0s autopkgtest [15:46:29]: starting date and time: 2024-03-23 15:46:29+0000 0s autopkgtest [15:46:29]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [15:46:29]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.i2ozpotd/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-3@bos01-ppc64el-5.secgroup --name adt-noble-ppc64el-flye-20240323-154629-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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://us.ports.ubuntu.com/ubuntu-ports/ 130s autopkgtest [15:48:39]: testbed dpkg architecture: ppc64el 130s autopkgtest [15:48:39]: testbed apt version: 2.7.12 130s autopkgtest [15:48:39]: @@@@@@@@@@@@@@@@@@@@ test bed setup 130s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 131s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3969 kB] 131s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB] 131s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [493 kB] 131s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 131s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [659 kB] 131s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 131s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 131s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 131s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4248 kB] 131s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 131s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [60.8 kB] 131s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 135s Fetched 9623 kB in 2s (4307 kB/s) 135s Reading package lists... 138s Reading package lists... 138s Building dependency tree... 138s Reading state information... 138s Calculating upgrade... 138s The following packages will be REMOVED: 138s libssl3 138s The following NEW packages will be installed: 138s libssl3t64 138s The following packages have been kept back: 138s curl 138s The following packages will be upgraded: 138s cloud-init fonts-ubuntu-console libbsd0 libc-bin libc6 locales openssl 138s python3-markupsafe 138s 8 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 138s Need to get 12.1 MB of archives. 138s After this operation, 10.2 kB of additional disk space will be used. 138s Get:1 http://ftpmaster.internal/ubuntu noble/main ppc64el libc6 ppc64el 2.39-0ubuntu6 [3274 kB] 139s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libc-bin ppc64el 2.39-0ubuntu6 [751 kB] 139s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu2 [1026 kB] 139s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu2 [2125 kB] 139s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el libbsd0 ppc64el 0.12.1-1 [56.9 kB] 139s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el locales all 2.39-0ubuntu6 [4232 kB] 139s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-ubuntu-console all 0.869+git20240321-0ubuntu1 [18.7 kB] 139s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-markupsafe ppc64el 2.1.5-1build1 [13.2 kB] 139s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el cloud-init all 24.1.2-0ubuntu1 [597 kB] 140s Preconfiguring packages ... 140s Fetched 12.1 MB in 1s (9007 kB/s) 140s (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 ... 70157 files and directories currently installed.) 140s Preparing to unpack .../libc6_2.39-0ubuntu6_ppc64el.deb ... 140s Unpacking libc6:ppc64el (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 140s Setting up libc6:ppc64el (2.39-0ubuntu6) ... 141s (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 ... 70157 files and directories currently installed.) 141s Preparing to unpack .../libc-bin_2.39-0ubuntu6_ppc64el.deb ... 141s Unpacking libc-bin (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 141s Setting up libc-bin (2.39-0ubuntu6) ... 141s (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 ... 70157 files and directories currently installed.) 141s Preparing to unpack .../openssl_3.0.13-0ubuntu2_ppc64el.deb ... 141s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 141s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested: 141s wget depends on libssl3 (>= 3.0.0). 141s tnftp depends on libssl3 (>= 3.0.0). 141s tcpdump depends on libssl3 (>= 3.0.0). 141s systemd-resolved depends on libssl3 (>= 3.0.0). 141s systemd depends on libssl3 (>= 3.0.0). 141s sudo depends on libssl3 (>= 3.0.0). 141s rsync depends on libssl3 (>= 3.0.0). 141s python3-cryptography depends on libssl3 (>= 3.0.0). 141s openssh-server depends on libssl3 (>= 3.0.10). 141s openssh-client depends on libssl3 (>= 3.0.10). 141s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 141s libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0). 141s libssh-4:ppc64el depends on libssl3 (>= 3.0.0). 141s libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0). 141s libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0). 141s libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0). 141s libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0). 141s libnvme1 depends on libssl3 (>= 3.0.0). 141s libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0). 141s libkmod2:ppc64el depends on libssl3 (>= 3.0.0). 141s libfido2-1:ppc64el depends on libssl3 (>= 3.0.0). 141s libcurl4:ppc64el depends on libssl3 (>= 3.0.0). 141s libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0). 141s kmod depends on libssl3 (>= 3.0.0). 141s dhcpcd-base depends on libssl3 (>= 3.0.0). 141s bind9-libs:ppc64el depends on libssl3 (>= 3.0.0). 141s 141s (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 ... 70157 files and directories currently installed.) 141s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ... 141s Selecting previously unselected package libssl3t64:ppc64el. 141s (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 ... 70146 files and directories currently installed.) 141s Preparing to unpack .../0-libssl3t64_3.0.13-0ubuntu2_ppc64el.deb ... 141s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 141s Preparing to unpack .../1-libbsd0_0.12.1-1_ppc64el.deb ... 141s Unpacking libbsd0:ppc64el (0.12.1-1) over (0.11.8-1) ... 141s Preparing to unpack .../2-locales_2.39-0ubuntu6_all.deb ... 141s Unpacking locales (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 142s Preparing to unpack .../3-fonts-ubuntu-console_0.869+git20240321-0ubuntu1_all.deb ... 142s Unpacking fonts-ubuntu-console (0.869+git20240321-0ubuntu1) over (0.869-0ubuntu1) ... 142s Preparing to unpack .../4-python3-markupsafe_2.1.5-1build1_ppc64el.deb ... 142s Unpacking python3-markupsafe (2.1.5-1build1) over (2.1.5-1) ... 142s Preparing to unpack .../5-cloud-init_24.1.2-0ubuntu1_all.deb ... 142s Unpacking cloud-init (24.1.2-0ubuntu1) over (24.1.1-0ubuntu1) ... 142s Setting up fonts-ubuntu-console (0.869+git20240321-0ubuntu1) ... 142s Setting up cloud-init (24.1.2-0ubuntu1) ... 143s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 143s Setting up locales (2.39-0ubuntu6) ... 144s Generating locales (this might take a while)... 145s en_US.UTF-8... done 145s Generation complete. 145s Setting up python3-markupsafe (2.1.5-1build1) ... 145s Setting up openssl (3.0.13-0ubuntu2) ... 145s Setting up libbsd0:ppc64el (0.12.1-1) ... 145s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 145s Processing triggers for man-db (2.12.0-3) ... 146s Processing triggers for libc-bin (2.39-0ubuntu6) ... 147s Reading package lists... 147s Building dependency tree... 147s Reading state information... 147s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 148s sh: Attempting to set up Debian/Ubuntu apt sources automatically 148s sh: Distribution appears to be Ubuntu 148s Reading package lists... 149s Building dependency tree... 149s Reading state information... 149s eatmydata is already the newest version (131-1). 149s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 149s Reading package lists... 149s Building dependency tree... 149s Reading state information... 149s dbus is already the newest version (1.14.10-4ubuntu1). 149s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 149s Reading package lists... 149s Building dependency tree... 149s Reading state information... 149s rng-tools-debian is already the newest version (2.4). 149s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 149s Reading package lists... 150s Building dependency tree... 150s Reading state information... 150s The following packages will be REMOVED: 150s cloud-init* python3-configobj* python3-debconf* 150s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 150s After this operation, 3256 kB disk space will be freed. 150s (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 ... 70158 files and directories currently installed.) 150s Removing cloud-init (24.1.2-0ubuntu1) ... 150s Removing python3-configobj (5.0.8-3) ... 150s Removing python3-debconf (1.5.86) ... 151s Processing triggers for man-db (2.12.0-3) ... 151s (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 ... 69769 files and directories currently installed.) 151s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 151s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 151s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 151s invoke-rc.d: policy-rc.d denied execution of try-restart. 152s Reading package lists... 152s Building dependency tree... 152s Reading state information... 152s linux-generic is already the newest version (6.8.0-11.11+1). 152s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 152s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 152s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 152s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 155s Reading package lists... 155s Reading package lists... 155s Building dependency tree... 155s Reading state information... 155s Calculating upgrade... 155s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 155s Reading package lists... 155s Building dependency tree... 155s Reading state information... 156s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 156s autopkgtest [15:49:05]: rebooting testbed after setup commands that affected boot 325s autopkgtest [15:51:54]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 327s autopkgtest [15:51:56]: @@@@@@@@@@@@@@@@@@@@ apt-source flye 329s Get:1 http://ftpmaster.internal/ubuntu noble/universe flye 2.9.3+dfsg2-1 (dsc) [2110 B] 329s Get:2 http://ftpmaster.internal/ubuntu noble/universe flye 2.9.3+dfsg2-1 (tar) [22.8 MB] 329s Get:3 http://ftpmaster.internal/ubuntu noble/universe flye 2.9.3+dfsg2-1 (diff) [14.4 kB] 330s gpgv: Signature made Fri Feb 2 13:53:41 2024 UTC 330s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 330s gpgv: issuer "tille@debian.org" 330s gpgv: Can't check signature: No public key 330s dpkg-source: warning: cannot verify inline signature for ./flye_2.9.3+dfsg2-1.dsc: no acceptable signature found 330s autopkgtest [15:51:59]: testing package flye version 2.9.3+dfsg2-1 331s autopkgtest [15:52:00]: build not needed 333s autopkgtest [15:52:02]: test run-unit-test: preparing testbed 362s Reading package lists... 362s Building dependency tree... 362s Reading state information... 362s Starting pkgProblemResolver with broken count: 0 362s Starting 2 pkgProblemResolver with broken count: 0 362s Done 362s The following additional packages will be installed: 362s flye libdeflate0 libhts3 libhtscodecs2 minimap2 samtools 362s Suggested packages: 362s cwltool 362s The following NEW packages will be installed: 362s autopkgtest-satdep flye libdeflate0 libhts3 libhtscodecs2 minimap2 samtools 362s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 362s Need to get 25.1 MB/25.1 MB of archives. 362s After this operation, 42.0 MB of additional disk space will be used. 362s Get:1 /tmp/autopkgtest.YxqNRc/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [704 B] 363s Get:2 http://ftpmaster.internal/ubuntu noble/universe ppc64el minimap2 ppc64el 2.24+dfsg-3build2 [396 kB] 363s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 363s Get:4 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 363s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB] 363s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el samtools ppc64el 1.19.2-1 [669 kB] 363s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el flye ppc64el 2.9.3+dfsg2-1 [23.3 MB] 364s Fetched 25.1 MB in 1s (19.1 MB/s) 364s Selecting previously unselected package minimap2. 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 ... 69714 files and directories currently installed.) 364s Preparing to unpack .../0-minimap2_2.24+dfsg-3build2_ppc64el.deb ... 364s Unpacking minimap2 (2.24+dfsg-3build2) ... 364s Selecting previously unselected package libdeflate0:ppc64el. 364s Preparing to unpack .../1-libdeflate0_1.19-1_ppc64el.deb ... 364s Unpacking libdeflate0:ppc64el (1.19-1) ... 364s Selecting previously unselected package libhtscodecs2:ppc64el. 364s Preparing to unpack .../2-libhtscodecs2_1.6.0-1_ppc64el.deb ... 364s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 364s Selecting previously unselected package libhts3:ppc64el. 364s Preparing to unpack .../3-libhts3_1.18+ds-1_ppc64el.deb ... 364s Unpacking libhts3:ppc64el (1.18+ds-1) ... 364s Selecting previously unselected package samtools. 364s Preparing to unpack .../4-samtools_1.19.2-1_ppc64el.deb ... 364s Unpacking samtools (1.19.2-1) ... 364s Selecting previously unselected package flye. 364s Preparing to unpack .../5-flye_2.9.3+dfsg2-1_ppc64el.deb ... 364s Unpacking flye (2.9.3+dfsg2-1) ... 364s Selecting previously unselected package autopkgtest-satdep. 364s Preparing to unpack .../6-1-autopkgtest-satdep.deb ... 364s Unpacking autopkgtest-satdep (0) ... 365s Setting up libhtscodecs2:ppc64el (1.6.0-1) ... 365s Setting up minimap2 (2.24+dfsg-3build2) ... 365s Setting up libdeflate0:ppc64el (1.19-1) ... 365s Setting up libhts3:ppc64el (1.18+ds-1) ... 365s Setting up samtools (1.19.2-1) ... 365s Setting up flye (2.9.3+dfsg2-1) ... 365s Setting up autopkgtest-satdep (0) ... 365s Processing triggers for man-db (2.12.0-3) ... 365s Processing triggers for libc-bin (2.39-0ubuntu6) ... 367s (Reading database ... 69919 files and directories currently installed.) 367s Removing autopkgtest-satdep (0) ... 368s autopkgtest [15:52:37]: test run-unit-test: [----------------------- 368s usage: flye (--pacbio-raw | --pacbio-corr | --pacbio-hifi | --nano-raw | 368s --nano-corr | --nano-hq ) file1 [file_2 ...] 368s --out-dir PATH 368s 368s [--genome-size SIZE] [--threads int] [--iterations int] 368s [--meta] [--polish-target] [--min-overlap SIZE] 368s [--keep-haplotypes] [--debug] [--version] [--help] 368s [--scaffold] [--resume] [--resume-from] [--stop-after] 368s [--read-error float] [--extra-params] 368s [--deterministic] 368s 368s Assembly of long reads with repeat graphs 368s 368s options: 368s -h, --help show this help message and exit 368s --pacbio-raw path [path ...] 368s PacBio regular CLR reads (<20% error) 368s --pacbio-corr path [path ...] 368s PacBio reads that were corrected with other methods 368s (<3% error) 368s --pacbio-hifi path [path ...] 368s PacBio HiFi reads (<1% error) 368s --nano-raw path [path ...] 368s ONT regular reads, pre-Guppy5 (<20% error) 368s --nano-corr path [path ...] 368s ONT reads that were corrected with other methods (<3% 368s error) 368s --nano-hq path [path ...] 368s ONT high-quality reads: Guppy5+ SUP or Q20 (<5% error) 368s --subassemblies path [path ...] 368s [deprecated] high-quality contigs input 368s -g size, --genome-size size 368s estimated genome size (for example, 5m or 2.6g) 368s -o path, --out-dir path 368s Output directory 368s -t int, --threads int 368s number of parallel threads [1] 368s -i int, --iterations int 368s number of polishing iterations [1] 368s -m int, --min-overlap int 368s minimum overlap between reads [auto] 368s --asm-coverage int reduced coverage for initial disjointig assembly [not 368s set] 368s --hifi-error float [deprecated] same as --read-error 368s --read-error float adjust parameters for given read error rate (as 368s fraction e.g. 0.03) 368s --extra-params extra_params 368s extra configuration parameters list (comma-separated) 368s --plasmids unused (retained for backward compatibility) 368s --meta metagenome / uneven coverage mode 368s --keep-haplotypes do not collapse alternative haplotypes 368s --no-alt-contigs do not output contigs representing alternative 368s haplotypes 368s --scaffold enable scaffolding using graph [disabled by default] 368s --trestle [deprecated] enable Trestle [disabled by default] 368s --polish-target path run polisher on the target sequence 368s --resume resume from the last completed stage 368s --resume-from stage_name 368s resume from a custom stage 368s --stop-after stage_name 368s stop after the specified stage completed 368s --debug enable debug output 368s -v, --version show program's version number and exit 368s --deterministic perform disjointig assembly single-threaded 368s 368s Input reads can be in FASTA or FASTQ format, uncompressed 368s or compressed with gz. Currently, PacBio (CLR, HiFi, corrected) 368s and ONT reads (regular, HQ, corrected) are supported. Expected error rates are 368s <15% for PB CLR/regular ONT; <5% for ONT HQ, <3% for corrected, and <1% for HiFi. Note that Flye 368s was primarily developed to run on uncorrected reads. You may specify multiple 368s files with reads (separated by spaces). Mixing different read 368s types is not yet supported. The --meta option enables the mode 368s for metagenome/uneven coverage assembly. 368s 368s To reduce memory consumption for large genome assemblies, 368s you can use a subset of the longest reads for initial disjointig 368s assembly by specifying --asm-coverage and --genome-size options. Typically, 368s 40x coverage is enough to produce good disjointigs. 368s 368s You can run Flye polisher as a standalone tool using 368s --polish-target option. 368s Test is downloading large databases. Set "REALLYRUNTEST=yes" to run this test 369s autopkgtest [15:52:38]: test run-unit-test: -----------------------] 369s autopkgtest [15:52:38]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 369s run-unit-test PASS 369s autopkgtest [15:52:38]: @@@@@@@@@@@@@@@@@@@@ summary 369s run-unit-test PASS 382s Creating nova instance adt-noble-ppc64el-flye-20240323-154629-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-ppc64el-server-20240321.img (UUID 024d6af5-fcba-4a84-85f9-01f41e1878d6)...