0s autopkgtest [17:10:57]: starting date and time: 2025-03-15 17:10:57+0000 0s autopkgtest [17:10:57]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [17:10:57]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.tizj5qeq/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/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-38.secgroup --name adt-plucky-arm64-tvc-20250315-171057-juju-7f2275-prod-proposed-migration-environment-2-a141f67e-c1ee-484a-98e6-8127c8e09452 --image adt/ubuntu-plucky-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,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 138s autopkgtest [17:13:15]: testbed dpkg architecture: arm64 138s autopkgtest [17:13:15]: testbed apt version: 2.9.33 139s autopkgtest [17:13:16]: @@@@@@@@@@@@@@@@@@@@ test bed setup 139s autopkgtest [17:13:16]: testbed release detected to be: None 140s autopkgtest [17:13:17]: updating testbed package index (apt update) 140s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 141s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 141s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 141s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 141s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 141s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 141s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 141s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [111 kB] 141s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1856 B] 141s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 141s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [324 kB] 142s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [14.7 kB] 142s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 142s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [268 B] 142s Fetched 1078 kB in 2s (669 kB/s) 143s Reading package lists... 144s Reading package lists... 144s Building dependency tree... 144s Reading state information... 145s Calculating upgrade... 145s Calculating upgrade... 146s The following packages will be upgraded: 146s pinentry-curses python3-jinja2 strace 146s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 146s Need to get 647 kB of archives. 146s After this operation, 11.3 kB of additional disk space will be used. 146s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 147s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pinentry-curses arm64 1.3.1-2ubuntu3 [39.2 kB] 147s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 147s Fetched 647 kB in 1s (555 kB/s) 148s (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 ... 117701 files and directories currently installed.) 148s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 148s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 148s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_arm64.deb ... 148s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 148s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 148s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 148s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 148s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 148s Setting up strace (6.13+ds-1ubuntu1) ... 148s Processing triggers for man-db (2.13.0-1) ... 149s Reading package lists... 150s Building dependency tree... 150s Reading state information... 150s Solving dependencies... 151s The following packages will be REMOVED: 151s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 151s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 151s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 151s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 151s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 151s After this operation, 267 MB disk space will be freed. 151s (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 ... 117701 files and directories currently installed.) 151s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 151s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 151s Removing libpython3.12t64:arm64 (3.12.9-1) ... 151s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 151s Removing libnsl2:arm64 (1.3.0-3build3) ... 151s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 151s Removing libunwind8:arm64 (1.6.2-3.1) ... 151s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 152s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 154s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 154s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 154s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 154s /etc/kernel/postrm.d/initramfs-tools: 154s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 154s /etc/kernel/postrm.d/zz-flash-kernel: 154s flash-kernel: Kernel 6.11.0-8-generic has been removed. 154s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 155s /etc/kernel/postrm.d/zz-update-grub: 155s Sourcing file `/etc/default/grub' 155s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 155s Generating grub configuration file ... 155s Found linux image: /boot/vmlinuz-6.14.0-10-generic 155s Found initrd image: /boot/initrd.img-6.14.0-10-generic 155s Warning: os-prober will not be executed to detect other bootable partitions. 155s Systems on them will not be added to the GRUB boot configuration. 155s Check GRUB_DISABLE_OS_PROBER documentation entry. 155s Adding boot menu entry for UEFI Firmware Settings ... 155s done 155s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 156s Processing triggers for libc-bin (2.41-1ubuntu1) ... 156s (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 ... 81650 files and directories currently installed.) 156s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 156s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 156s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 156s autopkgtest [17:13:33]: upgrading testbed (apt dist-upgrade and autopurge) 156s Reading package lists... 157s Building dependency tree... 157s Reading state information... 158s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 158s Starting 2 pkgProblemResolver with broken count: 0 158s Done 159s Entering ResolveByKeep 159s 159s Calculating upgrade... 160s The following packages will be upgraded: 160s libc-bin libc-dev-bin libc6 libc6-dev locales 160s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 160s Need to get 9530 kB of archives. 160s After this operation, 0 B of additional disk space will be used. 160s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 162s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 162s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 165s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 166s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 171s Preconfiguring packages ... 171s Fetched 9530 kB in 10s (923 kB/s) 171s (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 ... 81647 files and directories currently installed.) 171s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 171s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 171s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 171s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 171s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 171s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 172s Setting up libc6:arm64 (2.41-1ubuntu2) ... 172s (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 ... 81647 files and directories currently installed.) 172s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 172s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 172s Setting up libc-bin (2.41-1ubuntu2) ... 172s (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 ... 81647 files and directories currently installed.) 172s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 172s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 172s Setting up locales (2.41-1ubuntu2) ... 173s Generating locales (this might take a while)... 175s en_US.UTF-8... done 175s Generation complete. 175s Setting up libc-dev-bin (2.41-1ubuntu2) ... 175s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 175s Processing triggers for man-db (2.13.0-1) ... 176s Processing triggers for systemd (257.3-1ubuntu3) ... 177s Reading package lists... 177s Building dependency tree... 177s Reading state information... 177s Starting pkgProblemResolver with broken count: 0 178s Starting 2 pkgProblemResolver with broken count: 0 178s Done 178s Solving dependencies... 178s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 179s autopkgtest [17:13:56]: rebooting testbed after setup commands that affected boot 202s autopkgtest [17:14:19]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 205s autopkgtest [17:14:22]: @@@@@@@@@@@@@@@@@@@@ apt-source tvc 208s Get:1 http://ftpmaster.internal/ubuntu plucky/universe tvc 5.0.3+git20151221.80e144e+dfsg-5build4 (dsc) [2304 B] 208s Get:2 http://ftpmaster.internal/ubuntu plucky/universe tvc 5.0.3+git20151221.80e144e+dfsg-5build4 (tar) [745 kB] 208s Get:3 http://ftpmaster.internal/ubuntu plucky/universe tvc 5.0.3+git20151221.80e144e+dfsg-5build4 (diff) [10.1 kB] 209s gpgv: Signature made Sun Nov 10 11:21:31 2024 UTC 209s gpgv: using RSA key B8340990283D8D9BC1949AC74799A35146D12B35 209s gpgv: Can't check signature: No public key 209s dpkg-source: warning: cannot verify inline signature for ./tvc_5.0.3+git20151221.80e144e+dfsg-5build4.dsc: no acceptable signature found 209s autopkgtest [17:14:26]: testing package tvc version 5.0.3+git20151221.80e144e+dfsg-5build4 209s autopkgtest [17:14:26]: build not needed 210s autopkgtest [17:14:27]: test run-unit-test: preparing testbed 210s Reading package lists... 210s Building dependency tree... 210s Reading state information... 211s Starting pkgProblemResolver with broken count: 0 211s Starting 2 pkgProblemResolver with broken count: 0 211s Done 212s The following NEW packages will be installed: 212s libarmadillo14 libarpack2t64 libbamtools2.5.2 libblas3 libdisorder0 212s libgfortran5 libjsoncpp26 liblapack3 libsmithwaterman0 tvc 212s 0 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. 212s Need to get 4442 kB of archives. 212s After this operation, 13.5 MB of additional disk space will be used. 212s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 212s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB] 212s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 215s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 libarpack2t64 arm64 3.9.1-4 [94.4 kB] 215s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libarmadillo14 arm64 1:14.2.3+dfsg-1 [105 kB] 215s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 libbamtools2.5.2 arm64 2.5.2+dfsg-6build1 [132 kB] 216s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 libdisorder0 arm64 0.0.2+git20130809.8062ee1-4build1 [4604 B] 216s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libjsoncpp26 arm64 1.9.6-3 [78.7 kB] 216s Get:9 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsmithwaterman0 arm64 0.0+git20160702.2610e25-12 [35.9 kB] 216s Get:10 http://ftpmaster.internal/ubuntu plucky/universe arm64 tvc arm64 5.0.3+git20151221.80e144e+dfsg-5build4 [1080 kB] 217s Fetched 4442 kB in 6s (801 kB/s) 218s Selecting previously unselected package libblas3:arm64. 218s (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 ... 81647 files and directories currently installed.) 218s Preparing to unpack .../0-libblas3_3.12.1-2_arm64.deb ... 218s Unpacking libblas3:arm64 (3.12.1-2) ... 218s Selecting previously unselected package libgfortran5:arm64. 218s Preparing to unpack .../1-libgfortran5_15-20250222-0ubuntu1_arm64.deb ... 218s Unpacking libgfortran5:arm64 (15-20250222-0ubuntu1) ... 218s Selecting previously unselected package liblapack3:arm64. 218s Preparing to unpack .../2-liblapack3_3.12.1-2_arm64.deb ... 218s Unpacking liblapack3:arm64 (3.12.1-2) ... 218s Selecting previously unselected package libarpack2t64:arm64. 218s Preparing to unpack .../3-libarpack2t64_3.9.1-4_arm64.deb ... 218s Unpacking libarpack2t64:arm64 (3.9.1-4) ... 218s Selecting previously unselected package libarmadillo14. 218s Preparing to unpack .../4-libarmadillo14_1%3a14.2.3+dfsg-1_arm64.deb ... 218s Unpacking libarmadillo14 (1:14.2.3+dfsg-1) ... 218s Selecting previously unselected package libbamtools2.5.2:arm64. 218s Preparing to unpack .../5-libbamtools2.5.2_2.5.2+dfsg-6build1_arm64.deb ... 218s Unpacking libbamtools2.5.2:arm64 (2.5.2+dfsg-6build1) ... 218s Selecting previously unselected package libdisorder0:arm64. 218s Preparing to unpack .../6-libdisorder0_0.0.2+git20130809.8062ee1-4build1_arm64.deb ... 218s Unpacking libdisorder0:arm64 (0.0.2+git20130809.8062ee1-4build1) ... 218s Selecting previously unselected package libjsoncpp26:arm64. 218s Preparing to unpack .../7-libjsoncpp26_1.9.6-3_arm64.deb ... 218s Unpacking libjsoncpp26:arm64 (1.9.6-3) ... 218s Selecting previously unselected package libsmithwaterman0:arm64. 218s Preparing to unpack .../8-libsmithwaterman0_0.0+git20160702.2610e25-12_arm64.deb ... 218s Unpacking libsmithwaterman0:arm64 (0.0+git20160702.2610e25-12) ... 218s Selecting previously unselected package tvc. 218s Preparing to unpack .../9-tvc_5.0.3+git20151221.80e144e+dfsg-5build4_arm64.deb ... 218s Unpacking tvc (5.0.3+git20151221.80e144e+dfsg-5build4) ... 218s Setting up libdisorder0:arm64 (0.0.2+git20130809.8062ee1-4build1) ... 218s Setting up libsmithwaterman0:arm64 (0.0+git20160702.2610e25-12) ... 218s Setting up libblas3:arm64 (3.12.1-2) ... 218s 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 218s Setting up libjsoncpp26:arm64 (1.9.6-3) ... 218s Setting up libbamtools2.5.2:arm64 (2.5.2+dfsg-6build1) ... 218s Setting up libgfortran5:arm64 (15-20250222-0ubuntu1) ... 218s Setting up liblapack3:arm64 (3.12.1-2) ... 218s 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 218s Setting up libarpack2t64:arm64 (3.9.1-4) ... 218s Setting up libarmadillo14 (1:14.2.3+dfsg-1) ... 218s Setting up tvc (5.0.3+git20151221.80e144e+dfsg-5build4) ... 218s Processing triggers for man-db (2.13.0-1) ... 219s Processing triggers for libc-bin (2.41-1ubuntu2) ... 220s autopkgtest [17:14:37]: test run-unit-test: [----------------------- 220s Running Tests 220s [ Sat 2025-03-15 17:14:37 UTC ] 220s [ Sat 2025-03-15 17:14:37 UTC ] Task : Write effective bed 220s [ Sat 2025-03-15 17:14:37 UTC ] Command : /usr/bin/tvcutils validate_bed --reference "reference.fasta" --target-regions-bed "test_unmerged_detail.bed" --effective-bed "./effective_regions.bed" 220s [ Sat 2025-03-15 17:14:37 UTC ] 220s test_unmerged_detail.bed: Validation successful with 0 warnings and 0 errors 220s 220s [ Sat 2025-03-15 17:14:37 UTC ] Calling small INDELs and SNPs using tvc ... 220s [ Sat 2025-03-15 17:14:37 UTC ] 220s [ Sat 2025-03-15 17:14:37 UTC ] Task : Call small indels and SNPs 220s [ Sat 2025-03-15 17:14:37 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 220s [ Sat 2025-03-15 17:14:37 UTC ] 220s tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller 220s 220s INFO: No input VCF (Hotspot) file specified via -c,--input-vcf 220s INFO: Systematic error motif file not specified via -e 220s prefix-exclude = 6 220s hp-max-length = 8 (integer, builtin default) 220s sse-prob-threshold = 0.2 (double, builtin default) 220s min-ratio-reads-non-sse-strand = 0.2 (double, builtin default) 220s sse-relative-safety-level = 0.025 (double, builtin default) 220s do-snp-realignment = true (boolean, builtin default) 220s do-mnp-realignment = true (boolean, builtin default) 220s realignment-threshold = 1 (double, builtin default) 220s indel-as-hpindel = false (boolean, builtin default) 220s data-quality-stringency = 4 (double, builtin default) 220s read-rejection-threshold = 0.5 (double, builtin default) 220s use-position-bias = false (boolean, builtin default) 220s position-bias-ref-fraction = 0.05 (double, builtin default) 220s position-bias = 0.75 (double, builtin default) 220s position-bias-pval = 0.05 (double, builtin default) 220s downsample-to-coverage = 2000 (integer, builtin default) 220s tune-sbias = 0.01 (double, builtin default) 220s suppress-reference-genotypes = true (boolean, builtin default) 220s suppress-nocall-genotypes = true (boolean, builtin default) 220s suppress-no-calls = true (boolean, builtin default) 220s heal-snps = true (boolean, builtin default) 220s snp-min-cov-each-strand = 0 (integer, builtin default) 220s snp-min-variant-score = 10 (double, builtin default) 220s snp-min-allele-freq = 0.2 (double, builtin default) 220s snp-min-coverage = 6 (integer, builtin default) 220s snp-strand-bias = 0.95 (double, builtin default) 220s snp-strand-bias-pval = 1 (double, builtin default) 220s mnp-min-cov-each-strand = 0 (integer, builtin default) 220s mnp-min-variant-score = 10 (double, builtin default) 220s mnp-min-allele-freq = 0.2 (double, builtin default) 220s mnp-min-coverage = 6 (integer, builtin default) 220s mnp-strand-bias = 0.95 (double, builtin default) 220s mnp-strand-bias-pval = 1 (double, builtin default) 220s indel-min-cov-each-strand = 1 (integer, builtin default) 220s indel-min-variant-score = 10 (double, builtin default) 220s indel-min-allele-freq = 0.2 (double, builtin default) 220s indel-min-coverage = 15 (integer, builtin default) 220s indel-strand-bias = 0.85 (double, builtin default) 220s indel-strand-bias-pval = 1 (double, builtin default) 220s hotspot-min-cov-each-strand = 0 (integer, builtin default) 220s hotspot-min-variant-score = 10 (double, builtin default) 220s hotspot-min-allele-freq = 0.2 (double, builtin default) 220s hotspot-min-coverage = 6 (integer, builtin default) 220s hotspot-strand-bias = 0.95 (double, builtin default) 220s hotspot-strand-bias-pval = 1 (double, builtin default) 220s max-flows-to-test = 10 (integer, builtin default) 220s min-delta-for-flow = 0.1 (double, builtin default) 220s prediction-precision = 30 (double, builtin default) 220s outlier-probability = 0.01 (double, builtin default) 220s germline-prior-strength = 0 (double, builtin default) 220s heavy-tailed = 3 (integer, builtin default) 220s filter-unusual-predictions = 0.3 (double, builtin default) 220s soft-clip-bias-checker = 0.1 (double, builtin default) 220s filter-deletion-predictions = 100 (double, builtin default) 220s filter-insertion-predictions = 100 (double, builtin default) 220s max-detail-level = 0 (integer, builtin default) 220s shift-likelihood-penalty = 0.3 (double, builtin default) 220s minimum-sigma-prior = 0.085 (double, builtin default) 220s slope-sigma-prior = 0.0084 (double, builtin default) 220s sigma-prior-weight = 1 (double, builtin default) 220s k-zero = 3 (double, builtin default) 220s num-threads = 12 (integer, command line option) 220s num-variants-per-thread = 250 (integer, builtin default) 220s use-sse-basecaller = false (boolean, builtin default) 220s do-json-diagnostic = false (boolean, builtin default) 220s do-minimal-diagnostic = false (boolean, builtin default) 220s process-input-positions-only = false (boolean, builtin default) 220s suppress-recalibration = true (boolean, builtin default) 220s resolve-clipped-bases = false (boolean, builtin default) 220s allow-indels = true (boolean, builtin default) 220s allow-snps = true (boolean, builtin default) 220s allow-mnps = true (boolean, builtin default) 220s allow-complex = false (boolean, builtin default) 220s left-align-indels = false (boolean, builtin default) 220s use-best-n-alleles = 2 (integer, builtin default) 220s use-input-allele-only = false (boolean, builtin default) 220s min-mapping-qv = 4 (integer, builtin default) 220s read-snp-limit = 10 (integer, builtin default) 220s read-max-mismatch-fraction = 1 (double, builtin default) 220s max-complex-gap = 1 (integer, builtin default) 220s gen-min-alt-allele-freq = 0.2 (double, builtin default) 220s gen-min-coverage = 6 (integer, builtin default) 220s gen-min-indel-alt-allele-freq = 0.2 (double, builtin default) 220s override-limits = false (boolean, builtin default) 220s Limit check parameter hp-max-length: lim. 1 <= 8? OK! 220s Limit check parameter sse-prob-threshold: lim. 0 <= 0.2 <= lim. 1? OK! 220s Limit check parameter min-ratio-reads-non-sse-strand: lim. 0 <= 0.2 <= lim. 1? OK! 220s Limit check parameter sse-relative-safety-level: lim. 0 <= 0.025 <= lim. 1? OK! 220s Limit check parameter realignment-threshold: lim. 0 <= 1 <= lim. 1? OK! 220s Limit check parameter data-quality-stringency: lim. 0 <= 4? OK! 220s Limit check parameter read-rejection-threshold: lim. 0 <= 0.5 <= lim. 1? OK! 220s Limit check parameter downsample-to-coverage: lim. 20 <= 2000 <= lim. 100000? OK! 220s Limit check parameter position-bias-ref-fraction: lim. 0 <= 0.05 <= lim. 1? OK! 220s Limit check parameter position-bias: lim. 0 <= 0.75 <= lim. 1? OK! 220s Limit check parameter position-bias-pval: lim. 0 <= 0.05 <= lim. 1? OK! 220s Limit check parameter tune-sbias: lim. 0.001 <= 0.01 <= lim. 1000? OK! 220s Limit check parameter snp-min-cov-each-strand: lim. 0 <= 0? OK! 220s Limit check parameter snp-min-variant-score: lim. 0 <= 10? OK! 220s Limit check parameter snp-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 220s Limit check parameter snp-min-coverage: lim. 0 <= 6? OK! 220s Limit check parameter snp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 220s Limit check parameter snp-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 220s Limit check parameter mnp-min-cov-each-strand: lim. 0 <= 0? OK! 220s Limit check parameter mnp-min-variant-score: lim. 0 <= 10? OK! 220s Limit check parameter mnp-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 220s Limit check parameter mnp-min-coverage: lim. 0 <= 6? OK! 220s Limit check parameter mnp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 220s Limit check parameter mnp-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 220s Limit check parameter indel-min-cov-each-strand: lim. 0 <= 1? OK! 220s Limit check parameter indel-min-variant-score: lim. 0 <= 10? OK! 220s Limit check parameter indel-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 220s Limit check parameter indel-min-coverage: lim. 0 <= 15? OK! 220s Limit check parameter indel-strand-bias: lim. 0.5 <= 0.85 <= lim. 1? OK! 220s Limit check parameter indel-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 220s Limit check parameter hotspot-min-cov-each-strand: lim. 0 <= 0? OK! 220s Limit check parameter hotspot-min-variant-score: lim. 0 <= 10? OK! 220s Limit check parameter hotspot-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 220s Limit check parameter hotspot-min-coverage: lim. 0 <= 6? OK! 220s Limit check parameter hotspot-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 220s Limit check parameter hotspot-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 220s Limit check parameter max-flows-to-test: lim. 1 <= 10 <= lim. 100? OK! 220s Limit check parameter min-delta-for-flow: lim. 0.01 <= 0.1 <= lim. 0.5? OK! 220s Limit check parameter prediction-precision: lim. 0.1 <= 30? OK! 220s Limit check parameter outlier-probability: lim. 0 <= 0.01 <= lim. 1? OK! 220s Limit check parameter germline-prior-strength: lim. 0 <= 0 <= lim. 1000? OK! 220s Limit check parameter heavy-tailed: lim. 1 <= 3? OK! 220s Limit check parameter filter-unusual-predictions: lim. 0 <= 0.3? OK! 220s Limit check parameter soft-clip-bias-checker: lim. 0 <= 0.1 <= lim. 1? OK! 220s Limit check parameter filter-deletion-predictions: lim. 0 <= 100? OK! 220s Limit check parameter filter-insertion-predictions: lim. 0 <= 100? OK! 220s Limit check parameter max-detail-level: lim. 0 <= 0 <= lim. 10000? OK! 220s Limit check parameter shift-likelihood-penalty: lim. 0.01 <= 0.3? OK! 220s Limit check parameter minimum-sigma-prior: lim. 0.01 <= 0.085? OK! 220s Limit check parameter slope-sigma-prior: lim. 0 <= 0.0084? OK! 220s Limit check parameter sigma-prior-weight: lim. 0.01 <= 1? OK! 220s Limit check parameter k-zero: lim. 0 <= 3? OK! 220s Limit check parameter num-threads: lim. 1 <= 12 <= lim. 128? OK! 220s Limit check parameter num-variants-per-thread: lim. 1 <= 250 <= lim. 10000? OK! 220s Limit check parameter use-best-n-alleles: lim. 0 <= 2 <= lim. 20? OK! 220s Limit check parameter min-mapping-qv: lim. 0 <= 4? OK! 220s Limit check parameter read-snp-limit: lim. 0 <= 10? OK! 220s Limit check parameter read-max-mismatch-fraction: lim. 0 <= 1 <= lim. 1? OK! 220s Limit check parameter gen-min-alt-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 220s Limit check parameter gen-min-coverage: lim. 0 <= 6? OK! 220s Limit check parameter gen-min-indel-alt-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 220s TargetsManager: Loaded targets file test_unmerged_detail.bed 220s TargetsManager: 1 target(s) 220s TargetsManager: Trimming of AmpliSeq primers is enabled 220s SampleManager: Found 1 read group(s) and 1 sample(s). 220s SampleManager: Primary sample "85" (default) present in 1 read group(s) 220s TVC found a total of 1 different flow orders of max flow lengths: 500 220s Recalibration was detected from comment lines in bam file(s): 220s 1 unique blocks of recalibration info detected. 220s Recalibration model: suppressed 220s 220s [tvc] Normal termination. Processing time: 0 seconds. 220s 220s [ Sat 2025-03-15 17:14:37 UTC ] 220s [ Sat 2025-03-15 17:14:37 UTC ] Task : Assemble long indels 220s [ Sat 2025-03-15 17:14:37 UTC ] Command : /usr/bin/tvcassembly --reference reference.fasta --input-bam test.bam --target-file test_merged_plain.bed --output-vcf ./indel_assembly.vcf 220s [ Sat 2025-03-15 17:14:37 UTC ] 220s tvcassembly 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller - Long Indel Assembly 220s 220s kmer-len = 19 (integer, builtin default) 220s min-var-count = 5 (integer, builtin default) 220s short-suffix-match = 5 (integer, builtin default) 220s min-indel-size = 4 (integer, builtin default) 220s max-hp-length = 8 (integer, builtin default) 220s min-var-freq = 0.15 (double, builtin default) 220s min-var-score = 10 (double, builtin default) 220s relative-strand-bias = 0.8 (double, builtin default) 220s output-mnv = 0 (integer, builtin default) 220s TargetsManager: Loaded targets file test_merged_plain.bed 220s TargetsManager: 1 target(s) 220s SampleManager: Found 1 read group(s) and 1 sample(s). 220s SampleManager: Primary sample "85" (default) present in 1 read group(s) 220s [ Sat 2025-03-15 17:14:37 UTC ] 220s [ Sat 2025-03-15 17:14:37 UTC ] Task : Unify variants and annotations from all sources (tvc,IndelAssembly,hotpots) 220s [ Sat 2025-03-15 17:14:37 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" 220s [ Sat 2025-03-15 17:14:37 UTC ] 220s TargetsManager: Loaded targets file test_merged_plain.bed 220s TargetsManager: 1 target(s) 220s [ Sat 2025-03-15 17:14:37 UTC ] 220s [ Sat 2025-03-15 17:14:37 UTC ] Task : Generate uncompressed vcf 220s [ Sat 2025-03-15 17:14:37 UTC ] Command : gzip -dcf "./TSVC_variants.vcf.gz" > "./TSVC_variants.vcf" 220s [ Sat 2025-03-15 17:14:37 UTC ] 220s PASS 221s autopkgtest [17:14:38]: test run-unit-test: -----------------------] 221s run-unit-test PASS 221s autopkgtest [17:14:38]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 222s autopkgtest [17:14:39]: @@@@@@@@@@@@@@@@@@@@ summary 222s run-unit-test PASS 239s nova [W] Using flock in prodstack6-arm64 239s Creating nova instance adt-plucky-arm64-tvc-20250315-171057-juju-7f2275-prod-proposed-migration-environment-2-a141f67e-c1ee-484a-98e6-8127c8e09452 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 239s nova [W] Timed out waiting for 5c38dfad-6e7c-483d-8267-84ee8bf15fd3 to get deleted.