0s autopkgtest [21:44:02]: starting date and time: 2025-10-18 21:44:02+0000 0s autopkgtest [21:44:02]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [21:44:02]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.d6as_m75/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-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-10.secgroup --name adt-resolute-amd64-flye-20251018-214402-juju-7f2275-prod-proposed-migration-environment-2-28d6c952-ca88-4427-8f8f-60748f84ed88 --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/ 4s Creating nova instance adt-resolute-amd64-flye-20251018-214402-juju-7f2275-prod-proposed-migration-environment-2-28d6c952-ca88-4427-8f8f-60748f84ed88 from image adt/ubuntu-resolute-amd64-server-20251018.img (UUID dd697a48-b6cc-4a02-84bf-0f9f2fad5f89)... 28s autopkgtest [21:44:30]: testbed dpkg architecture: amd64 28s autopkgtest [21:44:30]: testbed apt version: 3.1.6ubuntu2 28s autopkgtest [21:44:30]: @@@@@@@@@@@@@@@@@@@@ test bed setup 28s autopkgtest [21:44:30]: testbed release detected to be: None 29s autopkgtest [21:44:31]: updating testbed package index (apt update) 29s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 29s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 29s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 29s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 29s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [431 kB] 29s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 29s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [54.3 kB] 29s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [18.2 kB] 29s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [108 kB] 29s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [65.5 kB] 30s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [28.0 kB] 30s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3208 B] 30s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [125 kB] 30s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [319 kB] 30s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [3088 B] 30s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [9188 B] 30s Fetched 1253 kB in 1s (2193 kB/s) 30s Reading package lists... 31s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 31s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 31s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 31s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 31s Reading package lists... 31s Reading package lists... 31s Building dependency tree... 31s Reading state information... 32s Calculating upgrade... 32s The following packages will be upgraded: 32s apt gir1.2-girepository-2.0 libapt-pkg7.0 libgirepository-1.0-1 32s libpython3-stdlib python3 python3-minimal 32s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 32s Need to get 2751 kB of archives. 32s After this operation, 2048 B of additional disk space will be used. 32s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-minimal amd64 3.13.7-2 [27.8 kB] 32s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3 amd64 3.13.7-2 [23.9 kB] 32s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libpython3-stdlib amd64 3.13.7-2 [10.6 kB] 32s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 libapt-pkg7.0 amd64 3.1.8ubuntu1 [1140 kB] 32s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 apt amd64 3.1.8ubuntu1 [1438 kB] 32s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libgirepository-1.0-1 amd64 1.86.0-6 [85.9 kB] 32s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-girepository-2.0 amd64 1.86.0-6 [25.3 kB] 32s dpkg-preconfigure: unable to re-open stdin: No such file or directory 32s Fetched 2751 kB in 0s (8308 kB/s) 32s (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.) 32s Preparing to unpack .../python3-minimal_3.13.7-2_amd64.deb ... 32s Unpacking python3-minimal (3.13.7-2) over (3.13.7-1) ... 32s Setting up python3-minimal (3.13.7-2) ... 32s (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.) 32s Preparing to unpack .../0-python3_3.13.7-2_amd64.deb ... 33s running python pre-rtupdate hooks for python3.13... 33s Unpacking python3 (3.13.7-2) over (3.13.7-1) ... 33s Preparing to unpack .../1-libpython3-stdlib_3.13.7-2_amd64.deb ... 33s Unpacking libpython3-stdlib:amd64 (3.13.7-2) over (3.13.7-1) ... 33s Preparing to unpack .../2-libapt-pkg7.0_3.1.8ubuntu1_amd64.deb ... 33s Unpacking libapt-pkg7.0:amd64 (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 33s Preparing to unpack .../3-apt_3.1.8ubuntu1_amd64.deb ... 33s Unpacking apt (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 33s Preparing to unpack .../4-libgirepository-1.0-1_1.86.0-6_amd64.deb ... 33s Unpacking libgirepository-1.0-1:amd64 (1.86.0-6) over (1.84.0-1) ... 33s Preparing to unpack .../5-gir1.2-girepository-2.0_1.86.0-6_amd64.deb ... 33s Unpacking gir1.2-girepository-2.0:amd64 (1.86.0-6) over (1.84.0-1) ... 33s Setting up libgirepository-1.0-1:amd64 (1.86.0-6) ... 33s Setting up libapt-pkg7.0:amd64 (3.1.8ubuntu1) ... 33s Setting up libpython3-stdlib:amd64 (3.13.7-2) ... 33s Setting up apt (3.1.8ubuntu1) ... 33s Setting up python3 (3.13.7-2) ... 33s running python rtupdate hooks for python3.13... 33s running python post-rtupdate hooks for python3.13... 33s Setting up gir1.2-girepository-2.0:amd64 (1.86.0-6) ... 33s Processing triggers for man-db (2.13.1-1) ... 34s Processing triggers for libc-bin (2.42-0ubuntu3) ... 34s autopkgtest [21:44:36]: upgrading testbed (apt dist-upgrade and autopurge) 35s Reading package lists... 35s Building dependency tree... 35s Reading state information... 35s Calculating upgrade... 35s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 35s Reading package lists... 35s Building dependency tree... 35s Reading state information... 35s Solving dependencies... 36s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 36s autopkgtest [21:44:38]: rebooting testbed after setup commands that affected boot 50s autopkgtest [21:44:52]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 10:00:33 UTC 2025 52s autopkgtest [21:44:54]: @@@@@@@@@@@@@@@@@@@@ apt-source flye 54s Get:1 http://ftpmaster.internal/ubuntu resolute/universe flye 2.9.5+dfsg-1 (dsc) [2222 B] 54s Get:2 http://ftpmaster.internal/ubuntu resolute/universe flye 2.9.5+dfsg-1 (tar) [22.8 MB] 54s Get:3 http://ftpmaster.internal/ubuntu resolute/universe flye 2.9.5+dfsg-1 (diff) [14.2 kB] 54s gpgv: Signature made Sat Aug 31 11:11:18 2024 UTC 54s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 54s gpgv: issuer "emollier@debian.org" 54s gpgv: Can't check signature: No public key 54s dpkg-source: warning: cannot verify inline signature for ./flye_2.9.5+dfsg-1.dsc: no acceptable signature found 54s autopkgtest [21:44:56]: testing package flye version 2.9.5+dfsg-1 54s autopkgtest [21:44:56]: build not needed 56s autopkgtest [21:44:58]: test run-unit-test: preparing testbed 56s Reading package lists... 56s Building dependency tree... 56s Reading state information... 56s Solving dependencies... 57s The following NEW packages will be installed: 57s flye libdeflate0 libhts3t64 libhtscodecs2 minimap2 python3-six samtools 57s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 57s Need to get 25.0 MB of archives. 57s After this operation, 41.1 MB of additional disk space will be used. 57s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-six all 1.17.0-1 [13.2 kB] 57s Get:2 http://ftpmaster.internal/ubuntu resolute/universe amd64 minimap2 amd64 2.27+dfsg-1build2 [389 kB] 57s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 57s Get:4 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhtscodecs2 amd64 1.6.1-2 [132 kB] 57s Get:5 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhts3t64 amd64 1.21+ds-1 [514 kB] 57s Get:6 http://ftpmaster.internal/ubuntu resolute/universe amd64 samtools amd64 1.21-1 [655 kB] 57s Get:7 http://ftpmaster.internal/ubuntu resolute/universe amd64 flye amd64 2.9.5+dfsg-1 [23.2 MB] 59s Fetched 25.0 MB in 2s (10.8 MB/s) 59s Selecting previously unselected package python3-six. 59s (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.) 59s Preparing to unpack .../0-python3-six_1.17.0-1_all.deb ... 59s Unpacking python3-six (1.17.0-1) ... 59s Selecting previously unselected package minimap2. 59s Preparing to unpack .../1-minimap2_2.27+dfsg-1build2_amd64.deb ... 59s Unpacking minimap2 (2.27+dfsg-1build2) ... 59s Selecting previously unselected package libdeflate0:amd64. 59s Preparing to unpack .../2-libdeflate0_1.23-2_amd64.deb ... 59s Unpacking libdeflate0:amd64 (1.23-2) ... 59s Selecting previously unselected package libhtscodecs2:amd64. 59s Preparing to unpack .../3-libhtscodecs2_1.6.1-2_amd64.deb ... 59s Unpacking libhtscodecs2:amd64 (1.6.1-2) ... 59s Selecting previously unselected package libhts3t64:amd64. 59s Preparing to unpack .../4-libhts3t64_1.21+ds-1_amd64.deb ... 59s Unpacking libhts3t64:amd64 (1.21+ds-1) ... 59s Selecting previously unselected package samtools. 59s Preparing to unpack .../5-samtools_1.21-1_amd64.deb ... 59s Unpacking samtools (1.21-1) ... 59s Selecting previously unselected package flye. 59s Preparing to unpack .../6-flye_2.9.5+dfsg-1_amd64.deb ... 59s Unpacking flye (2.9.5+dfsg-1) ... 59s Setting up libhtscodecs2:amd64 (1.6.1-2) ... 59s Setting up minimap2 (2.27+dfsg-1build2) ... 59s Setting up libdeflate0:amd64 (1.23-2) ... 59s Setting up python3-six (1.17.0-1) ... 59s Setting up libhts3t64:amd64 (1.21+ds-1) ... 59s Setting up samtools (1.21-1) ... 59s Setting up flye (2.9.5+dfsg-1) ... 59s Processing triggers for man-db (2.13.1-1) ... 60s Processing triggers for libc-bin (2.42-0ubuntu3) ... 61s autopkgtest [21:45:03]: test run-unit-test: [----------------------- 61s usage: flye (--pacbio-raw | --pacbio-corr | --pacbio-hifi | --nano-raw | 61s --nano-corr | --nano-hq ) file1 [file_2 ...] 61s --out-dir PATH 61s 61s [--genome-size SIZE] [--threads int] [--iterations int] 61s [--meta] [--polish-target] [--min-overlap SIZE] 61s [--keep-haplotypes] [--debug] [--version] [--help] 61s [--scaffold] [--resume] [--resume-from] [--stop-after] 61s [--read-error float] [--extra-params] 61s [--deterministic] 61s 61s Assembly of long reads with repeat graphs 61s 61s options: 61s -h, --help show this help message and exit 61s --pacbio-raw path [path ...] 61s PacBio regular CLR reads (<20% error) 61s --pacbio-corr path [path ...] 61s PacBio reads that were corrected with other methods 61s (<3% error) 61s --pacbio-hifi path [path ...] 61s PacBio HiFi reads (<1% error) 61s --nano-raw path [path ...] 61s ONT regular reads, pre-Guppy5 (<20% error) 61s --nano-corr path [path ...] 61s ONT reads that were corrected with other methods (<3% 61s error) 61s --nano-hq path [path ...] 61s ONT high-quality reads: Guppy5+ SUP or Q20 (<5% error) 61s --subassemblies path [path ...] 61s [deprecated] high-quality contigs input 61s -g, --genome-size size 61s estimated genome size (for example, 5m or 2.6g) 61s -o, --out-dir path Output directory 61s -t, --threads int number of parallel threads [1] 61s -i, --iterations int number of polishing iterations [1] 61s -m, --min-overlap int 61s minimum overlap between reads [auto] 61s --asm-coverage int reduced coverage for initial disjointig assembly [not 61s set] 61s --hifi-error float [deprecated] same as --read-error 61s --read-error float adjust parameters for given read error rate (as 61s fraction e.g. 0.03) 61s --extra-params extra_params 61s extra configuration parameters list (comma-separated) 61s --plasmids unused (retained for backward compatibility) 61s --meta metagenome / uneven coverage mode 61s --keep-haplotypes do not collapse alternative haplotypes 61s --no-alt-contigs do not output contigs representing alternative 61s haplotypes 61s --scaffold enable scaffolding using graph [disabled by default] 61s --trestle [deprecated] enable Trestle [disabled by default] 61s --polish-target path run polisher on the target sequence 61s --resume resume from the last completed stage 61s --resume-from stage_name 61s resume from a custom stage 61s --stop-after stage_name 61s stop after the specified stage completed 61s --debug enable debug output 61s -v, --version show program's version number and exit 61s --deterministic perform disjointig assembly single-threaded 61s 61s Input reads can be in FASTA or FASTQ format, uncompressed 61s or compressed with gz. Currently, PacBio (CLR, HiFi, corrected) 61s and ONT reads (regular, HQ, corrected) are supported. Expected error rates are 61s <15% for PB CLR/regular ONT; <5% for ONT HQ, <3% for corrected, and <1% for HiFi. Note that Flye 61s was primarily developed to run on uncorrected reads. You may specify multiple 61s files with reads (separated by spaces). Mixing different read 61s types is not yet supported. The --meta option enables the mode 61s for metagenome/uneven coverage assembly. 61s 61s To reduce memory consumption for large genome assemblies, 61s you can use a subset of the longest reads for initial disjointig 61s assembly by specifying --asm-coverage and --genome-size options. Typically, 61s 40x coverage is enough to produce good disjointigs. 61s 61s You can run Flye polisher as a standalone tool using 61s --polish-target option. 61s Test is downloading large databases. Set "REALLYRUNTEST=yes" to run this test 61s autopkgtest [21:45:03]: test run-unit-test: -----------------------] 62s run-unit-test PASS 62s autopkgtest [21:45:04]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 62s autopkgtest [21:45:04]: @@@@@@@@@@@@@@@@@@@@ summary 62s run-unit-test PASS