0s autopkgtest [16:31:22]: starting date and time: 2025-10-18 16:31:22+0000 0s autopkgtest [16:31:22]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [16:31:22]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ttpe_gid/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-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-6.secgroup --name adt-resolute-amd64-cat-bat-20251018-163122-juju-7f2275-prod-proposed-migration-environment-2-8b508d28-c1f3-4367-bcf1-ae79283a9f8c --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-amd64-cat-bat-20251018-163122-juju-7f2275-prod-proposed-migration-environment-2-8b508d28-c1f3-4367-bcf1-ae79283a9f8c from image adt/ubuntu-resolute-amd64-server-20251018.img (UUID dd697a48-b6cc-4a02-84bf-0f9f2fad5f89)... 27s autopkgtest [16:31:49]: testbed dpkg architecture: amd64 27s autopkgtest [16:31:49]: testbed apt version: 3.1.6ubuntu2 27s autopkgtest [16:31:49]: @@@@@@@@@@@@@@@@@@@@ test bed setup 27s autopkgtest [16:31:49]: testbed release detected to be: None 28s autopkgtest [16:31:50]: updating testbed package index (apt update) 28s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 28s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 28s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 28s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 28s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 28s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [345 kB] 28s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [28.4 kB] 28s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [15.4 kB] 28s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [46.6 kB] 28s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [85.2 kB] 28s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3208 B] 29s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [28.0 kB] 29s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [233 kB] 29s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [87.6 kB] 29s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [8376 B] 29s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [2772 B] 29s Fetched 972 kB in 1s (1460 kB/s) 29s Reading package lists... 30s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 30s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 30s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 30s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 30s Reading package lists... 30s Reading package lists... 31s Building dependency tree... 31s Reading state information... 31s Calculating upgrade... 31s The following packages will be upgraded: 31s apt gir1.2-girepository-2.0 libapt-pkg7.0 libgirepository-1.0-1 31s libpython3-stdlib python3 python3-minimal 31s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 31s Need to get 2751 kB of archives. 31s After this operation, 2048 B of additional disk space will be used. 31s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-minimal amd64 3.13.7-2 [27.8 kB] 31s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3 amd64 3.13.7-2 [23.9 kB] 31s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libpython3-stdlib amd64 3.13.7-2 [10.6 kB] 31s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 libapt-pkg7.0 amd64 3.1.8ubuntu1 [1140 kB] 31s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 apt amd64 3.1.8ubuntu1 [1438 kB] 31s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libgirepository-1.0-1 amd64 1.86.0-6 [85.9 kB] 31s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-girepository-2.0 amd64 1.86.0-6 [25.3 kB] 31s dpkg-preconfigure: unable to re-open stdin: No such file or directory 31s Fetched 2751 kB in 0s (11.8 MB/s) 31s (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 ... 78439 files and directories currently installed.) 31s Preparing to unpack .../python3-minimal_3.13.7-2_amd64.deb ... 31s Unpacking python3-minimal (3.13.7-2) over (3.13.7-1) ... 31s Setting up python3-minimal (3.13.7-2) ... 31s (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 ... 78439 files and directories currently installed.) 31s Preparing to unpack .../0-python3_3.13.7-2_amd64.deb ... 31s running python pre-rtupdate hooks for python3.13... 31s Unpacking python3 (3.13.7-2) over (3.13.7-1) ... 31s Preparing to unpack .../1-libpython3-stdlib_3.13.7-2_amd64.deb ... 31s Unpacking libpython3-stdlib:amd64 (3.13.7-2) over (3.13.7-1) ... 31s Preparing to unpack .../2-libapt-pkg7.0_3.1.8ubuntu1_amd64.deb ... 31s Unpacking libapt-pkg7.0:amd64 (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 32s Preparing to unpack .../3-apt_3.1.8ubuntu1_amd64.deb ... 32s Unpacking apt (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 32s Preparing to unpack .../4-libgirepository-1.0-1_1.86.0-6_amd64.deb ... 32s Unpacking libgirepository-1.0-1:amd64 (1.86.0-6) over (1.84.0-1) ... 32s Preparing to unpack .../5-gir1.2-girepository-2.0_1.86.0-6_amd64.deb ... 32s Unpacking gir1.2-girepository-2.0:amd64 (1.86.0-6) over (1.84.0-1) ... 32s Setting up libgirepository-1.0-1:amd64 (1.86.0-6) ... 32s Setting up libapt-pkg7.0:amd64 (3.1.8ubuntu1) ... 32s Setting up libpython3-stdlib:amd64 (3.13.7-2) ... 32s Setting up apt (3.1.8ubuntu1) ... 32s Setting up python3 (3.13.7-2) ... 32s running python rtupdate hooks for python3.13... 32s running python post-rtupdate hooks for python3.13... 32s Setting up gir1.2-girepository-2.0:amd64 (1.86.0-6) ... 32s Processing triggers for man-db (2.13.1-1) ... 33s Processing triggers for libc-bin (2.42-0ubuntu3) ... 33s autopkgtest [16:31:55]: upgrading testbed (apt dist-upgrade and autopurge) 34s Reading package lists... 34s Building dependency tree... 34s Reading state information... 34s Calculating upgrade... 34s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 34s Reading package lists... 34s Building dependency tree... 34s Reading state information... 34s Solving dependencies... 34s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 35s autopkgtest [16:31:57]: rebooting testbed after setup commands that affected boot 49s autopkgtest [16:32:11]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 10:00:33 UTC 2025 51s autopkgtest [16:32:13]: @@@@@@@@@@@@@@@@@@@@ apt-source cat-bat 52s Get:1 http://ftpmaster.internal/ubuntu resolute/universe cat-bat 5.3-2 (dsc) [2007 B] 52s Get:2 http://ftpmaster.internal/ubuntu resolute/universe cat-bat 5.3-2 (tar) [39.2 kB] 52s Get:3 http://ftpmaster.internal/ubuntu resolute/universe cat-bat 5.3-2 (diff) [5260 B] 52s gpgv: Signature made Thu Jan 11 10:25:13 2024 UTC 52s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 52s gpgv: issuer "tille@debian.org" 52s gpgv: Can't check signature: No public key 52s dpkg-source: warning: cannot verify inline signature for ./cat-bat_5.3-2.dsc: no acceptable signature found 52s autopkgtest [16:32:14]: testing package cat-bat version 5.3-2 53s autopkgtest [16:32:15]: build not needed 53s autopkgtest [16:32:15]: test run-unit-test: preparing testbed 53s Reading package lists... 53s Building dependency tree... 53s Reading state information... 53s Solving dependencies... 53s The following NEW packages will be installed: 53s cat-bat diamond-aligner prodigal 53s 0 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. 53s Need to get 3253 kB of archives. 53s After this operation, 21.9 MB of additional disk space will be used. 53s Get:1 http://ftpmaster.internal/ubuntu resolute/universe amd64 diamond-aligner amd64 2.1.11-2 [2572 kB] 54s Get:2 http://ftpmaster.internal/ubuntu resolute/universe amd64 prodigal amd64 1:2.6.3-6 [643 kB] 54s Get:3 http://ftpmaster.internal/ubuntu resolute/universe amd64 cat-bat amd64 5.3-2 [38.1 kB] 54s Fetched 3253 kB in 1s (3264 kB/s) 54s Selecting previously unselected package diamond-aligner. 55s (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 ... 78439 files and directories currently installed.) 55s Preparing to unpack .../diamond-aligner_2.1.11-2_amd64.deb ... 55s Unpacking diamond-aligner (2.1.11-2) ... 55s Selecting previously unselected package prodigal. 55s Preparing to unpack .../prodigal_1%3a2.6.3-6_amd64.deb ... 55s Unpacking prodigal (1:2.6.3-6) ... 55s Selecting previously unselected package cat-bat. 55s Preparing to unpack .../cat-bat_5.3-2_amd64.deb ... 55s Unpacking cat-bat (5.3-2) ... 55s Setting up prodigal (1:2.6.3-6) ... 55s Setting up diamond-aligner (2.1.11-2) ... 55s Setting up cat-bat (5.3-2) ... 55s Processing triggers for man-db (2.13.1-1) ... 56s autopkgtest [16:32:18]: test run-unit-test: [----------------------- 56s [2025-10-18 16:32:17] WARNING: At least 200GB of memory is recommended for large database construction (e.g. nr). 3.8GB 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/. 56s [2025-10-18 16:32:17] Taxonomy folder /tmp/autopkgtest.1aVy5a/autopkgtest_tmp/data/output_db/tax is created. 56s [2025-10-18 16:32:17] Copying nodes.dmp in taxonomy folder. 56s [2025-10-18 16:32:17] Copying names.dmp in taxonomy folder. 56s [2025-10-18 16:32:17] Database folder /tmp/autopkgtest.1aVy5a/autopkgtest_tmp/data/output_db/db is created. 56s [2025-10-18 16:32:17] Constructing DIAMOND database 2025-10-18_CAT.dmnd from ./prepare/small.fa using 2 cores. 56s [2025-10-18 16:32:17] DIAMOND database constructed. 56s [2025-10-18 16:32:17] Loading file ./prepare/nodes.dmp. 56s [2025-10-18 16:32:17] Loading file ./prepare/small.fa. 56s [2025-10-18 16:32:17] Loading file ./prepare/prot2acc.txt. 56s [2025-10-18 16:32:17] Finding LCA of all protein accession numbers in fasta headers. 56s [2025-10-18 16:32:17] Done! File /tmp/autopkgtest.1aVy5a/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. 56s [2025-10-18 16:32:17] Searching database for taxids with multiple offspring. 56s [2025-10-18 16:32:17] Writing /tmp/autopkgtest.1aVy5a/autopkgtest_tmp/data/output_db/db/2025-10-18_CAT.taxids_with_multiple_offspring. 56s 56s ----------------- 56s 56s [2025-10-18 16:32:17] CAT prepare is done! 56s 56s Supply the following arguments to CAT or BAT if you want to use this database: 56s -d / --database_folder /tmp/autopkgtest.1aVy5a/autopkgtest_tmp/data/output_db/db 56s -t / --taxonomy_folder /tmp/autopkgtest.1aVy5a/autopkgtest_tmp/data/output_db/tax 56s # CAT v5.3. 56s 56s CAT is running. Protein prediction, alignment, and contig classification are carried out. 56s Rarw! 56s 56s Supplied command: /usr/bin/CAT contigs -c ./prepare/small.fa -d ./output_db/db -t ./output_db/tax 56s 56s Contigs fasta: ./prepare/small.fa 56s Taxonomy folder: ./output_db/tax/ 56s Database folder: ./output_db/db/ 56s Parameter r: 10 56s Parameter f: 0.5 56s Log file: ./out.CAT.log 56s 56s ----------------- 56s 56s Doing some pre-flight checks first. 56s [2025-10-18 16:32:17] Prodigal found: Prodigal V2.6.3: February, 2016. 56s [2025-10-18 16:32:17] DIAMOND found: diamond version 2.1.11. 56s Ready to fly! 56s 56s ----------------- 56s 56s [2025-10-18 16:32:17] Importing contig names from ./prepare/small.fa. 56s [2025-10-18 16:32:17] 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. 56s [2025-10-18 16:32:17] ORF prediction done! 56s [2025-10-18 16:32:17] Parsing ORF file ./out.CAT.predicted_proteins.faa 56s [2025-10-18 16:32:17] ORFs found on 2 / 4 contigs (50.00%). 56s [2025-10-18 16:32:17] 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. 56s [2025-10-18 16:32:17] Homology search with DIAMOND is starting. Please be patient. Do not forget to cite DIAMOND when using CAT or BAT in your publication. 56s query: ./out.CAT.predicted_proteins.faa 56s database: ./output_db/db/2025-10-18_CAT.dmnd 56s mode: fast 56s top: 11 56s no-self-hits: False 56s number of cores: 2 56s block-size (billions of letters): 12.0 56s index-chunks: 1 56s tmpdir: ./ 56s compress: 0 56s [2025-10-18 16:32:17] Homology search done! File ./out.CAT.alignment.diamond created. 56s [2025-10-18 16:32:17] Parsing alignment file ./out.CAT.alignment.diamond. 56s [2025-10-18 16:32:17] Loading file ./output_db/tax/nodes.dmp. 56s [2025-10-18 16:32:17] Loading file ./output_db/db/2025-10-18_CAT.fastaid2LCAtaxid. 56s [2025-10-18 16:32:17] Loading file ./output_db/db/2025-10-18_CAT.taxids_with_multiple_offspring. 56s [2025-10-18 16:32:17] CAT is spinning! Files ./out.CAT.contig2classification.txt and ./out.CAT.ORF2LCA.txt are created. 56s 56s ----------------- 56s 56s [2025-10-18 16:32:17] CAT is done! 0/4 contigs (0.00%) have taxonomy assigned. 56s Final Classification Files Generated 56s # CAT v5.3. 56s 56s BAT is running. Protein prediction, alignment, and bin classification are carried out. 56s Rarw! 56s 56s Supplied command: /usr/bin/CAT bins -b prepare/small.fa -d output_db/db -t output_db/tax 56s 56s Bin fasta: ./prepare/small.fa 56s Taxonomy folder: ./output_db/tax/ 56s Database folder: ./output_db/db/ 56s Parameter r: 5 56s Parameter f: 0.3 56s Log file: ./out.BAT.log 56s 56s ----------------- 56s 56s Doing some pre-flight checks first. 56s [2025-10-18 16:32:17] Prodigal found: Prodigal V2.6.3: February, 2016. 56s [2025-10-18 16:32:17] DIAMOND found: diamond version 2.1.11. 56s Ready to fly! 56s 56s ----------------- 56s 56s [2025-10-18 16:32:17] Importing contig names from ./prepare/small.fa. 56s [2025-10-18 16:32:17] Writing ./out.BAT.concatenated.fasta. 56s [2025-10-18 16:32:17] 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. 56s [2025-10-18 16:32:17] ORF prediction done! 56s [2025-10-18 16:32:17] Parsing ORF file ./out.BAT.concatenated.predicted_proteins.faa 56s [2025-10-18 16:32:17] ORFs found on 2 / 4 contigs (50.00%). 56s [2025-10-18 16:32:17] 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. 56s [2025-10-18 16:32:17] Homology search with DIAMOND is starting. Please be patient. Do not forget to cite DIAMOND when using CAT or BAT in your publication. 56s query: ./out.BAT.concatenated.predicted_proteins.faa 56s database: ./output_db/db/2025-10-18_CAT.dmnd 56s mode: fast 56s top: 11 56s no-self-hits: False 56s number of cores: 2 56s block-size (billions of letters): 12.0 56s index-chunks: 1 56s tmpdir: ./ 56s compress: 0 56s [2025-10-18 16:32:17] Homology search done! File ./out.BAT.concatenated.alignment.diamond created. 56s [2025-10-18 16:32:17] Parsing alignment file ./out.BAT.concatenated.alignment.diamond. 56s [2025-10-18 16:32:17] Loading file ./output_db/tax/nodes.dmp. 56s [2025-10-18 16:32:17] Loading file ./output_db/db/2025-10-18_CAT.fastaid2LCAtaxid. 56s [2025-10-18 16:32:17] Loading file ./output_db/db/2025-10-18_CAT.taxids_with_multiple_offspring. 56s [2025-10-18 16:32:17] BAT is flying! Files ./out.BAT.bin2classification.txt and ./out.BAT.ORF2LCA.txt are created. 56s 56s ----------------- 56s 56s [2025-10-18 16:32:17] BAT is done! 0/1 bins (0.00%) have taxonomy assigned. 56s WARNING: since f is set to smaller than 0.5, one bin may have multiple classifications. 56s Final Classification Files Generated 56s autopkgtest [16:32:18]: test run-unit-test: -----------------------] 57s run-unit-test PASS 57s autopkgtest [16:32:19]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 57s autopkgtest [16:32:19]: @@@@@@@@@@@@@@@@@@@@ summary 57s run-unit-test PASS