0s autopkgtest [21:55:27]: starting date and time: 2024-03-17 21:55:27+0000
  0s autopkgtest [21:55:27]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data
  0s autopkgtest [21:55:27]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.gyep1v6y/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:ncbi-blast+,src:mbedtls --apt-upgrade kraken2 --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=ncbi-blast+/2.12.0+ds-4build1 mbedtls/2.28.7-1.1ubuntu1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-s390x-13.secgroup --name adt-noble-s390x-kraken2-20240317-215527-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-s390x-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,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
217s autopkgtest [21:59:04]: testbed dpkg architecture: s390x
218s autopkgtest [21:59:05]: testbed apt version: 2.7.12
218s autopkgtest [21:59:05]: @@@@@@@@@@@@@@@@@@@@ test bed setup
218s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
219s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [484 kB]
219s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B]
219s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3676 kB]
220s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB]
220s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [639 kB]
220s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B]
220s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B]
220s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B]
220s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [3877 kB]
221s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B]
221s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [33.2 kB]
221s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B]
222s Fetched 8895 kB in 3s (2919 kB/s)
222s Reading package lists...
225s Reading package lists...
225s Building dependency tree...
225s Reading state information...
225s Calculating upgrade...
225s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
225s Reading package lists...
225s Building dependency tree...
225s Reading state information...
225s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
226s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease
226s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease
226s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease
226s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease
227s Reading package lists...
227s Reading package lists...
227s Building dependency tree...
227s Reading state information...
227s Calculating upgrade...
227s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
227s Reading package lists...
228s Building dependency tree...
228s Reading state information...
228s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
230s autopkgtest [21:59:17]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024
230s autopkgtest [21:59:17]: @@@@@@@@@@@@@@@@@@@@ apt-source kraken2
232s Get:1 http://ftpmaster.internal/ubuntu noble/universe kraken2 2.1.3-1 (dsc) [1973 B]
232s Get:2 http://ftpmaster.internal/ubuntu noble/universe kraken2 2.1.3-1 (tar) [219 kB]
232s Get:3 http://ftpmaster.internal/ubuntu noble/universe kraken2 2.1.3-1 (diff) [339 kB]
232s gpgv: Signature made Tue Nov 28 19:25:57 2023 UTC
232s gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
232s gpgv:                issuer "tille@debian.org"
232s gpgv: Can't check signature: No public key
232s dpkg-source: warning: cannot verify inline signature for ./kraken2_2.1.3-1.dsc: no acceptable signature found
232s autopkgtest [21:59:19]: testing package kraken2 version 2.1.3-1
233s autopkgtest [21:59:20]: build not needed
233s autopkgtest [21:59:20]: test run-unit-test: preparing testbed
234s Reading package lists...
235s Building dependency tree...
235s Reading state information...
235s Starting pkgProblemResolver with broken count: 0
235s Starting 2 pkgProblemResolver with broken count: 0
235s Done
235s The following additional packages will be installed:
235s   kraken2 libgomp1 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64
235s   ncbi-blast+ ncbi-data
235s The following NEW packages will be installed:
235s   autopkgtest-satdep kraken2 libgomp1 libmbedcrypto7t64 libmbedtls14t64
235s   libmbedx509-1t64 ncbi-blast+ ncbi-data
235s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded.
235s Need to get 18.5 MB/18.5 MB of archives.
235s After this operation, 76.9 MB of additional disk space will be used.
235s Get:1 /tmp/autopkgtest.k8qDLp/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [704 B]
235s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libgomp1 s390x 14-20240303-1ubuntu1 [151 kB]
235s Get:3 http://ftpmaster.internal/ubuntu noble/universe s390x ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB]
236s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libmbedcrypto7t64 s390x 2.28.7-1.1ubuntu1 [216 kB]
236s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libmbedx509-1t64 s390x 2.28.7-1.1ubuntu1 [46.2 kB]
236s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libmbedtls14t64 s390x 2.28.7-1.1ubuntu1 [84.7 kB]
236s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x ncbi-blast+ s390x 2.12.0+ds-4build1 [12.8 MB]
236s Get:8 http://ftpmaster.internal/ubuntu noble/universe s390x kraken2 s390x 2.1.3-1 [875 kB]
236s Fetched 18.5 MB in 1s (17.4 MB/s)
236s Selecting previously unselected package libgomp1:s390x.
236s (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 ... 52171 files and directories currently installed.)
236s Preparing to unpack .../0-libgomp1_14-20240303-1ubuntu1_s390x.deb ...
236s Unpacking libgomp1:s390x (14-20240303-1ubuntu1) ...
236s Selecting previously unselected package ncbi-data.
236s Preparing to unpack .../1-ncbi-data_6.1.20170106+dfsg1-10_all.deb ...
236s Unpacking ncbi-data (6.1.20170106+dfsg1-10) ...
237s Selecting previously unselected package libmbedcrypto7t64:s390x.
237s Preparing to unpack .../2-libmbedcrypto7t64_2.28.7-1.1ubuntu1_s390x.deb ...
237s Unpacking libmbedcrypto7t64:s390x (2.28.7-1.1ubuntu1) ...
237s Selecting previously unselected package libmbedx509-1t64:s390x.
237s Preparing to unpack .../3-libmbedx509-1t64_2.28.7-1.1ubuntu1_s390x.deb ...
237s Unpacking libmbedx509-1t64:s390x (2.28.7-1.1ubuntu1) ...
237s Selecting previously unselected package libmbedtls14t64:s390x.
237s Preparing to unpack .../4-libmbedtls14t64_2.28.7-1.1ubuntu1_s390x.deb ...
237s Unpacking libmbedtls14t64:s390x (2.28.7-1.1ubuntu1) ...
237s Selecting previously unselected package ncbi-blast+.
237s Preparing to unpack .../5-ncbi-blast+_2.12.0+ds-4build1_s390x.deb ...
237s Unpacking ncbi-blast+ (2.12.0+ds-4build1) ...
237s Selecting previously unselected package kraken2.
237s Preparing to unpack .../6-kraken2_2.1.3-1_s390x.deb ...
237s Unpacking kraken2 (2.1.3-1) ...
237s Selecting previously unselected package autopkgtest-satdep.
237s Preparing to unpack .../7-1-autopkgtest-satdep.deb ...
237s Unpacking autopkgtest-satdep (0) ...
237s Setting up ncbi-data (6.1.20170106+dfsg1-10) ...
237s Setting up libmbedcrypto7t64:s390x (2.28.7-1.1ubuntu1) ...
237s Setting up libgomp1:s390x (14-20240303-1ubuntu1) ...
237s Setting up libmbedx509-1t64:s390x (2.28.7-1.1ubuntu1) ...
237s Setting up libmbedtls14t64:s390x (2.28.7-1.1ubuntu1) ...
237s Setting up ncbi-blast+ (2.12.0+ds-4build1) ...
237s Setting up kraken2 (2.1.3-1) ...
237s Setting up autopkgtest-satdep (0) ...
237s Processing triggers for man-db (2.12.0-3) ...
237s Processing triggers for libc-bin (2.39-0ubuntu2) ...
239s (Reading database ... 52496 files and directories currently installed.)
239s Removing autopkgtest-satdep (0) ...
240s autopkgtest [21:59:27]: test run-unit-test: [-----------------------
240s Masking low-complexity regions of new file... done.
240s Added "Acartia_tonsa.fasta" to library (test_db)
240s Masking low-complexity regions of new file... done.
240s Added "Acinetobacter_phage.fasta" to library (test_db)
241s autopkgtest [21:59:28]: test run-unit-test: -----------------------]
241s autopkgtest [21:59:28]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
241s run-unit-test        PASS
241s autopkgtest [21:59:28]: @@@@@@@@@@@@@@@@@@@@ summary
241s run-unit-test        PASS
259s Creating nova instance adt-noble-s390x-kraken2-20240317-215527-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-s390x-server-20240316.img (UUID 7afe023c-7cb8-41b6-91a7-c69e7d1e7c0d)...