0s autopkgtest [15:13:18]: starting date and time: 2025-10-18 15:13:18+0000 0s autopkgtest [15:13:18]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [15:13:18]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.wrq5gpk5/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-9.secgroup --name adt-resolute-arm64-cat-bat-20251018-151318-juju-7f2275-prod-proposed-migration-environment-2-f2e5cafb-7548-4b6d-9c15-61bae4fcbd9f --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-arm64-cat-bat-20251018-151318-juju-7f2275-prod-proposed-migration-environment-2-f2e5cafb-7548-4b6d-9c15-61bae4fcbd9f from image adt/ubuntu-resolute-arm64-server-20251018.img (UUID f7a49384-4e4d-4350-9a26-1f59236f89dd)... 57s autopkgtest [15:14:15]: testbed dpkg architecture: arm64 57s autopkgtest [15:14:15]: testbed apt version: 3.1.6ubuntu2 57s autopkgtest [15:14:15]: @@@@@@@@@@@@@@@@@@@@ test bed setup 57s autopkgtest [15:14:15]: testbed release detected to be: None 58s autopkgtest [15:14:16]: updating testbed package index (apt update) 59s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 59s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 59s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 59s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 59s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 59s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [15.4 kB] 59s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [345 kB] 59s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [28.4 kB] 59s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [81.1 kB] 59s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [43.8 kB] 59s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [223 kB] 59s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [5672 B] 59s Fetched 831 kB in 1s (895 kB/s) 60s Reading package lists... 61s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 61s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 61s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 61s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 62s Reading package lists... 62s Reading package lists... 62s Building dependency tree... 62s Reading state information... 63s Calculating upgrade... 63s The following packages will be upgraded: 63s apt flash-kernel gir1.2-girepository-2.0 libapt-pkg7.0 libgirepository-1.0-1 63s libpython3-stdlib lto-disabled-list python3 python3-minimal 63s 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 63s Need to get 2671 kB of archives. 63s After this operation, 66.6 kB of additional disk space will be used. 63s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-minimal arm64 3.13.7-2 [27.8 kB] 63s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3 arm64 3.13.7-2 [23.9 kB] 63s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libpython3-stdlib arm64 3.13.7-2 [10.6 kB] 63s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libapt-pkg7.0 arm64 3.1.8ubuntu1 [1055 kB] 64s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 apt arm64 3.1.8ubuntu1 [1373 kB] 64s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libgirepository-1.0-1 arm64 1.86.0-6 [84.5 kB] 64s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 gir1.2-girepository-2.0 arm64 1.86.0-6 [25.3 kB] 64s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 flash-kernel arm64 3.109ubuntu7 [58.8 kB] 64s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 lto-disabled-list all 71 [12.5 kB] 64s dpkg-preconfigure: unable to re-open stdin: No such file or directory 64s Fetched 2671 kB in 1s (2735 kB/s) 65s (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 ... 83359 files and directories currently installed.) 65s Preparing to unpack .../python3-minimal_3.13.7-2_arm64.deb ... 65s Unpacking python3-minimal (3.13.7-2) over (3.13.7-1) ... 65s Setting up python3-minimal (3.13.7-2) ... 65s (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 ... 83359 files and directories currently installed.) 65s Preparing to unpack .../0-python3_3.13.7-2_arm64.deb ... 65s running python pre-rtupdate hooks for python3.13... 65s Unpacking python3 (3.13.7-2) over (3.13.7-1) ... 65s Preparing to unpack .../1-libpython3-stdlib_3.13.7-2_arm64.deb ... 65s Unpacking libpython3-stdlib:arm64 (3.13.7-2) over (3.13.7-1) ... 65s Preparing to unpack .../2-libapt-pkg7.0_3.1.8ubuntu1_arm64.deb ... 65s Unpacking libapt-pkg7.0:arm64 (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 65s Preparing to unpack .../3-apt_3.1.8ubuntu1_arm64.deb ... 66s Unpacking apt (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 66s Preparing to unpack .../4-libgirepository-1.0-1_1.86.0-6_arm64.deb ... 66s Unpacking libgirepository-1.0-1:arm64 (1.86.0-6) over (1.84.0-1) ... 66s Preparing to unpack .../5-gir1.2-girepository-2.0_1.86.0-6_arm64.deb ... 66s Unpacking gir1.2-girepository-2.0:arm64 (1.86.0-6) over (1.84.0-1) ... 66s Preparing to unpack .../6-flash-kernel_3.109ubuntu7_arm64.deb ... 66s Unpacking flash-kernel (3.109ubuntu7) over (3.109ubuntu6) ... 66s Preparing to unpack .../7-lto-disabled-list_71_all.deb ... 66s Unpacking lto-disabled-list (71) over (69) ... 66s Setting up lto-disabled-list (71) ... 66s Setting up libgirepository-1.0-1:arm64 (1.86.0-6) ... 66s Setting up libapt-pkg7.0:arm64 (3.1.8ubuntu1) ... 66s Setting up libpython3-stdlib:arm64 (3.13.7-2) ... 66s Setting up apt (3.1.8ubuntu1) ... 67s Setting up python3 (3.13.7-2) ... 67s running python rtupdate hooks for python3.13... 67s running python post-rtupdate hooks for python3.13... 67s Setting up gir1.2-girepository-2.0:arm64 (1.86.0-6) ... 67s Setting up flash-kernel (3.109ubuntu7) ... 68s flash-kernel: deferring update (trigger activated) 68s Processing triggers for libc-bin (2.42-0ubuntu3) ... 68s Processing triggers for man-db (2.13.1-1) ... 69s Processing triggers for initramfs-tools (0.150ubuntu3) ... 69s update-initramfs: Generating /boot/initrd.img-6.17.0-5-generic 87s System running in EFI mode, skipping. 87s Processing triggers for flash-kernel (3.109ubuntu7) ... 87s System running in EFI mode, skipping. 87s autopkgtest [15:14:45]: upgrading testbed (apt dist-upgrade and autopurge) 88s Reading package lists... 89s Building dependency tree... 89s Reading state information... 89s Calculating upgrade... 89s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 89s Reading package lists... 90s Building dependency tree... 90s Reading state information... 90s Solving dependencies... 90s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 90s autopkgtest [15:14:48]: rebooting testbed after setup commands that affected boot 117s autopkgtest [15:15:15]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 09:50:31 UTC 2025 120s autopkgtest [15:15:18]: @@@@@@@@@@@@@@@@@@@@ apt-source cat-bat 122s Get:1 http://ftpmaster.internal/ubuntu resolute/universe cat-bat 5.3-2 (dsc) [2007 B] 122s Get:2 http://ftpmaster.internal/ubuntu resolute/universe cat-bat 5.3-2 (tar) [39.2 kB] 122s Get:3 http://ftpmaster.internal/ubuntu resolute/universe cat-bat 5.3-2 (diff) [5260 B] 122s gpgv: Signature made Thu Jan 11 10:25:13 2024 UTC 122s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 122s gpgv: issuer "tille@debian.org" 122s gpgv: Can't check signature: No public key 122s dpkg-source: warning: cannot verify inline signature for ./cat-bat_5.3-2.dsc: no acceptable signature found 122s autopkgtest [15:15:20]: testing package cat-bat version 5.3-2 122s autopkgtest [15:15:20]: build not needed 123s autopkgtest [15:15:21]: test run-unit-test: preparing testbed 123s Reading package lists... 123s Building dependency tree... 123s Reading state information... 123s Solving dependencies... 124s The following NEW packages will be installed: 124s cat-bat diamond-aligner prodigal 124s 0 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. 124s Need to get 2887 kB of archives. 124s After this operation, 19.2 MB of additional disk space will be used. 124s Get:1 http://ftpmaster.internal/ubuntu resolute/universe arm64 diamond-aligner arm64 2.1.11-2 [2027 kB] 125s Get:2 http://ftpmaster.internal/ubuntu resolute/universe arm64 prodigal arm64 1:2.6.3-6 [822 kB] 125s Get:3 http://ftpmaster.internal/ubuntu resolute/universe arm64 cat-bat arm64 5.3-2 [38.1 kB] 125s Fetched 2887 kB in 1s (2991 kB/s) 125s Selecting previously unselected package diamond-aligner. 125s (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 ... 83359 files and directories currently installed.) 125s Preparing to unpack .../diamond-aligner_2.1.11-2_arm64.deb ... 125s Unpacking diamond-aligner (2.1.11-2) ... 125s Selecting previously unselected package prodigal. 125s Preparing to unpack .../prodigal_1%3a2.6.3-6_arm64.deb ... 125s Unpacking prodigal (1:2.6.3-6) ... 125s Selecting previously unselected package cat-bat. 125s Preparing to unpack .../cat-bat_5.3-2_arm64.deb ... 125s Unpacking cat-bat (5.3-2) ... 125s Setting up prodigal (1:2.6.3-6) ... 125s Setting up diamond-aligner (2.1.11-2) ... 125s Setting up cat-bat (5.3-2) ... 126s Processing triggers for man-db (2.13.1-1) ... 127s autopkgtest [15:15:25]: test run-unit-test: [----------------------- 127s [2025-10-18 15:15:25] 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/. 127s [2025-10-18 15:15:25] Taxonomy folder /tmp/autopkgtest.X0qZZa/autopkgtest_tmp/data/output_db/tax is created. 127s [2025-10-18 15:15:25] Copying nodes.dmp in taxonomy folder. 127s [2025-10-18 15:15:25] Copying names.dmp in taxonomy folder. 127s [2025-10-18 15:15:25] Database folder /tmp/autopkgtest.X0qZZa/autopkgtest_tmp/data/output_db/db is created. 127s [2025-10-18 15:15:25] Constructing DIAMOND database 2025-10-18_CAT.dmnd from ./prepare/small.fa using 2 cores. 127s [2025-10-18 15:15:25] DIAMOND database constructed. 127s [2025-10-18 15:15:25] Loading file ./prepare/nodes.dmp. 127s [2025-10-18 15:15:25] Loading file ./prepare/small.fa. 127s [2025-10-18 15:15:25] Loading file ./prepare/prot2acc.txt. 127s [2025-10-18 15:15:25] Finding LCA of all protein accession numbers in fasta headers. 127s [2025-10-18 15:15:25] Done! File /tmp/autopkgtest.X0qZZa/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. 127s [2025-10-18 15:15:25] Searching database for taxids with multiple offspring. 127s [2025-10-18 15:15:25] Writing /tmp/autopkgtest.X0qZZa/autopkgtest_tmp/data/output_db/db/2025-10-18_CAT.taxids_with_multiple_offspring. 127s 127s ----------------- 127s 127s [2025-10-18 15:15:25] CAT prepare is done! 127s 127s Supply the following arguments to CAT or BAT if you want to use this database: 127s -d / --database_folder /tmp/autopkgtest.X0qZZa/autopkgtest_tmp/data/output_db/db 127s -t / --taxonomy_folder /tmp/autopkgtest.X0qZZa/autopkgtest_tmp/data/output_db/tax 128s # CAT v5.3. 128s 128s CAT is running. Protein prediction, alignment, and contig classification are carried out. 128s Rarw! 128s 128s Supplied command: /usr/bin/CAT contigs -c ./prepare/small.fa -d ./output_db/db -t ./output_db/tax 128s 128s Contigs fasta: ./prepare/small.fa 128s Taxonomy folder: ./output_db/tax/ 128s Database folder: ./output_db/db/ 128s Parameter r: 10 128s Parameter f: 0.5 128s Log file: ./out.CAT.log 128s 128s ----------------- 128s 128s Doing some pre-flight checks first. 128s [2025-10-18 15:15:26] Prodigal found: Prodigal V2.6.3: February, 2016. 128s [2025-10-18 15:15:26] DIAMOND found: diamond version 2.1.11. 128s Ready to fly! 128s 128s ----------------- 128s 128s [2025-10-18 15:15:26] Importing contig names from ./prepare/small.fa. 128s [2025-10-18 15:15:26] 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. 128s [2025-10-18 15:15:26] ORF prediction done! 128s [2025-10-18 15:15:26] Parsing ORF file ./out.CAT.predicted_proteins.faa 128s [2025-10-18 15:15:26] ORFs found on 2 / 4 contigs (50.00%). 128s [2025-10-18 15:15:26] 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. 128s [2025-10-18 15:15:26] Homology search with DIAMOND is starting. Please be patient. Do not forget to cite DIAMOND when using CAT or BAT in your publication. 128s query: ./out.CAT.predicted_proteins.faa 128s database: ./output_db/db/2025-10-18_CAT.dmnd 128s mode: fast 128s top: 11 128s no-self-hits: False 128s number of cores: 2 128s block-size (billions of letters): 12.0 128s index-chunks: 1 128s tmpdir: ./ 128s compress: 0 128s [2025-10-18 15:15:26] Homology search done! File ./out.CAT.alignment.diamond created. 128s [2025-10-18 15:15:26] Parsing alignment file ./out.CAT.alignment.diamond. 128s [2025-10-18 15:15:26] Loading file ./output_db/tax/nodes.dmp. 128s [2025-10-18 15:15:26] Loading file ./output_db/db/2025-10-18_CAT.fastaid2LCAtaxid. 128s [2025-10-18 15:15:26] Loading file ./output_db/db/2025-10-18_CAT.taxids_with_multiple_offspring. 128s [2025-10-18 15:15:26] CAT is spinning! Files ./out.CAT.contig2classification.txt and ./out.CAT.ORF2LCA.txt are created. 128s 128s ----------------- 128s 128s [2025-10-18 15:15:26] CAT is done! 0/4 contigs (0.00%) have taxonomy assigned. 128s Final Classification Files Generated 128s # CAT v5.3. 128s 128s BAT is running. Protein prediction, alignment, and bin classification are carried out. 128s Rarw! 128s 128s Supplied command: /usr/bin/CAT bins -b prepare/small.fa -d output_db/db -t output_db/tax 128s 128s Bin fasta: ./prepare/small.fa 128s Taxonomy folder: ./output_db/tax/ 128s Database folder: ./output_db/db/ 128s Parameter r: 5 128s Parameter f: 0.3 128s Log file: ./out.BAT.log 128s 128s ----------------- 128s 128s Doing some pre-flight checks first. 128s [2025-10-18 15:15:26] Prodigal found: Prodigal V2.6.3: February, 2016. 128s [2025-10-18 15:15:26] DIAMOND found: diamond version 2.1.11. 128s Ready to fly! 128s 128s ----------------- 128s 128s [2025-10-18 15:15:26] Importing contig names from ./prepare/small.fa. 128s [2025-10-18 15:15:26] Writing ./out.BAT.concatenated.fasta. 128s [2025-10-18 15:15:26] 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. 128s [2025-10-18 15:15:26] ORF prediction done! 128s [2025-10-18 15:15:26] Parsing ORF file ./out.BAT.concatenated.predicted_proteins.faa 128s [2025-10-18 15:15:26] ORFs found on 2 / 4 contigs (50.00%). 128s [2025-10-18 15:15:26] 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. 128s [2025-10-18 15:15:26] Homology search with DIAMOND is starting. Please be patient. Do not forget to cite DIAMOND when using CAT or BAT in your publication. 128s query: ./out.BAT.concatenated.predicted_proteins.faa 128s database: ./output_db/db/2025-10-18_CAT.dmnd 128s mode: fast 128s top: 11 128s no-self-hits: False 128s number of cores: 2 128s block-size (billions of letters): 12.0 128s index-chunks: 1 128s tmpdir: ./ 128s compress: 0 128s [2025-10-18 15:15:26] Homology search done! File ./out.BAT.concatenated.alignment.diamond created. 128s [2025-10-18 15:15:26] Parsing alignment file ./out.BAT.concatenated.alignment.diamond. 128s [2025-10-18 15:15:26] Loading file ./output_db/tax/nodes.dmp. 128s [2025-10-18 15:15:26] Loading file ./output_db/db/2025-10-18_CAT.fastaid2LCAtaxid. 128s [2025-10-18 15:15:26] Loading file ./output_db/db/2025-10-18_CAT.taxids_with_multiple_offspring. 128s [2025-10-18 15:15:26] BAT is flying! Files ./out.BAT.bin2classification.txt and ./out.BAT.ORF2LCA.txt are created. 128s 128s ----------------- 128s 128s [2025-10-18 15:15:26] BAT is done! 0/1 bins (0.00%) have taxonomy assigned. 128s WARNING: since f is set to smaller than 0.5, one bin may have multiple classifications. 128s Final Classification Files Generated 128s autopkgtest [15:15:26]: test run-unit-test: -----------------------] 129s autopkgtest [15:15:27]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 129s run-unit-test PASS 129s autopkgtest [15:15:27]: @@@@@@@@@@@@@@@@@@@@ summary 129s run-unit-test PASS