0s autopkgtest [05:39:40]: starting date and time: 2024-07-13 05:39:40+0000 0s autopkgtest [05:39:40]: git checkout: fd3bed09 nova: allow more retries for quota issues 0s autopkgtest [05:39:40]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.5cv0lqx4/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/2.39-3.1ubuntu3 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos02-s390x-18.secgroup --name adt-oracular-s390x-tvc-20240713-053940-juju-7f2275-prod-proposed-migration-environment-3-e56fc32e-f8f4-437d-be38-c3e434334461 --image adt/ubuntu-oracular-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 62s autopkgtest [05:40:42]: testbed dpkg architecture: s390x 62s autopkgtest [05:40:42]: testbed apt version: 2.9.6 62s autopkgtest [05:40:42]: @@@@@@@@@@@@@@@@@@@@ test bed setup 63s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB] 63s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [358 kB] 64s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8548 B] 64s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2576 B] 64s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [46.9 kB] 64s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x Packages [92.7 kB] 64s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x c-n-f Metadata [2112 B] 64s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted s390x Packages [1368 B] 64s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted s390x c-n-f Metadata [120 B] 64s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe s390x Packages [401 kB] 64s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe s390x c-n-f Metadata [8372 B] 64s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse s390x Packages [1448 B] 64s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse s390x c-n-f Metadata [120 B] 64s Fetched 1049 kB in 1s (1403 kB/s) 64s Reading package lists... 66s Reading package lists... 66s Building dependency tree... 66s Reading state information... 67s Calculating upgrade... 67s The following packages will be upgraded: 67s inetutils-telnet libc-bin libc-dev-bin libc-devtools libc6 libc6-dev locales 67s telnet 67s 8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 67s Need to get 9505 kB of archives. 67s After this operation, 121 kB of additional disk space will be used. 67s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libc-devtools s390x 2.39-3.1ubuntu3 [30.7 kB] 67s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libc6-dev s390x 2.39-3.1ubuntu3 [1626 kB] 67s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libc-dev-bin s390x 2.39-3.1ubuntu3 [20.2 kB] 67s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libc6 s390x 2.39-3.1ubuntu3 [2841 kB] 68s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libc-bin s390x 2.39-3.1ubuntu3 [654 kB] 68s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x locales all 2.39-3.1ubuntu3 [4220 kB] 69s Get:7 http://ftpmaster.internal/ubuntu oracular/main s390x inetutils-telnet s390x 2:2.5-5ubuntu1 [110 kB] 69s Get:8 http://ftpmaster.internal/ubuntu oracular/main s390x telnet all 0.17+2.5-5ubuntu1 [3688 B] 69s Preconfiguring packages ... 69s Fetched 9505 kB in 2s (4161 kB/s) 69s (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 ... 54720 files and directories currently installed.) 69s Preparing to unpack .../libc-devtools_2.39-3.1ubuntu3_s390x.deb ... 69s Unpacking libc-devtools (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 69s Preparing to unpack .../libc6-dev_2.39-3.1ubuntu3_s390x.deb ... 69s Unpacking libc6-dev:s390x (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 70s Preparing to unpack .../libc-dev-bin_2.39-3.1ubuntu3_s390x.deb ... 70s Unpacking libc-dev-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 70s Preparing to unpack .../libc6_2.39-3.1ubuntu3_s390x.deb ... 70s Unpacking libc6:s390x (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 70s Setting up libc6:s390x (2.39-3.1ubuntu3) ... 70s Error: Could not restart systemd, systemd binary not working 70s (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 ... 54720 files and directories currently installed.) 70s Preparing to unpack .../libc-bin_2.39-3.1ubuntu3_s390x.deb ... 70s Unpacking libc-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 70s Setting up libc-bin (2.39-3.1ubuntu3) ... 70s (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 ... 54720 files and directories currently installed.) 70s Preparing to unpack .../locales_2.39-3.1ubuntu3_all.deb ... 70s Unpacking locales (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 70s Preparing to unpack .../inetutils-telnet_2%3a2.5-5ubuntu1_s390x.deb ... 70s Unpacking inetutils-telnet (2:2.5-5ubuntu1) over (2:2.5-3ubuntu4) ... 70s Preparing to unpack .../telnet_0.17+2.5-5ubuntu1_all.deb ... 70s Unpacking telnet (0.17+2.5-5ubuntu1) over (0.17+2.5-3ubuntu4) ... 70s Setting up inetutils-telnet (2:2.5-5ubuntu1) ... 70s Setting up locales (2.39-3.1ubuntu3) ... 71s Generating locales (this might take a while)... 72s en_US.UTF-8... done 72s Generation complete. 72s Setting up libc-dev-bin (2.39-3.1ubuntu3) ... 72s Setting up libc-devtools (2.39-3.1ubuntu3) ... 72s Setting up telnet (0.17+2.5-5ubuntu1) ... 72s Setting up libc6-dev:s390x (2.39-3.1ubuntu3) ... 72s Processing triggers for man-db (2.12.1-2) ... 73s Processing triggers for systemd (256-1ubuntu1) ... 74s Reading package lists... 74s Building dependency tree... 74s Reading state information... 74s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 75s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 75s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 75s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 75s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 76s Reading package lists... 76s Reading package lists... 76s Building dependency tree... 76s Reading state information... 76s Calculating upgrade... 76s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 76s Reading package lists... 76s Building dependency tree... 76s Reading state information... 76s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 79s autopkgtest [05:40:59]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP Sat Apr 20 00:14:26 UTC 2024 79s autopkgtest [05:40:59]: @@@@@@@@@@@@@@@@@@@@ apt-source tvc 81s Get:1 http://ftpmaster.internal/ubuntu oracular/universe tvc 5.0.3+git20151221.80e144e+dfsg-5build2 (dsc) [2301 B] 81s Get:2 http://ftpmaster.internal/ubuntu oracular/universe tvc 5.0.3+git20151221.80e144e+dfsg-5build2 (tar) [745 kB] 81s Get:3 http://ftpmaster.internal/ubuntu oracular/universe tvc 5.0.3+git20151221.80e144e+dfsg-5build2 (diff) [9976 B] 81s gpgv: Signature made Fri Oct 27 16:50:16 2023 UTC 81s gpgv: using RSA key 4D0BE12F0E4776D8AACE9696E66C775AEBFE6C7D 81s gpgv: Can't check signature: No public key 81s dpkg-source: warning: cannot verify inline signature for ./tvc_5.0.3+git20151221.80e144e+dfsg-5build2.dsc: no acceptable signature found 81s autopkgtest [05:41:01]: testing package tvc version 5.0.3+git20151221.80e144e+dfsg-5build2 82s autopkgtest [05:41:02]: build not needed 82s autopkgtest [05:41:02]: test run-unit-test: preparing testbed 83s Reading package lists... 83s Building dependency tree... 83s Reading state information... 83s Starting pkgProblemResolver with broken count: 0 83s Starting 2 pkgProblemResolver with broken count: 0 83s Done 84s The following additional packages will be installed: 84s libarmadillo12 libarpack2t64 libbamtools2.5.2 libblas3 libdisorder0 84s libgfortran5 libjsoncpp25 liblapack3 libsmithwaterman0 libsuperlu6 tvc 84s The following NEW packages will be installed: 84s autopkgtest-satdep libarmadillo12 libarpack2t64 libbamtools2.5.2 libblas3 84s libdisorder0 libgfortran5 libjsoncpp25 liblapack3 libsmithwaterman0 84s libsuperlu6 tvc 84s 0 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 84s Need to get 5662 kB/5663 kB of archives. 84s After this operation, 16.3 MB of additional disk space will be used. 84s Get:1 /tmp/autopkgtest.KKcvdK/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [700 B] 84s Get:2 http://ftpmaster.internal/ubuntu oracular/main s390x libblas3 s390x 3.12.0-3build1 [245 kB] 84s Get:3 http://ftpmaster.internal/ubuntu oracular/main s390x libgfortran5 s390x 14.1.0-1ubuntu1 [600 kB] 84s Get:4 http://ftpmaster.internal/ubuntu oracular/main s390x liblapack3 s390x 3.12.0-3build1 [2976 kB] 85s Get:5 http://ftpmaster.internal/ubuntu oracular/universe s390x libarpack2t64 s390x 3.9.1-1.1build2 [113 kB] 85s Get:6 http://ftpmaster.internal/ubuntu oracular/universe s390x libsuperlu6 s390x 6.0.1+dfsg1-1build1 [232 kB] 85s Get:7 http://ftpmaster.internal/ubuntu oracular/universe s390x libarmadillo12 s390x 1:12.8.2+dfsg-1 [110 kB] 85s Get:8 http://ftpmaster.internal/ubuntu oracular/universe s390x libbamtools2.5.2 s390x 2.5.2+dfsg-5ubuntu1 [139 kB] 85s Get:9 http://ftpmaster.internal/ubuntu oracular/universe s390x libdisorder0 s390x 0.0.2+git20130809.8062ee1-4build1 [4734 B] 85s Get:10 http://ftpmaster.internal/ubuntu oracular/main s390x libjsoncpp25 s390x 1.9.5-6build1 [82.5 kB] 85s Get:11 http://ftpmaster.internal/ubuntu oracular/universe s390x libsmithwaterman0 s390x 0.0+git20160702.2610e25-12 [36.5 kB] 85s Get:12 http://ftpmaster.internal/ubuntu oracular/universe s390x tvc s390x 5.0.3+git20151221.80e144e+dfsg-5build2 [1124 kB] 85s Fetched 5662 kB in 1s (4387 kB/s) 85s Selecting previously unselected package libblas3:s390x. 85s (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 ... 54720 files and directories currently installed.) 85s Preparing to unpack .../00-libblas3_3.12.0-3build1_s390x.deb ... 85s Unpacking libblas3:s390x (3.12.0-3build1) ... 85s Selecting previously unselected package libgfortran5:s390x. 85s Preparing to unpack .../01-libgfortran5_14.1.0-1ubuntu1_s390x.deb ... 85s Unpacking libgfortran5:s390x (14.1.0-1ubuntu1) ... 85s Selecting previously unselected package liblapack3:s390x. 85s Preparing to unpack .../02-liblapack3_3.12.0-3build1_s390x.deb ... 85s Unpacking liblapack3:s390x (3.12.0-3build1) ... 85s Selecting previously unselected package libarpack2t64:s390x. 85s Preparing to unpack .../03-libarpack2t64_3.9.1-1.1build2_s390x.deb ... 85s Unpacking libarpack2t64:s390x (3.9.1-1.1build2) ... 85s Selecting previously unselected package libsuperlu6:s390x. 85s Preparing to unpack .../04-libsuperlu6_6.0.1+dfsg1-1build1_s390x.deb ... 85s Unpacking libsuperlu6:s390x (6.0.1+dfsg1-1build1) ... 85s Selecting previously unselected package libarmadillo12. 85s Preparing to unpack .../05-libarmadillo12_1%3a12.8.2+dfsg-1_s390x.deb ... 85s Unpacking libarmadillo12 (1:12.8.2+dfsg-1) ... 85s Selecting previously unselected package libbamtools2.5.2:s390x. 85s Preparing to unpack .../06-libbamtools2.5.2_2.5.2+dfsg-5ubuntu1_s390x.deb ... 85s Unpacking libbamtools2.5.2:s390x (2.5.2+dfsg-5ubuntu1) ... 86s Selecting previously unselected package libdisorder0:s390x. 86s Preparing to unpack .../07-libdisorder0_0.0.2+git20130809.8062ee1-4build1_s390x.deb ... 86s Unpacking libdisorder0:s390x (0.0.2+git20130809.8062ee1-4build1) ... 86s Selecting previously unselected package libjsoncpp25:s390x. 86s Preparing to unpack .../08-libjsoncpp25_1.9.5-6build1_s390x.deb ... 86s Unpacking libjsoncpp25:s390x (1.9.5-6build1) ... 86s Selecting previously unselected package libsmithwaterman0:s390x. 86s Preparing to unpack .../09-libsmithwaterman0_0.0+git20160702.2610e25-12_s390x.deb ... 86s Unpacking libsmithwaterman0:s390x (0.0+git20160702.2610e25-12) ... 86s Selecting previously unselected package tvc. 86s Preparing to unpack .../10-tvc_5.0.3+git20151221.80e144e+dfsg-5build2_s390x.deb ... 86s Unpacking tvc (5.0.3+git20151221.80e144e+dfsg-5build2) ... 86s Selecting previously unselected package autopkgtest-satdep. 86s Preparing to unpack .../11-1-autopkgtest-satdep.deb ... 86s Unpacking autopkgtest-satdep (0) ... 86s Setting up libdisorder0:s390x (0.0.2+git20130809.8062ee1-4build1) ... 86s Setting up libsmithwaterman0:s390x (0.0+git20160702.2610e25-12) ... 86s Setting up libblas3:s390x (3.12.0-3build1) ... 86s 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 86s Setting up libjsoncpp25:s390x (1.9.5-6build1) ... 86s Setting up libbamtools2.5.2:s390x (2.5.2+dfsg-5ubuntu1) ... 86s Setting up libgfortran5:s390x (14.1.0-1ubuntu1) ... 86s Setting up liblapack3:s390x (3.12.0-3build1) ... 86s 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 86s Setting up libarpack2t64:s390x (3.9.1-1.1build2) ... 86s Setting up libsuperlu6:s390x (6.0.1+dfsg1-1build1) ... 86s Setting up libarmadillo12 (1:12.8.2+dfsg-1) ... 86s Setting up tvc (5.0.3+git20151221.80e144e+dfsg-5build2) ... 86s Setting up autopkgtest-satdep (0) ... 86s Processing triggers for man-db (2.12.1-2) ... 86s Processing triggers for libc-bin (2.39-3.1ubuntu3) ... 88s (Reading database ... 54815 files and directories currently installed.) 88s Removing autopkgtest-satdep (0) ... 88s autopkgtest [05:41:08]: test run-unit-test: [----------------------- 89s Running Tests 89s [ Sat 2024-07-13 05:41:07 UTC ] 89s [ Sat 2024-07-13 05:41:07 UTC ] Task : Write effective bed 89s [ Sat 2024-07-13 05:41:07 UTC ] Command : /usr/bin/tvcutils validate_bed --reference "reference.fasta" --target-regions-bed "test_unmerged_detail.bed" --effective-bed "./effective_regions.bed" 89s [ Sat 2024-07-13 05:41:07 UTC ] 89s test_unmerged_detail.bed: Validation successful with 0 warnings and 0 errors 89s 89s [ Sat 2024-07-13 05:41:07 UTC ] Calling small INDELs and SNPs using tvc ... 89s [ Sat 2024-07-13 05:41:07 UTC ] 89s [ Sat 2024-07-13 05:41:07 UTC ] Task : Call small indels and SNPs 89s [ Sat 2024-07-13 05:41:07 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 89s [ Sat 2024-07-13 05:41:07 UTC ] 89s tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller 89s 89s hp-max-length = 8 (integer, builtin default) 89s sse-prob-threshold = 0.2 (double, builtin default) 89s min-ratio-reads-non-sse-strand = 0.2 (double, builtin default) 89s INFO: No input VCF (Hotspot) file specified via -c,--input-vcf 89s INFO: Systematic error motif file not specified via -e 89s prefix-exclude = sse-relative-safety-level = 0.025 (double, builtin default) 89s do-snp-realignment = true (boolean, builtin default) 89s do-mnp-realignment = true (boolean, builtin default) 89s realignment-threshold = 1 (double, builtin default) 89s indel-as-hpindel = false (boolean, builtin default) 89s data-quality-stringency = 4 (double, builtin default) 89s read-rejection-threshold = 0.5 (double, builtin default) 89s use-position-bias = false (boolean, builtin default) 89s position-bias-ref-fraction = 0.05 (double, builtin default) 89s position-bias = 0.75 (double, builtin default) 89s position-bias-pval = 0.05 (double, builtin default) 89s downsample-to-coverage = 2000 (integer, builtin default) 89s tune-sbias = 0.01 (double, builtin default) 89s suppress-reference-genotypes = true (boolean, builtin default) 89s suppress-nocall-genotypes = true (boolean, builtin default) 89s suppress-no-calls = true (boolean, builtin default) 89s heal-snps = true (boolean, builtin default) 89s snp-min-cov-each-strand = 0 (integer, builtin default) 89s snp-min-variant-score = 10 (double, builtin default) 89s snp-min-allele-freq = 0.2 (double, builtin default) 89s snp-min-coverage = 6 (integer, builtin default) 89s snp-strand-bias = 0.95 (double, builtin default) 89s snp-strand-bias-pval = 1 (double, builtin default) 89s mnp-min-cov-each-strand = 0 (integer, builtin default) 89s mnp-min-variant-score = 10 (double, builtin default) 89s mnp-min-allele-freq = 0.2 (double, builtin default) 89s mnp-min-coverage = 6 (integer, builtin default) 89s mnp-strand-bias = 0.95 (double, builtin default) 89s mnp-strand-bias-pval = 1 (double, builtin default) 89s indel-min-cov-each-strand = 1 (integer, builtin default) 89s indel-min-variant-score = 10 (double, builtin default) 89s indel-min-allele-freq = 0.2 (double, builtin default) 89s indel-min-coverage = 15 (integer, builtin default) 89s indel-strand-bias = 0.85 (double, builtin default) 89s indel-strand-bias-pval = 1 (double, builtin default) 89s hotspot-min-cov-each-strand = 0 (integer, builtin default) 89s hotspot-min-variant-score = 10 (double, builtin default) 89s hotspot-min-allele-freq = 0.2 (double, builtin default) 89s hotspot-min-coverage = 6 (integer, builtin default) 89s hotspot-strand-bias = 0.95 (double, builtin default) 89s hotspot-strand-bias-pval = 1 (double, builtin default) 89s max-flows-to-test = 10 (integer, builtin default) 89s min-delta-for-flow = 0.1 (double, builtin default) 89s prediction-precision = 30 (double, builtin default) 89s outlier-probability = 0.01 (double, builtin default) 89s germline-prior-strength = 0 (double, builtin default) 89s heavy-tailed = 3 (integer, builtin default) 89s filter-unusual-predictions = 0.3 (double, builtin default) 89s soft-clip-bias-checker = 0.1 (double, builtin default) 89s filter-deletion-predictions = 100 (double, builtin default) 89s filter-insertion-predictions = 100 (double, builtin default) 89s max-detail-level = 0 (integer, builtin default) 89s shift-likelihood-penalty = 0.3 (double, builtin default) 89s minimum-sigma-prior = 0.085 (double, builtin default) 89s slope-sigma-prior = 0.0084 (double, builtin default) 89s sigma-prior-weight = 1 (double, builtin default) 89s k-zero = 3 (double, builtin default) 89s num-threads = 12 (integer, command line option) 89s num-variants-per-thread = 250 (integer, builtin default) 89s use-sse-basecaller = false (boolean, builtin default) 89s do-json-diagnostic = false (boolean, builtin default) 89s do-minimal-diagnostic = false (boolean, builtin default) 89s process-input-positions-only = false (boolean, builtin default) 89s suppress-recalibration = true (boolean, builtin default) 89s resolve-clipped-bases = false (boolean, builtin default) 89s 6 allow-indels = true (boolean, builtin default) 89s allow-snps = true (boolean, builtin default) 89s allow-mnps = true (boolean, builtin default) 89s allow-complex = false (boolean, builtin default) 89s left-align-indels = false (boolean, builtin default) 89s use-best-n-alleles = 2 (integer, builtin default) 89s use-input-allele-only = false (boolean, builtin default) 89s min-mapping-qv = 4 (integer, builtin default) 89s read-snp-limit = 10 (integer, builtin default) 89s read-max-mismatch-fraction = 1 (double, builtin default) 89s max-complex-gap = 1 (integer, builtin default) 89s 89s gen-min-alt-allele-freq = 0.2 (double, builtin default) 89s gen-min-coverage = 6 (integer, builtin default) 89s gen-min-indel-alt-allele-freq = 0.2 (double, builtin default) 89s override-limits = false (boolean, builtin default) 89s Limit check parameter hp-max-length: lim. 1 <= 8? OK! 89s Limit check parameter sse-prob-threshold: lim. 0 <= 0.2 <= lim. 1? OK! 89s Limit check parameter min-ratio-reads-non-sse-strand: lim. 0 <= 0.2 <= lim. 1? OK! 89s Limit check parameter sse-relative-safety-level: lim. 0 <= 0.025 <= lim. 1? OK! 89s Limit check parameter realignment-threshold: lim. 0 <= 1 <= lim. 1? OK! 89s Limit check parameter data-quality-stringency: lim. 0 <= 4? OK! 89s Limit check parameter read-rejection-threshold: lim. 0 <= 0.5 <= lim. 1? OK! 89s Limit check parameter downsample-to-coverage: lim. 20 <= 2000 <= lim. 100000? OK! 89s Limit check parameter position-bias-ref-fraction: lim. 0 <= 0.05 <= lim. 1? OK! 89s Limit check parameter position-bias: lim. 0 <= 0.75 <= lim. 1? OK! 89s Limit check parameter position-bias-pval: lim. 0 <= 0.05 <= lim. 1? OK! 89s Limit check parameter tune-sbias: lim. 0.001 <= 0.01 <= lim. 1000? OK! 89s Limit check parameter snp-min-cov-each-strand: lim. 0 <= 0? OK! 89s Limit check parameter snp-min-variant-score: lim. 0 <= 10? OK! 89s Limit check parameter snp-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 89s Limit check parameter snp-min-coverage: lim. 0 <= 6? OK! 89s Limit check parameter snp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 89s Limit check parameter snp-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 89s Limit check parameter mnp-min-cov-each-strand: lim. 0 <= 0? OK! 89s Limit check parameter mnp-min-variant-score: lim. 0 <= 10? OK! 89s Limit check parameter mnp-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 89s Limit check parameter mnp-min-coverage: lim. 0 <= 6? OK! 89s Limit check parameter mnp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 89s Limit check parameter mnp-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 89s Limit check parameter indel-min-cov-each-strand: lim. 0 <= 1? OK! 89s Limit check parameter indel-min-variant-score: lim. 0 <= 10? OK! 89s Limit check parameter indel-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 89s Limit check parameter indel-min-coverage: lim. 0 <= 15? OK! 89s Limit check parameter indel-strand-bias: lim. 0.5 <= 0.85 <= lim. 1? OK! 89s Limit check parameter indel-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 89s Limit check parameter hotspot-min-cov-each-strand: lim. 0 <= 0? OK! 89s Limit check parameter hotspot-min-variant-score: lim. 0 <= 10? OK! 89s Limit check parameter hotspot-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 89s Limit check parameter hotspot-min-coverage: lim. 0 <= 6? OK! 89s Limit check parameter hotspot-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 89s Limit check parameter hotspot-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 89s Limit check parameter max-flows-to-test: lim. 1 <= 10 <= lim. 100? OK! 89s Limit check parameter min-delta-for-flow: lim. 0.01 <= 0.1 <= lim. 0.5? OK! 89s Limit check parameter prediction-precision: lim. 0.1 <= 30? OK! 89s Limit check parameter outlier-probability: lim. 0 <= 0.01 <= lim. 1? OK! 89s Limit check parameter germline-prior-strength: lim. 0 <= 0 <= lim. 1000? OK! 89s Limit check parameter heavy-tailed: lim. 1 <= 3? OK! 89s Limit check parameter filter-unusual-predictions: lim. 0 <= 0.3? OK! 89s Limit check parameter soft-clip-bias-checker: lim. 0 <= 0.1 <= lim. 1? OK! 89s Limit check parameter filter-deletion-predictions: lim. 0 <= 100? OK! 89s Limit check parameter filter-insertion-predictions: lim. 0 <= 100? OK! 89s Limit check parameter max-detail-level: lim. 0 <= 0 <= lim. 10000? OK! 89s Limit check parameter shift-likelihood-penalty: lim. 0.01 <= 0.3? OK! 89s Limit check parameter minimum-sigma-prior: lim. 0.01 <= 0.085? OK! 89s Limit check parameter slope-sigma-prior: lim. 0 <= 0.0084? OK! 89s Limit check parameter sigma-prior-weight: lim. 0.01 <= 1? OK! 89s Limit check parameter k-zero: lim. 0 <= 3? OK! 89s Limit check parameter num-threads: lim. 1 <= 12 <= lim. 128? OK! 89s Limit check parameter num-variants-per-thread: lim. 1 <= 250 <= lim. 10000? OK! 89s Limit check parameter use-best-n-alleles: lim. 0 <= 2 <= lim. 20? OK! 89s Limit check parameter min-mapping-qv: lim. 0 <= 4? OK! 89s Limit check parameter read-snp-limit: lim. 0 <= 10? OK! 89s Limit check parameter read-max-mismatch-fraction: lim. 0 <= 1 <= lim. 1? OK! 89s Limit check parameter gen-min-alt-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 89s Limit check parameter gen-min-coverage: lim. 0 <= 6? OK! 89s Limit check parameter gen-min-indel-alt-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 89s TargetsManager: Loaded targets file test_unmerged_detail.bed 89s TargetsManager: 1 target(s) 89s TargetsManager: Trimming of AmpliSeq primers is enabled 89s SampleManager: Found 1 read group(s) and 1 sample(s). 89s SampleManager: Primary sample "85" (default) present in 1 read group(s) 89s TVC found a total of 1 different flow orders of max flow lengths: 500 89s Recalibration was detected from comment lines in bam file(s): 89s 1 unique blocks of recalibration info detected. 89s Recalibration model: suppressed 89s 89s [tvc] Normal termination. Processing time: 0 seconds. 89s 89s [ Sat 2024-07-13 05:41:07 UTC ] 89s [ Sat 2024-07-13 05:41:07 UTC ] Task : Assemble long indels 89s [ Sat 2024-07-13 05:41:07 UTC ] Command : /usr/bin/tvcassembly --reference reference.fasta --input-bam test.bam --target-file test_merged_plain.bed --output-vcf ./indel_assembly.vcf 89s [ Sat 2024-07-13 05:41:07 UTC ] 89s tvcassembly 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller - Long Indel Assembly 89s 89s kmer-len = 19 (integer, builtin default) 89s min-var-count = 5 (integer, builtin default) 89s short-suffix-match = 5 (integer, builtin default) 89s min-indel-size = 4 (integer, builtin default) 89s max-hp-length = 8 (integer, builtin default) 89s min-var-freq = 0.15 (double, builtin default) 89s min-var-score = 10 (double, builtin default) 89s relative-strand-bias = 0.8 (double, builtin default) 89s output-mnv = 0 (integer, builtin default) 89s TargetsManager: Loaded targets file test_merged_plain.bed 89s TargetsManager: 1 target(s) 89s SampleManager: Found 1 read group(s) and 1 sample(s). 89s SampleManager: Primary sample "85" (default) present in 1 read group(s) 89s [ Sat 2024-07-13 05:41:07 UTC ] 89s [ Sat 2024-07-13 05:41:07 UTC ] Task : Unify variants and annotations from all sources (tvc,IndelAssembly,hotpots) 89s [ Sat 2024-07-13 05:41:07 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" 89s [ Sat 2024-07-13 05:41:07 UTC ] 89s TargetsManager: Loaded targets file test_merged_plain.bed 89s TargetsManager: 1 target(s) 89s [ Sat 2024-07-13 05:41:07 UTC ] 89s [ Sat 2024-07-13 05:41:07 UTC ] Task : Generate uncompressed vcf 89s [ Sat 2024-07-13 05:41:07 UTC ] Command : gzip -dcf "./TSVC_variants.vcf.gz" > "./TSVC_variants.vcf" 89s [ Sat 2024-07-13 05:41:07 UTC ] 89s PASS 89s autopkgtest [05:41:09]: test run-unit-test: -----------------------] 89s run-unit-test PASS 89s autopkgtest [05:41:09]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 90s autopkgtest [05:41:10]: @@@@@@@@@@@@@@@@@@@@ summary 90s run-unit-test PASS 100s nova [W] Using flock in scalingstack-bos02-s390x 100s Creating nova instance adt-oracular-s390x-tvc-20240713-053940-juju-7f2275-prod-proposed-migration-environment-3-e56fc32e-f8f4-437d-be38-c3e434334461 from image adt/ubuntu-oracular-s390x-server-20240712.img (UUID a92f8916-bf1f-48b9-acf3-c27787ac0cdf)...