0s autopkgtest [13:15:19]: starting date and time: 2025-01-11 13:15:19+0000 0s autopkgtest [13:15:19]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [13:15:19]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.2yuol1_9/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:blasr --apt-upgrade pbsuite --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=blasr/5.3.5+dfsg-7 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-20.secgroup --name adt-plucky-amd64-pbsuite-20250111-131518-juju-7f2275-prod-proposed-migration-environment-15-0dbc6bac-4107-42a9-b7bc-11cb89586b6f --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-amd64 -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/ 114s autopkgtest [13:17:13]: testbed dpkg architecture: amd64 114s autopkgtest [13:17:13]: testbed apt version: 2.9.18 114s autopkgtest [13:17:13]: @@@@@@@@@@@@@@@@@@@@ test bed setup 114s autopkgtest [13:17:13]: testbed release detected to be: None 115s autopkgtest [13:17:14]: updating testbed package index (apt update) 115s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 116s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 116s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 116s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 116s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [131 kB] 116s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [778 kB] 116s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.7 kB] 116s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 116s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [164 kB] 116s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [296 kB] 116s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [40.1 kB] 116s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2408 B] 116s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [380 kB] 116s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [979 kB] 116s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [3516 B] 116s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [13.0 kB] 116s Fetched 2884 kB in 1s (3078 kB/s) 117s Reading package lists... 118s Reading package lists... 118s Building dependency tree... 118s Reading state information... 118s Calculating upgrade... 118s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 118s Reading package lists... 118s Building dependency tree... 118s Reading state information... 119s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 119s autopkgtest [13:17:18]: upgrading testbed (apt dist-upgrade and autopurge) 119s Reading package lists... 119s Building dependency tree... 119s Reading state information... 119s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 119s Starting 2 pkgProblemResolver with broken count: 0 119s Done 120s Entering ResolveByKeep 120s 120s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 120s Reading package lists... 120s Building dependency tree... 120s Reading state information... 121s Starting pkgProblemResolver with broken count: 0 121s Starting 2 pkgProblemResolver with broken count: 0 121s Done 121s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 123s autopkgtest [13:17:22]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 124s autopkgtest [13:17:23]: @@@@@@@@@@@@@@@@@@@@ apt-source pbsuite 127s Get:1 http://ftpmaster.internal/ubuntu plucky/universe pbsuite 15.8.24+dfsg-8 (dsc) [2316 B] 127s Get:2 http://ftpmaster.internal/ubuntu plucky/universe pbsuite 15.8.24+dfsg-8 (tar) [1615 kB] 127s Get:3 http://ftpmaster.internal/ubuntu plucky/universe pbsuite 15.8.24+dfsg-8 (diff) [26.9 kB] 127s gpgv: Signature made Mon Dec 9 19:47:53 2024 UTC 127s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 127s gpgv: issuer "tille@debian.org" 127s gpgv: Can't check signature: No public key 127s dpkg-source: warning: cannot verify inline signature for ./pbsuite_15.8.24+dfsg-8.dsc: no acceptable signature found 128s autopkgtest [13:17:27]: testing package pbsuite version 15.8.24+dfsg-8 128s autopkgtest [13:17:27]: build not needed 129s autopkgtest [13:17:28]: test run-unit-test: preparing testbed 129s Reading package lists... 129s Building dependency tree... 129s Reading state information... 129s Starting pkgProblemResolver with broken count: 0 130s Starting 2 pkgProblemResolver with broken count: 0 130s Done 130s The following NEW packages will be installed: 130s blasr libaec0 libblas3 libblasr5.3.5 libdeflate0 libgfortran5 130s libhdf5-103-1t64 libhdf5-cpp-103-1t64 libhdf5-hl-100t64 libhts3t64 130s libhtscodecs2 liblapack3 liblzf1 libpbbam2.4.0 libpbcopper2.3.0 libpbseq 130s libsz2 pbdagcon pbhoney pbjelly pbsuite python3-h5py python3-h5py-serial 130s python3-intervaltree python3-intervaltree-bio python3-networkx python3-numpy 130s python3-pbbanana python3-pbsuite-utils python3-pysam 130s python3-sortedcontainers samtools 130s 0 upgraded, 32 newly installed, 0 to remove and 0 not upgraded. 130s Need to get 36.1 MB of archives. 130s After this operation, 208 MB of additional disk space will be used. 130s Get:1 http://ftpmaster.internal/ubuntu plucky/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB] 130s Get:2 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsz2 amd64 1.1.3-1 [5456 B] 130s Get:3 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-103-1t64 amd64 1.10.10+repack-5ubuntu1 [1367 kB] 130s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-cpp-103-1t64 amd64 1.10.10+repack-5ubuntu1 [131 kB] 130s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 130s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-1 [132 kB] 130s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.20+ds-2 [501 kB] 130s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpbcopper2.3.0 amd64 2.3.0+dfsg-2 [575 kB] 131s Get:9 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpbbam2.4.0 amd64 2.4.0+dfsg-1build2 [679 kB] 131s Get:10 http://ftpmaster.internal/ubuntu plucky/universe amd64 libblasr5.3.5 amd64 5.3.5+dfsg-9 [1248 kB] 131s Get:11 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpbseq amd64 5.3.5+dfsg-9 [3056 B] 131s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 blasr amd64 5.3.5+dfsg-7 [269 kB] 131s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-4 [332 kB] 131s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-12ubuntu1 [909 kB] 131s Get:15 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-5ubuntu1 [59.5 kB] 131s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-4 [3177 kB] 131s Get:17 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblzf1 amd64 3.6-4 [7624 B] 131s Get:18 http://ftpmaster.internal/ubuntu plucky/universe amd64 pbdagcon amd64 0.3+git20180411.c14c422+dfsg-9 [268 kB] 131s Get:19 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pysam amd64 0.22.1+ds-2build1 [4446 kB] 131s Get:20 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pbsuite-utils all 15.8.24+dfsg-8 [537 kB] 131s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 131s Get:22 http://ftpmaster.internal/ubuntu plucky/universe amd64 pbjelly all 15.8.24+dfsg-8 [1055 kB] 131s Get:23 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pbbanana all 15.8.24+dfsg-8 [16.7 kB] 131s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-12 [5319 kB] 131s Get:25 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py-serial amd64 3.11.0-8ubuntu3 [1689 kB] 131s Get:26 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py all 3.11.0-8ubuntu3 [7982 B] 131s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-sortedcontainers all 2.4.0-2 [27.6 kB] 131s Get:28 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-intervaltree all 3.0.2-1.1 [22.4 kB] 131s Get:29 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-intervaltree-bio all 1.0.1-4 [8260 B] 131s Get:30 http://ftpmaster.internal/ubuntu plucky/universe amd64 samtools amd64 1.20-3 [599 kB] 131s Get:31 http://ftpmaster.internal/ubuntu plucky/universe amd64 pbhoney all 15.8.24+dfsg-8 [1152 kB] 131s Get:32 http://ftpmaster.internal/ubuntu plucky/universe amd64 pbsuite all 15.8.24+dfsg-8 [1894 B] 132s Fetched 36.1 MB in 1s (25.5 MB/s) 132s Selecting previously unselected package libaec0:amd64. 132s (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 ... 75820 files and directories currently installed.) 132s Preparing to unpack .../00-libaec0_1.1.3-1_amd64.deb ... 132s Unpacking libaec0:amd64 (1.1.3-1) ... 132s Selecting previously unselected package libsz2:amd64. 132s Preparing to unpack .../01-libsz2_1.1.3-1_amd64.deb ... 132s Unpacking libsz2:amd64 (1.1.3-1) ... 132s Selecting previously unselected package libhdf5-103-1t64:amd64. 132s Preparing to unpack .../02-libhdf5-103-1t64_1.10.10+repack-5ubuntu1_amd64.deb ... 132s Unpacking libhdf5-103-1t64:amd64 (1.10.10+repack-5ubuntu1) ... 132s Selecting previously unselected package libhdf5-cpp-103-1t64:amd64. 132s Preparing to unpack .../03-libhdf5-cpp-103-1t64_1.10.10+repack-5ubuntu1_amd64.deb ... 132s Unpacking libhdf5-cpp-103-1t64:amd64 (1.10.10+repack-5ubuntu1) ... 132s Selecting previously unselected package libdeflate0:amd64. 132s Preparing to unpack .../04-libdeflate0_1.22-1_amd64.deb ... 132s Unpacking libdeflate0:amd64 (1.22-1) ... 132s Selecting previously unselected package libhtscodecs2:amd64. 132s Preparing to unpack .../05-libhtscodecs2_1.6.1-1_amd64.deb ... 132s Unpacking libhtscodecs2:amd64 (1.6.1-1) ... 132s Selecting previously unselected package libhts3t64:amd64. 132s Preparing to unpack .../06-libhts3t64_1.20+ds-2_amd64.deb ... 132s Unpacking libhts3t64:amd64 (1.20+ds-2) ... 132s Selecting previously unselected package libpbcopper2.3.0:amd64. 132s Preparing to unpack .../07-libpbcopper2.3.0_2.3.0+dfsg-2_amd64.deb ... 132s Unpacking libpbcopper2.3.0:amd64 (2.3.0+dfsg-2) ... 132s Selecting previously unselected package libpbbam2.4.0:amd64. 132s Preparing to unpack .../08-libpbbam2.4.0_2.4.0+dfsg-1build2_amd64.deb ... 132s Unpacking libpbbam2.4.0:amd64 (2.4.0+dfsg-1build2) ... 132s Selecting previously unselected package libblasr5.3.5:amd64. 132s Preparing to unpack .../09-libblasr5.3.5_5.3.5+dfsg-9_amd64.deb ... 132s Unpacking libblasr5.3.5:amd64 (5.3.5+dfsg-9) ... 132s Selecting previously unselected package libpbseq:amd64. 132s Preparing to unpack .../10-libpbseq_5.3.5+dfsg-9_amd64.deb ... 132s Unpacking libpbseq:amd64 (5.3.5+dfsg-9) ... 132s Selecting previously unselected package blasr. 132s Preparing to unpack .../11-blasr_5.3.5+dfsg-7_amd64.deb ... 132s Unpacking blasr (5.3.5+dfsg-7) ... 132s Selecting previously unselected package libblas3:amd64. 132s Preparing to unpack .../12-libblas3_3.12.0-4_amd64.deb ... 132s Unpacking libblas3:amd64 (3.12.0-4) ... 132s Selecting previously unselected package libgfortran5:amd64. 132s Preparing to unpack .../13-libgfortran5_14.2.0-12ubuntu1_amd64.deb ... 132s Unpacking libgfortran5:amd64 (14.2.0-12ubuntu1) ... 132s Selecting previously unselected package libhdf5-hl-100t64:amd64. 132s Preparing to unpack .../14-libhdf5-hl-100t64_1.10.10+repack-5ubuntu1_amd64.deb ... 132s Unpacking libhdf5-hl-100t64:amd64 (1.10.10+repack-5ubuntu1) ... 132s Selecting previously unselected package liblapack3:amd64. 132s Preparing to unpack .../15-liblapack3_3.12.0-4_amd64.deb ... 132s Unpacking liblapack3:amd64 (3.12.0-4) ... 132s Selecting previously unselected package liblzf1:amd64. 132s Preparing to unpack .../16-liblzf1_3.6-4_amd64.deb ... 132s Unpacking liblzf1:amd64 (3.6-4) ... 132s Selecting previously unselected package pbdagcon. 132s Preparing to unpack .../17-pbdagcon_0.3+git20180411.c14c422+dfsg-9_amd64.deb ... 132s Unpacking pbdagcon (0.3+git20180411.c14c422+dfsg-9) ... 132s Selecting previously unselected package python3-pysam. 132s Preparing to unpack .../18-python3-pysam_0.22.1+ds-2build1_amd64.deb ... 132s Unpacking python3-pysam (0.22.1+ds-2build1) ... 133s Selecting previously unselected package python3-pbsuite-utils. 133s Preparing to unpack .../19-python3-pbsuite-utils_15.8.24+dfsg-8_all.deb ... 133s Unpacking python3-pbsuite-utils (15.8.24+dfsg-8) ... 133s Selecting previously unselected package python3-networkx. 133s Preparing to unpack .../20-python3-networkx_3.2.1-4ubuntu1_all.deb ... 133s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 133s Selecting previously unselected package pbjelly. 133s Preparing to unpack .../21-pbjelly_15.8.24+dfsg-8_all.deb ... 133s Unpacking pbjelly (15.8.24+dfsg-8) ... 133s Selecting previously unselected package python3-pbbanana. 133s Preparing to unpack .../22-python3-pbbanana_15.8.24+dfsg-8_all.deb ... 133s Unpacking python3-pbbanana (15.8.24+dfsg-8) ... 133s Selecting previously unselected package python3-numpy. 133s Preparing to unpack .../23-python3-numpy_1%3a1.26.4+ds-12_amd64.deb ... 133s Unpacking python3-numpy (1:1.26.4+ds-12) ... 134s Selecting previously unselected package python3-h5py-serial. 134s Preparing to unpack .../24-python3-h5py-serial_3.11.0-8ubuntu3_amd64.deb ... 134s Unpacking python3-h5py-serial (3.11.0-8ubuntu3) ... 134s Selecting previously unselected package python3-h5py. 134s Preparing to unpack .../25-python3-h5py_3.11.0-8ubuntu3_all.deb ... 134s Unpacking python3-h5py (3.11.0-8ubuntu3) ... 134s Selecting previously unselected package python3-sortedcontainers. 134s Preparing to unpack .../26-python3-sortedcontainers_2.4.0-2_all.deb ... 134s Unpacking python3-sortedcontainers (2.4.0-2) ... 134s Selecting previously unselected package python3-intervaltree. 134s Preparing to unpack .../27-python3-intervaltree_3.0.2-1.1_all.deb ... 134s Unpacking python3-intervaltree (3.0.2-1.1) ... 134s Selecting previously unselected package python3-intervaltree-bio. 134s Preparing to unpack .../28-python3-intervaltree-bio_1.0.1-4_all.deb ... 134s Unpacking python3-intervaltree-bio (1.0.1-4) ... 134s Selecting previously unselected package samtools. 134s Preparing to unpack .../29-samtools_1.20-3_amd64.deb ... 134s Unpacking samtools (1.20-3) ... 134s Selecting previously unselected package pbhoney. 134s Preparing to unpack .../30-pbhoney_15.8.24+dfsg-8_all.deb ... 134s Unpacking pbhoney (15.8.24+dfsg-8) ... 134s Selecting previously unselected package pbsuite. 134s Preparing to unpack .../31-pbsuite_15.8.24+dfsg-8_all.deb ... 134s Unpacking pbsuite (15.8.24+dfsg-8) ... 134s Setting up libhtscodecs2:amd64 (1.6.1-1) ... 134s Setting up libdeflate0:amd64 (1.22-1) ... 134s Setting up python3-sortedcontainers (2.4.0-2) ... 134s Setting up python3-networkx (3.2.1-4ubuntu1) ... 135s Setting up libaec0:amd64 (1.1.3-1) ... 135s Setting up libblas3:amd64 (3.12.0-4) ... 135s 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 135s Setting up liblzf1:amd64 (3.6-4) ... 135s Setting up libgfortran5:amd64 (14.2.0-12ubuntu1) ... 135s Setting up libhts3t64:amd64 (1.20+ds-2) ... 135s Setting up libsz2:amd64 (1.1.3-1) ... 135s Setting up libpbcopper2.3.0:amd64 (2.3.0+dfsg-2) ... 135s Setting up liblapack3:amd64 (3.12.0-4) ... 135s 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 135s Setting up python3-pysam (0.22.1+ds-2build1) ... 135s Setting up python3-intervaltree (3.0.2-1.1) ... 135s Setting up python3-pbsuite-utils (15.8.24+dfsg-8) ... 135s Setting up libpbbam2.4.0:amd64 (2.4.0+dfsg-1build2) ... 135s Setting up samtools (1.20-3) ... 135s Setting up python3-numpy (1:1.26.4+ds-12) ... 137s Setting up python3-intervaltree-bio (1.0.1-4) ... 137s Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-5ubuntu1) ... 137s Setting up libhdf5-hl-100t64:amd64 (1.10.10+repack-5ubuntu1) ... 137s Setting up libhdf5-cpp-103-1t64:amd64 (1.10.10+repack-5ubuntu1) ... 137s Setting up python3-h5py-serial (3.11.0-8ubuntu3) ... 137s Setting up libblasr5.3.5:amd64 (5.3.5+dfsg-9) ... 137s Setting up python3-h5py (3.11.0-8ubuntu3) ... 137s Setting up libpbseq:amd64 (5.3.5+dfsg-9) ... 137s Setting up blasr (5.3.5+dfsg-7) ... 137s Setting up pbdagcon (0.3+git20180411.c14c422+dfsg-9) ... 137s Setting up pbjelly (15.8.24+dfsg-8) ... 137s Setting up python3-pbbanana (15.8.24+dfsg-8) ... 137s Setting up pbhoney (15.8.24+dfsg-8) ... 137s Setting up pbsuite (15.8.24+dfsg-8) ... 137s Processing triggers for man-db (2.13.0-1) ... 138s Processing triggers for libc-bin (2.40-4ubuntu1) ... 140s autopkgtest [13:17:39]: test run-unit-test: [----------------------- 140s PIEMapping 140s 140s Please Cite: English, Adam C., William J. Salerno, Jeffery G. 140s Reid. "PBHoney: identyfying genomic variants via 140s long-read discordance and interrupted mapping." 140s BMC Bioinformatics 2014, 15:180 (June 10, 2014). 140s doi:10.1186/1471-2105-15-180 140s 140s 2025-01-11 13:17:39,847 [INFO] Running /usr/bin/Honey pie filtered_subreads.fastq lambda_modified.fasta -o mappingFinal.sam 140s 2025-01-11 13:17:39,847 [INFO] Running Blasr 170s 2025-01-11 13:18:09,355 [INFO] [0, b'[INFO] 2025-01-11T13:17:39 [blasr] started.\n[INFO] 2025-01-11T13:18:09 [blasr] ended.\n', None] 170s 2025-01-11 13:18:09,356 [INFO] Mapping Tails 170s 2025-01-11 13:18:09,356 [INFO] Extracting tails 170s 2025-01-11 13:18:09,499 [INFO] Parsed 433 reads 170s 2025-01-11 13:18:09,499 [INFO] Found 278 tails 170s 2025-01-11 13:18:09,499 [INFO] 21 reads had double tails 170s 2025-01-11 13:18:09,500 [INFO] Running Blasr 171s 2025-01-11 13:18:10,779 [ERROR] blasr mapping failed! 171s 2025-01-11 13:18:10,779 [ERROR] RETCODE 134 171s 2025-01-11 13:18:10,779 [ERROR] STDOUT b"[INFO] 2025-01-11T13:18:09 [blasr] started.\n/usr/include/c++/14/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = ChainedMatchPos; _Alloc = std::allocator; reference = ChainedMatchPos&; size_type = long unsigned int]: Assertion '__n < this->size()' failed.\nAborted (core dumped)\n" 171s 2025-01-11 13:18:10,779 [ERROR] STDERR None 171s 2025-01-11 13:18:10,779 [ERROR] Exiting 171s Sam To Bam 171s [E::hts_open_format] Failed to open file "mappingFinal.sam" : No such file or directory 171s samtools view: failed to open "mappingFinal.sam" for reading: No such file or directory 171s [W::hts_set_opt] Cannot change block size for this format 171s samtools sort: failed to read header from "-" 171s Calling Tails 171s samtools index: "mappingFinal.bam" is in a format that cannot be usefully indexed 172s 172s Please Cite: English, Adam C., William J. Salerno, Jeffery G. 172s Reid. "PBHoney: identyfying genomic variants via 172s long-read discordance and interrupted mapping." 172s BMC Bioinformatics 2014, 15:180 (June 10, 2014). 172s doi:10.1186/1471-2105-15-180 172s 172s 2025-01-11 13:18:11,079 [INFO] Running /usr/bin/Honey tails mappingFinal.bam 172s Traceback (most recent call last): 172s File "/usr/bin/Honey", line 51, in 172s parseArgs() 172s File "/usr/bin/Honey", line 48, in parseArgs 172s STAGES[args.stage](args.options) 172s File "/usr/lib/python3/dist-packages/pbsuite/honey/TGraf.py", line 665, in run 172s bam = pysam.Samfile(args.bam,'rb') 172s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 172s File "pysam/libcalignmentfile.pyx", line 751, in pysam.libcalignmentfile.AlignmentFile.__cinit__ 172s File "pysam/libcalignmentfile.pyx", line 956, in pysam.libcalignmentfile.AlignmentFile._open 172s ValueError: file does not contain alignment data 172s Calling Spots 173s 173s Please Cite: English, Adam C., William J. Salerno, Jeffery G. 173s Reid. "PBHoney: identyfying genomic variants via 173s long-read discordance and interrupted mapping." 173s BMC Bioinformatics 2014, 15:180 (June 10, 2014). 173s doi:10.1186/1471-2105-15-180 173s 173s 2025-01-11 13:18:12,114 [INFO] Running /usr/bin/Honey spots --reference lambda_modified.fasta mappingFinal.bam 173s Traceback (most recent call last): 173s File "/usr/bin/Honey", line 51, in 173s parseArgs() 173s File "/usr/bin/Honey", line 48, in parseArgs 173s STAGES[args.stage](args.options) 173s File "/usr/lib/python3/dist-packages/pbsuite/honey/HSpots.py", line 1092, in run 173s bam = pysam.Samfile(args.bam) 173s ^^^^^^^^^^^^^^^^^^^^^^^ 173s File "pysam/libcalignmentfile.pyx", line 751, in pysam.libcalignmentfile.AlignmentFile.__cinit__ 173s File "pysam/libcalignmentfile.pyx", line 956, in pysam.libcalignmentfile.AlignmentFile._open 173s ValueError: file does not contain alignment data 174s autopkgtest [13:18:13]: test run-unit-test: -----------------------] 174s run-unit-test FAIL non-zero exit status 1 174s autopkgtest [13:18:13]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 175s autopkgtest [13:18:14]: @@@@@@@@@@@@@@@@@@@@ summary 175s run-unit-test FAIL non-zero exit status 1 215s nova [W] Skipping flock for amd64 215s Creating nova instance adt-plucky-amd64-pbsuite-20250111-131518-juju-7f2275-prod-proposed-migration-environment-15-0dbc6bac-4107-42a9-b7bc-11cb89586b6f from image adt/ubuntu-plucky-amd64-server-20250111.img (UUID 583b1e24-63f4-4305-9a48-aa6a34658dc0)... 215s nova [W] Timed out waiting for 8c371011-651a-474e-9fd6-096f9a1238d2 to get deleted.