0s autopkgtest [17:49:14]: starting date and time: 2025-03-15 17:49:14+0000 0s autopkgtest [17:49:14]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [17:49:14]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.3ioi1wyr/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:glibc --apt-upgrade tvc --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- lxd -r lxd-armhf-10.145.243.239 lxd-armhf-10.145.243.239:autopkgtest/ubuntu/plucky/armhf 21s autopkgtest [17:49:35]: testbed dpkg architecture: armhf 23s autopkgtest [17:49:37]: testbed apt version: 2.9.33 26s autopkgtest [17:49:40]: @@@@@@@@@@@@@@@@@@@@ test bed setup 28s autopkgtest [17:49:42]: testbed release detected to be: None 35s autopkgtest [17:49:49]: updating testbed package index (apt update) 37s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 38s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 38s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 38s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 38s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 38s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 38s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 39s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [114 kB] 39s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1832 B] 39s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 39s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [312 kB] 39s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [11.1 kB] 39s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 39s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [240 B] 39s Get:15 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 58s Get:16 http://ftpmaster.internal/ubuntu plucky/main Sources [1394 kB] 59s Get:17 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 59s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 60s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 60s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 60s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 69s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 71s Fetched 41.0 MB in 34s (1218 kB/s) 72s Reading package lists... 78s autopkgtest [17:50:32]: upgrading testbed (apt dist-upgrade and autopurge) 80s Reading package lists... 80s Building dependency tree... 80s Reading state information... 81s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 81s Starting 2 pkgProblemResolver with broken count: 0 81s Done 82s Entering ResolveByKeep 82s 82s Calculating upgrade... 83s The following packages will be upgraded: 83s libc-bin libc6 locales pinentry-curses python3-jinja2 sos strace 83s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 83s Need to get 8683 kB of archives. 83s After this operation, 23.6 kB of additional disk space will be used. 83s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 86s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 87s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 92s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 92s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf pinentry-curses armhf 1.3.1-2ubuntu3 [40.6 kB] 92s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 92s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 93s Preconfiguring packages ... 93s Fetched 8683 kB in 9s (921 kB/s) 93s (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 ... 64655 files and directories currently installed.) 93s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 93s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 94s Setting up libc6:armhf (2.41-1ubuntu2) ... 94s (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 ... 64655 files and directories currently installed.) 94s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 94s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 94s Setting up libc-bin (2.41-1ubuntu2) ... 94s (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 ... 64655 files and directories currently installed.) 94s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 94s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 94s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 94s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 94s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_armhf.deb ... 94s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 94s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 95s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 95s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 95s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 95s Setting up sos (4.9.0-5) ... 96s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 96s Setting up locales (2.41-1ubuntu2) ... 97s Generating locales (this might take a while)... 99s en_US.UTF-8... done 99s Generation complete. 99s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 99s Setting up strace (6.13+ds-1ubuntu1) ... 99s Processing triggers for man-db (2.13.0-1) ... 101s Processing triggers for systemd (257.3-1ubuntu3) ... 103s Reading package lists... 104s Building dependency tree... 104s Reading state information... 104s Starting pkgProblemResolver with broken count: 0 104s Starting 2 pkgProblemResolver with broken count: 0 104s Done 105s Solving dependencies... 105s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 107s autopkgtest [17:51:01]: rebooting testbed after setup commands that affected boot 150s autopkgtest [17:51:44]: testbed running kernel: Linux 6.8.0-52-generic #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 18:10:51 UTC 2 175s autopkgtest [17:52:09]: @@@@@@@@@@@@@@@@@@@@ apt-source tvc 185s Get:1 http://ftpmaster.internal/ubuntu plucky/universe tvc 5.0.3+git20151221.80e144e+dfsg-5build4 (dsc) [2304 B] 185s Get:2 http://ftpmaster.internal/ubuntu plucky/universe tvc 5.0.3+git20151221.80e144e+dfsg-5build4 (tar) [745 kB] 185s Get:3 http://ftpmaster.internal/ubuntu plucky/universe tvc 5.0.3+git20151221.80e144e+dfsg-5build4 (diff) [10.1 kB] 186s gpgv: Signature made Sun Nov 10 11:21:31 2024 UTC 186s gpgv: using RSA key B8340990283D8D9BC1949AC74799A35146D12B35 186s gpgv: Can't check signature: No public key 186s dpkg-source: warning: cannot verify inline signature for ./tvc_5.0.3+git20151221.80e144e+dfsg-5build4.dsc: no acceptable signature found 186s autopkgtest [17:52:20]: testing package tvc version 5.0.3+git20151221.80e144e+dfsg-5build4 188s autopkgtest [17:52:22]: build not needed 190s autopkgtest [17:52:24]: test run-unit-test: preparing testbed 192s Reading package lists... 192s Building dependency tree... 192s Reading state information... 193s Starting pkgProblemResolver with broken count: 0 193s Starting 2 pkgProblemResolver with broken count: 0 193s Done 194s The following NEW packages will be installed: 194s libarmadillo14 libarpack2t64 libbamtools2.5.2 libblas3 libdisorder0 194s libgfortran5 libjsoncpp26 liblapack3 libsmithwaterman0 tvc 194s 0 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. 194s Need to get 4097 kB of archives. 194s After this operation, 9730 kB of additional disk space will be used. 194s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.1-2 [132 kB] 194s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 15-20250222-0ubuntu1 [330 kB] 194s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.1-2 [2091 kB] 196s Get:4 http://ftpmaster.internal/ubuntu plucky/universe armhf libarpack2t64 armhf 3.9.1-4 [86.7 kB] 196s Get:5 http://ftpmaster.internal/ubuntu plucky/universe armhf libarmadillo14 armhf 1:14.2.3+dfsg-1 [102 kB] 196s Get:6 http://ftpmaster.internal/ubuntu plucky/universe armhf libbamtools2.5.2 armhf 2.5.2+dfsg-6build1 [154 kB] 196s Get:7 http://ftpmaster.internal/ubuntu plucky/universe armhf libdisorder0 armhf 0.0.2+git20130809.8062ee1-4build1 [4880 B] 196s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf libjsoncpp26 armhf 1.9.6-3 [75.5 kB] 196s Get:9 http://ftpmaster.internal/ubuntu plucky/universe armhf libsmithwaterman0 armhf 0.0+git20160702.2610e25-12 [35.8 kB] 196s Get:10 http://ftpmaster.internal/ubuntu plucky/universe armhf tvc armhf 5.0.3+git20151221.80e144e+dfsg-5build4 [1085 kB] 197s Fetched 4097 kB in 3s (1197 kB/s) 197s Selecting previously unselected package libblas3:armhf. 197s (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 ... 64655 files and directories currently installed.) 197s Preparing to unpack .../0-libblas3_3.12.1-2_armhf.deb ... 197s Unpacking libblas3:armhf (3.12.1-2) ... 197s Selecting previously unselected package libgfortran5:armhf. 198s Preparing to unpack .../1-libgfortran5_15-20250222-0ubuntu1_armhf.deb ... 198s Unpacking libgfortran5:armhf (15-20250222-0ubuntu1) ... 198s Selecting previously unselected package liblapack3:armhf. 198s Preparing to unpack .../2-liblapack3_3.12.1-2_armhf.deb ... 198s Unpacking liblapack3:armhf (3.12.1-2) ... 198s Selecting previously unselected package libarpack2t64:armhf. 198s Preparing to unpack .../3-libarpack2t64_3.9.1-4_armhf.deb ... 198s Unpacking libarpack2t64:armhf (3.9.1-4) ... 198s Selecting previously unselected package libarmadillo14. 198s Preparing to unpack .../4-libarmadillo14_1%3a14.2.3+dfsg-1_armhf.deb ... 198s Unpacking libarmadillo14 (1:14.2.3+dfsg-1) ... 198s Selecting previously unselected package libbamtools2.5.2:armhf. 198s Preparing to unpack .../5-libbamtools2.5.2_2.5.2+dfsg-6build1_armhf.deb ... 198s Unpacking libbamtools2.5.2:armhf (2.5.2+dfsg-6build1) ... 198s Selecting previously unselected package libdisorder0:armhf. 198s Preparing to unpack .../6-libdisorder0_0.0.2+git20130809.8062ee1-4build1_armhf.deb ... 198s Unpacking libdisorder0:armhf (0.0.2+git20130809.8062ee1-4build1) ... 198s Selecting previously unselected package libjsoncpp26:armhf. 198s Preparing to unpack .../7-libjsoncpp26_1.9.6-3_armhf.deb ... 198s Unpacking libjsoncpp26:armhf (1.9.6-3) ... 198s Selecting previously unselected package libsmithwaterman0:armhf. 198s Preparing to unpack .../8-libsmithwaterman0_0.0+git20160702.2610e25-12_armhf.deb ... 198s Unpacking libsmithwaterman0:armhf (0.0+git20160702.2610e25-12) ... 198s Selecting previously unselected package tvc. 198s Preparing to unpack .../9-tvc_5.0.3+git20151221.80e144e+dfsg-5build4_armhf.deb ... 198s Unpacking tvc (5.0.3+git20151221.80e144e+dfsg-5build4) ... 198s Setting up libdisorder0:armhf (0.0.2+git20130809.8062ee1-4build1) ... 198s Setting up libsmithwaterman0:armhf (0.0+git20160702.2610e25-12) ... 198s Setting up libblas3:armhf (3.12.1-2) ... 198s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 198s Setting up libjsoncpp26:armhf (1.9.6-3) ... 198s Setting up libbamtools2.5.2:armhf (2.5.2+dfsg-6build1) ... 198s Setting up libgfortran5:armhf (15-20250222-0ubuntu1) ... 198s Setting up liblapack3:armhf (3.12.1-2) ... 198s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 198s Setting up libarpack2t64:armhf (3.9.1-4) ... 198s Setting up libarmadillo14 (1:14.2.3+dfsg-1) ... 198s Setting up tvc (5.0.3+git20151221.80e144e+dfsg-5build4) ... 198s Processing triggers for man-db (2.13.0-1) ... 198s Processing triggers for libc-bin (2.41-1ubuntu2) ... 206s autopkgtest [17:52:40]: test run-unit-test: [----------------------- 208s Running Tests 208s [ Sat 2025-03-15 17:52:42 UTC ] 208s [ Sat 2025-03-15 17:52:42 UTC ] Task : Write effective bed 208s [ Sat 2025-03-15 17:52:42 UTC ] Command : /usr/bin/tvcutils validate_bed --reference "reference.fasta" --target-regions-bed "test_unmerged_detail.bed" --effective-bed "./effective_regions.bed" 208s [ Sat 2025-03-15 17:52:42 UTC ] 208s test_unmerged_detail.bed: Validation successful with 0 warnings and 0 errors 208s 208s [ Sat 2025-03-15 17:52:42 UTC ] Calling small INDELs and SNPs using tvc ... 208s [ Sat 2025-03-15 17:52:42 UTC ] 208s [ Sat 2025-03-15 17:52:42 UTC ] Task : Call small indels and SNPs 208s [ Sat 2025-03-15 17:52:42 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 208s [ Sat 2025-03-15 17:52:42 UTC ] 208s INFO: No input VCF (Hotspot) file specified via -c,--input-vcf 208s INFO: Systematic error motif file not specified via -e 208s prefix-exclude = 6 208s tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller 208s 208s hp-max-length = 8 (integer, builtin default) 208s sse-prob-threshold = 0.2 (double, builtin default) 208s min-ratio-reads-non-sse-strand = 0.2 (double, builtin default) 208s sse-relative-safety-level = 0.025 (double, builtin default) 208s do-snp-realignment = true (boolean, builtin default) 208s do-mnp-realignment = true (boolean, builtin default) 208s realignment-threshold = 1 (double, builtin default) 208s indel-as-hpindel = false (boolean, builtin default) 208s data-quality-stringency = 4 (double, builtin default) 208s read-rejection-threshold = 0.5 (double, builtin default) 208s use-position-bias = false (boolean, builtin default) 208s position-bias-ref-fraction = 0.05 (double, builtin default) 208s position-bias = 0.75 (double, builtin default) 208s position-bias-pval = 0.05 (double, builtin default) 208s downsample-to-coverage = 2000 (integer, builtin default) 208s tune-sbias = 0.01 (double, builtin default) 208s suppress-reference-genotypes = true (boolean, builtin default) 208s suppress-nocall-genotypes = true (boolean, builtin default) 208s suppress-no-calls = true (boolean, builtin default) 208s heal-snps = true (boolean, builtin default) 208s snp-min-cov-each-strand = 0 (integer, builtin default) 208s snp-min-variant-score = 10 (double, builtin default) 208s snp-min-allele-freq = 0.2 (double, builtin default) 208s snp-min-coverage = 6 (integer, builtin default) 208s snp-strand-bias = 0.95 (double, builtin default) 208s snp-strand-bias-pval = 1 (double, builtin default) 208s mnp-min-cov-each-strand = 0 (integer, builtin default) 208s mnp-min-variant-score = 10 (double, builtin default) 208s mnp-min-allele-freq = 0.2 (double, builtin default) 208s mnp-min-coverage = 6 (integer, builtin default) 208s mnp-strand-bias = 0.95 (double, builtin default) 208s mnp-strand-bias-pval = 1 (double, builtin default) 208s indel-min-cov-each-strand = 1 (integer, builtin default) 208s indel-min-variant-score = 10 (double, builtin default) 208s indel-min-allele-freq = 0.2 (double, builtin default) 208s indel-min-coverage = 15 (integer, builtin default) 208s indel-strand-bias = 0.85 (double, builtin default) 208s indel-strand-bias-pval = 1 (double, builtin default) 208s hotspot-min-cov-each-strand = 0 (integer, builtin default) 208s hotspot-min-variant-score = 10 (double, builtin default) 208s hotspot-min-allele-freq = 0.2 (double, builtin default) 208s hotspot-min-coverage = 6 (integer, builtin default) 208s hotspot-strand-bias = 0.95 (double, builtin default) 208s hotspot-strand-bias-pval = 1 (double, builtin default) 208s max-flows-to-test = 10 (integer, builtin default) 208s min-delta-for-flow = 0.1 (double, builtin default) 208s prediction-precision = 30 (double, builtin default) 208s outlier-probability = 0.01 (double, builtin default) 208s germline-prior-strength = 0 (double, builtin default) 208s heavy-tailed = 3 (integer, builtin default) 208s filter-unusual-predictions = 0.3 (double, builtin default) 208s soft-clip-bias-checker = 0.1 (double, builtin default) 208s filter-deletion-predictions = 100 (double, builtin default) 208s filter-insertion-predictions = 100 (double, builtin default) 208s max-detail-level = 0 (integer, builtin default) 208s shift-likelihood-penalty = 0.3 (double, builtin default) 208s minimum-sigma-prior = 0.085 (double, builtin default) 208s slope-sigma-prior = 0.0084 (double, builtin default) 208s sigma-prior-weight = 1 (double, builtin default) 208s k-zero = 3 (double, builtin default) 208s num-threads = 12 (integer, command line option) 208s num-variants-per-thread = 250 (integer, builtin default) 208s use-sse-basecaller = false (boolean, builtin default) 208s do-json-diagnostic = false (boolean, builtin default) 208s do-minimal-diagnostic = false (boolean, builtin default) 208s process-input-positions-only = false (boolean, builtin default) 208s suppress-recalibration = true (boolean, builtin default) 208s resolve-clipped-bases = false (boolean, builtin default) 208s allow-indels = true (boolean, builtin default) 208s allow-snps = true (boolean, builtin default) 208s allow-mnps = true (boolean, builtin default) 208s allow-complex = false (boolean, builtin default) 208s left-align-indels = false (boolean, builtin default) 208s use-best-n-alleles = 2 (integer, builtin default) 208s use-input-allele-only = false (boolean, builtin default) 208s min-mapping-qv = 4 (integer, builtin default) 208s read-snp-limit = 10 (integer, builtin default) 208s read-max-mismatch-fraction = 1 (double, builtin default) 208s max-complex-gap = 1 (integer, builtin default) 208s gen-min-alt-allele-freq = 0.2 (double, builtin default) 208s gen-min-coverage = 6 (integer, builtin default) 208s gen-min-indel-alt-allele-freq = 0.2 (double, builtin default) 208s override-limits = false (boolean, builtin default) 208s Limit check parameter hp-max-length: lim. 1 <= 8? OK! 208s Limit check parameter sse-prob-threshold: lim. 0 <= 0.2 <= lim. 1? OK! 208s Limit check parameter min-ratio-reads-non-sse-strand: lim. 0 <= 0.2 <= lim. 1? OK! 208s Limit check parameter sse-relative-safety-level: lim. 0 <= 0.025 <= lim. 1? OK! 208s Limit check parameter realignment-threshold: lim. 0 <= 1 <= lim. 1? OK! 208s Limit check parameter data-quality-stringency: lim. 0 <= 4? OK! 208s Limit check parameter read-rejection-threshold: lim. 0 <= 0.5 <= lim. 1? OK! 208s Limit check parameter downsample-to-coverage: lim. 20 <= 2000 <= lim. 100000? OK! 208s Limit check parameter position-bias-ref-fraction: lim. 0 <= 0.05 <= lim. 1? OK! 208s Limit check parameter position-bias: lim. 0 <= 0.75 <= lim. 1? OK! 208s Limit check parameter position-bias-pval: lim. 0 <= 0.05 <= lim. 1? OK! 208s Limit check parameter tune-sbias: lim. 0.001 <= 0.01 <= lim. 1000? OK! 208s Limit check parameter snp-min-cov-each-strand: lim. 0 <= 0? OK! 208s Limit check parameter snp-min-variant-score: lim. 0 <= 10? OK! 208s Limit check parameter snp-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 208s Limit check parameter snp-min-coverage: lim. 0 <= 6? OK! 208s Limit check parameter snp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 208s Limit check parameter snp-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 208s Limit check parameter mnp-min-cov-each-strand: lim. 0 <= 0? OK! 208s Limit check parameter mnp-min-variant-score: lim. 0 <= 10? OK! 208s Limit check parameter mnp-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 208s Limit check parameter mnp-min-coverage: lim. 0 <= 6? OK! 208s Limit check parameter mnp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 208s Limit check parameter mnp-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 208s Limit check parameter indel-min-cov-each-strand: lim. 0 <= 1? OK! 208s Limit check parameter indel-min-variant-score: lim. 0 <= 10? OK! 208s Limit check parameter indel-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 208s Limit check parameter indel-min-coverage: lim. 0 <= 15? OK! 208s Limit check parameter indel-strand-bias: lim. 0.5 <= 0.85 <= lim. 1? OK! 208s Limit check parameter indel-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 208s Limit check parameter hotspot-min-cov-each-strand: lim. 0 <= 0? OK! 208s Limit check parameter hotspot-min-variant-score: lim. 0 <= 10? OK! 208s Limit check parameter hotspot-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 208s Limit check parameter hotspot-min-coverage: lim. 0 <= 6? OK! 208s Limit check parameter hotspot-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 208s Limit check parameter hotspot-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 208s Limit check parameter max-flows-to-test: lim. 1 <= 10 <= lim. 100? OK! 208s Limit check parameter min-delta-for-flow: lim. 0.01 <= 0.1 <= lim. 0.5? OK! 208s Limit check parameter prediction-precision: lim. 0.1 <= 30? OK! 208s Limit check parameter outlier-probability: lim. 0 <= 0.01 <= lim. 1? OK! 208s Limit check parameter germline-prior-strength: lim. 0 <= 0 <= lim. 1000? OK! 208s Limit check parameter heavy-tailed: lim. 1 <= 3? OK! 208s Limit check parameter filter-unusual-predictions: lim. 0 <= 0.3? OK! 208s Limit check parameter soft-clip-bias-checker: lim. 0 <= 0.1 <= lim. 1? OK! 208s Limit check parameter filter-deletion-predictions: lim. 0 <= 100? OK! 208s Limit check parameter filter-insertion-predictions: lim. 0 <= 100? OK! 208s Limit check parameter max-detail-level: lim. 0 <= 0 <= lim. 10000? OK! 208s Limit check parameter shift-likelihood-penalty: lim. 0.01 <= 0.3? OK! 208s Limit check parameter minimum-sigma-prior: lim. 0.01 <= 0.085? OK! 208s Limit check parameter slope-sigma-prior: lim. 0 <= 0.0084? OK! 208s Limit check parameter sigma-prior-weight: lim. 0.01 <= 1? OK! 208s Limit check parameter k-zero: lim. 0 <= 3? OK! 208s Limit check parameter num-threads: lim. 1 <= 12 <= lim. 128? OK! 208s Limit check parameter num-variants-per-thread: lim. 1 <= 250 <= lim. 10000? OK! 208s Limit check parameter use-best-n-alleles: lim. 0 <= 2 <= lim. 20? OK! 208s Limit check parameter min-mapping-qv: lim. 0 <= 4? OK! 208s Limit check parameter read-snp-limit: lim. 0 <= 10? OK! 208s Limit check parameter read-max-mismatch-fraction: lim. 0 <= 1 <= lim. 1? OK! 208s Limit check parameter gen-min-alt-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 208s Limit check parameter gen-min-coverage: lim. 0 <= 6? OK! 208s Limit check parameter gen-min-indel-alt-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 208s TargetsManager: Loaded targets file test_unmerged_detail.bed 208s TargetsManager: 1 target(s) 208s TargetsManager: Trimming of AmpliSeq primers is enabled 208s SampleManager: Found 1 read group(s) and 1 sample(s). 208s SampleManager: Primary sample "85" (default) present in 1 read group(s) 208s TVC found a total of 1 different flow orders of max flow lengths: 500 208s Recalibration was detected from comment lines in bam file(s): 208s 1 unique blocks of recalibration info detected. 208s 208s Recalibration model: suppressed 208s 208s [tvc] Normal termination. Processing time: 0 seconds. 208s [ Sat 2025-03-15 17:52:42 UTC ] 208s [ Sat 2025-03-15 17:52:42 UTC ] Task : Assemble long indels 208s [ Sat 2025-03-15 17:52:42 UTC ] Command : /usr/bin/tvcassembly --reference reference.fasta --input-bam test.bam --target-file test_merged_plain.bed --output-vcf ./indel_assembly.vcf 208s [ Sat 2025-03-15 17:52:42 UTC ] 208s tvcassembly 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller - Long Indel Assembly 208s 208s kmer-len = 19 (integer, builtin default) 208s min-var-count = 5 (integer, builtin default) 208s short-suffix-match = 5 (integer, builtin default) 208s min-indel-size = 4 (integer, builtin default) 208s max-hp-length = 8 (integer, builtin default) 208s min-var-freq = 0.15 (double, builtin default) 208s min-var-score = 10 (double, builtin default) 208s relative-strand-bias = 0.8 (double, builtin default) 208s output-mnv = 0 (integer, builtin default) 208s TargetsManager: Loaded targets file test_merged_plain.bed 208s TargetsManager: 1 target(s) 208s SampleManager: Found 1 read group(s) and 1 sample(s). 208s SampleManager: Primary sample "85" (default) present in 1 read group(s) 208s [ Sat 2025-03-15 17:52:42 UTC ] 208s [ Sat 2025-03-15 17:52:42 UTC ] Task : Unify variants and annotations from all sources (tvc,IndelAssembly,hotpots) 208s [ Sat 2025-03-15 17:52:42 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" 208s [ Sat 2025-03-15 17:52:42 UTC ] 208s TargetsManager: Loaded targets file test_merged_plain.bed 208s TargetsManager: 1 target(s) 208s [ Sat 2025-03-15 17:52:42 UTC ] 208s [ Sat 2025-03-15 17:52:42 UTC ] Task : Generate uncompressed vcf 208s [ Sat 2025-03-15 17:52:42 UTC ] Command : gzip -dcf "./TSVC_variants.vcf.gz" > "./TSVC_variants.vcf" 208s [ Sat 2025-03-15 17:52:42 UTC ] 208s PASS 208s autopkgtest [17:52:42]: test run-unit-test: -----------------------] 212s autopkgtest [17:52:46]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 212s run-unit-test PASS 216s autopkgtest [17:52:50]: @@@@@@@@@@@@@@@@@@@@ summary 216s run-unit-test PASS