0s autopkgtest [01:29:09]: starting date and time: 2024-11-05 01:29:09+0000 0s autopkgtest [01:29:09]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [01:29:09]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.7aganyow/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:openjdk-24 --apt-upgrade bbmap --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=openjdk-24/24~22ea-1' -- lxd -r lxd-armhf-10.145.243.201 lxd-armhf-10.145.243.201:autopkgtest/ubuntu/plucky/armhf 51s autopkgtest [01:30:00]: testbed dpkg architecture: armhf 53s autopkgtest [01:30:02]: testbed apt version: 2.9.8 53s autopkgtest [01:30:02]: @@@@@@@@@@@@@@@@@@@@ test bed setup 61s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 61s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [22.2 kB] 62s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [177 kB] 62s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1772 kB] 62s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 62s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [217 kB] 62s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [1332 kB] 62s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [20.3 kB] 62s Fetched 3622 kB in 1s (3184 kB/s) 62s Reading package lists... 79s tee: /proc/self/fd/2: Permission denied 100s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 101s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 101s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 101s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 102s Reading package lists... 102s Reading package lists... 102s Building dependency tree... 102s Reading state information... 103s Calculating upgrade... 103s The following packages were automatically installed and are no longer required: 103s libperl5.38t64 perl-modules-5.38 103s Use 'apt autoremove' to remove them. 103s The following NEW packages will be installed: 103s libperl5.40 perl-modules-5.40 103s The following packages will be upgraded: 103s base-files distro-info-data fwupd gcc-14-base info install-info iproute2 103s libatomic1 libblockdev-crypto3 libblockdev-fs3 libblockdev-loop3 103s libblockdev-mdraid3 libblockdev-nvme3 libblockdev-part3 libblockdev-swap3 103s libblockdev-utils3 libblockdev3 libdb5.3t64 libdw1t64 libelf1t64 libevdev2 103s libftdi1-2 libfwupd2 libgcc-s1 libinih1 libkeyutils1 libldap-common libldap2 103s liblocale-gettext-perl libpipeline1 libsgutils2-1.46-2 libstdc++6 103s libtext-charwidth-perl libtext-iconv-perl libtraceevent1 103s libtraceevent1-plugin motd-news-config nano perl perl-base python3-configobj 103s python3-json-pointer python3-lazr.uri python3-oauthlib python3-zipp 103s sg3-utils sg3-utils-udev vim-common vim-tiny xxd 103s 50 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 103s Need to get 20.0 MB of archives. 103s After this operation, 42.8 MB of additional disk space will be used. 103s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf motd-news-config all 13.5ubuntu2 [5274 B] 104s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf base-files armhf 13.5ubuntu2 [68.6 kB] 104s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf perl-modules-5.40 all 5.40.0-6 [3214 kB] 104s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libperl5.40 armhf 5.40.0-6 [4140 kB] 104s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf perl armhf 5.40.0-6 [262 kB] 104s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf perl-base armhf 5.40.0-6 [1674 kB] 104s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf liblocale-gettext-perl armhf 1.07-7build1 [15.0 kB] 104s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf libtext-iconv-perl armhf 1.7-8build4 [12.8 kB] 104s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf libtext-charwidth-perl armhf 0.04-11build4 [9128 B] 104s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libdb5.3t64 armhf 5.3.28+dfsg2-9 [655 kB] 104s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libatomic1 armhf 14.2.0-7ubuntu1 [7842 B] 104s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14-base armhf 14.2.0-7ubuntu1 [51.2 kB] 104s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libstdc++6 armhf 14.2.0-7ubuntu1 [711 kB] 104s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf libgcc-s1 armhf 14.2.0-7ubuntu1 [40.8 kB] 104s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf install-info armhf 7.1.1-1 [61.4 kB] 104s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf distro-info-data all 0.63 [6588 B] 104s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libdw1t64 armhf 0.192-4 [243 kB] 104s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf libelf1t64 armhf 0.192-4 [50.2 kB] 104s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf iproute2 armhf 6.10.0-2ubuntu1 [1082 kB] 104s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libkeyutils1 armhf 1.6.3-4ubuntu2 [8712 B] 104s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf vim-tiny armhf 2:9.1.0777-1ubuntu1 [693 kB] 104s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf vim-common all 2:9.1.0777-1ubuntu1 [394 kB] 104s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf xxd armhf 2:9.1.0777-1ubuntu1 [66.8 kB] 104s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf info armhf 7.1.1-1 [126 kB] 104s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf libevdev2 armhf 1.13.3+dfsg-1 [29.7 kB] 104s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf libpipeline1 armhf 1.5.8-1 [26.9 kB] 104s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libtraceevent1-plugin armhf 1:1.8.3-1ubuntu1 [18.1 kB] 104s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf libtraceevent1 armhf 1:1.8.3-1ubuntu1 [52.1 kB] 104s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf nano armhf 8.2-1 [276 kB] 104s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf libfwupd2 armhf 1.9.26-2 [125 kB] 104s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf fwupd armhf 1.9.26-2 [4404 kB] 105s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-utils3 armhf 3.2.0-2 [17.4 kB] 105s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-crypto3 armhf 3.2.0-2 [22.3 kB] 105s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-fs3 armhf 3.2.0-2 [34.3 kB] 105s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-loop3 armhf 3.2.0-2 [6552 B] 105s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-mdraid3 armhf 3.2.0-2 [13.4 kB] 105s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-nvme3 armhf 3.2.0-2 [17.6 kB] 105s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-part3 armhf 3.2.0-2 [16.5 kB] 105s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-swap3 armhf 3.2.0-2 [8942 B] 105s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev3 armhf 3.2.0-2 [44.2 kB] 105s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf libftdi1-2 armhf 1.5-7 [25.7 kB] 105s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf libinih1 armhf 58-1ubuntu1 [6750 B] 105s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf libldap-common all 2.6.8+dfsg-1~exp4ubuntu3 [32.3 kB] 105s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf libldap2 armhf 2.6.8+dfsg-1~exp4ubuntu3 [173 kB] 105s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf libsgutils2-1.46-2 armhf 1.46-3ubuntu5 [82.5 kB] 105s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf python3-configobj all 5.0.9-1 [33.9 kB] 105s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf python3-json-pointer all 2.4-2 [8396 B] 105s Get:48 http://ftpmaster.internal/ubuntu plucky/main armhf python3-lazr.uri all 1.0.6-4 [13.6 kB] 105s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf python3-oauthlib all 3.2.2-2 [89.8 kB] 105s Get:50 http://ftpmaster.internal/ubuntu plucky/main armhf python3-zipp all 3.20.2-1 [10.1 kB] 105s Get:51 http://ftpmaster.internal/ubuntu plucky/main armhf sg3-utils armhf 1.46-3ubuntu5 [816 kB] 105s Get:52 http://ftpmaster.internal/ubuntu plucky/main armhf sg3-utils-udev all 1.46-3ubuntu5 [5916 B] 105s Preconfiguring packages ... 105s Fetched 20.0 MB in 2s (12.9 MB/s) 105s (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.) 105s Preparing to unpack .../motd-news-config_13.5ubuntu2_all.deb ... 105s Unpacking motd-news-config (13.5ubuntu2) over (13.3ubuntu6) ... 105s Preparing to unpack .../base-files_13.5ubuntu2_armhf.deb ... 106s Unpacking base-files (13.5ubuntu2) over (13.3ubuntu6) ... 106s Setting up base-files (13.5ubuntu2) ... 106s Installing new version of config file /etc/issue ... 106s Installing new version of config file /etc/issue.net ... 106s Installing new version of config file /etc/lsb-release ... 106s motd-news.service is a disabled or a static unit not running, not starting it. 106s (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.) 106s Preparing to unpack .../perl_5.40.0-6_armhf.deb ... 106s Unpacking perl (5.40.0-6) over (5.38.2-5) ... 106s Selecting previously unselected package perl-modules-5.40. 106s Preparing to unpack .../perl-modules-5.40_5.40.0-6_all.deb ... 106s Unpacking perl-modules-5.40 (5.40.0-6) ... 107s Selecting previously unselected package libperl5.40:armhf. 107s Preparing to unpack .../libperl5.40_5.40.0-6_armhf.deb ... 107s Unpacking libperl5.40:armhf (5.40.0-6) ... 107s Preparing to unpack .../perl-base_5.40.0-6_armhf.deb ... 107s Unpacking perl-base (5.40.0-6) over (5.38.2-5) ... 107s Setting up perl-base (5.40.0-6) ... 107s (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.) 107s Preparing to unpack .../liblocale-gettext-perl_1.07-7build1_armhf.deb ... 107s Unpacking liblocale-gettext-perl (1.07-7build1) over (1.07-7) ... 107s Preparing to unpack .../libtext-iconv-perl_1.7-8build4_armhf.deb ... 107s Unpacking libtext-iconv-perl:armhf (1.7-8build4) over (1.7-8build3) ... 107s Preparing to unpack .../libtext-charwidth-perl_0.04-11build4_armhf.deb ... 107s Unpacking libtext-charwidth-perl:armhf (0.04-11build4) over (0.04-11build3) ... 107s Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-9_armhf.deb ... 107s Unpacking libdb5.3t64:armhf (5.3.28+dfsg2-9) over (5.3.28+dfsg2-7) ... 107s Setting up libdb5.3t64:armhf (5.3.28+dfsg2-9) ... 107s (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.) 107s Preparing to unpack .../libatomic1_14.2.0-7ubuntu1_armhf.deb ... 107s Unpacking libatomic1:armhf (14.2.0-7ubuntu1) over (14.2.0-4ubuntu2) ... 107s Preparing to unpack .../gcc-14-base_14.2.0-7ubuntu1_armhf.deb ... 107s Unpacking gcc-14-base:armhf (14.2.0-7ubuntu1) over (14.2.0-4ubuntu2) ... 107s Setting up gcc-14-base:armhf (14.2.0-7ubuntu1) ... 107s (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.) 107s Preparing to unpack .../libstdc++6_14.2.0-7ubuntu1_armhf.deb ... 108s Unpacking libstdc++6:armhf (14.2.0-7ubuntu1) over (14.2.0-4ubuntu2) ... 108s Setting up libstdc++6:armhf (14.2.0-7ubuntu1) ... 108s (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.) 108s Preparing to unpack .../libgcc-s1_14.2.0-7ubuntu1_armhf.deb ... 108s Unpacking libgcc-s1:armhf (14.2.0-7ubuntu1) over (14.2.0-4ubuntu2) ... 108s Setting up libgcc-s1:armhf (14.2.0-7ubuntu1) ... 108s (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.) 108s Preparing to unpack .../install-info_7.1.1-1_armhf.deb ... 108s Unpacking install-info (7.1.1-1) over (7.1-3build2) ... 108s Setting up install-info (7.1.1-1) ... 108s (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.) 108s Preparing to unpack .../00-distro-info-data_0.63_all.deb ... 108s Unpacking distro-info-data (0.63) over (0.62) ... 108s Preparing to unpack .../01-libdw1t64_0.192-4_armhf.deb ... 108s Unpacking libdw1t64:armhf (0.192-4) over (0.191-2) ... 108s Preparing to unpack .../02-libelf1t64_0.192-4_armhf.deb ... 108s Unpacking libelf1t64:armhf (0.192-4) over (0.191-2) ... 108s Preparing to unpack .../03-iproute2_6.10.0-2ubuntu1_armhf.deb ... 108s Unpacking iproute2 (6.10.0-2ubuntu1) over (6.10.0-2) ... 108s Preparing to unpack .../04-libkeyutils1_1.6.3-4ubuntu2_armhf.deb ... 108s Unpacking libkeyutils1:armhf (1.6.3-4ubuntu2) over (1.6.3-3build1) ... 108s Preparing to unpack .../05-vim-tiny_2%3a9.1.0777-1ubuntu1_armhf.deb ... 108s Unpacking vim-tiny (2:9.1.0777-1ubuntu1) over (2:9.1.0496-1ubuntu6) ... 108s Preparing to unpack .../06-vim-common_2%3a9.1.0777-1ubuntu1_all.deb ... 108s Unpacking vim-common (2:9.1.0777-1ubuntu1) over (2:9.1.0496-1ubuntu6) ... 108s Preparing to unpack .../07-xxd_2%3a9.1.0777-1ubuntu1_armhf.deb ... 108s Unpacking xxd (2:9.1.0777-1ubuntu1) over (2:9.1.0496-1ubuntu6) ... 108s Preparing to unpack .../08-info_7.1.1-1_armhf.deb ... 108s Unpacking info (7.1.1-1) over (7.1-3build2) ... 108s Preparing to unpack .../09-libevdev2_1.13.3+dfsg-1_armhf.deb ... 108s Unpacking libevdev2:armhf (1.13.3+dfsg-1) over (1.13.2+dfsg-1) ... 109s Preparing to unpack .../10-libpipeline1_1.5.8-1_armhf.deb ... 109s Unpacking libpipeline1:armhf (1.5.8-1) over (1.5.7-2) ... 109s Preparing to unpack .../11-libtraceevent1-plugin_1%3a1.8.3-1ubuntu1_armhf.deb ... 109s Unpacking libtraceevent1-plugin:armhf (1:1.8.3-1ubuntu1) over (1:1.8.2-1ubuntu3) ... 109s Preparing to unpack .../12-libtraceevent1_1%3a1.8.3-1ubuntu1_armhf.deb ... 109s Unpacking libtraceevent1:armhf (1:1.8.3-1ubuntu1) over (1:1.8.2-1ubuntu3) ... 109s Preparing to unpack .../13-nano_8.2-1_armhf.deb ... 109s Unpacking nano (8.2-1) over (8.1-1) ... 109s Preparing to unpack .../14-libfwupd2_1.9.26-2_armhf.deb ... 109s Unpacking libfwupd2:armhf (1.9.26-2) over (1.9.24-1) ... 109s Preparing to unpack .../15-fwupd_1.9.26-2_armhf.deb ... 109s Unpacking fwupd (1.9.26-2) over (1.9.24-1) ... 109s Preparing to unpack .../16-libblockdev-utils3_3.2.0-2_armhf.deb ... 109s Unpacking libblockdev-utils3:armhf (3.2.0-2) over (3.1.1-2) ... 109s Preparing to unpack .../17-libblockdev-crypto3_3.2.0-2_armhf.deb ... 109s Unpacking libblockdev-crypto3:armhf (3.2.0-2) over (3.1.1-2) ... 109s Preparing to unpack .../18-libblockdev-fs3_3.2.0-2_armhf.deb ... 109s Unpacking libblockdev-fs3:armhf (3.2.0-2) over (3.1.1-2) ... 109s Preparing to unpack .../19-libblockdev-loop3_3.2.0-2_armhf.deb ... 109s Unpacking libblockdev-loop3:armhf (3.2.0-2) over (3.1.1-2) ... 109s Preparing to unpack .../20-libblockdev-mdraid3_3.2.0-2_armhf.deb ... 109s Unpacking libblockdev-mdraid3:armhf (3.2.0-2) over (3.1.1-2) ... 109s Preparing to unpack .../21-libblockdev-nvme3_3.2.0-2_armhf.deb ... 109s Unpacking libblockdev-nvme3:armhf (3.2.0-2) over (3.1.1-2) ... 109s Preparing to unpack .../22-libblockdev-part3_3.2.0-2_armhf.deb ... 109s Unpacking libblockdev-part3:armhf (3.2.0-2) over (3.1.1-2) ... 109s Preparing to unpack .../23-libblockdev-swap3_3.2.0-2_armhf.deb ... 109s Unpacking libblockdev-swap3:armhf (3.2.0-2) over (3.1.1-2) ... 109s Preparing to unpack .../24-libblockdev3_3.2.0-2_armhf.deb ... 109s Unpacking libblockdev3:armhf (3.2.0-2) over (3.1.1-2) ... 109s Preparing to unpack .../25-libftdi1-2_1.5-7_armhf.deb ... 109s Unpacking libftdi1-2:armhf (1.5-7) over (1.5-6build5) ... 109s Preparing to unpack .../26-libinih1_58-1ubuntu1_armhf.deb ... 109s Unpacking libinih1:armhf (58-1ubuntu1) over (55-1ubuntu2) ... 109s Preparing to unpack .../27-libldap-common_2.6.8+dfsg-1~exp4ubuntu3_all.deb ... 109s Unpacking libldap-common (2.6.8+dfsg-1~exp4ubuntu3) over (2.6.8+dfsg-1~exp4ubuntu1) ... 109s Preparing to unpack .../28-libldap2_2.6.8+dfsg-1~exp4ubuntu3_armhf.deb ... 109s Unpacking libldap2:armhf (2.6.8+dfsg-1~exp4ubuntu3) over (2.6.8+dfsg-1~exp4ubuntu1) ... 109s Preparing to unpack .../29-libsgutils2-1.46-2_1.46-3ubuntu5_armhf.deb ... 109s Unpacking libsgutils2-1.46-2:armhf (1.46-3ubuntu5) over (1.46-3ubuntu4) ... 109s Preparing to unpack .../30-python3-configobj_5.0.9-1_all.deb ... 109s Unpacking python3-configobj (5.0.9-1) over (5.0.8-3) ... 110s Preparing to unpack .../31-python3-json-pointer_2.4-2_all.deb ... 110s Unpacking python3-json-pointer (2.4-2) over (2.0-0ubuntu1) ... 110s Preparing to unpack .../32-python3-lazr.uri_1.0.6-4_all.deb ... 110s Unpacking python3-lazr.uri (1.0.6-4) over (1.0.6-3) ... 110s Preparing to unpack .../33-python3-oauthlib_3.2.2-2_all.deb ... 110s Unpacking python3-oauthlib (3.2.2-2) over (3.2.2-1) ... 110s Preparing to unpack .../34-python3-zipp_3.20.2-1_all.deb ... 110s Unpacking python3-zipp (3.20.2-1) over (3.20.0-1) ... 110s Preparing to unpack .../35-sg3-utils_1.46-3ubuntu5_armhf.deb ... 110s Unpacking sg3-utils (1.46-3ubuntu5) over (1.46-3ubuntu4) ... 110s Preparing to unpack .../36-sg3-utils-udev_1.46-3ubuntu5_all.deb ... 110s Unpacking sg3-utils-udev (1.46-3ubuntu5) over (1.46-3ubuntu4) ... 110s Setting up libpipeline1:armhf (1.5.8-1) ... 110s Setting up motd-news-config (13.5ubuntu2) ... 110s Setting up libtext-iconv-perl:armhf (1.7-8build4) ... 110s Setting up libtext-charwidth-perl:armhf (0.04-11build4) ... 110s Setting up libkeyutils1:armhf (1.6.3-4ubuntu2) ... 110s Setting up distro-info-data (0.63) ... 110s Setting up libinih1:armhf (58-1ubuntu1) ... 110s Setting up libfwupd2:armhf (1.9.26-2) ... 110s Setting up libsgutils2-1.46-2:armhf (1.46-3ubuntu5) ... 110s Setting up python3-lazr.uri (1.0.6-4) ... 110s Setting up python3-zipp (3.20.2-1) ... 110s Setting up libldap-common (2.6.8+dfsg-1~exp4ubuntu3) ... 110s Setting up xxd (2:9.1.0777-1ubuntu1) ... 110s Setting up libelf1t64:armhf (0.192-4) ... 110s Setting up libdw1t64:armhf (0.192-4) ... 110s Setting up libftdi1-2:armhf (1.5-7) ... 110s Setting up python3-oauthlib (3.2.2-2) ... 111s Setting up python3-configobj (5.0.9-1) ... 111s Setting up vim-common (2:9.1.0777-1ubuntu1) ... 111s Installing new version of config file /etc/vim/vimrc ... 111s Setting up libblockdev-utils3:armhf (3.2.0-2) ... 111s Setting up libatomic1:armhf (14.2.0-7ubuntu1) ... 111s Setting up libblockdev-nvme3:armhf (3.2.0-2) ... 111s Setting up nano (8.2-1) ... 111s Setting up libblockdev-fs3:armhf (3.2.0-2) ... 111s Setting up perl-modules-5.40 (5.40.0-6) ... 111s Setting up python3-json-pointer (2.4-2) ... 111s Setting up libtraceevent1:armhf (1:1.8.3-1ubuntu1) ... 111s Setting up libevdev2:armhf (1.13.3+dfsg-1) ... 111s Setting up libldap2:armhf (2.6.8+dfsg-1~exp4ubuntu3) ... 111s Setting up fwupd (1.9.26-2) ... 111s fwupd-offline-update.service is a disabled or a static unit not running, not starting it. 111s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 111s fwupd.service is a disabled or a static unit not running, not starting it. 111s Setting up info (7.1.1-1) ... 111s Setting up liblocale-gettext-perl (1.07-7build1) ... 111s Setting up sg3-utils (1.46-3ubuntu5) ... 111s Setting up libblockdev-mdraid3:armhf (3.2.0-2) ... 111s Setting up libblockdev-crypto3:armhf (3.2.0-2) ... 111s Setting up libblockdev-swap3:armhf (3.2.0-2) ... 111s Setting up iproute2 (6.10.0-2ubuntu1) ... 112s Setting up libblockdev-loop3:armhf (3.2.0-2) ... 112s Setting up vim-tiny (2:9.1.0777-1ubuntu1) ... 112s Setting up libblockdev3:armhf (3.2.0-2) ... 112s Installing new version of config file /etc/libblockdev/3/conf.d/00-default.cfg ... 112s Setting up libblockdev-part3:armhf (3.2.0-2) ... 112s Setting up sg3-utils-udev (1.46-3ubuntu5) ... 112s update-initramfs: deferring update (trigger activated) 112s Setting up libperl5.40:armhf (5.40.0-6) ... 112s Setting up perl (5.40.0-6) ... 112s Setting up libtraceevent1-plugin:armhf (1:1.8.3-1ubuntu1) ... 112s Processing triggers for initramfs-tools (0.142ubuntu34) ... 112s Processing triggers for libc-bin (2.40-1ubuntu3) ... 112s Processing triggers for man-db (2.12.1-3) ... 113s Processing triggers for plymouth-theme-ubuntu-text (24.004.60-1ubuntu10) ... 113s update-initramfs: deferring update (trigger activated) 113s Processing triggers for dbus (1.14.10-4ubuntu5) ... 113s Processing triggers for install-info (7.1.1-1) ... 113s Processing triggers for initramfs-tools (0.142ubuntu34) ... 114s Reading package lists... 114s Building dependency tree... 114s Reading state information... 115s The following packages will be REMOVED: 115s libperl5.38t64* perl-modules-5.38* 115s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 115s After this operation, 41.6 MB disk space will be freed. 115s (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.) 115s Removing libperl5.38t64:armhf (5.38.2-5) ... 115s Removing perl-modules-5.38 (5.38.2-5) ... 115s Processing triggers for man-db (2.12.1-3) ... 115s Processing triggers for libc-bin (2.40-1ubuntu3) ... 118s autopkgtest [01:31:07]: rebooting testbed after setup commands that affected boot 184s autopkgtest [01:32:13]: 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 210s autopkgtest [01:32:39]: @@@@@@@@@@@@@@@@@@@@ apt-source bbmap 224s Get:1 http://ftpmaster.internal/ubuntu plucky/universe bbmap 39.08+dfsg-1 (dsc) [2286 B] 224s Get:2 http://ftpmaster.internal/ubuntu plucky/universe bbmap 39.08+dfsg-1 (tar) [5396 kB] 224s Get:3 http://ftpmaster.internal/ubuntu plucky/universe bbmap 39.08+dfsg-1 (diff) [25.4 kB] 224s gpgv: Signature made Fri Aug 9 08:31:18 2024 UTC 224s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 224s gpgv: issuer "emollier@debian.org" 224s gpgv: Can't check signature: No public key 224s dpkg-source: warning: cannot verify inline signature for ./bbmap_39.08+dfsg-1.dsc: no acceptable signature found 225s autopkgtest [01:32:54]: testing package bbmap version 39.08+dfsg-1 227s autopkgtest [01:32:56]: build not needed 229s autopkgtest [01:32:58]: test run-unit-test: preparing testbed 239s Reading package lists... 239s Building dependency tree... 239s Reading state information... 240s Starting pkgProblemResolver with broken count: 0 240s Starting 2 pkgProblemResolver with broken count: 0 240s Done 240s The following additional packages will be installed: 240s bbmap bbmap-jni ca-certificates-java java-common libapache-pom-java 240s libcommons-cli-java libcommons-codec-java libcommons-io-java 240s libcommons-parent-java libjpeg-turbo8 libjpeg8 liblcms2-2 liblog4j1.2-java 240s libmpj-java libpcsclite1 openjdk-17-jre-headless python-biopython-doc 240s Suggested packages: 240s default-jre liblcms2-utils liblog4j1.2-java-doc libmail-java pcscd 240s libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho 240s fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic 240s Recommended packages: 240s pigz libcups2t64 libfontconfig1 libfreetype6 libharfbuzz0b libasound2t64 240s python3-biopython 241s The following NEW packages will be installed: 241s autopkgtest-satdep bbmap bbmap-jni ca-certificates-java java-common 241s libapache-pom-java libcommons-cli-java libcommons-codec-java 241s libcommons-io-java libcommons-parent-java libjpeg-turbo8 libjpeg8 liblcms2-2 241s liblog4j1.2-java libmpj-java libpcsclite1 openjdk-17-jre-headless 241s python-biopython-doc 241s 0 upgraded, 18 newly installed, 0 to remove and 0 not upgraded. 241s Need to get 71.6 MB/71.6 MB of archives. 241s After this operation, 197 MB of additional disk space will be used. 241s Get:1 /tmp/autopkgtest.071bZE/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [720 B] 241s Get:2 http://ftpmaster.internal/ubuntu plucky/universe armhf libcommons-cli-java all 1.6.0-1 [59.9 kB] 241s Get:3 http://ftpmaster.internal/ubuntu plucky/universe armhf libapache-pom-java all 33-2 [5874 B] 241s Get:4 http://ftpmaster.internal/ubuntu plucky/universe armhf libcommons-parent-java all 56-1 [10.7 kB] 241s Get:5 http://ftpmaster.internal/ubuntu plucky/universe armhf libcommons-codec-java all 1.17.1-1 [302 kB] 241s Get:6 http://ftpmaster.internal/ubuntu plucky/universe armhf libcommons-io-java all 2.16.1-1 [451 kB] 241s Get:7 http://ftpmaster.internal/ubuntu plucky/universe armhf liblog4j1.2-java all 1.2.17-11 [439 kB] 241s Get:8 http://ftpmaster.internal/ubuntu plucky/universe armhf libmpj-java all 0.44+dfsg-4 [443 kB] 241s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf ca-certificates-java all 20240118 [11.6 kB] 241s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf java-common all 0.76 [6852 B] 241s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf liblcms2-2 armhf 2.14-2build1 [132 kB] 241s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8 armhf 2.1.5-2ubuntu2 [125 kB] 241s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 241s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf libpcsclite1 armhf 2.3.0-1 [24.8 kB] 241s Get:15 http://ftpmaster.internal/ubuntu plucky/universe armhf openjdk-17-jre-headless armhf 17.0.13+11-2build1 [42.1 MB] 243s Get:16 http://ftpmaster.internal/ubuntu plucky/universe armhf bbmap all 39.08+dfsg-1 [10.0 MB] 243s Get:17 http://ftpmaster.internal/ubuntu plucky/universe armhf bbmap-jni armhf 39.08+dfsg-1 [20.9 kB] 243s Get:18 http://ftpmaster.internal/ubuntu plucky/universe armhf python-biopython-doc all 1.83+dfsg1-3 [17.4 MB] 245s Fetched 71.6 MB in 4s (20.1 MB/s) 245s Selecting previously unselected package libcommons-cli-java. 245s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59532 files and directories currently installed.) 245s Preparing to unpack .../00-libcommons-cli-java_1.6.0-1_all.deb ... 245s Unpacking libcommons-cli-java (1.6.0-1) ... 245s Selecting previously unselected package libapache-pom-java. 245s Preparing to unpack .../01-libapache-pom-java_33-2_all.deb ... 245s Unpacking libapache-pom-java (33-2) ... 245s Selecting previously unselected package libcommons-parent-java. 245s Preparing to unpack .../02-libcommons-parent-java_56-1_all.deb ... 245s Unpacking libcommons-parent-java (56-1) ... 245s Selecting previously unselected package libcommons-codec-java. 245s Preparing to unpack .../03-libcommons-codec-java_1.17.1-1_all.deb ... 245s Unpacking libcommons-codec-java (1.17.1-1) ... 245s Selecting previously unselected package libcommons-io-java. 245s Preparing to unpack .../04-libcommons-io-java_2.16.1-1_all.deb ... 245s Unpacking libcommons-io-java (2.16.1-1) ... 245s Selecting previously unselected package liblog4j1.2-java. 245s Preparing to unpack .../05-liblog4j1.2-java_1.2.17-11_all.deb ... 245s Unpacking liblog4j1.2-java (1.2.17-11) ... 245s Selecting previously unselected package libmpj-java. 245s Preparing to unpack .../06-libmpj-java_0.44+dfsg-4_all.deb ... 245s Unpacking libmpj-java (0.44+dfsg-4) ... 245s Selecting previously unselected package ca-certificates-java. 245s Preparing to unpack .../07-ca-certificates-java_20240118_all.deb ... 245s Unpacking ca-certificates-java (20240118) ... 245s Selecting previously unselected package java-common. 245s Preparing to unpack .../08-java-common_0.76_all.deb ... 245s Unpacking java-common (0.76) ... 245s Selecting previously unselected package liblcms2-2:armhf. 245s Preparing to unpack .../09-liblcms2-2_2.14-2build1_armhf.deb ... 245s Unpacking liblcms2-2:armhf (2.14-2build1) ... 245s Selecting previously unselected package libjpeg-turbo8:armhf. 245s Preparing to unpack .../10-libjpeg-turbo8_2.1.5-2ubuntu2_armhf.deb ... 245s Unpacking libjpeg-turbo8:armhf (2.1.5-2ubuntu2) ... 245s Selecting previously unselected package libjpeg8:armhf. 245s Preparing to unpack .../11-libjpeg8_8c-2ubuntu11_armhf.deb ... 245s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 245s Selecting previously unselected package libpcsclite1:armhf. 245s Preparing to unpack .../12-libpcsclite1_2.3.0-1_armhf.deb ... 245s Unpacking libpcsclite1:armhf (2.3.0-1) ... 245s Selecting previously unselected package openjdk-17-jre-headless:armhf. 245s Preparing to unpack .../13-openjdk-17-jre-headless_17.0.13+11-2build1_armhf.deb ... 245s Unpacking openjdk-17-jre-headless:armhf (17.0.13+11-2build1) ... 246s Selecting previously unselected package bbmap. 246s Preparing to unpack .../14-bbmap_39.08+dfsg-1_all.deb ... 246s Unpacking bbmap (39.08+dfsg-1) ... 246s Selecting previously unselected package bbmap-jni. 246s Preparing to unpack .../15-bbmap-jni_39.08+dfsg-1_armhf.deb ... 246s Unpacking bbmap-jni (39.08+dfsg-1) ... 246s Selecting previously unselected package python-biopython-doc. 246s Preparing to unpack .../16-python-biopython-doc_1.83+dfsg1-3_all.deb ... 246s Unpacking python-biopython-doc (1.83+dfsg1-3) ... 247s Selecting previously unselected package autopkgtest-satdep. 247s Preparing to unpack .../17-1-autopkgtest-satdep.deb ... 247s Unpacking autopkgtest-satdep (0) ... 247s Setting up liblcms2-2:armhf (2.14-2build1) ... 247s Setting up java-common (0.76) ... 247s Setting up libcommons-cli-java (1.6.0-1) ... 247s Setting up liblog4j1.2-java (1.2.17-11) ... 247s Setting up libapache-pom-java (33-2) ... 247s Setting up libpcsclite1:armhf (2.3.0-1) ... 247s Setting up libjpeg-turbo8:armhf (2.1.5-2ubuntu2) ... 247s Setting up python-biopython-doc (1.83+dfsg1-3) ... 247s Setting up bbmap-jni (39.08+dfsg-1) ... 247s Setting up ca-certificates-java (20240118) ... 247s No JRE found. Skipping Java certificates setup. 247s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 247s Setting up libcommons-parent-java (56-1) ... 247s Setting up openjdk-17-jre-headless:armhf (17.0.13+11-2build1) ... 247s update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/java to provide /usr/bin/java (java) in auto mode 247s update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 247s update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 247s update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 247s update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 247s Setting up libcommons-codec-java (1.17.1-1) ... 247s Setting up libcommons-io-java (2.16.1-1) ... 247s Setting up libmpj-java (0.44+dfsg-4) ... 247s Processing triggers for libc-bin (2.40-1ubuntu3) ... 247s Processing triggers for man-db (2.12.1-3) ... 247s Processing triggers for ca-certificates-java (20240118) ... 248s Adding debian:ACCVRAIZ1.pem 248s Adding debian:AC_RAIZ_FNMT-RCM.pem 248s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 248s Adding debian:ANF_Secure_Server_Root_CA.pem 248s Adding debian:Actalis_Authentication_Root_CA.pem 248s Adding debian:AffirmTrust_Commercial.pem 248s Adding debian:AffirmTrust_Networking.pem 248s Adding debian:AffirmTrust_Premium.pem 248s Adding debian:AffirmTrust_Premium_ECC.pem 248s Adding debian:Amazon_Root_CA_1.pem 248s Adding debian:Amazon_Root_CA_2.pem 248s Adding debian:Amazon_Root_CA_3.pem 248s Adding debian:Amazon_Root_CA_4.pem 248s Adding debian:Atos_TrustedRoot_2011.pem 248s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 248s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 248s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 248s Adding debian:BJCA_Global_Root_CA1.pem 248s Adding debian:BJCA_Global_Root_CA2.pem 248s Adding debian:Baltimore_CyberTrust_Root.pem 248s Adding debian:Buypass_Class_2_Root_CA.pem 248s Adding debian:Buypass_Class_3_Root_CA.pem 248s Adding debian:CA_Disig_Root_R2.pem 248s Adding debian:CFCA_EV_ROOT.pem 248s Adding debian:COMODO_Certification_Authority.pem 248s Adding debian:COMODO_ECC_Certification_Authority.pem 248s Adding debian:COMODO_RSA_Certification_Authority.pem 248s Adding debian:Certainly_Root_E1.pem 248s Adding debian:Certainly_Root_R1.pem 248s Adding debian:Certigna.pem 248s Adding debian:Certigna_Root_CA.pem 248s Adding debian:Certum_EC-384_CA.pem 248s Adding debian:Certum_Trusted_Network_CA.pem 248s Adding debian:Certum_Trusted_Network_CA_2.pem 248s Adding debian:Certum_Trusted_Root_CA.pem 248s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 248s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 248s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 248s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 248s Adding debian:Comodo_AAA_Services_root.pem 248s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 248s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 248s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 248s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 248s Adding debian:DigiCert_Assured_ID_Root_CA.pem 248s Adding debian:DigiCert_Assured_ID_Root_G2.pem 248s Adding debian:DigiCert_Assured_ID_Root_G3.pem 248s Adding debian:DigiCert_Global_Root_CA.pem 248s Adding debian:DigiCert_Global_Root_G2.pem 248s Adding debian:DigiCert_Global_Root_G3.pem 248s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 248s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 248s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 248s Adding debian:DigiCert_Trusted_Root_G4.pem 248s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 248s Adding debian:Entrust_Root_Certification_Authority.pem 248s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 248s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 248s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem 248s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 248s Adding debian:GLOBALTRUST_2020.pem 248s Adding debian:GTS_Root_R1.pem 248s Adding debian:GTS_Root_R2.pem 248s Adding debian:GTS_Root_R3.pem 248s Adding debian:GTS_Root_R4.pem 248s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 248s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 248s Adding debian:GlobalSign_Root_CA.pem 248s Adding debian:GlobalSign_Root_CA_-_R3.pem 248s Adding debian:GlobalSign_Root_CA_-_R6.pem 248s Adding debian:GlobalSign_Root_E46.pem 248s Adding debian:GlobalSign_Root_R46.pem 248s Adding debian:Go_Daddy_Class_2_CA.pem 248s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 248s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 248s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 248s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 248s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 248s Adding debian:HiPKI_Root_CA_-_G1.pem 248s Adding debian:Hongkong_Post_Root_CA_3.pem 248s Adding debian:ISRG_Root_X1.pem 248s Adding debian:ISRG_Root_X2.pem 248s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 248s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 248s Adding debian:Izenpe.com.pem 248s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 248s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 248s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 248s Adding debian:NAVER_Global_Root_Certification_Authority.pem 248s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 248s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 248s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 248s Adding debian:QuoVadis_Root_CA_1_G3.pem 248s Adding debian:QuoVadis_Root_CA_2.pem 248s Adding debian:QuoVadis_Root_CA_2_G3.pem 248s Adding debian:QuoVadis_Root_CA_3.pem 248s Adding debian:QuoVadis_Root_CA_3_G3.pem 248s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 248s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 248s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 248s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 248s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 248s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 248s Adding debian:SZAFIR_ROOT_CA2.pem 248s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 248s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 248s Adding debian:SecureSign_RootCA11.pem 248s Adding debian:SecureTrust_CA.pem 248s Adding debian:Secure_Global_CA.pem 248s Adding debian:Security_Communication_ECC_RootCA1.pem 248s Adding debian:Security_Communication_RootCA2.pem 248s Adding debian:Security_Communication_RootCA3.pem 248s Adding debian:Security_Communication_Root_CA.pem 248s Adding debian:Starfield_Class_2_CA.pem 248s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 248s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 248s Adding debian:SwissSign_Gold_CA_-_G2.pem 248s Adding debian:SwissSign_Silver_CA_-_G2.pem 248s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 248s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 248s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 248s Adding debian:TWCA_Global_Root_CA.pem 248s Adding debian:TWCA_Root_Certification_Authority.pem 248s Adding debian:TeliaSonera_Root_CA_v1.pem 248s Adding debian:Telia_Root_CA_v2.pem 248s Adding debian:TrustAsia_Global_Root_CA_G3.pem 248s Adding debian:TrustAsia_Global_Root_CA_G4.pem 248s Adding debian:Trustwave_Global_Certification_Authority.pem 248s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 248s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 248s Adding debian:TunTrust_Root_CA.pem 248s Adding debian:UCA_Extended_Validation_Root.pem 248s Adding debian:UCA_Global_G2_Root.pem 248s Adding debian:USERTrust_ECC_Certification_Authority.pem 248s Adding debian:USERTrust_RSA_Certification_Authority.pem 248s Adding debian:XRamp_Global_CA_Root.pem 248s Adding debian:certSIGN_ROOT_CA.pem 248s Adding debian:certSIGN_Root_CA_G2.pem 248s Adding debian:e-Szigno_Root_CA_2017.pem 248s Adding debian:ePKI_Root_Certification_Authority.pem 248s Adding debian:emSign_ECC_Root_CA_-_C3.pem 248s Adding debian:emSign_ECC_Root_CA_-_G3.pem 248s Adding debian:emSign_Root_CA_-_C1.pem 248s Adding debian:emSign_Root_CA_-_G1.pem 248s Adding debian:vTrus_ECC_Root_CA.pem 248s Adding debian:vTrus_Root_CA.pem 248s done. 248s Setting up bbmap (39.08+dfsg-1) ... 248s Setting up autopkgtest-satdep (0) ... 261s (Reading database ... 62076 files and directories currently installed.) 261s Removing autopkgtest-satdep (0) ... 268s autopkgtest [01:33:37]: test run-unit-test: [----------------------- 270s 270s # bbmap 270s bbmap.sh --version 270s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 270s java -ea -Xmx2200m -Xms2200m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 --version 270s BBTools version 39.08 270s For help, please run the shellscript with no parameters, or look in /docs/. 270s bbmap.sh --help 270s 270s BBMap 270s Written by Brian Bushnell, from Dec. 2010 - present 270s Last modified September 15, 2022 270s 270s Description: Fast and accurate splice-aware read aligner. 270s Please read bbmap/docs/guides/BBMapGuide.txt for more information. 270s 270s To index: bbmap.sh ref= 270s To map: bbmap.sh in= out= 270s To map without writing an index: 270s bbmap.sh ref= in= out= nodisk 270s 270s in=stdin will accept reads from standard in, and out=stdout will write to 270s standard out, but file extensions are still needed to specify the format of the 270s input and output files e.g. in=stdin.fa.gz will read gzipped fasta from 270s standard in; out=stdout.sam.gz will write gzipped sam. 270s 270s Indexing Parameters (required when building the index): 270s nodisk=f Set to true to build index in memory and write nothing 270s to disk except output. 270s ref= Specify the reference sequence. Only do this ONCE, 270s when building the index (unless using 'nodisk'). 270s build=1 If multiple references are indexed in the same directory, 270s each needs a unique numeric ID (unless using 'nodisk'). 270s k=13 Kmer length, range 8-15. Longer is faster but uses 270s more memory. Shorter is more sensitive. 270s If indexing and mapping are done in two steps, K should 270s be specified each time. 270s path=<.> Specify the location to write the index, if you don't 270s want it in the current working directory. 270s usemodulo=f Throw away ~80% of kmers based on remainder modulo a 270s number (reduces RAM by 50% and sensitivity slightly). 270s Should be enabled both when building the index AND 270s when mapping. 270s rebuild=f Force a rebuild of the index (ref= should be set). 270s 270s Input Parameters: 270s build=1 Designate index to use. Corresponds to the number 270s specified when building the index. 270s in= Primary reads input; required parameter. 270s in2= For paired reads in two files. 270s interleaved=auto True forces paired/interleaved input; false forces 270s single-ended mapping. If not specified, interleaved 270s status will be autodetected from read names. 270s fastareadlen=500 Break up FASTA reads longer than this. Max is 500 for 270s BBMap and 6000 for BBMapPacBio. Only works for FASTA 270s input (use 'maxlen' for FASTQ input). The default for 270s bbmap.sh is 500, and for mapPacBio.sh is 6000. 270s unpigz=f Spawn a pigz (parallel gzip) process for faster 270s decompression than using Java. 270s Requires pigz to be installed. 270s touppercase=t (tuc) Convert lowercase letters in reads to upper case 270s (otherwise they will not match the reference). 270s 270s Sampling Parameters: 270s 270s reads=-1 Set to a positive number N to only process the first N 270s reads (or pairs), then quit. -1 means use all reads. 270s samplerate=1 Set to a number from 0 to 1 to randomly select that 270s fraction of reads for mapping. 1 uses all reads. 270s skipreads=0 Set to a number N to skip the first N reads (or pairs), 270s then map the rest. 270s 270s Mapping Parameters: 270s fast=f This flag is a macro which sets other paramters to run 270s faster, at reduced sensitivity. Bad for RNA-seq. 270s slow=f This flag is a macro which sets other paramters to run 270s slower, at greater sensitivity. 'vslow' is even slower. 270s maxindel=16000 Don't look for indels longer than this. Lower is faster. 270s Set to >=100k for RNAseq with long introns like mammals. 270s strictmaxindel=f When enabled, do not allow indels longer than 'maxindel'. 270s By default these are not sought, but may be found anyway. 270s tipsearch=100 Look this far for read-end deletions with anchors 270s shorter than K, using brute force. 270s minid=0.76 Approximate minimum alignment identity to look for. 270s Higher is faster and less sensitive. 270s minhits=1 Minimum number of seed hits required for candidate sites. 270s Higher is faster. 270s local=f Set to true to use local, rather than global, alignments. 270s This will soft-clip ugly ends of poor alignments. 270s perfectmode=f Allow only perfect mappings when set to true (very fast). 270s semiperfectmode=f Allow only perfect and semiperfect (perfect except for 270s N's in the reference) mappings. 270s threads=auto (t) Set to number of threads desired. By default, uses 270s all cores available. 270s ambiguous=best (ambig) Set behavior on ambiguously-mapped reads (with 270s multiple top-scoring mapping locations). 270s best (use the first best site) 270s toss (consider unmapped) 270s random (select one top-scoring site randomly) 270s all (retain all top-scoring sites) 270s samestrandpairs=f (ssp) Specify whether paired reads should map to the 270s same strand or opposite strands. 270s requirecorrectstrand=t (rcs) Forbid pairing of reads without correct strand 270s orientation. Set to false for long-mate-pair libraries. 270s killbadpairs=f (kbp) If a read pair is mapped with an inappropriate 270s insert size or orientation, the read with the lower 270s mapping quality is marked unmapped. 270s pairedonly=f (po) Treat unpaired reads as unmapped. Thus they will 270s be sent to 'outu' but not 'outm'. 270s rcomp=f Reverse complement both reads prior to mapping (for LMP 270s outward-facing libraries). 270s rcompmate=f Reverse complement read2 prior to mapping. 270s pairlen=32000 Set max allowed distance between paired reads. 270s (insert size)=(pairlen)+(read1 length)+(read2 length) 270s rescuedist=1200 Don't try to rescue paired reads if avg. insert size 270s greater than this. Lower is faster. 270s rescuemismatches=32 Maximum mismatches allowed in a rescued read. Lower 270s is faster. 270s averagepairdist=100 (apd) Initial average distance between paired reads. 270s Varies dynamically; does not need to be specified. 270s deterministic=f Run in deterministic mode. In this case it is good 270s to set averagepairdist. BBMap is deterministic 270s without this flag if using single-ended reads, 270s or run singlethreaded. 270s bandwidthratio=0 (bwr) If above zero, restrict alignment band to this 270s fraction of read length. Faster but less accurate. 270s bandwidth=0 (bw) Set the bandwidth directly. 270s fraction of read length. Faster but less accurate. 270s usejni=f (jni) Do alignments faster, in C code. Requires 270s compiling the C code; details are in /jni/README.txt. 270s maxsites2=800 Don't analyze (or print) more than this many alignments 270s per read. 270s ignorefrequentkmers=t (ifk) Discard low-information kmers that occur often. 270s excludefraction=0.03 (ef) Fraction of kmers to ignore. For example, 0.03 270s will ignore the most common 3% of kmers. 270s greedy=t Use a greedy algorithm to discard the least-useful 270s kmers on a per-read basis. 270s kfilter=0 If positive, potential mapping sites must have at 270s least this many consecutive exact matches. 270s 270s 270s Quality and Trimming Parameters: 270s qin=auto Set to 3 bbmap.sh ref=example.fasta 270s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 270s java -ea -Xmx2200m -Xms2200m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta 270s 3 or 64 to specify input quality value ASCII 270s offset. 33 is Sanger, 64 is old Solexa. 270s qout=auto Set to 33 or 64 to specify output quality value ASCII 270s offset (only if output format is fastq). 270s qtrim=f Quality-trim ends before mapping. Options are: 270s 'f' (false), 'l' (left), 'r' (right), and 'lr' (both). 270s untrim=f Undo trimming after mapping. Untrimmed bases will be 270s soft-clipped in cigar strings. 270s trimq=6 Trim regions with average quality below this 270s (phred algorithm). 270s mintrimlength=60 (mintl) Don't trim reads to be shorter than this. 270s fakefastaquality=-1 (ffq) Set to a positive number 1-50 to generate fake 270s quality strings for fasta input reads. 270s ignorebadquality=f (ibq) Keep going, rather than crashing, if a read has 270s out-of-range quality values. 270s usequality=t Use quality scores when determining which read kmers 270s to use as seeds. 270s minaveragequality=0 (maq) Do not map reads with average quality below this. 270s maqb=0 If positive, calculate maq from this many initial bases. 270s 270s Output Parameters: 270s out= Write all reads to this file. 270s outu= Write only unmapped reads to this file. Does not 270s include unmapped paired reads with a mapped mate. 270s outm= Write only mapped reads to this file. Includes 270s unmapped paired reads with a mapped mate. 270s mappedonly=f If true, treats 'out' like 'outm'. 270s bamscript= (bs) Write a shell script to that will turn 270s the sam output into a sorted, indexed bam file. 270s ordered=f Set to true to output reads in same order as input. 270s Slower and uses more memory. 270s overwrite=f (ow) Allow process to overwrite existing files. 270s secondary=f Print secondary alignments. 270s sssr=0.95 (secondarysitescoreratio) Print only secondary alignments 270s with score of at least this fraction of primary. 270s ssao=f (secondarysiteasambiguousonly) Only print secondary 270s alignments for ambiguously-mapped reads. 270s maxsites=5 Maximum number of total alignments to print per read. 270s Only relevant when secondary=t. 270s quickmatch=f Generate cigar strings more quickly. 270s trimreaddescriptions=f (trd) Truncate read and ref names at the first whitespace, 270s assuming that the remainder is a comment or description. 270s ziplevel=2 (zl) Compression level for zip or gzip output. 270s pigz=f Spawn a pigz (parallel gzip) process for faster 270s compression than Java. Requires pigz to be installed. 270s machineout=f Set to true to output statistics in machine-friendly 270s 'key=value' format. 270s printunmappedcount=f Print the total number of unmapped reads and bases. 270s If input is paired, the number will be of pairs 270s for which both reads are unmapped. 270s showprogress=0 If positive, print a '.' every X reads. 270s showprogress2=0 If positive, print the number of seconds since the 270s last progress update (instead of a '.'). 270s renamebyinsert=f Renames reads based on their mapped insert size. 270s 270s Bloom-Filtering Parameters (bloomfilter.sh is the standalone version). 270s bloom=f Use a Bloom filter to ignore reads not sharing kmers 270s with the reference. This uses more memory, but speeds 270s mapping when most reads don't match the reference. 270s bloomhashes=2 Number of hash functions. 270s bloomminhits=3 Number of consecutive hits to be considered matched. 270s bloomk=31 Bloom filter kmer length. 270s bloomserial=t Use the serialized Bloom filter for greater loading 270s speed, if available. If not, generate and write one. 270s 270s Post-Filtering Parameters: 270s idfilter=0 Independant of minid; sets exact minimum identity 270s allowed for alignments to be printed. Range 0 to 1. 270s subfilter=-1 Ban alignments with more than this many substitutions. 270s insfilter=-1 Ban alignments with more than this many insertions. 270s delfilter=-1 Ban alignments with more than this many deletions. 270s indelfilter=-1 Ban alignments with more than this many indels. 270s editfilter=-1 Ban alignments with more than this many edits. 270s inslenfilter=-1 Ban alignments with an insertion longer than this. 270s dellenfilter=-1 Ban alignments with a deletion longer than this. 270s nfilter=-1 Ban alignments with more than this many ns. This 270s includes nocall, noref, and off scaffold ends. 270s 270s Sam flags and settings: 270s noheader=f Disable generation of header lines. 270s sam=1.4 Set to 1.4 to write Sam version 1.4 cigar strings, 270s with = and X, or 1.3 to use M. 270s saa=t (secondaryalignmentasterisks) Use asterisks instead of 270s bases for sam secondary alignments. 270s cigar=t Set to 'f' to skip generation of cigar strings (faster). 270s keepnames=f Keep original names of paired reads, rather than 270s ensuring both reads have the same name. 270s intronlen=999999999 Set to a lower number like 10 to change 'D' to 'N' in 270s cigar strings for deletions of at least that length. 270s rgid= Set readgroup ID. All other readgroup fields 270s can be set similarly, with the flag rgXX= 270s If you set a readgroup flag to the word 'filename', 270s e.g. rgid=filename, the input file name will be used. 270s mdtag=f Write MD tags. 270s nhtag=f Write NH tags. 270s xmtag=f Write XM tags (may only work correctly with ambig=all). 270s amtag=f Write AM tags. 270s nmtag=f Write NM tags. 270s xstag=f Set to 'xs=fs', 'xs=ss', or 'xs=us' to write XS tags 270s for RNAseq using firststrand, secondstrand, or 270s unstranded libraries. Needed by Cufflinks. 270s JGI mainly uses 'firststrand'. 270s stoptag=f Write a tag indicating read stop location, prefixed by YS:i: 270s lengthtag=f Write a tag indicating (query,ref) alignment lengths, 270s prefixed by YL:Z: 270s idtag=f Write a tag indicating percent identity, prefixed by YI:f: 270s inserttag=f Write a tag indicating insert size, prefixed by X8:Z: 270s scoretag=f Write a tag indicating BBMap's raw score, prefixed by YR:i: 270s timetag=f Write a tag indicating this read's mapping time, prefixed by X0:i: 270s boundstag=f Write a tag indicating whether either read in the pair 270s goes off the end of the reference, prefixed by XB:Z: 270s notags=f Turn off all optional tags. 270s 270s Histogram and statistics output parameters: 270s scafstats= Statistics on how many reads mapped to which scaffold. 270s refstats= Statistics on how many reads mapped to which reference 270s file; only for BBSplit. 270s sortscafs=t Sort scaffolds or references by read count. 270s bhist= Base composition histogram by position. 270s qhist= Quality histogram by position. 270s aqhist= Histogram of average read quality. 270s bqhist= Quality histogram designed for box plots. 270s lhist= Read length histogram. 270s ihist= Write histogram of insert sizes (for paired reads). 270s ehist= Errors-per-read histogram. 270s qahist= Quality accuracy histogram of error rates versus 270s quality score. 270s indelhist= Indel length histogram. 270s mhist= Histogram of match, sub, del, and ins rates by 270s read location. 270s gchist= Read GC content histogram. 270s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 270s gcpairs=t Use average GC of paired reads. 270s idhist= Histogram of read count versus percent identity. 270s idbins=100 Number idhist bins. Set to 'auto' to use read length. 270s statsfile=stderr Mapping statistics are printed here. 270s 270s Coverage output parameters (these may reduce speed and use more RAM): 270s covstats= Per-scaffold coverage info. 270s rpkm= Per-scaffold RPKM/FPKM counts. 270s covhist= Histogram of # occurrences of each depth level. 270s basecov= Coverage per base location. 270s bincov= Print binned coverage per location (one line per X bases). 270s covbinsize=1000 Set the binsize for binned coverage output. 270s nzo=t Only print scaffolds with nonzero coverage. 270s twocolumn=f Change to true to print only ID and Avg_fold instead of 270s all 6 columns to the 'out=' file. 270s 32bit=f Set to true if you need per-base coverage over 64k. 270s strandedcov=f Track coverage for plus and minus strand independently. 270s startcov=f Only track start positions of reads. 270s secondarycov=t Include coverage of secondary alignments. 270s physcov=f Calculate physical coverage for paired reads. 270s This includes the unsequenced bases. 270s delcoverage=t (delcov) Count bases covered by deletions as covered. 270s True is faster than false. 270s covk=0 If positive, calculate kmer coverage statistics. 270s 270s Java Parameters: 270s -Xmx This will set Java's memory usage, 270s overriding autodetection. 270s -Xmx20g will specify 20 gigs of RAM, and -Xmx800m 270s will specify 800 megs. The max is typically 85% of 270s physical memory. The human genome requires around 24g, 270s or 12g with the 'usemodulo' flag. The index uses 270s roughly 6 bytes per reference base. 270s -eoom This flag will cause the process to exit if an 270s out-of-memory exception occurs. Requires Java 8u92+. 270s -da Disable assertions. 270s 270s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter 270s any problems, or post at: http://seqanswers.com/forums/showthread.php?t=41057 270s 270s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta] 270s Version 39.08 270s 270s No output file. 270s Writing reference. 270s Executing dna.FastaToChromArrays2 [example.fasta, 1, writeinthread=false, genscaffoldinfo=true, retain, waitforwriting=false, gz=true, maxlen=536670912, writechroms=true, minscaf=1, midpad=300, startpad=8000, stoppad=8000, nodisk=false] 270s 270s Set genScaffoldInfo=true 270s Writing chunk 1 270s Set genome to 1 270s 270s Loaded Reference: 0.006 seconds. 270s Loading index for chunk 1-1, build 1 270s No index available; generating from reference genome: /tmp/autopkgtest.071bZE/autopkgtest_tmp/ref/index/1/chr1_index_k13_c16_b1.block 270s Indexing threads started for block 0-1 270s Indexing threads finished for block 0-1 272s Generated Index: 1.496 seconds. 272s No reads to process; quitting. 272s 272s Total time: 1.675 seconds. 272s test -d ref 272s bbmap.sh in=misc_dna_as_sanger.fastq out=out.sam 272s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 272s java -ea -Xmx2200m -Xms2200m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 in=misc_dna_as_sanger.fastq out=out.sam 272s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, in=misc_dna_as_sanger.fastq, out=out.sam] 272s Version 39.08 272s 272s Retaining first best site only for ambiguous mappings. 272s Set genome to 1 272s 272s Loaded Reference: 0.033 seconds. 272s Loading index for chunk 1-1, build 1 273s Generated Index: 0.662 seconds. 276s Analyzed Index: 3.468 seconds. 276s Started output stream: 0.030 seconds. 276s Cleared Memory: 0.111 seconds. 276s Processing reads in single-ended mode. 276s Started read stream. 276s Started 8 mapping threads. 276s Detecting finished threads: 0, 1, 2, 3, 4, 5, 6, 7 276s 276s ------------------ Results ------------------ 276s 276s Genome: 1 276s Key Length: 13 276s Max Indel: 16000 276s Minimum Score Ratio: 0.56 276s Mapping Mode: normal 276s Reads Used: 4 (153 bases) 276s 276s Mapping: 0.135 seconds. 276s Reads/sec: 29.68 276s kBases/sec: 1.14 276s 276s 276s Read 1 data: pct reads num reads pct bases num bases 276s 276s mapped: 0.0000% 0 0.0000% 0 276s unambiguous: 0.0000% 0 0.0000% 0 276s ambiguous: 0.0000% 0 0.0000% 0 276s low-Q discards: 25.0000% 1 19.6078% 30 276s 276s perfect best site: 0.0000% 0 0.0000% 0 276s semiperfect site: 0.0000% 0 0.0000% 0 276s 276s Match Rate: NA NA NaN% 0 276s Error Rate: NaN% 0 NaN% 0 276s Sub Rate: NaN% 0 NaN% 0 276s Del Rate: NaN% 0 NaN% 0 276s Ins Rate: NaN% 0 NaN% 0 276s N Rate: NaN% 0 NaN% 0 276s 276s Total time: 4.567 seconds. 276s test -r out.sam 276s bbmap.sh ref=example.fasta in=example.fastq out=out2.sam nodisk 276s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 276s java -ea -Xmx2200m -Xms2200m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta in=example.fastq out=out2.sam nodisk 277s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta, in=example.fastq, out=out2.sam, nodisk] 277s Version 39.08 277s 277s Retaining first best site only for ambiguous mappings. 277s Executing dna.FastaToChromArrays2 [example.fasta, 1, writeinthread=false, genscaffoldinfo=true, retain, waitforwriting=false, gz=true, maxlen=536670912, writechroms=false, minscaf=1, midpad=300, startpad=8000, stoppad=8000, nodisk=true] 277s 277s Set genScaffoldInfo=true 277s Set genome to 1 277s 277s Loaded Reference: 0.002 seconds. 277s Loading index for chunk 1-1, build 1 277s Indexing threads started for block 0-1 277s Indexing threads finished for block 0-1 277s Generated Index: 0.251 seconds. 280s Analyzed Index: 3.442 seconds. 280s Started output stream: 0.029 seconds. 281s Cleared Memory: 0.116 seconds. 281s Processing reads in single-ended mode. 281s Started read stream. 281s Started 8 mapping threads. 281s Detecting finished threads: 0, 1, 2, 3, 4, 5, 6, 7 281s 281s ------------------ Results ------------------ 281s 281s Genome: 1 281s Key Length: 13 281s Max Indel: 16000 281s Minimum Score Ratio: 0.56 281s Mapping Mode: normal 281s Reads Used: 3 (75 bases) 281s 281s Mapping: 0.144 seconds. 281s Reads/sec: 20.80 281s kBases/sec: 0.52 281s 281s 281s Read 1 data: pct reads num reads pct bases num bases 281s 281s mapped: 100.0000% 3 100.0000% 75 281s unambiguous: 100.0000% 3 100.0000% 75 281s ambiguous: 0.0000% 0 0.0000% 0 281s low-Q discards: 0.0000% 0 0.0000% 0 281s 281s perfect best site: 100.0000% 3 100.0000% 75 281s semiperfect site: 100.0000% 3 100.0000% 75 281s 281s Match Rate: NA NA 100.0000% 75 281s Error Rate: 0.0000% 0 0.0000% 0 281s Sub Rate: 0.0000% 0 0.0000% 0 281s Del Rate: 0.0000% 0 0.0000% 0 281s Ins Rate: 0.0000% 0 0.0000% 0 281s N Rate: 0.0000% 0 0.0000% 0 281s 281s Total time: 4.158 seconds. 281s test -r out2.sam 281s 281s # bbduk 281s bbduk.sh --version 281s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 281s java -ea -Xmx2200m -Xms2200m -cp /usr/share/java/bbmap.jar jgi.BBDuk --version 281s BBTools version 39.08 281s For help, please run the shellscript with no parameters, or look in /docs/. 281s bbduk.sh --help 281s 281s Written by Brian Bushnell 281s Last modified November 9, 2023 281s 281s Description: Compares reads to the kmers in a reference dataset, optionally 281s allowing an edit distance. Splits the reads into two outputs - those that 281s match the reference, and those that don't. Can also trim (remove) the matching 281s parts of the reads rather than binning the reads. 281s Please read bbmap/docs/guides/BBDukGuide.txt for more information. 281s 281s Usage: bbduk.sh in= out= ref= 281s 281s Input may be stdin or a fasta or fastq file, compressed or uncompressed. 281s If you pipe via stdin/stdout, please include the file type; e.g. for gzipped 281s fasta input, set in=stdin.fa.gz 281s 281s Input parameters: 281s in= Main input. in=stdin.fq will pipe from stdin. 281s in2= Input for 2nd read of pairs in a different file. 281s ref= Comma-delimited list of reference files. 281s In addition to filenames, you may also use the keywords: 281s adapters, artifacts, phix, lambda, pjet, mtst, kapa 281s literal= Comma-delimited list of literal reference sequences. 281s touppercase=f (tuc) Change all bases upper-case. 281s interleaved=auto (int) t/f overrides interleaved autodetection. 281s Must be set mainually when streaming fastq input. 281s qin=auto Input quality offset: 33 (Sanger), 64, or auto. 281s reads=-1 If positive, quit after processing X reads or pairs. 281s copyundefined=f (cu) Process non-AGCT IUPAC reference bases by making all 281s possible unambiguous copies. Intended for short motifs 281s or adapter barcodes, as time/memory use is exponential. 281s samplerate=1 Set lower to only process a fraction of input reads. 281s samref= Optional reference fasta for processing sam files. 281s 281s Output parameters: 281s out= (outnonmatch) Write reads here that do not contain 281s kmers matching the database. 'out=stdout.fq' will pipe 281s to standard out. 281s out2= (outnonmatch2) Use this to write 2nd read of pairs to a 281s different file. 281s outm= (outmatch) Write reads here that fail filters. In default 281s kfilter mode, this means any read with a matching kmer. 281s In any mode, it also includes reads that fail filters such 281s as minlength, mingc, maxgc, entropy, etc. In other words, 281s it includes all reads that do not go to 'out'. 281s outm2= (outmatch2) Use this to write 2nd read of pairs to a 281s different file. 281s outs= (outsingle) Use this to write singleton reads whose mate 281s was trimmed shorter than minlen. 281s stats= Write statistics about which contamininants were detected. 281s refstats= Write statistics on a per-reference-file basis. 281s rpkm= Write RPKM for each reference sequence (for RNA-seq). 281s dump= Dump kmer tables to a file, in fasta format. 281s duk= Write statistics in duk's format. *DEPRECATED* 281s nzo=t Only write statistics about ref sequences with nonzero hits. 281s overwrite=t (ow) Grant permission to overwrite files. 281s showspeed=t (ss) 'f' suppresses display of processing speed. 281s ziplevel=2 (zl) Compression level; 1 (min) through 9 (max). 281s fastawrap=70 Length of lines in fasta output. 281s qout=auto Output quality offset: 33 (Sanger), 64, or auto. 281s statscolumns=3 (cols) Number of columns for stats output, 3 or 5. 281s 5 includes base counts. 281s rename=f Rename reads to indicate which sequences they matched. 281s refnames=f Use names of reference files rather than scaffold IDs. 281s trd=f Truncate read and ref names at the first whitespace. 281s ordered=f Set to true to output reads in same order as input. 281s bbduk.sh in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq \ 281s qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 281s maxbasesout=-1 If positive, quit after writing approximately this many 281s bases to out (outu/outnonmatch). 281s maxbasesoutm=-1 If positive, quit after writing approximately this many 281s bases to outm (outmatch). 281s json=f Print to screen in json format. 281s 281s Histogram output parameters: 281s bhist= Base composition histogram by position. 281s qhist= Quality histogram by position. 281s qchist= Count of bases with each quality value. 281s aqhist= Histogram of average read quality. 281s bqhist= Quality histogram designed for box plots. 281s lhist= Read length histogram. 281s phist= Polymer length histogram. 281s gchist= Read GC content histogram. 281s enthist= Read entropy histogram. 281s ihist= Insert size histogram, for paired reads in mapped sam. 281s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 281s maxhistlen=6000 Set an upper bound for histogram lengths; higher uses 281s more memory. The default is 6000 for some histograms 281s and 80000 for others. 281s 281s Histograms for mapped sam/bam files only: 281s histbefore=t Calculate histograms from reads before processing. 281s ehist= Errors-per-read histogram. 281s qahist= Quality accuracy histogram of error rates versus quality 281s score. 281s indelhist= Indel length histogram. 281s mhist= Histogram of match, sub, del, and ins rates by position. 281s idhist= Histogram of read count versus percent identity. 281s idbins=100 Number idhist bins. Set to 'auto' to use read length. 281s varfile= Ignore substitution errors listed in this file when 281s calculating error rates. Can be generated with 281s CallVariants. 281s vcf= Ignore substitution errors listed in this VCF file 281s when calculating error rates. 281s ignorevcfindels=t Also ignore indels listed in the VCF. 281s 281s Processing parameters: 281s k=27 Kmer length used for finding contaminants. Contaminants 281s shorter than k will not be found. k must be at least 1. 281s rcomp=t Look for reverse-complements of kmers in addition to 281s forward kmers. 281s maskmiddle=t (mm) Treat the middle base of a kmer as a wildcard, to 281s increase sensitivity in the presence of errors. This may 281s also be set to a number, e.g. mm=3, to mask that many bp. 281s The default mm=t corresponds to mm=1 for odd-length kmers 281s and mm=2 for even-length kmers (as of v39.04), while 281s mm=f is always equivalent to mm=0. 281s minkmerhits=1 (mkh) Reads need at least this many matching kmers 281s to be considered as matching the reference. 281s minkmerfraction=0.0 (mkf) A reads needs at least this fraction of its total 281s kmers to hit a ref, in order to be considered a match. 281s If this and minkmerhits are set, the greater is used. 281s mincovfraction=0.0 (mcf) A reads needs at least this fraction of its total 281s bases to be covered by ref kmers to be considered a match. 281s If specified, mcf overrides mkh and mkf. 281s hammingdistance=0 (hdist) Maximum Hamming distance for ref kmers (subs only). 281s Memory use is proportional to (3*K)^hdist. 281s qhdist=0 Hamming distance for query kmers; impacts speed, not memory. 281s editdistance=0 (edist) Maximum edit distance from ref kmers (subs 281s and indels). Memory use is proportional to (8*K)^edist. 281s hammingdistance2=0 (hdist2) Sets hdist for short kmers, when using mink. 281s qhdist2=0 Sets qhdist for short kmers, when using mink. 281s editdistance2=0 (edist2) Sets edist for short kmers, when using mink. 281s forbidn=f (fn) Forbids matching of read kmers containing N. 281s By default, these will match a reference 'A' if 281s hdist>0 or edist>0, to increase sensitivity. 281s removeifeitherbad=t (rieb) Paired reads get sent to 'outmatch' if either is 281s match (or either is trimmed shorter than minlen). 281s Set to false to require both. 281s trimfailures=f Instead of discarding failed reads, trim them to 1bp. 281s This makes the statistics a bit odd. 281s findbestmatch=f (fbm) If multiple matches, associate read with sequence 281s sharing most kmers. Reduces speed. 281s skipr1=f Don't do kmer-based operations on read 1. 281s skipr2=f Don't do kmer-based operations on read 2. 281s ecco=f For overlapping paired reads only. Performs error- 281s correction with BBMerge prior to kmer operations. 281s recalibrate=f (recal) Recalibrate quality scores. Requires calibration 281s matrices generated by CalcTrueQuality. 281s sam= If recalibration is desired, and matrices have not already 281s been generated, BBDuk will create them from the sam file. 281s amino=f Run in amino acid mode. Some features have not been 281s tested, but kmer-matching works fine. Maximum k is 12. 281s 281s Speed and Memory parameters: 281s threads=auto (t) Set number of threads to use; default is number of 281s logical processors. 281s prealloc=f Preallocate memory in table. Allows faster table loading 281s and more efficient memory usage, for a large reference. 281s monitor=f Kill this process if it crashes. monitor=600,0.01 would 281s kill after 600 seconds under 1% usage. 281s minrskip=1 (mns) Force minimal skip interval when indexing reference 281s kmers. 1 means use all, 2 means use every other kmer, etc. 281s maxrskip=1 (mxs) Restrict maximal skip interval when indexing 281s reference kmers. Normally all are used for scaffolds<100kb, 281s but with longer scaffolds, up to maxrskip-1 are skipped. 281s rskip= Set both minrskip and maxrskip to the same value. 281s If not set, rskip will vary based on sequence length. 281s qskip=1 Skip query kmers to increase speed. 1 means use all. 281s speed=0 Ignore this fraction of kmer space (0-15 out of 16) in both 281s reads and reference. Increases speed and reduces memory. 281s Note: Do not use more than one of 'speed', 'qskip', and 'rskip'. 281s 281s Trimming/Filtering/Masking parameters: 281s Note - if ktrim, kmask, and ksplit are unset, the default behavior is kfilter. 281s All kmer processing modes are mutually exclusive. 281s Reads only get sent to 'outm' purely based on kmer matches in kfilter mode. 281s 281s ktrim=f Trim reads to remove bases matching reference kmers, plus 281s all bases to the left or right. 281s Values: 281s f (don't trim), 281s r (trim to the right), 281s l (trim to the left) 281s ktrimtips=0 Set this to a positive number to perform ktrim on both 281s ends, examining only the outermost X bases. 281s kmask= Replace bases matching ref kmers with another symbol. 281s Allows any non-whitespace character, and processes short 281s kmers on both ends if mink is set. 'kmask=lc' will 281s convert masked bases to lowercase. 281s maskfullycovered=f (mfc) Only mask bases that are fully covered by kmers. 281s ksplit=f For single-ended reads only. Reads will be split into 281s pairs around the kmer. If the kmer is at the end of the 281s read, it will be trimmed instead. Singletons will go to 281s out, and pairs will go to outm. Do not use ksplit with 281s other operations such as quality-trimming or filtering. 281s mink=0 Look for shorter kmers at read tips down to this length, 281s when k-trimming or masking. 0 means disabled. Enabling 281s this will disable maskmiddle. 281s qtrim=f Trim read ends to remove bases with quality below trimq. 281s Performed AFTER looking for kmers. Values: 281s rl (trim both ends), 281s f (neither end), 281s r (right end only), 281s l (left end only), 281s w (sliding window). 281s trimq=6 Regions with average quality BELOW this will be trimmed, 281s if qtrim is set to something other than f. Can be a 281s floating-point number like 7.3. 281s trimclip=f Trim soft-clipped bases from sam files. 281s minlength=10 (ml) Reads shorter than this after trimming will be 281s discarded. Pairs will be discarded if both are shorter. 281s mlf=0 (minlengthfraction) Reads shorter than this fraction of 281s original length after trimming will be discarded. 281s maxlength= Reads longer than this after trimming will be discarded. 281s minavgquality=0 (maq) Reads with average quality (after trimming) below 281s this will be discarded. 281s maqb=0 If positive, calculate maq from this many initial bases. 281s minbasequality=0 (mbq) Reads with any base below this quality (after 281s trimming) will be discarded. 281s maxns=-1 If non-negative, reads with more Ns than this 281s (after trimming) will be discarded. 281s mcb=0 (minconsecutivebases) Discard reads without at least 281s this many consecutive called bases. 281s ottm=f (outputtrimmedtomatch) Output reads trimmed to shorter 281s than minlength to outm rather than discarding. 281s tp=0 (trimpad) Trim this much extra around matching kmers. 281s tbo=f (trimbyoverlap) Trim adapters based on where paired 281s reads overlap. 281s strictoverlap=t Adjust sensitivity for trimbyoverlap mode. 281s minoverlap=14 Require this many bases of overlap for detection. 281s mininsert=40 Require insert size of at least this for overlap. 281s Should be reduced to 16 for small RNA sequencing. 281s tpe=f (trimpairsevenly) When kmer right-trimming, trim both 281s reads to the minimum length of either. 281s forcetrimleft=0 (ftl) If positive, trim bases to the left of this position 281s (exclusive, 0-based). 281s forcetrimright=0 (ftr) If positive, trim bases to the right of this position 281s (exclusive, 0-based). 281s forcetrimright2=0 (ftr2) If positive, trim this many bases on the right end. 281s forcetrimmod=0 (ftm) If positive, right-trim length to be equal to zero, 281s modulo this number. 281s restrictleft=0 If positive, only look for kmer matches in the 281s leftmost X bases. 281s restrictright=0 If positive, only look for kmer matches in the 281s rightmost X bases. 281s NOTE: restrictleft and restrictright are mutually exclusive. If trimming 281s both ends is desired, use ktrimtips. 281s mingc=0 Discard reads with GC content below this. 281s maxgc=1 Discard reads with GC content above this. 281s gcpairs=t Use average GC of paired reads. 281s Also affects gchist. 281s tossjunk=f Discard reads with invalid characters as bases. 281s swift=f Trim Swift sequences: Trailing C/T/N R1, leading G/A/N R2. 281s 281s Header-parsing parameters - these require Illumina headers: 281s chastityfilter=f (cf) Discard reads with id containing ' 1:Y:' or ' 2:Y:'. 281s barcodefilter=f Remove reads with unexpected barcodes if barcodes is set, 281s or barcodes containing 'N' otherwise. A barcode must be 281s the last part of the read header. Values: 281s t: Remove reads with bad barcodes. 281s f: Ignore barcodes. 281s crash: Crash upon encountering bad barcodes. 281s barcodes= Comma-delimited list of barcodes or files of barcodes. 281s xmin=-1 If positive, discard reads with a lesser X coordinate. 281s ymin=-1 If positive, discard reads with a lesser Y coordinate. 281s xmax=-1 If positive, discard reads with a greater X coordinate. 281s ymax=-1 If positive, discard reads with a greater Y coordinate. 281s 281s Polymer trimming: 281s trimpolya=0 If greater than 0, trim poly-A or poly-T tails of 281s at least this length on either end of reads. 281s trimpolygleft=0 If greater than 0, trim poly-G prefixes of at least this 281s length on the left end of reads. Does not trim poly-C. 281s trimpolygright=0 If greater than 0, trim poly-G tails of at least this 281s length on the right end of reads. Does not trim poly-C. 281s trimpolyg=0 This sets both left and right at once. 281s filterpolyg=0 If greater than 0, remove reads with a poly-G prefix of 281s at least this length (on the left). 281s Note: there are also equivalent poly-C flags. 281s 281s Polymer tracking: 281s pratio=base,base 'pratio=G,C' will print the ratio of G to C polymers. 281s plen=20 Length of homopolymers to count. 281s 281s Entropy/Complexity parameters: 281s entropy=-1 Set between 0 and 1 to filter reads with entropy below 281s that value. Higher is more stringent. 281s entropywindow=50 Calculate entropy using a sliding window of this length. 281s entropyk=5 Calculate entropy using kmers of this length. 281s minbasefrequency=0 Discard reads with a minimum base frequency below this. 281s entropytrim=f Values: 281s f: (false) Do not entropy-trim. 281s r: (right) Trim low entropy on the right end only. 281s l: (left) Trim low entropy on the left end only. 281s rl: (both) Trim low entropy on both ends. 281s entropymask=f Values: 281s f: (filter) Discard low-entropy sequences. 281s t: (true) Mask low-entropy parts of sequences with N. 281s lc: Change low-entropy parts of sequences to lowercase. 281s entropymark=f Mark each base with its entropy value. This is on a scale 281s of 0-41 and is reported as quality scores, so the output 281s should be fastq or fasta+qual. 281s NOTE: If set, entropytrim overrides entropymask. 281s 281s Cardinality estimation: 281s cardinality=f (loglog) Count unique kmers using the LogLog algorithm. 281s cardinalityout=f (loglogout) Count unique kmers in output reads. 281s loglogk=31 Use this kmer length for counting. 281s loglogbuckets=2048 Use this many buckets for counting. 281s khist= Kmer frequency histogram; plots number of kmers versus 281s kmer depth. This is approximate. 281s khistout= Kmer frequency histogram for output reads. 281s 281s Java Parameters: 281s 281s -Xmx This will set Java's memory usage, overriding autodetection. 281s -Xmx20g will 281s specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 281s The max is typically 85% of physical memory. 281s -eoom This flag will cause the process to exit if an 281s out-of-memory exception occurs. Requires Java 8u92+. 281s -da Disable assertions. 281s 281s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 281s 281s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 281s java -ea -Xmx2200m -Xms2200m -cp /usr/share/java/bbmap.jar jgi.BBDuk in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 281s Executing jgi.BBDuk [in1=misc_dna_as_illumina.fastq, in2=misc_rna_as_illumina.fastq, qtrim=rl, trimq=15, minlen=75, out=out.fastq.gz] 281s Version 39.08 281s 281s Changed from ASCII-33 to ASCII-64 on input quality X (Q55) for base A at lines 1 and 3, position 24 while prescanning. 281s Changed from ASCII-33 to ASCII-64 on input quality X (Q55) for base A at lines 1 and 3, position 24 while prescanning. 281s 0.025 seconds. 281s Initial: 281s Memory: max=2306m, total=2306m, free=2287m, used=19m 281s 281s Input is being processed as paired 281s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 281s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 281s Started output streams: 0.027 seconds. 281s Processing time: 0.009 seconds. 281s 281s Input: 8 reads 306 bases. 281s QTrimmed: 0 reads (0.00%) 0 bases (0.00%) 281s Total Removed: 8 reads (100.00%) 306 bases (100.00%) 281s Result: 0 reads (0.00%) 0 bases (0.00%) 281s 281s Time: 0.038 seconds. 281s Reads Processed: 8 0.21k reads/sec 281s Bases Processed: 306 0.01m bases/sec 281s test -r out.fastq.gz 281s 281s # bbnorm 281s bbnorm.sh --version 281s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 282s java -ea -Xmx2200m -Xms2200m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 --version 282s BBTools version 39.08 282s For help, please run the shellscript with no parameters, or look in /docs/. 282s bbnorm.sh --help 282s 282s Written by Brian Bushnell 282s Last modified October 19, 2017 282s 282s Description: Normalizes read depth based on kmer counts. 282s Can also error-correct, bin reads by kmer depth, and generate a kmer depth histogram. 282s However, Tadpole has superior error-correction to BBNorm. 282s Please read bbmap/docs/guides/BBNormGuide.txt for more information. 282s 282s Usage: bbnorm.sh in= out= outt= hist= 282s 282s Input parameters: 282s in=null Primary input. Use in2 for paired reads in a second file 282s in2=null Second input file for paired reads in two files 282s extra=null Additional files to use for input (generating hash table) but not for output 282s fastareadlen=2^31 Break up FASTA reads longer than this. Can be useful when processing scaffolded genomes 282s tablereads=-1 Use at most this many reads when building the hashtable (-1 means all) 282s kmersample=1 Process every nth kmer, and skip the rest 282s readsample=1 Process every nth read, and skip the rest 282s interleaved=auto May be set to true or false to force the input read file to ovverride autodetection of the input file as paired interleaved. 282s qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto. 282s 282s Output parameters: 282s out= File for normalized or corrected reads. Use out2 for paired reads in a second file 282s outt= (outtoss) File for reads that were excluded from primary output 282s reads=-1 Only process this number of reads, then quit (-1 means all) 282s sampleoutput=t Use sampling on output as well as input (not used if sample rates are 1) 282s keepall=f Set to true to keep all reads (e.g. if you just want error correction). 282s zerobin=f Set to true if you want kmers with a count of 0 to go in the 0 bin instead of the 1 bin in histograms. 282s Default is false, to prevent confusion about how there can be 0-count kmers. 282s The reason is that based on the 'minq' and 'minprob' settings, some kmers may be excluded from the bloom filter. 282s tmpdir= This will specify a directory for temp files (only needed for multipass runs). If null, they will be written to the output directory. 282s usetempdir=t Allows enabling/disabling of temporary directory; if disabled, temp files will be written to the output directory. 282s qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input). 282s rename=f Rename reads based on their kmer depth. 282s 282s Hashing parameters: 282s k=31 Kmer length (values under 32 are most efficient, but arbitrarily high values are supported) 282s bits=32 Bits per cell in bloom filter; must be 2, 4, 8, 16, or 32. Maximum kmer depth recorded is 2^cbits. Automatically reduced to 16 in 2-pass. 282s Large values decrease accuracy for a fixed amount of memory, so use the lowest number you can that will still capture highest-depth kmers. 282s hashes=3 Number of times each kmer is hashed and stored. Higher is slower. 282s Higher is MORE accurate if there is enough memory, and LESS accurate if there is not enough memory. 282s prefilter=f True is slower, but generally more accurate; filters out low-depth kmers from the main hashtable. The prefilter is more memory-efficient because it uses 2-bit cells. 282s prehashes=2 Number of hashes for prefilter. 282s prefilterbits=2 (pbits) Bits per cell in prefilter. 282s prefiltersize=0.35 Fraction of memory to allocate to prefilter. 282s buildpasses=1 More passes can sometimes increase accuracy by iteratively removing low-depth kmers 282s minq=6 Ignore kmers containing bases with quality below this 282s minprob=0.5 Ignore kmers with overall probability of correctness below this 282s threads=auto (t) Spawn exactly X hashing threads (default is number of logical processors). Total active threads may exceed X due to I/O threads. 282s rdk=t (removeduplicatekmers) When true, a kmer's count will only be incremented once per read pair, even if that kmer occurs more than once. 282s 282s Normalization parameters: 282s fixspikes=f (fs) Do a slower, high-precision bloom filter lookup of kmers that appear to have an abnormally high depth due to collisions. 282s target=100 (tgt) Target normalization depth. NOTE: All depth parameters control kmer depth, not read depth. 282s For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1)) 282s maxdepth=-1 (max) Reads will not be downsampled when below this depth, even if they are above the target depth. 282s mindepth=5 (min) Kmers with depth below this number will not be included when calculating the depth of a read. 282s minkmers=15 (mgkpr) Reads must have at least this many kmers over min depth to be retained. Aka 'mingoodkmersperread'. 282s percentile=54.0 (dp) Read depth is by default inferred from the 54th percentile of kmer depth, but this may be changed to any number 1-100. 282s uselowerdepth=t (uld) For pairs, use the depth of the lower read as the depth proxy. 282s deterministic=t (dr) Generate random numbers deterministically to ensure identical output between multiple runs. May decrease speed with a huge number of threads. 282s passes=2 (p) 1 pass is the basic mode. 2 passes (default) allows greater accuracy, error detection, better contol of output depth. 282s 282s Error detection parameters: 282s hdp=90.0 (highdepthpercentile) Position in sorted kmer depth array used as proxy of a read's high kmer depth. 282s ldp=25.0 (lowdepthpercentile) Position in sorted kmer depth array used as proxy of a read's low kmer depth. 282s tossbadreads=f (tbr) Throw away reads detected as containing errors. 282s requirebothbad=f (rbb) Only toss bad pairs if both reads are bad. 282s errordetectratio=125 (edr) Reads with a ratio of at least this much between their high and low depth kmers will be classified as error reads. 282s highthresh=12 (ht) Threshold for high kmer. A high kmer at this or above are considered non-error. 282s lowthresh=3 (lt) Threshold for low kmer. Kmers at this and below are always considered errors. 282s 282s Error correction parameters: 282s ecc=f Set to true to correct errors. NOTE: Tadpole is now preferred for ecc as it does a better job. 282s ecclimit=3 Correct up to this many errors per read. If more are detected, the read will remain unchanged. 282s errorcorrectratio=140 (ecr) Adjacent kmers with a depth ratio of at least this much between will be classified as an error. 282s echighthresh=22 (echt) Threshold for high kmer. A kmer at this or above may be considered non-error. 282s eclowthresh=2 (eclt) Threshold for low kmer. Kmers at this and below are considered errors. 282s eccmaxqual=127 Do not correct bases with quality above this value. 282s aec=f (aggressiveErrorCorrection) Sets more aggressive values of ecr=100, ecclimit=7, echt=16, eclt=3. 282s cec=f (conservativeErrorCorrection) Sets more conservative values of ecr=180, ecclimit=2, echt=30, eclt=1, sl=4, pl=4. 282s meo=f (markErrorsOnly) Marks errors by reducing quality value of suspected errors; does not correct anything. 282s mue=t (markUncorrectableErrors) Marks errors only on uncorrectable reads; requires 'ecc=t'. 282s overlap=f (ecco) Error correct by read overlap. 282s 282s Depth binning parameters: 282s lowbindepth=10 (lbd) Cutoff for low depth bin. 282s highbindepth=80 (hbd) Cutoff for high depth bin. 282s outlow= Pairs in which both reads have a median below lbd go into this file. 282s outhigh= Pairs in which both reads have a median above hbd go into this file. 282s outmid= All other pairs go into this file. 282s 282s Histogram parameters: 282s hist= Specify a file to write the input kmer depth histogram. 282s histout= Specify a file to write the output kmer depth histogram. 282s histcol=3 (histogramcolumns) Number of histogram columns, 2 or 3. 282s pzc=f (printzerocoverage) Print lines in the histogram with zero coverage. 282s histlen=1048576 Max kmer depth displayed in histogram. Also affe bbnorm.sh in=sanger_full_range_original_sanger.fastq qin=33 \ 282s out=out3.fastq outt=outt.fastq hist=hist.plt 282s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 282s java -ea -Xmx2200m -Xms2200m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 in=sanger_full_range_original_sanger.fastq qin=33 out=out3.fastq outt=outt.fastq hist=hist.plt 282s cts statistics displayed, but does not affect normalization. 282s 282s Peak calling parameters: 282s peaks= Write the peaks to this file. Default is stdout. 282s minHeight=2 (h) Ignore peaks shorter than this. 282s minVolume=5 (v) Ignore peaks with less area than this. 282s minWidth=3 (w) Ignore peaks narrower than this. 282s minPeak=2 (minp) Ignore peaks with an X-value below this. 282s maxPeak=BIG (maxp) Ignore peaks with an X-value above this. 282s maxPeakCount=8 (maxpc) Print up to this many peaks (prioritizing height). 282s 282s Java Parameters: 282s -Xmx This will set Java's memory usage, overriding autodetection. 282s -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 282s The max is typically 85% of physical memory. 282s -eoom This flag will cause the process to exit if an 282s out-of-memory exception occurs. Requires Java 8u92+. 282s -da Disable assertions. 282s 282s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 282s 282s Executing jgi.KmerNormalize [bits=32, in=sanger_full_range_original_sanger.fastq, qin=33, out=out3.fastq, outt=outt.fastq, hist=hist.plt] 282s 282s 282s *********** Pass 1 ********** 282s 282s 282s Settings: 282s threads: 8 282s k: 31 282s deterministic: true 282s toss error reads: false 282s passes: 1 282s bits per cell: 16 282s cells: 806.44M 282s hashes: 3 282s base min quality: 5 282s kmer min prob: 0.5 282s 282s target depth: 400 282s min depth: 3 282s max depth: 500 282s min good kmers: 15 282s depth percentile: 64.8 282s ignore dupe kmers: true 282s fix spikes: false 282s histogram length: 65536 282s print zero cov: false 282s 282s Made hash table: hashes = 3 mem = 1.50 GB cells = 806.41M used = 0.000% 282s 282s Estimated unique kmers: 4 282s 282s Table creation time: 0.564 seconds. 282s Started output threads. 282s Started output threads. 282s Table read time: 0.011 seconds. 17.46 kb/sec 282s Total reads in: 2 0.000% Kept 282s Total bases in: 188 0.000% Kept 282s Error reads in: 2 100.000% 282s Error type 1: 2 100.000% 283s Error type 2: 0 0.000% 283s Error type 3: 0 0.000% 283s 283s Wrote histogram to hist.plt 283s Total kmers counted: 128 283s Total unique kmer count: 128 283s Includes forward kmers only. 283s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 283s The most accurate value is the greater of the two. 283s 283s Percent unique: 100.00% 283s Depth average: 1.00 (unique kmers) 283s Depth median: 1 (unique kmers) 283s Depth standard deviation: 0.00 (unique kmers) 283s Corrected depth average: 0.00 283s 283s Depth average: 1.00 (all kmers) 283s Depth median: 1 (all kmers) 283s Depth standard deviation: 0.00 (all kmers) 283s 283s Approx. read depth median: 1.47 283s 283s *********** Pass 2 ********** 283s 283s 283s Settings: 283s threads: 8 283s k: 31 283s deterministic: true 283s toss error reads: false 283s passes: 1 283s bits per cell: 16 283s cells: 806.44M 283s hashes: 3 283s base min quality: 5 283s kmer min prob: 0.5 283s 283s target depth: 100 283s min depth: 5 283s max depth: 100 283s min good kmers: 15 283s depth percentile: 54.0 283s ignore dupe kmers: true 283s fix spikes: false 283s histogram length: 65536 283s 283s Made hash table: hashes = 3 mem = 1.50 GB cells = 806.41M used = 0.000% 283s 283s Estimated unique kmers: 0 283s 283s Table creation time: 0.332 seconds. 283s Started output threads. 283s Started output threads. 283s Table read time: 0.003 seconds. 0.00 kb/sec 283s Total reads in: 0 NaN% Kept 283s Total bases in: 0 NaN% Kept 283s Error reads in: 0 NaN% 283s Error type 1: 0 NaN% 283s Error type 2: 0 NaN% 283s Error type 3: 0 NaN% 283s Total kmers counted: 0 283s Total unique kmer count: 0 283s Includes forward kmers only. 283s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 283s The most accurate value is the greater of the two. 283s 283s Percent unique: NaN% 283s Depth average: NaN (unique kmers) 283s Depth median: 0 (unique kmers) 283s Depth standard deviation: NaN (unique kmers) 283s Corrected depth average: NaN 283s 283s Depth average: NaN (all kmers) 283s Depth median: 0 (all kmers) 283s Depth standard deviation: 0.00 (all kmers) 283s 283s Approx. read depth median: NaN 283s 283s Removing temp files. 283s 283s Total time: 0.994 seconds. 0.19 kb/sec 283s test -r out3.fastq 283s test -r outt.fastq 283s test -r hist.plt 283s bbnorm.sh in=illumina_full_range_original_illumina.fastq qin=64 \ 283s out=out4.fastq outt=outt2.fastq hist=hist2.plt 283s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 283s java -ea -Xmx2200m -Xms2200m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 in=illumina_full_range_original_illumina.fastq qin=64 out=out4.fastq outt=outt2.fastq hist=hist2.plt 283s Executing jgi.KmerNormalize [bits=32, in=illumina_full_range_original_illumina.fastq, qin=64, out=out4.fastq, outt=outt2.fastq, hist=hist2.plt] 283s 283s 283s *********** Pass 1 ********** 283s 283s 283s Settings: 283s threads: 8 283s k: 31 283s deterministic: true 283s toss error reads: false 283s passes: 1 283s bits per cell: 16 283s cells: 806.44M 283s hashes: 3 283s base min quality: 5 283s kmer min prob: 0.5 283s 283s target depth: 400 283s min depth: 3 283s max depth: 500 283s min good kmers: 15 283s depth percentile: 64.8 283s ignore dupe kmers: true 283s fix spikes: false 283s histogram length: 65536 283s print zero cov: false 283s 284s Made hash table: hashes = 3 mem = 1.50 GB cells = 806.41M used = 0.000% 284s 284s Estimated unique kmers: 4 284s 284s Table creation time: 0.563 seconds. 284s Started output threads. 284s Started output threads. 284s Table read time: 0.011 seconds. 11.66 kb/sec 284s Total reads in: 2 0.000% Kept 284s Total bases in: 126 0.000% Kept 284s Error reads in: 2 100.000% 284s Error type 1: 2 100.000% 284s Error type 2: 0 0.000% 284s Error type 3: 0 0.000% 284s 284s Wrote histogram to hist2.plt 284s Total kmers counted: 66 284s Total unique kmer count: 66 284s Includes forward kmers only. 284s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 284s The most accurate value is the greater of the two. 284s 284s Percent unique: 100.00% 284s Depth average: 1.00 (unique kmers) 284s Depth median: 1 (unique kmers) 284s Depth standard deviation: 0.00 (unique kmers) 284s Corrected depth average: 0.00 284s 284s Depth average: 1.00 (all kmers) 284s Depth median: 1 (all kmers) 284s Depth standard deviation: 0.00 (all kmers) 284s 284s Approx. read depth median: 1.91 284s 284s *********** Pass 2 ********** 284s 284s 284s Settings: 284s threads: 8 284s k: 31 284s deterministic: true 284s toss error reads: false 284s passes: 1 284s bits per cell: 16 284s cells: 806.44M 284s hashes: 3 284s base min quality: 5 284s kmer min prob: 0.5 284s 284s target depth: 100 284s min depth: 5 284s max depth: 100 284s min good kmers: 15 284s depth percentile: 54.0 284s ignore dupe kmers: true 284s fix spikes: false 284s histogram length: 65536 284s 284s Made hash table: hashes = 3 mem = 1.50 GB cells = 806.41M used = 0.000% 284s 284s Estimated unique kmers: 0 284s 284s Table creation time: 0.332 seconds. 284s Started output threads. 284s Started output threads. 284s Table read time: 0.003 seconds. 0.00 kb/sec 284s Total reads in: 0 NaN% Kept 284s Total bases in: 0 NaN% Kept 284s Error reads in: 0 NaN% 284s Error type 1: 0 NaN% 284s Error type 2: 0 NaN% 284s Error type 3: 0 NaN% 284s Total kmers counted: 0 284s Total unique kmer count: 0 284s Includes forward kmers only. 284s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 284s The most accurate value is the greater of the two. 284s 284s Percent unique: NaN% 284s Depth average: NaN (unique kmers) 284s Depth median: 0 (unique kmers) 284s Depth standard deviation: NaN (unique kmers) 284s Corrected depth average: NaN 284s 284s Depth average: NaN (all kmers) 284s Depth median: 0 (all kmers) 284s Depth standard deviation: 0.00 (all kmers) 284s 284s Approx. read depth median: NaN 284s 284s Removing temp files. 284s 284s Total time: 0.993 seconds. 0.13 kb/sec 284s test -r out4.fastq 284s test -r outt2.fastq 284s test -r hist2.plt 285s autopkgtest [01:33:54]: test run-unit-test: -----------------------] 288s autopkgtest [01:33:57]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 288s run-unit-test PASS 293s autopkgtest [01:34:01]: @@@@@@@@@@@@@@@@@@@@ summary 293s run-unit-test PASS