0s autopkgtest [16:01:52]: starting date and time: 2025-10-18 16:01:52+0000 0s autopkgtest [16:01:52]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [16:01:52]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.sbfmiuri/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-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-ppc64el-20.secgroup --name adt-resolute-ppc64el-cat-bat-20251018-160152-juju-7f2275-prod-proposed-migration-environment-2-4b0143e6-b9df-44ce-91f0-60a4fc8e7c05 --image adt/ubuntu-resolute-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-ppc64el -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-ppc64el-cat-bat-20251018-160152-juju-7f2275-prod-proposed-migration-environment-2-4b0143e6-b9df-44ce-91f0-60a4fc8e7c05 from image adt/ubuntu-resolute-ppc64el-server-20251018.img (UUID 746a0a80-14f1-4bf7-89b6-cbb5ab236a4e)... 64s autopkgtest [16:02:56]: testbed dpkg architecture: ppc64el 64s autopkgtest [16:02:56]: testbed apt version: 3.1.8ubuntu1 65s autopkgtest [16:02:57]: @@@@@@@@@@@@@@@@@@@@ test bed setup 65s autopkgtest [16:02:57]: testbed release detected to be: None 66s autopkgtest [16:02:58]: updating testbed package index (apt update) 66s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 66s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 66s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 66s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 66s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [345 kB] 67s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 67s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [28.4 kB] 67s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [15.4 kB] 67s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el Packages [73.4 kB] 67s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted ppc64el Packages [940 B] 67s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el Packages [222 kB] 67s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse ppc64el Packages [3808 B] 67s Fetched 777 kB in 1s (789 kB/s) 68s Reading package lists... 68s Failed to check for VM: Permission denied 69s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 69s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 69s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 69s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 70s Reading package lists... 70s Reading package lists... 70s Building dependency tree... 70s Reading state information... 70s Calculating upgrade... 70s The following packages will be upgraded: 70s gir1.2-girepository-2.0 libgirepository-1.0-1 libpython3-stdlib python3 70s python3-minimal 70s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 70s Need to get 185 kB of archives. 70s After this operation, 2048 B of additional disk space will be used. 70s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el python3-minimal ppc64el 3.13.7-2 [27.8 kB] 70s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el python3 ppc64el 3.13.7-2 [23.9 kB] 70s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el libpython3-stdlib ppc64el 3.13.7-2 [10.6 kB] 70s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgirepository-1.0-1 ppc64el 1.86.0-6 [97.4 kB] 70s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el gir1.2-girepository-2.0 ppc64el 1.86.0-6 [25.3 kB] 71s dpkg-preconfigure: unable to re-open stdin: No such file or directory 71s Fetched 185 kB in 0s (414 kB/s) 71s (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 ... 76461 files and directories currently installed.) 71s Preparing to unpack .../python3-minimal_3.13.7-2_ppc64el.deb ... 71s Unpacking python3-minimal (3.13.7-2) over (3.13.7-1) ... 71s Setting up python3-minimal (3.13.7-2) ... 71s (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 ... 76461 files and directories currently installed.) 71s Preparing to unpack .../python3_3.13.7-2_ppc64el.deb ... 71s running python pre-rtupdate hooks for python3.13... 71s Unpacking python3 (3.13.7-2) over (3.13.7-1) ... 71s Preparing to unpack .../libpython3-stdlib_3.13.7-2_ppc64el.deb ... 71s Unpacking libpython3-stdlib:ppc64el (3.13.7-2) over (3.13.7-1) ... 71s Preparing to unpack .../libgirepository-1.0-1_1.86.0-6_ppc64el.deb ... 71s Unpacking libgirepository-1.0-1:ppc64el (1.86.0-6) over (1.84.0-1) ... 71s Preparing to unpack .../gir1.2-girepository-2.0_1.86.0-6_ppc64el.deb ... 71s Unpacking gir1.2-girepository-2.0:ppc64el (1.86.0-6) over (1.84.0-1) ... 71s Setting up libgirepository-1.0-1:ppc64el (1.86.0-6) ... 71s Setting up libpython3-stdlib:ppc64el (3.13.7-2) ... 71s Setting up python3 (3.13.7-2) ... 71s running python rtupdate hooks for python3.13... 71s running python post-rtupdate hooks for python3.13... 72s Setting up gir1.2-girepository-2.0:ppc64el (1.86.0-6) ... 72s Processing triggers for man-db (2.13.1-1) ... 72s Processing triggers for libc-bin (2.42-0ubuntu3) ... 72s autopkgtest [16:03:04]: upgrading testbed (apt dist-upgrade and autopurge) 73s Reading package lists... 73s Building dependency tree... 73s Reading state information... 73s Calculating upgrade... 73s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 73s Reading package lists... 73s Building dependency tree... 73s Reading state information... 73s Solving dependencies... 73s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 76s autopkgtest [16:03:08]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 10:02:41 UTC 2025 76s autopkgtest [16:03:08]: @@@@@@@@@@@@@@@@@@@@ apt-source cat-bat 78s Get:1 http://ftpmaster.internal/ubuntu resolute/universe cat-bat 5.3-2 (dsc) [2007 B] 78s Get:2 http://ftpmaster.internal/ubuntu resolute/universe cat-bat 5.3-2 (tar) [39.2 kB] 78s Get:3 http://ftpmaster.internal/ubuntu resolute/universe cat-bat 5.3-2 (diff) [5260 B] 78s gpgv: Signature made Thu Jan 11 10:25:13 2024 UTC 78s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 78s gpgv: issuer "tille@debian.org" 78s gpgv: Can't check signature: No public key 78s dpkg-source: warning: cannot verify inline signature for ./cat-bat_5.3-2.dsc: no acceptable signature found 78s autopkgtest [16:03:10]: testing package cat-bat version 5.3-2 78s autopkgtest [16:03:10]: build not needed 79s autopkgtest [16:03:11]: test run-unit-test: preparing testbed 79s Reading package lists... 79s Building dependency tree... 79s Reading state information... 79s Solving dependencies... 79s The following NEW packages will be installed: 79s cat-bat diamond-aligner prodigal 79s 0 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. 79s Need to get 3330 kB of archives. 79s After this operation, 18.8 MB of additional disk space will be used. 79s Get:1 http://ftpmaster.internal/ubuntu resolute/universe ppc64el diamond-aligner ppc64el 2.1.11-2 [1978 kB] 80s Get:2 http://ftpmaster.internal/ubuntu resolute/universe ppc64el prodigal ppc64el 1:2.6.3-6 [1314 kB] 81s Get:3 http://ftpmaster.internal/ubuntu resolute/universe ppc64el cat-bat ppc64el 5.3-2 [38.1 kB] 81s Fetched 3330 kB in 2s (2165 kB/s) 81s Selecting previously unselected package diamond-aligner. 81s (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 ... 76461 files and directories currently installed.) 81s Preparing to unpack .../diamond-aligner_2.1.11-2_ppc64el.deb ... 81s Unpacking diamond-aligner (2.1.11-2) ... 81s Selecting previously unselected package prodigal. 81s Preparing to unpack .../prodigal_1%3a2.6.3-6_ppc64el.deb ... 81s Unpacking prodigal (1:2.6.3-6) ... 81s Selecting previously unselected package cat-bat. 81s Preparing to unpack .../cat-bat_5.3-2_ppc64el.deb ... 81s Unpacking cat-bat (5.3-2) ... 81s Setting up prodigal (1:2.6.3-6) ... 81s Setting up diamond-aligner (2.1.11-2) ... 81s Setting up cat-bat (5.3-2) ... 81s Processing triggers for man-db (2.13.1-1) ... 82s autopkgtest [16:03:14]: test run-unit-test: [----------------------- 83s [2025-10-18 16:03:14] 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/. 83s [2025-10-18 16:03:14] Taxonomy folder /tmp/autopkgtest.3f7kNx/autopkgtest_tmp/data/output_db/tax is created. 83s [2025-10-18 16:03:14] Copying nodes.dmp in taxonomy folder. 83s [2025-10-18 16:03:14] Copying names.dmp in taxonomy folder. 83s [2025-10-18 16:03:14] Database folder /tmp/autopkgtest.3f7kNx/autopkgtest_tmp/data/output_db/db is created. 83s [2025-10-18 16:03:14] Constructing DIAMOND database 2025-10-18_CAT.dmnd from ./prepare/small.fa using 2 cores. 83s [2025-10-18 16:03:14] DIAMOND database constructed. 83s [2025-10-18 16:03:14] Loading file ./prepare/nodes.dmp. 83s [2025-10-18 16:03:14] Loading file ./prepare/small.fa. 83s [2025-10-18 16:03:14] Loading file ./prepare/prot2acc.txt. 83s [2025-10-18 16:03:14] Finding LCA of all protein accession numbers in fasta headers. 83s [2025-10-18 16:03:14] Done! File /tmp/autopkgtest.3f7kNx/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. 83s [2025-10-18 16:03:14] Searching database for taxids with multiple offspring. 83s [2025-10-18 16:03:14] Writing /tmp/autopkgtest.3f7kNx/autopkgtest_tmp/data/output_db/db/2025-10-18_CAT.taxids_with_multiple_offspring. 83s 83s ----------------- 83s 83s [2025-10-18 16:03:14] CAT prepare is done! 83s 83s Supply the following arguments to CAT or BAT if you want to use this database: 83s -d / --database_folder /tmp/autopkgtest.3f7kNx/autopkgtest_tmp/data/output_db/db 83s -t / --taxonomy_folder /tmp/autopkgtest.3f7kNx/autopkgtest_tmp/data/output_db/tax 83s # CAT v5.3. 83s 83s CAT is running. Protein prediction, alignment, and contig classification are carried out. 83s Rarw! 83s 83s Supplied command: /usr/bin/CAT contigs -c ./prepare/small.fa -d ./output_db/db -t ./output_db/tax 83s 83s Contigs fasta: ./prepare/small.fa 83s Taxonomy folder: ./output_db/tax/ 83s Database folder: ./output_db/db/ 83s Parameter r: 10 83s Parameter f: 0.5 83s Log file: ./out.CAT.log 83s 83s ----------------- 83s 83s Doing some pre-flight checks first. 83s [2025-10-18 16:03:15] Prodigal found: Prodigal V2.6.3: February, 2016. 83s [2025-10-18 16:03:15] DIAMOND found: diamond version 2.1.11. 83s Ready to fly! 83s 83s ----------------- 83s 83s [2025-10-18 16:03:15] Importing contig names from ./prepare/small.fa. 83s [2025-10-18 16:03:15] 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. 83s [2025-10-18 16:03:15] ORF prediction done! 83s [2025-10-18 16:03:15] Parsing ORF file ./out.CAT.predicted_proteins.faa 83s [2025-10-18 16:03:15] ORFs found on 2 / 4 contigs (50.00%). 83s [2025-10-18 16:03:15] 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. 83s [2025-10-18 16:03:15] Homology search with DIAMOND is starting. Please be patient. Do not forget to cite DIAMOND when using CAT or BAT in your publication. 83s query: ./out.CAT.predicted_proteins.faa 83s database: ./output_db/db/2025-10-18_CAT.dmnd 83s mode: fast 83s top: 11 83s no-self-hits: False 83s number of cores: 2 83s block-size (billions of letters): 12.0 83s index-chunks: 1 83s tmpdir: ./ 83s compress: 0 83s [2025-10-18 16:03:15] Homology search done! File ./out.CAT.alignment.diamond created. 83s [2025-10-18 16:03:15] Parsing alignment file ./out.CAT.alignment.diamond. 83s [2025-10-18 16:03:15] Loading file ./output_db/tax/nodes.dmp. 83s [2025-10-18 16:03:15] Loading file ./output_db/db/2025-10-18_CAT.fastaid2LCAtaxid. 83s [2025-10-18 16:03:15] Loading file ./output_db/db/2025-10-18_CAT.taxids_with_multiple_offspring. 83s [2025-10-18 16:03:15] CAT is spinning! Files ./out.CAT.contig2classification.txt and ./out.CAT.ORF2LCA.txt are created. 83s 83s ----------------- 83s 83s [2025-10-18 16:03:15] CAT is done! 0/4 contigs (0.00%) have taxonomy assigned. 83s Final Classification Files Generated 83s # CAT v5.3. 83s 83s BAT is running. Protein prediction, alignment, and bin classification are carried out. 83s Rarw! 83s 83s Supplied command: /usr/bin/CAT bins -b prepare/small.fa -d output_db/db -t output_db/tax 83s 83s Bin fasta: ./prepare/small.fa 83s Taxonomy folder: ./output_db/tax/ 83s Database folder: ./output_db/db/ 83s Parameter r: 5 83s Parameter f: 0.3 83s Log file: ./out.BAT.log 83s 83s ----------------- 83s 83s Doing some pre-flight checks first. 83s [2025-10-18 16:03:15] Prodigal found: Prodigal V2.6.3: February, 2016. 83s [2025-10-18 16:03:15] DIAMOND found: diamond version 2.1.11. 83s Ready to fly! 83s 83s ----------------- 83s 83s [2025-10-18 16:03:15] Importing contig names from ./prepare/small.fa. 83s [2025-10-18 16:03:15] Writing ./out.BAT.concatenated.fasta. 83s [2025-10-18 16:03:15] 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. 83s [2025-10-18 16:03:15] ORF prediction done! 83s [2025-10-18 16:03:15] Parsing ORF file ./out.BAT.concatenated.predicted_proteins.faa 83s [2025-10-18 16:03:15] ORFs found on 2 / 4 contigs (50.00%). 83s [2025-10-18 16:03:15] 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. 83s [2025-10-18 16:03:15] Homology search with DIAMOND is starting. Please be patient. Do not forget to cite DIAMOND when using CAT or BAT in your publication. 83s query: ./out.BAT.concatenated.predicted_proteins.faa 83s database: ./output_db/db/2025-10-18_CAT.dmnd 83s mode: fast 83s top: 11 83s no-self-hits: False 83s number of cores: 2 83s block-size (billions of letters): 12.0 83s index-chunks: 1 83s tmpdir: ./ 83s compress: 0 83s [2025-10-18 16:03:15] Homology search done! File ./out.BAT.concatenated.alignment.diamond created. 83s [2025-10-18 16:03:15] Parsing alignment file ./out.BAT.concatenated.alignment.diamond. 83s [2025-10-18 16:03:15] Loading file ./output_db/tax/nodes.dmp. 83s [2025-10-18 16:03:15] Loading file ./output_db/db/2025-10-18_CAT.fastaid2LCAtaxid. 83s [2025-10-18 16:03:15] Loading file ./output_db/db/2025-10-18_CAT.taxids_with_multiple_offspring. 83s [2025-10-18 16:03:15] BAT is flying! Files ./out.BAT.bin2classification.txt and ./out.BAT.ORF2LCA.txt are created. 83s 83s ----------------- 83s 83s [2025-10-18 16:03:15] BAT is done! 0/1 bins (0.00%) have taxonomy assigned. 83s WARNING: since f is set to smaller than 0.5, one bin may have multiple classifications. 83s Final Classification Files Generated 83s autopkgtest [16:03:15]: test run-unit-test: -----------------------] 83s run-unit-test PASS 83s autopkgtest [16:03:15]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 84s autopkgtest [16:03:16]: @@@@@@@@@@@@@@@@@@@@ summary 84s run-unit-test PASS