0s autopkgtest [18:41:08]: starting date: 2024-03-09 0s autopkgtest [18:41:08]: git checkout: d9c0295 adt_testbed.py: supress warnings from apt using a shell pipeline 0s autopkgtest [18:41:08]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.91b_uwj8/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:sqlite3,src:readline --apt-upgrade pyfastx --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=sqlite3/3.45.1-1ubuntu1 readline/8.2-3.1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-8.secgroup --name adt-noble-arm64-pyfastx-20240309-184108-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/ 87s autopkgtest [18:42:35]: @@@@@@@@@@@@@@@@@@@@ test bed setup 88s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 88s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [3976 B] 88s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [429 kB] 89s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [2629 kB] 89s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [37.3 kB] 89s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [579 kB] 89s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 89s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [20.3 kB] 89s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 89s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [2931 kB] 89s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 89s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [39.6 kB] 89s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 91s Fetched 6798 kB in 2s (3689 kB/s) 91s Reading package lists... 94s Reading package lists... 95s Building dependency tree... 95s Reading state information... 96s Calculating upgrade... 96s The following package was automatically installed and is no longer required: 96s ubuntu-advantage-tools 96s Use 'sudo apt autoremove' to remove it. 96s The following NEW packages will be installed: 96s libnuma1 libsensors-config libsensors5 numactl sysstat 96s The following packages will be upgraded: 96s efibootmgr libsqlite3-0 python3-attr readline-common ubuntu-minimal 96s ubuntu-standard 96s 6 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. 96s Need to get 1437 kB of archives. 96s After this operation, 2215 kB of additional disk space will be used. 96s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsqlite3-0 arm64 3.45.1-1ubuntu1 [704 kB] 97s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 readline-common all 8.2-3.1 [56.4 kB] 97s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.535 [10.5 kB] 97s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libnuma1 arm64 2.0.18-1 [23.5 kB] 97s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.535 [10.5 kB] 97s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 efibootmgr arm64 18-1build1 [31.5 kB] 97s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libsensors-config all 1:3.6.0-9 [5458 B] 97s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libsensors5 arm64 1:3.6.0-9 [26.9 kB] 97s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 numactl arm64 2.0.18-1 [39.5 kB] 97s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 python3-attr all 23.2.0-2 [48.6 kB] 97s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 sysstat arm64 12.6.1-1ubuntu1 [480 kB] 98s Preconfiguring packages ... 99s Fetched 1437 kB in 1s (1938 kB/s) 99s (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 ... 74662 files and directories currently installed.) 99s Preparing to unpack .../00-libsqlite3-0_3.45.1-1ubuntu1_arm64.deb ... 99s Unpacking libsqlite3-0:arm64 (3.45.1-1ubuntu1) over (3.45.1-1) ... 99s Preparing to unpack .../01-readline-common_8.2-3.1_all.deb ... 99s Unpacking readline-common (8.2-3.1) over (8.2-3) ... 100s Preparing to unpack .../02-ubuntu-minimal_1.535_arm64.deb ... 100s Unpacking ubuntu-minimal (1.535) over (1.534) ... 100s Selecting previously unselected package libnuma1:arm64. 100s Preparing to unpack .../03-libnuma1_2.0.18-1_arm64.deb ... 100s Unpacking libnuma1:arm64 (2.0.18-1) ... 100s Preparing to unpack .../04-ubuntu-standard_1.535_arm64.deb ... 100s Unpacking ubuntu-standard (1.535) over (1.534) ... 100s Preparing to unpack .../05-efibootmgr_18-1build1_arm64.deb ... 100s Unpacking efibootmgr (18-1build1) over (18-1) ... 100s Selecting previously unselected package libsensors-config. 100s Preparing to unpack .../06-libsensors-config_1%3a3.6.0-9_all.deb ... 100s Unpacking libsensors-config (1:3.6.0-9) ... 100s Selecting previously unselected package libsensors5:arm64. 100s Preparing to unpack .../07-libsensors5_1%3a3.6.0-9_arm64.deb ... 100s Unpacking libsensors5:arm64 (1:3.6.0-9) ... 100s Selecting previously unselected package numactl. 100s Preparing to unpack .../08-numactl_2.0.18-1_arm64.deb ... 100s Unpacking numactl (2.0.18-1) ... 100s Preparing to unpack .../09-python3-attr_23.2.0-2_all.deb ... 101s Unpacking python3-attr (23.2.0-2) over (23.2.0-1) ... 101s Selecting previously unselected package sysstat. 101s Preparing to unpack .../10-sysstat_12.6.1-1ubuntu1_arm64.deb ... 101s Unpacking sysstat (12.6.1-1ubuntu1) ... 101s Setting up python3-attr (23.2.0-2) ... 101s Setting up efibootmgr (18-1build1) ... 101s Setting up ubuntu-minimal (1.535) ... 101s Setting up libsqlite3-0:arm64 (3.45.1-1ubuntu1) ... 101s Setting up libsensors-config (1:3.6.0-9) ... 101s Setting up ubuntu-standard (1.535) ... 101s Setting up libsensors5:arm64 (1:3.6.0-9) ... 101s Setting up libnuma1:arm64 (2.0.18-1) ... 101s Setting up readline-common (8.2-3.1) ... 101s Setting up sysstat (12.6.1-1ubuntu1) ... 101s 101s Creating config file /etc/default/sysstat with new version 101s update-alternatives: using /usr/bin/sar.sysstat to provide /usr/bin/sar (sar) in auto mode 103s Created symlink /etc/systemd/system/sysstat.service.wants/sysstat-collect.timer → /usr/lib/systemd/system/sysstat-collect.timer. 103s Created symlink /etc/systemd/system/sysstat.service.wants/sysstat-summary.timer → /usr/lib/systemd/system/sysstat-summary.timer. 103s Created symlink /etc/systemd/system/multi-user.target.wants/sysstat.service → /usr/lib/systemd/system/sysstat.service. 105s Setting up numactl (2.0.18-1) ... 105s Processing triggers for man-db (2.12.0-3) ... 106s Processing triggers for install-info (7.1-3) ... 106s Processing triggers for libc-bin (2.39-0ubuntu2) ... 107s Reading package lists... 107s Building dependency tree... 107s Reading state information... 108s The following packages will be REMOVED: 108s ubuntu-advantage-tools* 109s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. 109s After this operation, 71.7 kB disk space will be freed. 109s (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 ... 74755 files and directories currently installed.) 109s Removing ubuntu-advantage-tools (31.1) ... 109s (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 ... 74749 files and directories currently installed.) 109s Purging configuration files for ubuntu-advantage-tools (31.1) ... 111s sh: Attempting to set up Debian/Ubuntu apt sources automatically 111s sh: Distribution appears to be Ubuntu 112s Reading package lists... 113s Building dependency tree... 113s Reading state information... 113s eatmydata is already the newest version (131-1). 113s dbus is already the newest version (1.14.10-4ubuntu1). 113s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 113s Reading package lists... 114s Building dependency tree... 114s Reading state information... 114s rng-tools-debian is already the newest version (2.4). 114s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 114s Reading package lists... 115s Building dependency tree... 115s Reading state information... 115s haveged is already the newest version (1.9.14-1ubuntu1). 115s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 115s Reading package lists... 116s Building dependency tree... 116s Reading state information... 116s The following packages will be REMOVED: 116s cloud-init* python3-configobj* python3-debconf* 117s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 117s After this operation, 3248 kB disk space will be freed. 117s (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 ... 74748 files and directories currently installed.) 117s Removing cloud-init (24.1-0ubuntu1) ... 117s Removing python3-configobj (5.0.8-3) ... 118s Removing python3-debconf (1.5.86) ... 118s Processing triggers for man-db (2.12.0-3) ... 118s (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 ... 74359 files and directories currently installed.) 118s Purging configuration files for cloud-init (24.1-0ubuntu1) ... 120s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 120s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 120s Reading package lists... 120s Building dependency tree... 120s Reading state information... 121s linux-generic is already the newest version (6.8.0-11.11+1). 121s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 122s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 122s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 122s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 122s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 124s Reading package lists... 124s Reading package lists... 124s Building dependency tree... 124s Reading state information... 124s Calculating upgrade... 125s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 125s Reading package lists... 125s Building dependency tree... 125s Reading state information... 126s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 126s autopkgtest [18:43:14]: rebooting testbed after setup commands that affected boot 340s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 346s autopkgtest [18:46:54]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 347s autopkgtest [18:46:55]: testbed dpkg architecture: arm64 355s autopkgtest [18:47:03]: @@@@@@@@@@@@@@@@@@@@ apt-source pyfastx 359s Get:1 http://ftpmaster.internal/ubuntu noble/universe pyfastx 2.0.2-2 (dsc) [2292 B] 359s Get:2 http://ftpmaster.internal/ubuntu noble/universe pyfastx 2.0.2-2 (tar) [230 kB] 359s Get:3 http://ftpmaster.internal/ubuntu noble/universe pyfastx 2.0.2-2 (diff) [33.6 kB] 359s gpgv: Signature made Wed Dec 13 10:25:09 2023 UTC 359s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 359s gpgv: issuer "emollier@debian.org" 359s gpgv: Can't check signature: No public key 359s dpkg-source: warning: cannot verify inline signature for ./pyfastx_2.0.2-2.dsc: no acceptable signature found 359s autopkgtest [18:47:07]: testing package pyfastx version 2.0.2-2 359s autopkgtest [18:47:07]: build not needed 360s autopkgtest [18:47:08]: test run-unit-test: preparing testbed 364s Reading package lists... 364s Building dependency tree... 364s Reading state information... 365s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 365s Starting 2 pkgProblemResolver with broken count: 0 365s Done 365s Done 365s Starting pkgProblemResolver with broken count: 0 365s Starting 2 pkgProblemResolver with broken count: 0 365s Done 366s The following additional packages will be installed: 366s pyfastx python3-all python3-distutils python3-importlib-metadata 366s python3-lib2to3 python3-more-itertools python3-pyfaidx python3-pyfastx 366s python3-zipp 366s Recommended packages: 366s python3-biopython 366s The following NEW packages will be installed: 366s pyfastx python3-all python3-distutils python3-importlib-metadata 366s python3-lib2to3 python3-more-itertools python3-pyfaidx python3-pyfastx 366s python3-zipp 366s 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. 366s 1 not fully installed or removed. 366s Need to get 505 kB of archives. 366s After this operation, 2036 kB of additional disk space will be used. 366s Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 python3-more-itertools all 10.2.0-1 [52.9 kB] 367s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 python3-zipp all 1.0.0-6 [6090 B] 367s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 python3-importlib-metadata all 4.12.0-1 [17.8 kB] 367s Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pyfaidx all 0.8.1.1-1 [29.6 kB] 367s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pyfastx arm64 2.0.2-2 [66.0 kB] 367s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 pyfastx arm64 2.0.2-2 [123 kB] 367s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 python3-lib2to3 all 3.11.5-1 [79.0 kB] 367s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 python3-distutils all 3.11.5-1 [131 kB] 367s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 python3-all arm64 3.12.1-0ubuntu2 [906 B] 368s Fetched 505 kB in 1s (597 kB/s) 368s Selecting previously unselected package python3-more-itertools. 368s (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 ... 74304 files and directories currently installed.) 368s Preparing to unpack .../0-python3-more-itertools_10.2.0-1_all.deb ... 368s Unpacking python3-more-itertools (10.2.0-1) ... 368s Selecting previously unselected package python3-zipp. 368s Preparing to unpack .../1-python3-zipp_1.0.0-6_all.deb ... 368s Unpacking python3-zipp (1.0.0-6) ... 368s Selecting previously unselected package python3-importlib-metadata. 368s Preparing to unpack .../2-python3-importlib-metadata_4.12.0-1_all.deb ... 368s Unpacking python3-importlib-metadata (4.12.0-1) ... 368s Selecting previously unselected package python3-pyfaidx. 368s Preparing to unpack .../3-python3-pyfaidx_0.8.1.1-1_all.deb ... 368s Unpacking python3-pyfaidx (0.8.1.1-1) ... 368s Selecting previously unselected package python3-pyfastx. 368s Preparing to unpack .../4-python3-pyfastx_2.0.2-2_arm64.deb ... 368s Unpacking python3-pyfastx (2.0.2-2) ... 368s Selecting previously unselected package pyfastx. 368s Preparing to unpack .../5-pyfastx_2.0.2-2_arm64.deb ... 368s Unpacking pyfastx (2.0.2-2) ... 368s Selecting previously unselected package python3-lib2to3. 368s Preparing to unpack .../6-python3-lib2to3_3.11.5-1_all.deb ... 368s Unpacking python3-lib2to3 (3.11.5-1) ... 368s Selecting previously unselected package python3-distutils. 368s Preparing to unpack .../7-python3-distutils_3.11.5-1_all.deb ... 368s Unpacking python3-distutils (3.11.5-1) ... 368s Selecting previously unselected package python3-all. 368s Preparing to unpack .../8-python3-all_3.12.1-0ubuntu2_arm64.deb ... 368s Unpacking python3-all (3.12.1-0ubuntu2) ... 368s Setting up python3-more-itertools (10.2.0-1) ... 369s Setting up python3-zipp (1.0.0-6) ... 369s Setting up python3-lib2to3 (3.11.5-1) ... 369s Setting up python3-distutils (3.11.5-1) ... 369s python3.12: can't get files for byte-compilation 369s Setting up python3-importlib-metadata (4.12.0-1) ... 369s Setting up python3-all (3.12.1-0ubuntu2) ... 369s Setting up python3-pyfaidx (0.8.1.1-1) ... 369s Setting up python3-pyfastx (2.0.2-2) ... 369s Setting up pyfastx (2.0.2-2) ... 369s Setting up autopkgtest-satdep (0) ... 369s Processing triggers for man-db (2.12.0-3) ... 375s (Reading database ... 74617 files and directories currently installed.) 375s Removing autopkgtest-satdep (0) ... 376s autopkgtest [18:47:24]: test run-unit-test: [----------------------- 377s test_id_exception (tests.test_fakeys.IdentifierTest.test_id_exception) ... ok 377s test_key_identifier (tests.test_fakeys.IdentifierTest.test_key_identifier) ... ok 377s test_key_repr (tests.test_fakeys.IdentifierTest.test_key_repr) ... ok 378s test_key_slice (tests.test_fakeys.IdentifierTest.test_key_slice) ... ok 378s test_keys_filter (tests.test_fakeys.IdentifierTest.test_keys_filter) ... ok 378s test_keys_sort (tests.test_fakeys.IdentifierTest.test_keys_sort) ... ok 378s test_build (tests.test_fasta.FastaTest.test_build) ... ok 378s test_exception (tests.test_fasta.FastaTest.test_exception) ... ok 378s test_fasta (tests.test_fasta.FastaTest.test_fasta) ... ok 378s test_iter_full_name (tests.test_fasta.FastaTest.test_iter_full_name) ... ok 378s test_iter_object (tests.test_fasta.FastaTest.test_iter_object) ... ok 378s test_iter_tuple (tests.test_fasta.FastaTest.test_iter_tuple) ... ok 378s test_iter_upper (tests.test_fasta.FastaTest.test_iter_upper) ... ok 378s test_iter_upper_full_name (tests.test_fasta.FastaTest.test_iter_upper_full_name) ... ok 378s test_key_func (tests.test_fasta.FastaTest.test_key_func) ... ok 378s test_module (tests.test_fasta.FastaTest.test_module) ... ok 378s test_no_upper (tests.test_fasta.FastaTest.test_no_upper) ... ok 378s test_repr (tests.test_fasta.FastaTest.test_repr) ... ok 378s test_seq_fetch (tests.test_fasta.FastaTest.test_seq_fetch) ... ok 378s test_seq_flank (tests.test_fasta.FastaTest.test_seq_flank) ... ok 378s test_seq_type (tests.test_fasta.FastaTest.test_seq_type) ... ok 378s test_statistics (tests.test_fasta.FastaTest.test_statistics) ... ok 378s test_build (tests.test_fastq.FastqTest.test_build) ... ok 378s test_exception (tests.test_fastq.FastqTest.test_exception) ... ok 379s test_fastq (tests.test_fastq.FastqTest.test_fastq) ... ok 379s test_full_name (tests.test_fastq.FastqTest.test_full_name) ... ok 379s test_iter_object (tests.test_fastq.FastqTest.test_iter_object) ... ok 379s test_iter_tuple (tests.test_fastq.FastqTest.test_iter_tuple) ... ok 379s test_negative (tests.test_fastq.FastqTest.test_negative) ... ok 379s test_platform (tests.test_fastq.FastqTest.test_platform) ... ok 379s test_read_len (tests.test_fastq.FastqTest.test_read_len) ... ok 379s test_repr (tests.test_fastq.FastqTest.test_repr) ... ok 379s test_exception (tests.test_fastx.FastxTest.test_exception) ... ok 379s test_fasta_iter (tests.test_fastx.FastxTest.test_fasta_iter) ... ok 379s test_fasta_upper (tests.test_fastx.FastxTest.test_fasta_upper) ... ok 379s test_fastq_iter (tests.test_fastx.FastxTest.test_fastq_iter) ... ok 379s test_fastx_repr (tests.test_fastx.FastxTest.test_fastx_repr) ... ok 379s test_exception (tests.test_fqkeys.FastxTest.test_exception) ... ok 379s test_fastq_key (tests.test_fqkeys.FastxTest.test_fastq_key) ... ok 379s test_read (tests.test_read.ReadTest.test_read) ... ok 379s test_read_description (tests.test_read.ReadTest.test_read_description) ... ok 379s test_read_raw (tests.test_read.ReadTest.test_read_raw) ... ok 379s test_read_seq (tests.test_read.ReadTest.test_read_seq) ... ok 380s test_repr (tests.test_read.ReadTest.test_repr) ... ok 380s test_full_compo (tests.test_sequence.SequenceTest.test_full_compo) ... ok 380s test_seq_by_index (tests.test_sequence.SequenceTest.test_seq_by_index) ... ok 380s test_seq_by_key (tests.test_sequence.SequenceTest.test_seq_by_key) ... ok 380s test_seq_content (tests.test_sequence.SequenceTest.test_seq_content) ... ok 380s test_seq_exception (tests.test_sequence.SequenceTest.test_seq_exception) ... ok 380s test_seq_iter (tests.test_sequence.SequenceTest.test_seq_iter) ... ok 380s test_seq_raw (tests.test_sequence.SequenceTest.test_seq_raw) ... ok 380s test_seq_repr (tests.test_sequence.SequenceTest.test_seq_repr) ... ok 380s test_seq_reverse_complement (tests.test_sequence.SequenceTest.test_seq_reverse_complement) ... ok 380s test_seq_slice (tests.test_sequence.SequenceTest.test_seq_slice) ... ok 380s test_seq_by_index (tests.test_sequence_error.SequenceErrorTest.test_seq_by_index) ... ok 380s test_seq_by_key (tests.test_sequence_error.SequenceErrorTest.test_seq_by_key) ... pyfastx: 2.0.2; zlib: 1.3; sqlite: 3.44.2; zran: 1.7.0 380s ok 380s 380s ---------------------------------------------------------------------- 380s Ran 56 tests in 3.223s 380s 380s OK 381s autopkgtest [18:47:29]: test run-unit-test: -----------------------] 381s autopkgtest [18:47:29]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 381s run-unit-test PASS 381s autopkgtest [18:47:29]: test test-cli: preparing testbed 470s autopkgtest [18:48:58]: @@@@@@@@@@@@@@@@@@@@ test bed setup 470s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 471s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [3976 B] 471s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [2629 kB] 471s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [429 kB] 471s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [37.3 kB] 471s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [579 kB] 471s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 471s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [20.3 kB] 471s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 471s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [2931 kB] 471s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 471s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [39.6 kB] 471s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 473s Fetched 6798 kB in 1s (4628 kB/s) 473s Reading package lists... 475s Reading package lists... 475s Building dependency tree... 475s Reading state information... 475s Calculating upgrade... 476s The following package was automatically installed and is no longer required: 476s ubuntu-advantage-tools 476s Use 'sudo apt autoremove' to remove it. 476s The following NEW packages will be installed: 476s libnuma1 libsensors-config libsensors5 numactl sysstat 476s The following packages will be upgraded: 476s efibootmgr libsqlite3-0 python3-attr readline-common ubuntu-minimal 476s ubuntu-standard 476s 6 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. 476s Need to get 1437 kB of archives. 476s After this operation, 2215 kB of additional disk space will be used. 476s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsqlite3-0 arm64 3.45.1-1ubuntu1 [704 kB] 476s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 readline-common all 8.2-3.1 [56.4 kB] 476s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.535 [10.5 kB] 476s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libnuma1 arm64 2.0.18-1 [23.5 kB] 476s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.535 [10.5 kB] 476s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 efibootmgr arm64 18-1build1 [31.5 kB] 476s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libsensors-config all 1:3.6.0-9 [5458 B] 476s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libsensors5 arm64 1:3.6.0-9 [26.9 kB] 476s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 numactl arm64 2.0.18-1 [39.5 kB] 476s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 python3-attr all 23.2.0-2 [48.6 kB] 476s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 sysstat arm64 12.6.1-1ubuntu1 [480 kB] 477s Preconfiguring packages ... 477s Fetched 1437 kB in 1s (2124 kB/s) 477s (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 ... 74662 files and directories currently installed.) 477s Preparing to unpack .../00-libsqlite3-0_3.45.1-1ubuntu1_arm64.deb ... 477s Unpacking libsqlite3-0:arm64 (3.45.1-1ubuntu1) over (3.45.1-1) ... 477s Preparing to unpack .../01-readline-common_8.2-3.1_all.deb ... 477s Unpacking readline-common (8.2-3.1) over (8.2-3) ... 477s Preparing to unpack .../02-ubuntu-minimal_1.535_arm64.deb ... 477s Unpacking ubuntu-minimal (1.535) over (1.534) ... 477s Selecting previously unselected package libnuma1:arm64. 477s Preparing to unpack .../03-libnuma1_2.0.18-1_arm64.deb ... 477s Unpacking libnuma1:arm64 (2.0.18-1) ... 477s Preparing to unpack .../04-ubuntu-standard_1.535_arm64.deb ... 477s Unpacking ubuntu-standard (1.535) over (1.534) ... 477s Preparing to unpack .../05-efibootmgr_18-1build1_arm64.deb ... 477s Unpacking efibootmgr (18-1build1) over (18-1) ... 477s Selecting previously unselected package libsensors-config. 478s Preparing to unpack .../06-libsensors-config_1%3a3.6.0-9_all.deb ... 478s Unpacking libsensors-config (1:3.6.0-9) ... 478s Selecting previously unselected package libsensors5:arm64. 478s Preparing to unpack .../07-libsensors5_1%3a3.6.0-9_arm64.deb ... 478s Unpacking libsensors5:arm64 (1:3.6.0-9) ... 478s Selecting previously unselected package numactl. 478s Preparing to unpack .../08-numactl_2.0.18-1_arm64.deb ... 478s Unpacking numactl (2.0.18-1) ... 478s Preparing to unpack .../09-python3-attr_23.2.0-2_all.deb ... 478s Unpacking python3-attr (23.2.0-2) over (23.2.0-1) ... 478s Selecting previously unselected package sysstat. 478s Preparing to unpack .../10-sysstat_12.6.1-1ubuntu1_arm64.deb ... 478s Unpacking sysstat (12.6.1-1ubuntu1) ... 478s Setting up python3-attr (23.2.0-2) ... 478s Setting up efibootmgr (18-1build1) ... 478s Setting up ubuntu-minimal (1.535) ... 478s Setting up libsqlite3-0:arm64 (3.45.1-1ubuntu1) ... 478s Setting up libsensors-config (1:3.6.0-9) ... 478s Setting up ubuntu-standard (1.535) ... 478s Setting up libsensors5:arm64 (1:3.6.0-9) ... 479s Setting up libnuma1:arm64 (2.0.18-1) ... 479s Setting up readline-common (8.2-3.1) ... 479s Setting up sysstat (12.6.1-1ubuntu1) ... 479s 479s Creating config file /etc/default/sysstat with new version 479s update-alternatives: using /usr/bin/sar.sysstat to provide /usr/bin/sar (sar) in auto mode 479s Created symlink /etc/systemd/system/sysstat.service.wants/sysstat-collect.timer → /usr/lib/systemd/system/sysstat-collect.timer. 479s Created symlink /etc/systemd/system/sysstat.service.wants/sysstat-summary.timer → /usr/lib/systemd/system/sysstat-summary.timer. 479s Created symlink /etc/systemd/system/multi-user.target.wants/sysstat.service → /usr/lib/systemd/system/sysstat.service. 481s Setting up numactl (2.0.18-1) ... 481s Processing triggers for man-db (2.12.0-3) ... 482s Processing triggers for install-info (7.1-3) ... 482s Processing triggers for libc-bin (2.39-0ubuntu2) ... 483s Reading package lists... 483s Building dependency tree... 483s Reading state information... 483s The following packages will be REMOVED: 483s ubuntu-advantage-tools* 484s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. 484s After this operation, 71.7 kB disk space will be freed. 484s (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 ... 74755 files and directories currently installed.) 484s Removing ubuntu-advantage-tools (31.1) ... 484s (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 ... 74749 files and directories currently installed.) 484s Purging configuration files for ubuntu-advantage-tools (31.1) ... 485s sh: Attempting to set up Debian/Ubuntu apt sources automatically 485s sh: Distribution appears to be Ubuntu 485s Reading package lists... 485s Building dependency tree... 485s Reading state information... 486s eatmydata is already the newest version (131-1). 486s dbus is already the newest version (1.14.10-4ubuntu1). 486s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 486s Reading package lists... 486s Building dependency tree... 486s Reading state information... 487s rng-tools-debian is already the newest version (2.4). 487s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 487s Reading package lists... 487s Building dependency tree... 487s Reading state information... 488s haveged is already the newest version (1.9.14-1ubuntu1). 488s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 488s Reading package lists... 488s Building dependency tree... 488s Reading state information... 489s The following packages will be REMOVED: 489s cloud-init* python3-configobj* python3-debconf* 489s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 489s After this operation, 3248 kB disk space will be freed. 489s (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 ... 74748 files and directories currently installed.) 489s Removing cloud-init (24.1-0ubuntu1) ... 490s Removing python3-configobj (5.0.8-3) ... 490s Removing python3-debconf (1.5.86) ... 490s Processing triggers for man-db (2.12.0-3) ... 490s (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 ... 74359 files and directories currently installed.) 490s Purging configuration files for cloud-init (24.1-0ubuntu1) ... 491s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 491s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 492s Reading package lists... 492s Building dependency tree... 492s Reading state information... 493s linux-generic is already the newest version (6.8.0-11.11+1). 493s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 493s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 493s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 493s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 493s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 495s Reading package lists... 495s Reading package lists... 495s Building dependency tree... 495s Reading state information... 495s Calculating upgrade... 496s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 496s Reading package lists... 496s Building dependency tree... 496s Reading state information... 496s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 497s autopkgtest [18:49:25]: rebooting testbed after setup commands that affected boot 757s autopkgtest [18:53:45]: testbed dpkg architecture: arm64 762s Reading package lists... 762s Building dependency tree... 762s Reading state information... 763s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 763s Starting 2 pkgProblemResolver with broken count: 0 763s Done 763s Done 763s Starting pkgProblemResolver with broken count: 0 763s Starting 2 pkgProblemResolver with broken count: 0 763s Done 764s The following additional packages will be installed: 764s pyfastx python3-importlib-metadata python3-more-itertools python3-pyfaidx 764s python3-pyfastx python3-zipp 764s Recommended packages: 764s python3-biopython 765s The following NEW packages will be installed: 765s pyfastx python3-importlib-metadata python3-more-itertools python3-pyfaidx 765s python3-pyfastx python3-zipp 765s 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. 765s 1 not fully installed or removed. 765s Need to get 295 kB of archives. 765s After this operation, 995 kB of additional disk space will be used. 765s Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 python3-more-itertools all 10.2.0-1 [52.9 kB] 765s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 python3-zipp all 1.0.0-6 [6090 B] 765s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 python3-importlib-metadata all 4.12.0-1 [17.8 kB] 765s Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pyfaidx all 0.8.1.1-1 [29.6 kB] 765s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pyfastx arm64 2.0.2-2 [66.0 kB] 765s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 pyfastx arm64 2.0.2-2 [123 kB] 766s Fetched 295 kB in 1s (487 kB/s) 766s Selecting previously unselected package python3-more-itertools. 766s (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 ... 74304 files and directories currently installed.) 766s Preparing to unpack .../0-python3-more-itertools_10.2.0-1_all.deb ... 766s Unpacking python3-more-itertools (10.2.0-1) ... 766s Selecting previously unselected package python3-zipp. 766s Preparing to unpack .../1-python3-zipp_1.0.0-6_all.deb ... 766s Unpacking python3-zipp (1.0.0-6) ... 766s Selecting previously unselected package python3-importlib-metadata. 766s Preparing to unpack .../2-python3-importlib-metadata_4.12.0-1_all.deb ... 766s Unpacking python3-importlib-metadata (4.12.0-1) ... 766s Selecting previously unselected package python3-pyfaidx. 766s Preparing to unpack .../3-python3-pyfaidx_0.8.1.1-1_all.deb ... 766s Unpacking python3-pyfaidx (0.8.1.1-1) ... 766s Selecting previously unselected package python3-pyfastx. 766s Preparing to unpack .../4-python3-pyfastx_2.0.2-2_arm64.deb ... 766s Unpacking python3-pyfastx (2.0.2-2) ... 766s Selecting previously unselected package pyfastx. 766s Preparing to unpack .../5-pyfastx_2.0.2-2_arm64.deb ... 766s Unpacking pyfastx (2.0.2-2) ... 766s Setting up python3-more-itertools (10.2.0-1) ... 767s Setting up python3-zipp (1.0.0-6) ... 767s Setting up python3-importlib-metadata (4.12.0-1) ... 767s Setting up python3-pyfaidx (0.8.1.1-1) ... 767s Setting up python3-pyfastx (2.0.2-2) ... 767s Setting up pyfastx (2.0.2-2) ... 767s Setting up autopkgtest-satdep (0) ... 767s Processing triggers for man-db (2.12.0-3) ... 772s (Reading database ... 74400 files and directories currently installed.) 772s Removing autopkgtest-satdep (0) ... 774s autopkgtest [18:54:02]: test test-cli: [----------------------- 774s $ pyfastx --help 774s usage: pyfastx COMMAND [OPTIONS] 774s 774s A command line tool for FASTA/Q file manipulation 774s 774s options: 774s -h, --help show this help message and exit 774s -v, --version show program's version number and exit 774s 774s Commands: 774s 774s index build index for fasta/q file 774s stat show detailed statistics information of fasta/q file 774s split split fasta/q file into multiple files 774s fq2fa convert fastq file to fasta file 774s subseq get subsequences from fasta file by region 774s sample randomly sample sequences from fasta or fastq file 774s extract extract full sequences or reads from fasta/q file 775s $ # Found pyfastx commands: 'index stat split fq2fa subseq sample extract' 775s $ pyfastx index --help 775s usage: pyfastx index [-h] [-f] fastx [fastx ...] 775s 775s positional arguments: 775s fastx fasta or fastq file, gzip support 775s 775s options: 775s -h, --help show this help message and exit 775s -f, --full build full index, base composition will be calculated 775s $ pyfastx stat --help 775s usage: pyfastx stat [-h] fastx [fastx ...] 775s 775s positional arguments: 775s fastx fasta or fastq file, gzip support 775s 775s options: 775s -h, --help show this help message and exit 775s $ pyfastx split --help 775s usage: pyfastx split [-h] (-n int | -c int) [-o str] fastx 775s 775s positional arguments: 775s fastx fasta or fastq file, gzip support 775s 775s options: 775s -h, --help show this help message and exit 775s -n int split a fasta/q file into N new files with even size 775s -c int split a fasta/q file into multiple files containing 775s the same sequence counts 775s -o str, --out-dir str 775s output directory, default is current folder 775s $ pyfastx fq2fa --help 775s usage: pyfastx fq2fa [-h] [-o str] fastx 775s 775s positional arguments: 775s fastx fastq file, gzip support 775s 775s options: 775s -h, --help show this help message and exit 775s -o str, --out-file str 775s output file, default: output to stdout 775s $ pyfastx subseq --help 775s usage: pyfastx subseq [-h] [-r str | -b str] [-o str] fastx [region ...] 775s 775s positional arguments: 775s fastx input fasta file, gzip support 775s region format is chr:start-end, start and end position is 775s 1-based, multiple regions were separated by space 775s 775s options: 775s -h, --help show this help message and exit 775s -r str, --region-file str 775s tab-delimited file, one region per line, both start 775s and end position are 1-based 775s -b str, --bed-file str 775s tab-delimited BED file, 0-based start position and 775s 1-based end position 775s -o str, --out-file str 775s output file, default: output to stdout 775s $ pyfastx sample --help 775s usage: pyfastx sample [-h] (-n int | -p float) [-s int] [--sequential-read] 775s [-o str] 775s fastx 775s 775s positional arguments: 775s fastx fasta or fastq file, gzip support 775s 775s options: 775s -h, --help show this help message and exit 775s -n int number of sequences to be sampled 775s -p float proportion of sequences to be sampled, 0~1 775s -s int, --seed int random seed, default is the current system time 775s --sequential-read start sequential reading, particularly suitable for 775s sampling large numbers of sequences 775s -o str, --out-file str 775s output file, default: output to stdout 775s $ pyfastx extract --help 776s usage: pyfastx extract [-h] [-l str] [--reverse-complement] [--out-fasta] 776s [-o str] [--sequential-read] 776s fastx [name ...] 776s 776s positional arguments: 776s fastx fasta or fastq file, gzip support 776s name sequence name or read name, multiple names were 776s separated by space 776s 776s options: 776s -h, --help show this help message and exit 776s -l str, --list-file str 776s a file containing sequence or read names, one name per 776s line 776s --reverse-complement output reverse complement sequence 776s --out-fasta output fasta format when extract reads from fastq, 776s default output fastq format 776s -o str, --out-file str 776s output file, default: output to stdout 776s --sequential-read start sequential reading, particularly suitable for 776s extracting large numbers of sequences 776s $ pyfastx --version 776s pyfastx version 2.0.2 776s $ pyfastx index protein.fa 776s $ pyfastx index rna.fa 776s $ pyfastx index test.fa 776s $ pyfastx index test.fq 777s $ pyfastx index test.fa.gz 777s $ pyfastx index test.fq.gz 777s $ pyfastx stat protein.fa 777s fileName seqType seqCounts totalBases GC% avgLen medianLen maxLen minLen N50 L50 777s protein.fa protein 17 2265 - 133.235 80.0 419 23 263 4 777s $ pyfastx split -n 2 protein.fa 778s $ pyfastx fq2fa test.fq -o test.fa 778s $ pyfastx subseq protein.fa UPI0000000011:1-4 778s >UPI0000000011:1-4 778s MVDA 778s $ pyfastx sample -n 1 test.fq.gz -o sample.fq 778s $ pyfastx extract protein.fa UPI0000000011 778s >UPI0000000011 status=active 778s MVDAITVLTAIGITVLMLLMVISGAAMIVKELNPNDIFTMQSLKFNRAVTIFKYIGLFIY 778s IPGTIILYATYVKSLLMKS 779s autopkgtest [18:54:07]: test test-cli: -----------------------] 779s autopkgtest [18:54:07]: test test-cli: - - - - - - - - - - results - - - - - - - - - - 779s test-cli PASS 780s autopkgtest [18:54:08]: @@@@@@@@@@@@@@@@@@@@ summary 780s run-unit-test PASS 780s test-cli PASS 791s Creating nova instance adt-noble-arm64-pyfastx-20240309-184108-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240308.img (UUID ddbc0ee7-bb97-4aa3-b5e1-9386758c2ba2)... 791s Creating nova instance adt-noble-arm64-pyfastx-20240309-184108-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240308.img (UUID ddbc0ee7-bb97-4aa3-b5e1-9386758c2ba2)...