0s autopkgtest [22:44:45]: starting date and time: 2025-01-09 22:44:45+0000 0s autopkgtest [22:44:45]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [22:44:45]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.1aaak423/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 autopkgtest-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-ppc64el-11.secgroup --name adt-plucky-ppc64el-pbsuite-20250109-224445-juju-7f2275-prod-proposed-migration-environment-15-2c4b72b9-7687-469c-b0f5-faddc70e24b8 --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-ppc64el -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/ 96s autopkgtest [22:46:21]: testbed dpkg architecture: ppc64el 96s autopkgtest [22:46:21]: testbed apt version: 2.9.18 97s autopkgtest [22:46:22]: @@@@@@@@@@@@@@@@@@@@ test bed setup 97s autopkgtest [22:46:22]: testbed release detected to be: None 97s autopkgtest [22:46:22]: updating testbed package index (apt update) 98s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 98s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 98s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 98s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 98s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.0 kB] 98s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [781 kB] 98s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [126 kB] 98s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 98s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [268 kB] 98s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted ppc64el Packages [756 B] 98s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [1002 kB] 99s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [5088 B] 99s Fetched 2281 kB in 1s (2098 kB/s) 100s Reading package lists... 100s Reading package lists... 101s Building dependency tree... 101s Reading state information... 101s Calculating upgrade... 101s The following packages will be upgraded: 101s firmware-sof-signed 101s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 101s Need to get 7093 kB of archives. 101s After this operation, 0 B of additional disk space will be used. 101s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el firmware-sof-signed all 2024.06-1ubuntu4 [7093 kB] 102s Fetched 7093 kB in 1s (8528 kB/s) 102s (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 ... 74025 files and directories currently installed.) 102s Preparing to unpack .../firmware-sof-signed_2024.06-1ubuntu4_all.deb ... 103s Unpacking firmware-sof-signed (2024.06-1ubuntu4) over (2024.06-1ubuntu3) ... 103s Setting up firmware-sof-signed (2024.06-1ubuntu4) ... 103s Reading package lists... 103s Building dependency tree... 103s Reading state information... 103s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 103s autopkgtest [22:46:28]: upgrading testbed (apt dist-upgrade and autopurge) 103s Reading package lists... 104s Building dependency tree... 104s Reading state information... 104s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 104s Starting 2 pkgProblemResolver with broken count: 0 104s Done 104s Entering ResolveByKeep 105s 105s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 105s Starting pkgProblemResolver with broken count: 0 105s Starting 2 pkgProblemResolver with broken count: 0 105s Done 106s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 108s autopkgtest [22:46:33]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 13:49:23 UTC 2024 108s autopkgtest [22:46:33]: @@@@@@@@@@@@@@@@@@@@ apt-source pbsuite 112s Get:1 http://ftpmaster.internal/ubuntu plucky/universe pbsuite 15.8.24+dfsg-8 (dsc) [2316 B] 112s Get:2 http://ftpmaster.internal/ubuntu plucky/universe pbsuite 15.8.24+dfsg-8 (tar) [1615 kB] 112s Get:3 http://ftpmaster.internal/ubuntu plucky/universe pbsuite 15.8.24+dfsg-8 (diff) [26.9 kB] 112s gpgv: Signature made Mon Dec 9 19:47:53 2024 UTC 112s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 112s gpgv: issuer "tille@debian.org" 112s gpgv: Can't check signature: No public key 112s dpkg-source: warning: cannot verify inline signature for ./pbsuite_15.8.24+dfsg-8.dsc: no acceptable signature found 113s autopkgtest [22:46:38]: testing package pbsuite version 15.8.24+dfsg-8 113s autopkgtest [22:46:38]: build not needed 114s autopkgtest [22:46:39]: test run-unit-test: preparing testbed 114s Reading package lists... 114s Building dependency tree... 114s Reading state information... 115s Starting pkgProblemResolver with broken count: 0 115s Starting 2 pkgProblemResolver with broken count: 0 115s Done 115s The following NEW packages will be installed: 115s blasr libaec0 libblas3 libblasr5.3.5 libdeflate0 libgfortran5 115s libhdf5-103-1t64 libhdf5-cpp-103-1t64 libhdf5-hl-100t64 libhts3t64 115s libhtscodecs2 liblapack3 liblzf1 libpbbam2.4.0 libpbcopper2.3.0 libpbseq 115s libsz2 pbdagcon pbhoney pbjelly pbsuite python3-h5py python3-h5py-serial 115s python3-intervaltree python3-intervaltree-bio python3-networkx python3-numpy 115s python3-pbbanana python3-pbsuite-utils python3-pysam 115s python3-sortedcontainers samtools 115s 0 upgraded, 32 newly installed, 0 to remove and 0 not upgraded. 115s Need to get 35.1 MB of archives. 115s After this operation, 212 MB of additional disk space will be used. 115s Get:1 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libaec0 ppc64el 1.1.3-1 [30.1 kB] 115s Get:2 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libsz2 ppc64el 1.1.3-1 [5566 B] 115s Get:3 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhdf5-103-1t64 ppc64el 1.10.10+repack-5ubuntu1 [1394 kB] 116s Get:4 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhdf5-cpp-103-1t64 ppc64el 1.10.10+repack-5ubuntu1 [128 kB] 116s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdeflate0 ppc64el 1.22-1 [63.3 kB] 116s Get:6 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhtscodecs2 ppc64el 1.6.1-1 [113 kB] 116s Get:7 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhts3t64 ppc64el 1.20+ds-2 [574 kB] 116s Get:8 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libpbcopper2.3.0 ppc64el 2.3.0+dfsg-2 [594 kB] 116s Get:9 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libpbbam2.4.0 ppc64el 2.4.0+dfsg-1build2 [752 kB] 116s Get:10 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libblasr5.3.5 ppc64el 5.3.5+dfsg-9 [1258 kB] 116s Get:11 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libpbseq ppc64el 5.3.5+dfsg-9 [3054 B] 116s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el blasr ppc64el 5.3.5+dfsg-7 [269 kB] 116s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el libblas3 ppc64el 3.12.0-4 [222 kB] 116s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 14.2.0-12ubuntu1 [571 kB] 117s Get:15 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhdf5-hl-100t64 ppc64el 1.10.10+repack-5ubuntu1 [71.2 kB] 117s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblapack3 ppc64el 3.12.0-4 [2814 kB] 117s Get:17 http://ftpmaster.internal/ubuntu plucky/universe ppc64el liblzf1 ppc64el 3.6-4 [7920 B] 117s Get:18 http://ftpmaster.internal/ubuntu plucky/universe ppc64el pbdagcon ppc64el 0.3+git20180411.c14c422+dfsg-9 [279 kB] 117s Get:19 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pysam ppc64el 0.22.1+ds-2build1 [4445 kB] 118s Get:20 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pbsuite-utils all 15.8.24+dfsg-8 [537 kB] 118s Get:21 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 118s Get:22 http://ftpmaster.internal/ubuntu plucky/universe ppc64el pbjelly all 15.8.24+dfsg-8 [1055 kB] 118s Get:23 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pbbanana all 15.8.24+dfsg-8 [16.7 kB] 118s Get:24 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-12 [4917 kB] 118s Get:25 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-h5py-serial ppc64el 3.11.0-8ubuntu3 [1598 kB] 118s Get:26 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-h5py all 3.11.0-8ubuntu3 [7982 B] 118s Get:27 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-sortedcontainers all 2.4.0-2 [27.6 kB] 118s Get:28 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-intervaltree all 3.0.2-1.1 [22.4 kB] 118s Get:29 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-intervaltree-bio all 1.0.1-4 [8260 B] 118s Get:30 http://ftpmaster.internal/ubuntu plucky/universe ppc64el samtools ppc64el 1.20-3 [676 kB] 118s Get:31 http://ftpmaster.internal/ubuntu plucky/universe ppc64el pbhoney all 15.8.24+dfsg-8 [1152 kB] 118s Get:32 http://ftpmaster.internal/ubuntu plucky/universe ppc64el pbsuite all 15.8.24+dfsg-8 [1894 B] 119s Fetched 35.1 MB in 3s (10.3 MB/s) 119s Selecting previously unselected package libaec0:ppc64el. 119s (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 ... 74025 files and directories currently installed.) 119s Preparing to unpack .../00-libaec0_1.1.3-1_ppc64el.deb ... 119s Unpacking libaec0:ppc64el (1.1.3-1) ... 119s Selecting previously unselected package libsz2:ppc64el. 119s Preparing to unpack .../01-libsz2_1.1.3-1_ppc64el.deb ... 119s Unpacking libsz2:ppc64el (1.1.3-1) ... 119s Selecting previously unselected package libhdf5-103-1t64:ppc64el. 119s Preparing to unpack .../02-libhdf5-103-1t64_1.10.10+repack-5ubuntu1_ppc64el.deb ... 119s Unpacking libhdf5-103-1t64:ppc64el (1.10.10+repack-5ubuntu1) ... 119s Selecting previously unselected package libhdf5-cpp-103-1t64:ppc64el. 119s Preparing to unpack .../03-libhdf5-cpp-103-1t64_1.10.10+repack-5ubuntu1_ppc64el.deb ... 119s Unpacking libhdf5-cpp-103-1t64:ppc64el (1.10.10+repack-5ubuntu1) ... 119s Selecting previously unselected package libdeflate0:ppc64el. 119s Preparing to unpack .../04-libdeflate0_1.22-1_ppc64el.deb ... 119s Unpacking libdeflate0:ppc64el (1.22-1) ... 119s Selecting previously unselected package libhtscodecs2:ppc64el. 119s Preparing to unpack .../05-libhtscodecs2_1.6.1-1_ppc64el.deb ... 119s Unpacking libhtscodecs2:ppc64el (1.6.1-1) ... 119s Selecting previously unselected package libhts3t64:ppc64el. 119s Preparing to unpack .../06-libhts3t64_1.20+ds-2_ppc64el.deb ... 119s Unpacking libhts3t64:ppc64el (1.20+ds-2) ... 119s Selecting previously unselected package libpbcopper2.3.0:ppc64el. 119s Preparing to unpack .../07-libpbcopper2.3.0_2.3.0+dfsg-2_ppc64el.deb ... 119s Unpacking libpbcopper2.3.0:ppc64el (2.3.0+dfsg-2) ... 119s Selecting previously unselected package libpbbam2.4.0:ppc64el. 119s Preparing to unpack .../08-libpbbam2.4.0_2.4.0+dfsg-1build2_ppc64el.deb ... 119s Unpacking libpbbam2.4.0:ppc64el (2.4.0+dfsg-1build2) ... 119s Selecting previously unselected package libblasr5.3.5:ppc64el. 119s Preparing to unpack .../09-libblasr5.3.5_5.3.5+dfsg-9_ppc64el.deb ... 119s Unpacking libblasr5.3.5:ppc64el (5.3.5+dfsg-9) ... 119s Selecting previously unselected package libpbseq:ppc64el. 119s Preparing to unpack .../10-libpbseq_5.3.5+dfsg-9_ppc64el.deb ... 119s Unpacking libpbseq:ppc64el (5.3.5+dfsg-9) ... 119s Selecting previously unselected package blasr. 119s Preparing to unpack .../11-blasr_5.3.5+dfsg-7_ppc64el.deb ... 119s Unpacking blasr (5.3.5+dfsg-7) ... 119s Selecting previously unselected package libblas3:ppc64el. 119s Preparing to unpack .../12-libblas3_3.12.0-4_ppc64el.deb ... 119s Unpacking libblas3:ppc64el (3.12.0-4) ... 119s Selecting previously unselected package libgfortran5:ppc64el. 119s Preparing to unpack .../13-libgfortran5_14.2.0-12ubuntu1_ppc64el.deb ... 119s Unpacking libgfortran5:ppc64el (14.2.0-12ubuntu1) ... 119s Selecting previously unselected package libhdf5-hl-100t64:ppc64el. 119s Preparing to unpack .../14-libhdf5-hl-100t64_1.10.10+repack-5ubuntu1_ppc64el.deb ... 119s Unpacking libhdf5-hl-100t64:ppc64el (1.10.10+repack-5ubuntu1) ... 119s Selecting previously unselected package liblapack3:ppc64el. 119s Preparing to unpack .../15-liblapack3_3.12.0-4_ppc64el.deb ... 119s Unpacking liblapack3:ppc64el (3.12.0-4) ... 119s Selecting previously unselected package liblzf1:ppc64el. 119s Preparing to unpack .../16-liblzf1_3.6-4_ppc64el.deb ... 119s Unpacking liblzf1:ppc64el (3.6-4) ... 119s Selecting previously unselected package pbdagcon. 119s Preparing to unpack .../17-pbdagcon_0.3+git20180411.c14c422+dfsg-9_ppc64el.deb ... 119s Unpacking pbdagcon (0.3+git20180411.c14c422+dfsg-9) ... 119s Selecting previously unselected package python3-pysam. 119s Preparing to unpack .../18-python3-pysam_0.22.1+ds-2build1_ppc64el.deb ... 119s Unpacking python3-pysam (0.22.1+ds-2build1) ... 120s Selecting previously unselected package python3-pbsuite-utils. 120s Preparing to unpack .../19-python3-pbsuite-utils_15.8.24+dfsg-8_all.deb ... 120s Unpacking python3-pbsuite-utils (15.8.24+dfsg-8) ... 120s Selecting previously unselected package python3-networkx. 120s Preparing to unpack .../20-python3-networkx_3.2.1-4ubuntu1_all.deb ... 120s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 120s Selecting previously unselected package pbjelly. 120s Preparing to unpack .../21-pbjelly_15.8.24+dfsg-8_all.deb ... 120s Unpacking pbjelly (15.8.24+dfsg-8) ... 120s Selecting previously unselected package python3-pbbanana. 120s Preparing to unpack .../22-python3-pbbanana_15.8.24+dfsg-8_all.deb ... 120s Unpacking python3-pbbanana (15.8.24+dfsg-8) ... 120s Selecting previously unselected package python3-numpy. 120s Preparing to unpack .../23-python3-numpy_1%3a1.26.4+ds-12_ppc64el.deb ... 120s Unpacking python3-numpy (1:1.26.4+ds-12) ... 121s Selecting previously unselected package python3-h5py-serial. 121s Preparing to unpack .../24-python3-h5py-serial_3.11.0-8ubuntu3_ppc64el.deb ... 121s Unpacking python3-h5py-serial (3.11.0-8ubuntu3) ... 121s Selecting previously unselected package python3-h5py. 121s Preparing to unpack .../25-python3-h5py_3.11.0-8ubuntu3_all.deb ... 121s Unpacking python3-h5py (3.11.0-8ubuntu3) ... 121s Selecting previously unselected package python3-sortedcontainers. 121s Preparing to unpack .../26-python3-sortedcontainers_2.4.0-2_all.deb ... 121s Unpacking python3-sortedcontainers (2.4.0-2) ... 121s Selecting previously unselected package python3-intervaltree. 121s Preparing to unpack .../27-python3-intervaltree_3.0.2-1.1_all.deb ... 121s Unpacking python3-intervaltree (3.0.2-1.1) ... 121s Selecting previously unselected package python3-intervaltree-bio. 121s Preparing to unpack .../28-python3-intervaltree-bio_1.0.1-4_all.deb ... 121s Unpacking python3-intervaltree-bio (1.0.1-4) ... 121s Selecting previously unselected package samtools. 121s Preparing to unpack .../29-samtools_1.20-3_ppc64el.deb ... 121s Unpacking samtools (1.20-3) ... 121s Selecting previously unselected package pbhoney. 121s Preparing to unpack .../30-pbhoney_15.8.24+dfsg-8_all.deb ... 121s Unpacking pbhoney (15.8.24+dfsg-8) ... 121s Selecting previously unselected package pbsuite. 121s Preparing to unpack .../31-pbsuite_15.8.24+dfsg-8_all.deb ... 121s Unpacking pbsuite (15.8.24+dfsg-8) ... 121s Setting up libhtscodecs2:ppc64el (1.6.1-1) ... 121s Setting up libdeflate0:ppc64el (1.22-1) ... 121s Setting up python3-sortedcontainers (2.4.0-2) ... 121s Setting up python3-networkx (3.2.1-4ubuntu1) ... 123s Setting up libaec0:ppc64el (1.1.3-1) ... 123s Setting up libblas3:ppc64el (3.12.0-4) ... 123s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 123s Setting up liblzf1:ppc64el (3.6-4) ... 123s Setting up libgfortran5:ppc64el (14.2.0-12ubuntu1) ... 123s Setting up libhts3t64:ppc64el (1.20+ds-2) ... 123s Setting up libsz2:ppc64el (1.1.3-1) ... 123s Setting up libpbcopper2.3.0:ppc64el (2.3.0+dfsg-2) ... 123s Setting up liblapack3:ppc64el (3.12.0-4) ... 123s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 123s Setting up python3-pysam (0.22.1+ds-2build1) ... 123s Setting up python3-intervaltree (3.0.2-1.1) ... 123s Setting up python3-pbsuite-utils (15.8.24+dfsg-8) ... 123s Setting up libpbbam2.4.0:ppc64el (2.4.0+dfsg-1build2) ... 123s Setting up samtools (1.20-3) ... 123s Setting up python3-numpy (1:1.26.4+ds-12) ... 125s Setting up python3-intervaltree-bio (1.0.1-4) ... 125s Setting up libhdf5-103-1t64:ppc64el (1.10.10+repack-5ubuntu1) ... 125s Setting up libhdf5-hl-100t64:ppc64el (1.10.10+repack-5ubuntu1) ... 126s Setting up libhdf5-cpp-103-1t64:ppc64el (1.10.10+repack-5ubuntu1) ... 126s Setting up python3-h5py-serial (3.11.0-8ubuntu3) ... 126s Setting up libblasr5.3.5:ppc64el (5.3.5+dfsg-9) ... 126s Setting up python3-h5py (3.11.0-8ubuntu3) ... 126s Setting up libpbseq:ppc64el (5.3.5+dfsg-9) ... 126s Setting up blasr (5.3.5+dfsg-7) ... 126s Setting up pbdagcon (0.3+git20180411.c14c422+dfsg-9) ... 126s Setting up pbjelly (15.8.24+dfsg-8) ... 126s Setting up python3-pbbanana (15.8.24+dfsg-8) ... 126s Setting up pbhoney (15.8.24+dfsg-8) ... 126s Setting up pbsuite (15.8.24+dfsg-8) ... 126s Processing triggers for man-db (2.13.0-1) ... 127s Processing triggers for libc-bin (2.40-4ubuntu1) ... 129s autopkgtest [22:46:54]: test run-unit-test: [----------------------- 129s PIEMapping 130s 130s Please Cite: English, Adam C., William J. Salerno, Jeffery G. 130s Reid. "PBHoney: identyfying genomic variants via 130s long-read discordance and interrupted mapping." 130s BMC Bioinformatics 2014, 15:180 (June 10, 2014). 130s doi:10.1186/1471-2105-15-180 130s 130s 2025-01-09 22:46:55,116 [INFO] Running /usr/bin/Honey pie filtered_subreads.fastq lambda_modified.fasta -o mappingFinal.sam 130s 2025-01-09 22:46:55,117 [INFO] Running Blasr 170s 2025-01-09 22:47:35,598 [INFO] [0, b'[INFO] 2025-01-09T22:46:55 [blasr] started.\n[INFO] 2025-01-09T22:47:35 [blasr] ended.\n', None] 170s 2025-01-09 22:47:35,600 [INFO] Mapping Tails 170s 2025-01-09 22:47:35,605 [INFO] Extracting tails 170s 2025-01-09 22:47:35,912 [INFO] Parsed 433 reads 170s 2025-01-09 22:47:35,912 [INFO] Found 278 tails 170s 2025-01-09 22:47:35,912 [INFO] 21 reads had double tails 170s 2025-01-09 22:47:35,913 [INFO] Running Blasr 172s 2025-01-09 22:47:37,936 [ERROR] blasr mapping failed! 172s 2025-01-09 22:47:37,936 [ERROR] RETCODE 134 172s 2025-01-09 22:47:37,936 [ERROR] STDOUT b"[INFO] 2025-01-09T22:47:35 [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" 172s 2025-01-09 22:47:37,937 [ERROR] STDERR None 172s 2025-01-09 22:47:37,937 [ERROR] Exiting 173s Sam To Bam 173s [E::hts_open_format] Failed to open file "mappingFinal.sam" : No such file or directory 173s samtools view: failed to open "mappingFinal.sam" for reading: No such file or directory 173s [W::hts_set_opt] Cannot change block size for this format 173s samtools sort: failed to read header from "-" 173s Calling Tails 173s samtools index: "mappingFinal.bam" is in a format that cannot be usefully indexed 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 2025-01-09 22:47:38,311 [INFO] Running /usr/bin/Honey tails mappingFinal.bam 174s Traceback (most recent call last): 174s File "/usr/bin/Honey", line 51, in 174s parseArgs() 174s File "/usr/bin/Honey", line 48, in parseArgs 174s STAGES[args.stage](args.options) 174s File "/usr/lib/python3/dist-packages/pbsuite/honey/TGraf.py", line 665, in run 174s bam = pysam.Samfile(args.bam,'rb') 174s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 174s File "pysam/libcalignmentfile.pyx", line 751, in pysam.libcalignmentfile.AlignmentFile.__cinit__ 174s File "pysam/libcalignmentfile.pyx", line 956, in pysam.libcalignmentfile.AlignmentFile._open 174s ValueError: file does not contain alignment data 174s Calling Spots 174s 174s Please Cite: English, Adam C., William J. Salerno, Jeffery G. 174s Reid. "PBHoney: identyfying genomic variants via 174s long-read discordance and interrupted mapping." 174s BMC Bioinformatics 2014, 15:180 (June 10, 2014). 174s doi:10.1186/1471-2105-15-180 174s 174s 2025-01-09 22:47:39,525 [INFO] Running /usr/bin/Honey spots --reference lambda_modified.fasta mappingFinal.bam 175s Traceback (most recent call last): 175s File "/usr/bin/Honey", line 51, in 175s parseArgs() 175s File "/usr/bin/Honey", line 48, in parseArgs 175s STAGES[args.stage](args.options) 175s File "/usr/lib/python3/dist-packages/pbsuite/honey/HSpots.py", line 1092, in run 175s bam = pysam.Samfile(args.bam) 175s ^^^^^^^^^^^^^^^^^^^^^^^ 175s File "pysam/libcalignmentfile.pyx", line 751, in pysam.libcalignmentfile.AlignmentFile.__cinit__ 175s File "pysam/libcalignmentfile.pyx", line 956, in pysam.libcalignmentfile.AlignmentFile._open 175s ValueError: file does not contain alignment data 175s autopkgtest [22:47:40]: test run-unit-test: -----------------------] 176s autopkgtest [22:47:41]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 176s run-unit-test FAIL non-zero exit status 1 176s autopkgtest [22:47:41]: @@@@@@@@@@@@@@@@@@@@ summary 176s run-unit-test FAIL non-zero exit status 1 193s nova [W] Using flock in prodstack6-ppc64el 193s Creating nova instance adt-plucky-ppc64el-pbsuite-20250109-224445-juju-7f2275-prod-proposed-migration-environment-15-2c4b72b9-7687-469c-b0f5-faddc70e24b8 from image adt/ubuntu-plucky-ppc64el-server-20250109.img (UUID 64b5f774-d527-428e-8e51-6eba74faf5f9)... 193s nova [W] Timed out waiting for 43878a34-bcaa-4ffd-888b-dc5f6c9a1fb7 to get deleted.