0s autopkgtest [01:17:21]: starting date and time: 2024-07-13 01:17:21+0000 0s autopkgtest [01:17:21]: git checkout: fd3bed09 nova: allow more retries for quota issues 0s autopkgtest [01:17:21]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work._zo6zpwt/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-ppc64el-8.secgroup --name adt-oracular-ppc64el-tvc-20240713-011720-juju-7f2275-prod-proposed-migration-environment-3-16b03b41-fc3b-4349-8e32-8c680be4fddd --image adt/ubuntu-oracular-ppc64el-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/ 104s autopkgtest [01:19:05]: testbed dpkg architecture: ppc64el 104s autopkgtest [01:19:05]: testbed apt version: 2.9.6 104s autopkgtest [01:19:05]: @@@@@@@@@@@@@@@@@@@@ test bed setup 105s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB] 106s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [48.2 kB] 106s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8548 B] 106s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [3860 B] 106s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [366 kB] 106s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el Packages [92.7 kB] 106s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el c-n-f Metadata [2116 B] 106s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted ppc64el Packages [1368 B] 106s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted ppc64el c-n-f Metadata [120 B] 106s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe ppc64el Packages [423 kB] 106s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe ppc64el c-n-f Metadata [8952 B] 106s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse ppc64el Packages [2088 B] 106s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse ppc64el c-n-f Metadata [120 B] 108s Fetched 1083 kB in 1s (976 kB/s) 108s Reading package lists... 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s Calculating upgrade... 111s The following packages will be upgraded: 111s libc-bin libc-dev-bin libc-devtools libc6 libc6-dev locales 111s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 111s Need to get 10.1 MB of archives. 111s After this operation, 1843 kB disk space will be freed. 111s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el libc-devtools ppc64el 2.39-3.1ubuntu3 [29.5 kB] 112s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el libc6-dev ppc64el 2.39-3.1ubuntu3 [1982 kB] 112s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el libc-dev-bin ppc64el 2.39-3.1ubuntu3 [21.0 kB] 112s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el libc6 ppc64el 2.39-3.1ubuntu3 [3174 kB] 113s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el libc-bin ppc64el 2.39-3.1ubuntu3 [720 kB] 113s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el locales all 2.39-3.1ubuntu3 [4220 kB] 114s Preconfiguring packages ... 114s Fetched 10.1 MB in 3s (3993 kB/s) 114s (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 ... 72754 files and directories currently installed.) 114s Preparing to unpack .../libc-devtools_2.39-3.1ubuntu3_ppc64el.deb ... 114s Unpacking libc-devtools (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 114s Preparing to unpack .../libc6-dev_2.39-3.1ubuntu3_ppc64el.deb ... 114s Unpacking libc6-dev:ppc64el (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 115s Preparing to unpack .../libc-dev-bin_2.39-3.1ubuntu3_ppc64el.deb ... 115s Unpacking libc-dev-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 115s Preparing to unpack .../libc6_2.39-3.1ubuntu3_ppc64el.deb ... 115s Unpacking libc6:ppc64el (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 115s Setting up libc6:ppc64el (2.39-3.1ubuntu3) ... 115s Error: Could not restart systemd, systemd binary not working 115s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 72754 files and directories currently installed.) 115s Preparing to unpack .../libc-bin_2.39-3.1ubuntu3_ppc64el.deb ... 115s Unpacking libc-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 115s Setting up libc-bin (2.39-3.1ubuntu3) ... 115s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 72754 files and directories currently installed.) 115s Preparing to unpack .../locales_2.39-3.1ubuntu3_all.deb ... 115s Unpacking locales (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 116s Setting up locales (2.39-3.1ubuntu3) ... 116s Generating locales (this might take a while)... 118s en_US.UTF-8... done 118s Generation complete. 118s Setting up libc-dev-bin (2.39-3.1ubuntu3) ... 118s Setting up libc-devtools (2.39-3.1ubuntu3) ... 118s Setting up libc6-dev:ppc64el (2.39-3.1ubuntu3) ... 118s Processing triggers for man-db (2.12.1-2) ... 119s Processing triggers for systemd (256-1ubuntu1) ... 120s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 121s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 121s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 121s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 121s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 123s Reading package lists... 123s Reading package lists... 123s Building dependency tree... 123s Reading state information... 123s Calculating upgrade... 123s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 123s Reading package lists... 123s Building dependency tree... 123s Reading state information... 124s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 126s autopkgtest [01:19:27]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP Sat Apr 20 00:05:55 UTC 2024 126s autopkgtest [01:19:27]: @@@@@@@@@@@@@@@@@@@@ apt-source tvc 128s Get:1 http://ftpmaster.internal/ubuntu oracular/universe tvc 5.0.3+git20151221.80e144e+dfsg-5build2 (dsc) [2301 B] 128s Get:2 http://ftpmaster.internal/ubuntu oracular/universe tvc 5.0.3+git20151221.80e144e+dfsg-5build2 (tar) [745 kB] 128s Get:3 http://ftpmaster.internal/ubuntu oracular/universe tvc 5.0.3+git20151221.80e144e+dfsg-5build2 (diff) [9976 B] 129s gpgv: Signature made Fri Oct 27 16:50:16 2023 UTC 129s gpgv: using RSA key 4D0BE12F0E4776D8AACE9696E66C775AEBFE6C7D 129s gpgv: Can't check signature: No public key 129s dpkg-source: warning: cannot verify inline signature for ./tvc_5.0.3+git20151221.80e144e+dfsg-5build2.dsc: no acceptable signature found 129s autopkgtest [01:19:30]: testing package tvc version 5.0.3+git20151221.80e144e+dfsg-5build2 129s autopkgtest [01:19:30]: build not needed 130s autopkgtest [01:19:31]: test run-unit-test: preparing testbed 131s Reading package lists... 131s Building dependency tree... 131s Reading state information... 131s Starting pkgProblemResolver with broken count: 0 131s Starting 2 pkgProblemResolver with broken count: 0 131s Done 132s The following additional packages will be installed: 132s libarmadillo12 libarpack2t64 libbamtools2.5.2 libblas3 libdisorder0 132s libgfortran5 libjsoncpp25 liblapack3 libsmithwaterman0 libsuperlu6 tvc 132s The following NEW packages will be installed: 132s autopkgtest-satdep libarmadillo12 libarpack2t64 libbamtools2.5.2 libblas3 132s libdisorder0 libgfortran5 libjsoncpp25 liblapack3 libsmithwaterman0 132s libsuperlu6 tvc 132s 0 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 132s Need to get 5522 kB/5522 kB of archives. 132s After this operation, 17.6 MB of additional disk space will be used. 132s Get:1 /tmp/autopkgtest.CaLRSz/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [708 B] 132s Get:2 http://ftpmaster.internal/ubuntu oracular/main ppc64el libblas3 ppc64el 3.12.0-3build1 [227 kB] 132s Get:3 http://ftpmaster.internal/ubuntu oracular/main ppc64el libgfortran5 ppc64el 14.1.0-1ubuntu1 [573 kB] 132s Get:4 http://ftpmaster.internal/ubuntu oracular/main ppc64el liblapack3 ppc64el 3.12.0-3build1 [2804 kB] 133s Get:5 http://ftpmaster.internal/ubuntu oracular/universe ppc64el libarpack2t64 ppc64el 3.9.1-1.1build2 [107 kB] 133s Get:6 http://ftpmaster.internal/ubuntu oracular/universe ppc64el libsuperlu6 ppc64el 6.0.1+dfsg1-1build1 [238 kB] 133s Get:7 http://ftpmaster.internal/ubuntu oracular/universe ppc64el libarmadillo12 ppc64el 1:12.8.2+dfsg-1 [110 kB] 133s Get:8 http://ftpmaster.internal/ubuntu oracular/universe ppc64el libbamtools2.5.2 ppc64el 2.5.2+dfsg-5ubuntu1 [150 kB] 133s Get:9 http://ftpmaster.internal/ubuntu oracular/universe ppc64el libdisorder0 ppc64el 0.0.2+git20130809.8062ee1-4build1 [5046 B] 133s Get:10 http://ftpmaster.internal/ubuntu oracular/main ppc64el libjsoncpp25 ppc64el 1.9.5-6build1 [89.0 kB] 133s Get:11 http://ftpmaster.internal/ubuntu oracular/universe ppc64el libsmithwaterman0 ppc64el 0.0+git20160702.2610e25-12 [46.6 kB] 133s Get:12 http://ftpmaster.internal/ubuntu oracular/universe ppc64el tvc ppc64el 5.0.3+git20151221.80e144e+dfsg-5build2 [1172 kB] 133s Fetched 5522 kB in 1s (4157 kB/s) 133s Selecting previously unselected package libblas3:ppc64el. 133s (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 ... 72754 files and directories currently installed.) 133s Preparing to unpack .../00-libblas3_3.12.0-3build1_ppc64el.deb ... 133s Unpacking libblas3:ppc64el (3.12.0-3build1) ... 133s Selecting previously unselected package libgfortran5:ppc64el. 133s Preparing to unpack .../01-libgfortran5_14.1.0-1ubuntu1_ppc64el.deb ... 133s Unpacking libgfortran5:ppc64el (14.1.0-1ubuntu1) ... 133s Selecting previously unselected package liblapack3:ppc64el. 133s Preparing to unpack .../02-liblapack3_3.12.0-3build1_ppc64el.deb ... 133s Unpacking liblapack3:ppc64el (3.12.0-3build1) ... 133s Selecting previously unselected package libarpack2t64:ppc64el. 133s Preparing to unpack .../03-libarpack2t64_3.9.1-1.1build2_ppc64el.deb ... 133s Unpacking libarpack2t64:ppc64el (3.9.1-1.1build2) ... 133s Selecting previously unselected package libsuperlu6:ppc64el. 133s Preparing to unpack .../04-libsuperlu6_6.0.1+dfsg1-1build1_ppc64el.deb ... 133s Unpacking libsuperlu6:ppc64el (6.0.1+dfsg1-1build1) ... 133s Selecting previously unselected package libarmadillo12. 133s Preparing to unpack .../05-libarmadillo12_1%3a12.8.2+dfsg-1_ppc64el.deb ... 133s Unpacking libarmadillo12 (1:12.8.2+dfsg-1) ... 133s Selecting previously unselected package libbamtools2.5.2:ppc64el. 133s Preparing to unpack .../06-libbamtools2.5.2_2.5.2+dfsg-5ubuntu1_ppc64el.deb ... 133s Unpacking libbamtools2.5.2:ppc64el (2.5.2+dfsg-5ubuntu1) ... 133s Selecting previously unselected package libdisorder0:ppc64el. 133s Preparing to unpack .../07-libdisorder0_0.0.2+git20130809.8062ee1-4build1_ppc64el.deb ... 133s Unpacking libdisorder0:ppc64el (0.0.2+git20130809.8062ee1-4build1) ... 133s Selecting previously unselected package libjsoncpp25:ppc64el. 134s Preparing to unpack .../08-libjsoncpp25_1.9.5-6build1_ppc64el.deb ... 134s Unpacking libjsoncpp25:ppc64el (1.9.5-6build1) ... 134s Selecting previously unselected package libsmithwaterman0:ppc64el. 134s Preparing to unpack .../09-libsmithwaterman0_0.0+git20160702.2610e25-12_ppc64el.deb ... 134s Unpacking libsmithwaterman0:ppc64el (0.0+git20160702.2610e25-12) ... 134s Selecting previously unselected package tvc. 134s Preparing to unpack .../10-tvc_5.0.3+git20151221.80e144e+dfsg-5build2_ppc64el.deb ... 134s Unpacking tvc (5.0.3+git20151221.80e144e+dfsg-5build2) ... 134s Selecting previously unselected package autopkgtest-satdep. 134s Preparing to unpack .../11-1-autopkgtest-satdep.deb ... 134s Unpacking autopkgtest-satdep (0) ... 134s Setting up libdisorder0:ppc64el (0.0.2+git20130809.8062ee1-4build1) ... 134s Setting up libsmithwaterman0:ppc64el (0.0+git20160702.2610e25-12) ... 134s Setting up libblas3:ppc64el (3.12.0-3build1) ... 134s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 134s Setting up libjsoncpp25:ppc64el (1.9.5-6build1) ... 134s Setting up libbamtools2.5.2:ppc64el (2.5.2+dfsg-5ubuntu1) ... 134s Setting up libgfortran5:ppc64el (14.1.0-1ubuntu1) ... 134s Setting up liblapack3:ppc64el (3.12.0-3build1) ... 134s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 134s Setting up libarpack2t64:ppc64el (3.9.1-1.1build2) ... 134s Setting up libsuperlu6:ppc64el (6.0.1+dfsg1-1build1) ... 134s Setting up libarmadillo12 (1:12.8.2+dfsg-1) ... 134s Setting up tvc (5.0.3+git20151221.80e144e+dfsg-5build2) ... 134s Setting up autopkgtest-satdep (0) ... 134s Processing triggers for man-db (2.12.1-2) ... 134s Processing triggers for libc-bin (2.39-3.1ubuntu3) ... 136s (Reading database ... 72849 files and directories currently installed.) 136s Removing autopkgtest-satdep (0) ... 137s autopkgtest [01:19:38]: test run-unit-test: [----------------------- 137s Running Tests 137s [ Sat 2024-07-13 01:19:38 UTC ] 137s [ Sat 2024-07-13 01:19:38 UTC ] Task : Write effective bed 137s [ Sat 2024-07-13 01:19:38 UTC ] Command : /usr/bin/tvcutils validate_bed --reference "reference.fasta" --target-regions-bed "test_unmerged_detail.bed" --effective-bed "./effective_regions.bed" 137s [ Sat 2024-07-13 01:19:38 UTC ] 137s test_unmerged_detail.bed: Validation successful with 0 warnings and 0 errors 137s 137s [ Sat 2024-07-13 01:19:38 UTC ] Calling small INDELs and SNPs using tvc ... 137s [ Sat 2024-07-13 01:19:38 UTC ] 137s [ Sat 2024-07-13 01:19:38 UTC ] Task : Call small indels and SNPs 137s [ Sat 2024-07-13 01:19:38 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 137s [ Sat 2024-07-13 01:19:38 UTC ] 137s tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller 137s 137s INFO: No input VCF (Hotspot) file specified via -c,--input-vcf 137s INFO: Systematic error motif file not specified via -e 137s hp-max-length = 8 (integer, builtin default) 137s sse-prob-threshold = 0.2 (double, builtin default) 137s min-ratio-reads-non-sse-strand = 0.2 (double, builtin default) 137s sse-relative-safety-level = 0.025 (double, builtin default) 137s do-snp-realignment = true (boolean, builtin default) 137s do-mnp-realignment = true (boolean, builtin default) 137s realignment-threshold = 1 (double, builtin default) 137s indel-as-hpindel = false (boolean, builtin default) 137s data-quality-stringency = 4 (double, builtin default) 137s read-rejection-threshold = 0.5 (double, builtin default) 137s use-position-bias = false (boolean, builtin default) 137s position-bias-ref-fraction = 0.05 (double, builtin default) 137s position-bias = 0.75 (double, builtin default) 137s position-bias-pval = 0.05 (double, builtin default) 137s downsample-to-coverage = 2000 (integer, builtin default) 137s tune-sbias = 0.01 (double, builtin default) 137s suppress-reference-genotypes = true (boolean, builtin default) 137s suppress-nocall-genotypes = true (boolean, builtin default) 137s suppress-no-calls = true (boolean, builtin default) 137s heal-snps = true (boolean, builtin default) 137s snp-min-cov-each-strand = 0 (integer, builtin default) 137s snp-min-variant-score = 10 (double, builtin default) 137s snp-min-allele-freq = 0.2 (double, builtin default) 137s snp-min-coverage = 6 (integer, builtin default) 137s snp-strand-bias = 0.95 (double, builtin default) 137s snp-strand-bias-pval = 1 (double, builtin default) 137s mnp-min-cov-each-strand = 0 (integer, builtin default) 137s mnp-min-variant-score = 10 (double, builtin default) 137s mnp-min-allele-freq = 0.2 (double, builtin default) 137s mnp-min-coverage = 6 (integer, builtin default) 137s mnp-strand-bias = 0.95 (double, builtin default) 137s mnp-strand-bias-pval = 1 (double, builtin default) 137s indel-min-cov-each-strand = 1 (integer, builtin default) 137s indel-min-variant-score = 10 (double, builtin default) 137s indel-min-allele-freq = 0.2 (double, builtin default) 137s indel-min-coverage = 15 (integer, builtin default) 137s indel-strand-bias = 0.85 (double, builtin default) 137s indel-strand-bias-pval = 1 (double, builtin default) 137s hotspot-min-cov-each-strand = 0 (integer, builtin default) 137s hotspot-min-variant-score = 10 (double, builtin default) 137s hotspot-min-allele-freq = 0.2 (double, builtin default) 137s hotspot-min-coverage = 6 (integer, builtin default) 137s hotspot-strand-bias = 0.95 (double, builtin default) 137s hotspot-strand-bias-pval = 1 (double, builtin default) 137s max-flows-to-test = 10 (integer, builtin default) 137s min-delta-for-flow = 0.1 (double, builtin default) 137s prediction-precision = 30 (double, builtin default) 137s outlier-probability = 0.01 (double, builtin default) 137s germline-prior-strength = 0 (double, builtin default) 137s heavy-tailed = 3 (integer, builtin default) 137s filter-unusual-predictions = 0.3 (double, builtin default) 137s soft-clip-bias-checker = 0.1 (double, builtin default) 137s filter-deletion-predictions = 100 (double, builtin default) 137s filter-insertion-predictions = 100 (double, builtin default) 137s max-detail-level = 0 (integer, builtin default) 137s shift-likelihood-penalty = 0.3 (double, builtin default) 137s minimum-sigma-prior = 0.085 (double, builtin default) 137s slope-sigma-prior = 0.0084 (double, builtin default) 137s sigma-prior-weight = 1 (double, builtin default) 137s k-zero = 3 (double, builtin default) 137s num-threads = 12 (integer, command line option) 137s num-variants-per-thread = 250 (integer, builtin default) 137s use-sse-basecaller = false (boolean, builtin default) 137s do-json-diagnostic = false (boolean, builtin default) 137s do-minimal-diagnostic = false (boolean, builtin default) 137s process-input-positions-only = false (boolean, builtin default) 137s suppress-recalibration = true (boolean, builtin default) 137s resolve-clipped-bases = false (boolean, builtin default) 137s allow-indels = true (boolean, builtin default) 137s allow-snps = true (boolean, builtin default) 137s allow-mnps = true (boolean, builtin default) 137s allow-complex = false (boolean, builtin default) 137s left-align-indels = false (boolean, builtin default) 137s use-best-n-alleles = 2 (integer, builtin default) 137s use-input-allele-only = false (boolean, builtin default) 137s min-mapping-qv = 4 (integer, builtin default) 137s read-snp-limit = 10 (integer, builtin default) 137s read-max-mismatch-fraction = 1 (double, builtin default) 137s max-complex-gap = 1 (integer, builtin default) 137s gen-min-alt-allele-freq = 0.2 (double, builtin default) 137s gen-min-coverage = 6 (integer, builtin default) 137s gen-min-indel-alt-allele-freq = 0.2 (double, builtin default) 137s override-limits = false (boolean, builtin default) 137s Limit check parameter hp-max-length: lim. 1 <= 8? OK! 137s Limit check parameter sse-prob-threshold: lim. 0 <= 0.2 <= lim. 1? OK! 137s Limit check parameter min-ratio-reads-non-sse-strand: lim. 0 <= 0.2 <= lim. 1? OK! 137s Limit check parameter sse-relative-safety-level: lim. 0 <= 0.025 <= lim. 1? OK! 137s Limit check parameter realignment-threshold: lim. 0 <= 1 <= lim. 1? OK! 137s Limit check parameter data-quality-stringency: lim. 0 <= 4? OK! 137s Limit check parameter read-rejection-threshold: lim. 0 <= 0.5 <= lim. 1? OK! 137s Limit check parameter downsample-to-coverage: lim. 20 <= 2000 <= lim. 100000? OK! 137s Limit check parameter position-bias-ref-fraction: lim. 0 <= 0.05 <= lim. 1? OK! 137s Limit check parameter position-bias: lim. 0 <= 0.75 <= lim. 1? OK! 137s Limit check parameter position-bias-pval: lim. 0 <= 0.05 <= lim. 1? OK! 137s Limit check parameter tune-sbias: lim. 0.001 <= 0.01 <= lim. 1000? OK! 137s Limit check parameter snp-min-cov-each-strand: lim. 0 <= 0? OK! 137s Limit check parameter snp-min-variant-score: lim. 0 <= 10? OK! 137s Limit check parameter snp-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 137s Limit check parameter snp-min-coverage: lim. 0 <= 6? OK! 137s Limit check parameter snp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 137s Limit check parameter snp-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 137s Limit check parameter mnp-min-cov-each-strand: lim. 0 <= 0? OK! 137s Limit check parameter mnp-min-variant-score: lim. 0 <= 10? OK! 137s Limit check parameter mnp-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 137s Limit check parameter mnp-min-coverage: lim. 0 <= 6? OK! 137s Limit check parameter mnp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 137s Limit check parameter mnp-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 137s Limit check parameter indel-min-cov-each-strand: lim. 0 <= 1? OK! 137s Limit check parameter indel-min-variant-score: lim. 0 <= 10? OK! 137s Limit check parameter indel-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 137s Limit check parameter indel-min-coverage: lim. 0 <= 15? OK! 137s Limit check parameter indel-strand-bias: lim. 0.5 <= 0.85 <= lim. 1? OK! 137s Limit check parameter indel-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 137s Limit check parameter hotspot-min-cov-each-strand: lim. 0 <= 0? OK! 137s Limit check parameter hotspot-min-variant-score: lim. 0 <= 10? OK! 137s Limit check parameter hotspot-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 137s Limit check parameter hotspot-min-coverage: lim. 0 <= 6? OK! 137s Limit check parameter hotspot-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 137s Limit check parameter hotspot-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 137s Limit check parameter max-flows-to-test: lim. 1 <= 10 <= lim. 100? OK! 137s Limit check parameter min-delta-for-flow: lim. 0.01 <= 0.1 <= lim. 0.5? OK! 137s Limit check parameter prediction-precision: lim. 0.1 <= 30? OK! 137s Limit check parameter outlier-probability: lim. 0 <= 0.01 <= lim. 1? OK! 137s Limit check parameter germline-prior-strength: lim. 0 <= 0 <= lim. 1000? OK! 137s Limitprefix-exclude = 6 137s check parameter heavy-tailed: lim. 1 <= 3? OK! 137s Limit check parameter filter-unusual-predictions: lim. 0 <= 0.3? OK! 137s Limit check parameter soft-clip-bias-checker: lim. 0 <= 0.1 <= lim. 1? OK! 137s Limit check parameter filter-deletion-predictions: lim. 0 <= 100? OK! 137s Limit check parameter filter-insertion-predictions: lim. 0 <= 100? OK! 137s Limit check parameter max-detail-level: lim. 0 <= 0 <= lim. 10000? OK! 137s Limit check parameter shift-likelihood-penalty: lim. 0.01 <= 0.3? OK! 137s Limit check parameter minimum-sigma-prior: lim. 0.01 <= 0.085? OK! 137s Limit check parameter slope-sigma-prior: lim. 0 <= 0.0084? OK! 137s Limit check parameter sigma-prior-weight: lim. 0.01 <= 1? OK! 137s Limit check parameter k-zero: lim. 0 <= 3? OK! 137s Limit check parameter num-threads: lim. 1 <= 12 <= lim. 128? OK! 137s Limit check parameter num-variants-per-thread: lim. 1 <= 250 <= lim. 10000? OK! 137s Limit check parameter use-best-n-alleles: lim. 0 <= 2 <= lim. 20? OK! 137s Limit check parameter min-mapping-qv: lim. 0 <= 4? OK! 137s Limit check parameter read-snp-limit: lim. 0 <= 10? OK! 137s Limit check parameter read-max-mismatch-fraction: lim. 0 <= 1 <= lim. 1? OK! 137s Limit check parameter gen-min-alt-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 137s Limit check parameter gen-min-coverage: lim. 0 <= 6? OK! 137s Limit check parameter gen-min-indel-alt-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 137s TargetsManager: Loaded targets file test_unmerged_detail.bed 137s TargetsManager: 1 target(s) 137s TargetsManager: Trimming of AmpliSeq primers is enabled 137s SampleManager: Found 1 read group(s) and 1 sample(s). 137s SampleManager: Primary sample "85" (default) present in 1 read group(s) 137s TVC found a total of 1 different flow orders of max flow lengths: 500 137s Recalibration was detected from comment lines in bam file(s): 137s 1 unique blocks of recalibration info detected. 137s Recalibration model: suppressed 137s 137s [tvc] Normal termination. Processing time: 0 seconds. 137s 137s [ Sat 2024-07-13 01:19:38 UTC ] 137s [ Sat 2024-07-13 01:19:38 UTC ] Task : Assemble long indels 137s [ Sat 2024-07-13 01:19:38 UTC ] Command : /usr/bin/tvcassembly --reference reference.fasta --input-bam test.bam --target-file test_merged_plain.bed --output-vcf ./indel_assembly.vcf 137s [ Sat 2024-07-13 01:19:38 UTC ] 137s tvcassembly 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller - Long Indel Assembly 137s 137s kmer-len = 19 (integer, builtin default) 137s min-var-count = 5 (integer, builtin default) 137s short-suffix-match = 5 (integer, builtin default) 137s min-indel-size = 4 (integer, builtin default) 137s max-hp-length = 8 (integer, builtin default) 137s min-var-freq = 0.15 (double, builtin default) 137s min-var-score = 10 (double, builtin default) 137s relative-strand-bias = 0.8 (double, builtin default) 137s output-mnv = 0 (integer, builtin default) 137s TargetsManager: Loaded targets file test_merged_plain.bed 137s TargetsManager: 1 target(s) 137s SampleManager: Found 1 read group(s) and 1 sample(s). 137s SampleManager: Primary sample "85" (default) present in 1 read group(s) 137s [ Sat 2024-07-13 01:19:38 UTC ] 137s [ Sat 2024-07-13 01:19:38 UTC ] Task : Unify variants and annotations from all sources (tvc,IndelAssembly,hotpots) 137s [ Sat 2024-07-13 01:19:38 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" 137s [ Sat 2024-07-13 01:19:38 UTC ] 137s TargetsManager: Loaded targets file test_merged_plain.bed 137s TargetsManager: 1 target(s) 137s [ Sat 2024-07-13 01:19:38 UTC ] 137s [ Sat 2024-07-13 01:19:38 UTC ] Task : Generate uncompressed vcf 137s [ Sat 2024-07-13 01:19:38 UTC ] Command : gzip -dcf "./TSVC_variants.vcf.gz" > "./TSVC_variants.vcf" 137s [ Sat 2024-07-13 01:19:38 UTC ] 137s PASS 138s autopkgtest [01:19:39]: test run-unit-test: -----------------------] 138s autopkgtest [01:19:39]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 138s run-unit-test PASS 139s autopkgtest [01:19:40]: @@@@@@@@@@@@@@@@@@@@ summary 139s run-unit-test PASS 149s nova [W] Using flock in scalingstack-bos02-ppc64el 149s Creating nova instance adt-oracular-ppc64el-tvc-20240713-011720-juju-7f2275-prod-proposed-migration-environment-3-16b03b41-fc3b-4349-8e32-8c680be4fddd from image adt/ubuntu-oracular-ppc64el-server-20240713.img (UUID b28bdc0e-67ab-46b9-adc7-daedcc93171c)...