0s autopkgtest [14:39:46]: starting date and time: 2024-11-03 14:39:46+0000 0s autopkgtest [14:39:46]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [14:39:46]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.xpz4ywip/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --apt-pocket=proposed=src:htslib --apt-upgrade stacks --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=htslib/1.20+ds-2 -- lxd -r lxd-armhf-10.145.243.158 lxd-armhf-10.145.243.158:autopkgtest/ubuntu/plucky/armhf 57s autopkgtest [14:40:43]: testbed dpkg architecture: armhf 59s autopkgtest [14:40:45]: testbed apt version: 2.9.8 59s autopkgtest [14:40:45]: @@@@@@@@@@@@@@@@@@@@ test bed setup 68s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 69s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [31.2 kB] 69s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [2268 kB] 89s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 89s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [177 kB] 90s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [209 kB] 91s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [1640 kB] 109s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [23.9 kB] 109s Fetched 4430 kB in 41s (108 kB/s) 109s Reading package lists... 132s tee: /proc/self/fd/2: Permission denied 469s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 469s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 469s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 470s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 471s Reading package lists... 471s Reading package lists... 472s Building dependency tree... 472s Reading state information... 474s Calculating upgrade... 475s The following packages were automatically installed and are no longer required: 475s libperl5.38t64 perl-modules-5.38 475s Use 'apt autoremove' to remove them. 475s The following NEW packages will be installed: 475s libperl5.40 perl-modules-5.40 475s The following packages will be upgraded: 475s base-files distro-info-data fwupd gcc-14-base info install-info iproute2 475s libatomic1 libblockdev-crypto3 libblockdev-fs3 libblockdev-loop3 475s libblockdev-mdraid3 libblockdev-nvme3 libblockdev-part3 libblockdev-swap3 475s libblockdev-utils3 libblockdev3 libdb5.3t64 libdw1t64 libelf1t64 libevdev2 475s libftdi1-2 libfwupd2 libgcc-s1 libinih1 libkeyutils1 liblocale-gettext-perl 475s libpipeline1 libsgutils2-1.46-2 libstdc++6 libtext-charwidth-perl 475s libtext-iconv-perl motd-news-config nano perl perl-base python3-configobj 475s python3-json-pointer python3-lazr.uri python3-zipp sg3-utils sg3-utils-udev 475s vim-common vim-tiny xxd 475s 45 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 475s Need to get 19.6 MB of archives. 475s After this operation, 42.8 MB of additional disk space will be used. 475s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf motd-news-config all 13.5ubuntu2 [5274 B] 475s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf base-files armhf 13.5ubuntu2 [68.6 kB] 476s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf perl-modules-5.40 all 5.40.0-6 [3214 kB] 479s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libperl5.40 armhf 5.40.0-6 [4140 kB] 480s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf perl armhf 5.40.0-6 [262 kB] 480s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf perl-base armhf 5.40.0-6 [1674 kB] 480s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf liblocale-gettext-perl armhf 1.07-7build1 [15.0 kB] 480s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf libtext-iconv-perl armhf 1.7-8build4 [12.8 kB] 480s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf libtext-charwidth-perl armhf 0.04-11build4 [9128 B] 480s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libdb5.3t64 armhf 5.3.28+dfsg2-9 [655 kB] 480s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libatomic1 armhf 14.2.0-7ubuntu1 [7842 B] 480s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14-base armhf 14.2.0-7ubuntu1 [51.2 kB] 480s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libstdc++6 armhf 14.2.0-7ubuntu1 [711 kB] 480s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf libgcc-s1 armhf 14.2.0-7ubuntu1 [40.8 kB] 480s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf install-info armhf 7.1.1-1 [61.4 kB] 480s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf distro-info-data all 0.63 [6588 B] 480s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libdw1t64 armhf 0.192-4 [243 kB] 480s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf libelf1t64 armhf 0.192-4 [50.2 kB] 480s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf iproute2 armhf 6.10.0-2ubuntu1 [1082 kB] 480s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libkeyutils1 armhf 1.6.3-4ubuntu2 [8712 B] 480s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf vim-tiny armhf 2:9.1.0777-1ubuntu1 [693 kB] 480s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf vim-common all 2:9.1.0777-1ubuntu1 [394 kB] 480s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf xxd armhf 2:9.1.0777-1ubuntu1 [66.8 kB] 480s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf info armhf 7.1.1-1 [126 kB] 480s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf libevdev2 armhf 1.13.3+dfsg-1 [29.7 kB] 480s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf libpipeline1 armhf 1.5.8-1 [26.9 kB] 480s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf nano armhf 8.2-1 [276 kB] 481s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf libfwupd2 armhf 1.9.26-2 [125 kB] 481s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf fwupd armhf 1.9.26-2 [4404 kB] 481s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-utils3 armhf 3.2.0-2 [17.4 kB] 481s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-crypto3 armhf 3.2.0-2 [22.3 kB] 481s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-fs3 armhf 3.2.0-2 [34.3 kB] 481s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-loop3 armhf 3.2.0-2 [6552 B] 481s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-mdraid3 armhf 3.2.0-2 [13.4 kB] 481s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-nvme3 armhf 3.2.0-2 [17.6 kB] 481s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-part3 armhf 3.2.0-2 [16.5 kB] 481s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-swap3 armhf 3.2.0-2 [8942 B] 481s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev3 armhf 3.2.0-2 [44.2 kB] 481s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf libftdi1-2 armhf 1.5-7 [25.7 kB] 481s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf libinih1 armhf 58-1ubuntu1 [6750 B] 481s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf libsgutils2-1.46-2 armhf 1.46-3ubuntu5 [82.5 kB] 481s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf python3-configobj all 5.0.9-1 [33.9 kB] 481s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf python3-json-pointer all 2.4-2 [8396 B] 481s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf python3-lazr.uri all 1.0.6-4 [13.6 kB] 481s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf python3-zipp all 3.20.2-1 [10.1 kB] 481s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf sg3-utils armhf 1.46-3ubuntu5 [816 kB] 481s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf sg3-utils-udev all 1.46-3ubuntu5 [5916 B] 482s Preconfiguring packages ... 482s Fetched 19.6 MB in 6s (3263 kB/s) 482s (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 ... 59386 files and directories currently installed.) 482s Preparing to unpack .../motd-news-config_13.5ubuntu2_all.deb ... 482s Unpacking motd-news-config (13.5ubuntu2) over (13.3ubuntu6) ... 482s Preparing to unpack .../base-files_13.5ubuntu2_armhf.deb ... 482s Unpacking base-files (13.5ubuntu2) over (13.3ubuntu6) ... 482s Setting up base-files (13.5ubuntu2) ... 482s Installing new version of config file /etc/issue ... 482s Installing new version of config file /etc/issue.net ... 482s Installing new version of config file /etc/lsb-release ... 483s motd-news.service is a disabled or a static unit not running, not starting it. 483s (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 ... 59386 files and directories currently installed.) 483s Preparing to unpack .../perl_5.40.0-6_armhf.deb ... 483s Unpacking perl (5.40.0-6) over (5.38.2-5) ... 483s Selecting previously unselected package perl-modules-5.40. 483s Preparing to unpack .../perl-modules-5.40_5.40.0-6_all.deb ... 483s Unpacking perl-modules-5.40 (5.40.0-6) ... 483s Selecting previously unselected package libperl5.40:armhf. 483s Preparing to unpack .../libperl5.40_5.40.0-6_armhf.deb ... 483s Unpacking libperl5.40:armhf (5.40.0-6) ... 483s Preparing to unpack .../perl-base_5.40.0-6_armhf.deb ... 484s Unpacking perl-base (5.40.0-6) over (5.38.2-5) ... 484s Setting up perl-base (5.40.0-6) ... 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 ... 61462 files and directories currently installed.) 484s Preparing to unpack .../liblocale-gettext-perl_1.07-7build1_armhf.deb ... 484s Unpacking liblocale-gettext-perl (1.07-7build1) over (1.07-7) ... 484s Preparing to unpack .../libtext-iconv-perl_1.7-8build4_armhf.deb ... 484s Unpacking libtext-iconv-perl:armhf (1.7-8build4) over (1.7-8build3) ... 484s Preparing to unpack .../libtext-charwidth-perl_0.04-11build4_armhf.deb ... 484s Unpacking libtext-charwidth-perl:armhf (0.04-11build4) over (0.04-11build3) ... 484s Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-9_armhf.deb ... 484s Unpacking libdb5.3t64:armhf (5.3.28+dfsg2-9) over (5.3.28+dfsg2-7) ... 484s Setting up libdb5.3t64:armhf (5.3.28+dfsg2-9) ... 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 ... 61462 files and directories currently installed.) 484s Preparing to unpack .../libatomic1_14.2.0-7ubuntu1_armhf.deb ... 484s Unpacking libatomic1:armhf (14.2.0-7ubuntu1) over (14.2.0-4ubuntu2) ... 484s Preparing to unpack .../gcc-14-base_14.2.0-7ubuntu1_armhf.deb ... 484s Unpacking gcc-14-base:armhf (14.2.0-7ubuntu1) over (14.2.0-4ubuntu2) ... 484s Setting up gcc-14-base:armhf (14.2.0-7ubuntu1) ... 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 ... 61462 files and directories currently installed.) 484s Preparing to unpack .../libstdc++6_14.2.0-7ubuntu1_armhf.deb ... 484s Unpacking libstdc++6:armhf (14.2.0-7ubuntu1) over (14.2.0-4ubuntu2) ... 484s Setting up libstdc++6:armhf (14.2.0-7ubuntu1) ... 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 ... 61462 files and directories currently installed.) 484s Preparing to unpack .../libgcc-s1_14.2.0-7ubuntu1_armhf.deb ... 484s Unpacking libgcc-s1:armhf (14.2.0-7ubuntu1) over (14.2.0-4ubuntu2) ... 484s Setting up libgcc-s1:armhf (14.2.0-7ubuntu1) ... 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 ... 61462 files and directories currently installed.) 484s Preparing to unpack .../install-info_7.1.1-1_armhf.deb ... 484s Unpacking install-info (7.1.1-1) over (7.1-3build2) ... 484s Setting up install-info (7.1.1-1) ... 485s (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 ... 61462 files and directories currently installed.) 485s Preparing to unpack .../00-distro-info-data_0.63_all.deb ... 485s Unpacking distro-info-data (0.63) over (0.62) ... 485s Preparing to unpack .../01-libdw1t64_0.192-4_armhf.deb ... 485s Unpacking libdw1t64:armhf (0.192-4) over (0.191-2) ... 485s Preparing to unpack .../02-libelf1t64_0.192-4_armhf.deb ... 485s Unpacking libelf1t64:armhf (0.192-4) over (0.191-2) ... 485s Preparing to unpack .../03-iproute2_6.10.0-2ubuntu1_armhf.deb ... 485s Unpacking iproute2 (6.10.0-2ubuntu1) over (6.10.0-2) ... 485s Preparing to unpack .../04-libkeyutils1_1.6.3-4ubuntu2_armhf.deb ... 485s Unpacking libkeyutils1:armhf (1.6.3-4ubuntu2) over (1.6.3-3build1) ... 485s Preparing to unpack .../05-vim-tiny_2%3a9.1.0777-1ubuntu1_armhf.deb ... 485s Unpacking vim-tiny (2:9.1.0777-1ubuntu1) over (2:9.1.0496-1ubuntu6) ... 485s Preparing to unpack .../06-vim-common_2%3a9.1.0777-1ubuntu1_all.deb ... 485s Unpacking vim-common (2:9.1.0777-1ubuntu1) over (2:9.1.0496-1ubuntu6) ... 485s Preparing to unpack .../07-xxd_2%3a9.1.0777-1ubuntu1_armhf.deb ... 485s Unpacking xxd (2:9.1.0777-1ubuntu1) over (2:9.1.0496-1ubuntu6) ... 485s Preparing to unpack .../08-info_7.1.1-1_armhf.deb ... 485s Unpacking info (7.1.1-1) over (7.1-3build2) ... 485s Preparing to unpack .../09-libevdev2_1.13.3+dfsg-1_armhf.deb ... 485s Unpacking libevdev2:armhf (1.13.3+dfsg-1) over (1.13.2+dfsg-1) ... 485s Preparing to unpack .../10-libpipeline1_1.5.8-1_armhf.deb ... 485s Unpacking libpipeline1:armhf (1.5.8-1) over (1.5.7-2) ... 485s Preparing to unpack .../11-nano_8.2-1_armhf.deb ... 485s Unpacking nano (8.2-1) over (8.1-1) ... 485s Preparing to unpack .../12-libfwupd2_1.9.26-2_armhf.deb ... 485s Unpacking libfwupd2:armhf (1.9.26-2) over (1.9.24-1) ... 485s Preparing to unpack .../13-fwupd_1.9.26-2_armhf.deb ... 486s Unpacking fwupd (1.9.26-2) over (1.9.24-1) ... 486s Preparing to unpack .../14-libblockdev-utils3_3.2.0-2_armhf.deb ... 486s Unpacking libblockdev-utils3:armhf (3.2.0-2) over (3.1.1-2) ... 486s Preparing to unpack .../15-libblockdev-crypto3_3.2.0-2_armhf.deb ... 486s Unpacking libblockdev-crypto3:armhf (3.2.0-2) over (3.1.1-2) ... 486s Preparing to unpack .../16-libblockdev-fs3_3.2.0-2_armhf.deb ... 486s Unpacking libblockdev-fs3:armhf (3.2.0-2) over (3.1.1-2) ... 486s Preparing to unpack .../17-libblockdev-loop3_3.2.0-2_armhf.deb ... 486s Unpacking libblockdev-loop3:armhf (3.2.0-2) over (3.1.1-2) ... 486s Preparing to unpack .../18-libblockdev-mdraid3_3.2.0-2_armhf.deb ... 486s Unpacking libblockdev-mdraid3:armhf (3.2.0-2) over (3.1.1-2) ... 486s Preparing to unpack .../19-libblockdev-nvme3_3.2.0-2_armhf.deb ... 486s Unpacking libblockdev-nvme3:armhf (3.2.0-2) over (3.1.1-2) ... 486s Preparing to unpack .../20-libblockdev-part3_3.2.0-2_armhf.deb ... 486s Unpacking libblockdev-part3:armhf (3.2.0-2) over (3.1.1-2) ... 486s Preparing to unpack .../21-libblockdev-swap3_3.2.0-2_armhf.deb ... 486s Unpacking libblockdev-swap3:armhf (3.2.0-2) over (3.1.1-2) ... 486s Preparing to unpack .../22-libblockdev3_3.2.0-2_armhf.deb ... 486s Unpacking libblockdev3:armhf (3.2.0-2) over (3.1.1-2) ... 486s Preparing to unpack .../23-libftdi1-2_1.5-7_armhf.deb ... 486s Unpacking libftdi1-2:armhf (1.5-7) over (1.5-6build5) ... 486s Preparing to unpack .../24-libinih1_58-1ubuntu1_armhf.deb ... 486s Unpacking libinih1:armhf (58-1ubuntu1) over (55-1ubuntu2) ... 486s Preparing to unpack .../25-libsgutils2-1.46-2_1.46-3ubuntu5_armhf.deb ... 486s Unpacking libsgutils2-1.46-2:armhf (1.46-3ubuntu5) over (1.46-3ubuntu4) ... 486s Preparing to unpack .../26-python3-configobj_5.0.9-1_all.deb ... 486s Unpacking python3-configobj (5.0.9-1) over (5.0.8-3) ... 486s Preparing to unpack .../27-python3-json-pointer_2.4-2_all.deb ... 486s Unpacking python3-json-pointer (2.4-2) over (2.0-0ubuntu1) ... 486s Preparing to unpack .../28-python3-lazr.uri_1.0.6-4_all.deb ... 486s Unpacking python3-lazr.uri (1.0.6-4) over (1.0.6-3) ... 486s Preparing to unpack .../29-python3-zipp_3.20.2-1_all.deb ... 487s Unpacking python3-zipp (3.20.2-1) over (3.20.0-1) ... 487s Preparing to unpack .../30-sg3-utils_1.46-3ubuntu5_armhf.deb ... 487s Unpacking sg3-utils (1.46-3ubuntu5) over (1.46-3ubuntu4) ... 487s Preparing to unpack .../31-sg3-utils-udev_1.46-3ubuntu5_all.deb ... 487s Unpacking sg3-utils-udev (1.46-3ubuntu5) over (1.46-3ubuntu4) ... 487s Setting up libpipeline1:armhf (1.5.8-1) ... 487s Setting up motd-news-config (13.5ubuntu2) ... 487s Setting up libtext-iconv-perl:armhf (1.7-8build4) ... 487s Setting up libtext-charwidth-perl:armhf (0.04-11build4) ... 487s Setting up libkeyutils1:armhf (1.6.3-4ubuntu2) ... 487s Setting up distro-info-data (0.63) ... 487s Setting up libinih1:armhf (58-1ubuntu1) ... 487s Setting up libfwupd2:armhf (1.9.26-2) ... 487s Setting up libsgutils2-1.46-2:armhf (1.46-3ubuntu5) ... 487s Setting up python3-lazr.uri (1.0.6-4) ... 487s Setting up python3-zipp (3.20.2-1) ... 487s Setting up xxd (2:9.1.0777-1ubuntu1) ... 487s Setting up libelf1t64:armhf (0.192-4) ... 487s Setting up libdw1t64:armhf (0.192-4) ... 487s Setting up libftdi1-2:armhf (1.5-7) ... 487s Setting up python3-configobj (5.0.9-1) ... 487s Setting up vim-common (2:9.1.0777-1ubuntu1) ... 487s Installing new version of config file /etc/vim/vimrc ... 487s Setting up libblockdev-utils3:armhf (3.2.0-2) ... 487s Setting up libatomic1:armhf (14.2.0-7ubuntu1) ... 487s Setting up 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information... 492s The following packages will be REMOVED: 492s libperl5.38t64* perl-modules-5.38* 492s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 492s After this operation, 41.6 MB disk space will be freed. 492s (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 ... 61462 files and directories currently installed.) 492s Removing libperl5.38t64:armhf (5.38.2-5) ... 492s Removing perl-modules-5.38 (5.38.2-5) ... 492s Processing triggers for man-db (2.12.1-3) ... 492s Processing triggers for libc-bin (2.40-1ubuntu3) ... 495s autopkgtest [14:48:01]: rebooting testbed after setup commands that affected boot 571s autopkgtest [14:49:17]: testbed running kernel: Linux 6.8.0-47-generic #47~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Oct 2 16:39:14 UTC 2 609s autopkgtest [14:49:55]: @@@@@@@@@@@@@@@@@@@@ apt-source stacks 623s Get:1 http://ftpmaster.internal/ubuntu plucky/universe stacks 2.67+dfsg-1 (dsc) [2041 B] 623s Get:2 http://ftpmaster.internal/ubuntu plucky/universe stacks 2.67+dfsg-1 (tar) [348 kB] 623s Get:3 http://ftpmaster.internal/ubuntu plucky/universe stacks 2.67+dfsg-1 (diff) [12.2 kB] 623s gpgv: Signature made Sat Aug 10 12:47:16 2024 UTC 623s gpgv: using RSA key 4A31DB5A1EE4096C87399880903649294C33F9B7 623s gpgv: Can't check signature: No public key 623s dpkg-source: warning: cannot verify inline signature for ./stacks_2.67+dfsg-1.dsc: no acceptable signature found 623s autopkgtest [14:50:09]: testing package stacks version 2.67+dfsg-1 626s autopkgtest [14:50:12]: build not needed 629s autopkgtest [14:50:15]: test run-unit-test: preparing testbed 641s Reading package lists... 642s Building dependency tree... 642s Reading state information... 642s Starting pkgProblemResolver with broken count: 0 642s Starting 2 pkgProblemResolver with broken count: 0 642s Done 643s The following additional packages will be installed: 643s libdbi-perl libdeflate0 libgomp1 libhts3t64 libhtscodecs2 samtools stacks 643s Suggested packages: 643s libclone-perl libmldbm-perl libnet-daemon-perl libsql-statement-perl cwltool 643s gdb 643s Recommended packages: 643s libspreadsheet-writeexcel-perl littler 643s The following NEW packages will be installed: 643s autopkgtest-satdep libdbi-perl libdeflate0 libgomp1 libhts3t64 libhtscodecs2 643s samtools stacks 643s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. 643s Need to get 3239 kB/3240 kB of archives. 643s After this operation, 8553 kB of additional disk space will be used. 643s Get:1 /tmp/autopkgtest.2Zq7eo/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [700 B] 644s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libdbi-perl armhf 1.645-1 [822 kB] 645s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.21-1 [38.8 kB] 645s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 14.2.0-7ubuntu1 [125 kB] 645s Get:5 http://ftpmaster.internal/ubuntu plucky/universe armhf libhtscodecs2 armhf 1.6.0-1build1 [65.8 kB] 645s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf libhts3t64 armhf 1.20+ds-2 [394 kB] 646s Get:7 http://ftpmaster.internal/ubuntu plucky/universe armhf samtools armhf 1.20-3 [607 kB] 650s Get:8 http://ftpmaster.internal/ubuntu plucky/universe armhf stacks armhf 2.67+dfsg-1 [1187 kB] 661s Fetched 3239 kB in 17s (192 kB/s) 661s Selecting previously unselected package libdbi-perl:armhf. 661s (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 ... 59532 files and directories currently installed.) 661s Preparing to unpack .../0-libdbi-perl_1.645-1_armhf.deb ... 661s Unpacking libdbi-perl:armhf (1.645-1) ... 661s Selecting previously unselected package libdeflate0:armhf. 661s Preparing to unpack .../1-libdeflate0_1.21-1_armhf.deb ... 661s Unpacking libdeflate0:armhf (1.21-1) ... 661s Selecting previously unselected package libgomp1:armhf. 661s Preparing to unpack .../2-libgomp1_14.2.0-7ubuntu1_armhf.deb ... 661s Unpacking libgomp1:armhf (14.2.0-7ubuntu1) ... 661s Selecting previously unselected package libhtscodecs2:armhf. 661s Preparing to unpack .../3-libhtscodecs2_1.6.0-1build1_armhf.deb ... 661s Unpacking libhtscodecs2:armhf (1.6.0-1build1) ... 661s Selecting previously unselected package libhts3t64:armhf. 661s Preparing to unpack .../4-libhts3t64_1.20+ds-2_armhf.deb ... 661s Unpacking libhts3t64:armhf (1.20+ds-2) ... 661s Selecting previously unselected package samtools. 661s Preparing to unpack .../5-samtools_1.20-3_armhf.deb ... 661s Unpacking samtools (1.20-3) ... 661s Selecting previously unselected package stacks. 661s Preparing to unpack .../6-stacks_2.67+dfsg-1_armhf.deb ... 661s Unpacking stacks (2.67+dfsg-1) ... 661s Selecting previously unselected package autopkgtest-satdep. 661s Preparing to unpack .../7-1-autopkgtest-satdep.deb ... 661s Unpacking autopkgtest-satdep (0) ... 661s Setting up libhtscodecs2:armhf (1.6.0-1build1) ... 661s Setting up libdeflate0:armhf (1.21-1) ... 661s Setting up libgomp1:armhf (14.2.0-7ubuntu1) ... 661s Setting up libhts3t64:armhf (1.20+ds-2) ... 661s Setting up libdbi-perl:armhf (1.645-1) ... 661s Setting up samtools (1.20-3) ... 661s Setting up stacks (2.67+dfsg-1) ... 661s Setting up autopkgtest-satdep (0) ... 661s Processing triggers for man-db (2.12.1-3) ... 661s Processing triggers for libc-bin (2.40-1ubuntu3) ... 675s (Reading database ... 59851 files and directories currently installed.) 675s Removing autopkgtest-satdep (0) ... 682s autopkgtest [14:51:08]: test run-unit-test: [----------------------- 685s Stacks - a pipeline for building loci from short-read sequences 685s v2.67+dfsg http://creskolab.uoregon.edu/stacks/ 685s 685s This is the Stacks wrapper script for Debian. Usage: 685s stacks 685s 685s Programs available are: 685s clone_filter ref_map 685s cstacks sstacks 685s denovo_map stacks-dist-extract 685s gstacks stacks-gdb 685s kmer_filter stacks-integrate-alignments 685s phasedstacks stacks-private-alleles 685s populations stacks-samtools-tview 685s process_radtags tsv2bam 685s process_shortreads ustacks 685s 685s Or else add /usr/libexec/stacks/bin to your $PATH to invoke the commands directly. 685s 685s clone_filter 2.67 685s clone_filter [-f in_file | -p in_dir [-P] [-I] | -1 pair_1 -2 pair_2] -o out_dir [-i type] [-y type] [-D] [-h] 685s f: path to the input file if processing single-end sequences. 685s p: path to a directory of files. 685s P: files contained within directory specified by '-p' are paired. 685s 1: first input file in a set of paired-end sequences. 685s 2: second input file in a set of paired-end sequences. 685s i: input file type, either 'bustard', 'fastq', 'fasta', 'gzfasta', or 'gzfastq' (default 'fastq'). 685s o: path to output the processed files. 685s y: output type, either 'fastq', 'fasta', 'gzfasta', or 'gzfastq' (default same as input type). 685s D: capture discarded reads to a file. 685s h: display this help message. 685s --oligo-len-1 len: length of the single-end oligo sequence in data set. 685s --oligo-len-2 len: length of the paired-end oligo sequence in data set. 685s --retain-oligo: do not trim off the random oligo sequence (if oligo is inline). 685s 685s Oligo sequence options: 685s --inline-null: random oligo is inline with sequence, occurs only on single-end read (default). 685s --null-inline: random oligo is inline with sequence, occurs only on the paired-end read. 685s --null-index: random oligo is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 685s --index-null: random oligo is provded in FASTQ header (Illumina i5 or i7 read). 685s --inline-inline: random oligo is inline with sequence, occurs on single and paired-end read. 685s --index-index: random oligo is provded in FASTQ header (Illumina i5 and i7 read). 685s --inline-index: random oligo is inline with sequence on single-end read and second oligo occurs in FASTQ header. 685s --index-inline: random oligo occurs in FASTQ header (Illumina i5 or i7 read) and is inline with sequence on single-end read (if single read data) or paired-end read (if paired data). 685s 685s cstacks 2.67 685s cstacks -P in_dir -M popmap [-n num_mismatches] [-t num_threads] 685s cstacks -s sample1_path [-s sample2_path ...] -o path [-n num_mismatches] [-t num_threads] 685s 685s -P,--in-path: path to the directory containing Stacks files. 685s -M,--popmap: path to a population map file. 685s -n: number of mismatches allowed between sample loci when build the catalog (default 1; suggested: set to ustacks -M). 685s -t,--threads: enable parallel execution with num_threads threads. 685s -s: sample prefix from which to load loci into the catalog. 685s -o,--outpath: output path to write results. 685s -c,--catalog : add to an existing catalog. 685s 685s Gapped assembly options: 685s --max-gaps: number of gaps allowed between stacks before merging (default: 2). 685s --min-aln-len: minimum length of aligned sequence in a gapped alignment (default: 0.80). 685s --disable-gapped: disable gapped alignments between stacks (default: use gapped alignments). 685s 685s Advanced options: 685s --k-len : specify k-mer size for matching between between catalog loci (automatically calculated by default). 685s --report-mmatches: report query loci that match more than one catalog locus. 685s denovo_map.pl 2.67 685s denovo_map.pl --samples dir --popmap path --out-path dir [--paired [--rm-pcr-duplicates]] (assembly options) (filtering options) [-X prog:"opts" ...] 685s 685s Input/Output files: 685s --samples: path to the directory containing the reads files for each sample. 685s --popmap: path to a population map file (format is " TAB ", one sample per line). 685s -o,--out-path: path to an output directory. 685s 685s General options: 685s -X: additional options for specific pipeline components, e.g. -X "populations: --min-maf 0.05". 685s -T, --threads: the number of threads/CPUs to use (default: 1). 685s --dry-run: dry run. Do not actually execute anything, just print the commands that would be executed. 685s --resume: resume executing the pipeline from a previous run. 685s 685s Stack assembly options: 685s -M: number of mismatches allowed between stacks within individuals (for ustacks). 685s -n: number of mismatches allowed between stacks between individuals (for cstacks; default: set to ustacks -M). 685s 685s SNP model options: 685s --var-alpha: significance level at which to call variant sites (for gstacks; default: 0.05). 685s --gt-alpha: significance level at which to call genotypes (for gstacks; default: 0.05). 685s 685s Paired-end options: 685s --paired: after assembling RAD loci, assemble mini-contigs with paired-end reads. 685s --rm-pcr-duplicates: remove all but one set of read pairs of the same sample that have 685s the same insert length. 685s 685s Population filtering options: 685s -r,--min-samples-per-pop: minimum percentage of individuals in a population required to process a locus for that population (for populations; default: 0) 685s -p,--min-populations: minimum number of populations a locus must be present in to process a locus (for populations; default: 1) 685s 685s For large datasets: 685s --catalog-popmap: path to a second population map file containing a subset of samples for use only in building the catalog. 685s 685s Miscellaneous: 685s --time-components (for benchmarking) 685s gstacks 2.67 685s 685s De novo mode: 685s gstacks -P stacks_dir -M popmap 685s 685s -P: input directory containing '*.matches.bam' files created by the 685s de novo Stacks pipeline, ustacks-cstacks-sstacks-tsv2bam 685s 685s Reference-based mode: 685s gstacks -I bam_dir -M popmap [-S suffix] -O out_dir 685s gstacks -B bam_file [-B ...] -O out_dir 685s 685s -I: input directory containing BAM files 685s -S: with -I/-M, suffix to use to build BAM file names: by default this 685s is just '.bam', i.e. the program expects 'SAMPLE_NAME.bam' 685s -B: input BAM file(s) 685s 685s The input BAM file(s) must be sorted by coordinate. 685s With -B, records must be assigned to samples using BAM "reads groups" 685s (gstacks uses the ID/identifier and SM/sample name fields). Read groups 685s must be consistent if repeated different files. Note that with -I, read 685s groups are unneeded and ignored. 685s 685s For both modes: 685s -M: path to a population map giving the list of samples 685s -O: output directory (default: none with -B; with -P same as the input 685s directory) 685s -t,--threads: number of threads to use (default: 1) 685s 685s SNP Model options: 685s --model: model to use to call variants and genotypes; one of 685s marukilow (default), marukihigh, or snp 685s --var-alpha: alpha threshold for discovering SNPs (default: 0.01 for marukilow) 685s --gt-alpha: alpha threshold for calling genotypes (default: 0.05) 685s 685s Paired-end options: 685s --rm-pcr-duplicates: remove all but one set ofread pairs of the same sample that 685s have the same insert length (implies --rm-unpaired-reads) 685s --rm-unpaired-reads: discard unpaired reads 685s --ignore-pe-reads: ignore paired-end reads even if present in the input 685s --unpaired: ignore read pairing (only for paired-end GBS; treat READ2's as if they were READ1's) 685s 685s Advanced options: 685s (De novo mode) 685s --kmer-length: kmer length for the de Bruijn graph (default: 31, max. 31) 685s --max-debruijn-reads: maximum number of reads to use in the de Bruijn graph (default: 1000) 685s --min-kmer-cov: minimum coverage to consider a kmer (default: 2) 685s --write-alignments: save read alignments (heavy BAM files) 685s 685s (Reference-based mode) 685s --methyl-status: assumes a methylation-aware molecular protocol used; calls methylated bases. 685s --min-mapq: minimum PHRED-scaled mapping quality to consider a read (default: 10) 685s --max-clipped: maximum soft-clipping level, in fraction of read length (default: 0.20) 685s --max-insert-len: maximum allowed sequencing insert length (default: 1000) 685s 685s --details: write a heavier output 685s --phasing-cooccurrences-thr-range: range of edge coverage thresholds to 685s iterate over when building the graph of allele cooccurrences for 685s SNP phasing (default: 1,2) 685s --phasing-dont-prune-hets: don't try to ignore dubious heterozygote 685s genotypes during phasing 685s 685s kmer_filter 2.67 685s kmer_filter [-f in_file_1 [-f in_file_2...] | -p in_dir] [-1 pair_1 -2 pair_2 [-1 pair_1...]] -o out_dir [-i type] [-y type] [-D] [-h] 685s f: path to the input file if processing single-end seqeunces. 685s i: input file type, either 'bustard' for the Illumina BUSTARD output files, 'fasta', 'fastq', 'gzfasta', or 'gzfastq' (default 'fastq'). 685s p: path to a directory of files (for single-end files only). 685s 1: specify the first in a pair of files to be processed together. 685s 2: specify the second in a pair of files to be processed together. 685s o: path to output the processed files. 685s y: output type, either 'fastq' or 'fasta' (default fastq). 685s D: capture discarded reads to a file. 685s h: display this help message. 685s 685s Filtering options: 685s --rare: turn on filtering based on rare k-mers. 685s --abundant: turn on filtering based on abundant k-mers. 685s --k-len : specify k-mer size (default 15). 685s 685s Advanced filtering options: 685s --max-k-freq : specify the number of times a kmer must occur to be considered abundant (default 20,000). 685s --min-lim : specify number of rare kmers occurring in a row required to discard a read (default 80% of the k-mer length). 685s --max-lim : specify number of abundant kmers required to discard a read (default 80% of the k-mers in a read). 685s 685s Normalize data: 685s --normalize : normalize read depth according to k-mer coverage. 685s 685s Characterizing K-mers: 685s --write-k-freq: write kmers along with their frequency of occurrence and exit. 685s --k-dist: print k-mer frequency distribution and exit. 685s 685s Advanced input options: 685s --read-k-freq : read a set of kmers along with their frequencies of occurrence instead of reading raw input files. 685s 685s phasedstacks 2.67 685s phasedstacks -b id -S path -P path -t file_type [-p threads] [-M popmap] [-v] [-h] 685s b: Stacks batch ID. 685s P: path to the phased output files. 685s S: path to the Stacks output files. 685s t: input file type. Supported types: fastphase, and beagle. 685s p: number of processes to run in parallel sections of code. 685s M: path to the population map, a tab separated file describing which individuals belong in which population. 685s v: print program version. 685s h: display this help message. 685s --haplotypes: data were phased as RAD locus haplotypes. 685s --dprime-bin-size: size of buckets for binning SNPs at a particular distance to calculate the mean D' value. 685s --dprime-threshold : if D' values fall above , set the D' to 1, otherwise set D' to 0. 685s 685s Filtering options: 685s --skip-zeros: do not include D' values of zero in the D' output. 685s --minor-allele-freq: specify a minimum minor allele frequency required to process a nucleotide site (0 < a < 0.5). 685s --min-inform-pairs: when building D' haplotype blocks, the minimum number of informative D' measures to combine two blocks (default 0.9). 685s 685s populations 2.67 685s Usage: 685s populations -P dir [-O dir] [-M popmap] (filters) [--fstats] [-k [--sigma=150000] [--bootstrap [-N 100]]] (output formats) 685s populations -V vcf -O dir [-M popmap] (filters) [--fstats] [-k [--sigma=150000] [--bootstrap [-N 100]]] (output formats) 685s 685s -P,--in-path: path to a directory containing Stacks output files. 685s -V,--in-vcf: path to a standalone input VCF file. 685s -O,--out-path: path to a directory where to write the output files. (Required by -V; otherwise defaults to value of -P.) 685s -M,--popmap: path to a population map. (Format is 'SAMPLE1 \t POP1 \n SAMPLE2 ...'.) 685s -t,--threads: number of threads to run in parallel sections of code. 685s --batch-size [int]: the number of loci to process in a batch (default: 10,000 in de novo mode; in reference mode, one chromosome 685s per batch). Increase to speed analysis, uses more memory, decrease to save memory). 685s 685s Data Filtering: 685s -p,--min-populations [int]: minimum number of populations a locus must be present in to process a locus. 685s -r,--min-samples-per-pop [float]: minimum percentage of individuals in a population required to process a locus for that population. 685s -R,--min-samples-overall [float]: minimum percentage of individuals across populations required to process a locus. 685s -H,--filter-haplotype-wise: apply the above filters haplotype wise 685s (unshared SNPs will be pruned to reduce haplotype-wise missing data). 685s --min-maf [float]: specify a minimum minor allele frequency required to process a SNP (0 < min_maf < 0.5; applied to the metapopulation). 685s --min-mac [int]: specify a minimum minor allele count required to process a SNP (applied to the metapopulation). 685s --max-obs-het [float]: specify a maximum observed heterozygosity required to process a SNP (applied ot the metapopulation). 685s --min-gt-depth [int]: specify a minimum number of reads to include a called SNP (otherwise marked as missing data). 685s 685s --write-single-snp: restrict data analysis to only the first SNP per locus (implies --no-haps). 685s --write-random-snp: restrict data analysis to one random SNP per locus (implies --no-haps). 685s -B,--blacklist: path to a file containing Blacklisted markers to be excluded from the export. 685s -W,--whitelist: path to a file containing Whitelisted markers to include in the export. 685s 685s Locus stats: 685s --hwe: calculate divergence from Hardy-Weinberg equilibrium for each locus. 685s 685s Fstats: 685s --fstats: enable SNP and haplotype-based F statistics. 685s --fst-correction: specify a p-value correction to be applied to Fst values based on a Fisher's exact test. Default: off. 685s --p-value-cutoff [float]: maximum p-value to keep an Fst measurement. Default: 0.05. 685s 685s Kernel-smoothing algorithm: 685s -k,--smooth: enable kernel-smoothed Pi, Fis, Fst, Fst', and Phi_st calculations. 685s --smooth-fstats: enable kernel-smoothed Fst, Fst', and Phi_st calculations. 685s --smooth-popstats: enable kernel-smoothed Pi and Fis calculations. 685s (Note: turning on smoothing implies --ordered-export.) 685s --sigma [int]: standard deviation of the kernel smoothing weight distribution. Sliding window size is defined as 3 x sigma; (default sigma = 150kbp). 685s --bootstrap-archive: archive statistical values for use in bootstrap resampling in a subsequent run, statistics must be enabled to be archived. 685s --bootstrap: turn on boostrap resampling for all kernel-smoothed statistics. 685s -N,--bootstrap-reps [int]: number of bootstrap resamplings to calculate (default 100). 685s --bootstrap-pifis: turn on boostrap resampling for smoothed SNP-based Pi and Fis calculations. 685s --bootstrap-fst: turn on boostrap resampling for smoothed Fst calculations based on pairwise population comparison of SNPs. 685s --bootstrap-div: turn on boostrap resampling for smoothed haplotype diveristy and gene diversity calculations based on haplotypes. 685s --bootstrap-phist: turn on boostrap resampling for smoothed Phi_st calculations based on haplotypes. 685s --bootstrap-wl [path]: only bootstrap loci contained in this whitelist. 685s 685s File output options: 685s --ordered-export: if data is reference aligned, exports will be ordered; only a single representative of each overlapping site. 685s --fasta-loci: output locus consensus sequences in FASTA format. 685s --fasta-samples: output the sequences of the two haplotypes of each (diploid) sample, for each locus, in FASTA format. 685s --vcf: output SNPs and haplotypes in Variant Call Format (VCF). 685s --vcf-all: output all sites in Variant Call Format (VCF). 685s --genepop: output SNPs and haplotypes in GenePop format. 685s --structure: output results in Structure format. 685s --radpainter: output results in fineRADstructure/RADpainter format. 685s --plink: output genotypes in PLINK format. 685s --hzar: output genotypes in Hybrid Zone Analysis using R (HZAR) format. 685s --phylip: output nucleotides that are fixed-within, and variant among populations in Phylip format for phylogenetic tree construction. 685s --phylip-var: include variable sites in the phylip output encoded using IUPAC notation. 685s --phylip-var-all: include all sequence as well as variable sites in the phylip output encoded using IUPAC notation. 685s --treemix: output SNPs in a format useable for the TreeMix program (Pickrell and Pritchard). 685s --gtf: output locus positions in a GTF annotation file. 685s --no-hap-exports: omit haplotype outputs. 685s --fasta-samples-raw: output all haplotypes observed in each sample, for each locus, in FASTA format. 685s 685s Genetic map output options (population map must specify a genetic cross): 685s --map-type: genetic map type to write. 'CP', 'DH', 'F2', and 'BC1' are the currently supported map types. 685s --map-format: mapping program format to write, 'joinmap', 'onemap', and 'rqtl' are currently supported. 685s 685s Additional options: 685s -h,--help: display this help message. 685s -v,--version: print program version. 685s --verbose: turn on additional logging. 685s --log-fst-comp: log components of Fst/Phi_st calculations to a file. 685s process_radtags 2.67 685s process_radtags -p in_dir [-P] [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 685s process_radtags -f in_file [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 685s process_radtags --in-path in_dir [--paired] [--barcodes barcode_file] --out-path out_dir --renz-1 enz [--renz-2 enz] [--threads num] [-c] [-q] [-r] [-t len] 685s process_radtags -1 pair_1 -2 pair_2 [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 685s 685s -p,--in-path: path to a directory of files. 685s -P,--paired: files contained within the directory are paired. 685s -I,--interleaved: specify that the paired-end reads are interleaved in single files. 685s -b,--barcodes: path to a file containing barcodes for this run, omit to ignore any barcoding or for already demultiplexed data. 685s -f: path to the input file if processing single-end sequences. 685s -1: first input file in a set of paired-end sequences. 685s -2: second input file in a set of paired-end sequences. 685s -o,--out-path: path to output the processed files. 685s --basename: specify the prefix of the output files when using -f or -1/-2. 685s 685s --threads: number of threads to run. 685s -c,--clean: clean data, remove any read with an uncalled base ('N'). 685s -q,--quality: discard reads with low quality (phred) scores. 685s -r,--rescue: rescue barcodes and RAD-Tag cut sites. 685s -t,--truncate: truncate final read length to this value. 685s -D,--discards: capture discarded reads to a file. 685s 685s Barcode options: 685s --inline-null: barcode is inline with sequence, occurs only on single-end read (default). 685s --index-null: barcode is provded in FASTQ header (Illumina i5 or i7 read). 685s --null-index: barcode is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 685s --inline-inline: barcode is inline with sequence, occurs on single and paired-end read. 685s --index-index: barcode is provded in FASTQ header (Illumina i5 and i7 reads). 685s --inline-index: barcode is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read). 685s --index-inline: barcode occurs in FASTQ header (Illumina i5 or i7 read) and is inline with single-end sequence (for single-end data) on paired-end read (for paired-end data). 685s 685s Restriction enzyme options: 685s -e [enz], --renz-1 [enz]: provide the restriction enzyme used (cut site occurs on single-end read) 685s --renz-2 [enz]: if a double digest was used, provide the second restriction enzyme used (cut site occurs on the paired-end read). 685s Currently supported enzymes include: 685s 'aciI', 'aclI', 'ageI', 'aluI', 'apaLI', 'apeKI', 'apoI', 'aseI', 685s 'bamHI', 'bbvCI', 'bfaI', 'bfuCI', 'bgIII', 'bsaHI', 'bspDI', 'bstYI', 685s 'btgI', 'cac8I', 'claI', 'csp6I', 'ddeI', 'dpnII', 'eaeI', 'ecoRI', 685s 'ecoRV', 'ecoT22I', 'haeII', 'haeIII', 'hhaI', 'hinP1I', 'hindIII', 'hpaII', 685s 'hpyCH4IV', 'kpnI', 'mluCI', 'mseI', 'mslI', 'mspI', 'ncoI', 'ndeI', 685s 'ngoMIV', 'nheI', 'nlaIII', 'notI', 'nsiI', 'nspI', 'pacI', 'pspXI', 685s 'pstI', 'pstIshi', 'rsaI', 'sacI', 'sau3AI', 'sbfI', 'sexAI', 'sgrAI', 685s 'speI', 'sphI', 'taqI', 'xbaI', or 'xhoI' 685s 685s Protocol-specific options: 685s --bestrad: library was generated using BestRAD, check for restriction enzyme on either read and potentially tranpose reads. 685s --methylrad: library was generated using enzymatic methyl-seq (EM-seq) or bisulphite sequencing. 685s 685s Adapter options: 685s --adapter-1 : provide adaptor sequence that may occur on the single-end read for filtering. 685s --adapter-2 : provide adaptor sequence that may occur on the paired-read for filtering. 685s --adapter-mm : number of mismatches allowed in the adapter sequence. 685s 685s Input/Output options: 685s --in-type: input file type, either 'fastq', 'gzfastq' (gzipped fastq), 'bam', or 'bustard' (default: guess, or gzfastq if unable to). 685s --out-type: output type, either 'fastq', 'gzfastq', 'fasta', or 'gzfasta' (default: match input type). 685s --retain-header: retain unmodified FASTQ headers in the output. 685s --merge: if no barcodes are specified, merge all input files into a single output file. 685s 685s Advanced options: 685s --filter-illumina: discard reads that have been marked by Illumina's chastity/purity filter as failing. 685s --disable-rad-check: disable checking if the RAD cut site is intact. 685s --force-poly-g-check: force a check for runs of poly-Gs (default: autodetect based on machine type in FASTQ header). 685s --disable-poly-g-check: disable checking for runs of poly-Gs (default: autodetect based on machine type in FASTQ header). 685s --encoding: specify how quality scores are encoded, 'phred33' (Illumina 1.8+/Sanger, default) or 'phred64' (Illumina 1.3-1.5). 685s --window-size: set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15). 685s --score-limit: set the phred score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10). 685s --len-limit : specify a minimum sequence length (useful if your data has already been trimmed). 685s --barcode-dist-1: the number of allowed mismatches when rescuing single-end barcodes (default 1). 685s --barcode-dist-2: the number of allowed mismatches when rescuing paired-end barcodes (defaults to --barcode-dist-1). 685s process_shortreads 2.67 685s process_shortreads [-f in_file | -p in_dir [-P] [-I] | -1 pair_1 -2 pair_2] -b barcode_file -o out_dir [-i type] [-y type] [-c] [-q] [-r] [-E encoding] [-t len] [-D] [-w size] [-s lim] [-h] 685s f: path to the input file if processing single-end seqeunces. 685s i: input file type, either 'bustard' for the Illumina BUSTARD format, 'bam', 'fastq' (default), or 'gzfastq' for gzipped FASTQ. 685s p: path to a directory of single-end Illumina files. 685s 1: first input file in a set of paired-end sequences. 685s 2: second input file in a set of paired-end sequences. 685s P: specify that input is paired (for use with '-p'). 685s I: specify that the paired-end reads are interleaved in single files. 685s o: path to output the processed files. 685s y: output type, either 'fastq' or 'fasta' (default gzfastq). 685s b: a list of barcodes for this run. 685s c: clean data, remove any read with an uncalled base. 685s q: discard reads with low quality scores. 685s r: rescue barcodes. 685s t: truncate final read length to this value. 685s E: specify how quality scores are encoded, 'phred33' (Illumina 1.8+/Sanger, default) or 'phred64' (Illumina 1.3-1.5). 685s D: capture discarded reads to a file. 685s w: set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15). 685s s: set the score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10). 685s h: display this help message. 685s 685s Barcode options: 685s --inline-null: barcode is inline with sequence, occurs only on single-end read (default). 685s --index-null: barcode is provded in FASTQ header (Illumina i5 or i7 read). 685s --null-index: barcode is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 685s --inline-inline: barcode is inline with sequence, occurs on single and paired-end read. 685s --index-index: barcode is provded in FASTQ header (Illumina i5 and i7 reads). 685s --inline-index: barcode is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read). 685s --index-inline: barcode occurs in FASTQ header (Illumina i5 or i7 read) and is inline with single-end sequence (for single-end data) on paired-end read (for paired-end data). 685s 685s Adapter options: 685s --adapter-1 : provide adaptor sequence that may occur on the first read for filtering. 685s --adapter-2 : provide adaptor sequence that may occur on the paired-read for filtering. 685s --adapter-mm : number of mismatches allowed in the adapter sequence. 685s 685s Output options: 685s --retain-header: retain unmodified FASTQ headers in the output. 685s --merge: if no barcodes are specified, merge all input files into a single output file (or single pair of files). 685s 685s Advanced options: 685s --no-read-trimming: do not trim low quality reads, just discard them. 685s --len-limit : when trimming sequences, specify the minimum length a sequence must be to keep it (default 31bp). 685s --filter-illumina: discard reads that have been marked by Illumina's chastity/purity filter as failing. 685s --barcode-dist: provide the distace between barcodes to allow for barcode rescue (default 2) 685s --mate-pair: raw reads are circularized mate-pair data, first read will be reverse complemented. 685s --no-overhang: data does not contain an overhang nucleotide between barcode and seqeunce. 685s ref_map.pl 2.67 685s ref_map.pl --samples path --popmap path [-s spacer] --out-path path [--rm-pcr-duplicates] [-X prog:"opts" ...] 685s 685s Input/Output files: 685s --samples: path to the directory containing the samples BAM (or SAM) alignment files. 685s --popmap: path to a population map file (format is " TAB ", one sample per line). 685s -s: spacer for file names: by default this is empty and the program looks for files 685s named 'SAMPLE_NAME.bam'; if this option is given the program looks for files 685s named 'SAMPLE_NAME.SPACER.bam'. 685s -o,--out-path: path to an output directory. 685s 685s General options: 685s -X: additional options for specific pipeline components, e.g. -X "populations: -p 3 -r 0.50" 685s -T: the number of threads/CPUs to use (default: 1). 685s -d: Dry run. Do not actually execute anything, just print the individual pipeline commands 685s that would be executed. 685s 685s SNP model options: 685s --var-alpha: significance level at which to call variant sites (for gstacks; default: 0.05). 685s --gt-alpha: significance level at which to call genotypes (for gstacks; default: 0.05). 685s 685s Paired-end options: 685s --rm-pcr-duplicates: remove all but one copy of read pairs of the same sample that have 685s the same insert length. 685s --ignore-pe-reads: ignore paired-end reads even if present in the input 685s --unpaired: ignore read pairing (for paired-end GBS; treat READ2's as if they were READ1's) 685s 685s Population filtering options: 685s -r,--min-samples-per-pop: minimum percentage of individuals in a population required to process a locus for that population (for populations; default: 0) 685s -p,--min-populations: minimum number of populations a locus must be present in to process a locus (for populations; default: 1) 685s 685s Miscellaneous: 685s --time-components (for benchmarking) 685s sstacks 2.67 685s sstacks -P dir -M popmap [-t n_threads] 685s sstacks -c catalog_path -s sample_path [-s sample_path ...] -o path [-t n_threads] 685s -P,--in-path: path to the directory containing Stacks files. 685s -M,--popmap: path to a population map file from which to take sample names. 685s -s,--sample: filename prefix from which to load sample loci. 685s -c,--catalog: path to the catalog. 685s -t,--threads: enable parallel execution with n_threads threads. 685s -o,--out-path: output path to write results. 685s -x: don't verify haplotype of matching locus. 685s 685s Gapped assembly options: 685s --disable-gapped: disable gapped alignments between stacks (default: enable gapped alignments). 685s usage: 685s stacks-dist-extract logfile [section] 685s stacks-dist-extract [--pretty] [--out-path path] logfile [section] 685s cat logfile | stacks-dist-extract [--pretty] [--section section] 685s 685s Export a paricular section of a Stacks log or distribs file. If you supply a 685s log path alone, stacks-dist-extract will print the available sections to 685s output. The log file can also be supplied via stdin. 685s 685s options: 685s -h, --help show this help message and exit 685s -p, --pretty Output data as a table with columns lined up. 685s -o path, --out-path path 685s Path to output file. 685s -s section, --section section 685s Name of section to output from the log file. 685s Usage: 685s stacks-gdb PROGRAM ARGUMENTS 685s 685s e.g. 685s stacks-gdb populations -P . -p 3 -r 0.5 --vcf 685s 685s This utility will run the `PROGRAM ARGUMENTS` command as specified, but in 685s case of a crash it will print additional information, helping us in fixing the 685s crash. 685s 685s This utility requires GDB, the GNU Debugger, to be installed on the system where 685s Stacks is run. You can check whether this is the case by just typing: 685s 685s gdb --version 685s 685s at the command prompt. Note that you may need to load the corresponding module. 685s GDB is standard scientific software, but may not be installed on some systems. 685s For further information please contact the administrators of your system; 685s trying to install GDB without administrator priviledges is not recommended. 685s 685s For questions please contact us, e.g. at stacks-users@googlegroups.com 685s usage: stacks-integrate-alignments [-h] -P path -B path -O path [-q MIN_MAPQ] 685s [-a MIN_ALNCOV] [-p MIN_PCTID] [--verbose] 685s [--version] 685s 685s Extracts the coordinates of the RAD loci from the given BAM file into a 685s 'locus_coordinates.tsv' table, then rewrites the 'catalog.fa.gz' and 685s 'catalog.calls' files so that they include the genomic coordinates given in 685s the input BAM file. 685s 685s options: 685s -h, --help show this help message and exit 685s -P path, --in-path path 685s Path to a directory containing Stacks ouput files. 685s -B path, --bam-path path 685s Path to a SAM or BAM file containing alignment of de 685s novo catalog loci to a reference genome. 685s -O path, --out-path path 685s Path to write the integrated ouput files. 685s -q MIN_MAPQ, --min_mapq MIN_MAPQ 685s Minimum mapping quality as listed in the BAM file 685s (default 20). 685s -a MIN_ALNCOV, --min_alncov MIN_ALNCOV 685s Minimum fraction of the de novo catalog locus that 685s must participate in the alignment (default 0.6). 685s -p MIN_PCTID, --min_pctid MIN_PCTID 685s Minimum BLAST-style percent identity of the largest 685s alignment fragment for a de novo catalog locus 685s (default 0.6). 685s --verbose Provide verbose output. 685s --version show program's version number and exit 685s usage: 685s stacks-samtools-tview -P gstacks_dir -c catalog_locus_id -s sample_name 685s 685s Displays the read alignments of the given sample for the given locus, in text 685s format, to the standard output. Requires gstacks to have been run with the 685s --write-alignments option. (This is a convenience wrapper around samtools-tview.) 685s tsv2bam 2.67 685s tsv2bam -P stacks_dir -M popmap [-R paired_reads_dir] 685s tsv2bam -P stacks_dir -s sample [-s sample ...] [-R paired_reads_dir] 685s 685s -P,--in-dir: input directory. 685s -M,--popmap: population map. 685s -s,--sample: name of one sample. 685s -R,--pe-reads-dir: directory where to find the paired-end reads files (in fastq/fasta/bam (gz) format). 685s -t: number of threads to use (default: 1). 685s 685s ustacks 2.67 685s ustacks -f in_path -o out_path [-M max_dist] [-m min_reads] [-t num_threads] 685s -f,--file: input file path. 685s -o,--out-path: output path to write results. 685s -M: Maximum distance (in nucleotides) allowed between stacks (default 2). 685s -m: Minimum number of reads to seed a new stack (default 3). 685s -N: Maximum distance allowed to align secondary reads to primary stacks (default: M + 2). 685s -t,--threads: enable parallel execution with num_threads threads. 685s -i,--in-type: input file type. Supported types: fasta, fastq, gzfasta, or gzfastq (default: guess). 685s -n,--name: a name for the sample (default: input file name minus the suffix). 685s -R: retain unused reads. 685s -H: disable calling haplotypes from secondary reads. 685s 685s Stack assembly options: 685s --force-diff-len: allow raw input reads of different lengths, e.g. after trimming (default: ustacks prefers raw input reads of uniform length). 685s --keep-high-cov: disable the algorithm that removes highly-repetitive stacks and nearby errors. 685s --high-cov-thres: highly-repetitive stacks threshold, in standard deviation units (default: 3.0). 685s --max-locus-stacks : maximum number of stacks at a single de novo locus (default 3). 685s --k-len : specify k-mer size for matching between alleles and loci (automatically calculated by default). 685s --deleverage: enable the Deleveraging algorithm, used for resolving over merged tags. 685s 685s Gapped assembly options: 685s --max-gaps: number of gaps allowed between stacks before merging (default: 2). 685s --min-aln-len: minimum length of aligned sequence in a gapped alignment (default: 0.80). 685s --disable-gapped: do not preform gapped alignments between stacks (default: gapped alignements enabled). 685s 685s Model options: 685s --model-type: either 'snp' (default), 'bounded', or 'fixed' 685s For the SNP or Bounded SNP model: 685s --alpha : chi square significance level required to call a heterozygote or homozygote, either 0.1, 0.05 (default), 0.01, or 0.001. 685s For the Bounded SNP model: 685s --bound-low : lower bound for epsilon, the error rate, between 0 and 1.0 (default 0). 685s --bound-high : upper bound for epsilon, the error rate, between 0 and 1.0 (default 1). 685s For the Fixed model: 685s --bc-err-freq : specify the barcode error frequency, between 0 and 1.0. 685s 685s h: display this help message. 685s autopkgtest [14:51:11]: test run-unit-test: -----------------------] 691s run-unit-test PASS (superficial) 691s autopkgtest [14:51:17]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 696s autopkgtest [14:51:22]: @@@@@@@@@@@@@@@@@@@@ summary 696s run-unit-test PASS (superficial)