0s autopkgtest [16:38:10]: starting date and time: 2025-10-18 16:38:10+0000 0s autopkgtest [16:38:10]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [16:38:10]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.pxik0mv3/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-14.secgroup --name adt-resolute-arm64-flye-20251018-163810-juju-7f2275-prod-proposed-migration-environment-20-34780f99-353c-4de8-aba3-9f4d4945358b --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-arm64-flye-20251018-163810-juju-7f2275-prod-proposed-migration-environment-20-34780f99-353c-4de8-aba3-9f4d4945358b from image adt/ubuntu-resolute-arm64-server-20251018.img (UUID f7a49384-4e4d-4350-9a26-1f59236f89dd)... 68s autopkgtest [16:39:18]: testbed dpkg architecture: arm64 68s autopkgtest [16:39:18]: testbed apt version: 3.1.6ubuntu2 68s autopkgtest [16:39:18]: @@@@@@@@@@@@@@@@@@@@ test bed setup 69s autopkgtest [16:39:19]: testbed release detected to be: None 69s autopkgtest [16:39:19]: updating testbed package index (apt update) 70s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 70s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 70s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 70s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 70s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [15.4 kB] 70s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 70s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [345 kB] 70s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [28.4 kB] 70s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [81.1 kB] 70s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [43.8 kB] 71s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [223 kB] 71s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [5672 B] 71s Fetched 831 kB in 1s (769 kB/s) 71s Reading package lists... 72s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 72s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 72s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 72s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 73s Reading package lists... 73s Reading package lists... 74s Building dependency tree... 74s Reading state information... 74s Calculating upgrade... 74s The following packages will be upgraded: 74s apt flash-kernel gir1.2-girepository-2.0 libapt-pkg7.0 libgirepository-1.0-1 74s libpython3-stdlib lto-disabled-list python3 python3-minimal 74s 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 74s Need to get 2671 kB of archives. 74s After this operation, 66.6 kB of additional disk space will be used. 74s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-minimal arm64 3.13.7-2 [27.8 kB] 75s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3 arm64 3.13.7-2 [23.9 kB] 75s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libpython3-stdlib arm64 3.13.7-2 [10.6 kB] 75s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libapt-pkg7.0 arm64 3.1.8ubuntu1 [1055 kB] 75s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 apt arm64 3.1.8ubuntu1 [1373 kB] 75s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libgirepository-1.0-1 arm64 1.86.0-6 [84.5 kB] 75s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 gir1.2-girepository-2.0 arm64 1.86.0-6 [25.3 kB] 75s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 flash-kernel arm64 3.109ubuntu7 [58.8 kB] 75s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 lto-disabled-list all 71 [12.5 kB] 76s dpkg-preconfigure: unable to re-open stdin: No such file or directory 76s Fetched 2671 kB in 1s (2517 kB/s) 76s (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.) 76s Preparing to unpack .../python3-minimal_3.13.7-2_arm64.deb ... 76s Unpacking python3-minimal (3.13.7-2) over (3.13.7-1) ... 76s Setting up python3-minimal (3.13.7-2) ... 76s (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.) 76s Preparing to unpack .../0-python3_3.13.7-2_arm64.deb ... 76s running python pre-rtupdate hooks for python3.13... 76s Unpacking python3 (3.13.7-2) over (3.13.7-1) ... 76s Preparing to unpack .../1-libpython3-stdlib_3.13.7-2_arm64.deb ... 76s Unpacking libpython3-stdlib:arm64 (3.13.7-2) over (3.13.7-1) ... 77s Preparing to unpack .../2-libapt-pkg7.0_3.1.8ubuntu1_arm64.deb ... 77s Unpacking libapt-pkg7.0:arm64 (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 77s Preparing to unpack .../3-apt_3.1.8ubuntu1_arm64.deb ... 77s Unpacking apt (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 77s Preparing to unpack .../4-libgirepository-1.0-1_1.86.0-6_arm64.deb ... 77s Unpacking libgirepository-1.0-1:arm64 (1.86.0-6) over (1.84.0-1) ... 77s Preparing to unpack .../5-gir1.2-girepository-2.0_1.86.0-6_arm64.deb ... 77s Unpacking gir1.2-girepository-2.0:arm64 (1.86.0-6) over (1.84.0-1) ... 77s Preparing to unpack .../6-flash-kernel_3.109ubuntu7_arm64.deb ... 77s Unpacking flash-kernel (3.109ubuntu7) over (3.109ubuntu6) ... 77s Preparing to unpack .../7-lto-disabled-list_71_all.deb ... 77s Unpacking lto-disabled-list (71) over (69) ... 77s Setting up lto-disabled-list (71) ... 77s Setting up libgirepository-1.0-1:arm64 (1.86.0-6) ... 77s Setting up libapt-pkg7.0:arm64 (3.1.8ubuntu1) ... 77s Setting up libpython3-stdlib:arm64 (3.13.7-2) ... 77s Setting up apt (3.1.8ubuntu1) ... 78s Setting up python3 (3.13.7-2) ... 78s running python rtupdate hooks for python3.13... 78s running python post-rtupdate hooks for python3.13... 78s Setting up gir1.2-girepository-2.0:arm64 (1.86.0-6) ... 78s Setting up flash-kernel (3.109ubuntu7) ... 79s flash-kernel: deferring update (trigger activated) 79s Processing triggers for libc-bin (2.42-0ubuntu3) ... 79s Processing triggers for man-db (2.13.1-1) ... 81s Processing triggers for initramfs-tools (0.150ubuntu3) ... 81s update-initramfs: Generating /boot/initrd.img-6.17.0-5-generic 99s System running in EFI mode, skipping. 99s Processing triggers for flash-kernel (3.109ubuntu7) ... 99s System running in EFI mode, skipping. 100s autopkgtest [16:39:50]: upgrading testbed (apt dist-upgrade and autopurge) 100s Reading package lists... 101s Building dependency tree... 101s Reading state information... 101s Calculating upgrade... 101s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 102s Reading package lists... 102s Building dependency tree... 102s Reading state information... 102s Solving dependencies... 102s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 103s autopkgtest [16:39:53]: rebooting testbed after setup commands that affected boot 130s autopkgtest [16:40:20]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 09:50:31 UTC 2025 132s autopkgtest [16:40:22]: @@@@@@@@@@@@@@@@@@@@ apt-source flye 139s Get:1 http://ftpmaster.internal/ubuntu resolute/universe flye 2.9.5+dfsg-1 (dsc) [2222 B] 139s Get:2 http://ftpmaster.internal/ubuntu resolute/universe flye 2.9.5+dfsg-1 (tar) [22.8 MB] 139s Get:3 http://ftpmaster.internal/ubuntu resolute/universe flye 2.9.5+dfsg-1 (diff) [14.2 kB] 139s gpgv: Signature made Sat Aug 31 11:11:18 2024 UTC 139s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 139s gpgv: issuer "emollier@debian.org" 139s gpgv: Can't check signature: No public key 139s dpkg-source: warning: cannot verify inline signature for ./flye_2.9.5+dfsg-1.dsc: no acceptable signature found 140s autopkgtest [16:40:30]: testing package flye version 2.9.5+dfsg-1 140s autopkgtest [16:40:30]: build not needed 142s autopkgtest [16:40:32]: test run-unit-test: preparing testbed 142s Reading package lists... 143s Building dependency tree... 143s Reading state information... 143s Solving dependencies... 143s The following NEW packages will be installed: 143s flye libdeflate0 libhts3t64 libhtscodecs2 minimap2 python3-six samtools 143s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 143s Need to get 24.8 MB of archives. 143s After this operation, 41.2 MB of additional disk space will be used. 143s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-six all 1.17.0-1 [13.2 kB] 143s Get:2 http://ftpmaster.internal/ubuntu resolute/universe arm64 minimap2 arm64 2.27+dfsg-1build2 [384 kB] 144s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB] 144s Get:4 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhtscodecs2 arm64 1.6.1-2 [82.7 kB] 144s Get:5 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhts3t64 arm64 1.21+ds-1 [441 kB] 144s Get:6 http://ftpmaster.internal/ubuntu resolute/universe arm64 samtools arm64 1.21-1 [609 kB] 144s Get:7 http://ftpmaster.internal/ubuntu resolute/universe arm64 flye arm64 2.9.5+dfsg-1 [23.2 MB] 148s Fetched 24.8 MB in 4s (6374 kB/s) 148s Selecting previously unselected package python3-six. 148s (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.) 148s Preparing to unpack .../0-python3-six_1.17.0-1_all.deb ... 148s Unpacking python3-six (1.17.0-1) ... 148s Selecting previously unselected package minimap2. 148s Preparing to unpack .../1-minimap2_2.27+dfsg-1build2_arm64.deb ... 148s Unpacking minimap2 (2.27+dfsg-1build2) ... 148s Selecting previously unselected package libdeflate0:arm64. 148s Preparing to unpack .../2-libdeflate0_1.23-2_arm64.deb ... 148s Unpacking libdeflate0:arm64 (1.23-2) ... 148s Selecting previously unselected package libhtscodecs2:arm64. 148s Preparing to unpack .../3-libhtscodecs2_1.6.1-2_arm64.deb ... 148s Unpacking libhtscodecs2:arm64 (1.6.1-2) ... 148s Selecting previously unselected package libhts3t64:arm64. 148s Preparing to unpack .../4-libhts3t64_1.21+ds-1_arm64.deb ... 148s Unpacking libhts3t64:arm64 (1.21+ds-1) ... 148s Selecting previously unselected package samtools. 148s Preparing to unpack .../5-samtools_1.21-1_arm64.deb ... 148s Unpacking samtools (1.21-1) ... 148s Selecting previously unselected package flye. 148s Preparing to unpack .../6-flye_2.9.5+dfsg-1_arm64.deb ... 148s Unpacking flye (2.9.5+dfsg-1) ... 148s Setting up libhtscodecs2:arm64 (1.6.1-2) ... 148s Setting up minimap2 (2.27+dfsg-1build2) ... 148s Setting up libdeflate0:arm64 (1.23-2) ... 148s Setting up python3-six (1.17.0-1) ... 148s Setting up libhts3t64:arm64 (1.21+ds-1) ... 148s Setting up samtools (1.21-1) ... 148s Setting up flye (2.9.5+dfsg-1) ... 149s Processing triggers for man-db (2.13.1-1) ... 149s Processing triggers for libc-bin (2.42-0ubuntu3) ... 150s autopkgtest [16:40:40]: test run-unit-test: [----------------------- 151s usage: flye (--pacbio-raw | --pacbio-corr | --pacbio-hifi | --nano-raw | 151s --nano-corr | --nano-hq ) file1 [file_2 ...] 151s --out-dir PATH 151s 151s [--genome-size SIZE] [--threads int] [--iterations int] 151s [--meta] [--polish-target] [--min-overlap SIZE] 151s [--keep-haplotypes] [--debug] [--version] [--help] 151s [--scaffold] [--resume] [--resume-from] [--stop-after] 151s [--read-error float] [--extra-params] 151s [--deterministic] 151s 151s Assembly of long reads with repeat graphs 151s 151s options: 151s -h, --help show this help message and exit 151s --pacbio-raw path [path ...] 151s PacBio regular CLR reads (<20% error) 151s --pacbio-corr path [path ...] 151s PacBio reads that were corrected with other methods 151s (<3% error) 151s --pacbio-hifi path [path ...] 151s PacBio HiFi reads (<1% error) 151s --nano-raw path [path ...] 151s ONT regular reads, pre-Guppy5 (<20% error) 151s --nano-corr path [path ...] 151s ONT reads that were corrected with other methods (<3% 151s error) 151s --nano-hq path [path ...] 151s ONT high-quality reads: Guppy5+ SUP or Q20 (<5% error) 151s --subassemblies path [path ...] 151s [deprecated] high-quality contigs input 151s -g, --genome-size size 151s estimated genome size (for example, 5m or 2.6g) 151s -o, --out-dir path Output directory 151s -t, --threads int number of parallel threads [1] 151s -i, --iterations int number of polishing iterations [1] 151s -m, --min-overlap int 151s minimum overlap between reads [auto] 151s --asm-coverage int reduced coverage for initial disjointig assembly [not 151s set] 151s --hifi-error float [deprecated] same as --read-error 151s --read-error float adjust parameters for given read error rate (as 151s fraction e.g. 0.03) 151s --extra-params extra_params 151s extra configuration parameters list (comma-separated) 151s --plasmids unused (retained for backward compatibility) 151s --meta metagenome / uneven coverage mode 151s --keep-haplotypes do not collapse alternative haplotypes 151s --no-alt-contigs do not output contigs representing alternative 151s haplotypes 151s --scaffold enable scaffolding using graph [disabled by default] 151s --trestle [deprecated] enable Trestle [disabled by default] 151s --polish-target path run polisher on the target sequence 151s --resume resume from the last completed stage 151s --resume-from stage_name 151s resume from a custom stage 151s --stop-after stage_name 151s stop after the specified stage completed 151s --debug enable debug output 151s -v, --version show program's version number and exit 151s --deterministic perform disjointig assembly single-threaded 151s 151s Input reads can be in FASTA or FASTQ format, uncompressed 151s or compressed with gz. Currently, PacBio (CLR, HiFi, corrected) 151s and ONT reads (regular, HQ, corrected) are supported. Expected error rates are 151s <15% for PB CLR/regular ONT; <5% for ONT HQ, <3% for corrected, and <1% for HiFi. Note that Flye 151s was primarily developed to run on uncorrected reads. You may specify multiple 151s files with reads (separated by spaces). Mixing different read 151s types is not yet supported. The --meta option enables the mode 151s for metagenome/uneven coverage assembly. 151s 151s To reduce memory consumption for large genome assemblies, 151s you can use a subset of the longest reads for initial disjointig 151s assembly by specifying --asm-coverage and --genome-size options. Typically, 151s 40x coverage is enough to produce good disjointigs. 151s 151s You can run Flye polisher as a standalone tool using 151s --polish-target option. 151s Test is downloading large databases. Set "REALLYRUNTEST=yes" to run this test 151s autopkgtest [16:40:41]: test run-unit-test: -----------------------] 152s run-unit-test PASS 152s autopkgtest [16:40:42]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 152s autopkgtest [16:40:42]: @@@@@@@@@@@@@@@@@@@@ summary 152s run-unit-test PASS