0s autopkgtest [16:35:26]: starting date and time: 2025-10-18 16:35:26+0000 0s autopkgtest [16:35:26]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [16:35:26]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.msk5eeyq/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade cat-bat --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.13.7-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-s390x-13.secgroup --name adt-resolute-s390x-cat-bat-20251018-163526-juju-7f2275-prod-proposed-migration-environment-20-09ab1f88-11bd-441a-a581-a313b91dd92c --image adt/ubuntu-resolute-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-s390x -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-s390x-cat-bat-20251018-163526-juju-7f2275-prod-proposed-migration-environment-20-09ab1f88-11bd-441a-a581-a313b91dd92c from image adt/ubuntu-resolute-s390x-server-20251018.img (UUID c47ab411-f9be-46ce-b861-20d934d06dba)... 51s autopkgtest [16:36:17]: testbed dpkg architecture: s390x 51s autopkgtest [16:36:17]: testbed apt version: 3.1.6ubuntu2 51s autopkgtest [16:36:17]: @@@@@@@@@@@@@@@@@@@@ test bed setup 51s autopkgtest [16:36:17]: testbed release detected to be: None 52s autopkgtest [16:36:18]: updating testbed package index (apt update) 52s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 53s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 53s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 53s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 53s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 53s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [28.4 kB] 53s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [15.4 kB] 53s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [345 kB] 53s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x Packages [74.0 kB] 53s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted s390x Packages [940 B] 53s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x Packages [226 kB] 53s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse s390x Packages [3812 B] 53s Fetched 781 kB in 1s (731 kB/s) 54s Reading package lists... 55s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 55s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 55s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 55s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 56s Reading package lists... 56s Reading package lists... 56s Building dependency tree... 56s Reading state information... 56s Calculating upgrade... 56s The following packages will be upgraded: 56s apt gir1.2-girepository-2.0 libapt-pkg7.0 libgirepository-1.0-1 56s libpython3-stdlib lto-disabled-list python3 python3-minimal 56s 8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 56s Need to get 2763 kB of archives. 56s After this operation, 14.3 kB of additional disk space will be used. 56s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3-minimal s390x 3.13.7-2 [27.8 kB] 56s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3 s390x 3.13.7-2 [23.9 kB] 56s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x libpython3-stdlib s390x 3.13.7-2 [10.6 kB] 56s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x libapt-pkg7.0 s390x 3.1.8ubuntu1 [1144 kB] 58s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x apt s390x 3.1.8ubuntu1 [1432 kB] 58s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x libgirepository-1.0-1 s390x 1.86.0-6 [86.9 kB] 58s Get:7 http://ftpmaster.internal/ubuntu resolute/main s390x gir1.2-girepository-2.0 s390x 1.86.0-6 [25.1 kB] 58s Get:8 http://ftpmaster.internal/ubuntu resolute/main s390x lto-disabled-list all 71 [12.5 kB] 59s dpkg-preconfigure: unable to re-open stdin: No such file or directory 59s Fetched 2763 kB in 3s (1095 kB/s) 59s (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 ... 56852 files and directories currently installed.) 59s Preparing to unpack .../python3-minimal_3.13.7-2_s390x.deb ... 59s Unpacking python3-minimal (3.13.7-2) over (3.13.7-1) ... 59s Setting up python3-minimal (3.13.7-2) ... 59s (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 ... 56852 files and directories currently installed.) 59s Preparing to unpack .../0-python3_3.13.7-2_s390x.deb ... 59s running python pre-rtupdate hooks for python3.13... 59s Unpacking python3 (3.13.7-2) over (3.13.7-1) ... 59s Preparing to unpack .../1-libpython3-stdlib_3.13.7-2_s390x.deb ... 59s Unpacking libpython3-stdlib:s390x (3.13.7-2) over (3.13.7-1) ... 59s Preparing to unpack .../2-libapt-pkg7.0_3.1.8ubuntu1_s390x.deb ... 59s Unpacking libapt-pkg7.0:s390x (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 59s Preparing to unpack .../3-apt_3.1.8ubuntu1_s390x.deb ... 59s Unpacking apt (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 59s Preparing to unpack .../4-libgirepository-1.0-1_1.86.0-6_s390x.deb ... 59s Unpacking libgirepository-1.0-1:s390x (1.86.0-6) over (1.84.0-1) ... 59s Preparing to unpack .../5-gir1.2-girepository-2.0_1.86.0-6_s390x.deb ... 59s Unpacking gir1.2-girepository-2.0:s390x (1.86.0-6) over (1.84.0-1) ... 59s Preparing to unpack .../6-lto-disabled-list_71_all.deb ... 59s Unpacking lto-disabled-list (71) over (69) ... 59s Setting up lto-disabled-list (71) ... 59s Setting up libgirepository-1.0-1:s390x (1.86.0-6) ... 59s Setting up libapt-pkg7.0:s390x (3.1.8ubuntu1) ... 59s Setting up libpython3-stdlib:s390x (3.13.7-2) ... 59s Setting up apt (3.1.8ubuntu1) ... 60s Setting up python3 (3.13.7-2) ... 60s running python rtupdate hooks for python3.13... 60s running python post-rtupdate hooks for python3.13... 60s Setting up gir1.2-girepository-2.0:s390x (1.86.0-6) ... 60s Processing triggers for man-db (2.13.1-1) ... 61s Processing triggers for libc-bin (2.42-0ubuntu3) ... 61s autopkgtest [16:36:27]: upgrading testbed (apt dist-upgrade and autopurge) 62s Reading package lists... 62s Building dependency tree... 62s Reading state information... 62s Calculating upgrade... 62s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 62s Reading package lists... 62s Building dependency tree... 62s Reading state information... 62s Solving dependencies... 63s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 63s autopkgtest [16:36:29]: rebooting testbed after setup commands that affected boot 77s autopkgtest [16:36:43]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP Mon Sep 22 08:56:47 UTC 2025 80s autopkgtest [16:36:46]: @@@@@@@@@@@@@@@@@@@@ apt-source cat-bat 81s Get:1 http://ftpmaster.internal/ubuntu resolute/universe cat-bat 5.3-2 (dsc) [2007 B] 81s Get:2 http://ftpmaster.internal/ubuntu resolute/universe cat-bat 5.3-2 (tar) [39.2 kB] 81s Get:3 http://ftpmaster.internal/ubuntu resolute/universe cat-bat 5.3-2 (diff) [5260 B] 81s gpgv: Signature made Thu Jan 11 10:25:13 2024 UTC 81s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 81s gpgv: issuer "tille@debian.org" 81s gpgv: Can't check signature: No public key 81s dpkg-source: warning: cannot verify inline signature for ./cat-bat_5.3-2.dsc: no acceptable signature found 81s autopkgtest [16:36:47]: testing package cat-bat version 5.3-2 82s autopkgtest [16:36:48]: build not needed 82s autopkgtest [16:36:48]: test run-unit-test: preparing testbed 82s Reading package lists... 82s Building dependency tree... 82s Reading state information... 82s Solving dependencies... 82s The following NEW packages will be installed: 82s cat-bat diamond-aligner prodigal 83s 0 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. 83s Need to get 2997 kB of archives. 83s After this operation, 18.9 MB of additional disk space will be used. 83s Get:1 http://ftpmaster.internal/ubuntu resolute/universe s390x diamond-aligner s390x 2.1.11-2 [2296 kB] 84s Get:2 http://ftpmaster.internal/ubuntu resolute/universe s390x prodigal s390x 1:2.6.3-6 [663 kB] 84s Get:3 http://ftpmaster.internal/ubuntu resolute/universe s390x cat-bat s390x 5.3-2 [38.1 kB] 84s Fetched 2997 kB in 2s (1646 kB/s) 84s Selecting previously unselected package diamond-aligner. 85s (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 ... 56852 files and directories currently installed.) 85s Preparing to unpack .../diamond-aligner_2.1.11-2_s390x.deb ... 85s Unpacking diamond-aligner (2.1.11-2) ... 85s Selecting previously unselected package prodigal. 85s Preparing to unpack .../prodigal_1%3a2.6.3-6_s390x.deb ... 85s Unpacking prodigal (1:2.6.3-6) ... 85s Selecting previously unselected package cat-bat. 85s Preparing to unpack .../cat-bat_5.3-2_s390x.deb ... 85s Unpacking cat-bat (5.3-2) ... 85s Setting up prodigal (1:2.6.3-6) ... 85s Setting up diamond-aligner (2.1.11-2) ... 85s Setting up cat-bat (5.3-2) ... 85s Processing triggers for man-db (2.13.1-1) ... 86s autopkgtest [16:36:52]: test run-unit-test: [----------------------- 86s [2025-10-18 16:36:52] WARNING: At least 200GB of memory is recommended for large database construction (e.g. nr). 3.9GB is found on your system. You can try to find a machine with more memory if you run into issues or download preconstructed database files from tbb.bio.uu.nl/bastiaan/CAT_prepare/. 86s [2025-10-18 16:36:52] Taxonomy folder /tmp/autopkgtest.xJAsM1/autopkgtest_tmp/data/output_db/tax is created. 86s [2025-10-18 16:36:52] Copying nodes.dmp in taxonomy folder. 86s [2025-10-18 16:36:52] Copying names.dmp in taxonomy folder. 86s [2025-10-18 16:36:52] Database folder /tmp/autopkgtest.xJAsM1/autopkgtest_tmp/data/output_db/db is created. 86s [2025-10-18 16:36:52] Constructing DIAMOND database 2025-10-18_CAT.dmnd from ./prepare/small.fa using 2 cores. 86s [2025-10-18 16:36:52] DIAMOND database constructed. 86s [2025-10-18 16:36:52] Loading file ./prepare/nodes.dmp. 86s [2025-10-18 16:36:52] Loading file ./prepare/small.fa. 86s [2025-10-18 16:36:52] Loading file ./prepare/prot2acc.txt. 86s [2025-10-18 16:36:52] Finding LCA of all protein accession numbers in fasta headers. 86s [2025-10-18 16:36:52] Done! File /tmp/autopkgtest.xJAsM1/autopkgtest_tmp/data/output_db/db/2025-10-18_CAT.fastaid2LCAtaxid is created. 0 of 4 headers (0.0%) corrected. 0 headers (0.0%) do not have a taxid assigned. 86s [2025-10-18 16:36:52] Searching database for taxids with multiple offspring. 86s [2025-10-18 16:36:52] Writing /tmp/autopkgtest.xJAsM1/autopkgtest_tmp/data/output_db/db/2025-10-18_CAT.taxids_with_multiple_offspring. 86s 86s ----------------- 86s 86s [2025-10-18 16:36:52] CAT prepare is done! 86s 86s Supply the following arguments to CAT or BAT if you want to use this database: 86s -d / --database_folder /tmp/autopkgtest.xJAsM1/autopkgtest_tmp/data/output_db/db 86s -t / --taxonomy_folder /tmp/autopkgtest.xJAsM1/autopkgtest_tmp/data/output_db/tax 86s # CAT v5.3. 86s 86s CAT is running. Protein prediction, alignment, and contig classification are carried out. 86s Rarw! 86s 86s Supplied command: /usr/bin/CAT contigs -c ./prepare/small.fa -d ./output_db/db -t ./output_db/tax 86s 86s Contigs fasta: ./prepare/small.fa 86s Taxonomy folder: ./output_db/tax/ 86s Database folder: ./output_db/db/ 86s Parameter r: 10 86s Parameter f: 0.5 86s Log file: ./out.CAT.log 86s 86s ----------------- 86s 86s Doing some pre-flight checks first. 86s [2025-10-18 16:36:52] Prodigal found: Prodigal V2.6.3: February, 2016. 86s [2025-10-18 16:36:52] DIAMOND found: diamond version 2.1.11. 86s Ready to fly! 86s 86s ----------------- 86s 86s [2025-10-18 16:36:52] Importing contig names from ./prepare/small.fa. 86s [2025-10-18 16:36:52] Running Prodigal for ORF prediction. Files ./out.CAT.predicted_proteins.faa and ./out.CAT.predicted_proteins.gff will be generated. Do not forget to cite Prodigal when using CAT or BAT in your publication. 86s [2025-10-18 16:36:52] ORF prediction done! 86s [2025-10-18 16:36:52] Parsing ORF file ./out.CAT.predicted_proteins.faa 86s [2025-10-18 16:36:52] ORFs found on 2 / 4 contigs (50.00%). 86s [2025-10-18 16:36:52] WARNING: only 50.00% contigs found with ORF predictions. This may indicate that some contigs were missing from the protein prediction. Please make sure that the protein prediction was based on all contigs. 86s [2025-10-18 16:36:52] Homology search with DIAMOND is starting. Please be patient. Do not forget to cite DIAMOND when using CAT or BAT in your publication. 86s query: ./out.CAT.predicted_proteins.faa 86s database: ./output_db/db/2025-10-18_CAT.dmnd 86s mode: fast 86s top: 11 86s no-self-hits: False 86s number of cores: 2 86s block-size (billions of letters): 12.0 86s index-chunks: 1 86s tmpdir: ./ 86s compress: 0 86s [2025-10-18 16:36:52] Homology search done! File ./out.CAT.alignment.diamond created. 86s [2025-10-18 16:36:52] Parsing alignment file ./out.CAT.alignment.diamond. 86s [2025-10-18 16:36:52] Loading file ./output_db/tax/nodes.dmp. 86s [2025-10-18 16:36:52] Loading file ./output_db/db/2025-10-18_CAT.fastaid2LCAtaxid. 86s [2025-10-18 16:36:52] Loading file ./output_db/db/2025-10-18_CAT.taxids_with_multiple_offspring. 86s [2025-10-18 16:36:52] CAT is spinning! Files ./out.CAT.contig2classification.txt and ./out.CAT.ORF2LCA.txt are created. 86s 86s ----------------- 86s 86s [2025-10-18 16:36:52] CAT is done! 0/4 contigs (0.00%) have taxonomy assigned. 86s Final Classification Files Generated 86s # CAT v5.3. 86s 86s BAT is running. Protein prediction, alignment, and bin classification are carried out. 86s Rarw! 86s 86s Supplied command: /usr/bin/CAT bins -b prepare/small.fa -d output_db/db -t output_db/tax 86s 86s Bin fasta: ./prepare/small.fa 86s Taxonomy folder: ./output_db/tax/ 86s Database folder: ./output_db/db/ 86s Parameter r: 5 86s Parameter f: 0.3 86s Log file: ./out.BAT.log 86s 86s ----------------- 86s 86s Doing some pre-flight checks first. 86s [2025-10-18 16:36:52] Prodigal found: Prodigal V2.6.3: February, 2016. 86s [2025-10-18 16:36:52] DIAMOND found: diamond version 2.1.11. 86s Ready to fly! 86s 86s ----------------- 86s 86s [2025-10-18 16:36:52] Importing contig names from ./prepare/small.fa. 86s [2025-10-18 16:36:52] Writing ./out.BAT.concatenated.fasta. 86s [2025-10-18 16:36:52] Running Prodigal for ORF prediction. Files ./out.BAT.concatenated.predicted_proteins.faa and ./out.BAT.concatenated.predicted_proteins.gff will be generated. Do not forget to cite Prodigal when using CAT or BAT in your publication. 86s [2025-10-18 16:36:52] ORF prediction done! 86s [2025-10-18 16:36:52] Parsing ORF file ./out.BAT.concatenated.predicted_proteins.faa 86s [2025-10-18 16:36:52] ORFs found on 2 / 4 contigs (50.00%). 86s [2025-10-18 16:36:52] WARNING: only 50.00% contigs found with ORF predictions. This may indicate that some contigs were missing from the protein prediction. Please make sure that the protein prediction was based on all contigs. 86s [2025-10-18 16:36:52] Homology search with DIAMOND is starting. Please be patient. Do not forget to cite DIAMOND when using CAT or BAT in your publication. 86s query: ./out.BAT.concatenated.predicted_proteins.faa 86s database: ./output_db/db/2025-10-18_CAT.dmnd 86s mode: fast 86s top: 11 86s no-self-hits: False 86s number of cores: 2 86s block-size (billions of letters): 12.0 86s index-chunks: 1 86s tmpdir: ./ 86s compress: 0 86s [2025-10-18 16:36:52] Homology search done! File ./out.BAT.concatenated.alignment.diamond created. 86s [2025-10-18 16:36:52] Parsing alignment file ./out.BAT.concatenated.alignment.diamond. 86s [2025-10-18 16:36:52] Loading file ./output_db/tax/nodes.dmp. 86s [2025-10-18 16:36:52] Loading file ./output_db/db/2025-10-18_CAT.fastaid2LCAtaxid. 86s [2025-10-18 16:36:52] Loading file ./output_db/db/2025-10-18_CAT.taxids_with_multiple_offspring. 86s [2025-10-18 16:36:52] BAT is flying! Files ./out.BAT.bin2classification.txt and ./out.BAT.ORF2LCA.txt are created. 86s 86s ----------------- 86s 86s [2025-10-18 16:36:52] BAT is done! 0/1 bins (0.00%) have taxonomy assigned. 86s WARNING: since f is set to smaller than 0.5, one bin may have multiple classifications. 86s Final Classification Files Generated 87s autopkgtest [16:36:53]: test run-unit-test: -----------------------] 87s run-unit-test PASS 87s autopkgtest [16:36:53]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 88s autopkgtest [16:36:54]: @@@@@@@@@@@@@@@@@@@@ summary 88s run-unit-test PASS