0s autopkgtest [10:21:47]: starting date and time: 2024-06-16 10:21:47+0000
  1s autopkgtest [10:21:48]: git checkout: 433ed4cb Merge branch 'skia/nova_flock' into 'ubuntu/5.34+prod'
  1s autopkgtest [10:21:48]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.0jvgwx5k/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@lcy02-95.secgroup --name adt-oracular-amd64-pbdagcon-20240616-102147-juju-7f2275-prod-proposed-migration-environment-3-b650d5de-e8c9-4b1b-bb64-4decf4bab773 --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/
111s autopkgtest [10:23:38]: testbed dpkg architecture: amd64
111s autopkgtest [10:23:38]: testbed apt version: 2.9.3
111s autopkgtest [10:23:38]: @@@@@@@@@@@@@@@@@@@@ test bed setup
112s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [110 kB]
112s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [7052 B]
112s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2576 B]
112s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [389 kB]
112s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [36.1 kB]
112s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main i386 Packages [38.2 kB]
112s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 Packages [53.8 kB]
112s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 Packages [28.9 kB]
112s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted i386 Packages [6732 B]
112s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 Packages [317 kB]
112s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe i386 Packages [138 kB]
112s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse i386 Packages [3884 B]
112s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 Packages [8364 B]
112s Fetched 1140 kB in 0s (4972 kB/s)
112s Reading package lists...
113s Reading package lists...
114s Building dependency tree...
114s Reading state information...
114s Calculating upgrade...
114s The following packages will be upgraded:
114s   apt apt-utils libapt-pkg6.0t64 libldap-common libldap2
114s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
114s Need to get 2875 kB of archives.
114s After this operation, 11.3 kB of additional disk space will be used.
114s Get:1 http://ftpmaster.internal/ubuntu oracular/main amd64 libapt-pkg6.0t64 amd64 2.9.5 [1023 kB]
114s Get:2 http://ftpmaster.internal/ubuntu oracular/main amd64 apt amd64 2.9.5 [1403 kB]
114s Get:3 http://ftpmaster.internal/ubuntu oracular/main amd64 apt-utils amd64 2.9.5 [223 kB]
114s Get:4 http://ftpmaster.internal/ubuntu oracular/main amd64 libldap-common all 2.6.7+dfsg-1~exp1ubuntu9 [31.5 kB]
114s Get:5 http://ftpmaster.internal/ubuntu oracular/main amd64 libldap2 amd64 2.6.7+dfsg-1~exp1ubuntu9 [195 kB]
115s Fetched 2875 kB in 0s (50.6 MB/s)
115s (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 ... 74430 files and directories currently installed.)
115s Preparing to unpack .../libapt-pkg6.0t64_2.9.5_amd64.deb ...
115s Unpacking libapt-pkg6.0t64:amd64 (2.9.5) over (2.9.3) ...
115s Setting up libapt-pkg6.0t64:amd64 (2.9.5) ...
115s (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 ... 74430 files and directories currently installed.)
115s Preparing to unpack .../archives/apt_2.9.5_amd64.deb ...
115s Unpacking apt (2.9.5) over (2.9.3) ...
115s Setting up apt (2.9.5) ...
116s (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 ... 74430 files and directories currently installed.)
116s Preparing to unpack .../apt-utils_2.9.5_amd64.deb ...
116s Unpacking apt-utils (2.9.5) over (2.9.3) ...
116s Preparing to unpack .../libldap-common_2.6.7+dfsg-1~exp1ubuntu9_all.deb ...
116s Unpacking libldap-common (2.6.7+dfsg-1~exp1ubuntu9) over (2.6.7+dfsg-1~exp1ubuntu8) ...
116s Preparing to unpack .../libldap2_2.6.7+dfsg-1~exp1ubuntu9_amd64.deb ...
116s Unpacking libldap2:amd64 (2.6.7+dfsg-1~exp1ubuntu9) over (2.6.7+dfsg-1~exp1ubuntu8) ...
116s Setting up apt-utils (2.9.5) ...
116s Setting up libldap-common (2.6.7+dfsg-1~exp1ubuntu9) ...
116s Setting up libldap2:amd64 (2.6.7+dfsg-1~exp1ubuntu9) ...
116s Processing triggers for man-db (2.12.1-2) ...
118s Processing triggers for libc-bin (2.39-0ubuntu9) ...
119s Reading package lists...
119s Building dependency tree...
119s Reading state information...
120s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
120s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease
120s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease
120s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease
120s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease
121s Reading package lists...
121s Reading package lists...
121s Building dependency tree...
121s Reading state information...
121s Calculating upgrade...
122s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
122s Reading package lists...
122s Building dependency tree...
122s Reading state information...
122s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
122s autopkgtest [10:23:49]: rebooting testbed after setup commands that affected boot
126s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds...
136s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds...
140s autopkgtest [10:24:07]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 00:40:06 UTC 2024
141s autopkgtest [10:24:08]: @@@@@@@@@@@@@@@@@@@@ apt-source pbdagcon
142s Get:1 http://ftpmaster.internal/ubuntu oracular/universe pbdagcon 0.3+git20180411.c14c422+dfsg-8build3 (dsc) [2475 B]
142s Get:2 http://ftpmaster.internal/ubuntu oracular/universe pbdagcon 0.3+git20180411.c14c422+dfsg-8build3 (tar) [79.8 kB]
142s Get:3 http://ftpmaster.internal/ubuntu oracular/universe pbdagcon 0.3+git20180411.c14c422+dfsg-8build3 (diff) [58.3 kB]
142s gpgv: Signature made Mon Nov 13 17:59:32 2023 UTC
142s gpgv:                using RSA key 92978A6E195E4921825F7FF0F34F09744E9F5DD9
142s gpgv: Can't check signature: No public key
142s dpkg-source: warning: cannot verify inline signature for ./pbdagcon_0.3+git20180411.c14c422+dfsg-8build3.dsc: no acceptable signature found
142s autopkgtest [10:24:09]: testing package pbdagcon version 0.3+git20180411.c14c422+dfsg-8build3
142s autopkgtest [10:24:09]: build not needed
142s autopkgtest [10:24:09]: test run-unit-test: preparing testbed
143s Reading package lists...
143s Building dependency tree...
143s Reading state information...
144s Starting pkgProblemResolver with broken count: 0
144s Starting 2 pkgProblemResolver with broken count: 0
144s Done
144s The following additional packages will be installed:
144s   blasr daligner dazzdb libaec0 libblasr5.3.5 libhdf5-103-1t64
144s   libhdf5-cpp-103-1t64 libhts3t64 libhtscodecs2 libpbbam2.4.0 libpbcopper2.3.0
144s   libpbseq libsz2 pbdagcon
144s Suggested packages:
144s   dascrubber
144s The following NEW packages will be installed:
144s   autopkgtest-satdep blasr daligner dazzdb libaec0 libblasr5.3.5
144s   libhdf5-103-1t64 libhdf5-cpp-103-1t64 libhts3t64 libhtscodecs2 libpbbam2.4.0
144s   libpbcopper2.3.0 libpbseq libsz2 pbdagcon
144s 0 upgraded, 15 newly installed, 0 to remove and 0 not upgraded.
144s Need to get 5266 kB/5267 kB of archives.
144s After this operation, 15.4 MB of additional disk space will be used.
144s Get:1 /tmp/autopkgtest.xnSSIJ/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [736 B]
144s Get:2 http://ftpmaster.internal/ubuntu oracular/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB]
144s Get:3 http://ftpmaster.internal/ubuntu oracular/universe amd64 libsz2 amd64 1.1.3-1 [5456 B]
144s Get:4 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhdf5-103-1t64 amd64 1.10.10+repack-3.1ubuntu4 [1270 kB]
144s Get:5 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhdf5-cpp-103-1t64 amd64 1.10.10+repack-3.1ubuntu4 [128 kB]
144s Get:6 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhtscodecs2 amd64 1.6.0-1build1 [98.8 kB]
144s Get:7 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhts3t64 amd64 1.20+ds-1 [439 kB]
144s Get:8 http://ftpmaster.internal/ubuntu oracular/universe amd64 libpbcopper2.3.0 amd64 2.3.0+dfsg-2 [575 kB]
144s Get:9 http://ftpmaster.internal/ubuntu oracular/universe amd64 libpbbam2.4.0 amd64 2.4.0+dfsg-1build2 [679 kB]
144s Get:10 http://ftpmaster.internal/ubuntu oracular/universe amd64 libblasr5.3.5 amd64 5.3.5+dfsg-6build5 [1234 kB]
145s Get:11 http://ftpmaster.internal/ubuntu oracular/universe amd64 libpbseq amd64 5.3.5+dfsg-6build5 [3064 B]
145s Get:12 http://ftpmaster.internal/ubuntu oracular/universe amd64 blasr amd64 5.3.5+dfsg-6build5 [230 kB]
145s Get:13 http://ftpmaster.internal/ubuntu oracular/universe amd64 daligner amd64 1.0+git20240119.335105d-2 [161 kB]
145s Get:14 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 dazzdb amd64 1.0+git20240115.be65e59-1 [150 kB]
145s Get:15 http://ftpmaster.internal/ubuntu oracular/universe amd64 pbdagcon amd64 0.3+git20180411.c14c422+dfsg-8build3 [269 kB]
145s Fetched 5266 kB in 0s (13.0 MB/s)
145s Selecting previously unselected package libaec0:amd64.
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 ... 74430 files and directories currently installed.)
145s Preparing to unpack .../00-libaec0_1.1.3-1_amd64.deb ...
145s Unpacking libaec0:amd64 (1.1.3-1) ...
145s Selecting previously unselected package libsz2:amd64.
145s Preparing to unpack .../01-libsz2_1.1.3-1_amd64.deb ...
145s Unpacking libsz2:amd64 (1.1.3-1) ...
145s Selecting previously unselected package libhdf5-103-1t64:amd64.
145s Preparing to unpack .../02-libhdf5-103-1t64_1.10.10+repack-3.1ubuntu4_amd64.deb ...
145s Unpacking libhdf5-103-1t64:amd64 (1.10.10+repack-3.1ubuntu4) ...
145s Selecting previously unselected package libhdf5-cpp-103-1t64:amd64.
145s Preparing to unpack .../03-libhdf5-cpp-103-1t64_1.10.10+repack-3.1ubuntu4_amd64.deb ...
145s Unpacking libhdf5-cpp-103-1t64:amd64 (1.10.10+repack-3.1ubuntu4) ...
145s Selecting previously unselected package libhtscodecs2:amd64.
145s Preparing to unpack .../04-libhtscodecs2_1.6.0-1build1_amd64.deb ...
145s Unpacking libhtscodecs2:amd64 (1.6.0-1build1) ...
145s Selecting previously unselected package libhts3t64:amd64.
145s Preparing to unpack .../05-libhts3t64_1.20+ds-1_amd64.deb ...
145s Unpacking libhts3t64:amd64 (1.20+ds-1) ...
145s Selecting previously unselected package libpbcopper2.3.0:amd64.
145s Preparing to unpack .../06-libpbcopper2.3.0_2.3.0+dfsg-2_amd64.deb ...
145s Unpacking libpbcopper2.3.0:amd64 (2.3.0+dfsg-2) ...
145s Selecting previously unselected package libpbbam2.4.0:amd64.
145s Preparing to unpack .../07-libpbbam2.4.0_2.4.0+dfsg-1build2_amd64.deb ...
145s Unpacking libpbbam2.4.0:amd64 (2.4.0+dfsg-1build2) ...
145s Selecting previously unselected package libblasr5.3.5:amd64.
145s Preparing to unpack .../08-libblasr5.3.5_5.3.5+dfsg-6build5_amd64.deb ...
145s Unpacking libblasr5.3.5:amd64 (5.3.5+dfsg-6build5) ...
145s Selecting previously unselected package libpbseq:amd64.
145s Preparing to unpack .../09-libpbseq_5.3.5+dfsg-6build5_amd64.deb ...
145s Unpacking libpbseq:amd64 (5.3.5+dfsg-6build5) ...
145s Selecting previously unselected package blasr.
145s Preparing to unpack .../10-blasr_5.3.5+dfsg-6build5_amd64.deb ...
145s Unpacking blasr (5.3.5+dfsg-6build5) ...
145s Selecting previously unselected package daligner.
145s Preparing to unpack .../11-daligner_1.0+git20240119.335105d-2_amd64.deb ...
145s Unpacking daligner (1.0+git20240119.335105d-2) ...
145s Selecting previously unselected package dazzdb.
145s Preparing to unpack .../12-dazzdb_1.0+git20240115.be65e59-1_amd64.deb ...
145s Unpacking dazzdb (1.0+git20240115.be65e59-1) ...
146s Selecting previously unselected package pbdagcon.
146s Preparing to unpack .../13-pbdagcon_0.3+git20180411.c14c422+dfsg-8build3_amd64.deb ...
146s Unpacking pbdagcon (0.3+git20180411.c14c422+dfsg-8build3) ...
146s Selecting previously unselected package autopkgtest-satdep.
146s Preparing to unpack .../14-1-autopkgtest-satdep.deb ...
146s Unpacking autopkgtest-satdep (0) ...
146s Setting up libhtscodecs2:amd64 (1.6.0-1build1) ...
146s Setting up libaec0:amd64 (1.1.3-1) ...
146s Setting up dazzdb (1.0+git20240115.be65e59-1) ...
146s Setting up daligner (1.0+git20240119.335105d-2) ...
146s Setting up libhts3t64:amd64 (1.20+ds-1) ...
146s Setting up libsz2:amd64 (1.1.3-1) ...
146s Setting up libpbcopper2.3.0:amd64 (2.3.0+dfsg-2) ...
146s Setting up libpbbam2.4.0:amd64 (2.4.0+dfsg-1build2) ...
146s Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-3.1ubuntu4) ...
146s Setting up libhdf5-cpp-103-1t64:amd64 (1.10.10+repack-3.1ubuntu4) ...
146s Setting up libblasr5.3.5:amd64 (5.3.5+dfsg-6build5) ...
146s Setting up libpbseq:amd64 (5.3.5+dfsg-6build5) ...
146s Setting up blasr (5.3.5+dfsg-6build5) ...
146s Setting up pbdagcon (0.3+git20180411.c14c422+dfsg-8build3) ...
146s Setting up autopkgtest-satdep (0) ...
146s Processing triggers for man-db (2.12.1-2) ...
146s Processing triggers for libc-bin (2.39-0ubuntu9) ...
149s (Reading database ... 74605 files and directories currently installed.)
149s Removing autopkgtest-satdep (0) ...
149s autopkgtest [10:24:16]: test run-unit-test: [-----------------------
149s Test 1
149s [INFO] 2024-06-16T10:24:16 [blasr] started.
149s [INFO] 2024-06-16T10:24:16 [blasr] ended.
149s 2024-06-16 10:24:16,313 INFO  [default] Multi-threaded. Input: mapped.m5, Threads: 4
149s 2024-06-16 10:24:16,315 DEBUG [Reader] [ubuntu@unknown-host] [FUNCTION] [FILE:0] Consensus candidate: random
149s 2024-06-16 10:24:16,315 INFO  [Consensus] Consensus calling: random Alignments: 21
149s md5sum: WARNING: 1 computed checksum did NOT match
149s consensus.fasta: OK
149s mapped.m5: OK
149s queries.fasta: OK
149s target.dam: FAILED
149s target.fasta: OK
149s autopkgtest [10:24:16]: test run-unit-test: -----------------------]
150s run-unit-test        FAIL non-zero exit status 1
150s autopkgtest [10:24:17]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
150s autopkgtest [10:24:17]: @@@@@@@@@@@@@@@@@@@@ summary
150s run-unit-test        FAIL non-zero exit status 1
163s nova [W] Skipping flock for amd64
163s Creating nova instance adt-oracular-amd64-pbdagcon-20240616-102147-juju-7f2275-prod-proposed-migration-environment-3-b650d5de-e8c9-4b1b-bb64-4decf4bab773 from image adt/ubuntu-oracular-amd64-server-20240615.img (UUID 94fd7b6f-4495-4684-bd31-1d1deeaa1788)...