0s autopkgtest [14:40:27]: starting date and time: 2025-03-15 14:40:27+0000 0s autopkgtest [14:40:27]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [14:40:27]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work._n9tz2l0/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade pyfastx --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-42.secgroup --name adt-plucky-arm64-pyfastx-20250315-144027-juju-7f2275-prod-proposed-migration-environment-15-44feb0e8-0750-4d65-8080-0fe4a179c58d --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --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,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 165s autopkgtest [14:43:12]: testbed dpkg architecture: arm64 166s autopkgtest [14:43:13]: testbed apt version: 2.9.33 166s autopkgtest [14:43:13]: @@@@@@@@@@@@@@@@@@@@ test bed setup 166s autopkgtest [14:43:13]: testbed release detected to be: None 167s autopkgtest [14:43:14]: updating testbed package index (apt update) 168s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 168s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 168s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 168s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 168s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 168s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 168s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 169s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [78.2 kB] 169s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1976 B] 169s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 169s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [346 kB] 169s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [15.8 kB] 169s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 169s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [572 B] 170s Fetched 1094 kB in 2s (584 kB/s) 174s Reading package lists... 174s + lsb_release --codename --short 174s Reading package lists... 174s Building dependency tree... 174s Reading state information... 174s Calculating upgrade... 174s Calculating upgrade...+ RELEASE=plucky 174s + cat 174s + [ plucky != trusty ] 174s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 174s 174s The following packages will be upgraded: 174s python3-jinja2 strace 175s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 175s Need to get 608 kB of archives. 175s After this operation, 11.3 kB of additional disk space will be used. 175s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 175s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 176s Fetched 608 kB in 1s (597 kB/s) 177s (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 ... 117701 files and directories currently installed.) 177s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 177s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 177s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 177s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 177s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 177s Setting up strace (6.13+ds-1ubuntu1) ... 177s Processing triggers for man-db (2.13.0-1) ... 178s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 178s + /usr/lib/apt/apt-helper analyze-pattern ?true 178s + + sed s/\./\\./g 178s uname -r 178s + running_kernel_pattern=^linux-.*6\.14\.0-10-generic.* 178s + apt list ?obsolete 178s + tail -n+2 178s + + cut -d/ -f1 178s grep -v ^linux-.*6\.14\.0-10-generic.* 178s + obsolete_pkgs=linux-headers-6.11.0-8-generic 178s linux-headers-6.11.0-8 178s linux-image-6.11.0-8-generic 178s linux-modules-6.11.0-8-generic 178s linux-tools-6.11.0-8-generic 178s linux-tools-6.11.0-8 178s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove linux-headers-6.11.0-8-generic linux-headers-6.11.0-8 linux-image-6.11.0-8-generic linux-modules-6.11.0-8-generic linux-tools-6.11.0-8-generic linux-tools-6.11.0-8 178s Reading package lists... 179s Building dependency tree... 179s Reading state information... 179s Solving dependencies... 179s The following packages will be REMOVED: 179s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 179s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 179s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 179s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 180s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 180s After this operation, 267 MB disk space will be freed. 180s (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 ... 117701 files and directories currently installed.) 180s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 180s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 180s Removing libpython3.12t64:arm64 (3.12.9-1) ... 180s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 180s Removing libnsl2:arm64 (1.3.0-3build3) ... 180s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 180s Removing libunwind8:arm64 (1.6.2-3.1) ... 180s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 181s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 182s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 183s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 183s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 183s /etc/kernel/postrm.d/initramfs-tools: 183s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 183s /etc/kernel/postrm.d/zz-flash-kernel: 183s flash-kernel: Kernel 6.11.0-8-generic has been removed. 183s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 183s /etc/kernel/postrm.d/zz-update-grub: 183s Sourcing file `/etc/default/grub' 183s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 183s Generating grub configuration file ... 183s Found linux image: /boot/vmlinuz-6.14.0-10-generic 183s Found initrd image: /boot/initrd.img-6.14.0-10-generic 184s Warning: os-prober will not be executed to detect other bootable partitions. 184s Systems on them will not be added to the GRUB boot configuration. 184s Check GRUB_DISABLE_OS_PROBER documentation entry. 184s Adding boot menu entry for UEFI Firmware Settings ... 184s done 184s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 184s Processing triggers for libc-bin (2.41-1ubuntu1) ... 184s (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 ... 81650 files and directories currently installed.) 184s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 185s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 185s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 185s + grep -q trusty /etc/lsb-release 185s + [ ! -d /usr/share/doc/unattended-upgrades ] 185s + [ ! -d /usr/share/doc/lxd ] 185s + [ ! -d /usr/share/doc/lxd-client ] 185s + [ ! -d /usr/share/doc/snapd ] 185s + type iptables 185s + cat 185s + chmod 755 /etc/rc.local 185s + . /etc/rc.local 185s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 185s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 185s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 185s + uname -m 185s + [ aarch64 = ppc64le ] 185s + [ -d /run/systemd/system ] 185s + systemd-detect-virt --quiet --vm 185s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 185s + cat 185s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 185s + echo COMPRESS=lz4 185s autopkgtest [14:43:32]: upgrading testbed (apt dist-upgrade and autopurge) 185s Reading package lists... 186s Building dependency tree... 186s Reading state information... 186s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 187s Starting 2 pkgProblemResolver with broken count: 0 187s Done 188s Entering ResolveByKeep 188s 189s Calculating upgrade... 189s The following packages will be upgraded: 189s libc-bin libc-dev-bin libc6 libc6-dev locales 190s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 190s Need to get 9530 kB of archives. 190s After this operation, 0 B of additional disk space will be used. 190s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 191s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 191s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 194s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 195s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 199s Preconfiguring packages ... 199s Fetched 9530 kB in 9s (1029 kB/s) 199s (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 ... 81647 files and directories currently installed.) 199s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 199s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 200s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 200s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 200s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 200s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 200s Setting up libc6:arm64 (2.41-1ubuntu2) ... 201s (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 ... 81647 files and directories currently installed.) 201s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 201s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 201s Setting up libc-bin (2.41-1ubuntu2) ... 201s (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 ... 81647 files and directories currently installed.) 201s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 201s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 201s Setting up locales (2.41-1ubuntu2) ... 202s Generating locales (this might take a while)... 205s en_US.UTF-8... done 205s Generation complete. 205s Setting up libc-dev-bin (2.41-1ubuntu2) ... 205s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 205s Processing triggers for man-db (2.13.0-1) ... 206s Processing triggers for systemd (257.3-1ubuntu3) ... 207s Reading package lists... 208s Building dependency tree... 208s Reading state information... 209s Starting pkgProblemResolver with broken count: 0 209s Starting 2 pkgProblemResolver with broken count: 0 209s Done 210s Solving dependencies... 211s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 211s autopkgtest [14:43:58]: rebooting testbed after setup commands that affected boot 235s autopkgtest [14:44:22]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 238s autopkgtest [14:44:25]: @@@@@@@@@@@@@@@@@@@@ apt-source pyfastx 241s Get:1 http://ftpmaster.internal/ubuntu plucky/universe pyfastx 2.2.0-1build1 (dsc) [2171 B] 241s Get:2 http://ftpmaster.internal/ubuntu plucky/universe pyfastx 2.2.0-1build1 (tar) [231 kB] 241s Get:3 http://ftpmaster.internal/ubuntu plucky/universe pyfastx 2.2.0-1build1 (diff) [7896 B] 241s gpgv: Signature made Tue Mar 4 15:58:37 2025 UTC 241s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 241s gpgv: Can't check signature: No public key 241s dpkg-source: warning: cannot verify inline signature for ./pyfastx_2.2.0-1build1.dsc: no acceptable signature found 241s autopkgtest [14:44:28]: testing package pyfastx version 2.2.0-1build1 242s autopkgtest [14:44:29]: build not needed 242s autopkgtest [14:44:29]: test run-unit-test: preparing testbed 242s Reading package lists... 243s Building dependency tree... 243s Reading state information... 243s Starting pkgProblemResolver with broken count: 0 243s Starting 2 pkgProblemResolver with broken count: 0 243s Done 244s The following NEW packages will be installed: 244s pyfastx python3-all python3-importlib-metadata python3-packaging 244s python3-pyfaidx python3-pyfastx 244s 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. 244s Need to get 281 kB of archives. 244s After this operation, 835 kB of additional disk space will be used. 244s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-importlib-metadata all 8.6.1-1 [20.7 kB] 244s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.2-1 [51.5 kB] 244s Get:3 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 244s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pyfastx arm64 2.2.0-1build1 [56.4 kB] 244s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 pyfastx arm64 2.2.0-1build1 [122 kB] 245s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.13.2-2 [886 B] 245s Fetched 281 kB in 1s (432 kB/s) 245s Selecting previously unselected package python3-importlib-metadata. 245s (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 ... 81647 files and directories currently installed.) 245s Preparing to unpack .../0-python3-importlib-metadata_8.6.1-1_all.deb ... 245s Unpacking python3-importlib-metadata (8.6.1-1) ... 245s Selecting previously unselected package python3-packaging. 245s Preparing to unpack .../1-python3-packaging_24.2-1_all.deb ... 245s Unpacking python3-packaging (24.2-1) ... 245s Selecting previously unselected package python3-pyfaidx. 245s Preparing to unpack .../2-python3-pyfaidx_0.8.1.3-1_all.deb ... 245s Unpacking python3-pyfaidx (0.8.1.3-1) ... 245s Selecting previously unselected package python3-pyfastx. 245s Preparing to unpack .../3-python3-pyfastx_2.2.0-1build1_arm64.deb ... 245s Unpacking python3-pyfastx (2.2.0-1build1) ... 245s Selecting previously unselected package pyfastx. 245s Preparing to unpack .../4-pyfastx_2.2.0-1build1_arm64.deb ... 245s Unpacking pyfastx (2.2.0-1build1) ... 245s Selecting previously unselected package python3-all. 245s Preparing to unpack .../5-python3-all_3.13.2-2_arm64.deb ... 245s Unpacking python3-all (3.13.2-2) ... 245s Setting up python3-importlib-metadata (8.6.1-1) ... 246s Setting up python3-all (3.13.2-2) ... 246s Setting up python3-packaging (24.2-1) ... 246s Setting up python3-pyfaidx (0.8.1.3-1) ... 246s Setting up python3-pyfastx (2.2.0-1build1) ... 246s Setting up pyfastx (2.2.0-1build1) ... 246s Processing triggers for man-db (2.13.0-1) ... 248s autopkgtest [14:44:35]: test run-unit-test: [----------------------- 248s test_id_exception (tests.test_fakeys.IdentifierTest.test_id_exception) ... ok 248s test_key_identifier (tests.test_fakeys.IdentifierTest.test_key_identifier) ... ok 248s test_key_repr (tests.test_fakeys.IdentifierTest.test_key_repr) ... ok 248s test_key_slice (tests.test_fakeys.IdentifierTest.test_key_slice) ... ok 248s test_keys_filter (tests.test_fakeys.IdentifierTest.test_keys_filter) ... ok 249s test_keys_sort (tests.test_fakeys.IdentifierTest.test_keys_sort) ... ok 249s test_build (tests.test_fasta.FastaTest.test_build) ... ok 249s test_exception (tests.test_fasta.FastaTest.test_exception) ... ok 249s test_fasta (tests.test_fasta.FastaTest.test_fasta) ... ok 249s test_iter_full_name (tests.test_fasta.FastaTest.test_iter_full_name) ... ok 249s test_iter_object (tests.test_fasta.FastaTest.test_iter_object) ... ok 249s test_iter_tuple (tests.test_fasta.FastaTest.test_iter_tuple) ... ok 249s test_iter_upper (tests.test_fasta.FastaTest.test_iter_upper) ... ok 249s test_iter_upper_full_name (tests.test_fasta.FastaTest.test_iter_upper_full_name) ... ok 249s test_key_func (tests.test_fasta.FastaTest.test_key_func) ... ok 249s test_module (tests.test_fasta.FastaTest.test_module) ... ok 249s test_no_upper (tests.test_fasta.FastaTest.test_no_upper) ... ok 249s test_repr (tests.test_fasta.FastaTest.test_repr) ... ok 249s test_seq_fetch (tests.test_fasta.FastaTest.test_seq_fetch) ... ok 249s test_seq_flank (tests.test_fasta.FastaTest.test_seq_flank) ... ok 249s test_seq_type (tests.test_fasta.FastaTest.test_seq_type) ... ok 250s test_statistics (tests.test_fasta.FastaTest.test_statistics) ... ok 250s test_build (tests.test_fastq.FastqTest.test_build) ... ok 250s test_exception (tests.test_fastq.FastqTest.test_exception) ... ok 250s test_fastq (tests.test_fastq.FastqTest.test_fastq) ... ok 250s test_full_name (tests.test_fastq.FastqTest.test_full_name) ... ok 250s test_iter_object (tests.test_fastq.FastqTest.test_iter_object) ... ok 250s test_iter_tuple (tests.test_fastq.FastqTest.test_iter_tuple) ... ok 250s test_negative (tests.test_fastq.FastqTest.test_negative) ... ok 251s test_platform (tests.test_fastq.FastqTest.test_platform) ... ok 251s test_read_len (tests.test_fastq.FastqTest.test_read_len) ... ok 251s test_repr (tests.test_fastq.FastqTest.test_repr) ... ok 251s test_exception (tests.test_fastx.FastxTest.test_exception) ... ok 251s test_fasta_iter (tests.test_fastx.FastxTest.test_fasta_iter) ... ok 251s test_fasta_upper (tests.test_fastx.FastxTest.test_fasta_upper) ... ok 251s test_fastq_iter (tests.test_fastx.FastxTest.test_fastq_iter) ... ok 251s test_fastx_repr (tests.test_fastx.FastxTest.test_fastx_repr) ... ok 251s test_exception (tests.test_fqkeys.FastxTest.test_exception) ... ok 251s test_fastq_key (tests.test_fqkeys.FastxTest.test_fastq_key) ... ok 251s test_read (tests.test_read.ReadTest.test_read) ... ok 251s test_read_description (tests.test_read.ReadTest.test_read_description) ... ok 251s test_read_raw (tests.test_read.ReadTest.test_read_raw) ... ok 251s test_read_seq (tests.test_read.ReadTest.test_read_seq) ... ok 251s test_repr (tests.test_read.ReadTest.test_repr) ... ok 251s test_full_compo (tests.test_sequence.SequenceTest.test_full_compo) ... ok 251s test_seq_by_index (tests.test_sequence.SequenceTest.test_seq_by_index) ... ok 251s test_seq_by_key (tests.test_sequence.SequenceTest.test_seq_by_key) ... ok 251s test_seq_content (tests.test_sequence.SequenceTest.test_seq_content) ... ok 251s test_seq_exception (tests.test_sequence.SequenceTest.test_seq_exception) ... ok 251s test_seq_iter (tests.test_sequence.SequenceTest.test_seq_iter) ... ok 251s test_seq_raw (tests.test_sequence.SequenceTest.test_seq_raw) ... ok 252s test_seq_repr (tests.test_sequence.SequenceTest.test_seq_repr) ... ok 252s test_seq_reverse_complement (tests.test_sequence.SequenceTest.test_seq_reverse_complement) ... ok 252s test_seq_slice (tests.test_sequence.SequenceTest.test_seq_slice) ... ok 252s test_seq_by_index (tests.test_sequence_error.SequenceErrorTest.test_seq_by_index) ... ok 252s test_seq_by_key (tests.test_sequence_error.SequenceErrorTest.test_seq_by_key) ... ok 252s 252s ---------------------------------------------------------------------- 252s Ran 56 tests in 3.482s 252s 252s OK 252s autopkgtest [14:44:39]: test run-unit-test: -----------------------] 252s run-unit-test PASS 252s autopkgtest [14:44:39]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 253s autopkgtest [14:44:40]: test test-cli: preparing testbed 425s autopkgtest [14:47:32]: testbed dpkg architecture: arm64 425s autopkgtest [14:47:32]: testbed apt version: 2.9.33 425s autopkgtest [14:47:32]: @@@@@@@@@@@@@@@@@@@@ test bed setup 425s autopkgtest [14:47:32]: testbed release detected to be: plucky 426s autopkgtest [14:47:33]: updating testbed package index (apt update) 427s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 427s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 427s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 427s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 427s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 427s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 427s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 428s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [78.2 kB] 428s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1976 B] 428s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 428s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [346 kB] 429s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [15.8 kB] 429s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 429s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [572 B] 429s Fetched 1094 kB in 2s (510 kB/s) 430s Reading package lists... 430s + lsb_release --codename --short 430s + RELEASE=plucky 430s + cat 430s + [ plucky != trusty ] 430s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 430s Reading package lists... 431s Building dependency tree... 431s Reading state information... 431s Calculating upgrade... 431s Calculating upgrade... 432s The following packages will be upgraded: 432s python3-jinja2 strace 432s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 432s Need to get 608 kB of archives. 432s After this operation, 11.3 kB of additional disk space will be used. 432s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 433s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 433s Fetched 608 kB in 1s (633 kB/s) 433s (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 ... 117701 files and directories currently installed.) 433s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 433s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 433s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 434s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 434s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 434s Setting up strace (6.13+ds-1ubuntu1) ... 434s Processing triggers for man-db (2.13.0-1) ... 434s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 434s + /usr/lib/apt/apt-helper analyze-pattern ?true 434s + uname -r 434s + sed s/\./\\./g 434s + running_kernel_pattern=^linux-.*6\.14\.0-10-generic.* 434s + apt list ?obsolete 434s + tail -n+2 434s + cut -d/ -f1 434s + grep -v ^linux-.*6\.14\.0-10-generic.* 435s + obsolete_pkgs=linux-headers-6.11.0-8-generic 435s linux-headers-6.11.0-8 435s linux-image-6.11.0-8-generic 435s linux-modules-6.11.0-8-generic 435s linux-tools-6.11.0-8-generic 435s linux-tools-6.11.0-8 435s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove linux-headers-6.11.0-8-generic linux-headers-6.11.0-8 linux-image-6.11.0-8-generic linux-modules-6.11.0-8-generic linux-tools-6.11.0-8-generic linux-tools-6.11.0-8 435s Reading package lists... 435s Building dependency tree... 435s Reading state information... 435s Solving dependencies... 436s The following packages will be REMOVED: 436s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 436s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 436s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 436s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 436s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 436s After this operation, 267 MB disk space will be freed. 436s (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 ... 117701 files and directories currently installed.) 436s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 436s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 436s Removing libpython3.12t64:arm64 (3.12.9-1) ... 436s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 436s Removing libnsl2:arm64 (1.3.0-3build3) ... 436s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 436s Removing libunwind8:arm64 (1.6.2-3.1) ... 436s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 437s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 438s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 438s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 438s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 438s /etc/kernel/postrm.d/initramfs-tools: 438s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 439s /etc/kernel/postrm.d/zz-flash-kernel: 439s flash-kernel: Kernel 6.11.0-8-generic has been removed. 439s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 439s /etc/kernel/postrm.d/zz-update-grub: 439s Sourcing file `/etc/default/grub' 439s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 439s Generating grub configuration file ... 439s Found linux image: /boot/vmlinuz-6.14.0-10-generic 439s Found initrd image: /boot/initrd.img-6.14.0-10-generic 439s Warning: os-prober will not be executed to detect other bootable partitions. 439s Systems on them will not be added to the GRUB boot configuration. 439s Check GRUB_DISABLE_OS_PROBER documentation entry. 439s Adding boot menu entry for UEFI Firmware Settings ... 439s done 439s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 440s Processing triggers for libc-bin (2.41-1ubuntu1) ... 440s (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 ... 81650 files and directories currently installed.) 440s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 440s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 440s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 440s + grep -q trusty /etc/lsb-release 440s + [ ! -d /usr/share/doc/unattended-upgrades ] 440s + [ ! -d /usr/share/doc/lxd ] 440s + [ ! -d /usr/share/doc/lxd-client ] 440s + [ ! -d /usr/share/doc/snapd ] 440s + type iptables 440s + cat 440s + chmod 755 /etc/rc.local 440s + . /etc/rc.local 440s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 440s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 440s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 440s + uname -m 440s + [ aarch64 = ppc64le ] 440s + [ -d /run/systemd/system ] 440s + systemd-detect-virt --quiet --vm 440s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 440s + cat 440s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 440s + echo COMPRESS=lz4 440s autopkgtest [14:47:47]: upgrading testbed (apt dist-upgrade and autopurge) 440s Reading package lists... 440s Building dependency tree... 440s Reading state information... 441s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 441s Starting 2 pkgProblemResolver with broken count: 0 441s Done 442s Entering ResolveByKeep 442s 442s Calculating upgrade... 443s The following packages will be upgraded: 443s libc-bin libc-dev-bin libc6 libc6-dev locales 443s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 443s Need to get 9530 kB of archives. 443s After this operation, 0 B of additional disk space will be used. 443s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 446s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 446s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 451s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 452s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 459s Preconfiguring packages ... 460s Fetched 9530 kB in 16s (582 kB/s) 460s (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 ... 81647 files and directories currently installed.) 460s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 460s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 460s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 460s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 460s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 460s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 460s Setting up libc6:arm64 (2.41-1ubuntu2) ... 460s (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 ... 81647 files and directories currently installed.) 460s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 460s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 460s Setting up libc-bin (2.41-1ubuntu2) ... 460s (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 ... 81647 files and directories currently installed.) 460s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 460s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 461s Setting up locales (2.41-1ubuntu2) ... 461s Generating locales (this might take a while)... 463s en_US.UTF-8... done 463s Generation complete. 463s Setting up libc-dev-bin (2.41-1ubuntu2) ... 463s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 463s Processing triggers for man-db (2.13.0-1) ... 464s Processing triggers for systemd (257.3-1ubuntu3) ... 465s Reading package lists... 465s Building dependency tree... 465s Reading state information... 466s Starting pkgProblemResolver with broken count: 0 466s Starting 2 pkgProblemResolver with broken count: 0 466s Done 466s Solving dependencies... 466s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 467s autopkgtest [14:48:14]: rebooting testbed after setup commands that affected boot 494s Reading package lists... 494s Building dependency tree... 494s Reading state information... 494s Starting pkgProblemResolver with broken count: 0 495s Starting 2 pkgProblemResolver with broken count: 0 495s Done 495s The following NEW packages will be installed: 495s pyfastx python3-importlib-metadata python3-packaging python3-pyfaidx 495s python3-pyfastx 496s 0 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. 496s Need to get 280 kB of archives. 496s After this operation, 828 kB of additional disk space will be used. 496s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-importlib-metadata all 8.6.1-1 [20.7 kB] 496s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.2-1 [51.5 kB] 496s Get:3 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 496s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pyfastx arm64 2.2.0-1build1 [56.4 kB] 496s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 pyfastx arm64 2.2.0-1build1 [122 kB] 496s Fetched 280 kB in 1s (419 kB/s) 496s Selecting previously unselected package python3-importlib-metadata. 497s (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 ... 81647 files and directories currently installed.) 497s Preparing to unpack .../python3-importlib-metadata_8.6.1-1_all.deb ... 497s Unpacking python3-importlib-metadata (8.6.1-1) ... 497s Selecting previously unselected package python3-packaging. 497s Preparing to unpack .../python3-packaging_24.2-1_all.deb ... 497s Unpacking python3-packaging (24.2-1) ... 497s Selecting previously unselected package python3-pyfaidx. 497s Preparing to unpack .../python3-pyfaidx_0.8.1.3-1_all.deb ... 497s Unpacking python3-pyfaidx (0.8.1.3-1) ... 497s Selecting previously unselected package python3-pyfastx. 497s Preparing to unpack .../python3-pyfastx_2.2.0-1build1_arm64.deb ... 497s Unpacking python3-pyfastx (2.2.0-1build1) ... 497s Selecting previously unselected package pyfastx. 497s Preparing to unpack .../pyfastx_2.2.0-1build1_arm64.deb ... 497s Unpacking pyfastx (2.2.0-1build1) ... 497s Setting up python3-importlib-metadata (8.6.1-1) ... 497s Setting up python3-packaging (24.2-1) ... 497s Setting up python3-pyfaidx (0.8.1.3-1) ... 497s Setting up python3-pyfastx (2.2.0-1build1) ... 497s Setting up pyfastx (2.2.0-1build1) ... 497s Processing triggers for man-db (2.13.0-1) ... 500s autopkgtest [14:48:47]: test test-cli: [----------------------- 501s $ pyfastx --help 501s usage: pyfastx COMMAND [OPTIONS] 501s 501s A command line tool for FASTA/Q file manipulation 501s 501s options: 501s -h, --help show this help message and exit 501s -v, --version show program's version number and exit 501s 501s Commands: 501s 501s index build index for fasta/q file 501s stat show detailed statistics information of fasta/q file 501s split split fasta/q file into multiple files 501s fq2fa convert fastq file to fasta file 501s subseq get subsequences from fasta file by region 501s sample randomly sample sequences from fasta or fastq file 501s extract extract full sequences or reads from fasta/q file 501s $ # Found pyfastx commands: 'index stat split fq2fa subseq sample extract' 501s $ pyfastx index --help 501s usage: pyfastx index [-h] [-f] fastx [fastx ...] 501s 501s positional arguments: 501s fastx fasta or fastq file, gzip support 501s 501s options: 501s -h, --help show this help message and exit 501s -f, --full build full index, base composition will be calculated 501s $ pyfastx stat --help 501s usage: pyfastx stat [-h] fastx [fastx ...] 501s 501s positional arguments: 501s fastx fasta or fastq file, gzip support 501s 501s options: 501s -h, --help show this help message and exit 501s $ pyfastx split --help 501s usage: pyfastx split [-h] (-n int | -c int) [-o str] fastx 501s 501s positional arguments: 501s fastx fasta or fastq file, gzip support 501s 501s options: 501s -h, --help show this help message and exit 501s -n int split a fasta/q file into N new files with even size 501s -c int split a fasta/q file into multiple files containing the 501s same sequence counts 501s -o, --out-dir str output directory, default is current folder 501s $ pyfastx fq2fa --help 501s usage: pyfastx fq2fa [-h] [-o str] fastx 501s 501s positional arguments: 501s fastx fastq file, gzip support 501s 501s options: 501s -h, --help show this help message and exit 501s -o, --out-file str output file, default: output to stdout 501s $ pyfastx subseq --help 501s usage: pyfastx subseq [-h] [-r str | -b str] [-o str] fastx [region ...] 501s 501s positional arguments: 501s fastx input fasta file, gzip support 501s region format is chr:start-end, start and end position is 501s 1-based, multiple regions were separated by space 501s 501s options: 501s -h, --help show this help message and exit 501s -r, --region-file str 501s tab-delimited file, one region per line, both start 501s and end position are 1-based 501s -b, --bed-file str tab-delimited BED file, 0-based start position and 501s 1-based end position 501s -o, --out-file str output file, default: output to stdout 501s $ pyfastx sample --help 501s usage: pyfastx sample [-h] (-n int | -p float) [-s int] [--sequential-read] 501s [-o str] 501s fastx 501s 501s positional arguments: 501s fastx fasta or fastq file, gzip support 501s 501s options: 501s -h, --help show this help message and exit 501s -n int number of sequences to be sampled 501s -p float proportion of sequences to be sampled, 0~1 501s -s, --seed int random seed, default is the current system time 501s --sequential-read start sequential reading, particularly suitable for 501s sampling large numbers of sequences 501s -o, --out-file str output file, default: output to stdout 501s $ pyfastx extract --help 501s usage: pyfastx extract [-h] [-l str] [--reverse-complement] [--out-fasta] 501s [-o str] [--sequential-read] 501s fastx [name ...] 501s 501s positional arguments: 501s fastx fasta or fastq file, gzip support 501s name sequence name or read name, multiple names were 501s separated by space 501s 501s options: 501s -h, --help show this help message and exit 501s -l, --list-file str a file containing sequence or read names, one name per 501s line 501s --reverse-complement output reverse complement sequence 501s --out-fasta output fasta format when extract reads from fastq, 501s default output fastq format 501s -o, --out-file str output file, default: output to stdout 501s --sequential-read start sequential reading, particularly suitable for 501s extracting large numbers of sequences 501s $ pyfastx --version 501s pyfastx version 2.2.0 501s $ pyfastx index protein.fa 501s $ pyfastx index rna.fa 501s $ pyfastx index test.fa 502s $ pyfastx index test.fq 502s $ pyfastx index test.fa.gz 502s $ pyfastx index test.fq.gz 502s $ pyfastx stat protein.fa 502s fileName seqType seqCounts totalBases GC% avgLen medianLen maxLen minLen N50 L50 502s protein.fa protein 17 2265 - 133.235 80.0 419 23 263 4 502s $ pyfastx split -n 2 protein.fa 502s $ pyfastx fq2fa test.fq -o test.fa 502s $ pyfastx subseq protein.fa UPI0000000011:1-4 502s >UPI0000000011:1-4 502s MVDA 502s $ pyfastx sample -n 1 test.fq.gz -o sample.fq 502s $ pyfastx extract protein.fa UPI0000000011 502s >UPI0000000011 status=active 502s MVDAITVLTAIGITVLMLLMVISGAAMIVKELNPNDIFTMQSLKFNRAVTIFKYIGLFIY 502s IPGTIILYATYVKSLLMKS 503s autopkgtest [14:48:50]: test test-cli: -----------------------] 506s test-cli PASS 506s autopkgtest [14:48:53]: test test-cli: - - - - - - - - - - results - - - - - - - - - - 507s autopkgtest [14:48:54]: @@@@@@@@@@@@@@@@@@@@ summary 507s run-unit-test PASS 507s test-cli PASS 525s nova [W] Using flock in prodstack6-arm64 525s Creating nova instance adt-plucky-arm64-pyfastx-20250315-144027-juju-7f2275-prod-proposed-migration-environment-15-44feb0e8-0750-4d65-8080-0fe4a179c58d from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 525s nova [W] Timed out waiting for 83724700-d407-4518-ad5b-8708be04fc1e to get deleted. 525s nova [W] Using flock in prodstack6-arm64 525s Creating nova instance adt-plucky-arm64-pyfastx-20250315-144027-juju-7f2275-prod-proposed-migration-environment-15-44feb0e8-0750-4d65-8080-0fe4a179c58d from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 525s nova [W] Timed out waiting for 81b68145-c0af-4796-af14-bc7777c3a247 to get deleted.