2s autopkgtest [16:06:53]: starting date and time: 2024-07-26 16:06:53+0000
  2s autopkgtest [16:06:53]: git checkout: fd3bed09 nova: allow more retries for quota issues
  2s autopkgtest [16:06:53]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ja4vgx6c/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:dazzdb --apt-upgrade pbdagcon --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=dazzdb/1.0+git20240115.be65e59-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@lcy02-32.secgroup --name adt-oracular-amd64-pbdagcon-20240726-160649-juju-7f2275-prod-proposed-migration-environment-3-8d3139c9-fa4f-4e39-ac46-d96463cf0c82 --image adt/ubuntu-oracular-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
123s autopkgtest [16:08:54]: testbed dpkg architecture: amd64
123s autopkgtest [16:08:54]: testbed apt version: 2.9.6
123s autopkgtest [16:08:54]: @@@@@@@@@@@@@@@@@@@@ test bed setup
123s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB]
123s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [436 kB]
123s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [50.6 kB]
123s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [4288 B]
123s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8548 B]
123s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 Packages [94.8 kB]
123s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main i386 Packages [53.4 kB]
123s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 c-n-f Metadata [2116 B]
123s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 Packages [34.9 kB]
123s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/restricted i386 Packages [6244 B]
123s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 c-n-f Metadata [368 B]
123s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/universe i386 Packages [296 kB]
123s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 Packages [498 kB]
123s Get:14 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 c-n-f Metadata [9900 B]
123s Get:15 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 Packages [8792 B]
123s Get:16 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse i386 Packages [3052 B]
123s Get:17 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 c-n-f Metadata [276 B]
125s Fetched 1634 kB in 0s (4613 kB/s)
125s Reading package lists...
127s Reading package lists...
127s Building dependency tree...
127s Reading state information...
127s Calculating upgrade...
128s The following packages will be upgraded:
128s   bpfcc-tools bpftrace libbpfcc liblz4-1 mawk python3-bpfcc
128s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
128s Need to get 13.9 MB of archives.
128s After this operation, 37.8 MB of additional disk space will be used.
128s Get:1 http://ftpmaster.internal/ubuntu oracular/main amd64 liblz4-1 amd64 1.9.4-3 [63.1 kB]
128s Get:2 http://ftpmaster.internal/ubuntu oracular/main amd64 mawk amd64 1.3.4.20240622-2 [127 kB]
128s Get:3 http://ftpmaster.internal/ubuntu oracular/main amd64 libbpfcc amd64 0.30.0+ds-1ubuntu2 [644 kB]
128s Get:4 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-bpfcc all 0.30.0+ds-1ubuntu2 [40.3 kB]
128s Get:5 http://ftpmaster.internal/ubuntu oracular/main amd64 bpfcc-tools all 0.30.0+ds-1ubuntu2 [697 kB]
128s Get:6 http://ftpmaster.internal/ubuntu oracular/main amd64 bpftrace amd64 0.21.0-1ubuntu6 [12.3 MB]
128s Fetched 13.9 MB in 0s (62.4 MB/s)
129s (Reading database ... 
(Reading database ... 5%
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(Reading database ... 15%
(Reading database ... 20%
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(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 ... 74523 files and directories currently installed.)
129s Preparing to unpack .../liblz4-1_1.9.4-3_amd64.deb ...
129s Unpacking liblz4-1:amd64 (1.9.4-3) over (1.9.4-2) ...
129s Setting up liblz4-1:amd64 (1.9.4-3) ...
129s (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 ... 74523 files and directories currently installed.)
129s Preparing to unpack .../mawk_1.3.4.20240622-2_amd64.deb ...
129s Unpacking mawk (1.3.4.20240622-2) over (1.3.4.20240622-1) ...
129s Preparing to unpack .../libbpfcc_0.30.0+ds-1ubuntu2_amd64.deb ...
129s Unpacking libbpfcc:amd64 (0.30.0+ds-1ubuntu2) over (0.29.1+ds-1ubuntu7) ...
129s Preparing to unpack .../python3-bpfcc_0.30.0+ds-1ubuntu2_all.deb ...
129s Unpacking python3-bpfcc (0.30.0+ds-1ubuntu2) over (0.29.1+ds-1ubuntu7) ...
129s Preparing to unpack .../bpfcc-tools_0.30.0+ds-1ubuntu2_all.deb ...
129s Unpacking bpfcc-tools (0.30.0+ds-1ubuntu2) over (0.29.1+ds-1ubuntu7) ...
129s Preparing to unpack .../bpftrace_0.21.0-1ubuntu6_amd64.deb ...
129s Unpacking bpftrace (0.21.0-1ubuntu6) over (0.20.2-1ubuntu4) ...
129s Setting up mawk (1.3.4.20240622-2) ...
129s Setting up libbpfcc:amd64 (0.30.0+ds-1ubuntu2) ...
129s Setting up python3-bpfcc (0.30.0+ds-1ubuntu2) ...
130s Setting up bpftrace (0.21.0-1ubuntu6) ...
130s Setting up bpfcc-tools (0.30.0+ds-1ubuntu2) ...
130s Processing triggers for man-db (2.12.1-2) ...
131s Processing triggers for libc-bin (2.39-0ubuntu9) ...
131s Reading package lists...
131s Building dependency tree...
131s Reading state information...
132s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
132s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease
132s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease
132s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease
132s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease
134s Reading package lists...
134s Reading package lists...
134s Building dependency tree...
134s Reading state information...
134s Calculating upgrade...
134s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
134s Reading package lists...
135s Building dependency tree...
135s Reading state information...
135s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
136s autopkgtest [16:09:07]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 00:40:06 UTC 2024
136s autopkgtest [16:09:07]: @@@@@@@@@@@@@@@@@@@@ apt-source pbdagcon
137s Get:1 http://ftpmaster.internal/ubuntu oracular/universe pbdagcon 0.3+git20180411.c14c422+dfsg-8build3 (dsc) [2475 B]
137s Get:2 http://ftpmaster.internal/ubuntu oracular/universe pbdagcon 0.3+git20180411.c14c422+dfsg-8build3 (tar) [79.8 kB]
137s Get:3 http://ftpmaster.internal/ubuntu oracular/universe pbdagcon 0.3+git20180411.c14c422+dfsg-8build3 (diff) [58.3 kB]
137s gpgv: Signature made Mon Nov 13 17:59:32 2023 UTC
137s gpgv:                using RSA key 92978A6E195E4921825F7FF0F34F09744E9F5DD9
137s gpgv: Can't check signature: No public key
137s dpkg-source: warning: cannot verify inline signature for ./pbdagcon_0.3+git20180411.c14c422+dfsg-8build3.dsc: no acceptable signature found
137s autopkgtest [16:09:08]: testing package pbdagcon version 0.3+git20180411.c14c422+dfsg-8build3
137s autopkgtest [16:09:08]: build not needed
137s autopkgtest [16:09:08]: test run-unit-test: preparing testbed
138s Reading package lists...
138s Building dependency tree...
138s Reading state information...
138s Starting pkgProblemResolver with broken count: 0
138s Starting 2 pkgProblemResolver with broken count: 0
138s Done
139s The following additional packages will be installed:
139s   blasr daligner dazzdb libaec0 libblasr5.3.5 libhdf5-103-1t64
139s   libhdf5-cpp-103-1t64 libhts3t64 libhtscodecs2 libpbbam2.4.0 libpbcopper2.3.0
139s   libpbseq libsz2 pbdagcon
139s Suggested packages:
139s   dascrubber
139s The following NEW packages will be installed:
139s   autopkgtest-satdep blasr daligner dazzdb libaec0 libblasr5.3.5
139s   libhdf5-103-1t64 libhdf5-cpp-103-1t64 libhts3t64 libhtscodecs2 libpbbam2.4.0
139s   libpbcopper2.3.0 libpbseq libsz2 pbdagcon
139s 0 upgraded, 15 newly installed, 0 to remove and 0 not upgraded.
139s Need to get 5266 kB/5267 kB of archives.
139s After this operation, 15.4 MB of additional disk space will be used.
139s Get:1 /tmp/autopkgtest.6fywlM/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [736 B]
139s Get:2 http://ftpmaster.internal/ubuntu oracular/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB]
139s Get:3 http://ftpmaster.internal/ubuntu oracular/universe amd64 libsz2 amd64 1.1.3-1 [5456 B]
139s Get:4 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhdf5-103-1t64 amd64 1.10.10+repack-3.1ubuntu4 [1270 kB]
139s Get:5 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhdf5-cpp-103-1t64 amd64 1.10.10+repack-3.1ubuntu4 [128 kB]
139s Get:6 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhtscodecs2 amd64 1.6.0-1build1 [98.8 kB]
139s Get:7 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhts3t64 amd64 1.20+ds-1 [439 kB]
139s Get:8 http://ftpmaster.internal/ubuntu oracular/universe amd64 libpbcopper2.3.0 amd64 2.3.0+dfsg-2 [575 kB]
139s Get:9 http://ftpmaster.internal/ubuntu oracular/universe amd64 libpbbam2.4.0 amd64 2.4.0+dfsg-1build2 [679 kB]
139s Get:10 http://ftpmaster.internal/ubuntu oracular/universe amd64 libblasr5.3.5 amd64 5.3.5+dfsg-6build5 [1234 kB]
139s Get:11 http://ftpmaster.internal/ubuntu oracular/universe amd64 libpbseq amd64 5.3.5+dfsg-6build5 [3064 B]
139s Get:12 http://ftpmaster.internal/ubuntu oracular/universe amd64 blasr amd64 5.3.5+dfsg-6build5 [230 kB]
139s Get:13 http://ftpmaster.internal/ubuntu oracular/universe amd64 daligner amd64 1.0+git20240119.335105d-3 [161 kB]
139s Get:14 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 dazzdb amd64 1.0+git20240115.be65e59-1 [150 kB]
139s Get:15 http://ftpmaster.internal/ubuntu oracular/universe amd64 pbdagcon amd64 0.3+git20180411.c14c422+dfsg-8build3 [269 kB]
140s Fetched 5266 kB in 0s (21.4 MB/s)
140s Selecting previously unselected package libaec0:amd64.
140s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
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(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 ... 74530 files and directories currently installed.)
140s Preparing to unpack .../00-libaec0_1.1.3-1_amd64.deb ...
140s Unpacking libaec0:amd64 (1.1.3-1) ...
140s Selecting previously unselected package libsz2:amd64.
140s Preparing to unpack .../01-libsz2_1.1.3-1_amd64.deb ...
140s Unpacking libsz2:amd64 (1.1.3-1) ...
140s Selecting previously unselected package libhdf5-103-1t64:amd64.
140s Preparing to unpack .../02-libhdf5-103-1t64_1.10.10+repack-3.1ubuntu4_amd64.deb ...
140s Unpacking libhdf5-103-1t64:amd64 (1.10.10+repack-3.1ubuntu4) ...
140s Selecting previously unselected package libhdf5-cpp-103-1t64:amd64.
140s Preparing to unpack .../03-libhdf5-cpp-103-1t64_1.10.10+repack-3.1ubuntu4_amd64.deb ...
140s Unpacking libhdf5-cpp-103-1t64:amd64 (1.10.10+repack-3.1ubuntu4) ...
140s Selecting previously unselected package libhtscodecs2:amd64.
140s Preparing to unpack .../04-libhtscodecs2_1.6.0-1build1_amd64.deb ...
140s Unpacking libhtscodecs2:amd64 (1.6.0-1build1) ...
140s Selecting previously unselected package libhts3t64:amd64.
140s Preparing to unpack .../05-libhts3t64_1.20+ds-1_amd64.deb ...
140s Unpacking libhts3t64:amd64 (1.20+ds-1) ...
140s Selecting previously unselected package libpbcopper2.3.0:amd64.
140s Preparing to unpack .../06-libpbcopper2.3.0_2.3.0+dfsg-2_amd64.deb ...
140s Unpacking libpbcopper2.3.0:amd64 (2.3.0+dfsg-2) ...
140s Selecting previously unselected package libpbbam2.4.0:amd64.
140s Preparing to unpack .../07-libpbbam2.4.0_2.4.0+dfsg-1build2_amd64.deb ...
140s Unpacking libpbbam2.4.0:amd64 (2.4.0+dfsg-1build2) ...
140s Selecting previously unselected package libblasr5.3.5:amd64.
140s Preparing to unpack .../08-libblasr5.3.5_5.3.5+dfsg-6build5_amd64.deb ...
140s Unpacking libblasr5.3.5:amd64 (5.3.5+dfsg-6build5) ...
140s Selecting previously unselected package libpbseq:amd64.
140s Preparing to unpack .../09-libpbseq_5.3.5+dfsg-6build5_amd64.deb ...
140s Unpacking libpbseq:amd64 (5.3.5+dfsg-6build5) ...
140s Selecting previously unselected package blasr.
140s Preparing to unpack .../10-blasr_5.3.5+dfsg-6build5_amd64.deb ...
140s Unpacking blasr (5.3.5+dfsg-6build5) ...
140s Selecting previously unselected package daligner.
140s Preparing to unpack .../11-daligner_1.0+git20240119.335105d-3_amd64.deb ...
140s Unpacking daligner (1.0+git20240119.335105d-3) ...
140s Selecting previously unselected package dazzdb.
140s Preparing to unpack .../12-dazzdb_1.0+git20240115.be65e59-1_amd64.deb ...
140s Unpacking dazzdb (1.0+git20240115.be65e59-1) ...
140s Selecting previously unselected package pbdagcon.
140s Preparing to unpack .../13-pbdagcon_0.3+git20180411.c14c422+dfsg-8build3_amd64.deb ...
140s Unpacking pbdagcon (0.3+git20180411.c14c422+dfsg-8build3) ...
140s Selecting previously unselected package autopkgtest-satdep.
140s Preparing to unpack .../14-1-autopkgtest-satdep.deb ...
140s Unpacking autopkgtest-satdep (0) ...
140s Setting up libhtscodecs2:amd64 (1.6.0-1build1) ...
140s Setting up libaec0:amd64 (1.1.3-1) ...
140s Setting up dazzdb (1.0+git20240115.be65e59-1) ...
140s Setting up daligner (1.0+git20240119.335105d-3) ...
140s Setting up libhts3t64:amd64 (1.20+ds-1) ...
140s Setting up libsz2:amd64 (1.1.3-1) ...
140s Setting up libpbcopper2.3.0:amd64 (2.3.0+dfsg-2) ...
140s Setting up libpbbam2.4.0:amd64 (2.4.0+dfsg-1build2) ...
140s Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-3.1ubuntu4) ...
140s Setting up libhdf5-cpp-103-1t64:amd64 (1.10.10+repack-3.1ubuntu4) ...
140s Setting up libblasr5.3.5:amd64 (5.3.5+dfsg-6build5) ...
140s Setting up libpbseq:amd64 (5.3.5+dfsg-6build5) ...
140s Setting up blasr (5.3.5+dfsg-6build5) ...
140s Setting up pbdagcon (0.3+git20180411.c14c422+dfsg-8build3) ...
140s Setting up autopkgtest-satdep (0) ...
140s Processing triggers for man-db (2.12.1-2) ...
141s Processing triggers for libc-bin (2.39-0ubuntu9) ...
143s (Reading database ... 74705 files and directories currently installed.)
143s Removing autopkgtest-satdep (0) ...
143s autopkgtest [16:09:14]: test run-unit-test: [-----------------------
143s Test 1
143s [INFO] 2024-07-26T16:09:14 [blasr] started.
144s [INFO] 2024-07-26T16:09:15 [blasr] ended.
144s 2024-07-26 16:09:15,054 INFO  [default] Multi-threaded. Input: mapped.m5, Threads: 4
144s 2024-07-26 16:09:15,057 DEBUG [Reader] [ubuntu@unknown-host] [FUNCTION] [FILE:0] Consensus candidate: random
144s 2024-07-26 16:09:15,057 INFO  [Consensus] Consensus calling: random Alignments: 21
144s consensus.fasta: OK
144s mapped.m5: OK
144s queries.fasta: OK
144s target.dam: FAILED
144s target.fasta: OK
144s md5sum: WARNING: 1 computed checksum did NOT match
144s autopkgtest [16:09:15]: test run-unit-test: -----------------------]
144s autopkgtest [16:09:15]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
144s run-unit-test        FAIL non-zero exit status 1
144s autopkgtest [16:09:15]: @@@@@@@@@@@@@@@@@@@@ summary
144s run-unit-test        FAIL non-zero exit status 1
156s nova [W] Skipping flock for amd64
156s Creating nova instance adt-oracular-amd64-pbdagcon-20240726-160649-juju-7f2275-prod-proposed-migration-environment-3-8d3139c9-fa4f-4e39-ac46-d96463cf0c82 from image adt/ubuntu-oracular-amd64-server-20240726.img (UUID 6c5f29e9-79d7-45b1-9721-03e2205f6a0e)...