0s autopkgtest [11:01:32]: starting date and time: 2024-03-20 11:01:32+0000 0s autopkgtest [11:01:32]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [11:01:32]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.8zu3qdym/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:minimap2 --apt-upgrade flye --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=minimap2/2.26+dfsg-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-s390x-6.secgroup --name adt-noble-s390x-flye-20240320-110132-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 63s autopkgtest [11:02:35]: testbed dpkg architecture: s390x 63s autopkgtest [11:02:35]: testbed apt version: 2.7.12 63s autopkgtest [11:02:35]: @@@@@@@@@@@@@@@@@@@@ test bed setup 64s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 64s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 65s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 65s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3766 kB] 67s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [52.7 kB] 67s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [653 kB] 67s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 67s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 67s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 67s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4051 kB] 67s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 67s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [34.4 kB] 67s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 69s Fetched 9188 kB in 4s (2188 kB/s) 69s Reading package lists... 72s Reading package lists... 72s Building dependency tree... 72s Reading state information... 72s Calculating upgrade... 72s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 72s Reading package lists... 72s Building dependency tree... 72s Reading state information... 72s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 73s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 73s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 73s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 73s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 74s Reading package lists... 74s Reading package lists... 74s Building dependency tree... 74s Reading state information... 74s Calculating upgrade... 74s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 74s Reading package lists... 75s Building dependency tree... 75s Reading state information... 75s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 77s autopkgtest [11:02:49]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 77s autopkgtest [11:02:49]: @@@@@@@@@@@@@@@@@@@@ apt-source flye 80s Get:1 http://ftpmaster.internal/ubuntu noble/universe flye 2.9.3+dfsg2-1 (dsc) [2110 B] 80s Get:2 http://ftpmaster.internal/ubuntu noble/universe flye 2.9.3+dfsg2-1 (tar) [22.8 MB] 80s Get:3 http://ftpmaster.internal/ubuntu noble/universe flye 2.9.3+dfsg2-1 (diff) [14.4 kB] 80s gpgv: Signature made Fri Feb 2 13:53:41 2024 UTC 80s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 80s gpgv: issuer "tille@debian.org" 80s gpgv: Can't check signature: No public key 80s dpkg-source: warning: cannot verify inline signature for ./flye_2.9.3+dfsg2-1.dsc: no acceptable signature found 81s autopkgtest [11:02:53]: testing package flye version 2.9.3+dfsg2-1 81s autopkgtest [11:02:53]: build not needed 85s autopkgtest [11:02:57]: test run-unit-test: preparing testbed 92s Reading package lists... 93s Building dependency tree... 93s Reading state information... 93s Starting pkgProblemResolver with broken count: 0 93s Starting 2 pkgProblemResolver with broken count: 0 93s Done 93s The following additional packages will be installed: 93s flye libdeflate0 libhts3 libhtscodecs2 minimap2 samtools 93s Suggested packages: 93s cwltool 93s The following NEW packages will be installed: 93s autopkgtest-satdep flye libdeflate0 libhts3 libhtscodecs2 minimap2 samtools 93s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 93s Need to get 24.9 MB/24.9 MB of archives. 93s After this operation, 40.8 MB of additional disk space will be used. 93s Get:1 /tmp/autopkgtest.JQMwWU/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [704 B] 93s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x minimap2 s390x 2.26+dfsg-1 [399 kB] 93s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x libdeflate0 s390x 1.19-1 [46.0 kB] 93s Get:4 http://ftpmaster.internal/ubuntu noble/universe s390x libhtscodecs2 s390x 1.6.0-1 [87.2 kB] 93s Get:5 http://ftpmaster.internal/ubuntu noble/universe s390x libhts3 s390x 1.18+ds-1 [463 kB] 94s Get:6 http://ftpmaster.internal/ubuntu noble/universe s390x samtools s390x 1.19.2-1 [613 kB] 94s Get:7 http://ftpmaster.internal/ubuntu noble/universe s390x flye s390x 2.9.3+dfsg2-1 [23.3 MB] 95s Fetched 24.9 MB in 1s (19.6 MB/s) 95s Selecting previously unselected package minimap2. 95s (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 ... 52171 files and directories currently installed.) 95s Preparing to unpack .../0-minimap2_2.26+dfsg-1_s390x.deb ... 95s Unpacking minimap2 (2.26+dfsg-1) ... 95s Selecting previously unselected package libdeflate0:s390x. 95s Preparing to unpack .../1-libdeflate0_1.19-1_s390x.deb ... 95s Unpacking libdeflate0:s390x (1.19-1) ... 95s Selecting previously unselected package libhtscodecs2:s390x. 95s Preparing to unpack .../2-libhtscodecs2_1.6.0-1_s390x.deb ... 95s Unpacking libhtscodecs2:s390x (1.6.0-1) ... 95s Selecting previously unselected package libhts3:s390x. 95s Preparing to unpack .../3-libhts3_1.18+ds-1_s390x.deb ... 95s Unpacking libhts3:s390x (1.18+ds-1) ... 95s Selecting previously unselected package samtools. 95s Preparing to unpack .../4-samtools_1.19.2-1_s390x.deb ... 95s Unpacking samtools (1.19.2-1) ... 95s Selecting previously unselected package flye. 95s Preparing to unpack .../5-flye_2.9.3+dfsg2-1_s390x.deb ... 95s Unpacking flye (2.9.3+dfsg2-1) ... 95s Selecting previously unselected package autopkgtest-satdep. 95s Preparing to unpack .../6-1-autopkgtest-satdep.deb ... 95s Unpacking autopkgtest-satdep (0) ... 95s Setting up libhtscodecs2:s390x (1.6.0-1) ... 95s Setting up minimap2 (2.26+dfsg-1) ... 95s Setting up libdeflate0:s390x (1.19-1) ... 95s Setting up libhts3:s390x (1.18+ds-1) ... 95s Setting up samtools (1.19.2-1) ... 95s Setting up flye (2.9.3+dfsg2-1) ... 95s Setting up autopkgtest-satdep (0) ... 95s Processing triggers for man-db (2.12.0-3) ... 96s Processing triggers for libc-bin (2.39-0ubuntu2) ... 98s (Reading database ... 52376 files and directories currently installed.) 98s Removing autopkgtest-satdep (0) ... 98s autopkgtest [11:03:10]: 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 size, --genome-size size 98s estimated genome size (for example, 5m or 2.6g) 98s -o path, --out-dir path 98s Output directory 98s -t int, --threads int 98s number of parallel threads [1] 98s -i int, --iterations int 98s number of polishing iterations [1] 98s -m int, --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 99s autopkgtest [11:03:11]: test run-unit-test: -----------------------] 99s run-unit-test PASS 99s autopkgtest [11:03:11]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 100s autopkgtest [11:03:12]: @@@@@@@@@@@@@@@@@@@@ summary 100s run-unit-test PASS 111s Creating nova instance adt-noble-s390x-flye-20240320-110132-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-s390x-server-20240320.img (UUID 6569a0ff-4984-4a4c-a4d0-b93f21cb5de9)...