0s autopkgtest [08:03:45]: starting date and time: 2024-07-13 08:03:45+0000 0s autopkgtest [08:03:45]: git checkout: fd3bed09 nova: allow more retries for quota issues 0s autopkgtest [08:03:45]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.xgzi1wy9/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-2@bos03-arm64-22.secgroup --name adt-oracular-arm64-tvc-20240713-080345-juju-7f2275-prod-proposed-migration-environment-2-f62d92dc-6e0c-4d3a-8fd1-34628e03e0f7 --image adt/ubuntu-oracular-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,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/ 523s autopkgtest [08:12:28]: testbed dpkg architecture: arm64 524s autopkgtest [08:12:29]: testbed apt version: 2.9.6 524s autopkgtest [08:12:29]: @@@@@@@@@@@@@@@@@@@@ test bed setup 524s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB] 525s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [375 kB] 525s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [51.3 kB] 525s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2576 B] 525s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8548 B] 525s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 Packages [112 kB] 525s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 c-n-f Metadata [2116 B] 525s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted arm64 Packages [43.9 kB] 525s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted arm64 c-n-f Metadata [364 B] 525s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 Packages [421 kB] 525s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 c-n-f Metadata [8752 B] 525s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse arm64 Packages [7596 B] 525s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse arm64 c-n-f Metadata [276 B] 532s Fetched 1159 kB in 2s (715 kB/s) 532s Reading package lists... 536s Reading package lists... 537s Building dependency tree... 537s Reading state information... 537s Calculating upgrade... 538s The following packages will be upgraded: 538s libc-bin libc-dev-bin libc-devtools libc6 libc6-dev locales 538s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 538s Need to get 9208 kB of archives. 538s After this operation, 29.7 kB disk space will be freed. 538s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libc-devtools arm64 2.39-3.1ubuntu3 [27.7 kB] 538s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libc6-dev arm64 2.39-3.1ubuntu3 [1591 kB] 539s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libc-dev-bin arm64 2.39-3.1ubuntu3 [19.7 kB] 539s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libc6 arm64 2.39-3.1ubuntu3 [2770 kB] 539s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libc-bin arm64 2.39-3.1ubuntu3 [579 kB] 539s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 locales all 2.39-3.1ubuntu3 [4220 kB] 544s Preconfiguring packages ... 555s Fetched 9208 kB in 1s (9723 kB/s) 558s (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 ... 78392 files and directories currently installed.) 558s Preparing to unpack .../libc-devtools_2.39-3.1ubuntu3_arm64.deb ... 558s Unpacking libc-devtools (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 559s Preparing to unpack .../libc6-dev_2.39-3.1ubuntu3_arm64.deb ... 559s Unpacking libc6-dev:arm64 (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 561s Preparing to unpack .../libc-dev-bin_2.39-3.1ubuntu3_arm64.deb ... 561s Unpacking libc-dev-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 565s Preparing to unpack .../libc6_2.39-3.1ubuntu3_arm64.deb ... 569s Unpacking libc6:arm64 (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 573s Setting up libc6:arm64 (2.39-3.1ubuntu3) ... 574s Error: Could not restart systemd, systemd binary not working 576s (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 ... 78392 files and directories currently installed.) 576s Preparing to unpack .../libc-bin_2.39-3.1ubuntu3_arm64.deb ... 576s Unpacking libc-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 578s Setting up libc-bin (2.39-3.1ubuntu3) ... 581s (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 ... 78392 files and directories currently installed.) 581s Preparing to unpack .../locales_2.39-3.1ubuntu3_all.deb ... 581s Unpacking locales (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 583s Setting up locales (2.39-3.1ubuntu3) ... 602s Generating locales (this might take a while)... 623s en_US.UTF-8... done 623s Generation complete. 625s Setting up libc-dev-bin (2.39-3.1ubuntu3) ... 625s Setting up libc-devtools (2.39-3.1ubuntu3) ... 625s Setting up libc6-dev:arm64 (2.39-3.1ubuntu3) ... 625s Processing triggers for man-db (2.12.1-2) ... 627s Processing triggers for systemd (256-1ubuntu1) ... 639s Reading package lists... 640s Building dependency tree... 640s Reading state information... 641s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 643s Hit:1 http://ftpmaster.internal/ubuntu oracular InRelease 643s Hit:2 http://ftpmaster.internal/ubuntu oracular-updates InRelease 643s Hit:3 http://ftpmaster.internal/ubuntu oracular-security InRelease 643s Hit:4 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 651s Reading package lists... 652s Reading package lists... 652s Building dependency tree... 652s Reading state information... 653s Calculating upgrade... 653s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 653s Reading package lists... 654s Building dependency tree... 654s Reading state information... 654s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 659s autopkgtest [08:14:44]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 02:32:42 UTC 2024 660s autopkgtest [08:14:45]: @@@@@@@@@@@@@@@@@@@@ apt-source tvc 664s Get:1 http://ftpmaster.internal/ubuntu oracular/universe tvc 5.0.3+git20151221.80e144e+dfsg-5build2 (dsc) [2301 B] 664s Get:2 http://ftpmaster.internal/ubuntu oracular/universe tvc 5.0.3+git20151221.80e144e+dfsg-5build2 (tar) [745 kB] 664s Get:3 http://ftpmaster.internal/ubuntu oracular/universe tvc 5.0.3+git20151221.80e144e+dfsg-5build2 (diff) [9976 B] 665s gpgv: Signature made Fri Oct 27 16:50:16 2023 UTC 665s gpgv: using RSA key 4D0BE12F0E4776D8AACE9696E66C775AEBFE6C7D 665s gpgv: Can't check signature: No public key 665s dpkg-source: warning: cannot verify inline signature for ./tvc_5.0.3+git20151221.80e144e+dfsg-5build2.dsc: no acceptable signature found 666s autopkgtest [08:14:51]: testing package tvc version 5.0.3+git20151221.80e144e+dfsg-5build2 666s autopkgtest [08:14:51]: build not needed 667s autopkgtest [08:14:52]: test run-unit-test: preparing testbed 669s Reading package lists... 669s Building dependency tree... 669s Reading state information... 669s Starting pkgProblemResolver with broken count: 0 669s Starting 2 pkgProblemResolver with broken count: 0 669s Done 670s The following additional packages will be installed: 670s libarmadillo12 libarpack2t64 libbamtools2.5.2 libblas3 libdisorder0 670s libgfortran5 libjsoncpp25 liblapack3 libsmithwaterman0 libsuperlu6 tvc 670s The following NEW packages will be installed: 670s autopkgtest-satdep libarmadillo12 libarpack2t64 libbamtools2.5.2 libblas3 670s libdisorder0 libgfortran5 libjsoncpp25 liblapack3 libsmithwaterman0 670s libsuperlu6 tvc 670s 0 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 670s Need to get 4493 kB/4494 kB of archives. 670s After this operation, 13.6 MB of additional disk space will be used. 670s Get:1 /tmp/autopkgtest.I0aAG9/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [700 B] 671s Get:2 http://ftpmaster.internal/ubuntu oracular/main arm64 libblas3 arm64 3.12.0-3build1 [143 kB] 671s Get:3 http://ftpmaster.internal/ubuntu oracular/main arm64 libgfortran5 arm64 14.1.0-1ubuntu1 [443 kB] 671s Get:4 http://ftpmaster.internal/ubuntu oracular/main arm64 liblapack3 arm64 3.12.0-3build1 [2241 kB] 671s Get:5 http://ftpmaster.internal/ubuntu oracular/universe arm64 libarpack2t64 arm64 3.9.1-1.1build2 [90.6 kB] 671s Get:6 http://ftpmaster.internal/ubuntu oracular/universe arm64 libsuperlu6 arm64 6.0.1+dfsg1-1build1 [166 kB] 671s Get:7 http://ftpmaster.internal/ubuntu oracular/universe arm64 libarmadillo12 arm64 1:12.8.2+dfsg-1 [105 kB] 671s Get:8 http://ftpmaster.internal/ubuntu oracular/universe arm64 libbamtools2.5.2 arm64 2.5.2+dfsg-5ubuntu1 [130 kB] 671s Get:9 http://ftpmaster.internal/ubuntu oracular/universe arm64 libdisorder0 arm64 0.0.2+git20130809.8062ee1-4build1 [4604 B] 671s Get:10 http://ftpmaster.internal/ubuntu oracular/main arm64 libjsoncpp25 arm64 1.9.5-6build1 [78.2 kB] 671s Get:11 http://ftpmaster.internal/ubuntu oracular/universe arm64 libsmithwaterman0 arm64 0.0+git20160702.2610e25-12 [35.9 kB] 671s Get:12 http://ftpmaster.internal/ubuntu oracular/universe arm64 tvc arm64 5.0.3+git20151221.80e144e+dfsg-5build2 [1056 kB] 673s Fetched 4493 kB in 1s (4998 kB/s) 673s Selecting previously unselected package libblas3:arm64. 673s (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 ... 78392 files and directories currently installed.) 673s Preparing to unpack .../00-libblas3_3.12.0-3build1_arm64.deb ... 674s Unpacking libblas3:arm64 (3.12.0-3build1) ... 674s Selecting previously unselected package libgfortran5:arm64. 674s Preparing to unpack .../01-libgfortran5_14.1.0-1ubuntu1_arm64.deb ... 674s Unpacking libgfortran5:arm64 (14.1.0-1ubuntu1) ... 674s Selecting previously unselected package liblapack3:arm64. 674s Preparing to unpack .../02-liblapack3_3.12.0-3build1_arm64.deb ... 674s Unpacking liblapack3:arm64 (3.12.0-3build1) ... 674s Selecting previously unselected package libarpack2t64:arm64. 675s Preparing to unpack .../03-libarpack2t64_3.9.1-1.1build2_arm64.deb ... 675s Unpacking libarpack2t64:arm64 (3.9.1-1.1build2) ... 675s Selecting previously unselected package libsuperlu6:arm64. 675s Preparing to unpack .../04-libsuperlu6_6.0.1+dfsg1-1build1_arm64.deb ... 675s Unpacking libsuperlu6:arm64 (6.0.1+dfsg1-1build1) ... 675s Selecting previously unselected package libarmadillo12. 675s Preparing to unpack .../05-libarmadillo12_1%3a12.8.2+dfsg-1_arm64.deb ... 675s Unpacking libarmadillo12 (1:12.8.2+dfsg-1) ... 675s Selecting previously unselected package libbamtools2.5.2:arm64. 675s Preparing to unpack .../06-libbamtools2.5.2_2.5.2+dfsg-5ubuntu1_arm64.deb ... 675s Unpacking libbamtools2.5.2:arm64 (2.5.2+dfsg-5ubuntu1) ... 675s Selecting previously unselected package libdisorder0:arm64. 675s Preparing to unpack .../07-libdisorder0_0.0.2+git20130809.8062ee1-4build1_arm64.deb ... 675s Unpacking libdisorder0:arm64 (0.0.2+git20130809.8062ee1-4build1) ... 675s Selecting previously unselected package libjsoncpp25:arm64. 676s Preparing to unpack .../08-libjsoncpp25_1.9.5-6build1_arm64.deb ... 676s Unpacking libjsoncpp25:arm64 (1.9.5-6build1) ... 676s Selecting previously unselected package libsmithwaterman0:arm64. 676s Preparing to unpack .../09-libsmithwaterman0_0.0+git20160702.2610e25-12_arm64.deb ... 676s Unpacking libsmithwaterman0:arm64 (0.0+git20160702.2610e25-12) ... 676s Selecting previously unselected package tvc. 676s Preparing to unpack .../10-tvc_5.0.3+git20151221.80e144e+dfsg-5build2_arm64.deb ... 676s Unpacking tvc (5.0.3+git20151221.80e144e+dfsg-5build2) ... 676s Selecting previously unselected package autopkgtest-satdep. 676s Preparing to unpack .../11-1-autopkgtest-satdep.deb ... 676s Unpacking autopkgtest-satdep (0) ... 678s Setting up libdisorder0:arm64 (0.0.2+git20130809.8062ee1-4build1) ... 678s Setting up libsmithwaterman0:arm64 (0.0+git20160702.2610e25-12) ... 678s Setting up libblas3:arm64 (3.12.0-3build1) ... 678s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 678s Setting up libjsoncpp25:arm64 (1.9.5-6build1) ... 678s Setting up libbamtools2.5.2:arm64 (2.5.2+dfsg-5ubuntu1) ... 678s Setting up libgfortran5:arm64 (14.1.0-1ubuntu1) ... 678s Setting up liblapack3:arm64 (3.12.0-3build1) ... 678s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 678s Setting up libarpack2t64:arm64 (3.9.1-1.1build2) ... 678s Setting up libsuperlu6:arm64 (6.0.1+dfsg1-1build1) ... 678s Setting up libarmadillo12 (1:12.8.2+dfsg-1) ... 678s Setting up tvc (5.0.3+git20151221.80e144e+dfsg-5build2) ... 678s Setting up autopkgtest-satdep (0) ... 678s Processing triggers for man-db (2.12.1-2) ... 678s Processing triggers for libc-bin (2.39-3.1ubuntu3) ... 684s (Reading database ... 78487 files and directories currently installed.) 684s Removing autopkgtest-satdep (0) ... 686s autopkgtest [08:15:11]: test run-unit-test: [----------------------- 691s Running Tests 691s [ Sat 2024-07-13 08:15:16 UTC ] 691s [ Sat 2024-07-13 08:15:16 UTC ] Task : Write effective bed 691s [ Sat 2024-07-13 08:15:16 UTC ] Command : /usr/bin/tvcutils validate_bed --reference "reference.fasta" --target-regions-bed "test_unmerged_detail.bed" --effective-bed "./effective_regions.bed" 691s [ Sat 2024-07-13 08:15:16 UTC ] 692s test_unmerged_detail.bed: Validation successful with 0 warnings and 0 errors 692s 692s [ Sat 2024-07-13 08:15:17 UTC ] Calling small INDELs and SNPs using tvc ... 692s [ Sat 2024-07-13 08:15:17 UTC ] 692s [ Sat 2024-07-13 08:15:17 UTC ] Task : Call small indels and SNPs 692s [ Sat 2024-07-13 08:15:17 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 692s [ Sat 2024-07-13 08:15:17 UTC ] 693s tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller 693s 693s INFO: No input VCF (Hotspot) file specified via -c,--input-vcf 693s INFO: Systematic error motif file not specified via -e 693s hp-max-length = 8 (integer, builtin default) 693s sse-prob-threshold = 0.2 (double, builtin default) 693s min-ratio-reads-non-sse-strand = 0.2 (double, builtin default) 693s sse-relative-safety-level = 0.025 (double, builtin default) 693s do-snp-realignment = true (boolean, builtin default) 693s do-mnp-realignment = true (boolean, builtin default) 693s realignment-threshold = 1 (double, builtin default) 693s indel-as-hpindel = false (boolean, builtin default) 693s prefix-exclude = 6 693s data-quality-stringency = 4 (double, builtin default) 693s read-rejection-threshold = 0.5 (double, builtin default) 693s use-position-bias = false (boolean, builtin default) 693s position-bias-ref-fraction = 0.05 (double, builtin default) 693s position-bias = 0.75 (double, builtin default) 693s position-bias-pval = 0.05 (double, builtin default) 693s downsample-to-coverage = 2000 (integer, builtin default) 693s tune-sbias = 0.01 (double, builtin default) 693s suppress-reference-genotypes = true (boolean, builtin default) 693s suppress-nocall-genotypes = true (boolean, builtin default) 693s suppress-no-calls = true (boolean, builtin default) 693s heal-snps = true (boolean, builtin default) 693s snp-min-cov-each-strand = 0 (integer, builtin default) 693s snp-min-variant-score = 10 (double, builtin default) 693s snp-min-allele-freq = 0.2 (double, builtin default) 693s snp-min-coverage = 6 (integer, builtin default) 693s snp-strand-bias = 0.95 (double, builtin default) 693s snp-strand-bias-pval = 1 (double, builtin default) 693s mnp-min-cov-each-strand = 0 (integer, builtin default) 693s mnp-min-variant-score = 10 (double, builtin default) 693s mnp-min-allele-freq = 0.2 (double, builtin default) 693s mnp-min-coverage = 6 (integer, builtin default) 693s mnp-strand-bias = 0.95 (double, builtin default) 693s mnp-strand-bias-pval = 1 (double, builtin default) 693s indel-min-cov-each-strand = 1 (integer, builtin default) 693s indel-min-variant-score = 10 (double, builtin default) 693s indel-min-allele-freq = 0.2 (double, builtin default) 693s indel-min-coverage = 15 (integer, builtin default) 693s indel-strand-bias = 0.85 (double, builtin default) 693s indel-strand-bias-pval = 1 (double, builtin default) 693s hotspot-min-cov-each-strand = 0 (integer, builtin default) 693s hotspot-min-variant-score = 10 (double, builtin default) 693s hotspot-min-allele-freq = 0.2 (double, builtin default) 693s hotspot-min-coverage = 6 (integer, builtin default) 693s hotspot-strand-bias = 0.95 (double, builtin default) 693s hotspot-strand-bias-pval = 1 (double, builtin default) 693s max-flows-to-test = 10 (integer, builtin default) 693s min-delta-for-flow = 0.1 (double, builtin default) 693s prediction-precision = 30 (double, builtin default) 693s outlier-probability = 0.01 (double, builtin default) 693s germline-prior-strength = 0 (double, builtin default) 693s heavy-tailed = 3 (integer, builtin default) 693s filter-unusual-predictions = 0.3 (double, builtin default) 693s soft-clip-bias-checker = 0.1 (double, builtin default) 693s filter-deletion-predictions = 100 (double, builtin default) 693s filter-insertion-predictions = 100 (double, builtin default) 693s max-detail-level = 0 (integer, builtin default) 693s shift-likelihood-penalty = 0.3 (double, builtin default) 693s minimum-sigma-prior = 0.085 (double, builtin default) 693s slope-sigma-prior = 0.0084 (double, builtin default) 693s sigma-prior-weight = 1 (double, builtin default) 693s k-zero = 3 (double, builtin default) 693s num-threads = 12 (integer, command line option) 693s num-variants-per-thread = 250 (integer, builtin default) 693s use-sse-basecaller = false (boolean, builtin default) 693s do-json-diagnostic = false (boolean, builtin default) 693s do-minimal-diagnostic = false (boolean, builtin default) 693s process-input-positions-only = false (boolean, builtin default) 693s suppress-recalibration = true (boolean, builtin default) 693s resolve-clipped-bases = false (boolean, builtin default) 693s allow-indels = true (boolean, builtin default) 693s allow-snps = true (boolean, builtin default) 693s allow-mnps = true (boolean, builtin default) 693s allow-complex = false (boolean, builtin default) 693s left-align-indels = false (boolean, builtin default) 693s use-best-n-alleles = 2 (integer, builtin default) 693s use-input-allele-only = false (boolean, builtin default) 693s min-mapping-qv = 4 (integer, builtin default) 693s read-snp-limit = 10 (integer, builtin default) 693s read-max-mismatch-fraction = 1 (double, builtin default) 693s max-complex-gap = 1 (integer, builtin default) 693s gen-min-alt-allele-freq = 0.2 (double, builtin default) 693s gen-min-coverage = 6 (integer, builtin default) 693s gen-min-indel-alt-allele-freq = 0.2 (double, builtin default) 693s override-limits = false (boolean, builtin default) 693s Limit check parameter hp-max-length: lim. 1 <= 8? OK! 693s Limit check parameter sse-prob-threshold: lim. 0 <= 0.2 <= lim. 1? OK! 693s Limit check parameter min-ratio-reads-non-sse-strand: lim. 0 <= 0.2 <= lim. 1? OK! 693s Limit check parameter sse-relative-safety-level: lim. 0 <= 0.025 <= lim. 1? OK! 693s Limit check parameter realignment-threshold: lim. 0 <= 1 <= lim. 1? OK! 693s Limit check parameter data-quality-stringency: lim. 0 <= 4? OK! 693s Limit check parameter read-rejection-threshold: lim. 0 <= 0.5 <= lim. 1? OK! 693s Limit check parameter downsample-to-coverage: lim. 20 <= 2000 <= lim. 100000? OK! 693s Limit check parameter position-bias-ref-fraction: lim. 0 <= 0.05 <= lim. 1? OK! 693s Limit check parameter position-bias: lim. 0 <= 0.75 <= lim. 1? OK! 693s Limit check parameter position-bias-pval: lim. 0 <= 0.05 <= lim. 1? OK! 693s Limit check parameter tune-sbias: lim. 0.001 <= 0.01 <= lim. 1000? OK! 693s Limit check parameter snp-min-cov-each-strand: lim. 0 <= 0? OK! 693s Limit check parameter snp-min-variant-score: lim. 0 <= 10? OK! 693s Limit check parameter snp-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 693s Limit check parameter snp-min-coverage: lim. 0 <= 6? OK! 693s Limit check parameter snp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 693s Limit check parameter snp-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 693s Limit check parameter mnp-min-cov-each-strand: lim. 0 <= 0? OK! 693s Limit check parameter mnp-min-variant-score: lim. 0 <= 10? OK! 693s Limit check parameter mnp-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 693s Limit check parameter mnp-min-coverage: lim. 0 <= 6? OK! 693s Limit check parameter mnp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 693s Limit check parameter mnp-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 693s Limit check parameter indel-min-cov-each-strand: lim. 0 <= 1? OK! 693s Limit check parameter indel-min-variant-score: lim. 0 <= 10? OK! 693s Limit check parameter indel-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 693s Limit check parameter indel-min-coverage: lim. 0 <= 15? OK! 693s Limit check parameter indel-strand-bias: lim. 0.5 <= 0.85 <= lim. 1? OK! 693s Limit check parameter indel-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 693s Limit check parameter hotspot-min-cov-each-strand: lim. 0 <= 0? OK! 693s Limit check parameter hotspot-min-variant-score: lim. 0 <= 10? OK! 693s Limit check parameter hotspot-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 693s Limit check parameter hotspot-min-coverage: lim. 0 <= 6? OK! 693s Limit check parameter hotspot-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 693s Limit check parameter hotspot-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 693s Limit check parameter max-flows-to-test: lim. 1 <= 10 <= lim. 100? OK! 693s Limit check parameter min-delta-for-flow: lim. 0.01 <= 0.1 <= lim. 0.5? OK! 693s Limit check parameter prediction-precision: lim. 0.1 <= 30? OK! 693s Limit check parameter outlier-probability: lim. 0 <= 0.01 <= lim. 1? OK! 693s Limit check parameter germline-prior-strength: lim. 0 <= 0 <= lim. 1000? OK! 693s Limit check parameter heavy-tailed: lim. 1 <= 3? OK! 693s Limit check parameter filter-unusual-predictions: lim. 0 <= 0.3? OK! 693s Limit check parameter soft-clip-bias-checker: lim. 0 <= 0.1 <= lim. 1? OK! 693s Limit check parameter filter-deletion-predictions: lim. 0 <= 100? OK! 693s Limit check parameter filter-insertion-predictions: lim. 0 <= 100? OK! 693s Limit check parameter max-detail-level: lim. 0 <= 0 <= lim. 10000? OK! 693s Limit check parameter shift-likelihood-penalty: lim. 0.01 <= 0.3? OK! 693s Limit check parameter minimum-sigma-prior: lim. 0.01 <= 0.085? OK! 693s Limit check parameter slope-sigma-prior: lim. 0 <= 0.0084? OK! 693s Limit check parameter sigma-prior-weight: lim. 0.01 <= 1? OK! 693s Limit check parameter k-zero: lim. 0 <= 3? OK! 693s Limit check parameter num-threads: lim. 1 <= 12 <= lim. 128? OK! 693s Limit check parameter num-variants-per-thread: lim. 1 <= 250 <= lim. 10000? OK! 693s Limit check parameter use-best-n-alleles: lim. 0 <= 2 <= lim. 20? OK! 693s Limit check parameter min-mapping-qv: lim. 0 <= 4? OK! 693s Limit check parameter read-snp-limit: lim. 0 <= 10? OK! 693s Limit check parameter read-max-mismatch-fraction: lim. 0 <= 1 <= lim. 1? OK! 693s Limit check parameter gen-min-alt-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 693s Limit check parameter gen-min-coverage: lim. 0 <= 6? OK! 693s Limit check parameter gen-min-indel-alt-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 693s TargetsManager: Loaded targets file test_unmerged_detail.bed 693s TargetsManager: 1 target(s) 693s TargetsManager: Trimming of AmpliSeq primers is enabled 693s SampleManager: Found 1 read group(s) and 1 sample(s). 693s SampleManager: Primary sample "85" (default) present in 1 read group(s) 693s TVC found a total of 1 different flow orders of max flow lengths: 500 693s Recalibration was detected from comment lines in bam file(s): 693s 1 unique blocks of recalibration info detected. 693s Recalibration model: suppressed 693s 693s [tvc] Normal termination. Processing time: 1 seconds. 693s 693s [ Sat 2024-07-13 08:15:18 UTC ] 693s [ Sat 2024-07-13 08:15:18 UTC ] Task : Assemble long indels 693s [ Sat 2024-07-13 08:15:18 UTC ] Command : /usr/bin/tvcassembly --reference reference.fasta --input-bam test.bam --target-file test_merged_plain.bed --output-vcf ./indel_assembly.vcf 693s [ Sat 2024-07-13 08:15:18 UTC ] 693s tvcassembly 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller - Long Indel Assembly 693s 693s kmer-len = 19 (integer, builtin default) 693s min-var-count = 5 (integer, builtin default) 693s short-suffix-match = 5 (integer, builtin default) 693s min-indel-size = 4 (integer, builtin default) 693s max-hp-length = 8 (integer, builtin default) 693s min-var-freq = 0.15 (double, builtin default) 693s min-var-score = 10 (double, builtin default) 693s relative-strand-bias = 0.8 (double, builtin default) 693s output-mnv = 0 (integer, builtin default) 693s TargetsManager: Loaded targets file test_merged_plain.bed 693s TargetsManager: 1 target(s) 693s SampleManager: Found 1 read group(s) and 1 sample(s). 693s SampleManager: Primary sample "85" (default) present in 1 read group(s) 693s [ Sat 2024-07-13 08:15:18 UTC ] 693s [ Sat 2024-07-13 08:15:18 UTC ] Task : Unify variants and annotations from all sources (tvc,IndelAssembly,hotpots) 693s [ Sat 2024-07-13 08:15:18 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" 693s [ Sat 2024-07-13 08:15:18 UTC ] 693s TargetsManager: Loaded targets file test_merged_plain.bed 693s TargetsManager: 1 target(s) 693s [ Sat 2024-07-13 08:15:18 UTC ] 693s [ Sat 2024-07-13 08:15:18 UTC ] Task : Generate uncompressed vcf 693s [ Sat 2024-07-13 08:15:18 UTC ] Command : gzip -dcf "./TSVC_variants.vcf.gz" > "./TSVC_variants.vcf" 693s [ Sat 2024-07-13 08:15:18 UTC ] 693s PASS 694s autopkgtest [08:15:19]: test run-unit-test: -----------------------] 696s run-unit-test PASS 696s autopkgtest [08:15:21]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 698s autopkgtest [08:15:23]: @@@@@@@@@@@@@@@@@@@@ summary 698s run-unit-test PASS 760s nova [W] Skipping flock in bos03-arm64 760s Creating nova instance adt-oracular-arm64-tvc-20240713-080345-juju-7f2275-prod-proposed-migration-environment-2-f62d92dc-6e0c-4d3a-8fd1-34628e03e0f7 from image adt/ubuntu-oracular-arm64-server-20240713.img (UUID 3c579e1a-9694-4cfa-8fb2-317ade717652)...