0s autopkgtest [19:34:26]: starting date and time: 2025-03-15 19:34:26+0000 0s autopkgtest [19:34:26]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [19:34:26]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.uy5lbq1a/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade tvc --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-11.secgroup --name adt-plucky-s390x-tvc-20250315-193426-juju-7f2275-prod-proposed-migration-environment-2-351dd80e-7fcb-4dc3-b6ab-415ec22c3235 --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/ 121s autopkgtest [19:36:27]: testbed dpkg architecture: s390x 121s autopkgtest [19:36:27]: testbed apt version: 2.9.33 122s autopkgtest [19:36:28]: @@@@@@@@@@@@@@@@@@@@ test bed setup 122s autopkgtest [19:36:28]: testbed release detected to be: None 123s autopkgtest [19:36:29]: updating testbed package index (apt update) 123s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 123s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 123s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 123s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 123s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.5 kB] 123s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [369 kB] 124s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [45.1 kB] 124s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [77.3 kB] 124s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1824 B] 124s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 124s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [314 kB] 124s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [13.3 kB] 124s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3532 B] 124s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [240 B] 124s Fetched 965 kB in 1s (1136 kB/s) 124s Reading package lists... 125s Reading package lists... 125s Building dependency tree... 125s Reading state information... 125s Calculating upgrade... 125s Calculating upgrade... 125s The following packages were automatically installed and are no longer required: 125s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 125s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 125s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 125s linux-tools-6.11.0-8-generic 125s Use 'sudo apt autoremove' to remove them. 125s The following packages will be upgraded: 125s pinentry-curses python3-jinja2 strace 126s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 126s Need to get 652 kB of archives. 126s After this operation, 27.6 kB of additional disk space will be used. 126s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB] 126s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pinentry-curses s390x 1.3.1-2ubuntu3 [42.9 kB] 126s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 126s Fetched 652 kB in 1s (1111 kB/s) 126s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81428 files and directories currently installed.) 126s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ... 126s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 126s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_s390x.deb ... 126s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 126s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 127s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 127s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 127s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 127s Setting up strace (6.13+ds-1ubuntu1) ... 127s Processing triggers for man-db (2.13.0-1) ... 127s Reading package lists... 127s Building dependency tree... 127s Reading state information... 127s Solving dependencies... 128s The following packages will be REMOVED: 128s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 128s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 128s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 128s linux-tools-6.11.0-8-generic* 128s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded. 128s After this operation, 167 MB disk space will be freed. 128s (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.) 128s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 128s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 128s Removing libpython3.12t64:s390x (3.12.9-1) ... 128s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 128s Removing libnsl2:s390x (1.3.0-3build3) ... 128s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 128s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 128s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 129s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 129s Processing triggers for libc-bin (2.41-1ubuntu1) ... 129s (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.) 129s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 129s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 129s autopkgtest [19:36:35]: upgrading testbed (apt dist-upgrade and autopurge) 129s Reading package lists... 129s Building dependency tree... 129s Reading state information... 130s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 130s Starting 2 pkgProblemResolver with broken count: 0 130s Done 130s Entering ResolveByKeep 130s 130s Calculating upgrade... 130s The following packages will be upgraded: 130s libc-bin libc-dev-bin libc6 libc6-dev locales 130s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 130s Need to get 9512 kB of archives. 130s After this operation, 8192 B of additional disk space will be used. 130s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB] 131s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB] 131s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB] 131s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB] 131s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB] 131s Preconfiguring packages ... 131s Fetched 9512 kB in 1s (8143 kB/s) 131s (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.) 131s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ... 131s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 132s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ... 132s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 132s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ... 132s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 132s Setting up libc6:s390x (2.41-1ubuntu2) ... 132s (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.) 132s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ... 132s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 132s Setting up libc-bin (2.41-1ubuntu2) ... 132s (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.) 132s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 132s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 132s Setting up locales (2.41-1ubuntu2) ... 132s Generating locales (this might take a while)... 133s en_US.UTF-8... done 133s Generation complete. 133s Setting up libc-dev-bin (2.41-1ubuntu2) ... 133s Setting up libc6-dev:s390x (2.41-1ubuntu2) ... 133s Processing triggers for man-db (2.13.0-1) ... 134s Processing triggers for systemd (257.3-1ubuntu3) ... 135s Reading package lists... 135s Building dependency tree... 135s Reading state information... 135s Starting pkgProblemResolver with broken count: 0 135s Starting 2 pkgProblemResolver with broken count: 0 135s Done 135s Solving dependencies... 135s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 136s autopkgtest [19:36:42]: rebooting testbed after setup commands that affected boot 154s autopkgtest [19:37:00]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025 157s autopkgtest [19:37:03]: @@@@@@@@@@@@@@@@@@@@ apt-source tvc 159s Get:1 http://ftpmaster.internal/ubuntu plucky/universe tvc 5.0.3+git20151221.80e144e+dfsg-5build4 (dsc) [2304 B] 159s Get:2 http://ftpmaster.internal/ubuntu plucky/universe tvc 5.0.3+git20151221.80e144e+dfsg-5build4 (tar) [745 kB] 159s Get:3 http://ftpmaster.internal/ubuntu plucky/universe tvc 5.0.3+git20151221.80e144e+dfsg-5build4 (diff) [10.1 kB] 159s gpgv: Signature made Sun Nov 10 11:21:31 2024 UTC 159s gpgv: using RSA key B8340990283D8D9BC1949AC74799A35146D12B35 159s gpgv: Can't check signature: No public key 159s dpkg-source: warning: cannot verify inline signature for ./tvc_5.0.3+git20151221.80e144e+dfsg-5build4.dsc: no acceptable signature found 159s autopkgtest [19:37:05]: testing package tvc version 5.0.3+git20151221.80e144e+dfsg-5build4 160s autopkgtest [19:37:06]: build not needed 161s autopkgtest [19:37:07]: test run-unit-test: preparing testbed 161s Reading package lists... 161s Building dependency tree... 161s Reading state information... 161s Starting pkgProblemResolver with broken count: 0 161s Starting 2 pkgProblemResolver with broken count: 0 161s Done 162s The following NEW packages will be installed: 162s libarmadillo14 libarpack2t64 libbamtools2.5.2 libblas3 libdisorder0 162s libgfortran5 libjsoncpp26 liblapack3 libsmithwaterman0 tvc 162s 0 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. 162s Need to get 5467 kB of archives. 162s After this operation, 16.0 MB of additional disk space will be used. 162s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.1-2 [252 kB] 162s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 15-20250222-0ubuntu1 [620 kB] 162s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.1-2 [2971 kB] 162s Get:4 http://ftpmaster.internal/ubuntu plucky/universe s390x libarpack2t64 s390x 3.9.1-4 [110 kB] 163s Get:5 http://ftpmaster.internal/ubuntu plucky/universe s390x libarmadillo14 s390x 1:14.2.3+dfsg-1 [110 kB] 163s Get:6 http://ftpmaster.internal/ubuntu plucky/universe s390x libbamtools2.5.2 s390x 2.5.2+dfsg-6build1 [142 kB] 163s Get:7 http://ftpmaster.internal/ubuntu plucky/universe s390x libdisorder0 s390x 0.0.2+git20130809.8062ee1-4build1 [4734 B] 163s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libjsoncpp26 s390x 1.9.6-3 [80.8 kB] 163s Get:9 http://ftpmaster.internal/ubuntu plucky/universe s390x libsmithwaterman0 s390x 0.0+git20160702.2610e25-12 [36.5 kB] 163s Get:10 http://ftpmaster.internal/ubuntu plucky/universe s390x tvc s390x 5.0.3+git20151221.80e144e+dfsg-5build4 [1140 kB] 163s Fetched 5467 kB in 1s (5249 kB/s) 163s Selecting previously unselected package libblas3:s390x. 163s (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.) 163s Preparing to unpack .../0-libblas3_3.12.1-2_s390x.deb ... 163s Unpacking libblas3:s390x (3.12.1-2) ... 163s Selecting previously unselected package libgfortran5:s390x. 163s Preparing to unpack .../1-libgfortran5_15-20250222-0ubuntu1_s390x.deb ... 163s Unpacking libgfortran5:s390x (15-20250222-0ubuntu1) ... 163s Selecting previously unselected package liblapack3:s390x. 163s Preparing to unpack .../2-liblapack3_3.12.1-2_s390x.deb ... 163s Unpacking liblapack3:s390x (3.12.1-2) ... 163s Selecting previously unselected package libarpack2t64:s390x. 163s Preparing to unpack .../3-libarpack2t64_3.9.1-4_s390x.deb ... 163s Unpacking libarpack2t64:s390x (3.9.1-4) ... 163s Selecting previously unselected package libarmadillo14. 163s Preparing to unpack .../4-libarmadillo14_1%3a14.2.3+dfsg-1_s390x.deb ... 163s Unpacking libarmadillo14 (1:14.2.3+dfsg-1) ... 163s Selecting previously unselected package libbamtools2.5.2:s390x. 163s Preparing to unpack .../5-libbamtools2.5.2_2.5.2+dfsg-6build1_s390x.deb ... 163s Unpacking libbamtools2.5.2:s390x (2.5.2+dfsg-6build1) ... 163s Selecting previously unselected package libdisorder0:s390x. 163s Preparing to unpack .../6-libdisorder0_0.0.2+git20130809.8062ee1-4build1_s390x.deb ... 163s Unpacking libdisorder0:s390x (0.0.2+git20130809.8062ee1-4build1) ... 163s Selecting previously unselected package libjsoncpp26:s390x. 163s Preparing to unpack .../7-libjsoncpp26_1.9.6-3_s390x.deb ... 163s Unpacking libjsoncpp26:s390x (1.9.6-3) ... 163s Selecting previously unselected package libsmithwaterman0:s390x. 163s Preparing to unpack .../8-libsmithwaterman0_0.0+git20160702.2610e25-12_s390x.deb ... 163s Unpacking libsmithwaterman0:s390x (0.0+git20160702.2610e25-12) ... 163s Selecting previously unselected package tvc. 163s Preparing to unpack .../9-tvc_5.0.3+git20151221.80e144e+dfsg-5build4_s390x.deb ... 163s Unpacking tvc (5.0.3+git20151221.80e144e+dfsg-5build4) ... 163s Setting up libdisorder0:s390x (0.0.2+git20130809.8062ee1-4build1) ... 163s Setting up libsmithwaterman0:s390x (0.0+git20160702.2610e25-12) ... 163s Setting up libblas3:s390x (3.12.1-2) ... 163s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 163s Setting up libjsoncpp26:s390x (1.9.6-3) ... 163s Setting up libbamtools2.5.2:s390x (2.5.2+dfsg-6build1) ... 163s Setting up libgfortran5:s390x (15-20250222-0ubuntu1) ... 163s Setting up liblapack3:s390x (3.12.1-2) ... 163s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 163s Setting up libarpack2t64:s390x (3.9.1-4) ... 163s Setting up libarmadillo14 (1:14.2.3+dfsg-1) ... 163s Setting up tvc (5.0.3+git20151221.80e144e+dfsg-5build4) ... 163s Processing triggers for man-db (2.13.0-1) ... 163s Processing triggers for libc-bin (2.41-1ubuntu2) ... 165s autopkgtest [19:37:11]: test run-unit-test: [----------------------- 165s Running Tests 165s [ Sat 2025-03-15 19:38:36 UTC ] 165s [ Sat 2025-03-15 19:38:36 UTC ] Task : Write effective bed 165s [ Sat 2025-03-15 19:38:36 UTC ] Command : /usr/bin/tvcutils validate_bed --reference "reference.fasta" --target-regions-bed "test_unmerged_detail.bed" --effective-bed "./effective_regions.bed" 165s [ Sat 2025-03-15 19:38:36 UTC ] 165s test_unmerged_detail.bed: Validation successful with 0 warnings and 0 errors 165s 165s [ Sat 2025-03-15 19:38:36 UTC ] Calling small INDELs and SNPs using tvc ... 165s [ Sat 2025-03-15 19:38:36 UTC ] 165s [ Sat 2025-03-15 19:38:36 UTC ] Task : Call small indels and SNPs 165s [ Sat 2025-03-15 19:38:36 UTC ] Command : /usr/bin/tvc --output-dir . --reference reference.fasta --num-threads 12 --target-file test_unmerged_detail.bed --trim-ampliseq-primers on --input-bam test.bam --output-vcf small_variants.vcf 165s [ Sat 2025-03-15 19:38:36 UTC ] 165s INFO: No input VCF (Hotspot) file specified via -c,--input-vcf 165s INFO: Systematic error motif file not specified via -e 165s prefix-exclude = 6 165s tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller 165s 165s hp-max-length = 8 (integer, builtin default) 165s sse-prob-threshold = 0.2 (double, builtin default) 165s min-ratio-reads-non-sse-strand = 0.2 (double, builtin default) 165s sse-relative-safety-level = 0.025 (double, builtin default) 165s do-snp-realignment = true (boolean, builtin default) 165s do-mnp-realignment = true (boolean, builtin default) 165s realignment-threshold = 1 (double, builtin default) 165s indel-as-hpindel = false (boolean, builtin default) 165s data-quality-stringency = 4 (double, builtin default) 165s read-rejection-threshold = 0.5 (double, builtin default) 165s use-position-bias = false (boolean, builtin default) 165s position-bias-ref-fraction = 0.05 (double, builtin default) 165s position-bias = 0.75 (double, builtin default) 165s position-bias-pval = 0.05 (double, builtin default) 165s downsample-to-coverage = 2000 (integer, builtin default) 165s tune-sbias = 0.01 (double, builtin default) 165s suppress-reference-genotypes = true (boolean, builtin default) 165s suppress-nocall-genotypes = true (boolean, builtin default) 165s suppress-no-calls = true (boolean, builtin default) 165s heal-snps = true (boolean, builtin default) 165s snp-min-cov-each-strand = 0 (integer, builtin default) 165s snp-min-variant-score = 10 (double, builtin default) 165s snp-min-allele-freq = 0.2 (double, builtin default) 165s snp-min-coverage = 6 (integer, builtin default) 165s snp-strand-bias = 0.95 (double, builtin default) 165s snp-strand-bias-pval = 1 (double, builtin default) 165s mnp-min-cov-each-strand = 0 (integer, builtin default) 165s mnp-min-variant-score = 10 (double, builtin default) 165s mnp-min-allele-freq = 0.2 (double, builtin default) 165s mnp-min-coverage = 6 (integer, builtin default) 165s mnp-strand-bias = 0.95 (double, builtin default) 165s mnp-strand-bias-pval = 1 (double, builtin default) 165s indel-min-cov-each-strand = 1 (integer, builtin default) 165s indel-min-variant-score = 10 (double, builtin default) 165s indel-min-allele-freq = 0.2 (double, builtin default) 165s indel-min-coverage = 15 (integer, builtin default) 165s indel-strand-bias = 0.85 (double, builtin default) 165s indel-strand-bias-pval = 1 (double, builtin default) 165s hotspot-min-cov-each-strand = 0 (integer, builtin default) 165s hotspot-min-variant-score = 10 (double, builtin default) 165s hotspot-min-allele-freq = 0.2 (double, builtin default) 165s hotspot-min-coverage = 6 (integer, builtin default) 165s hotspot-strand-bias = 0.95 (double, builtin default) 165s hotspot-strand-bias-pval = 1 (double, builtin default) 165s max-flows-to-test = 10 (integer, builtin default) 165s min-delta-for-flow = 0.1 (double, builtin default) 165s prediction-precision = 30 (double, builtin default) 165s outlier-probability = 0.01 (double, builtin default) 165s germline-prior-strength = 0 (double, builtin default) 165s heavy-tailed = 3 (integer, builtin default) 165s filter-unusual-predictions = 0.3 (double, builtin default) 165s soft-clip-bias-checker = 0.1 (double, builtin default) 165s filter-deletion-predictions = 100 (double, builtin default) 165s filter-insertion-predictions = 100 (double, builtin default) 165s max-detail-level = 0 (integer, builtin default) 165s shift-likelihood-penalty = 0.3 (double, builtin default) 165s minimum-sigma-prior = 0.085 (double, builtin default) 165s slope-sigma-prior = 0.0084 (double, builtin default) 165s sigma-prior-weight = 1 (double, builtin default) 165s k-zero = 3 (double, builtin default) 165s num-threads = 12 (integer, command line option) 165s num-variants-per-thread = 250 (integer, builtin default) 165s use-sse-basecaller = false (boolean, builtin default) 165s do-json-diagnostic = false (boolean, builtin default) 165s do-minimal-diagnostic = false (boolean, builtin default) 165s process-input-positions-only = false (boolean, builtin default) 165s suppress-recalibration = true (boolean, builtin default) 165s resolve-clipped-bases = false (boolean, builtin default) 165s allow-indels = true (boolean, builtin default) 165s allow-snps = true (boolean, builtin default) 165s allow-mnps = true (boolean, builtin default) 165s allow-complex = false (boolean, builtin default) 165s left-align-indels = false (boolean, builtin default) 165s use-best-n-alleles = 2 (integer, builtin default) 165s use-input-allele-only = false (boolean, builtin default) 165s min-mapping-qv = 4 (integer, builtin default) 165s read-snp-limit = 10 (integer, builtin default) 165s read-max-mismatch-fraction = 1 (double, builtin default) 165s max-complex-gap = 1 (integer, builtin default) 165s gen-min-alt-allele-freq = 0.2 (double, builtin default) 165s gen-min-coverage = 6 (integer, builtin default) 165s gen-min-indel-alt-allele-freq = 0.2 (double, builtin default) 165s override-limits = false (boolean, builtin default) 165s Limit check parameter hp-max-length: lim. 1 <= 8? OK! 165s Limit check parameter sse-prob-threshold: lim. 0 <= 0.2 <= lim. 1? OK! 165s Limit check parameter min-ratio-reads-non-sse-strand: lim. 0 <= 0.2 <= lim. 1? OK! 165s Limit check parameter sse-relative-safety-level: lim. 0 <= 0.025 <= lim. 1? OK! 165s Limit check parameter realignment-threshold: lim. 0 <= 1 <= lim. 1? OK! 165s Limit check parameter data-quality-stringency: lim. 0 <= 4? OK! 165s Limit check parameter read-rejection-threshold: lim. 0 <= 0.5 <= lim. 1? OK! 165s Limit check parameter downsample-to-coverage: lim. 20 <= 2000 <= lim. 100000? OK! 165s Limit check parameter position-bias-ref-fraction: lim. 0 <= 0.05 <= lim. 1? OK! 165s Limit check parameter position-bias: lim. 0 <= 0.75 <= lim. 1? OK! 165s Limit check parameter position-bias-pval: lim. 0 <= 0.05 <= lim. 1? OK! 165s Limit check parameter tune-sbias: lim. 0.001 <= 0.01 <= lim. 1000? OK! 165s Limit check parameter snp-min-cov-each-strand: lim. 0 <= 0? OK! 165s Limit check parameter snp-min-variant-score: lim. 0 <= 10? OK! 165s Limit check parameter snp-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 165s Limit check parameter snp-min-coverage: lim. 0 <= 6? OK! 165s Limit check parameter snp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 165s Limit check parameter snp-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 165s Limit check parameter mnp-min-cov-each-strand: lim. 0 <= 0? OK! 165s Limit check parameter mnp-min-variant-score: lim. 0 <= 10? OK! 165s Limit check parameter mnp-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 165s Limit check parameter mnp-min-coverage: lim. 0 <= 6? OK! 165s Limit check parameter mnp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 165s Limit check parameter mnp-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 165s Limit check parameter indel-min-cov-each-strand: lim. 0 <= 1? OK! 165s Limit check parameter indel-min-variant-score: lim. 0 <= 10? OK! 165s Limit check parameter indel-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 165s Limit check parameter indel-min-coverage: lim. 0 <= 15? OK! 165s Limit check parameter indel-strand-bias: lim. 0.5 <= 0.85 <= lim. 1? OK! 165s Limit check parameter indel-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 165s Limit check parameter hotspot-min-cov-each-strand: lim. 0 <= 0? OK! 165s Limit check parameter hotspot-min-variant-score: lim. 0 <= 10? OK! 165s Limit check parameter hotspot-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 165s Limit check parameter hotspot-min-coverage: lim. 0 <= 6? OK! 165s Limit check parameter hotspot-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 165s Limit check parameter hotspot-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 165s Limit check parameter max-flows-to-test: lim. 1 <= 10 <= lim. 100? OK! 165s Limit check parameter min-delta-for-flow: lim. 0.01 <= 0.1 <= lim. 0.5? OK! 165s Limit check parameter prediction-precision: lim. 0.1 <= 30? OK! 165s Limit check parameter outlier-probability: lim. 0 <= 0.01 <= lim. 1? OK! 165s Limit check parameter germline-prior-strength: lim. 0 <= 0 <= lim. 1000? OK! 165s Limit check parameter heavy-tailed: lim. 1 <= 3? OK! 165s Limit check parameter filter-unusual-predictions: lim. 0 <= 0.3? OK! 165s Limit check parameter soft-clip-bias-checker: lim. 0 <= 0.1 <= lim. 1? OK! 165s Limit check parameter filter-deletion-predictions: lim. 0 <= 100? OK! 165s Limit check parameter filter-insertion-predictions: lim. 0 <= 100? OK! 165s Limit check parameter max-detail-level: lim. 0 <= 0 <= lim. 10000? OK! 165s Limit check parameter shift-likelihood-penalty: lim. 0.01 <= 0.3? OK! 165s Limit check parameter minimum-sigma-prior: lim. 0.01 <= 0.085? OK! 165s Limit check parameter slope-sigma-prior: lim. 0 <= 0.0084? OK! 165s Limit check parameter sigma-prior-weight: lim. 0.01 <= 1? OK! 165s Limit check parameter k-zero: lim. 0 <= 3? OK! 165s Limit check parameter num-threads: lim. 1 <= 12 <= lim. 128? OK! 165s Limit check parameter num-variants-per-thread: lim. 1 <= 250 <= lim. 10000? OK! 165s Limit check parameter use-best-n-alleles: lim. 0 <= 2 <= lim. 20? OK! 165s Limit check parameter min-mapping-qv: lim. 0 <= 4? OK! 165s Limit check parameter read-snp-limit: lim. 0 <= 10? OK! 165s Limit check parameter read-max-mismatch-fraction: lim. 0 <= 1 <= lim. 1? OK! 165s Limit check parameter gen-min-alt-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 165s Limit check parameter gen-min-coverage: lim. 0 <= 6? OK! 165s Limit check parameter gen-min-indel-alt-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 165s TargetsManager: Loaded targets file test_unmerged_detail.bed 165s TargetsManager: 1 target(s) 165s TargetsManager: Trimming of AmpliSeq primers is enabled 165s SampleManager: Found 1 read group(s) and 1 sample(s). 165s SampleManager: Primary sample "85" (default) present in 1 read group(s) 165s TVC found a total of 1 different flow orders of max flow lengths: 500 165s Recalibration was detected from comment lines in bam file(s): 165s 1 unique blocks of recalibration info detected. 165s Recalibration model: suppressed 165s 165s [tvc] Normal termination. Processing time: 0 seconds. 165s 165s [ Sat 2025-03-15 19:38:36 UTC ] 165s [ Sat 2025-03-15 19:38:36 UTC ] Task : Assemble long indels 165s [ Sat 2025-03-15 19:38:36 UTC ] Command : /usr/bin/tvcassembly --reference reference.fasta --input-bam test.bam --target-file test_merged_plain.bed --output-vcf ./indel_assembly.vcf 165s [ Sat 2025-03-15 19:38:36 UTC ] 165s tvcassembly 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller - Long Indel Assembly 165s 165s kmer-len = 19 (integer, builtin default) 165s min-var-count = 5 (integer, builtin default) 165s short-suffix-match = 5 (integer, builtin default) 165s min-indel-size = 4 (integer, builtin default) 165s max-hp-length = 8 (integer, builtin default) 165s min-var-freq = 0.15 (double, builtin default) 165s min-var-score = 10 (double, builtin default) 165s relative-strand-bias = 0.8 (double, builtin default) 165s output-mnv = 0 (integer, builtin default) 165s TargetsManager: Loaded targets file test_merged_plain.bed 165s TargetsManager: 1 target(s) 165s SampleManager: Found 1 read group(s) and 1 sample(s). 165s SampleManager: Primary sample "85" (default) present in 1 read group(s) 165s [ Sat 2025-03-15 19:38:36 UTC ] 165s [ Sat 2025-03-15 19:38:36 UTC ] Task : Unify variants and annotations from all sources (tvc,IndelAssembly,hotpots) 165s [ Sat 2025-03-15 19:38:36 UTC ] Command : /usr/bin/tvcutils unify_vcf --novel-tvc-vcf ./small_variants.vcf --novel-assembly-vcf ./indel_assembly.vcf --output-vcf ./TSVC_variants.vcf.gz --reference-fasta reference.fasta --tvc-metrics ./tvc_metrics.json --target-file "test_merged_plain.bed" 165s [ Sat 2025-03-15 19:38:36 UTC ] 165s TargetsManager: Loaded targets file test_merged_plain.bed 165s TargetsManager: 1 target(s) 165s [ Sat 2025-03-15 19:38:36 UTC ] 165s [ Sat 2025-03-15 19:38:36 UTC ] Task : Generate uncompressed vcf 165s [ Sat 2025-03-15 19:38:36 UTC ] Command : gzip -dcf "./TSVC_variants.vcf.gz" > "./TSVC_variants.vcf" 165s [ Sat 2025-03-15 19:38:36 UTC ] 165s PASS 165s autopkgtest [19:37:11]: test run-unit-test: -----------------------] 166s autopkgtest [19:37:12]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 166s run-unit-test PASS 166s autopkgtest [19:37:12]: @@@@@@@@@@@@@@@@@@@@ summary 166s run-unit-test PASS 172s nova [W] Using flock in prodstack6-s390x 172s Creating nova instance adt-plucky-s390x-tvc-20250315-193426-juju-7f2275-prod-proposed-migration-environment-2-351dd80e-7fcb-4dc3-b6ab-415ec22c3235 from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 172s nova [W] Timed out waiting for 7c4207b0-da7e-48aa-a7d9-8e9e88d5b01c to get deleted.