0s autopkgtest [17:24:28]: starting date and time: 2024-03-24 17:24:28+0000 0s autopkgtest [17:24:28]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [17:24:28]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.q9_vpdkb/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:samtools,src:curl,src:gnutls28,src:htslib,src:libpsl,src:nettle,src:openssl --apt-upgrade flye --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=samtools/1.19.2-1build1 curl/8.5.0-2ubuntu7 gnutls28/3.8.3-1.1ubuntu2 htslib/1.19+ds-1.1build2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-arm64-4.secgroup --name adt-noble-arm64-flye-20240324-172428-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-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/ 304s autopkgtest [17:29:32]: testbed dpkg architecture: arm64 304s autopkgtest [17:29:32]: testbed apt version: 2.7.12 304s autopkgtest [17:29:32]: @@@@@@@@@@@@@@@@@@@@ test bed setup 307s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 308s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3986 kB] 310s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 310s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 310s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 310s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [708 kB] 310s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 310s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 310s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 310s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4364 kB] 311s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 311s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [70.1 kB] 311s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 335s Fetched 9850 kB in 10s (1034 kB/s) 337s Reading package lists... 349s Reading package lists... 350s Building dependency tree... 350s Reading state information... 355s Calculating upgrade... 357s The following packages will be REMOVED: 357s libssl3 357s The following NEW packages will be installed: 357s libssl3t64 357s The following packages have been kept back: 357s curl 357s The following packages will be upgraded: 357s openssl 358s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 358s Need to get 2777 kB of archives. 358s After this operation, 139 kB of additional disk space will be used. 358s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu2 [985 kB] 358s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu2 [1793 kB] 362s Fetched 2777 kB in 2s (1842 kB/s) 364s (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 ... 75911 files and directories currently installed.) 364s Preparing to unpack .../openssl_3.0.13-0ubuntu2_arm64.deb ... 364s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 366s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 366s wget depends on libssl3 (>= 3.0.0). 366s u-boot-tools depends on libssl3 (>= 3.0.0). 366s tnftp depends on libssl3 (>= 3.0.0). 366s tcpdump depends on libssl3 (>= 3.0.0). 366s systemd-resolved depends on libssl3 (>= 3.0.0). 366s systemd depends on libssl3 (>= 3.0.0). 366s sudo depends on libssl3 (>= 3.0.0). 366s sbsigntool depends on libssl3 (>= 3.0.0). 366s rsync depends on libssl3 (>= 3.0.0). 366s python3-cryptography depends on libssl3 (>= 3.0.0). 366s openssh-server depends on libssl3 (>= 3.0.10). 366s openssh-client depends on libssl3 (>= 3.0.10). 366s mtd-utils depends on libssl3 (>= 3.0.0). 366s mokutil depends on libssl3 (>= 3.0.0). 366s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 366s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 366s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 366s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 366s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 366s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 366s libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0). 366s libnvme1 depends on libssl3 (>= 3.0.0). 366s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 366s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 366s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 366s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 366s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 366s kmod depends on libssl3 (>= 3.0.0). 366s dhcpcd-base depends on libssl3 (>= 3.0.0). 366s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 366s 366s (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 ... 75911 files and directories currently installed.) 366s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 366s Selecting previously unselected package libssl3t64:arm64. 366s (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 ... 75900 files and directories currently installed.) 366s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_arm64.deb ... 366s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu2) ... 367s Setting up libssl3t64:arm64 (3.0.13-0ubuntu2) ... 367s Setting up openssl (3.0.13-0ubuntu2) ... 367s Processing triggers for man-db (2.12.0-3) ... 372s Processing triggers for libc-bin (2.39-0ubuntu6) ... 373s Reading package lists... 374s Building dependency tree... 374s Reading state information... 378s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 382s sh: Attempting to set up Debian/Ubuntu apt sources automatically 382s sh: Distribution appears to be Ubuntu 388s Reading package lists... 389s Building dependency tree... 389s Reading state information... 392s eatmydata is already the newest version (131-1). 392s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 392s Reading package lists... 393s Building dependency tree... 393s Reading state information... 396s dbus is already the newest version (1.14.10-4ubuntu1). 396s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 396s Reading package lists... 397s Building dependency tree... 397s Reading state information... 400s rng-tools-debian is already the newest version (2.4). 400s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 400s Reading package lists... 401s Building dependency tree... 401s Reading state information... 404s The following packages will be REMOVED: 404s cloud-init* python3-configobj* python3-debconf* 406s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 406s After this operation, 3256 kB disk space will be freed. 407s (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 ... 75913 files and directories currently installed.) 407s Removing cloud-init (24.1.2-0ubuntu1) ... 411s Removing python3-configobj (5.0.8-3) ... 412s Removing python3-debconf (1.5.86) ... 413s Processing triggers for man-db (2.12.0-3) ... 415s (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 ... 75524 files and directories currently installed.) 415s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 418s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 419s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 419s invoke-rc.d: policy-rc.d denied execution of try-restart. 420s Reading package lists... 421s Building dependency tree... 421s Reading state information... 424s linux-generic is already the newest version (6.8.0-11.11+1). 424s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 425s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 425s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 426s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 446s Reading package lists... 446s Reading package lists... 448s Building dependency tree... 448s Reading state information... 450s Calculating upgrade... 452s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 452s Reading package lists... 454s Building dependency tree... 454s Reading state information... 457s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 458s autopkgtest [17:32:06]: rebooting testbed after setup commands that affected boot 629s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 665s autopkgtest [17:35:33]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 673s autopkgtest [17:35:41]: @@@@@@@@@@@@@@@@@@@@ apt-source flye 684s Get:1 http://ftpmaster.internal/ubuntu noble/universe flye 2.9.3+dfsg2-1 (dsc) [2110 B] 684s Get:2 http://ftpmaster.internal/ubuntu noble/universe flye 2.9.3+dfsg2-1 (tar) [22.8 MB] 684s Get:3 http://ftpmaster.internal/ubuntu noble/universe flye 2.9.3+dfsg2-1 (diff) [14.4 kB] 686s gpgv: Signature made Fri Feb 2 13:53:41 2024 UTC 686s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 686s gpgv: issuer "tille@debian.org" 686s gpgv: Can't check signature: No public key 686s dpkg-source: warning: cannot verify inline signature for ./flye_2.9.3+dfsg2-1.dsc: no acceptable signature found 691s autopkgtest [17:35:59]: testing package flye version 2.9.3+dfsg2-1 691s autopkgtest [17:35:59]: build not needed 699s autopkgtest [17:36:07]: test run-unit-test: preparing testbed 713s Reading package lists... 714s Building dependency tree... 714s Reading state information... 716s Starting pkgProblemResolver with broken count: 0 716s Starting 2 pkgProblemResolver with broken count: 0 716s Done 719s The following additional packages will be installed: 719s flye libdeflate0 libhts3 libhtscodecs2 minimap2 samtools 719s Suggested packages: 719s cwltool 719s The following NEW packages will be installed: 719s autopkgtest-satdep flye libdeflate0 libhts3 libhtscodecs2 minimap2 samtools 719s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 719s Need to get 24.7 MB/24.7 MB of archives. 719s After this operation, 40.8 MB of additional disk space will be used. 719s Get:1 /tmp/autopkgtest.8YjJwe/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [700 B] 720s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 minimap2 arm64 2.24+dfsg-3build2 [379 kB] 720s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 720s Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 720s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 720s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 samtools arm64 1.19.2-1 [584 kB] 720s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 flye arm64 2.9.3+dfsg2-1 [23.2 MB] 728s Fetched 24.7 MB in 5s (5175 kB/s) 728s Selecting previously unselected package minimap2. 729s (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 ... 75469 files and directories currently installed.) 729s Preparing to unpack .../0-minimap2_2.24+dfsg-3build2_arm64.deb ... 729s Unpacking minimap2 (2.24+dfsg-3build2) ... 729s Selecting previously unselected package libdeflate0:arm64. 729s Preparing to unpack .../1-libdeflate0_1.19-1_arm64.deb ... 729s Unpacking libdeflate0:arm64 (1.19-1) ... 729s Selecting previously unselected package libhtscodecs2:arm64. 729s Preparing to unpack .../2-libhtscodecs2_1.6.0-1_arm64.deb ... 729s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 729s Selecting previously unselected package libhts3:arm64. 729s Preparing to unpack .../3-libhts3_1.18+ds-1_arm64.deb ... 729s Unpacking libhts3:arm64 (1.18+ds-1) ... 729s Selecting previously unselected package samtools. 730s Preparing to unpack .../4-samtools_1.19.2-1_arm64.deb ... 730s Unpacking samtools (1.19.2-1) ... 730s Selecting previously unselected package flye. 730s Preparing to unpack .../5-flye_2.9.3+dfsg2-1_arm64.deb ... 730s Unpacking flye (2.9.3+dfsg2-1) ... 733s Selecting previously unselected package autopkgtest-satdep. 733s Preparing to unpack .../6-1-autopkgtest-satdep.deb ... 733s Unpacking autopkgtest-satdep (0) ... 734s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 734s Setting up minimap2 (2.24+dfsg-3build2) ... 734s Setting up libdeflate0:arm64 (1.19-1) ... 734s Setting up libhts3:arm64 (1.18+ds-1) ... 734s Setting up samtools (1.19.2-1) ... 734s Setting up flye (2.9.3+dfsg2-1) ... 736s Setting up autopkgtest-satdep (0) ... 736s Processing triggers for man-db (2.12.0-3) ... 741s Processing triggers for libc-bin (2.39-0ubuntu6) ... 754s (Reading database ... 75674 files and directories currently installed.) 754s Removing autopkgtest-satdep (0) ... 756s autopkgtest [17:37:04]: test run-unit-test: [----------------------- 757s usage: flye (--pacbio-raw | --pacbio-corr | --pacbio-hifi | --nano-raw | 757s --nano-corr | --nano-hq ) file1 [file_2 ...] 757s --out-dir PATH 757s 757s [--genome-size SIZE] [--threads int] [--iterations int] 757s [--meta] [--polish-target] [--min-overlap SIZE] 757s [--keep-haplotypes] [--debug] [--version] [--help] 757s [--scaffold] [--resume] [--resume-from] [--stop-after] 757s [--read-error float] [--extra-params] 757s [--deterministic] 757s 757s Assembly of long reads with repeat graphs 757s 757s options: 757s -h, --help show this help message and exit 757s --pacbio-raw path [path ...] 757s PacBio regular CLR reads (<20% error) 757s --pacbio-corr path [path ...] 757s PacBio reads that were corrected with other methods 757s (<3% error) 757s --pacbio-hifi path [path ...] 757s PacBio HiFi reads (<1% error) 757s --nano-raw path [path ...] 757s ONT regular reads, pre-Guppy5 (<20% error) 757s --nano-corr path [path ...] 757s ONT reads that were corrected with other methods (<3% 757s error) 757s --nano-hq path [path ...] 757s ONT high-quality reads: Guppy5+ SUP or Q20 (<5% error) 757s --subassemblies path [path ...] 757s [deprecated] high-quality contigs input 757s -g size, --genome-size size 757s estimated genome size (for example, 5m or 2.6g) 757s -o path, --out-dir path 757s Output directory 757s -t int, --threads int 757s number of parallel threads [1] 757s -i int, --iterations int 757s number of polishing iterations [1] 757s -m int, --min-overlap int 757s minimum overlap between reads [auto] 757s --asm-coverage int reduced coverage for initial disjointig assembly [not 757s set] 757s --hifi-error float [deprecated] same as --read-error 757s --read-error float adjust parameters for given read error rate (as 757s fraction e.g. 0.03) 757s --extra-params extra_params 757s extra configuration parameters list (comma-separated) 757s --plasmids unused (retained for backward compatibility) 757s --meta metagenome / uneven coverage mode 757s --keep-haplotypes do not collapse alternative haplotypes 757s --no-alt-contigs do not output contigs representing alternative 757s haplotypes 757s --scaffold enable scaffolding using graph [disabled by default] 757s --trestle [deprecated] enable Trestle [disabled by default] 757s --polish-target path run polisher on the target sequence 757s --resume resume from the last completed stage 757s --resume-from stage_name 757s resume from a custom stage 757s --stop-after stage_name 757s stop after the specified stage completed 757s --debug enable debug output 757s -v, --version show program's version number and exit 757s --deterministic perform disjointig assembly single-threaded 757s 757s Input reads can be in FASTA or FASTQ format, uncompressed 757s or compressed with gz. Currently, PacBio (CLR, HiFi, corrected) 757s and ONT reads (regular, HQ, corrected) are supported. Expected error rates are 757s <15% for PB CLR/regular ONT; <5% for ONT HQ, <3% for corrected, and <1% for HiFi. Note that Flye 757s was primarily developed to run on uncorrected reads. You may specify multiple 757s files with reads (separated by spaces). Mixing different read 757s types is not yet supported. The --meta option enables the mode 757s for metagenome/uneven coverage assembly. 757s 757s To reduce memory consumption for large genome assemblies, 757s you can use a subset of the longest reads for initial disjointig 757s assembly by specifying --asm-coverage and --genome-size options. Typically, 757s 40x coverage is enough to produce good disjointigs. 757s 757s You can run Flye polisher as a standalone tool using 757s --polish-target option. 758s Test is downloading large databases. Set "REALLYRUNTEST=yes" to run this test 758s autopkgtest [17:37:06]: test run-unit-test: -----------------------] 759s autopkgtest [17:37:07]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 759s run-unit-test PASS 761s autopkgtest [17:37:09]: @@@@@@@@@@@@@@@@@@@@ summary 761s run-unit-test PASS 801s Creating nova instance adt-noble-arm64-flye-20240324-172428-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240324.img (UUID 86f9118c-691d-4fd3-ac71-bf5396ee0d8a)...