0s autopkgtest [21:14:05]: starting date and time: 2024-11-23 21:14:05+0000 0s autopkgtest [21:14:05]: git checkout: 0acbae0a WIP show VirtSubproc stderr in real-time 0s autopkgtest [21:14:05]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.drjz_m3z/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade pyfastx --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@lcy02-4.secgroup --name adt-plucky-amd64-pyfastx-20241123-203903-juju-7f2275-prod-proposed-migration-environment-2-c46afc55-44fe-46fa-a9bd-f10a91afb641 --image adt/ubuntu-plucky-amd64-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,keyserver.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/ 39s autopkgtest [21:14:44]: testbed dpkg architecture: amd64 39s autopkgtest [21:14:44]: testbed apt version: 2.9.8 39s autopkgtest [21:14:44]: @@@@@@@@@@@@@@@@@@@@ test bed setup 39s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 39s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [925 kB] 39s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9704 B] 39s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.6 kB] 39s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [53.2 kB] 39s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [89.4 kB] 39s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [41.5 kB] 39s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2408 B] 39s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [40.1 kB] 39s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [800 kB] 39s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [290 kB] 40s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [20.0 kB] 40s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [5528 B] 40s Fetched 2364 kB in 0s (7974 kB/s) 40s Reading package lists... 41s Reading package lists... 41s Building dependency tree... 41s Reading state information... 42s Calculating upgrade... 42s The following package was automatically installed and is no longer required: 42s libsgutils2-1.46-2 42s Use 'sudo apt autoremove' to remove it. 42s The following NEW packages will be installed: 42s libsgutils2-1.48 42s The following packages will be upgraded: 42s amd64-microcode bash bpftrace curl debconf debconf-i18n distro-info 42s dracut-install fwupd-signed gir1.2-girepository-2.0 gir1.2-glib-2.0 hostname 42s intel-microcode libaudit-common libaudit1 libcurl3t64-gnutls libcurl4t64 42s libgirepository-1.0-1 libglib2.0-0t64 libglib2.0-data libpam-modules 42s libpam-modules-bin libpam-runtime libpam0g libplymouth5 libpython3-stdlib 42s libselinux1 libsemanage-common libsemanage2 linux-base lxd-installer 42s openssh-client openssh-server openssh-sftp-server pinentry-curses plymouth 42s plymouth-theme-ubuntu-text python3 python3-blinker python3-debconf 42s python3-jsonschema-specifications python3-minimal python3-rpds-py sg3-utils 42s sg3-utils-udev vim-common vim-tiny xxd 42s 48 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 42s Need to get 19.4 MB of archives. 42s After this operation, 3523 kB of additional disk space will be used. 42s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 bash amd64 5.2.32-1ubuntu2 [918 kB] 42s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 hostname amd64 3.25 [11.1 kB] 42s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu1 [6578 B] 42s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu1 [53.9 kB] 42s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 debconf-i18n all 1.5.87ubuntu1 [204 kB] 42s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 42s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 42s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 42s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-debconf all 1.5.87ubuntu1 [4156 B] 42s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 debconf all 1.5.87ubuntu1 [124 kB] 42s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam0g amd64 1.5.3-7ubuntu4 [69.6 kB] 42s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libselinux1 amd64 3.7-3ubuntu1 [86.9 kB] 42s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam-modules-bin amd64 1.5.3-7ubuntu4 [53.7 kB] 42s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam-modules amd64 1.5.3-7ubuntu4 [294 kB] 42s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 openssh-sftp-server amd64 1:9.9p1-3ubuntu2 [41.2 kB] 42s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 openssh-server amd64 1:9.9p1-3ubuntu2 [625 kB] 42s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 openssh-client amd64 1:9.9p1-3ubuntu2 [1080 kB] 42s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam-runtime all 1.5.3-7ubuntu4 [40.8 kB] 42s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage-common all 3.7-2build1 [7186 B] 42s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage2 amd64 3.7-2build1 [105 kB] 42s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 distro-info amd64 1.12 [20.0 kB] 42s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-girepository-2.0 amd64 1.82.0-2 [25.3 kB] 42s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-glib-2.0 amd64 2.82.2-3 [182 kB] 42s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-0t64 amd64 2.82.2-3 [1655 kB] 42s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libgirepository-1.0-1 amd64 1.82.0-2 [88.7 kB] 42s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-data all 2.82.2-3 [51.7 kB] 42s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 vim-tiny amd64 2:9.1.0861-1ubuntu1 [1037 kB] 42s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 vim-common all 2:9.1.0861-1ubuntu1 [395 kB] 42s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 xxd amd64 2:9.1.0861-1ubuntu1 [67.8 kB] 42s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libplymouth5 amd64 24.004.60-2ubuntu3 [145 kB] 42s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 plymouth-theme-ubuntu-text amd64 24.004.60-2ubuntu3 [10.3 kB] 42s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 plymouth amd64 24.004.60-2ubuntu3 [140 kB] 42s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 bpftrace amd64 0.21.2-2ubuntu3 [1787 kB] 42s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 curl amd64 8.9.1-2ubuntu3 [243 kB] 42s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4t64 amd64 8.9.1-2ubuntu3 [420 kB] 42s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 dracut-install amd64 105-2ubuntu2 [35.9 kB] 42s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd-signed amd64 1.55+1.7-1 [30.6 kB] 42s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl3t64-gnutls amd64 8.9.1-2ubuntu3 [412 kB] 42s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libsgutils2-1.48 amd64 1.48-0ubuntu1 [124 kB] 42s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-base all 4.10.1ubuntu1 [34.8 kB] 42s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 lxd-installer all 10 [5264 B] 42s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 pinentry-curses amd64 1.3.1-0ubuntu2 [41.6 kB] 42s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-blinker all 1.9.0-1 [10.7 kB] 42s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-rpds-py amd64 0.21.0-2ubuntu1 [323 kB] 42s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jsonschema-specifications all 2023.12.1-2 [9116 B] 42s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 sg3-utils amd64 1.48-0ubuntu1 [1042 kB] 42s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 sg3-utils-udev all 1.48-0ubuntu1 [6608 B] 42s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 amd64-microcode amd64 3.20240820.1ubuntu1 [187 kB] 42s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 intel-microcode amd64 3.20241112.1ubuntu2 [7055 kB] 43s Preconfiguring packages ... 43s Fetched 19.4 MB in 0s (92.9 MB/s) 43s (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 ... 75624 files and directories currently installed.) 43s Preparing to unpack .../bash_5.2.32-1ubuntu2_amd64.deb ... 43s Unpacking bash (5.2.32-1ubuntu2) over (5.2.32-1ubuntu1) ... 43s Setting up bash (5.2.32-1ubuntu2) ... 43s update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode 43s (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 ... 75624 files and directories currently installed.) 43s Preparing to unpack .../hostname_3.25_amd64.deb ... 43s Unpacking hostname (3.25) over (3.23+nmu2ubuntu2) ... 43s Setting up hostname (3.25) ... 43s (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 ... 75624 files and directories currently installed.) 43s Preparing to unpack .../libaudit-common_1%3a4.0.2-2ubuntu1_all.deb ... 43s Unpacking libaudit-common (1:4.0.2-2ubuntu1) over (1:4.0.1-1ubuntu2) ... 43s Setting up libaudit-common (1:4.0.2-2ubuntu1) ... 43s (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 ... 75624 files and directories currently installed.) 43s Preparing to unpack .../libaudit1_1%3a4.0.2-2ubuntu1_amd64.deb ... 43s Unpacking libaudit1:amd64 (1:4.0.2-2ubuntu1) over (1:4.0.1-1ubuntu2) ... 43s Setting up libaudit1:amd64 (1:4.0.2-2ubuntu1) ... 43s (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 ... 75624 files and directories currently installed.) 43s Preparing to unpack .../debconf-i18n_1.5.87ubuntu1_all.deb ... 43s Unpacking debconf-i18n (1.5.87ubuntu1) over (1.5.86ubuntu1) ... 43s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 43s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 43s Setting up python3-minimal (3.12.7-1) ... 44s (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 ... 75624 files and directories currently installed.) 44s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 44s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 44s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 44s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 44s Preparing to unpack .../python3-debconf_1.5.87ubuntu1_all.deb ... 44s Unpacking python3-debconf (1.5.87ubuntu1) over (1.5.86ubuntu1) ... 44s Preparing to unpack .../debconf_1.5.87ubuntu1_all.deb ... 44s Unpacking debconf (1.5.87ubuntu1) over (1.5.86ubuntu1) ... 44s Setting up debconf (1.5.87ubuntu1) ... 44s (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 ... 75624 files and directories currently installed.) 44s Preparing to unpack .../libpam0g_1.5.3-7ubuntu4_amd64.deb ... 44s Unpacking libpam0g:amd64 (1.5.3-7ubuntu4) over (1.5.3-7ubuntu2) ... 44s Setting up libpam0g:amd64 (1.5.3-7ubuntu4) ... 44s (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 ... 75624 files and directories currently installed.) 44s Preparing to unpack .../libselinux1_3.7-3ubuntu1_amd64.deb ... 44s Unpacking libselinux1:amd64 (3.7-3ubuntu1) over (3.5-2ubuntu5) ... 44s Setting up libselinux1:amd64 (3.7-3ubuntu1) ... 44s (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 ... 75624 files and directories currently installed.) 44s Preparing to unpack .../libpam-modules-bin_1.5.3-7ubuntu4_amd64.deb ... 44s Unpacking libpam-modules-bin (1.5.3-7ubuntu4) over (1.5.3-7ubuntu2) ... 44s Setting up libpam-modules-bin (1.5.3-7ubuntu4) ... 45s pam_namespace.service is a disabled or a static unit not running, not starting it. 45s (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 ... 75624 files and directories currently installed.) 45s Preparing to unpack .../libpam-modules_1.5.3-7ubuntu4_amd64.deb ... 45s Unpacking libpam-modules:amd64 (1.5.3-7ubuntu4) over (1.5.3-7ubuntu2) ... 45s Setting up libpam-modules:amd64 (1.5.3-7ubuntu4) ... 45s (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 ... 75624 files and directories currently installed.) 45s Preparing to unpack .../openssh-sftp-server_1%3a9.9p1-3ubuntu2_amd64.deb ... 45s Unpacking openssh-sftp-server (1:9.9p1-3ubuntu2) over (1:9.7p1-7ubuntu5) ... 45s Preparing to unpack .../openssh-server_1%3a9.9p1-3ubuntu2_amd64.deb ... 45s Unpacking openssh-server (1:9.9p1-3ubuntu2) over (1:9.7p1-7ubuntu5) ... 45s Preparing to unpack .../openssh-client_1%3a9.9p1-3ubuntu2_amd64.deb ... 45s Unpacking openssh-client (1:9.9p1-3ubuntu2) over (1:9.7p1-7ubuntu5) ... 45s Preparing to unpack .../libpam-runtime_1.5.3-7ubuntu4_all.deb ... 45s Unpacking libpam-runtime (1.5.3-7ubuntu4) over (1.5.3-7ubuntu2) ... 45s Setting up libpam-runtime (1.5.3-7ubuntu4) ... 45s (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 ... 75626 files and directories currently installed.) 45s Preparing to unpack .../libsemanage-common_3.7-2build1_all.deb ... 45s Unpacking libsemanage-common (3.7-2build1) over (3.5-1build6) ... 46s Setting up libsemanage-common (3.7-2build1) ... 46s (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 ... 75625 files and directories currently installed.) 46s Preparing to unpack .../libsemanage2_3.7-2build1_amd64.deb ... 46s Unpacking libsemanage2:amd64 (3.7-2build1) over (3.5-1build6) ... 46s Setting up libsemanage2:amd64 (3.7-2build1) ... 46s (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 ... 75625 files and directories currently installed.) 46s Preparing to unpack .../00-distro-info_1.12_amd64.deb ... 46s Unpacking distro-info (1.12) over (1.9) ... 46s Preparing to unpack .../01-gir1.2-girepository-2.0_1.82.0-2_amd64.deb ... 46s Unpacking gir1.2-girepository-2.0:amd64 (1.82.0-2) over (1.80.1-4) ... 46s Preparing to unpack .../02-gir1.2-glib-2.0_2.82.2-3_amd64.deb ... 46s Unpacking gir1.2-glib-2.0:amd64 (2.82.2-3) over (2.82.1-0ubuntu1) ... 46s Preparing to unpack .../03-libglib2.0-0t64_2.82.2-3_amd64.deb ... 46s Unpacking libglib2.0-0t64:amd64 (2.82.2-3) over (2.82.1-0ubuntu1) ... 46s Preparing to unpack .../04-libgirepository-1.0-1_1.82.0-2_amd64.deb ... 46s Unpacking libgirepository-1.0-1:amd64 (1.82.0-2) over (1.80.1-4) ... 46s Preparing to unpack .../05-libglib2.0-data_2.82.2-3_all.deb ... 46s Unpacking libglib2.0-data (2.82.2-3) over (2.82.1-0ubuntu1) ... 46s Preparing to unpack .../06-vim-tiny_2%3a9.1.0861-1ubuntu1_amd64.deb ... 46s Unpacking vim-tiny (2:9.1.0861-1ubuntu1) over (2:9.1.0777-1ubuntu1) ... 46s Preparing to unpack .../07-vim-common_2%3a9.1.0861-1ubuntu1_all.deb ... 46s Unpacking vim-common (2:9.1.0861-1ubuntu1) over (2:9.1.0777-1ubuntu1) ... 46s Preparing to unpack .../08-xxd_2%3a9.1.0861-1ubuntu1_amd64.deb ... 46s Unpacking xxd (2:9.1.0861-1ubuntu1) over (2:9.1.0777-1ubuntu1) ... 46s Preparing to unpack .../09-libplymouth5_24.004.60-2ubuntu3_amd64.deb ... 46s Unpacking libplymouth5:amd64 (24.004.60-2ubuntu3) over (24.004.60-1ubuntu11) ... 46s Preparing to unpack .../10-plymouth-theme-ubuntu-text_24.004.60-2ubuntu3_amd64.deb ... 46s Unpacking plymouth-theme-ubuntu-text (24.004.60-2ubuntu3) over (24.004.60-1ubuntu11) ... 46s Preparing to unpack .../11-plymouth_24.004.60-2ubuntu3_amd64.deb ... 46s Unpacking plymouth (24.004.60-2ubuntu3) over (24.004.60-1ubuntu11) ... 46s Preparing to unpack .../12-bpftrace_0.21.2-2ubuntu3_amd64.deb ... 46s Unpacking bpftrace (0.21.2-2ubuntu3) over (0.21.2-2ubuntu2) ... 46s Preparing to unpack .../13-curl_8.9.1-2ubuntu3_amd64.deb ... 46s Unpacking curl (8.9.1-2ubuntu3) over (8.9.1-2ubuntu2) ... 46s Preparing to unpack .../14-libcurl4t64_8.9.1-2ubuntu3_amd64.deb ... 46s Unpacking libcurl4t64:amd64 (8.9.1-2ubuntu3) over (8.9.1-2ubuntu2) ... 46s Preparing to unpack .../15-dracut-install_105-2ubuntu2_amd64.deb ... 46s Unpacking dracut-install (105-2ubuntu2) over (105-1ubuntu1) ... 46s Preparing to unpack .../16-fwupd-signed_1.55+1.7-1_amd64.deb ... 46s Unpacking fwupd-signed (1.55+1.7-1) over (1.54+1.6-1build1) ... 46s Preparing to unpack .../17-libcurl3t64-gnutls_8.9.1-2ubuntu3_amd64.deb ... 46s Unpacking libcurl3t64-gnutls:amd64 (8.9.1-2ubuntu3) over (8.9.1-2ubuntu2) ... 46s Selecting previously unselected package libsgutils2-1.48:amd64. 46s Preparing to unpack .../18-libsgutils2-1.48_1.48-0ubuntu1_amd64.deb ... 46s Unpacking libsgutils2-1.48:amd64 (1.48-0ubuntu1) ... 46s Preparing to unpack .../19-linux-base_4.10.1ubuntu1_all.deb ... 46s Unpacking linux-base (4.10.1ubuntu1) over (4.5ubuntu9) ... 46s Preparing to unpack .../20-lxd-installer_10_all.deb ... 46s Unpacking lxd-installer (10) over (9) ... 46s Preparing to unpack .../21-pinentry-curses_1.3.1-0ubuntu2_amd64.deb ... 46s Unpacking pinentry-curses (1.3.1-0ubuntu2) over (1.2.1-3ubuntu5) ... 46s Preparing to unpack .../22-python3-blinker_1.9.0-1_all.deb ... 47s Unpacking python3-blinker (1.9.0-1) over (1.8.2-1) ... 47s Preparing to unpack .../23-python3-rpds-py_0.21.0-2ubuntu1_amd64.deb ... 47s Unpacking python3-rpds-py (0.21.0-2ubuntu1) over (0.20.0-0ubuntu3) ... 47s Preparing to unpack .../24-python3-jsonschema-specifications_2023.12.1-2_all.deb ... 47s Unpacking python3-jsonschema-specifications (2023.12.1-2) over (2023.12.1-1ubuntu1) ... 47s Preparing to unpack .../25-sg3-utils_1.48-0ubuntu1_amd64.deb ... 47s Unpacking sg3-utils (1.48-0ubuntu1) over (1.46-3ubuntu5) ... 47s Preparing to unpack .../26-sg3-utils-udev_1.48-0ubuntu1_all.deb ... 47s Unpacking sg3-utils-udev (1.48-0ubuntu1) over (1.46-3ubuntu5) ... 47s Preparing to unpack .../27-amd64-microcode_3.20240820.1ubuntu1_amd64.deb ... 47s Unpacking amd64-microcode (3.20240820.1ubuntu1) over (3.20240116.2+nmu1ubuntu1.1) ... 47s Preparing to unpack .../28-intel-microcode_3.20241112.1ubuntu2_amd64.deb ... 47s Unpacking intel-microcode (3.20241112.1ubuntu2) over (3.20241112.1ubuntu1) ... 47s Setting up pinentry-curses (1.3.1-0ubuntu2) ... 47s Setting up distro-info (1.12) ... 47s Setting up linux-base (4.10.1ubuntu1) ... 47s Setting up libcurl4t64:amd64 (8.9.1-2ubuntu3) ... 47s Setting up bpftrace (0.21.2-2ubuntu3) ... 47s Setting up openssh-client (1:9.9p1-3ubuntu2) ... 47s Setting up intel-microcode (3.20241112.1ubuntu2) ... 47s intel-microcode: microcode will be updated at next boot 47s Setting up libcurl3t64-gnutls:amd64 (8.9.1-2ubuntu3) ... 47s Setting up fwupd-signed (1.55+1.7-1) ... 47s Setting up libsgutils2-1.48:amd64 (1.48-0ubuntu1) ... 47s Setting up debconf-i18n (1.5.87ubuntu1) ... 47s Setting up amd64-microcode (3.20240820.1ubuntu1) ... 47s amd64-microcode: microcode will be updated at next boot 47s Setting up xxd (2:9.1.0861-1ubuntu1) ... 47s Setting up libglib2.0-0t64:amd64 (2.82.2-3) ... 47s No schema files found: doing nothing. 47s Setting up libglib2.0-data (2.82.2-3) ... 47s Setting up vim-common (2:9.1.0861-1ubuntu1) ... 47s Setting up gir1.2-glib-2.0:amd64 (2.82.2-3) ... 47s Setting up lxd-installer (10) ... 48s Setting up dracut-install (105-2ubuntu2) ... 48s Setting up libplymouth5:amd64 (24.004.60-2ubuntu3) ... 48s Setting up libgirepository-1.0-1:amd64 (1.82.0-2) ... 48s Setting up curl (8.9.1-2ubuntu3) ... 48s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 48s Setting up sg3-utils (1.48-0ubuntu1) ... 48s Setting up openssh-sftp-server (1:9.9p1-3ubuntu2) ... 48s Setting up openssh-server (1:9.9p1-3ubuntu2) ... 48s Installing new version of config file /etc/ssh/moduli ... 48s Replacing config file /etc/ssh/sshd_config with new version 49s Setting up plymouth (24.004.60-2ubuntu3) ... 49s update-initramfs: Generating /boot/initrd.img-6.11.0-8-generic 49s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 57s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 57s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 58s Setting up python3 (3.12.7-1) ... 58s Setting up vim-tiny (2:9.1.0861-1ubuntu1) ... 58s Setting up sg3-utils-udev (1.48-0ubuntu1) ... 58s update-initramfs: deferring update (trigger activated) 58s Setting up plymouth-theme-ubuntu-text (24.004.60-2ubuntu3) ... 58s update-initramfs: deferring update (trigger activated) 58s Setting up gir1.2-girepository-2.0:amd64 (1.82.0-2) ... 58s Setting up python3-rpds-py (0.21.0-2ubuntu1) ... 58s Setting up python3-jsonschema-specifications (2023.12.1-2) ... 58s Setting up python3-blinker (1.9.0-1) ... 58s Setting up python3-debconf (1.5.87ubuntu1) ... 58s Processing triggers for man-db (2.13.0-1) ... 60s Processing triggers for debianutils (5.21) ... 60s Processing triggers for install-info (7.1.1-1) ... 60s Processing triggers for initramfs-tools (0.142ubuntu35) ... 60s update-initramfs: Generating /boot/initrd.img-6.11.0-8-generic 60s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 68s Processing triggers for libc-bin (2.40-1ubuntu3) ... 68s Processing triggers for ufw (0.36.2-8) ... 69s Reading package lists... 69s Building dependency tree... 69s Reading state information... 69s The following packages will be REMOVED: 69s libsgutils2-1.46-2* 70s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. 70s After this operation, 294 kB disk space will be freed. 70s (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 ... 75656 files and directories currently installed.) 70s Removing libsgutils2-1.46-2:amd64 (1.46-3ubuntu5) ... 70s Processing triggers for libc-bin (2.40-1ubuntu3) ... 70s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 70s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 70s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 70s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 71s Reading package lists... 71s Reading package lists... 71s Building dependency tree... 71s Reading state information... 72s Calculating upgrade... 72s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 72s Reading package lists... 72s Building dependency tree... 72s Reading state information... 73s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 73s autopkgtest [21:15:18]: rebooting testbed after setup commands that affected boot 76s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 88s autopkgtest [21:15:33]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 89s autopkgtest [21:15:34]: @@@@@@@@@@@@@@@@@@@@ apt-source pyfastx 90s Get:1 http://ftpmaster.internal/ubuntu plucky/universe pyfastx 2.1.0-2 (dsc) [2289 B] 90s Get:2 http://ftpmaster.internal/ubuntu plucky/universe pyfastx 2.1.0-2 (tar) [230 kB] 90s Get:3 http://ftpmaster.internal/ubuntu plucky/universe pyfastx 2.1.0-2 (diff) [7412 B] 90s gpgv: Signature made Fri Aug 30 18:49:12 2024 UTC 90s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 90s gpgv: issuer "emollier@debian.org" 90s gpgv: Can't check signature: No public key 90s dpkg-source: warning: cannot verify inline signature for ./pyfastx_2.1.0-2.dsc: no acceptable signature found 90s autopkgtest [21:15:35]: testing package pyfastx version 2.1.0-2 90s autopkgtest [21:15:35]: build not needed 90s autopkgtest [21:15:35]: test run-unit-test: preparing testbed 90s Reading package lists... 91s Building dependency tree... 91s Reading state information... 91s Starting pkgProblemResolver with broken count: 0 91s Starting 2 pkgProblemResolver with broken count: 0 91s Done 92s The following additional packages will be installed: 92s libpython3.13-minimal libpython3.13-stdlib pyfastx python3-all 92s python3-importlib-metadata python3-packaging python3-pyfaidx python3-pyfastx 92s python3.13 python3.13-minimal 92s Suggested packages: 92s python3.13-venv python3.13-doc binfmt-support 92s Recommended packages: 92s python3-biopython 92s The following NEW packages will be installed: 92s autopkgtest-satdep libpython3.13-minimal libpython3.13-stdlib pyfastx 92s python3-all python3-importlib-metadata python3-packaging python3-pyfaidx 92s python3-pyfastx python3.13 python3.13-minimal 92s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. 92s Need to get 6174 kB/6175 kB of archives. 92s After this operation, 23.2 MB of additional disk space will be used. 92s Get:1 /tmp/autopkgtest.xYXzum/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [720 B] 92s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.0-2 [879 kB] 92s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.0-2 [2188 kB] 92s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [2107 kB] 92s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-importlib-metadata all 8.5.0-1 [20.7 kB] 92s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.2-1 [51.5 kB] 92s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 92s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyfastx amd64 2.1.0-2 [56.7 kB] 92s Get:9 http://ftpmaster.internal/ubuntu plucky/universe amd64 pyfastx amd64 2.1.0-2 [122 kB] 92s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.0-2 [719 kB] 92s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all amd64 3.12.7-1 [890 B] 92s Fetched 6174 kB in 0s (67.5 MB/s) 92s Selecting previously unselected package libpython3.13-minimal:amd64. 93s (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 ... 75651 files and directories currently installed.) 93s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_amd64.deb ... 93s Unpacking libpython3.13-minimal:amd64 (3.13.0-2) ... 93s Selecting previously unselected package python3.13-minimal. 93s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_amd64.deb ... 93s Unpacking python3.13-minimal (3.13.0-2) ... 93s Selecting previously unselected package libpython3.13-stdlib:amd64. 93s Preparing to unpack .../02-libpython3.13-stdlib_3.13.0-2_amd64.deb ... 93s Unpacking libpython3.13-stdlib:amd64 (3.13.0-2) ... 93s Selecting previously unselected package python3-importlib-metadata. 93s Preparing to unpack .../03-python3-importlib-metadata_8.5.0-1_all.deb ... 93s Unpacking python3-importlib-metadata (8.5.0-1) ... 93s Selecting previously unselected package python3-packaging. 93s Preparing to unpack .../04-python3-packaging_24.2-1_all.deb ... 93s Unpacking python3-packaging (24.2-1) ... 93s Selecting previously unselected package python3-pyfaidx. 93s Preparing to unpack .../05-python3-pyfaidx_0.8.1.3-1_all.deb ... 93s Unpacking python3-pyfaidx (0.8.1.3-1) ... 93s Selecting previously unselected package python3-pyfastx. 93s Preparing to unpack .../06-python3-pyfastx_2.1.0-2_amd64.deb ... 93s Unpacking python3-pyfastx (2.1.0-2) ... 93s Selecting previously unselected package pyfastx. 93s Preparing to unpack .../07-pyfastx_2.1.0-2_amd64.deb ... 93s Unpacking pyfastx (2.1.0-2) ... 93s Selecting previously unselected package python3.13. 93s Preparing to unpack .../08-python3.13_3.13.0-2_amd64.deb ... 93s Unpacking python3.13 (3.13.0-2) ... 93s Selecting previously unselected package python3-all. 93s Preparing to unpack .../09-python3-all_3.12.7-1_amd64.deb ... 93s Unpacking python3-all (3.12.7-1) ... 93s Selecting previously unselected package autopkgtest-satdep. 93s Preparing to unpack .../10-1-autopkgtest-satdep.deb ... 93s Unpacking autopkgtest-satdep (0) ... 93s Setting up python3-importlib-metadata (8.5.0-1) ... 93s Setting up libpython3.13-minimal:amd64 (3.13.0-2) ... 93s Setting up python3-packaging (24.2-1) ... 94s Setting up python3.13-minimal (3.13.0-2) ... 94s Setting up libpython3.13-stdlib:amd64 (3.13.0-2) ... 94s Setting up python3-pyfaidx (0.8.1.3-1) ... 95s Setting up python3.13 (3.13.0-2) ... 95s Setting up python3-pyfastx (2.1.0-2) ... 95s Setting up python3-all (3.12.7-1) ... 95s Setting up pyfastx (2.1.0-2) ... 95s Setting up autopkgtest-satdep (0) ... 95s Processing triggers for man-db (2.13.0-1) ... 96s Processing triggers for systemd (256.5-2ubuntu4) ... 99s (Reading database ... 76486 files and directories currently installed.) 99s Removing autopkgtest-satdep (0) ... 99s autopkgtest [21:15:44]: test run-unit-test: [----------------------- 99s tests.test_fakeys (unittest.loader._FailedTest.tests.test_fakeys) ... ERROR 99s tests.test_fasta (unittest.loader._FailedTest.tests.test_fasta) ... ERROR 99s tests.test_fastq (unittest.loader._FailedTest.tests.test_fastq) ... ERROR 99s tests.test_fastx (unittest.loader._FailedTest.tests.test_fastx) ... ERROR 99s tests.test_fqkeys (unittest.loader._FailedTest.tests.test_fqkeys) ... ERROR 99s tests.test_read (unittest.loader._FailedTest.tests.test_read) ... ERROR 99s tests.test_sequence (unittest.loader._FailedTest.tests.test_sequence) ... ERROR 99s tests.test_sequence_error (unittest.loader._FailedTest.tests.test_sequence_error) ... ERROR 99s 99s ====================================================================== 99s ERROR: tests.test_fakeys (unittest.loader._FailedTest.tests.test_fakeys) 99s ---------------------------------------------------------------------- 99s ImportError: Failed to import test module: tests.test_fakeys 99s Traceback (most recent call last): 99s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 99s module = self._get_module_from_name(name) 99s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 99s __import__(name) 99s ~~~~~~~~~~^^^^^^ 99s File "/tmp/autopkgtest.xYXzum/build.ulk/src/tests/test_fakeys.py", line 3, in 99s import pyfastx 99s ModuleNotFoundError: No module named 'pyfastx' 99s 99s 99s ====================================================================== 99s ERROR: tests.test_fasta (unittest.loader._FailedTest.tests.test_fasta) 99s ---------------------------------------------------------------------- 99s ImportError: Failed to import test module: tests.test_fasta 99s Traceback (most recent call last): 99s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 99s module = self._get_module_from_name(name) 99s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 99s __import__(name) 99s ~~~~~~~~~~^^^^^^ 99s File "/tmp/autopkgtest.xYXzum/build.ulk/src/tests/test_fasta.py", line 3, in 99s import pyfastx 99s ModuleNotFoundError: No module named 'pyfastx' 99s 99s 99s ====================================================================== 99s ERROR: tests.test_fastq (unittest.loader._FailedTest.tests.test_fastq) 99s ---------------------------------------------------------------------- 99s ImportError: Failed to import test module: tests.test_fastq 99s Traceback (most recent call last): 99s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 99s module = self._get_module_from_name(name) 99s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 99s __import__(name) 99s ~~~~~~~~~~^^^^^^ 99s File "/tmp/autopkgtest.xYXzum/build.ulk/src/tests/test_fastq.py", line 3, in 99s import pyfastx 99s ModuleNotFoundError: No module named 'pyfastx' 99s 99s 99s ====================================================================== 99s ERROR: tests.test_fastx (unittest.loader._FailedTest.tests.test_fastx) 99s ---------------------------------------------------------------------- 99s ImportError: Failed to import test module: tests.test_fastx 99s Traceback (most recent call last): 99s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 99s module = self._get_module_from_name(name) 99s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 99s __import__(name) 99s ~~~~~~~~~~^^^^^^ 99s File "/tmp/autopkgtest.xYXzum/build.ulk/src/tests/test_fastx.py", line 3, in 99s import pyfastx 99s ModuleNotFoundError: No module named 'pyfastx' 99s 99s 99s ====================================================================== 99s ERROR: tests.test_fqkeys (unittest.loader._FailedTest.tests.test_fqkeys) 99s ---------------------------------------------------------------------- 99s ImportError: Failed to import test module: tests.test_fqkeys 99s Traceback (most recent call last): 99s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 99s module = self._get_module_from_name(name) 99s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 99s __import__(name) 99s ~~~~~~~~~~^^^^^^ 99s File "/tmp/autopkgtest.xYXzum/build.ulk/src/tests/test_fqkeys.py", line 3, in 99s import pyfastx 99s ModuleNotFoundError: No module named 'pyfastx' 99s 99s 99s ====================================================================== 99s ERROR: tests.test_read (unittest.loader._FailedTest.tests.test_read) 99s ---------------------------------------------------------------------- 99s ImportError: Failed to import test module: tests.test_read 99s Traceback (most recent call last): 99s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 99s module = self._get_module_from_name(name) 99s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 99s __import__(name) 99s ~~~~~~~~~~^^^^^^ 99s File "/tmp/autopkgtest.xYXzum/build.ulk/src/tests/test_read.py", line 4, in 99s import pyfastx 99s ModuleNotFoundError: No module named 'pyfastx' 99s 99s 99s ====================================================================== 99s ERROR: tests.test_sequence (unittest.loader._FailedTest.tests.test_sequence) 99s ---------------------------------------------------------------------- 99s ImportError: Failed to import test module: tests.test_sequence 99s Traceback (most recent call last): 99s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 99s module = self._get_module_from_name(name) 99s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 99s __import__(name) 99s ~~~~~~~~~~^^^^^^ 99s File "/tmp/autopkgtest.xYXzum/build.ulk/src/tests/test_sequence.py", line 3, in 99s import pyfastx 99s ModuleNotFoundError: No module named 'pyfastx' 99s 99s 99s ====================================================================== 99s ERROR: tests.test_sequence_error (unittest.loader._FailedTest.tests.test_sequence_error) 99s ---------------------------------------------------------------------- 99s ImportError: Failed to import test module: tests.test_sequence_error 99s Traceback (most recent call last): 99s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 99s module = self._get_module_from_name(name) 99s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 99s __import__(name) 99s ~~~~~~~~~~^^^^^^ 99s File "/tmp/autopkgtest.xYXzum/build.ulk/src/tests/test_sequence_error.py", line 3, in 99s import pyfastx 99s ModuleNotFoundError: No module named 'pyfastx' 99s 99s 99s ---------------------------------------------------------------------- 99s Ran 8 tests in 0.001s 99s 99s FAILED (errors=8) 99s autopkgtest [21:15:44]: test run-unit-test: -----------------------] 100s run-unit-test FAIL non-zero exit status 1 100s autopkgtest [21:15:45]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 100s autopkgtest [21:15:45]: test test-cli: preparing testbed 161s autopkgtest [21:16:46]: testbed dpkg architecture: amd64 161s autopkgtest [21:16:46]: testbed apt version: 2.9.8 161s autopkgtest [21:16:46]: @@@@@@@@@@@@@@@@@@@@ test bed setup 161s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 161s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [53.2 kB] 161s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [925 kB] 161s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.6 kB] 161s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9704 B] 161s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [89.4 kB] 161s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [41.5 kB] 161s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2408 B] 161s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [40.1 kB] 161s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [800 kB] 161s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [290 kB] 161s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [20.0 kB] 161s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [5528 B] 161s Fetched 2364 kB in 0s (7559 kB/s) 162s Reading package lists... 163s Reading package lists... 163s Building dependency tree... 163s Reading state information... 164s Calculating upgrade... 164s The following package was automatically installed and is no longer required: 164s libsgutils2-1.46-2 164s Use 'sudo apt autoremove' to remove it. 164s The following NEW packages will be installed: 164s libsgutils2-1.48 164s The following packages will be upgraded: 164s amd64-microcode bash bpftrace curl debconf debconf-i18n distro-info 164s dracut-install fwupd-signed gir1.2-girepository-2.0 gir1.2-glib-2.0 hostname 164s intel-microcode libaudit-common libaudit1 libcurl3t64-gnutls libcurl4t64 164s libgirepository-1.0-1 libglib2.0-0t64 libglib2.0-data libpam-modules 164s libpam-modules-bin libpam-runtime libpam0g libplymouth5 libpython3-stdlib 164s libselinux1 libsemanage-common libsemanage2 linux-base lxd-installer 164s openssh-client openssh-server openssh-sftp-server pinentry-curses plymouth 164s plymouth-theme-ubuntu-text python3 python3-blinker python3-debconf 164s python3-jsonschema-specifications python3-minimal python3-rpds-py sg3-utils 164s sg3-utils-udev vim-common vim-tiny xxd 164s 48 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 164s Need to get 19.4 MB of archives. 164s After this operation, 3523 kB of additional disk space will be used. 164s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 bash amd64 5.2.32-1ubuntu2 [918 kB] 164s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 hostname amd64 3.25 [11.1 kB] 164s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu1 [6578 B] 164s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu1 [53.9 kB] 164s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 debconf-i18n all 1.5.87ubuntu1 [204 kB] 164s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 164s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 164s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 164s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-debconf all 1.5.87ubuntu1 [4156 B] 164s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 debconf all 1.5.87ubuntu1 [124 kB] 164s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam0g amd64 1.5.3-7ubuntu4 [69.6 kB] 164s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libselinux1 amd64 3.7-3ubuntu1 [86.9 kB] 164s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam-modules-bin amd64 1.5.3-7ubuntu4 [53.7 kB] 164s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam-modules amd64 1.5.3-7ubuntu4 [294 kB] 164s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 openssh-sftp-server amd64 1:9.9p1-3ubuntu2 [41.2 kB] 164s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 openssh-server amd64 1:9.9p1-3ubuntu2 [625 kB] 164s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 openssh-client amd64 1:9.9p1-3ubuntu2 [1080 kB] 164s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam-runtime all 1.5.3-7ubuntu4 [40.8 kB] 164s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage-common all 3.7-2build1 [7186 B] 164s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage2 amd64 3.7-2build1 [105 kB] 164s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 distro-info amd64 1.12 [20.0 kB] 164s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-girepository-2.0 amd64 1.82.0-2 [25.3 kB] 164s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-glib-2.0 amd64 2.82.2-3 [182 kB] 164s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-0t64 amd64 2.82.2-3 [1655 kB] 164s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libgirepository-1.0-1 amd64 1.82.0-2 [88.7 kB] 164s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-data all 2.82.2-3 [51.7 kB] 164s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 vim-tiny amd64 2:9.1.0861-1ubuntu1 [1037 kB] 164s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 vim-common all 2:9.1.0861-1ubuntu1 [395 kB] 164s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 xxd amd64 2:9.1.0861-1ubuntu1 [67.8 kB] 164s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libplymouth5 amd64 24.004.60-2ubuntu3 [145 kB] 164s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 plymouth-theme-ubuntu-text amd64 24.004.60-2ubuntu3 [10.3 kB] 164s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 plymouth amd64 24.004.60-2ubuntu3 [140 kB] 164s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 bpftrace amd64 0.21.2-2ubuntu3 [1787 kB] 164s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 curl amd64 8.9.1-2ubuntu3 [243 kB] 164s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4t64 amd64 8.9.1-2ubuntu3 [420 kB] 164s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 dracut-install amd64 105-2ubuntu2 [35.9 kB] 164s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd-signed amd64 1.55+1.7-1 [30.6 kB] 164s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl3t64-gnutls amd64 8.9.1-2ubuntu3 [412 kB] 164s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libsgutils2-1.48 amd64 1.48-0ubuntu1 [124 kB] 164s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-base all 4.10.1ubuntu1 [34.8 kB] 164s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 lxd-installer all 10 [5264 B] 164s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 pinentry-curses amd64 1.3.1-0ubuntu2 [41.6 kB] 164s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-blinker all 1.9.0-1 [10.7 kB] 164s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-rpds-py amd64 0.21.0-2ubuntu1 [323 kB] 164s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jsonschema-specifications all 2023.12.1-2 [9116 B] 164s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 sg3-utils amd64 1.48-0ubuntu1 [1042 kB] 164s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 sg3-utils-udev all 1.48-0ubuntu1 [6608 B] 164s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 amd64-microcode amd64 3.20240820.1ubuntu1 [187 kB] 164s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 intel-microcode amd64 3.20241112.1ubuntu2 [7055 kB] 165s Preconfiguring packages ... 165s Fetched 19.4 MB in 0s (80.0 MB/s) 165s (Reading database ... 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(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 ... 75624 files and directories currently installed.) 167s Preparing to unpack .../openssh-sftp-server_1%3a9.9p1-3ubuntu2_amd64.deb ... 167s Unpacking openssh-sftp-server (1:9.9p1-3ubuntu2) over (1:9.7p1-7ubuntu5) ... 167s Preparing to unpack .../openssh-server_1%3a9.9p1-3ubuntu2_amd64.deb ... 168s Unpacking openssh-server (1:9.9p1-3ubuntu2) over (1:9.7p1-7ubuntu5) ... 168s Preparing to unpack .../openssh-client_1%3a9.9p1-3ubuntu2_amd64.deb ... 168s Unpacking openssh-client (1:9.9p1-3ubuntu2) over (1:9.7p1-7ubuntu5) ... 168s Preparing to unpack .../libpam-runtime_1.5.3-7ubuntu4_all.deb ... 168s Unpacking libpam-runtime (1.5.3-7ubuntu4) over (1.5.3-7ubuntu2) ... 168s Setting up libpam-runtime (1.5.3-7ubuntu4) ... 168s (Reading database ... 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(2.82.2-3) ... 170s Setting up lxd-installer (10) ... 171s Setting up dracut-install (105-2ubuntu2) ... 171s Setting up libplymouth5:amd64 (24.004.60-2ubuntu3) ... 171s Setting up libgirepository-1.0-1:amd64 (1.82.0-2) ... 171s Setting up curl (8.9.1-2ubuntu3) ... 171s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 171s Setting up sg3-utils (1.48-0ubuntu1) ... 171s Setting up openssh-sftp-server (1:9.9p1-3ubuntu2) ... 171s Setting up openssh-server (1:9.9p1-3ubuntu2) ... 171s Installing new version of config file /etc/ssh/moduli ... 171s Replacing config file /etc/ssh/sshd_config with new version 172s Setting up plymouth (24.004.60-2ubuntu3) ... 172s update-initramfs: Generating /boot/initrd.img-6.11.0-8-generic 172s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 182s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 183s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 183s Setting up python3 (3.12.7-1) ... 183s Setting up vim-tiny (2:9.1.0861-1ubuntu1) ... 183s Setting up sg3-utils-udev (1.48-0ubuntu1) ... 183s update-initramfs: deferring update (trigger activated) 183s Setting up plymouth-theme-ubuntu-text (24.004.60-2ubuntu3) ... 183s update-initramfs: deferring update (trigger activated) 183s Setting up gir1.2-girepository-2.0:amd64 (1.82.0-2) ... 183s Setting up python3-rpds-py (0.21.0-2ubuntu1) ... 183s Setting up python3-jsonschema-specifications (2023.12.1-2) ... 184s Setting up python3-blinker (1.9.0-1) ... 184s Setting up python3-debconf (1.5.87ubuntu1) ... 184s Processing triggers for man-db (2.13.0-1) ... 186s Processing triggers for debianutils (5.21) ... 186s Processing triggers for install-info (7.1.1-1) ... 186s Processing triggers for initramfs-tools (0.142ubuntu35) ... 186s update-initramfs: Generating /boot/initrd.img-6.11.0-8-generic 186s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 196s Processing triggers for libc-bin (2.40-1ubuntu3) ... 196s Processing triggers for ufw (0.36.2-8) ... 196s Reading package lists... 197s Building dependency tree... 197s Reading state information... 197s The following packages will be REMOVED: 197s libsgutils2-1.46-2* 197s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. 197s After this operation, 294 kB disk space will be freed. 197s (Reading database ... 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Retrying in 3 seconds... 216s Reading package lists... 217s Building dependency tree... 217s Reading state information... 217s Starting pkgProblemResolver with broken count: 0 217s Starting 2 pkgProblemResolver with broken count: 0 217s Done 218s The following additional packages will be installed: 218s pyfastx python3-importlib-metadata python3-packaging python3-pyfaidx 218s python3-pyfastx 218s Recommended packages: 218s python3-biopython 218s The following NEW packages will be installed: 218s autopkgtest-satdep pyfastx python3-importlib-metadata python3-packaging 218s python3-pyfaidx python3-pyfastx 218s 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. 218s Need to get 280 kB/281 kB of archives. 218s After this operation, 812 kB of additional disk space will be used. 218s Get:1 /tmp/autopkgtest.xYXzum/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [716 B] 218s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-importlib-metadata all 8.5.0-1 [20.7 kB] 218s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.2-1 [51.5 kB] 218s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 218s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyfastx amd64 2.1.0-2 [56.7 kB] 218s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 pyfastx amd64 2.1.0-2 [122 kB] 218s Fetched 280 kB in 0s (5905 kB/s) 218s Selecting previously unselected package python3-importlib-metadata. 218s (Reading database ... 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.../2-python3-pyfaidx_0.8.1.3-1_all.deb ... 218s Unpacking python3-pyfaidx (0.8.1.3-1) ... 218s Selecting previously unselected package python3-pyfastx. 218s Preparing to unpack .../3-python3-pyfastx_2.1.0-2_amd64.deb ... 218s Unpacking python3-pyfastx (2.1.0-2) ... 218s Selecting previously unselected package pyfastx. 218s Preparing to unpack .../4-pyfastx_2.1.0-2_amd64.deb ... 218s Unpacking pyfastx (2.1.0-2) ... 218s Selecting previously unselected package autopkgtest-satdep. 218s Preparing to unpack .../5-2-autopkgtest-satdep.deb ... 218s Unpacking autopkgtest-satdep (0) ... 218s Setting up python3-importlib-metadata (8.5.0-1) ... 219s Setting up python3-packaging (24.2-1) ... 219s Setting up python3-pyfaidx (0.8.1.3-1) ... 219s Setting up python3-pyfastx (2.1.0-2) ... 219s Setting up pyfastx (2.1.0-2) ... 219s Setting up autopkgtest-satdep (0) ... 219s Processing triggers for man-db (2.13.0-1) ... 222s (Reading database ... 75751 files and directories currently installed.) 222s Removing autopkgtest-satdep (0) ... 222s autopkgtest [21:17:47]: test test-cli: [----------------------- 222s $ pyfastx --help 222s usage: pyfastx COMMAND [OPTIONS] 222s 222s A command line tool for FASTA/Q file manipulation 222s 222s options: 222s -h, --help show this help message and exit 222s -v, --version show program's version number and exit 222s 222s Commands: 222s 222s index build index for fasta/q file 222s stat show detailed statistics information of fasta/q file 222s split split fasta/q file into multiple files 222s fq2fa convert fastq file to fasta file 222s subseq get subsequences from fasta file by region 222s sample randomly sample sequences from fasta or fastq file 222s extract extract full sequences or reads from fasta/q file 223s $ # Found pyfastx commands: 'index stat split fq2fa subseq sample extract' 223s $ pyfastx index --help 223s usage: pyfastx index [-h] [-f] fastx [fastx ...] 223s 223s positional arguments: 223s fastx fasta or fastq file, gzip support 223s 223s options: 223s -h, --help show this help message and exit 223s -f, --full build full index, base composition will be calculated 223s $ pyfastx stat --help 223s usage: pyfastx stat [-h] fastx [fastx ...] 223s 223s positional arguments: 223s fastx fasta or fastq file, gzip support 223s 223s options: 223s -h, --help show this help message and exit 223s $ pyfastx split --help 223s usage: pyfastx split [-h] (-n int | -c int) [-o str] fastx 223s 223s positional arguments: 223s fastx fasta or fastq file, gzip support 223s 223s options: 223s -h, --help show this help message and exit 223s -n int split a fasta/q file into N new files with even size 223s -c int split a fasta/q file into multiple files containing 223s the same sequence counts 223s -o str, --out-dir str 223s output directory, default is current folder 223s $ pyfastx fq2fa --help 223s usage: pyfastx fq2fa [-h] [-o str] fastx 223s 223s positional arguments: 223s fastx fastq file, gzip support 223s 223s options: 223s -h, --help show this help message and exit 223s -o str, --out-file str 223s output file, default: output to stdout 223s $ pyfastx subseq --help 223s usage: pyfastx subseq [-h] [-r str | -b str] [-o str] fastx [region ...] 223s 223s positional arguments: 223s fastx input fasta file, gzip support 223s region format is chr:start-end, start and end position is 223s 1-based, multiple regions were separated by space 223s 223s options: 223s -h, --help show this help message and exit 223s -r str, --region-file str 223s tab-delimited file, one region per line, both start 223s and end position are 1-based 223s -b str, --bed-file str 223s tab-delimited BED file, 0-based start position and 223s 1-based end position 223s -o str, --out-file str 223s output file, default: output to stdout 223s $ pyfastx sample --help 223s usage: pyfastx sample [-h] (-n int | -p float) [-s int] [--sequential-read] 223s [-o str] 223s fastx 223s 223s positional arguments: 223s fastx fasta or fastq file, gzip support 223s 223s options: 223s -h, --help show this help message and exit 223s -n int number of sequences to be sampled 223s -p float proportion of sequences to be sampled, 0~1 223s -s int, --seed int random seed, default is the current system time 223s --sequential-read start sequential reading, particularly suitable for 223s sampling large numbers of sequences 223s -o str, --out-file str 223s output file, default: output to stdout 223s $ pyfastx extract --help 223s usage: pyfastx extract [-h] [-l str] [--reverse-complement] [--out-fasta] 223s [-o str] [--sequential-read] 223s fastx [name ...] 223s 223s positional arguments: 223s fastx fasta or fastq file, gzip support 223s name sequence name or read name, multiple names were 223s separated by space 223s 223s options: 223s -h, --help show this help message and exit 223s -l str, --list-file str 223s a file containing sequence or read names, one name per 223s line 223s --reverse-complement output reverse complement sequence 223s --out-fasta output fasta format when extract reads from fastq, 223s default output fastq format 223s -o str, --out-file str 223s output file, default: output to stdout 223s --sequential-read start sequential reading, particularly suitable for 223s extracting large numbers of sequences 223s $ pyfastx --version 223s pyfastx version 2.1.0 223s $ pyfastx index protein.fa 223s $ pyfastx index rna.fa 224s $ pyfastx index test.fa 224s $ pyfastx index test.fq 224s $ pyfastx index test.fa.gz 224s $ pyfastx index test.fq.gz 224s $ pyfastx stat protein.fa 224s fileName seqType seqCounts totalBases GC% avgLen medianLen maxLen minLen N50 L50 224s protein.fa protein 17 2265 - 133.235 80.0 419 23 263 4 224s $ pyfastx split -n 2 protein.fa 224s $ pyfastx fq2fa test.fq -o test.fa 224s $ pyfastx subseq protein.fa UPI0000000011:1-4 224s >UPI0000000011:1-4 224s MVDA 225s $ pyfastx sample -n 1 test.fq.gz -o sample.fq 225s $ pyfastx extract protein.fa UPI0000000011 225s >UPI0000000011 status=active 225s MVDAITVLTAIGITVLMLLMVISGAAMIVKELNPNDIFTMQSLKFNRAVTIFKYIGLFIY 225s IPGTIILYATYVKSLLMKS 225s autopkgtest [21:17:50]: test test-cli: -----------------------] 225s test-cli PASS 225s autopkgtest [21:17:50]: test test-cli: - - - - - - - - - - results - - - - - - - - - - 225s autopkgtest [21:17:50]: @@@@@@@@@@@@@@@@@@@@ summary 225s run-unit-test FAIL non-zero exit status 1 225s test-cli PASS 240s virt: nova [W] Skipping flock for amd64 240s virt: Creating nova instance adt-plucky-amd64-pyfastx-20241123-203903-juju-7f2275-prod-proposed-migration-environment-2-c46afc55-44fe-46fa-a9bd-f10a91afb641 from image adt/ubuntu-plucky-amd64-server-20241119.img (UUID 2f2a410e-3f09-433d-912b-264888c6382a)... 240s virt: nova [W] Skipping flock for amd64 240s virt: Creating nova instance adt-plucky-amd64-pyfastx-20241123-203903-juju-7f2275-prod-proposed-migration-environment-2-c46afc55-44fe-46fa-a9bd-f10a91afb641 from image adt/ubuntu-plucky-amd64-server-20241119.img (UUID 2f2a410e-3f09-433d-912b-264888c6382a)...