5s autopkgtest [19:50:39]: starting date and time: 2024-07-12 19:50:39+0000 5s autopkgtest [19:50:39]: git checkout: fd3bed09 nova: allow more retries for quota issues 5s autopkgtest [19:50:39]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work._u733ope/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@lcy02-133.secgroup --name adt-oracular-amd64-tvc-20240712-195025-juju-7f2275-prod-proposed-migration-environment-2-70034c9f-e004-414f-bcb3-f37f90a888f4 --image adt/ubuntu-oracular-amd64-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/ 183s autopkgtest [19:53:37]: testbed dpkg architecture: amd64 183s autopkgtest [19:53:37]: testbed apt version: 2.9.6 183s autopkgtest [19:53:37]: @@@@@@@@@@@@@@@@@@@@ test bed setup 204s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB] 204s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [371 kB] 204s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8548 B] 204s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [48.0 kB] 204s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [3288 B] 204s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 Packages [99.8 kB] 204s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main i386 Packages [71.2 kB] 204s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 c-n-f Metadata [2104 B] 204s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted i386 Packages [6244 B] 204s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 Packages [34.9 kB] 204s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 c-n-f Metadata [368 B] 204s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 Packages [393 kB] 204s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/universe i386 Packages [236 kB] 204s Get:14 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 c-n-f Metadata [9228 B] 204s Get:15 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse i386 Packages [3052 B] 204s Get:16 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 Packages [7976 B] 204s Get:17 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 c-n-f Metadata [276 B] 205s Fetched 1422 kB in 0s (5176 kB/s) 206s Reading package lists... 207s Reading package lists... 208s Building dependency tree... 208s Reading state information... 208s Calculating upgrade... 208s The following packages will be upgraded: 208s libc-bin libc-dev-bin libc-devtools libc6 libc6-dev locales 209s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 209s Need to get 10.3 MB of archives. 209s After this operation, 34.8 kB of additional disk space will be used. 209s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc-devtools amd64 2.39-3.1ubuntu3 [29.3 kB] 209s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc6-dev amd64 2.39-3.1ubuntu3 [2120 kB] 209s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc-dev-bin amd64 2.39-3.1ubuntu3 [20.4 kB] 209s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc6 amd64 2.39-3.1ubuntu3 [3262 kB] 209s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc-bin amd64 2.39-3.1ubuntu3 [680 kB] 209s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 locales all 2.39-3.1ubuntu3 [4220 kB] 209s Preconfiguring packages ... 209s Fetched 10.3 MB in 0s (70.5 MB/s) 209s (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 ... 74486 files and directories currently installed.) 209s Preparing to unpack .../libc-devtools_2.39-3.1ubuntu3_amd64.deb ... 209s Unpacking libc-devtools (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 209s Preparing to unpack .../libc6-dev_2.39-3.1ubuntu3_amd64.deb ... 209s Unpacking libc6-dev:amd64 (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 210s Preparing to unpack .../libc-dev-bin_2.39-3.1ubuntu3_amd64.deb ... 210s Unpacking libc-dev-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 210s Preparing to unpack .../libc6_2.39-3.1ubuntu3_amd64.deb ... 210s Unpacking libc6:amd64 (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 210s Setting up libc6:amd64 (2.39-3.1ubuntu3) ... 210s Error: Could not restart systemd, systemd binary not working 210s (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 ... 74486 files and directories currently installed.) 210s Preparing to unpack .../libc-bin_2.39-3.1ubuntu3_amd64.deb ... 210s Unpacking libc-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 210s Setting up libc-bin (2.39-3.1ubuntu3) ... 210s (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 ... 74486 files and directories currently installed.) 210s Preparing to unpack .../locales_2.39-3.1ubuntu3_all.deb ... 210s Unpacking locales (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 211s Setting up locales (2.39-3.1ubuntu3) ... 211s Generating locales (this might take a while)... 213s en_US.UTF-8... done 213s Generation complete. 213s Setting up libc-dev-bin (2.39-3.1ubuntu3) ... 213s Setting up libc-devtools (2.39-3.1ubuntu3) ... 213s Setting up libc6-dev:amd64 (2.39-3.1ubuntu3) ... 213s Processing triggers for man-db (2.12.1-2) ... 214s Processing triggers for systemd (256-1ubuntu1) ... 215s Reading package lists... 215s Building dependency tree... 215s Reading state information... 216s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 218s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 218s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 218s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 218s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 220s Reading package lists... 220s Reading package lists... 220s Building dependency tree... 220s Reading state information... 220s Calculating upgrade... 221s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 221s Reading package lists... 221s Building dependency tree... 221s Reading state information... 221s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 243s autopkgtest [19:54:37]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 00:40:06 UTC 2024 244s autopkgtest [19:54:38]: @@@@@@@@@@@@@@@@@@@@ apt-source tvc 246s Get:1 http://ftpmaster.internal/ubuntu oracular/universe tvc 5.0.3+git20151221.80e144e+dfsg-5build2 (dsc) [2301 B] 246s Get:2 http://ftpmaster.internal/ubuntu oracular/universe tvc 5.0.3+git20151221.80e144e+dfsg-5build2 (tar) [745 kB] 246s Get:3 http://ftpmaster.internal/ubuntu oracular/universe tvc 5.0.3+git20151221.80e144e+dfsg-5build2 (diff) [9976 B] 247s gpgv: Signature made Fri Oct 27 16:50:16 2023 UTC 247s gpgv: using RSA key 4D0BE12F0E4776D8AACE9696E66C775AEBFE6C7D 247s gpgv: Can't check signature: No public key 247s dpkg-source: warning: cannot verify inline signature for ./tvc_5.0.3+git20151221.80e144e+dfsg-5build2.dsc: no acceptable signature found 247s autopkgtest [19:54:41]: testing package tvc version 5.0.3+git20151221.80e144e+dfsg-5build2 247s autopkgtest [19:54:41]: build not needed 248s autopkgtest [19:54:42]: test run-unit-test: preparing testbed 253s Reading package lists... 253s Building dependency tree... 253s Reading state information... 253s Starting pkgProblemResolver with broken count: 0 253s Starting 2 pkgProblemResolver with broken count: 0 253s Done 254s The following additional packages will be installed: 254s libarmadillo12 libarpack2t64 libbamtools2.5.2 libblas3 libdisorder0 254s libgfortran5 libjsoncpp25 liblapack3 libsmithwaterman0 libsuperlu6 tvc 254s The following NEW packages will be installed: 254s autopkgtest-satdep libarmadillo12 libarpack2t64 libbamtools2.5.2 libblas3 254s libdisorder0 libgfortran5 libjsoncpp25 liblapack3 libsmithwaterman0 254s libsuperlu6 tvc 254s 0 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 254s Need to get 5582 kB/5583 kB of archives. 254s After this operation, 16.7 MB of additional disk space will be used. 254s Get:1 /tmp/autopkgtest.zLN0HD/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [700 B] 254s Get:2 http://ftpmaster.internal/ubuntu oracular/main amd64 libblas3 amd64 3.12.0-3build1 [238 kB] 254s Get:3 http://ftpmaster.internal/ubuntu oracular/main amd64 libgfortran5 amd64 14.1.0-1ubuntu1 [928 kB] 254s Get:4 http://ftpmaster.internal/ubuntu oracular/main amd64 liblapack3 amd64 3.12.0-3build1 [2650 kB] 254s Get:5 http://ftpmaster.internal/ubuntu oracular/universe amd64 libarpack2t64 amd64 3.9.1-1.1build2 [106 kB] 254s Get:6 http://ftpmaster.internal/ubuntu oracular/universe amd64 libsuperlu6 amd64 6.0.1+dfsg1-1build1 [180 kB] 254s Get:7 http://ftpmaster.internal/ubuntu oracular/universe amd64 libarmadillo12 amd64 1:12.8.2+dfsg-1 [106 kB] 254s Get:8 http://ftpmaster.internal/ubuntu oracular/universe amd64 libbamtools2.5.2 amd64 2.5.2+dfsg-5ubuntu1 [137 kB] 254s Get:9 http://ftpmaster.internal/ubuntu oracular/universe amd64 libdisorder0 amd64 0.0.2+git20130809.8062ee1-4build1 [4738 B] 254s Get:10 http://ftpmaster.internal/ubuntu oracular/main amd64 libjsoncpp25 amd64 1.9.5-6build1 [82.8 kB] 254s Get:11 http://ftpmaster.internal/ubuntu oracular/universe amd64 libsmithwaterman0 amd64 0.0+git20160702.2610e25-12 [37.6 kB] 254s Get:12 http://ftpmaster.internal/ubuntu oracular/universe amd64 tvc amd64 5.0.3+git20151221.80e144e+dfsg-5build2 [1113 kB] 254s Fetched 5582 kB in 0s (53.0 MB/s) 254s Selecting previously unselected package libblas3:amd64. 254s (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 ... 74486 files and directories currently installed.) 254s Preparing to unpack .../00-libblas3_3.12.0-3build1_amd64.deb ... 254s Unpacking libblas3:amd64 (3.12.0-3build1) ... 255s Selecting previously unselected package libgfortran5:amd64. 255s Preparing to unpack .../01-libgfortran5_14.1.0-1ubuntu1_amd64.deb ... 255s Unpacking libgfortran5:amd64 (14.1.0-1ubuntu1) ... 255s Selecting previously unselected package liblapack3:amd64. 255s Preparing to unpack .../02-liblapack3_3.12.0-3build1_amd64.deb ... 255s Unpacking liblapack3:amd64 (3.12.0-3build1) ... 255s Selecting previously unselected package libarpack2t64:amd64. 255s Preparing to unpack .../03-libarpack2t64_3.9.1-1.1build2_amd64.deb ... 255s Unpacking libarpack2t64:amd64 (3.9.1-1.1build2) ... 255s Selecting previously unselected package libsuperlu6:amd64. 255s Preparing to unpack .../04-libsuperlu6_6.0.1+dfsg1-1build1_amd64.deb ... 255s Unpacking libsuperlu6:amd64 (6.0.1+dfsg1-1build1) ... 255s Selecting previously unselected package libarmadillo12. 255s Preparing to unpack .../05-libarmadillo12_1%3a12.8.2+dfsg-1_amd64.deb ... 255s Unpacking libarmadillo12 (1:12.8.2+dfsg-1) ... 255s Selecting previously unselected package libbamtools2.5.2:amd64. 255s Preparing to unpack .../06-libbamtools2.5.2_2.5.2+dfsg-5ubuntu1_amd64.deb ... 255s Unpacking libbamtools2.5.2:amd64 (2.5.2+dfsg-5ubuntu1) ... 255s Selecting previously unselected package libdisorder0:amd64. 255s Preparing to unpack .../07-libdisorder0_0.0.2+git20130809.8062ee1-4build1_amd64.deb ... 255s Unpacking libdisorder0:amd64 (0.0.2+git20130809.8062ee1-4build1) ... 255s Selecting previously unselected package libjsoncpp25:amd64. 255s Preparing to unpack .../08-libjsoncpp25_1.9.5-6build1_amd64.deb ... 255s Unpacking libjsoncpp25:amd64 (1.9.5-6build1) ... 255s Selecting previously unselected package libsmithwaterman0:amd64. 255s Preparing to unpack .../09-libsmithwaterman0_0.0+git20160702.2610e25-12_amd64.deb ... 255s Unpacking libsmithwaterman0:amd64 (0.0+git20160702.2610e25-12) ... 255s Selecting previously unselected package tvc. 255s Preparing to unpack .../10-tvc_5.0.3+git20151221.80e144e+dfsg-5build2_amd64.deb ... 255s Unpacking tvc (5.0.3+git20151221.80e144e+dfsg-5build2) ... 255s Selecting previously unselected package autopkgtest-satdep. 255s Preparing to unpack .../11-1-autopkgtest-satdep.deb ... 255s Unpacking autopkgtest-satdep (0) ... 255s Setting up libdisorder0:amd64 (0.0.2+git20130809.8062ee1-4build1) ... 255s Setting up libsmithwaterman0:amd64 (0.0+git20160702.2610e25-12) ... 255s Setting up libblas3:amd64 (3.12.0-3build1) ... 255s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 255s Setting up libjsoncpp25:amd64 (1.9.5-6build1) ... 255s Setting up libbamtools2.5.2:amd64 (2.5.2+dfsg-5ubuntu1) ... 255s Setting up libgfortran5:amd64 (14.1.0-1ubuntu1) ... 255s Setting up liblapack3:amd64 (3.12.0-3build1) ... 255s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 255s Setting up libarpack2t64:amd64 (3.9.1-1.1build2) ... 255s Setting up libsuperlu6:amd64 (6.0.1+dfsg1-1build1) ... 255s Setting up libarmadillo12 (1:12.8.2+dfsg-1) ... 255s Setting up tvc (5.0.3+git20151221.80e144e+dfsg-5build2) ... 255s Setting up autopkgtest-satdep (0) ... 255s Processing triggers for man-db (2.12.1-2) ... 255s Processing triggers for libc-bin (2.39-3.1ubuntu3) ... 257s (Reading database ... 74581 files and directories currently installed.) 257s Removing autopkgtest-satdep (0) ... 258s autopkgtest [19:54:52]: test run-unit-test: [----------------------- 258s Running Tests 258s [ Fri 2024-07-12 19:54:52 UTC ] 258s [ Fri 2024-07-12 19:54:52 UTC ] Task : Write effective bed 258s [ Fri 2024-07-12 19:54:52 UTC ] Command : /usr/bin/tvcutils validate_bed --reference "reference.fasta" --target-regions-bed "test_unmerged_detail.bed" --effective-bed "./effective_regions.bed" 258s [ Fri 2024-07-12 19:54:52 UTC ] 258s test_unmerged_detail.bed: Validation successful with 0 warnings and 0 errors 258s 258s [ Fri 2024-07-12 19:54:52 UTC ] Calling small INDELs and SNPs using tvc ... 258s [ Fri 2024-07-12 19:54:52 UTC ] 258s [ Fri 2024-07-12 19:54:52 UTC ] Task : Call small indels and SNPs 258s [ Fri 2024-07-12 19:54:52 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 258s [ Fri 2024-07-12 19:54:52 UTC ] 258s tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller 258s 258s INFO: No input VCF (Hotspot) file specified via -c,--input-vcf 258s INFO: Systematic error motif file not specified via -e 258s prefix-exclude = 6 258s hp-max-length = 8 (integer, builtin default) 258s sse-prob-threshold = 0.2 (double, builtin default) 258s min-ratio-reads-non-sse-strand = 0.2 (double, builtin default) 258s sse-relative-safety-level = 0.025 (double, builtin default) 258s do-snp-realignment = true (boolean, builtin default) 258s do-mnp-realignment = true (boolean, builtin default) 258s realignment-threshold = 1 (double, builtin default) 258s indel-as-hpindel = false (boolean, builtin default) 258s data-quality-stringency = 4 (double, builtin default) 258s read-rejection-threshold = 0.5 (double, builtin default) 258s use-position-bias = false (boolean, builtin default) 258s position-bias-ref-fraction = 0.05 (double, builtin default) 258s position-bias = 0.75 (double, builtin default) 258s position-bias-pval = 0.05 (double, builtin default) 258s downsample-to-coverage = 2000 (integer, builtin default) 258s tune-sbias = 0.01 (double, builtin default) 258s suppress-reference-genotypes = true (boolean, builtin default) 258s suppress-nocall-genotypes = true (boolean, builtin default) 258s suppress-no-calls = true (boolean, builtin default) 258s heal-snps = true (boolean, builtin default) 258s snp-min-cov-each-strand = 0 (integer, builtin default) 258s snp-min-variant-score = 10 (double, builtin default) 258s snp-min-allele-freq = 0.2 (double, builtin default) 258s snp-min-coverage = 6 (integer, builtin default) 258s snp-strand-bias = 0.95 (double, builtin default) 258s snp-strand-bias-pval = 1 (double, builtin default) 258s mnp-min-cov-each-strand = 0 (integer, builtin default) 258s mnp-min-variant-score = 10 (double, builtin default) 258s mnp-min-allele-freq = 0.2 (double, builtin default) 258s mnp-min-coverage = 6 (integer, builtin default) 258s mnp-strand-bias = 0.95 (double, builtin default) 258s mnp-strand-bias-pval = 1 (double, builtin default) 258s indel-min-cov-each-strand = 1 (integer, builtin default) 258s indel-min-variant-score = 10 (double, builtin default) 258s indel-min-allele-freq = 0.2 (double, builtin default) 258s indel-min-coverage = 15 (integer, builtin default) 258s indel-strand-bias = 0.85 (double, builtin default) 258s indel-strand-bias-pval = 1 (double, builtin default) 258s hotspot-min-cov-each-strand = 0 (integer, builtin default) 258s hotspot-min-variant-score = 10 (double, builtin default) 258s hotspot-min-allele-freq = 0.2 (double, builtin default) 258s hotspot-min-coverage = 6 (integer, builtin default) 258s hotspot-strand-bias = 0.95 (double, builtin default) 258s hotspot-strand-bias-pval = 1 (double, builtin default) 258s max-flows-to-test = 10 (integer, builtin default) 258s min-delta-for-flow = 0.1 (double, builtin default) 258s prediction-precision = 30 (double, builtin default) 258s outlier-probability = 0.01 (double, builtin default) 258s germline-prior-strength = 0 (double, builtin default) 258s heavy-tailed = 3 (integer, builtin default) 258s filter-unusual-predictions = 0.3 (double, builtin default) 258s soft-clip-bias-checker = 0.1 (double, builtin default) 258s filter-deletion-predictions = 100 (double, builtin default) 258s filter-insertion-predictions = 100 (double, builtin default) 258s max-detail-level = 0 (integer, builtin default) 258s shift-likelihood-penalty = 0.3 (double, builtin default) 258s minimum-sigma-prior = 0.085 (double, builtin default) 258s slope-sigma-prior = 0.0084 (double, builtin default) 258s sigma-prior-weight = 1 (double, builtin default) 258s k-zero = 3 (double, builtin default) 258s num-threads = 12 (integer, command line option) 258s num-variants-per-thread = 250 (integer, builtin default) 258s use-sse-basecaller = true (boolean, builtin default) 258s do-json-diagnostic = false (boolean, builtin default) 258s do-minimal-diagnostic = false (boolean, builtin default) 258s process-input-positions-only = false (boolean, builtin default) 258s suppress-recalibration = true (boolean, builtin default) 258s resolve-clipped-bases = false (boolean, builtin default) 258s allow-indels = true (boolean, builtin default) 258s allow-snps = true (boolean, builtin default) 258s allow-mnps = true (boolean, builtin default) 258s allow-complex = false (boolean, builtin default) 258s left-align-indels = false (boolean, builtin default) 258s use-best-n-alleles = 2 (integer, builtin default) 258s use-input-allele-only = false (boolean, builtin default) 258s min-mapping-qv = 4 (integer, builtin default) 258s read-snp-limit = 10 (integer, builtin default) 258s read-max-mismatch-fraction = 1 (double, builtin default) 258s max-complex-gap = 1 (integer, builtin default) 258s gen-min-alt-allele-freq = 0.2 (double, builtin default) 258s gen-min-coverage = 6 (integer, builtin default) 258s gen-min-indel-alt-allele-freq = 0.2 (double, builtin default) 258s override-limits = false (boolean, builtin default) 258s Limit check parameter hp-max-length: lim. 1 <= 8? OK! 258s Limit check parameter sse-prob-threshold: lim. 0 <= 0.2 <= lim. 1? OK! 258s Limit check parameter min-ratio-reads-non-sse-strand: lim. 0 <= 0.2 <= lim. 1? OK! 258s Limit check parameter sse-relative-safety-level: lim. 0 <= 0.025 <= lim. 1? OK! 258s Limit check parameter realignment-threshold: lim. 0 <= 1 <= lim. 1? OK! 258s Limit check parameter data-quality-stringency: lim. 0 <= 4? OK! 258s Limit check parameter read-rejection-threshold: lim. 0 <= 0.5 <= lim. 1? OK! 258s Limit check parameter downsample-to-coverage: lim. 20 <= 2000 <= lim. 100000? OK! 258s Limit check parameter position-bias-ref-fraction: lim. 0 <= 0.05 <= lim. 1? OK! 258s Limit check parameter position-bias: lim. 0 <= 0.75 <= lim. 1? OK! 258s Limit check parameter position-bias-pval: lim. 0 <= 0.05 <= lim. 1? OK! 258s Limit check parameter tune-sbias: lim. 0.001 <= 0.01 <= lim. 1000? OK! 258s Limit check parameter snp-min-cov-each-strand: lim. 0 <= 0? OK! 258s Limit check parameter snp-min-variant-score: lim. 0 <= 10? OK! 258s Limit check parameter snp-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 258s Limit check parameter snp-min-coverage: lim. 0 <= 6? OK! 258s Limit check parameter snp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 258s Limit check parameter snp-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 258s Limit check parameter mnp-min-cov-each-strand: lim. 0 <= 0? OK! 258s Limit check parameter mnp-min-variant-score: lim. 0 <= 10? OK! 258s Limit check parameter mnp-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 258s Limit check parameter mnp-min-coverage: lim. 0 <= 6? OK! 258s Limit check parameter mnp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 258s Limit check parameter mnp-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 258s Limit check parameter indel-min-cov-each-strand: lim. 0 <= 1? OK! 258s Limit check parameter indel-min-variant-score: lim. 0 <= 10? OK! 258s Limit check parameter indel-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 258s Limit check parameter indel-min-coverage: lim. 0 <= 15? OK! 258s Limit check parameter indel-strand-bias: lim. 0.5 <= 0.85 <= lim. 1? OK! 258s Limit check parameter indel-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 258s Limit check parameter hotspot-min-cov-each-strand: lim. 0 <= 0? OK! 258s Limit check parameter hotspot-min-variant-score: lim. 0 <= 10? OK! 258s Limit check parameter hotspot-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 258s Limit check parameter hotspot-min-coverage: lim. 0 <= 6? OK! 258s Limit check parameter hotspot-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 258s Limit check parameter hotspot-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 258s Limit check parameter max-flows-to-test: lim. 1 <= 10 <= lim. 100? OK! 258s Limit check parameter min-delta-for-flow: lim. 0.01 <= 0.1 <= lim. 0.5? OK! 258s Limit check parameter prediction-precision: lim. 0.1 <= 30? OK! 258s Limit check parameter outlier-probability: lim. 0 <= 0.01 <= lim. 1? OK! 258s Limit check parameter germline-prior-strength: lim. 0 <= 0 <= lim. 1000? OK! 258s Limit check parameter heavy-tailed: lim. 1 <= 3? OK! 258s Limit check parameter filter-unusual-predictions: lim. 0 <= 0.3? OK! 258s Limit check parameter soft-clip-bias-checker: lim. 0 <= 0.1 <= lim. 1? OK! 258s Limit check parameter filter-deletion-predictions: lim. 0 <= 100? OK! 258s Limit check parameter filter-insertion-predictions: lim. 0 <= 100? OK! 258s Limit check parameter max-detail-level: lim. 0 <= 0 <= lim. 10000? OK! 258s Limit check parameter shift-likelihood-penalty: lim. 0.01 <= 0.3? OK! 258s Limit check parameter minimum-sigma-prior: lim. 0.01 <= 0.085? OK! 258s Limit check parameter slope-sigma-prior: lim. 0 <= 0.0084? OK! 258s Limit check parameter sigma-prior-weight: lim. 0.01 <= 1? OK! 258s Limit check parameter k-zero: lim. 0 <= 3? OK! 258s Limit check parameter num-threads: lim. 1 <= 12 <= lim. 128? OK! 258s Limit check parameter num-variants-per-thread: lim. 1 <= 250 <= lim. 10000? OK! 258s Limit check parameter use-best-n-alleles: lim. 0 <= 2 <= lim. 20? OK! 258s Limit check parameter min-mapping-qv: lim. 0 <= 4? OK! 258s Limit check parameter read-snp-limit: lim. 0 <= 10? OK! 258s Limit check parameter read-max-mismatch-fraction: lim. 0 <= 1 <= lim. 1? OK! 258s Limit check parameter gen-min-alt-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 258s Limit check parameter gen-min-coverage: lim. 0 <= 6? OK! 258s Limit check parameter gen-min-indel-alt-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 258s TargetsManager: Loaded targets file test_unmerged_detail.bed 258s TargetsManager: 1 target(s) 258s TargetsManager: Trimming of AmpliSeq primers is enabled 258s SampleManager: Found 1 read group(s) and 1 sample(s). 258s SampleManager: Primary sample "85" (default) present in 1 read group(s) 258s TVC found a total of 1 different flow orders of max flow lengths: 500 258s Recalibration was detected from comment lines in bam file(s): 258s 1 unique blocks of recalibration info detected. 258s Recalibration model: suppressed 258s 258s [tvc] Normal termination. Processing time: 0 seconds. 258s 258s [ Fri 2024-07-12 19:54:52 UTC ] 258s [ Fri 2024-07-12 19:54:52 UTC ] Task : Assemble long indels 258s [ Fri 2024-07-12 19:54:52 UTC ] Command : /usr/bin/tvcassembly --reference reference.fasta --input-bam test.bam --target-file test_merged_plain.bed --output-vcf ./indel_assembly.vcf 258s [ Fri 2024-07-12 19:54:52 UTC ] 258s tvcassembly 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller - Long Indel Assembly 258s 258s kmer-len = 19 (integer, builtin default) 258s min-var-count = 5 (integer, builtin default) 258s short-suffix-match = 5 (integer, builtin default) 258s min-indel-size = 4 (integer, builtin default) 258s max-hp-length = 8 (integer, builtin default) 258s min-var-freq = 0.15 (double, builtin default) 258s min-var-score = 10 (double, builtin default) 258s relative-strand-bias = 0.8 (double, builtin default) 258s output-mnv = 0 (integer, builtin default) 258s TargetsManager: Loaded targets file test_merged_plain.bed 258s TargetsManager: 1 target(s) 258s SampleManager: Found 1 read group(s) and 1 sample(s). 258s SampleManager: Primary sample "85" (default) present in 1 read group(s) 258s [ Fri 2024-07-12 19:54:52 UTC ] 258s [ Fri 2024-07-12 19:54:52 UTC ] Task : Unify variants and annotations from all sources (tvc,IndelAssembly,hotpots) 258s [ Fri 2024-07-12 19:54:52 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" 258s [ Fri 2024-07-12 19:54:52 UTC ] 258s TargetsManager: Loaded targets file test_merged_plain.bed 258s TargetsManager: 1 target(s) 258s [ Fri 2024-07-12 19:54:52 UTC ] 258s [ Fri 2024-07-12 19:54:52 UTC ] Task : Generate uncompressed vcf 258s [ Fri 2024-07-12 19:54:52 UTC ] Command : gzip -dcf "./TSVC_variants.vcf.gz" > "./TSVC_variants.vcf" 258s [ Fri 2024-07-12 19:54:52 UTC ] 258s PASS 258s autopkgtest [19:54:52]: test run-unit-test: -----------------------] 265s run-unit-test PASS 265s autopkgtest [19:54:59]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 273s autopkgtest [19:55:07]: @@@@@@@@@@@@@@@@@@@@ summary 273s run-unit-test PASS 358s nova [W] Skipping flock for amd64 358s Creating nova instance adt-oracular-amd64-tvc-20240712-195025-juju-7f2275-prod-proposed-migration-environment-2-70034c9f-e004-414f-bcb3-f37f90a888f4 from image adt/ubuntu-oracular-amd64-server-20240712.img (UUID 9132249a-6053-4497-bc26-981612ca03ad)...