0s autopkgtest [18:53:13]: starting date and time: 2025-10-18 18:53:13+0000 0s autopkgtest [18:53:13]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [18:53:13]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.zqofx6ji/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade flye --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-20@bos03-ppc64el-3.secgroup --name adt-resolute-ppc64el-flye-20251018-185313-juju-7f2275-prod-proposed-migration-environment-20-5fa15bf2-f515-420a-8001-e9b12b032a0c --image adt/ubuntu-resolute-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-ppc64el -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-ppc64el-flye-20251018-185313-juju-7f2275-prod-proposed-migration-environment-20-5fa15bf2-f515-420a-8001-e9b12b032a0c from image adt/ubuntu-resolute-ppc64el-server-20251018.img (UUID 746a0a80-14f1-4bf7-89b6-cbb5ab236a4e)... 50s autopkgtest [18:54:03]: testbed dpkg architecture: ppc64el 50s autopkgtest [18:54:03]: testbed apt version: 3.1.8ubuntu1 51s autopkgtest [18:54:04]: @@@@@@@@@@@@@@@@@@@@ test bed setup 51s autopkgtest [18:54:04]: testbed release detected to be: None 52s autopkgtest [18:54:05]: updating testbed package index (apt update) 52s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 52s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 52s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 52s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 53s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [50.7 kB] 53s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [456 kB] 53s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [16.7 kB] 53s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 53s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el Packages [92.0 kB] 53s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted ppc64el Packages [940 B] 53s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el Packages [317 kB] 53s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse ppc64el Packages [4660 B] 53s Fetched 1026 kB in 1s (896 kB/s) 54s Reading package lists... 54s Failed to check for VM: Permission denied 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 gir1.2-girepository-2.0 libgirepository-1.0-1 libpython3-stdlib python3 56s python3-minimal 56s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 56s Need to get 185 kB of archives. 56s After this operation, 2048 B of additional disk space will be used. 56s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el python3-minimal ppc64el 3.13.7-2 [27.8 kB] 56s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el python3 ppc64el 3.13.7-2 [23.9 kB] 56s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el libpython3-stdlib ppc64el 3.13.7-2 [10.6 kB] 56s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgirepository-1.0-1 ppc64el 1.86.0-6 [97.4 kB] 56s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el gir1.2-girepository-2.0 ppc64el 1.86.0-6 [25.3 kB] 57s dpkg-preconfigure: unable to re-open stdin: No such file or directory 57s Fetched 185 kB in 0s (390 kB/s) 57s (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.) 57s Preparing to unpack .../python3-minimal_3.13.7-2_ppc64el.deb ... 57s Unpacking python3-minimal (3.13.7-2) over (3.13.7-1) ... 57s Setting up python3-minimal (3.13.7-2) ... 57s (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.) 57s Preparing to unpack .../python3_3.13.7-2_ppc64el.deb ... 57s running python pre-rtupdate hooks for python3.13... 57s Unpacking python3 (3.13.7-2) over (3.13.7-1) ... 57s Preparing to unpack .../libpython3-stdlib_3.13.7-2_ppc64el.deb ... 57s Unpacking libpython3-stdlib:ppc64el (3.13.7-2) over (3.13.7-1) ... 57s Preparing to unpack .../libgirepository-1.0-1_1.86.0-6_ppc64el.deb ... 57s Unpacking libgirepository-1.0-1:ppc64el (1.86.0-6) over (1.84.0-1) ... 57s Preparing to unpack .../gir1.2-girepository-2.0_1.86.0-6_ppc64el.deb ... 57s Unpacking gir1.2-girepository-2.0:ppc64el (1.86.0-6) over (1.84.0-1) ... 57s Setting up libgirepository-1.0-1:ppc64el (1.86.0-6) ... 57s Setting up libpython3-stdlib:ppc64el (3.13.7-2) ... 57s Setting up python3 (3.13.7-2) ... 57s running python rtupdate hooks for python3.13... 57s running python post-rtupdate hooks for python3.13... 58s Setting up gir1.2-girepository-2.0:ppc64el (1.86.0-6) ... 58s Processing triggers for man-db (2.13.1-1) ... 58s Processing triggers for libc-bin (2.42-0ubuntu3) ... 58s autopkgtest [18:54:11]: upgrading testbed (apt dist-upgrade and autopurge) 59s Reading package lists... 59s Building dependency tree... 59s Reading state information... 59s Calculating upgrade... 59s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 59s Reading package lists... 59s Building dependency tree... 59s Reading state information... 59s Solving dependencies... 59s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 62s autopkgtest [18:54:15]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 10:02:41 UTC 2025 62s autopkgtest [18:54:15]: @@@@@@@@@@@@@@@@@@@@ apt-source flye 67s Get:1 http://ftpmaster.internal/ubuntu resolute/universe flye 2.9.5+dfsg-1 (dsc) [2222 B] 67s Get:2 http://ftpmaster.internal/ubuntu resolute/universe flye 2.9.5+dfsg-1 (tar) [22.8 MB] 67s Get:3 http://ftpmaster.internal/ubuntu resolute/universe flye 2.9.5+dfsg-1 (diff) [14.2 kB] 67s gpgv: Signature made Sat Aug 31 11:11:18 2024 UTC 67s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 67s gpgv: issuer "emollier@debian.org" 67s gpgv: Can't check signature: No public key 67s dpkg-source: warning: cannot verify inline signature for ./flye_2.9.5+dfsg-1.dsc: no acceptable signature found 67s autopkgtest [18:54:20]: testing package flye version 2.9.5+dfsg-1 68s autopkgtest [18:54:21]: build not needed 73s autopkgtest [18:54:26]: test run-unit-test: preparing testbed 73s Reading package lists... 74s Building dependency tree... 74s Reading state information... 74s Solving dependencies... 74s The following NEW packages will be installed: 74s flye libdeflate0 libhts3t64 libhtscodecs2 minimap2 python3-six samtools 74s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 74s Need to get 25.1 MB of archives. 74s After this operation, 42.2 MB of additional disk space will be used. 74s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-six all 1.17.0-1 [13.2 kB] 74s Get:2 http://ftpmaster.internal/ubuntu resolute/universe ppc64el minimap2 ppc64el 2.27+dfsg-1build2 [399 kB] 74s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdeflate0 ppc64el 1.23-2 [63.3 kB] 74s Get:4 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhtscodecs2 ppc64el 1.6.1-2 [113 kB] 74s Get:5 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhts3t64 ppc64el 1.21+ds-1 [585 kB] 75s Get:6 http://ftpmaster.internal/ubuntu resolute/universe ppc64el samtools ppc64el 1.21-1 [690 kB] 75s Get:7 http://ftpmaster.internal/ubuntu resolute/universe ppc64el flye ppc64el 2.9.5+dfsg-1 [23.3 MB] 79s Fetched 25.1 MB in 5s (5387 kB/s) 79s Selecting previously unselected package python3-six. 79s (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.) 79s Preparing to unpack .../0-python3-six_1.17.0-1_all.deb ... 79s Unpacking python3-six (1.17.0-1) ... 79s Selecting previously unselected package minimap2. 79s Preparing to unpack .../1-minimap2_2.27+dfsg-1build2_ppc64el.deb ... 79s Unpacking minimap2 (2.27+dfsg-1build2) ... 79s Selecting previously unselected package libdeflate0:ppc64el. 79s Preparing to unpack .../2-libdeflate0_1.23-2_ppc64el.deb ... 79s Unpacking libdeflate0:ppc64el (1.23-2) ... 79s Selecting previously unselected package libhtscodecs2:ppc64el. 79s Preparing to unpack .../3-libhtscodecs2_1.6.1-2_ppc64el.deb ... 79s Unpacking libhtscodecs2:ppc64el (1.6.1-2) ... 79s Selecting previously unselected package libhts3t64:ppc64el. 79s Preparing to unpack .../4-libhts3t64_1.21+ds-1_ppc64el.deb ... 79s Unpacking libhts3t64:ppc64el (1.21+ds-1) ... 79s Selecting previously unselected package samtools. 79s Preparing to unpack .../5-samtools_1.21-1_ppc64el.deb ... 79s Unpacking samtools (1.21-1) ... 79s Selecting previously unselected package flye. 79s Preparing to unpack .../6-flye_2.9.5+dfsg-1_ppc64el.deb ... 79s Unpacking flye (2.9.5+dfsg-1) ... 79s Setting up libhtscodecs2:ppc64el (1.6.1-2) ... 79s Setting up minimap2 (2.27+dfsg-1build2) ... 79s Setting up libdeflate0:ppc64el (1.23-2) ... 79s Setting up python3-six (1.17.0-1) ... 79s Setting up libhts3t64:ppc64el (1.21+ds-1) ... 79s Setting up samtools (1.21-1) ... 79s Setting up flye (2.9.5+dfsg-1) ... 79s Processing triggers for man-db (2.13.1-1) ... 80s Processing triggers for libc-bin (2.42-0ubuntu3) ... 81s autopkgtest [18:54:34]: test run-unit-test: [----------------------- 81s usage: flye (--pacbio-raw | --pacbio-corr | --pacbio-hifi | --nano-raw | 81s --nano-corr | --nano-hq ) file1 [file_2 ...] 81s --out-dir PATH 81s 81s [--genome-size SIZE] [--threads int] [--iterations int] 81s [--meta] [--polish-target] [--min-overlap SIZE] 81s [--keep-haplotypes] [--debug] [--version] [--help] 81s [--scaffold] [--resume] [--resume-from] [--stop-after] 81s [--read-error float] [--extra-params] 81s [--deterministic] 81s 81s Assembly of long reads with repeat graphs 81s 81s options: 81s -h, --help show this help message and exit 81s --pacbio-raw path [path ...] 81s PacBio regular CLR reads (<20% error) 81s --pacbio-corr path [path ...] 81s PacBio reads that were corrected with other methods 81s (<3% error) 81s --pacbio-hifi path [path ...] 81s PacBio HiFi reads (<1% error) 81s --nano-raw path [path ...] 81s ONT regular reads, pre-Guppy5 (<20% error) 81s --nano-corr path [path ...] 81s ONT reads that were corrected with other methods (<3% 81s error) 81s --nano-hq path [path ...] 81s ONT high-quality reads: Guppy5+ SUP or Q20 (<5% error) 81s --subassemblies path [path ...] 81s [deprecated] high-quality contigs input 81s -g, --genome-size size 81s estimated genome size (for example, 5m or 2.6g) 81s -o, --out-dir path Output directory 81s -t, --threads int number of parallel threads [1] 81s -i, --iterations int number of polishing iterations [1] 81s -m, --min-overlap int 81s minimum overlap between reads [auto] 81s --asm-coverage int reduced coverage for initial disjointig assembly [not 81s set] 81s --hifi-error float [deprecated] same as --read-error 81s --read-error float adjust parameters for given read error rate (as 81s fraction e.g. 0.03) 81s --extra-params extra_params 81s extra configuration parameters list (comma-separated) 81s --plasmids unused (retained for backward compatibility) 81s --meta metagenome / uneven coverage mode 81s --keep-haplotypes do not collapse alternative haplotypes 81s --no-alt-contigs do not output contigs representing alternative 81s haplotypes 81s --scaffold enable scaffolding using graph [disabled by default] 81s --trestle [deprecated] enable Trestle [disabled by default] 81s --polish-target path run polisher on the target sequence 81s --resume resume from the last completed stage 81s --resume-from stage_name 81s resume from a custom stage 81s --stop-after stage_name 81s stop after the specified stage completed 81s --debug enable debug output 81s -v, --version show program's version number and exit 81s --deterministic perform disjointig assembly single-threaded 81s 81s Input reads can be in FASTA or FASTQ format, uncompressed 81s or compressed with gz. Currently, PacBio (CLR, HiFi, corrected) 81s and ONT reads (regular, HQ, corrected) are supported. Expected error rates are 81s <15% for PB CLR/regular ONT; <5% for ONT HQ, <3% for corrected, and <1% for HiFi. Note that Flye 81s was primarily developed to run on uncorrected reads. You may specify multiple 81s files with reads (separated by spaces). Mixing different read 81s types is not yet supported. The --meta option enables the mode 81s for metagenome/uneven coverage assembly. 81s 81s To reduce memory consumption for large genome assemblies, 81s you can use a subset of the longest reads for initial disjointig 81s assembly by specifying --asm-coverage and --genome-size options. Typically, 81s 40x coverage is enough to produce good disjointigs. 81s 81s You can run Flye polisher as a standalone tool using 81s --polish-target option. 81s Test is downloading large databases. Set "REALLYRUNTEST=yes" to run this test 81s autopkgtest [18:54:34]: test run-unit-test: -----------------------] 82s autopkgtest [18:54:35]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 82s run-unit-test PASS 82s autopkgtest [18:54:35]: @@@@@@@@@@@@@@@@@@@@ summary 82s run-unit-test PASS