0s autopkgtest [00:07:59]: starting date and time: 2024-03-20 00:07:59+0000 0s autopkgtest [00:07:59]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [00:07:59]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.2rrszk7c/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-ppc64el-16.secgroup --name adt-noble-ppc64el-flye-20240320-000759-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-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/ 166s autopkgtest [00:10:45]: testbed dpkg architecture: ppc64el 166s autopkgtest [00:10:45]: testbed apt version: 2.7.12 166s autopkgtest [00:10:45]: @@@@@@@@@@@@@@@@@@@@ test bed setup 167s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 167s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 167s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3799 kB] 168s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [52.7 kB] 168s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [492 kB] 168s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [654 kB] 168s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 168s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 168s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 168s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4104 kB] 168s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 168s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [47.7 kB] 168s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 172s Fetched 9286 kB in 2s (3732 kB/s) 172s Reading package lists... 175s Reading package lists... 175s Building dependency tree... 175s Reading state information... 175s Calculating upgrade... 175s The following packages will be upgraded: 175s ubuntu-minimal ubuntu-standard 175s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 175s Need to get 21.5 kB of archives. 175s After this operation, 0 B of additional disk space will be used. 175s Get:1 http://ftpmaster.internal/ubuntu noble/main ppc64el ubuntu-minimal ppc64el 1.536build1 [10.7 kB] 176s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el ubuntu-standard ppc64el 1.536build1 [10.7 kB] 176s Fetched 21.5 kB in 0s (102 kB/s) 176s (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 ... 70095 files and directories currently installed.) 176s Preparing to unpack .../ubuntu-minimal_1.536build1_ppc64el.deb ... 176s Unpacking ubuntu-minimal (1.536build1) over (1.536) ... 176s Preparing to unpack .../ubuntu-standard_1.536build1_ppc64el.deb ... 176s Unpacking ubuntu-standard (1.536build1) over (1.536) ... 176s Setting up ubuntu-minimal (1.536build1) ... 176s Setting up ubuntu-standard (1.536build1) ... 176s Reading package lists... 176s Building dependency tree... 176s Reading state information... 177s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 177s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 177s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 177s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 177s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 179s Reading package lists... 179s Reading package lists... 179s Building dependency tree... 179s Reading state information... 179s Calculating upgrade... 179s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 179s Reading package lists... 179s Building dependency tree... 179s Reading state information... 180s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 183s autopkgtest [00:11:02]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 183s autopkgtest [00:11:02]: @@@@@@@@@@@@@@@@@@@@ apt-source flye 186s Get:1 http://ftpmaster.internal/ubuntu noble/universe flye 2.9.3+dfsg2-1 (dsc) [2110 B] 186s Get:2 http://ftpmaster.internal/ubuntu noble/universe flye 2.9.3+dfsg2-1 (tar) [22.8 MB] 186s Get:3 http://ftpmaster.internal/ubuntu noble/universe flye 2.9.3+dfsg2-1 (diff) [14.4 kB] 186s gpgv: Signature made Fri Feb 2 13:53:41 2024 UTC 186s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 186s gpgv: issuer "tille@debian.org" 186s gpgv: Can't check signature: No public key 186s dpkg-source: warning: cannot verify inline signature for ./flye_2.9.3+dfsg2-1.dsc: no acceptable signature found 187s autopkgtest [00:11:06]: testing package flye version 2.9.3+dfsg2-1 187s autopkgtest [00:11:06]: build not needed 192s autopkgtest [00:11:11]: test run-unit-test: preparing testbed 194s Reading package lists... 194s Building dependency tree... 194s Reading state information... 194s Starting pkgProblemResolver with broken count: 0 194s Starting 2 pkgProblemResolver with broken count: 0 194s Done 194s The following additional packages will be installed: 194s flye libdeflate0 libhts3 libhtscodecs2 minimap2 samtools 194s Suggested packages: 194s cwltool 194s The following NEW packages will be installed: 194s autopkgtest-satdep flye libdeflate0 libhts3 libhtscodecs2 minimap2 samtools 194s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 194s Need to get 25.1 MB/25.1 MB of archives. 194s After this operation, 42.1 MB of additional disk space will be used. 194s Get:1 /tmp/autopkgtest.2wSBgm/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [704 B] 195s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el minimap2 ppc64el 2.26+dfsg-1 [397 kB] 195s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 195s Get:4 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 195s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB] 195s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el samtools ppc64el 1.19.2-1 [669 kB] 195s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el flye ppc64el 2.9.3+dfsg2-1 [23.3 MB] 196s Fetched 25.1 MB in 1s (16.9 MB/s) 196s Selecting previously unselected package minimap2. 196s (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 ... 70095 files and directories currently installed.) 196s Preparing to unpack .../0-minimap2_2.26+dfsg-1_ppc64el.deb ... 196s Unpacking minimap2 (2.26+dfsg-1) ... 196s Selecting previously unselected package libdeflate0:ppc64el. 196s Preparing to unpack .../1-libdeflate0_1.19-1_ppc64el.deb ... 196s Unpacking libdeflate0:ppc64el (1.19-1) ... 196s Selecting previously unselected package libhtscodecs2:ppc64el. 196s Preparing to unpack .../2-libhtscodecs2_1.6.0-1_ppc64el.deb ... 196s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 196s Selecting previously unselected package libhts3:ppc64el. 196s Preparing to unpack .../3-libhts3_1.18+ds-1_ppc64el.deb ... 196s Unpacking libhts3:ppc64el (1.18+ds-1) ... 196s Selecting previously unselected package samtools. 196s Preparing to unpack .../4-samtools_1.19.2-1_ppc64el.deb ... 196s Unpacking samtools (1.19.2-1) ... 196s Selecting previously unselected package flye. 196s Preparing to unpack .../5-flye_2.9.3+dfsg2-1_ppc64el.deb ... 196s Unpacking flye (2.9.3+dfsg2-1) ... 197s Selecting previously unselected package autopkgtest-satdep. 197s Preparing to unpack .../6-1-autopkgtest-satdep.deb ... 197s Unpacking autopkgtest-satdep (0) ... 197s Setting up libhtscodecs2:ppc64el (1.6.0-1) ... 197s Setting up minimap2 (2.26+dfsg-1) ... 197s Setting up libdeflate0:ppc64el (1.19-1) ... 197s Setting up libhts3:ppc64el (1.18+ds-1) ... 197s Setting up samtools (1.19.2-1) ... 197s Setting up flye (2.9.3+dfsg2-1) ... 197s Setting up autopkgtest-satdep (0) ... 197s Processing triggers for man-db (2.12.0-3) ... 198s Processing triggers for libc-bin (2.39-0ubuntu2) ... 200s (Reading database ... 70300 files and directories currently installed.) 200s Removing autopkgtest-satdep (0) ... 201s autopkgtest [00:11:20]: test run-unit-test: [----------------------- 201s usage: flye (--pacbio-raw | --pacbio-corr | --pacbio-hifi | --nano-raw | 201s --nano-corr | --nano-hq ) file1 [file_2 ...] 201s --out-dir PATH 201s 201s [--genome-size SIZE] [--threads int] [--iterations int] 201s [--meta] [--polish-target] [--min-overlap SIZE] 201s [--keep-haplotypes] [--debug] [--version] [--help] 201s [--scaffold] [--resume] [--resume-from] [--stop-after] 201s [--read-error float] [--extra-params] 201s [--deterministic] 201s 201s Assembly of long reads with repeat graphs 201s 201s options: 201s -h, --help show this help message and exit 201s --pacbio-raw path [path ...] 201s PacBio regular CLR reads (<20% error) 201s --pacbio-corr path [path ...] 201s PacBio reads that were corrected with other methods 201s (<3% error) 201s --pacbio-hifi path [path ...] 201s PacBio HiFi reads (<1% error) 201s --nano-raw path [path ...] 201s ONT regular reads, pre-Guppy5 (<20% error) 201s --nano-corr path [path ...] 201s ONT reads that were corrected with other methods (<3% 201s error) 201s --nano-hq path [path ...] 201s ONT high-quality reads: Guppy5+ SUP or Q20 (<5% error) 201s --subassemblies path [path ...] 201s [deprecated] high-quality contigs input 201s -g size, --genome-size size 201s estimated genome size (for example, 5m or 2.6g) 201s -o path, --out-dir path 201s Output directory 201s -t int, --threads int 201s number of parallel threads [1] 201s -i int, --iterations int 201s number of polishing iterations [1] 201s -m int, --min-overlap int 201s minimum overlap between reads [auto] 201s --asm-coverage int reduced coverage for initial disjointig assembly [not 201s set] 201s --hifi-error float [deprecated] same as --read-error 201s --read-error float adjust parameters for given read error rate (as 201s fraction e.g. 0.03) 201s --extra-params extra_params 201s extra configuration parameters list (comma-separated) 201s --plasmids unused (retained for backward compatibility) 201s --meta metagenome / uneven coverage mode 201s --keep-haplotypes do not collapse alternative haplotypes 201s --no-alt-contigs do not output contigs representing alternative 201s haplotypes 201s --scaffold enable scaffolding using graph [disabled by default] 201s --trestle [deprecated] enable Trestle [disabled by default] 201s --polish-target path run polisher on the target sequence 201s --resume resume from the last completed stage 201s --resume-from stage_name 201s resume from a custom stage 201s --stop-after stage_name 201s stop after the specified stage completed 201s --debug enable debug output 201s -v, --version show program's version number and exit 201s --deterministic perform disjointig assembly single-threaded 201s 201s Input reads can be in FASTA or FASTQ format, uncompressed 201s or compressed with gz. Currently, PacBio (CLR, HiFi, corrected) 201s and ONT reads (regular, HQ, corrected) are supported. Expected error rates are 201s <15% for PB CLR/regular ONT; <5% for ONT HQ, <3% for corrected, and <1% for HiFi. Note that Flye 201s was primarily developed to run on uncorrected reads. You may specify multiple 201s files with reads (separated by spaces). Mixing different read 201s types is not yet supported. The --meta option enables the mode 201s for metagenome/uneven coverage assembly. 201s 201s To reduce memory consumption for large genome assemblies, 201s you can use a subset of the longest reads for initial disjointig 201s assembly by specifying --asm-coverage and --genome-size options. Typically, 201s 40x coverage is enough to produce good disjointigs. 201s 201s You can run Flye polisher as a standalone tool using 201s --polish-target option. 201s Test is downloading large databases. Set "REALLYRUNTEST=yes" to run this test 201s autopkgtest [00:11:20]: test run-unit-test: -----------------------] 202s autopkgtest [00:11:21]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 202s run-unit-test PASS 202s autopkgtest [00:11:21]: @@@@@@@@@@@@@@@@@@@@ summary 202s run-unit-test PASS 229s Creating nova instance adt-noble-ppc64el-flye-20240320-000759-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240319.img (UUID 6e7a6c13-d651-45a1-a24f-48d9d59effd9)...