0s autopkgtest [18:08:20]: starting date and time: 2025-10-18 18:08:20+0000 0s autopkgtest [18:08:20]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [18:08:20]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.9a1vzmts/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-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-s390x-15.secgroup --name adt-resolute-s390x-flye-20251018-180820-juju-7f2275-prod-proposed-migration-environment-15-850347ce-f159-4dee-a943-03e5e47596e6 --image adt/ubuntu-resolute-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-s390x -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-s390x-flye-20251018-180820-juju-7f2275-prod-proposed-migration-environment-15-850347ce-f159-4dee-a943-03e5e47596e6 from image adt/ubuntu-resolute-s390x-server-20251018.img (UUID c47ab411-f9be-46ce-b861-20d934d06dba)... 55s autopkgtest [18:09:15]: testbed dpkg architecture: s390x 55s autopkgtest [18:09:15]: testbed apt version: 3.1.6ubuntu2 55s autopkgtest [18:09:15]: @@@@@@@@@@@@@@@@@@@@ test bed setup 56s autopkgtest [18:09:16]: testbed release detected to be: None 56s autopkgtest [18:09:16]: updating testbed package index (apt update) 57s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 57s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 57s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 57s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 57s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 57s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [50.7 kB] 57s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [16.7 kB] 57s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [456 kB] 57s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x Packages [92.8 kB] 57s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted s390x Packages [940 B] 57s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x Packages [314 kB] 57s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse s390x Packages [4660 B] 58s Fetched 1023 kB in 1s (975 kB/s) 58s Reading package lists... 59s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 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 60s Reading package lists... 60s Reading package lists... 60s Building dependency tree... 60s Reading state information... 60s Calculating upgrade... 60s The following packages will be upgraded: 60s apt gir1.2-girepository-2.0 libapt-pkg7.0 libgirepository-1.0-1 60s libpython3-stdlib lto-disabled-list python3 python3-minimal 60s 8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 60s Need to get 2763 kB of archives. 60s After this operation, 14.3 kB of additional disk space will be used. 60s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3-minimal s390x 3.13.7-2 [27.8 kB] 60s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3 s390x 3.13.7-2 [23.9 kB] 60s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x libpython3-stdlib s390x 3.13.7-2 [10.6 kB] 60s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x libapt-pkg7.0 s390x 3.1.8ubuntu1 [1144 kB] 61s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x apt s390x 3.1.8ubuntu1 [1432 kB] 62s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x libgirepository-1.0-1 s390x 1.86.0-6 [86.9 kB] 62s Get:7 http://ftpmaster.internal/ubuntu resolute/main s390x gir1.2-girepository-2.0 s390x 1.86.0-6 [25.1 kB] 62s Get:8 http://ftpmaster.internal/ubuntu resolute/main s390x lto-disabled-list all 71 [12.5 kB] 62s dpkg-preconfigure: unable to re-open stdin: No such file or directory 62s Fetched 2763 kB in 2s (1313 kB/s) 63s (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.) 63s Preparing to unpack .../python3-minimal_3.13.7-2_s390x.deb ... 63s Unpacking python3-minimal (3.13.7-2) over (3.13.7-1) ... 63s Setting up python3-minimal (3.13.7-2) ... 63s (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.) 63s Preparing to unpack .../0-python3_3.13.7-2_s390x.deb ... 63s running python pre-rtupdate hooks for python3.13... 63s Unpacking python3 (3.13.7-2) over (3.13.7-1) ... 63s Preparing to unpack .../1-libpython3-stdlib_3.13.7-2_s390x.deb ... 63s Unpacking libpython3-stdlib:s390x (3.13.7-2) over (3.13.7-1) ... 63s Preparing to unpack .../2-libapt-pkg7.0_3.1.8ubuntu1_s390x.deb ... 63s Unpacking libapt-pkg7.0:s390x (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 63s Preparing to unpack .../3-apt_3.1.8ubuntu1_s390x.deb ... 63s Unpacking apt (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 63s Preparing to unpack .../4-libgirepository-1.0-1_1.86.0-6_s390x.deb ... 63s Unpacking libgirepository-1.0-1:s390x (1.86.0-6) over (1.84.0-1) ... 63s Preparing to unpack .../5-gir1.2-girepository-2.0_1.86.0-6_s390x.deb ... 63s Unpacking gir1.2-girepository-2.0:s390x (1.86.0-6) over (1.84.0-1) ... 63s Preparing to unpack .../6-lto-disabled-list_71_all.deb ... 63s Unpacking lto-disabled-list (71) over (69) ... 63s Setting up lto-disabled-list (71) ... 63s Setting up libgirepository-1.0-1:s390x (1.86.0-6) ... 63s Setting up libapt-pkg7.0:s390x (3.1.8ubuntu1) ... 63s Setting up libpython3-stdlib:s390x (3.13.7-2) ... 63s Setting up apt (3.1.8ubuntu1) ... 64s Setting up python3 (3.13.7-2) ... 64s running python rtupdate hooks for python3.13... 64s running python post-rtupdate hooks for python3.13... 64s Setting up gir1.2-girepository-2.0:s390x (1.86.0-6) ... 64s Processing triggers for man-db (2.13.1-1) ... 65s Processing triggers for libc-bin (2.42-0ubuntu3) ... 65s autopkgtest [18:09:25]: upgrading testbed (apt dist-upgrade and autopurge) 66s Reading package lists... 66s Building dependency tree... 66s Reading state information... 66s Calculating upgrade... 67s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 67s Reading package lists... 67s Building dependency tree... 67s Reading state information... 67s Solving dependencies... 67s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 67s autopkgtest [18:09:27]: rebooting testbed after setup commands that affected boot 81s autopkgtest [18:09:41]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP Mon Sep 22 08:56:47 UTC 2025 84s autopkgtest [18:09:44]: @@@@@@@@@@@@@@@@@@@@ apt-source flye 89s Get:1 http://ftpmaster.internal/ubuntu resolute/universe flye 2.9.5+dfsg-1 (dsc) [2222 B] 89s Get:2 http://ftpmaster.internal/ubuntu resolute/universe flye 2.9.5+dfsg-1 (tar) [22.8 MB] 89s Get:3 http://ftpmaster.internal/ubuntu resolute/universe flye 2.9.5+dfsg-1 (diff) [14.2 kB] 89s gpgv: Signature made Sat Aug 31 11:11:18 2024 UTC 89s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 89s gpgv: issuer "emollier@debian.org" 89s gpgv: Can't check signature: No public key 89s dpkg-source: warning: cannot verify inline signature for ./flye_2.9.5+dfsg-1.dsc: no acceptable signature found 90s autopkgtest [18:09:50]: testing package flye version 2.9.5+dfsg-1 90s autopkgtest [18:09:50]: build not needed 92s autopkgtest [18:09:52]: test run-unit-test: preparing testbed 92s Reading package lists... 92s Building dependency tree... 92s Reading state information... 92s Solving dependencies... 93s The following NEW packages will be installed: 93s flye libdeflate0 libhts3t64 libhtscodecs2 minimap2 python3-six samtools 93s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 93s Need to get 25.0 MB of archives. 93s After this operation, 41.0 MB of additional disk space will be used. 93s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x python3-six all 1.17.0-1 [13.2 kB] 93s Get:2 http://ftpmaster.internal/ubuntu resolute/universe s390x minimap2 s390x 2.27+dfsg-1build2 [402 kB] 93s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x libdeflate0 s390x 1.23-2 [46.0 kB] 93s Get:4 http://ftpmaster.internal/ubuntu resolute/universe s390x libhtscodecs2 s390x 1.6.1-2 [91.0 kB] 93s Get:5 http://ftpmaster.internal/ubuntu resolute/universe s390x libhts3t64 s390x 1.21+ds-1 [479 kB] 93s Get:6 http://ftpmaster.internal/ubuntu resolute/universe s390x samtools s390x 1.21-1 [633 kB] 93s Get:7 http://ftpmaster.internal/ubuntu resolute/universe s390x flye s390x 2.9.5+dfsg-1 [23.3 MB] 96s Fetched 25.0 MB in 3s (9139 kB/s) 96s Selecting previously unselected package python3-six. 96s (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.) 96s Preparing to unpack .../0-python3-six_1.17.0-1_all.deb ... 96s Unpacking python3-six (1.17.0-1) ... 96s Selecting previously unselected package minimap2. 96s Preparing to unpack .../1-minimap2_2.27+dfsg-1build2_s390x.deb ... 96s Unpacking minimap2 (2.27+dfsg-1build2) ... 96s Selecting previously unselected package libdeflate0:s390x. 96s Preparing to unpack .../2-libdeflate0_1.23-2_s390x.deb ... 96s Unpacking libdeflate0:s390x (1.23-2) ... 96s Selecting previously unselected package libhtscodecs2:s390x. 96s Preparing to unpack .../3-libhtscodecs2_1.6.1-2_s390x.deb ... 96s Unpacking libhtscodecs2:s390x (1.6.1-2) ... 96s Selecting previously unselected package libhts3t64:s390x. 96s Preparing to unpack .../4-libhts3t64_1.21+ds-1_s390x.deb ... 96s Unpacking libhts3t64:s390x (1.21+ds-1) ... 96s Selecting previously unselected package samtools. 96s Preparing to unpack .../5-samtools_1.21-1_s390x.deb ... 96s Unpacking samtools (1.21-1) ... 96s Selecting previously unselected package flye. 96s Preparing to unpack .../6-flye_2.9.5+dfsg-1_s390x.deb ... 96s Unpacking flye (2.9.5+dfsg-1) ... 96s Setting up libhtscodecs2:s390x (1.6.1-2) ... 96s Setting up minimap2 (2.27+dfsg-1build2) ... 96s Setting up libdeflate0:s390x (1.23-2) ... 96s Setting up python3-six (1.17.0-1) ... 96s Setting up libhts3t64:s390x (1.21+ds-1) ... 96s Setting up samtools (1.21-1) ... 96s Setting up flye (2.9.5+dfsg-1) ... 96s Processing triggers for man-db (2.13.1-1) ... 97s Processing triggers for libc-bin (2.42-0ubuntu3) ... 98s autopkgtest [18:09:58]: test run-unit-test: [----------------------- 98s usage: flye (--pacbio-raw | --pacbio-corr | --pacbio-hifi | --nano-raw | 98s --nano-corr | --nano-hq ) file1 [file_2 ...] 98s --out-dir PATH 98s 98s [--genome-size SIZE] [--threads int] [--iterations int] 98s [--meta] [--polish-target] [--min-overlap SIZE] 98s [--keep-haplotypes] [--debug] [--version] [--help] 98s [--scaffold] [--resume] [--resume-from] [--stop-after] 98s [--read-error float] [--extra-params] 98s [--deterministic] 98s 98s Assembly of long reads with repeat graphs 98s 98s options: 98s -h, --help show this help message and exit 98s --pacbio-raw path [path ...] 98s PacBio regular CLR reads (<20% error) 98s --pacbio-corr path [path ...] 98s PacBio reads that were corrected with other methods 98s (<3% error) 98s --pacbio-hifi path [path ...] 98s PacBio HiFi reads (<1% error) 98s --nano-raw path [path ...] 98s ONT regular reads, pre-Guppy5 (<20% error) 98s --nano-corr path [path ...] 98s ONT reads that were corrected with other methods (<3% 98s error) 98s --nano-hq path [path ...] 98s ONT high-quality reads: Guppy5+ SUP or Q20 (<5% error) 98s --subassemblies path [path ...] 98s [deprecated] high-quality contigs input 98s -g, --genome-size size 98s estimated genome size (for example, 5m or 2.6g) 98s -o, --out-dir path Output directory 98s -t, --threads int number of parallel threads [1] 98s -i, --iterations int number of polishing iterations [1] 98s -m, --min-overlap int 98s minimum overlap between reads [auto] 98s --asm-coverage int reduced coverage for initial disjointig assembly [not 98s set] 98s --hifi-error float [deprecated] same as --read-error 98s --read-error float adjust parameters for given read error rate (as 98s fraction e.g. 0.03) 98s --extra-params extra_params 98s extra configuration parameters list (comma-separated) 98s --plasmids unused (retained for backward compatibility) 98s --meta metagenome / uneven coverage mode 98s --keep-haplotypes do not collapse alternative haplotypes 98s --no-alt-contigs do not output contigs representing alternative 98s haplotypes 98s --scaffold enable scaffolding using graph [disabled by default] 98s --trestle [deprecated] enable Trestle [disabled by default] 98s --polish-target path run polisher on the target sequence 98s --resume resume from the last completed stage 98s --resume-from stage_name 98s resume from a custom stage 98s --stop-after stage_name 98s stop after the specified stage completed 98s --debug enable debug output 98s -v, --version show program's version number and exit 98s --deterministic perform disjointig assembly single-threaded 98s 98s Input reads can be in FASTA or FASTQ format, uncompressed 98s or compressed with gz. Currently, PacBio (CLR, HiFi, corrected) 98s and ONT reads (regular, HQ, corrected) are supported. Expected error rates are 98s <15% for PB CLR/regular ONT; <5% for ONT HQ, <3% for corrected, and <1% for HiFi. Note that Flye 98s was primarily developed to run on uncorrected reads. You may specify multiple 98s files with reads (separated by spaces). Mixing different read 98s types is not yet supported. The --meta option enables the mode 98s for metagenome/uneven coverage assembly. 98s 98s To reduce memory consumption for large genome assemblies, 98s you can use a subset of the longest reads for initial disjointig 98s assembly by specifying --asm-coverage and --genome-size options. Typically, 98s 40x coverage is enough to produce good disjointigs. 98s 98s You can run Flye polisher as a standalone tool using 98s --polish-target option. 98s Test is downloading large databases. Set "REALLYRUNTEST=yes" to run this test 98s autopkgtest [18:09:58]: test run-unit-test: -----------------------] 99s autopkgtest [18:09:59]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 99s run-unit-test PASS 99s autopkgtest [18:09:59]: @@@@@@@@@@@@@@@@@@@@ summary 99s run-unit-test PASS