0s autopkgtest [13:50:34]: starting date and time: 2025-01-09 13:50:34+0000 0s autopkgtest [13:50:34]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [13:50:34]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.6nupx2_p/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-35.secgroup --name adt-plucky-arm64-pbsuite-20250109-135034-juju-7f2275-prod-proposed-migration-environment-2-c3cf5c18-415b-42d7-98d4-d369d33e8cd8 --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 [13:52:52]: testbed dpkg architecture: arm64 139s autopkgtest [13:52:53]: testbed apt version: 2.9.18 139s autopkgtest [13:52:53]: @@@@@@@@@@@@@@@@@@@@ test bed setup 139s autopkgtest [13:52:53]: testbed release detected to be: None 140s autopkgtest [13:52:54]: updating testbed package index (apt update) 140s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 140s 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/main Sources [126 kB] 141s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 141s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.6 kB] 141s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [769 kB] 141s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [242 kB] 141s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [57.8 kB] 141s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [976 kB] 141s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [22.4 kB] 141s Fetched 2295 kB in 1s (2084 kB/s) 142s Reading package lists... 143s + lsb_release --codename --short 143s + RELEASE=plucky 143s + cat 143s + [ plucky != trusty ] 143s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 143s Reading package lists... 143s Building dependency tree... 143s Reading state information... 143s Calculating upgrade... 144s The following packages will be upgraded: 144s libgpgme11t64 python3-oauthlib 144s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 144s Need to get 232 kB of archives. 144s After this operation, 0 B of additional disk space will be used. 144s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libgpgme11t64 arm64 1.24.1-2ubuntu1 [142 kB] 144s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-oauthlib all 3.2.2-3 [89.9 kB] 145s Fetched 232 kB in 0s (542 kB/s) 145s (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 ... 80185 files and directories currently installed.) 145s Preparing to unpack .../libgpgme11t64_1.24.1-2ubuntu1_arm64.deb ... 145s Unpacking libgpgme11t64:arm64 (1.24.1-2ubuntu1) over (1.24.0-2ubuntu1) ... 145s Preparing to unpack .../python3-oauthlib_3.2.2-3_all.deb ... 145s Unpacking python3-oauthlib (3.2.2-3) over (3.2.2-2) ... 145s Setting up python3-oauthlib (3.2.2-3) ... 145s Setting up libgpgme11t64:arm64 (1.24.1-2ubuntu1) ... 145s Processing triggers for libc-bin (2.40-4ubuntu1) ... 146s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 146s + /usr/lib/apt/apt-helper analyze-pattern ?true 146s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove ?obsolete 146s Reading package lists... 146s Building dependency tree... 146s Reading state information... 147s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 147s + grep -q trusty /etc/lsb-release 147s + [ ! -d /usr/share/doc/unattended-upgrades ] 147s + [ ! -d /usr/share/doc/lxd ] 147s + [ ! -d /usr/share/doc/lxd-client ] 147s + [ ! -d /usr/share/doc/snapd ] 147s + type iptables 147s + cat 147s + chmod 755 /etc/rc.local 147s + . /etc/rc.local 147s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 147s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 147s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 147s + uname -m 147s + [ aarch64 = ppc64le ] 147s + [ -d /run/systemd/system ] 147s + systemd-detect-virt --quiet --vm 147s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 147s + cat 147s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 147s + echo COMPRESS=lz4 147s autopkgtest [13:53:01]: upgrading testbed (apt dist-upgrade and autopurge) 147s Reading package lists... 147s Building dependency tree... 147s Reading state information... 148s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 148s Starting 2 pkgProblemResolver with broken count: 0 148s Done 148s Entering ResolveByKeep 149s 149s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 149s Reading package lists... 150s Building dependency tree... 150s Reading state information... 150s Starting pkgProblemResolver with broken count: 0 150s Starting 2 pkgProblemResolver with broken count: 0 150s Done 151s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 153s autopkgtest [13:53:07]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 153s autopkgtest [13:53:07]: @@@@@@@@@@@@@@@@@@@@ apt-source pbsuite 157s Get:1 http://ftpmaster.internal/ubuntu plucky/universe pbsuite 15.8.24+dfsg-8 (dsc) [2316 B] 157s Get:2 http://ftpmaster.internal/ubuntu plucky/universe pbsuite 15.8.24+dfsg-8 (tar) [1615 kB] 157s Get:3 http://ftpmaster.internal/ubuntu plucky/universe pbsuite 15.8.24+dfsg-8 (diff) [26.9 kB] 157s gpgv: Signature made Mon Dec 9 19:47:53 2024 UTC 157s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 157s gpgv: issuer "tille@debian.org" 157s gpgv: Can't check signature: No public key 157s dpkg-source: warning: cannot verify inline signature for ./pbsuite_15.8.24+dfsg-8.dsc: no acceptable signature found 157s autopkgtest [13:53:11]: testing package pbsuite version 15.8.24+dfsg-8 158s autopkgtest [13:53:12]: build not needed 159s autopkgtest [13:53:13]: test run-unit-test: preparing testbed 159s Reading package lists... 159s Building dependency tree... 159s Reading state information... 160s Starting pkgProblemResolver with broken count: 0 160s Starting 2 pkgProblemResolver with broken count: 0 160s Done 160s The following NEW packages will be installed: 160s blasr libaec0 libblas3 libblasr5.3.5 libdeflate0 libgfortran5 160s libhdf5-103-1t64 libhdf5-cpp-103-1t64 libhdf5-hl-100t64 libhts3t64 160s libhtscodecs2 liblapack3 liblzf1 libpbbam2.4.0 libpbcopper2.3.0 libpbseq 160s libsz2 pbdagcon pbhoney pbjelly pbsuite python3-h5py python3-h5py-serial 160s python3-intervaltree python3-intervaltree-bio python3-networkx python3-numpy 160s python3-pbbanana python3-pbsuite-utils python3-pysam 160s python3-sortedcontainers samtools 161s 0 upgraded, 32 newly installed, 0 to remove and 0 not upgraded. 161s Need to get 32.2 MB of archives. 161s After this operation, 190 MB of additional disk space will be used. 161s Get:1 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 161s Get:2 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 161s Get:3 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-103-1t64 arm64 1.10.10+repack-5ubuntu1 [1210 kB] 161s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-cpp-103-1t64 arm64 1.10.10+repack-5ubuntu1 [118 kB] 161s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB] 161s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.1-1 [82.5 kB] 161s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts3t64 arm64 1.20+ds-2 [437 kB] 161s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 libpbcopper2.3.0 arm64 2.3.0+dfsg-2 [516 kB] 161s Get:9 http://ftpmaster.internal/ubuntu plucky/universe arm64 libpbbam2.4.0 arm64 2.4.0+dfsg-1build2 [634 kB] 161s Get:10 http://ftpmaster.internal/ubuntu plucky/universe arm64 libblasr5.3.5 arm64 5.3.5+dfsg-9 [1220 kB] 162s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 libpbseq arm64 5.3.5+dfsg-9 [3056 B] 162s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 blasr arm64 5.3.5+dfsg-7 [221 kB] 162s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-4 [152 kB] 162s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-12ubuntu1 [437 kB] 162s Get:15 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-5ubuntu1 [56.9 kB] 162s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-4 [2305 kB] 162s Get:17 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 162s Get:18 http://ftpmaster.internal/ubuntu plucky/universe arm64 pbdagcon arm64 0.3+git20180411.c14c422+dfsg-9 [256 kB] 162s Get:19 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pysam arm64 0.22.1+ds-2build1 [3987 kB] 162s Get:20 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pbsuite-utils all 15.8.24+dfsg-8 [537 kB] 162s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 163s Get:22 http://ftpmaster.internal/ubuntu plucky/universe arm64 pbjelly all 15.8.24+dfsg-8 [1055 kB] 163s Get:23 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pbbanana all 15.8.24+dfsg-8 [16.7 kB] 163s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-12 [4153 kB] 164s Get:25 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py-serial arm64 3.11.0-8ubuntu3 [1452 kB] 164s Get:26 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py all 3.11.0-8ubuntu3 [7982 B] 164s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-sortedcontainers all 2.4.0-2 [27.6 kB] 164s Get:28 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-intervaltree all 3.0.2-1.1 [22.4 kB] 164s Get:29 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-intervaltree-bio all 1.0.1-4 [8260 B] 164s Get:30 http://ftpmaster.internal/ubuntu plucky/universe arm64 samtools arm64 1.20-3 [590 kB] 164s Get:31 http://ftpmaster.internal/ubuntu plucky/universe arm64 pbhoney all 15.8.24+dfsg-8 [1152 kB] 164s Get:32 http://ftpmaster.internal/ubuntu plucky/universe arm64 pbsuite all 15.8.24+dfsg-8 [1894 B] 165s Fetched 32.2 MB in 4s (8930 kB/s) 165s Selecting previously unselected package libaec0:arm64. 165s (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 ... 80185 files and directories currently installed.) 165s Preparing to unpack .../00-libaec0_1.1.3-1_arm64.deb ... 165s Unpacking libaec0:arm64 (1.1.3-1) ... 165s Selecting previously unselected package libsz2:arm64. 165s Preparing to unpack .../01-libsz2_1.1.3-1_arm64.deb ... 165s Unpacking libsz2:arm64 (1.1.3-1) ... 165s Selecting previously unselected package libhdf5-103-1t64:arm64. 165s Preparing to unpack .../02-libhdf5-103-1t64_1.10.10+repack-5ubuntu1_arm64.deb ... 165s Unpacking libhdf5-103-1t64:arm64 (1.10.10+repack-5ubuntu1) ... 165s Selecting previously unselected package libhdf5-cpp-103-1t64:arm64. 165s Preparing to unpack .../03-libhdf5-cpp-103-1t64_1.10.10+repack-5ubuntu1_arm64.deb ... 165s Unpacking libhdf5-cpp-103-1t64:arm64 (1.10.10+repack-5ubuntu1) ... 165s Selecting previously unselected package libdeflate0:arm64. 165s Preparing to unpack .../04-libdeflate0_1.22-1_arm64.deb ... 165s Unpacking libdeflate0:arm64 (1.22-1) ... 165s Selecting previously unselected package libhtscodecs2:arm64. 165s Preparing to unpack .../05-libhtscodecs2_1.6.1-1_arm64.deb ... 165s Unpacking libhtscodecs2:arm64 (1.6.1-1) ... 165s Selecting previously unselected package libhts3t64:arm64. 165s Preparing to unpack .../06-libhts3t64_1.20+ds-2_arm64.deb ... 165s Unpacking libhts3t64:arm64 (1.20+ds-2) ... 165s Selecting previously unselected package libpbcopper2.3.0:arm64. 165s Preparing to unpack .../07-libpbcopper2.3.0_2.3.0+dfsg-2_arm64.deb ... 165s Unpacking libpbcopper2.3.0:arm64 (2.3.0+dfsg-2) ... 165s Selecting previously unselected package libpbbam2.4.0:arm64. 165s Preparing to unpack .../08-libpbbam2.4.0_2.4.0+dfsg-1build2_arm64.deb ... 165s Unpacking libpbbam2.4.0:arm64 (2.4.0+dfsg-1build2) ... 165s Selecting previously unselected package libblasr5.3.5:arm64. 165s Preparing to unpack .../09-libblasr5.3.5_5.3.5+dfsg-9_arm64.deb ... 165s Unpacking libblasr5.3.5:arm64 (5.3.5+dfsg-9) ... 165s Selecting previously unselected package libpbseq:arm64. 165s Preparing to unpack .../10-libpbseq_5.3.5+dfsg-9_arm64.deb ... 165s Unpacking libpbseq:arm64 (5.3.5+dfsg-9) ... 165s Selecting previously unselected package blasr. 165s Preparing to unpack .../11-blasr_5.3.5+dfsg-7_arm64.deb ... 165s Unpacking blasr (5.3.5+dfsg-7) ... 165s Selecting previously unselected package libblas3:arm64. 165s Preparing to unpack .../12-libblas3_3.12.0-4_arm64.deb ... 165s Unpacking libblas3:arm64 (3.12.0-4) ... 165s Selecting previously unselected package libgfortran5:arm64. 165s Preparing to unpack .../13-libgfortran5_14.2.0-12ubuntu1_arm64.deb ... 165s Unpacking libgfortran5:arm64 (14.2.0-12ubuntu1) ... 165s Selecting previously unselected package libhdf5-hl-100t64:arm64. 165s Preparing to unpack .../14-libhdf5-hl-100t64_1.10.10+repack-5ubuntu1_arm64.deb ... 165s Unpacking libhdf5-hl-100t64:arm64 (1.10.10+repack-5ubuntu1) ... 165s Selecting previously unselected package liblapack3:arm64. 165s Preparing to unpack .../15-liblapack3_3.12.0-4_arm64.deb ... 165s Unpacking liblapack3:arm64 (3.12.0-4) ... 165s Selecting previously unselected package liblzf1:arm64. 165s Preparing to unpack .../16-liblzf1_3.6-4_arm64.deb ... 165s Unpacking liblzf1:arm64 (3.6-4) ... 165s Selecting previously unselected package pbdagcon. 165s Preparing to unpack .../17-pbdagcon_0.3+git20180411.c14c422+dfsg-9_arm64.deb ... 165s Unpacking pbdagcon (0.3+git20180411.c14c422+dfsg-9) ... 165s Selecting previously unselected package python3-pysam. 165s Preparing to unpack .../18-python3-pysam_0.22.1+ds-2build1_arm64.deb ... 165s Unpacking python3-pysam (0.22.1+ds-2build1) ... 166s Selecting previously unselected package python3-pbsuite-utils. 166s Preparing to unpack .../19-python3-pbsuite-utils_15.8.24+dfsg-8_all.deb ... 166s Unpacking python3-pbsuite-utils (15.8.24+dfsg-8) ... 166s Selecting previously unselected package python3-networkx. 166s Preparing to unpack .../20-python3-networkx_3.2.1-4ubuntu1_all.deb ... 166s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 166s Selecting previously unselected package pbjelly. 166s Preparing to unpack .../21-pbjelly_15.8.24+dfsg-8_all.deb ... 166s Unpacking pbjelly (15.8.24+dfsg-8) ... 166s Selecting previously unselected package python3-pbbanana. 166s Preparing to unpack .../22-python3-pbbanana_15.8.24+dfsg-8_all.deb ... 166s Unpacking python3-pbbanana (15.8.24+dfsg-8) ... 166s Selecting previously unselected package python3-numpy. 166s Preparing to unpack .../23-python3-numpy_1%3a1.26.4+ds-12_arm64.deb ... 166s Unpacking python3-numpy (1:1.26.4+ds-12) ... 167s Selecting previously unselected package python3-h5py-serial. 167s Preparing to unpack .../24-python3-h5py-serial_3.11.0-8ubuntu3_arm64.deb ... 167s Unpacking python3-h5py-serial (3.11.0-8ubuntu3) ... 167s Selecting previously unselected package python3-h5py. 167s Preparing to unpack .../25-python3-h5py_3.11.0-8ubuntu3_all.deb ... 167s Unpacking python3-h5py (3.11.0-8ubuntu3) ... 167s Selecting previously unselected package python3-sortedcontainers. 167s Preparing to unpack .../26-python3-sortedcontainers_2.4.0-2_all.deb ... 167s Unpacking python3-sortedcontainers (2.4.0-2) ... 167s Selecting previously unselected package python3-intervaltree. 167s Preparing to unpack .../27-python3-intervaltree_3.0.2-1.1_all.deb ... 167s Unpacking python3-intervaltree (3.0.2-1.1) ... 167s Selecting previously unselected package python3-intervaltree-bio. 167s Preparing to unpack .../28-python3-intervaltree-bio_1.0.1-4_all.deb ... 167s Unpacking python3-intervaltree-bio (1.0.1-4) ... 167s Selecting previously unselected package samtools. 167s Preparing to unpack .../29-samtools_1.20-3_arm64.deb ... 167s Unpacking samtools (1.20-3) ... 167s Selecting previously unselected package pbhoney. 167s Preparing to unpack .../30-pbhoney_15.8.24+dfsg-8_all.deb ... 167s Unpacking pbhoney (15.8.24+dfsg-8) ... 167s Selecting previously unselected package pbsuite. 167s Preparing to unpack .../31-pbsuite_15.8.24+dfsg-8_all.deb ... 167s Unpacking pbsuite (15.8.24+dfsg-8) ... 167s Setting up libhtscodecs2:arm64 (1.6.1-1) ... 167s Setting up libdeflate0:arm64 (1.22-1) ... 167s Setting up python3-sortedcontainers (2.4.0-2) ... 167s Setting up python3-networkx (3.2.1-4ubuntu1) ... 168s Setting up libaec0:arm64 (1.1.3-1) ... 168s Setting up libblas3:arm64 (3.12.0-4) ... 168s 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 168s Setting up liblzf1:arm64 (3.6-4) ... 168s Setting up libgfortran5:arm64 (14.2.0-12ubuntu1) ... 169s Setting up libhts3t64:arm64 (1.20+ds-2) ... 169s Setting up libsz2:arm64 (1.1.3-1) ... 169s Setting up libpbcopper2.3.0:arm64 (2.3.0+dfsg-2) ... 169s Setting up liblapack3:arm64 (3.12.0-4) ... 169s 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 169s Setting up python3-pysam (0.22.1+ds-2build1) ... 169s Setting up python3-intervaltree (3.0.2-1.1) ... 169s Setting up python3-pbsuite-utils (15.8.24+dfsg-8) ... 169s Setting up libpbbam2.4.0:arm64 (2.4.0+dfsg-1build2) ... 169s Setting up samtools (1.20-3) ... 169s Setting up python3-numpy (1:1.26.4+ds-12) ... 171s Setting up python3-intervaltree-bio (1.0.1-4) ... 171s Setting up libhdf5-103-1t64:arm64 (1.10.10+repack-5ubuntu1) ... 171s Setting up libhdf5-hl-100t64:arm64 (1.10.10+repack-5ubuntu1) ... 171s Setting up libhdf5-cpp-103-1t64:arm64 (1.10.10+repack-5ubuntu1) ... 171s Setting up python3-h5py-serial (3.11.0-8ubuntu3) ... 171s Setting up libblasr5.3.5:arm64 (5.3.5+dfsg-9) ... 171s Setting up python3-h5py (3.11.0-8ubuntu3) ... 171s Setting up libpbseq:arm64 (5.3.5+dfsg-9) ... 171s Setting up blasr (5.3.5+dfsg-7) ... 171s Setting up pbdagcon (0.3+git20180411.c14c422+dfsg-9) ... 171s Setting up pbjelly (15.8.24+dfsg-8) ... 172s Setting up python3-pbbanana (15.8.24+dfsg-8) ... 172s Setting up pbhoney (15.8.24+dfsg-8) ... 172s Setting up pbsuite (15.8.24+dfsg-8) ... 172s Processing triggers for man-db (2.13.0-1) ... 173s Processing triggers for libc-bin (2.40-4ubuntu1) ... 175s autopkgtest [13:53:29]: test run-unit-test: [----------------------- 175s PIEMapping 175s 175s Please Cite: English, Adam C., William J. Salerno, Jeffery G. 175s Reid. "PBHoney: identyfying genomic variants via 175s long-read discordance and interrupted mapping." 175s BMC Bioinformatics 2014, 15:180 (June 10, 2014). 175s doi:10.1186/1471-2105-15-180 175s 175s 2025-01-09 13:53:29,705 [INFO] Running /usr/bin/Honey pie filtered_subreads.fastq lambda_modified.fasta -o mappingFinal.sam 175s 2025-01-09 13:53:29,705 [INFO] Running Blasr 208s 2025-01-09 13:54:02,222 [INFO] [0, b'[INFO] 2025-01-09T13:53:29 [blasr] started.\n[INFO] 2025-01-09T13:54:02 [blasr] ended.\n', None] 208s 2025-01-09 13:54:02,223 [INFO] Mapping Tails 208s 2025-01-09 13:54:02,223 [INFO] Extracting tails 208s 2025-01-09 13:54:02,433 [INFO] Parsed 433 reads 208s 2025-01-09 13:54:02,433 [INFO] Found 278 tails 208s 2025-01-09 13:54:02,433 [INFO] 21 reads had double tails 208s 2025-01-09 13:54:02,433 [INFO] Running Blasr 210s 2025-01-09 13:54:04,318 [ERROR] blasr mapping failed! 210s 2025-01-09 13:54:04,319 [ERROR] RETCODE 134 210s 2025-01-09 13:54:04,319 [ERROR] STDOUT b"[INFO] 2025-01-09T13:54:02 [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" 210s 2025-01-09 13:54:04,319 [ERROR] STDERR None 210s 2025-01-09 13:54:04,319 [ERROR] Exiting 210s Sam To Bam 210s [E::hts_open_format] Failed to open file "mappingFinal.sam" : No such file or directory 210s samtools view: failed to open "mappingFinal.sam" for reading: No such file or directory 210s [W::hts_set_opt] Cannot change block size for this format 210s samtools sort: failed to read header from "-" 210s samtools index: "mappingFinal.bam" is in a format that cannot be usefully indexed 210s Calling Tails 210s 210s Please Cite: English, Adam C., William J. Salerno, Jeffery G. 210s Reid. "PBHoney: identyfying genomic variants via 210s long-read discordance and interrupted mapping." 210s BMC Bioinformatics 2014, 15:180 (June 10, 2014). 210s doi:10.1186/1471-2105-15-180 210s 210s 2025-01-09 13:54:04,761 [INFO] Running /usr/bin/Honey tails mappingFinal.bam 212s Traceback (most recent call last): 212s File "/usr/bin/Honey", line 51, in 212s parseArgs() 212s File "/usr/bin/Honey", line 48, in parseArgs 212s STAGES[args.stage](args.options) 212s File "/usr/lib/python3/dist-packages/pbsuite/honey/TGraf.py", line 665, in run 212s bam = pysam.Samfile(args.bam,'rb') 212s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 212s File "pysam/libcalignmentfile.pyx", line 751, in pysam.libcalignmentfile.AlignmentFile.__cinit__ 212s File "pysam/libcalignmentfile.pyx", line 956, in pysam.libcalignmentfile.AlignmentFile._open 212s ValueError: file does not contain alignment data 212s Calling Spots 212s 212s Please Cite: English, Adam C., William J. Salerno, Jeffery G. 212s Reid. "PBHoney: identyfying genomic variants via 212s long-read discordance and interrupted mapping." 212s BMC Bioinformatics 2014, 15:180 (June 10, 2014). 212s doi:10.1186/1471-2105-15-180 212s 212s 2025-01-09 13:54:06,509 [INFO] Running /usr/bin/Honey spots --reference lambda_modified.fasta mappingFinal.bam 213s Traceback (most recent call last): 213s File "/usr/bin/Honey", line 51, in 213s parseArgs() 213s File "/usr/bin/Honey", line 48, in parseArgs 213s STAGES[args.stage](args.options) 213s File "/usr/lib/python3/dist-packages/pbsuite/honey/HSpots.py", line 1092, in run 213s bam = pysam.Samfile(args.bam) 213s ^^^^^^^^^^^^^^^^^^^^^^^ 213s File "pysam/libcalignmentfile.pyx", line 751, in pysam.libcalignmentfile.AlignmentFile.__cinit__ 213s File "pysam/libcalignmentfile.pyx", line 956, in pysam.libcalignmentfile.AlignmentFile._open 213s ValueError: file does not contain alignment data 214s autopkgtest [13:54:08]: test run-unit-test: -----------------------] 214s autopkgtest [13:54:08]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 214s run-unit-test FAIL non-zero exit status 1 215s autopkgtest [13:54:09]: @@@@@@@@@@@@@@@@@@@@ summary 215s run-unit-test FAIL non-zero exit status 1 233s nova [W] Using flock in prodstack6-arm64 233s Creating nova instance adt-plucky-arm64-pbsuite-20250109-135034-juju-7f2275-prod-proposed-migration-environment-2-c3cf5c18-415b-42d7-98d4-d369d33e8cd8 from image adt/ubuntu-plucky-arm64-server-20250108.img (UUID 053f5e9f-d810-4aac-9e57-cf8ac63865d2)... 233s nova [W] Timed out waiting for d22ad111-4169-4683-a17a-acec808c8b4a to get deleted.