0s autopkgtest [21:56:14]: starting date and time: 2025-01-09 21:56:14+0000 0s autopkgtest [21:56:14]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [21:56:14]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.7i200bln/out --timeout-copy=6000 -a i386 --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-2@bos03-22.secgroup --name adt-plucky-i386-pbsuite-20250109-215613-juju-7f2275-prod-proposed-migration-environment-2-adb572f8-7ad7-4298-9911-69dc3e84f1fa --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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/ 63s autopkgtest [21:57:17]: testbed dpkg architecture: amd64 63s autopkgtest [21:57:17]: testbed apt version: 2.9.18 64s autopkgtest [21:57:18]: @@@@@@@@@@@@@@@@@@@@ test bed setup 64s autopkgtest [21:57:18]: testbed release detected to be: None 65s autopkgtest [21:57:19]: updating testbed package index (apt update) 65s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 65s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 65s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 65s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 65s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 65s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [128 kB] 65s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.0 kB] 65s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [790 kB] 66s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [159 kB] 66s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [292 kB] 66s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [40.1 kB] 66s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2408 B] 66s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [1049 kB] 66s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [418 kB] 66s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [13.7 kB] 66s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [3100 B] 66s Fetched 2994 kB in 1s (3080 kB/s) 67s Reading package lists... 67s + lsb_release --codename --short 67s + RELEASE=plucky 67s + cat 67s + [ plucky != trusty ] 67s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 67s Reading package lists... 67s Building dependency tree... 67s Reading state information... 68s Calculating upgrade... 68s The following packages will be upgraded: 68s firmware-sof-signed 68s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 68s Need to get 7093 kB of archives. 68s After this operation, 0 B of additional disk space will be used. 68s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 firmware-sof-signed all 2024.06-1ubuntu4 [7093 kB] 69s Fetched 7093 kB in 1s (9116 kB/s) 69s (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 ... 75804 files and directories currently installed.) 69s Preparing to unpack .../firmware-sof-signed_2024.06-1ubuntu4_all.deb ... 69s Unpacking firmware-sof-signed (2024.06-1ubuntu4) over (2024.06-1ubuntu3) ... 69s Setting up firmware-sof-signed (2024.06-1ubuntu4) ... 69s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 69s + /usr/lib/apt/apt-helper analyze-pattern ?true 69s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove ?obsolete 69s Reading package lists... 70s Building dependency tree... 70s Reading state information... 70s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 70s + grep -q trusty /etc/lsb-release 70s + [ ! -d /usr/share/doc/unattended-upgrades ] 70s + [ ! -d /usr/share/doc/lxd ] 70s + [ ! -d /usr/share/doc/lxd-client ] 70s + [ ! -d /usr/share/doc/snapd ] 70s + type iptables 70s + cat 70s + chmod 755 /etc/rc.local 70s + . /etc/rc.local 70s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 70s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 70s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 70s + uname -m 70s + [ x86_64 = ppc64le ] 70s + [ -d /run/systemd/system ] 70s + systemd-detect-virt --quiet --vm 70s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 70s + cat 70s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 70s + echo COMPRESS=lz4 70s autopkgtest [21:57:24]: upgrading testbed (apt dist-upgrade and autopurge) 70s Reading package lists... 70s Building dependency tree... 70s Reading state information... 71s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 71s Starting 2 pkgProblemResolver with broken count: 0 71s Done 71s Entering ResolveByKeep 71s 71s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 72s Reading package lists... 72s Building dependency tree... 72s Reading state information... 72s Starting pkgProblemResolver with broken count: 0 72s Starting 2 pkgProblemResolver with broken count: 0 72s Done 72s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 73s autopkgtest [21:57:27]: rebooting testbed after setup commands that affected boot 98s autopkgtest [21:57:52]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 100s autopkgtest [21:57:54]: @@@@@@@@@@@@@@@@@@@@ apt-source pbsuite 104s Get:1 http://ftpmaster.internal/ubuntu plucky/universe pbsuite 15.8.24+dfsg-8 (dsc) [2316 B] 104s Get:2 http://ftpmaster.internal/ubuntu plucky/universe pbsuite 15.8.24+dfsg-8 (tar) [1615 kB] 104s Get:3 http://ftpmaster.internal/ubuntu plucky/universe pbsuite 15.8.24+dfsg-8 (diff) [26.9 kB] 104s gpgv: Signature made Mon Dec 9 19:47:53 2024 UTC 104s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 104s gpgv: issuer "tille@debian.org" 104s gpgv: Can't check signature: No public key 104s dpkg-source: warning: cannot verify inline signature for ./pbsuite_15.8.24+dfsg-8.dsc: no acceptable signature found 105s autopkgtest [21:57:59]: testing package pbsuite version 15.8.24+dfsg-8 105s autopkgtest [21:57:59]: build not needed 106s autopkgtest [21:58:00]: test run-unit-test: preparing testbed 106s Reading package lists... 106s Building dependency tree... 106s Reading state information... 107s Starting pkgProblemResolver with broken count: 0 107s Starting 2 pkgProblemResolver with broken count: 0 107s Done 107s The following NEW packages will be installed: 107s blasr libaec0 libblas3 libblasr5.3.5 libdeflate0 libgfortran5 107s libhdf5-103-1t64 libhdf5-cpp-103-1t64 libhdf5-hl-100t64 libhts3t64 107s libhtscodecs2 liblapack3 liblzf1 libpbbam2.4.0 libpbcopper2.3.0 libpbseq 107s libsz2 pbdagcon pbhoney pbjelly pbsuite python3-h5py python3-h5py-serial 107s python3-intervaltree python3-intervaltree-bio python3-networkx python3-numpy 107s python3-pbbanana python3-pbsuite-utils python3-pysam 107s python3-sortedcontainers samtools 107s 0 upgraded, 32 newly installed, 0 to remove and 0 not upgraded. 107s Need to get 36.1 MB of archives. 107s After this operation, 208 MB of additional disk space will be used. 107s Get:1 http://ftpmaster.internal/ubuntu plucky/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB] 108s Get:2 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsz2 amd64 1.1.3-1 [5456 B] 108s Get:3 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-103-1t64 amd64 1.10.10+repack-5ubuntu1 [1367 kB] 108s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-cpp-103-1t64 amd64 1.10.10+repack-5ubuntu1 [131 kB] 108s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 108s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-1 [132 kB] 108s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.20+ds-2 [501 kB] 108s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpbcopper2.3.0 amd64 2.3.0+dfsg-2 [575 kB] 108s Get:9 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpbbam2.4.0 amd64 2.4.0+dfsg-1build2 [679 kB] 108s Get:10 http://ftpmaster.internal/ubuntu plucky/universe amd64 libblasr5.3.5 amd64 5.3.5+dfsg-9 [1248 kB] 108s Get:11 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpbseq amd64 5.3.5+dfsg-9 [3056 B] 108s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 blasr amd64 5.3.5+dfsg-7 [269 kB] 108s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-4 [332 kB] 108s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-12ubuntu1 [909 kB] 108s Get:15 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-5ubuntu1 [59.5 kB] 108s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-4 [3177 kB] 109s Get:17 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblzf1 amd64 3.6-4 [7624 B] 109s Get:18 http://ftpmaster.internal/ubuntu plucky/universe amd64 pbdagcon amd64 0.3+git20180411.c14c422+dfsg-9 [268 kB] 109s Get:19 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pysam amd64 0.22.1+ds-2build1 [4446 kB] 109s Get:20 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pbsuite-utils all 15.8.24+dfsg-8 [537 kB] 109s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 110s Get:22 http://ftpmaster.internal/ubuntu plucky/universe amd64 pbjelly all 15.8.24+dfsg-8 [1055 kB] 110s Get:23 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pbbanana all 15.8.24+dfsg-8 [16.7 kB] 110s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-12 [5319 kB] 110s Get:25 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py-serial amd64 3.11.0-8ubuntu3 [1689 kB] 110s Get:26 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py all 3.11.0-8ubuntu3 [7982 B] 110s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-sortedcontainers all 2.4.0-2 [27.6 kB] 110s Get:28 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-intervaltree all 3.0.2-1.1 [22.4 kB] 110s Get:29 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-intervaltree-bio all 1.0.1-4 [8260 B] 110s Get:30 http://ftpmaster.internal/ubuntu plucky/universe amd64 samtools amd64 1.20-3 [599 kB] 110s Get:31 http://ftpmaster.internal/ubuntu plucky/universe amd64 pbhoney all 15.8.24+dfsg-8 [1152 kB] 110s Get:32 http://ftpmaster.internal/ubuntu plucky/universe amd64 pbsuite all 15.8.24+dfsg-8 [1894 B] 110s Fetched 36.1 MB in 3s (13.2 MB/s) 110s Selecting previously unselected package libaec0:amd64. 111s (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 ... 75804 files and directories currently installed.) 111s Preparing to unpack .../00-libaec0_1.1.3-1_amd64.deb ... 111s Unpacking libaec0:amd64 (1.1.3-1) ... 111s Selecting previously unselected package libsz2:amd64. 111s Preparing to unpack .../01-libsz2_1.1.3-1_amd64.deb ... 111s Unpacking libsz2:amd64 (1.1.3-1) ... 111s Selecting previously unselected package libhdf5-103-1t64:amd64. 111s Preparing to unpack .../02-libhdf5-103-1t64_1.10.10+repack-5ubuntu1_amd64.deb ... 111s Unpacking libhdf5-103-1t64:amd64 (1.10.10+repack-5ubuntu1) ... 111s Selecting previously unselected package libhdf5-cpp-103-1t64:amd64. 111s Preparing to unpack .../03-libhdf5-cpp-103-1t64_1.10.10+repack-5ubuntu1_amd64.deb ... 111s Unpacking libhdf5-cpp-103-1t64:amd64 (1.10.10+repack-5ubuntu1) ... 111s Selecting previously unselected package libdeflate0:amd64. 111s Preparing to unpack .../04-libdeflate0_1.22-1_amd64.deb ... 111s Unpacking libdeflate0:amd64 (1.22-1) ... 111s Selecting previously unselected package libhtscodecs2:amd64. 111s Preparing to unpack .../05-libhtscodecs2_1.6.1-1_amd64.deb ... 111s Unpacking libhtscodecs2:amd64 (1.6.1-1) ... 111s Selecting previously unselected package libhts3t64:amd64. 111s Preparing to unpack .../06-libhts3t64_1.20+ds-2_amd64.deb ... 111s Unpacking libhts3t64:amd64 (1.20+ds-2) ... 111s Selecting previously unselected package libpbcopper2.3.0:amd64. 111s Preparing to unpack .../07-libpbcopper2.3.0_2.3.0+dfsg-2_amd64.deb ... 111s Unpacking libpbcopper2.3.0:amd64 (2.3.0+dfsg-2) ... 111s Selecting previously unselected package libpbbam2.4.0:amd64. 111s Preparing to unpack .../08-libpbbam2.4.0_2.4.0+dfsg-1build2_amd64.deb ... 111s Unpacking libpbbam2.4.0:amd64 (2.4.0+dfsg-1build2) ... 111s Selecting previously unselected package libblasr5.3.5:amd64. 111s Preparing to unpack .../09-libblasr5.3.5_5.3.5+dfsg-9_amd64.deb ... 111s Unpacking libblasr5.3.5:amd64 (5.3.5+dfsg-9) ... 111s Selecting previously unselected package libpbseq:amd64. 111s Preparing to unpack .../10-libpbseq_5.3.5+dfsg-9_amd64.deb ... 111s Unpacking libpbseq:amd64 (5.3.5+dfsg-9) ... 111s Selecting previously unselected package blasr. 111s Preparing to unpack .../11-blasr_5.3.5+dfsg-7_amd64.deb ... 111s Unpacking blasr (5.3.5+dfsg-7) ... 111s Selecting previously unselected package libblas3:amd64. 111s Preparing to unpack .../12-libblas3_3.12.0-4_amd64.deb ... 111s Unpacking libblas3:amd64 (3.12.0-4) ... 111s Selecting previously unselected package libgfortran5:amd64. 111s Preparing to unpack .../13-libgfortran5_14.2.0-12ubuntu1_amd64.deb ... 111s Unpacking libgfortran5:amd64 (14.2.0-12ubuntu1) ... 111s Selecting previously unselected package libhdf5-hl-100t64:amd64. 111s Preparing to unpack .../14-libhdf5-hl-100t64_1.10.10+repack-5ubuntu1_amd64.deb ... 111s Unpacking libhdf5-hl-100t64:amd64 (1.10.10+repack-5ubuntu1) ... 111s Selecting previously unselected package liblapack3:amd64. 111s Preparing to unpack .../15-liblapack3_3.12.0-4_amd64.deb ... 111s Unpacking liblapack3:amd64 (3.12.0-4) ... 111s Selecting previously unselected package liblzf1:amd64. 111s Preparing to unpack .../16-liblzf1_3.6-4_amd64.deb ... 111s Unpacking liblzf1:amd64 (3.6-4) ... 111s Selecting previously unselected package pbdagcon. 111s Preparing to unpack .../17-pbdagcon_0.3+git20180411.c14c422+dfsg-9_amd64.deb ... 111s Unpacking pbdagcon (0.3+git20180411.c14c422+dfsg-9) ... 111s Selecting previously unselected package python3-pysam. 111s Preparing to unpack .../18-python3-pysam_0.22.1+ds-2build1_amd64.deb ... 111s Unpacking python3-pysam (0.22.1+ds-2build1) ... 111s Selecting previously unselected package python3-pbsuite-utils. 111s Preparing to unpack .../19-python3-pbsuite-utils_15.8.24+dfsg-8_all.deb ... 111s Unpacking python3-pbsuite-utils (15.8.24+dfsg-8) ... 111s Selecting previously unselected package python3-networkx. 111s Preparing to unpack .../20-python3-networkx_3.2.1-4ubuntu1_all.deb ... 111s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 112s Selecting previously unselected package pbjelly. 112s Preparing to unpack .../21-pbjelly_15.8.24+dfsg-8_all.deb ... 112s Unpacking pbjelly (15.8.24+dfsg-8) ... 112s Selecting previously unselected package python3-pbbanana. 112s Preparing to unpack .../22-python3-pbbanana_15.8.24+dfsg-8_all.deb ... 112s Unpacking python3-pbbanana (15.8.24+dfsg-8) ... 112s Selecting previously unselected package python3-numpy. 112s Preparing to unpack .../23-python3-numpy_1%3a1.26.4+ds-12_amd64.deb ... 112s Unpacking python3-numpy (1:1.26.4+ds-12) ... 112s Selecting previously unselected package python3-h5py-serial. 112s Preparing to unpack .../24-python3-h5py-serial_3.11.0-8ubuntu3_amd64.deb ... 112s Unpacking python3-h5py-serial (3.11.0-8ubuntu3) ... 112s Selecting previously unselected package python3-h5py. 112s Preparing to unpack .../25-python3-h5py_3.11.0-8ubuntu3_all.deb ... 112s Unpacking python3-h5py (3.11.0-8ubuntu3) ... 112s Selecting previously unselected package python3-sortedcontainers. 112s Preparing to unpack .../26-python3-sortedcontainers_2.4.0-2_all.deb ... 112s Unpacking python3-sortedcontainers (2.4.0-2) ... 112s Selecting previously unselected package python3-intervaltree. 112s Preparing to unpack .../27-python3-intervaltree_3.0.2-1.1_all.deb ... 112s Unpacking python3-intervaltree (3.0.2-1.1) ... 112s Selecting previously unselected package python3-intervaltree-bio. 112s Preparing to unpack .../28-python3-intervaltree-bio_1.0.1-4_all.deb ... 112s Unpacking python3-intervaltree-bio (1.0.1-4) ... 112s Selecting previously unselected package samtools. 112s Preparing to unpack .../29-samtools_1.20-3_amd64.deb ... 112s Unpacking samtools (1.20-3) ... 112s Selecting previously unselected package pbhoney. 112s Preparing to unpack .../30-pbhoney_15.8.24+dfsg-8_all.deb ... 112s Unpacking pbhoney (15.8.24+dfsg-8) ... 113s Selecting previously unselected package pbsuite. 113s Preparing to unpack .../31-pbsuite_15.8.24+dfsg-8_all.deb ... 113s Unpacking pbsuite (15.8.24+dfsg-8) ... 113s Setting up libhtscodecs2:amd64 (1.6.1-1) ... 113s Setting up libdeflate0:amd64 (1.22-1) ... 113s Setting up python3-sortedcontainers (2.4.0-2) ... 113s Setting up python3-networkx (3.2.1-4ubuntu1) ... 114s Setting up libaec0:amd64 (1.1.3-1) ... 114s Setting up libblas3:amd64 (3.12.0-4) ... 114s 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 114s Setting up liblzf1:amd64 (3.6-4) ... 114s Setting up libgfortran5:amd64 (14.2.0-12ubuntu1) ... 114s Setting up libhts3t64:amd64 (1.20+ds-2) ... 114s Setting up libsz2:amd64 (1.1.3-1) ... 114s Setting up libpbcopper2.3.0:amd64 (2.3.0+dfsg-2) ... 114s Setting up liblapack3:amd64 (3.12.0-4) ... 114s 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 114s Setting up python3-pysam (0.22.1+ds-2build1) ... 114s Setting up python3-intervaltree (3.0.2-1.1) ... 114s Setting up python3-pbsuite-utils (15.8.24+dfsg-8) ... 114s Setting up libpbbam2.4.0:amd64 (2.4.0+dfsg-1build2) ... 114s Setting up samtools (1.20-3) ... 114s Setting up python3-numpy (1:1.26.4+ds-12) ... 115s Setting up python3-intervaltree-bio (1.0.1-4) ... 115s Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-5ubuntu1) ... 115s Setting up libhdf5-hl-100t64:amd64 (1.10.10+repack-5ubuntu1) ... 115s Setting up libhdf5-cpp-103-1t64:amd64 (1.10.10+repack-5ubuntu1) ... 116s Setting up python3-h5py-serial (3.11.0-8ubuntu3) ... 116s Setting up libblasr5.3.5:amd64 (5.3.5+dfsg-9) ... 116s Setting up python3-h5py (3.11.0-8ubuntu3) ... 116s Setting up libpbseq:amd64 (5.3.5+dfsg-9) ... 116s Setting up blasr (5.3.5+dfsg-7) ... 116s Setting up pbdagcon (0.3+git20180411.c14c422+dfsg-9) ... 116s Setting up pbjelly (15.8.24+dfsg-8) ... 116s Setting up python3-pbbanana (15.8.24+dfsg-8) ... 116s Setting up pbhoney (15.8.24+dfsg-8) ... 116s Setting up pbsuite (15.8.24+dfsg-8) ... 116s Processing triggers for man-db (2.13.0-1) ... 117s Processing triggers for libc-bin (2.40-4ubuntu1) ... 119s autopkgtest [21:58:13]: testbed environment configured for cross-architecture building 119s autopkgtest [21:58:13]: test run-unit-test: [----------------------- 119s PIEMapping 120s 120s Please Cite: English, Adam C., William J. Salerno, Jeffery G. 120s Reid. "PBHoney: identyfying genomic variants via 120s long-read discordance and interrupted mapping." 120s BMC Bioinformatics 2014, 15:180 (June 10, 2014). 120s doi:10.1186/1471-2105-15-180 120s 120s 2025-01-09 21:58:13,982 [INFO] Running /usr/bin/Honey pie filtered_subreads.fastq lambda_modified.fasta -o mappingFinal.sam 120s 2025-01-09 21:58:13,982 [INFO] Running Blasr 150s 2025-01-09 21:58:44,235 [INFO] [0, b'[INFO] 2025-01-09T21:58:13 [blasr] started.\n[INFO] 2025-01-09T21:58:44 [blasr] ended.\n', None] 150s 2025-01-09 21:58:44,235 [INFO] Mapping Tails 150s 2025-01-09 21:58:44,235 [INFO] Extracting tails 150s 2025-01-09 21:58:44,383 [INFO] Parsed 433 reads 150s 2025-01-09 21:58:44,383 [INFO] Found 278 tails 150s 2025-01-09 21:58:44,383 [INFO] 21 reads had double tails 150s 2025-01-09 21:58:44,384 [INFO] Running Blasr 151s 2025-01-09 21:58:45,663 [ERROR] blasr mapping failed! 151s 2025-01-09 21:58:45,663 [ERROR] RETCODE 134 151s 2025-01-09 21:58:45,664 [ERROR] STDOUT b"[INFO] 2025-01-09T21:58:44 [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" 151s 2025-01-09 21:58:45,664 [ERROR] STDERR None 151s 2025-01-09 21:58:45,664 [ERROR] Exiting 151s Sam To Bam 151s [E::hts_open_format] Failed to open file "mappingFinal.sam" : No such file or directory 151s samtools view: failed to open "mappingFinal.sam" for reading: No such file or directory 151s [W::hts_set_opt] Cannot change block size for this format 151s samtools sort: failed to read header from "-" 151s samtools index: "mappingFinal.bam" is in a format that cannot be usefully indexed 151s Calling Tails 151s 151s Please Cite: English, Adam C., William J. Salerno, Jeffery G. 151s Reid. "PBHoney: identyfying genomic variants via 151s long-read discordance and interrupted mapping." 151s BMC Bioinformatics 2014, 15:180 (June 10, 2014). 151s doi:10.1186/1471-2105-15-180 151s 151s 2025-01-09 21:58:45,953 [INFO] Running /usr/bin/Honey tails mappingFinal.bam 152s Traceback (most recent call last): 152s File "/usr/bin/Honey", line 51, in 152s parseArgs() 152s File "/usr/bin/Honey", line 48, in parseArgs 152s STAGES[args.stage](args.options) 152s File "/usr/lib/python3/dist-packages/pbsuite/honey/TGraf.py", line 665, in run 152s bam = pysam.Samfile(args.bam,'rb') 152s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 152s File "pysam/libcalignmentfile.pyx", line 751, in pysam.libcalignmentfile.AlignmentFile.__cinit__ 152s File "pysam/libcalignmentfile.pyx", line 956, in pysam.libcalignmentfile.AlignmentFile._open 152s ValueError: file does not contain alignment data 152s Calling Spots 153s 153s Please Cite: English, Adam C., William J. Salerno, Jeffery G. 153s Reid. "PBHoney: identyfying genomic variants via 153s long-read discordance and interrupted mapping." 153s BMC Bioinformatics 2014, 15:180 (June 10, 2014). 153s doi:10.1186/1471-2105-15-180 153s 153s 2025-01-09 21:58:46,994 [INFO] Running /usr/bin/Honey spots --reference lambda_modified.fasta mappingFinal.bam 153s Traceback (most recent call last): 153s File "/usr/bin/Honey", line 51, in 153s parseArgs() 153s File "/usr/bin/Honey", line 48, in parseArgs 153s STAGES[args.stage](args.options) 153s File "/usr/lib/python3/dist-packages/pbsuite/honey/HSpots.py", line 1092, in run 153s bam = pysam.Samfile(args.bam) 153s ^^^^^^^^^^^^^^^^^^^^^^^ 153s File "pysam/libcalignmentfile.pyx", line 751, in pysam.libcalignmentfile.AlignmentFile.__cinit__ 153s File "pysam/libcalignmentfile.pyx", line 956, in pysam.libcalignmentfile.AlignmentFile._open 153s ValueError: file does not contain alignment data 154s autopkgtest [21:58:48]: test run-unit-test: -----------------------] 154s run-unit-test FAIL non-zero exit status 1 154s autopkgtest [21:58:48]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 154s autopkgtest [21:58:48]: @@@@@@@@@@@@@@@@@@@@ summary 154s run-unit-test FAIL non-zero exit status 1 159s nova [W] Skipping flock for amd64 159s Creating nova instance adt-plucky-i386-pbsuite-20250109-215613-juju-7f2275-prod-proposed-migration-environment-2-adb572f8-7ad7-4298-9911-69dc3e84f1fa from image adt/ubuntu-plucky-amd64-server-20250109.img (UUID 47fb0aba-d15c-4240-a5df-62aa479e218d)... 159s nova [W] Timed out waiting for 9e96d66e-0ace-435e-9135-3185db04fd95 to get deleted.