0s autopkgtest [18:09:49]: starting date and time: 2025-05-02 18:09:49+0000 0s autopkgtest [18:09:49]: git checkout: 9986aa8c Merge branch 'skia/fix_network_interface' into 'ubuntu/production' 0s autopkgtest [18:09:49]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.dpo32lcb/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,localhost,localdomain,internal,login.ubuntu.com,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:openjdk-25 --apt-upgrade bbmap --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=openjdk-25/25~20ea-1' -- lxd -r lxd-armhf-10.145.243.28 lxd-armhf-10.145.243.28:autopkgtest/ubuntu/questing/armhf 21s autopkgtest [18:10:10]: testbed dpkg architecture: armhf 23s autopkgtest [18:10:12]: testbed apt version: 3.0.0 27s autopkgtest [18:10:16]: @@@@@@@@@@@@@@@@@@@@ test bed setup 29s autopkgtest [18:10:18]: testbed release detected to be: None 36s autopkgtest [18:10:25]: updating testbed package index (apt update) 38s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB] 38s Get:2 http://ftpmaster.internal/ubuntu questing InRelease [110 kB] 38s Get:3 http://ftpmaster.internal/ubuntu questing-updates InRelease [110 kB] 38s Get:4 http://ftpmaster.internal/ubuntu questing-security InRelease [110 kB] 39s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [2005 kB] 39s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [43.1 kB] 39s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [170 kB] 39s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main armhf Packages [203 kB] 39s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/universe armhf Packages [1408 kB] 39s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/multiverse armhf Packages [12.9 kB] 39s Get:11 http://ftpmaster.internal/ubuntu questing/universe Sources [21.1 MB] 40s Get:12 http://ftpmaster.internal/ubuntu questing/main Sources [1398 kB] 40s Get:13 http://ftpmaster.internal/ubuntu questing/multiverse Sources [299 kB] 40s Get:14 http://ftpmaster.internal/ubuntu questing/main armhf Packages [1358 kB] 40s Get:15 http://ftpmaster.internal/ubuntu questing/universe armhf Packages [15.0 MB] 41s Get:16 http://ftpmaster.internal/ubuntu questing/multiverse armhf Packages [173 kB] 44s Fetched 43.6 MB in 6s (7551 kB/s) 45s Reading package lists... 50s autopkgtest [18:10:39]: upgrading testbed (apt dist-upgrade and autopurge) 52s Reading package lists... 52s Building dependency tree... 52s Reading state information... 53s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 53s Starting 2 pkgProblemResolver with broken count: 0 53s Done 54s Entering ResolveByKeep 54s 55s Calculating upgrade... 55s The following packages will be upgraded: 55s base-files distro-info-data dpkg dpkg-dev fwupd htop libdpkg-perl libftdi1-2 55s libfwupd3 libnpth0t64 libsensors-config libsensors5 liburcu8t64 55s motd-news-config nano ubuntu-pro-client ubuntu-pro-client-l10n usb.ids 55s 18 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 55s Need to get 5303 kB of archives. 55s After this operation, 3722 kB disk space will be freed. 55s Get:1 http://ftpmaster.internal/ubuntu questing/main armhf motd-news-config all 13.7ubuntu1 [5260 B] 55s Get:2 http://ftpmaster.internal/ubuntu questing/main armhf base-files armhf 13.7ubuntu1 [75.4 kB] 56s Get:3 http://ftpmaster.internal/ubuntu questing/main armhf dpkg armhf 1.22.18ubuntu3 [1254 kB] 56s Get:4 http://ftpmaster.internal/ubuntu questing/main armhf libnpth0t64 armhf 1.8-3 [7716 B] 56s Get:5 http://ftpmaster.internal/ubuntu questing/main armhf distro-info-data all 0.64 [6664 B] 56s Get:6 http://ftpmaster.internal/ubuntu questing/main armhf ubuntu-pro-client-l10n armhf 35.1ubuntu0 [19.7 kB] 56s Get:7 http://ftpmaster.internal/ubuntu questing/main armhf ubuntu-pro-client armhf 35.1ubuntu0 [258 kB] 56s Get:8 http://ftpmaster.internal/ubuntu questing/main armhf libsensors-config all 1:3.6.2-2 [6756 B] 56s Get:9 http://ftpmaster.internal/ubuntu questing/main armhf libsensors5 armhf 1:3.6.2-2 [26.8 kB] 56s Get:10 http://ftpmaster.internal/ubuntu questing/main armhf liburcu8t64 armhf 0.15.2-2 [57.3 kB] 56s Get:11 http://ftpmaster.internal/ubuntu questing/main armhf nano armhf 8.4-1 [278 kB] 56s Get:12 http://ftpmaster.internal/ubuntu questing/main armhf usb.ids all 2025.04.01-1 [223 kB] 56s Get:13 http://ftpmaster.internal/ubuntu questing/main armhf dpkg-dev all 1.22.18ubuntu3 [1089 kB] 56s Get:14 http://ftpmaster.internal/ubuntu questing/main armhf libdpkg-perl all 1.22.18ubuntu3 [281 kB] 56s Get:15 http://ftpmaster.internal/ubuntu questing/main armhf fwupd armhf 2.0.8-3 [1414 kB] 56s Get:16 http://ftpmaster.internal/ubuntu questing/main armhf libfwupd3 armhf 2.0.8-3 [126 kB] 56s Get:17 http://ftpmaster.internal/ubuntu questing/main armhf htop armhf 3.4.1-4 [147 kB] 56s Get:18 http://ftpmaster.internal/ubuntu questing/main armhf libftdi1-2 armhf 1.5-10 [27.8 kB] 57s Fetched 5303 kB in 1s (5627 kB/s) 57s (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 ... 63953 files and directories currently installed.) 57s Preparing to unpack .../motd-news-config_13.7ubuntu1_all.deb ... 57s Unpacking motd-news-config (13.7ubuntu1) over (13.6ubuntu2) ... 57s Preparing to unpack .../base-files_13.7ubuntu1_armhf.deb ... 57s Unpacking base-files (13.7ubuntu1) over (13.6ubuntu2) ... 57s Setting up base-files (13.7ubuntu1) ... 57s Installing new version of config file /etc/issue ... 57s Installing new version of config file /etc/issue.net ... 57s Installing new version of config file /etc/lsb-release ... 58s motd-news.service is a disabled or a static unit not running, not starting it. 58s (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 ... 63953 files and directories currently installed.) 58s Preparing to unpack .../dpkg_1.22.18ubuntu3_armhf.deb ... 58s Unpacking dpkg (1.22.18ubuntu3) over (1.22.18ubuntu2) ... 58s Setting up dpkg (1.22.18ubuntu3) ... 58s (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 ... 63953 files and directories currently installed.) 58s Preparing to unpack .../libnpth0t64_1.8-3_armhf.deb ... 58s Unpacking libnpth0t64:armhf (1.8-3) over (1.8-2) ... 58s Setting up libnpth0t64:armhf (1.8-3) ... 58s (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 ... 63953 files and directories currently installed.) 58s Preparing to unpack .../00-distro-info-data_0.64_all.deb ... 58s Unpacking distro-info-data (0.64) over (0.63) ... 58s Preparing to unpack .../01-ubuntu-pro-client-l10n_35.1ubuntu0_armhf.deb ... 58s Unpacking ubuntu-pro-client-l10n (35.1ubuntu0) over (35) ... 58s Preparing to unpack .../02-ubuntu-pro-client_35.1ubuntu0_armhf.deb ... 59s Unpacking ubuntu-pro-client (35.1ubuntu0) over (35) ... 59s Preparing to unpack .../03-libsensors-config_1%3a3.6.2-2_all.deb ... 59s Unpacking libsensors-config (1:3.6.2-2) over (1:3.6.0-10) ... 59s Preparing to unpack .../04-libsensors5_1%3a3.6.2-2_armhf.deb ... 59s Unpacking libsensors5:armhf (1:3.6.2-2) over (1:3.6.0-10) ... 59s Preparing to unpack .../05-liburcu8t64_0.15.2-2_armhf.deb ... 59s Unpacking liburcu8t64:armhf (0.15.2-2) over (0.15.1-1) ... 59s Preparing to unpack .../06-nano_8.4-1_armhf.deb ... 59s Unpacking nano (8.4-1) over (8.3-1) ... 59s Preparing to unpack .../07-usb.ids_2025.04.01-1_all.deb ... 59s Unpacking usb.ids (2025.04.01-1) over (2025.01.14-1) ... 59s Preparing to unpack .../08-dpkg-dev_1.22.18ubuntu3_all.deb ... 59s Unpacking dpkg-dev (1.22.18ubuntu3) over (1.22.18ubuntu2) ... 59s Preparing to unpack .../09-libdpkg-perl_1.22.18ubuntu3_all.deb ... 59s Unpacking libdpkg-perl (1.22.18ubuntu3) over (1.22.18ubuntu2) ... 59s Preparing to unpack .../10-fwupd_2.0.8-3_armhf.deb ... 59s Unpacking fwupd (2.0.8-3) over (2.0.7-1) ... 59s dpkg: warning: unable to delete old directory '/etc/grub.d': Directory not empty 60s Preparing to unpack .../11-libfwupd3_2.0.8-3_armhf.deb ... 60s Unpacking libfwupd3:armhf (2.0.8-3) over (2.0.7-1) ... 60s Preparing to unpack .../12-htop_3.4.1-4_armhf.deb ... 60s Unpacking htop (3.4.1-4) over (3.4.0-2) ... 60s Preparing to unpack .../13-libftdi1-2_1.5-10_armhf.deb ... 60s Unpacking libftdi1-2:armhf (1.5-10) over (1.5-8build1) ... 60s Setting up motd-news-config (13.7ubuntu1) ... 60s Setting up liburcu8t64:armhf (0.15.2-2) ... 60s Setting up distro-info-data (0.64) ... 60s Setting up htop (3.4.1-4) ... 60s Setting up libsensors-config (1:3.6.2-2) ... 60s Installing new version of config file /etc/sensors3.conf ... 60s Setting up libfwupd3:armhf (2.0.8-3) ... 60s Setting up libftdi1-2:armhf (1.5-10) ... 60s Setting up usb.ids (2025.04.01-1) ... 60s Setting up libsensors5:armhf (1:3.6.2-2) ... 60s Setting up libdpkg-perl (1.22.18ubuntu3) ... 60s Setting up nano (8.4-1) ... 60s Installing new version of config file /etc/nanorc ... 60s Setting up ubuntu-pro-client (35.1ubuntu0) ... 60s apparmor_parser: Unable to replace "ubuntu_pro_apt_news". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 60s 60s apparmor_parser: Unable to replace "apt_methods". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 60s 60s apparmor_parser: Unable to replace "ubuntu_pro_esm_cache". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 60s 61s Setting up fwupd (2.0.8-3) ... 62s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 62s fwupd.service is a disabled or a static unit not running, not starting it. 62s Setting up ubuntu-pro-client-l10n (35.1ubuntu0) ... 62s Setting up dpkg-dev (1.22.18ubuntu3) ... 62s Processing triggers for dbus (1.16.2-2ubuntu1) ... 62s Processing triggers for install-info (7.1.1-1) ... 62s Processing triggers for libc-bin (2.41-6ubuntu1) ... 62s Processing triggers for man-db (2.13.0-1) ... 64s Processing triggers for plymouth-theme-ubuntu-text (24.004.60-2ubuntu7) ... 64s Processing triggers for initramfs-tools (0.147ubuntu1) ... 66s Reading package lists... 66s Building dependency tree... 66s Reading state information... 67s Starting pkgProblemResolver with broken count: 0 67s Starting 2 pkgProblemResolver with broken count: 0 67s Done 67s Solving dependencies... 68s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 70s autopkgtest [18:10:59]: rebooting testbed after setup commands that affected boot 110s autopkgtest [18:11:39]: testbed running kernel: Linux 6.8.0-58-generic #60~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Fri Mar 28 14:48:37 UTC 2 134s autopkgtest [18:12:03]: @@@@@@@@@@@@@@@@@@@@ apt-source bbmap 149s Get:1 http://ftpmaster.internal/ubuntu questing/universe bbmap 39.20+dfsg-1 (dsc) [2286 B] 149s Get:2 http://ftpmaster.internal/ubuntu questing/universe bbmap 39.20+dfsg-1 (tar) [5748 kB] 149s Get:3 http://ftpmaster.internal/ubuntu questing/universe bbmap 39.20+dfsg-1 (diff) [26.7 kB] 149s gpgv: Signature made Sat Apr 5 12:21:02 2025 UTC 149s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 149s gpgv: issuer "emollier@debian.org" 149s gpgv: Can't check signature: No public key 149s dpkg-source: warning: cannot verify inline signature for ./bbmap_39.20+dfsg-1.dsc: no acceptable signature found 150s autopkgtest [18:12:19]: testing package bbmap version 39.20+dfsg-1 152s autopkgtest [18:12:21]: build not needed 155s autopkgtest [18:12:24]: test run-unit-test: preparing testbed 156s Reading package lists... 157s Building dependency tree... 157s Reading state information... 157s Starting pkgProblemResolver with broken count: 0 157s Starting 2 pkgProblemResolver with broken count: 0 157s Done 158s The following NEW packages will be installed: 158s bbmap bbmap-jni ca-certificates-java default-jre-headless java-common 158s libapache-pom-java libcommons-cli-java libcommons-codec-java 158s libcommons-io-java libcommons-parent-java libjpeg-turbo8 libjpeg8 158s libjs-jquery libjs-sphinxdoc libjs-underscore liblcms2-2 liblog4j1.2-java 158s libmpj-java libpcsclite1 openjdk-21-jre-headless python-biopython-doc 158s 0 upgraded, 21 newly installed, 0 to remove and 0 not upgraded. 158s Need to get 71.1 MB of archives. 158s After this operation, 223 MB of additional disk space will be used. 158s Get:1 http://ftpmaster.internal/ubuntu questing/universe armhf libcommons-cli-java all 1.6.0-1 [59.9 kB] 159s Get:2 http://ftpmaster.internal/ubuntu questing/universe armhf libapache-pom-java all 33-2 [5874 B] 159s Get:3 http://ftpmaster.internal/ubuntu questing/universe armhf libcommons-parent-java all 56-1 [10.7 kB] 159s Get:4 http://ftpmaster.internal/ubuntu questing/universe armhf libcommons-codec-java all 1.17.1-1 [302 kB] 159s Get:5 http://ftpmaster.internal/ubuntu questing/universe armhf libcommons-io-java all 2.18.0-1 [477 kB] 159s Get:6 http://ftpmaster.internal/ubuntu questing/universe armhf liblog4j1.2-java all 1.2.17-11 [439 kB] 159s Get:7 http://ftpmaster.internal/ubuntu questing/universe armhf libmpj-java all 0.44+dfsg-4 [443 kB] 159s Get:8 http://ftpmaster.internal/ubuntu questing/main armhf ca-certificates-java all 20240118 [11.6 kB] 159s Get:9 http://ftpmaster.internal/ubuntu questing/main armhf java-common all 0.76 [6852 B] 159s Get:10 http://ftpmaster.internal/ubuntu questing/main armhf liblcms2-2 armhf 2.16-2 [137 kB] 159s Get:11 http://ftpmaster.internal/ubuntu questing/main armhf libjpeg-turbo8 armhf 2.1.5-3ubuntu2 [127 kB] 159s Get:12 http://ftpmaster.internal/ubuntu questing/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 159s Get:13 http://ftpmaster.internal/ubuntu questing/main armhf libpcsclite1 armhf 2.3.1-1 [24.9 kB] 159s Get:14 http://ftpmaster.internal/ubuntu questing/main armhf openjdk-21-jre-headless armhf 21.0.7~8ea-1 [39.8 MB] 161s Get:15 http://ftpmaster.internal/ubuntu questing/main armhf default-jre-headless armhf 2:1.21-76 [3182 B] 161s Get:16 http://ftpmaster.internal/ubuntu questing/universe armhf bbmap all 39.20+dfsg-1 [10.6 MB] 161s Get:17 http://ftpmaster.internal/ubuntu questing/universe armhf bbmap-jni armhf 39.20+dfsg-1 [20.8 kB] 161s Get:18 http://ftpmaster.internal/ubuntu questing/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 161s Get:19 http://ftpmaster.internal/ubuntu questing/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 161s Get:20 http://ftpmaster.internal/ubuntu questing/main armhf libjs-sphinxdoc all 8.1.3-5 [31.0 kB] 161s Get:21 http://ftpmaster.internal/ubuntu questing/universe armhf python-biopython-doc all 1.85+dfsg-2build1 [18.2 MB] 163s Fetched 71.1 MB in 4s (16.7 MB/s) 163s Selecting previously unselected package libcommons-cli-java. 163s (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 ... 63951 files and directories currently installed.) 163s Preparing to unpack .../00-libcommons-cli-java_1.6.0-1_all.deb ... 163s Unpacking libcommons-cli-java (1.6.0-1) ... 163s Selecting previously unselected package libapache-pom-java. 163s Preparing to unpack .../01-libapache-pom-java_33-2_all.deb ... 163s Unpacking libapache-pom-java (33-2) ... 163s Selecting previously unselected package libcommons-parent-java. 163s Preparing to unpack .../02-libcommons-parent-java_56-1_all.deb ... 163s Unpacking libcommons-parent-java (56-1) ... 163s Selecting previously unselected package libcommons-codec-java. 163s Preparing to unpack .../03-libcommons-codec-java_1.17.1-1_all.deb ... 163s Unpacking libcommons-codec-java (1.17.1-1) ... 163s Selecting previously unselected package libcommons-io-java. 163s Preparing to unpack .../04-libcommons-io-java_2.18.0-1_all.deb ... 163s Unpacking libcommons-io-java (2.18.0-1) ... 163s Selecting previously unselected package liblog4j1.2-java. 163s Preparing to unpack .../05-liblog4j1.2-java_1.2.17-11_all.deb ... 163s Unpacking liblog4j1.2-java (1.2.17-11) ... 163s Selecting previously unselected package libmpj-java. 163s Preparing to unpack .../06-libmpj-java_0.44+dfsg-4_all.deb ... 163s Unpacking libmpj-java (0.44+dfsg-4) ... 163s Selecting previously unselected package ca-certificates-java. 163s Preparing to unpack .../07-ca-certificates-java_20240118_all.deb ... 163s Unpacking ca-certificates-java (20240118) ... 163s Selecting previously unselected package java-common. 163s Preparing to unpack .../08-java-common_0.76_all.deb ... 163s Unpacking java-common (0.76) ... 163s Selecting previously unselected package liblcms2-2:armhf. 163s Preparing to unpack .../09-liblcms2-2_2.16-2_armhf.deb ... 163s Unpacking liblcms2-2:armhf (2.16-2) ... 163s Selecting previously unselected package libjpeg-turbo8:armhf. 163s Preparing to unpack .../10-libjpeg-turbo8_2.1.5-3ubuntu2_armhf.deb ... 163s Unpacking libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 163s Selecting previously unselected package libjpeg8:armhf. 163s Preparing to unpack .../11-libjpeg8_8c-2ubuntu11_armhf.deb ... 163s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 163s Selecting previously unselected package libpcsclite1:armhf. 163s Preparing to unpack .../12-libpcsclite1_2.3.1-1_armhf.deb ... 163s Unpacking libpcsclite1:armhf (2.3.1-1) ... 163s Selecting previously unselected package openjdk-21-jre-headless:armhf. 164s Preparing to unpack .../13-openjdk-21-jre-headless_21.0.7~8ea-1_armhf.deb ... 164s Unpacking openjdk-21-jre-headless:armhf (21.0.7~8ea-1) ... 165s Selecting previously unselected package default-jre-headless. 165s Preparing to unpack .../14-default-jre-headless_2%3a1.21-76_armhf.deb ... 165s Unpacking default-jre-headless (2:1.21-76) ... 165s Selecting previously unselected package bbmap. 165s Preparing to unpack .../15-bbmap_39.20+dfsg-1_all.deb ... 165s Unpacking bbmap (39.20+dfsg-1) ... 165s Selecting previously unselected package bbmap-jni. 165s Preparing to unpack .../16-bbmap-jni_39.20+dfsg-1_armhf.deb ... 165s Unpacking bbmap-jni (39.20+dfsg-1) ... 165s Selecting previously unselected package libjs-jquery. 165s Preparing to unpack .../17-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 165s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 165s Selecting previously unselected package libjs-underscore. 165s Preparing to unpack .../18-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 165s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 165s Selecting previously unselected package libjs-sphinxdoc. 165s Preparing to unpack .../19-libjs-sphinxdoc_8.1.3-5_all.deb ... 165s Unpacking libjs-sphinxdoc (8.1.3-5) ... 165s Selecting previously unselected package python-biopython-doc. 165s Preparing to unpack .../20-python-biopython-doc_1.85+dfsg-2build1_all.deb ... 165s Unpacking python-biopython-doc (1.85+dfsg-2build1) ... 165s Setting up liblcms2-2:armhf (2.16-2) ... 165s Setting up java-common (0.76) ... 165s Setting up libcommons-cli-java (1.6.0-1) ... 165s Setting up liblog4j1.2-java (1.2.17-11) ... 165s Setting up libapache-pom-java (33-2) ... 165s Setting up libpcsclite1:armhf (2.3.1-1) ... 165s Setting up libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 165s Setting up bbmap-jni (39.20+dfsg-1) ... 165s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 165s Setting up ca-certificates-java (20240118) ... 165s No JRE found. Skipping Java certificates setup. 165s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 165s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 165s Setting up openjdk-21-jre-headless:armhf (21.0.7~8ea-1) ... 165s update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/java to provide /usr/bin/java (java) in auto mode 165s update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 165s update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 165s update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 165s update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 165s Setting up libcommons-parent-java (56-1) ... 165s Setting up libjs-sphinxdoc (8.1.3-5) ... 165s Setting up python-biopython-doc (1.85+dfsg-2build1) ... 165s Setting up libcommons-codec-java (1.17.1-1) ... 165s Setting up libcommons-io-java (2.18.0-1) ... 165s Setting up libmpj-java (0.44+dfsg-4) ... 165s Processing triggers for libc-bin (2.41-6ubuntu1) ... 166s Processing triggers for man-db (2.13.0-1) ... 166s Processing triggers for ca-certificates-java (20240118) ... 167s Adding debian:ACCVRAIZ1.pem 167s Adding debian:AC_RAIZ_FNMT-RCM.pem 167s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 167s Adding debian:ANF_Secure_Server_Root_CA.pem 167s Adding debian:Actalis_Authentication_Root_CA.pem 167s Adding debian:AffirmTrust_Commercial.pem 167s Adding debian:AffirmTrust_Networking.pem 167s Adding debian:AffirmTrust_Premium.pem 167s Adding debian:AffirmTrust_Premium_ECC.pem 167s Adding debian:Amazon_Root_CA_1.pem 167s Adding debian:Amazon_Root_CA_2.pem 167s Adding debian:Amazon_Root_CA_3.pem 167s Adding debian:Amazon_Root_CA_4.pem 167s Adding debian:Atos_TrustedRoot_2011.pem 167s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 167s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 167s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 167s Adding debian:BJCA_Global_Root_CA1.pem 167s Adding debian:BJCA_Global_Root_CA2.pem 167s Adding debian:Baltimore_CyberTrust_Root.pem 167s Adding debian:Buypass_Class_2_Root_CA.pem 167s Adding debian:Buypass_Class_3_Root_CA.pem 167s Adding debian:CA_Disig_Root_R2.pem 167s Adding debian:CFCA_EV_ROOT.pem 167s Adding debian:COMODO_Certification_Authority.pem 167s Adding debian:COMODO_ECC_Certification_Authority.pem 167s Adding debian:COMODO_RSA_Certification_Authority.pem 167s Adding debian:Certainly_Root_E1.pem 167s Adding debian:Certainly_Root_R1.pem 167s Adding debian:Certigna.pem 167s Adding debian:Certigna_Root_CA.pem 167s Adding debian:Certum_EC-384_CA.pem 167s Adding debian:Certum_Trusted_Network_CA.pem 167s Adding debian:Certum_Trusted_Network_CA_2.pem 167s Adding debian:Certum_Trusted_Root_CA.pem 167s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 167s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 167s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 167s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 167s Adding debian:Comodo_AAA_Services_root.pem 167s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 167s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 167s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 167s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 167s Adding debian:DigiCert_Assured_ID_Root_CA.pem 167s Adding debian:DigiCert_Assured_ID_Root_G2.pem 167s Adding debian:DigiCert_Assured_ID_Root_G3.pem 167s Adding debian:DigiCert_Global_Root_CA.pem 167s Adding debian:DigiCert_Global_Root_G2.pem 167s Adding debian:DigiCert_Global_Root_G3.pem 167s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 167s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 167s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 167s Adding debian:DigiCert_Trusted_Root_G4.pem 167s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 167s Adding debian:Entrust_Root_Certification_Authority.pem 167s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 167s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 167s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem 167s Adding debian:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem 167s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 167s Adding debian:GLOBALTRUST_2020.pem 167s Adding debian:GTS_Root_R1.pem 167s Adding debian:GTS_Root_R2.pem 167s Adding debian:GTS_Root_R3.pem 167s Adding debian:GTS_Root_R4.pem 167s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 167s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 167s Adding debian:GlobalSign_Root_CA.pem 167s Adding debian:GlobalSign_Root_CA_-_R3.pem 167s Adding debian:GlobalSign_Root_CA_-_R6.pem 167s Adding debian:GlobalSign_Root_E46.pem 167s Adding debian:GlobalSign_Root_R46.pem 167s Adding debian:Go_Daddy_Class_2_CA.pem 167s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 167s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 167s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 167s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 167s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 167s Adding debian:HiPKI_Root_CA_-_G1.pem 167s Adding debian:Hongkong_Post_Root_CA_3.pem 167s Adding debian:ISRG_Root_X1.pem 167s Adding debian:ISRG_Root_X2.pem 167s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 167s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 167s Adding debian:Izenpe.com.pem 167s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 167s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 167s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 167s Adding debian:NAVER_Global_Root_Certification_Authority.pem 167s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 167s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 167s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 167s Adding debian:QuoVadis_Root_CA_1_G3.pem 167s Adding debian:QuoVadis_Root_CA_2.pem 167s Adding debian:QuoVadis_Root_CA_2_G3.pem 167s Adding debian:QuoVadis_Root_CA_3.pem 167s Adding debian:QuoVadis_Root_CA_3_G3.pem 167s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 167s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 167s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 167s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 167s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 167s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 167s Adding debian:SZAFIR_ROOT_CA2.pem 167s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 167s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 167s Adding debian:SecureSign_RootCA11.pem 167s Adding debian:SecureSign_Root_CA12.pem 167s Adding debian:SecureSign_Root_CA14.pem 167s Adding debian:SecureSign_Root_CA15.pem 167s Adding debian:SecureTrust_CA.pem 167s Adding debian:Secure_Global_CA.pem 167s Adding debian:Security_Communication_ECC_RootCA1.pem 167s Adding debian:Security_Communication_RootCA2.pem 167s Adding debian:Security_Communication_RootCA3.pem 167s Adding debian:Starfield_Class_2_CA.pem 167s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 167s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 167s Adding debian:SwissSign_Gold_CA_-_G2.pem 167s Adding debian:SwissSign_Silver_CA_-_G2.pem 167s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 167s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 167s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 167s Adding debian:TWCA_CYBER_Root_CA.pem 167s Adding debian:TWCA_Global_Root_CA.pem 167s Adding debian:TWCA_Root_Certification_Authority.pem 167s Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem 167s Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem 167s Adding debian:TeliaSonera_Root_CA_v1.pem 167s Adding debian:Telia_Root_CA_v2.pem 167s Adding debian:TrustAsia_Global_Root_CA_G3.pem 167s Adding debian:TrustAsia_Global_Root_CA_G4.pem 167s Adding debian:Trustwave_Global_Certification_Authority.pem 167s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 167s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 167s Adding debian:TunTrust_Root_CA.pem 167s Adding debian:UCA_Extended_Validation_Root.pem 167s Adding debian:UCA_Global_G2_Root.pem 167s Adding debian:USERTrust_ECC_Certification_Authority.pem 167s Adding debian:USERTrust_RSA_Certification_Authority.pem 167s Adding debian:XRamp_Global_CA_Root.pem 167s Adding debian:certSIGN_ROOT_CA.pem 167s Adding debian:certSIGN_Root_CA_G2.pem 167s Adding debian:e-Szigno_Root_CA_2017.pem 167s Adding debian:ePKI_Root_Certification_Authority.pem 167s Adding debian:emSign_ECC_Root_CA_-_C3.pem 167s Adding debian:emSign_ECC_Root_CA_-_G3.pem 167s Adding debian:emSign_Root_CA_-_C1.pem 167s Adding debian:emSign_Root_CA_-_G1.pem 167s Adding debian:vTrus_ECC_Root_CA.pem 167s Adding debian:vTrus_Root_CA.pem 167s done. 167s Setting up bbmap (39.20+dfsg-1) ... 167s Setting up default-jre-headless (2:1.21-76) ... 176s autopkgtest [18:12:45]: test run-unit-test: [----------------------- 178s 178s # bbmap 178s bbmap.sh --version 178s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 178s java -ea -Xmx2200m -Xms2200m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 --version 179s BBTools version 39.20 179s For help, please run the shellscript with no parameters, or look in /docs/. 179s bbmap.sh --help 179s bbmap.sh ref=example.fasta 179s 179s BBMap 179s Written by Brian Bushnell, from Dec. 2010 - present 179s Last modified September 15, 2022 179s 179s Description: Fast and accurate splice-aware read aligner. 179s Please read bbmap/docs/guides/BBMapGuide.txt for more information. 179s 179s To index: bbmap.sh ref= 179s To map: bbmap.sh in= out= 179s To map without writing an index: 179s bbmap.sh ref= in= out= nodisk 179s 179s in=stdin will accept reads from standard in, and out=stdout will write to 179s standard out, but file extensions are still needed to specify the format of the 179s input and output files e.g. in=stdin.fa.gz will read gzipped fasta from 179s standard in; out=stdout.sam.gz will write gzipped sam. 179s 179s Indexing Parameters (required when building the index): 179s nodisk=f Set to true to build index in memory and write nothing 179s to disk except output. 179s ref= Specify the reference sequence. Only do this ONCE, 179s when building the index (unless using 'nodisk'). 179s build=1 If multiple references are indexed in the same directory, 179s each needs a unique numeric ID (unless using 'nodisk'). 179s k=13 Kmer length, range 8-15. Longer is faster but uses 179s more memory. Shorter is more sensitive. 179s If indexing and mapping are done in two steps, K should 179s be specified each time. 179s path=<.> Specify the location to write the index, if you don't 179s want it in the current working directory. 179s usemodulo=f Throw away ~80% of kmers based on remainder modulo a 179s number (reduces RAM by 50% and sensitivity slightly). 179s Should be enabled both when building the index AND 179s when mapping. 179s rebuild=f Force a rebuild of the index (ref= should be set). 179s 179s Input Parameters: 179s build=1 Designate index to use. Corresponds to the number 179s specified when building the index. 179s in= Primary reads input; required parameter. 179s in2= For paired reads in two files. 179s interleaved=auto True forces paired/interleaved input; false forces 179s single-ended mapping. If not specified, interleaved 179s status will be autodetected from read names. 179s fastareadlen=500 Break up FASTA reads longer than this. Max is 500 for 179s BBMap and 6000 for BBMapPacBio. Only works for FASTA 179s input (use 'maxlen' for FASTQ input). The default for 179s bbmap.sh is 500, and for mapPacBio.sh is 6000. 179s unpigz=f Spawn a pigz (parallel gzip) process for faster 179s decompression than using Java. 179s Requires pigz to be installed. 179s touppercase=t (tuc) Convert lowercase letters in reads to upper case 179s (otherwise they will not match the reference). 179s 179s Sampling Parameters: 179s 179s reads=-1 Set to a positive number N to only process the first N 179s reads (or pairs), then quit. -1 means use all reads. 179s samplerate=1 Set to a number from 0 to 1 to randomly select that 179s fraction of reads for mapping. 1 uses all reads. 179s skipreads=0 Set to a number N to skip the first N reads (or pairs), 179s then map the rest. 179s 179s Mapping Parameters: 179s fast=f This flag is a macro which sets other paramters to run 179s faster, at reduced sensitivity. Bad for RNA-seq. 179s slow=f This flag is a macro which sets other paramters to run 179s slower, at greater sensitivity. 'vslow' is even slower. 179s maxindel=16000 Don't look for indels longer than this. Lower is faster. 179s Set to >=100k for RNAseq with long introns like mammals. 179s strictmaxindel=f When enabled, do not allow indels longer than 'maxindel'. 179s By default these are not sought, but may be found anyway. 179s tipsearch=100 Look this far for read-end deletions with anchors 179s shorter than K, using brute force. 179s minid=0.76 Approximate minimum alignment identity to look for. 179s Higher is faster and less sensitive. 179s minhits=1 Minimum number of seed hits required for candidate sites. 179s Higher is faster. 179s local=f Set to true to use local, rather than global, alignments. 179s This will soft-clip ugly ends of poor alignments. 179s perfectmode=f Allow only perfect mappings when set to true (very fast). 179s semiperfectmode=f Allow only perfect and semiperfect (perfect except for 179s N's in the reference) mappings. 179s threads=auto (t) Set to number of threads desired. By default, uses 179s all cores available. 179s ambiguous=best (ambig) Set behavior on ambiguously-mapped reads (with 179s multiple top-scoring mapping locations). 179s best (use the first best site) 179s toss (consider unmapped) 179s random (select one top-scoring site randomly) 179s all (retain all top-scoring sites) 179s samestrandpairs=f (ssp) Specify whether paired reads should map to the 179s same strand or opposite strands. 179s requirecorrectstrand=t (rcs) Forbid pairing of reads without correct strand 179s orientation. Set to false for long-mate-pair libraries. 179s killbadpairs=f (kbp) If a read pair is mapped with an inappropriate 179s insert size or orientation, the read with the lower 179s mapping quality is marked unmapped. 179s pairedonly=f (po) Treat unpaired reads as unmapped. Thus they will 179s be sent to 'outu' but not 'outm'. 179s rcomp=f Reverse complement both reads prior to mapping (for LMP 179s outward-facing libraries). 179s rcompmate=f Reverse complement read2 prior to mapping. 179s pairlen=32000 Set max allowed distance between paired reads. 179s (insert size)=(pairlen)+(read1 length)+(read2 length) 179s rescuedist=1200 Don't try to rescue paired reads if avg. insert size 179s greater than this. Lower is faster. 179s rescuemismatches=32 Maximum mismatches allowed in a rescued read. Lower 179s is faster. 179s averagepairdist=100 (apd) Initial average distance between paired reads. 179s Varies dynamically; does not need to be specified. 179s deterministic=f Run in deterministic mode. In this case it is good 179s to set averagepairdist. BBMap is deterministic 179s without this flag if using single-ended reads, 179s or run singlethreaded. 179s bandwidthratio=0 (bwr) If above zero, restrict alignment band to this 179s fraction of read length. Faster but less accurate. 179s bandwidth=0 (bw) Set the bandwidth directly. 179s fraction of read length. Faster but less accurate. 179s usejni=f (jni) Do alignments faster, in C code. Requires 179s compiling the C code; details are in /jni/README.txt. 179s maxsites2=800 Don't analyze (or print) more than this many alignments 179s per read. 179s ignorefrequentkmers=t (ifk) Discard low-information kmers that occur often. 179s excludefraction=0.03 (ef) Fraction of kmers to ignore. For example, 0.03 179s will ignore the most common 3% of kmers. 179s greedy=t Use a greedy algorithm to discard the least-useful 179s kmers on a per-read basis. 179s kfilter=0 If positive, potential mapping sites must have at 179s least this many consecutive exact matches. 179s 179s 179s Quality and Trimming Parameters: 179s qin=auto Set to 33 or 64 to specify input quality value ASCII 179s offset. 33 is Sanger, 64 is old Solexa. 179s qout=auto Set to 33 or 64 to specify output quality value ASCII 179s offset (only if output format is fastq). 179s qtrim=f Quality-trim ends before mapping. Options are: 179s 'f' (false), 'l' (left), 'r' (right), and 'lr' (both). 179s untrim=f Undo trimming after mapping. Untrimmed bases will be 179s soft-clipped in cigar strings. 179s trimq=6 Trim regions with average quality below this 179s (phred algorithm). 179s mintrimlength=60 (mintl) Don't trim reads to be shorter than this. 179s fakefastaquality=-1 (ffq) Set to a positive number 1-50 to generate fake 179s quality strings for fasta input reads. 179s ignorebadquality=f (ibq) Keep going, rather than crashing, if a read has 179s out-of-range quality values. 179s usequality=t Use quality scores when determining which read kmers 179s to use as seeds. 179s minaveragequality=0 (maq) Do not map reads with average quality below this. 179s maqb=0 If positive, calculate maq from this many initial bases. 179s 179s Output Parameters: 179s out= Write all reads to this file. 179s outu= Write only unmapped reads to this file. Does not 179s include unmapped paired reads with a mapped mate. 179s outm= Write only mapped reads to this file. Includes 179s unmapped paired reads with a mapped mate. 179s mappedonly=f If true, treats 'out' like 'outm'. 179s bamscript= (bs) Write a shell script to that will turn 179s the sam output into a dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 179s sorted, indexed bam file. 179s ordered=f Set to true to output reads in same order as input. 179s Slower and uses more memory. 179s overwrite=f (ow) Allow process to overwrite existing files. 179s secondary=f Print secondary alignments. 179s sssr=0.95 (secondarysitescoreratio) Print only secondary alignments 179s with score of at least this fraction of primary. 179s ssao=f (secondarysiteasambiguousonly) Only print secondary 179s alignments for ambiguously-mapped reads. 179s maxsites=5 Maximum number of total alignments to print per read. 179s Only relevant when secondary=t. 179s quickmatch=f Generate cigar strings more quickly. 179s trimreaddescriptions=f (trd) Truncate read and ref names at the first whitespace, 179s assuming that the remainder is a comment or description. 179s ziplevel=2 (zl) Compression level for zip or gzip output. 179s pigz=f Spawn a pigz (parallel gzip) process for faster 179s compression than Java. Requires pigz to be installed. 179s machineout=f Set to true to output statistics in machine-friendly 179s 'key=value' format. 179s printunmappedcount=f Print the total number of unmapped reads and bases. 179s If input is paired, the number will be of pairs 179s for which both reads are unmapped. 179s showprogress=0 If positive, print a '.' every X reads. 179s showprogress2=0 If positive, print the number of seconds since the 179s last progress update (instead of a '.'). 179s renamebyinsert=f Renames reads based on their mapped insert size. 179s 179s Bloom-Filtering Parameters (bloomfilter.sh is the standalone version). 179s bloom=f Use a Bloom filter to ignore reads not sharing kmers 179s with the reference. This uses more memory, but speeds 179s mapping when most reads don't match the reference. 179s bloomhashes=2 Number of hash functions. 179s bloomminhits=3 Number of consecutive hits to be considered matched. 179s bloomk=31 Bloom filter kmer length. 179s bloomserial=t Use the serialized Bloom filter for greater loading 179s speed, if available. If not, generate and write one. 179s 179s Post-Filtering Parameters: 179s idfilter=0 Independant of minid; sets exact minimum identity 179s allowed for alignments to be printed. Range 0 to 1. 179s subfilter=-1 Ban alignments with more than this many substitutions. 179s insfilter=-1 Ban alignments with more than this many insertions. 179s delfilter=-1 Ban alignments with more than this many deletions. 179s indelfilter=-1 Ban alignments with more than this many indels. 179s editfilter=-1 Ban alignments with more than this many edits. 179s inslenfilter=-1 Ban alignments with an insertion longer than this. 179s dellenfilter=-1 Ban alignments with a deletion longer than this. 179s nfilter=-1 Ban alignments with more than this many ns. This 179s includes nocall, noref, and off scaffold ends. 179s 179s Sam flags and settings: 179s noheader=f Disable generation of header lines. 179s sam=1.4 Set to 1.4 to write Sam version 1.4 cigar strings, 179s with = and X, or 1.3 to use M. 179s saa=t (secondaryalignmentasterisks) Use asterisks instead of 179s bases for sam secondary alignments. 179s cigar=t Set to 'f' to skip generation of cigar strings (faster). 179s keepnames=f Keep original names of paired reads, rather than 179s ensuring both reads have the same name. 179s intronlen=999999999 Set to a lower number like 10 to change 'D' to 'N' in 179s cigar strings for deletions of at least that length. 179s rgid= Set readgroup ID. All other readgroup fields 179s can be set similarly, with the flag rgXX= 179s If you set a readgroup flag to the word 'filename', 179s e.g. rgid=filename, the input file name will be used. 179s mdtag=f Write MD tags. 179s nhtag=f Write NH tags. 179s xmtag=f Write XM tags (may only work correctly with ambig=all). 179s amtag=f Write AM tags. 179s nmtag=f Write NM tags. 179s xstag=f Set to 'xs=fs', 'xs=ss', or 'xs=us' to write XS tags 179s for RNAseq using firststrand, secondstrand, or 179s unstranded libraries. Needed by Cufflinks. 179s JGI mainly uses 'firststrand'. 179s stoptag=f Write a tag indicating read stop location, prefixed by YS:i: 179s lengthtag=f Write a tag indicating (query,ref) alignment lengths, 179s prefixed by YL:Z: 179s idtag=f Write a tag indicating percent identity, prefixed by YI:f: 179s inserttag=f Write a tag indicating insert size, prefixed by X8:Z: 179s scoretag=f Write a tag indicating BBMap's raw score, prefixed by YR:i: 179s timetag=f Write a tag indicating this read's mapping time, prefixed by X0:i: 179s boundstag=f Write a tag indicating whether either read in the pair 179s goes off the end of the reference, prefixed by XB:Z: 179s notags=f Turn off all optional tags. 179s 179s Histogram and statistics output parameters: 179s scafstats= Statistics on how many reads mapped to which scaffold. 179s refstats= Statistics on how many reads mapped to which reference 179s file; only for BBSplit. 179s sortscafs=t Sort scaffolds or references by read count. 179s bhist= Base composition histogram by position. 179s qhist= Quality histogram by position. 179s aqhist= Histogram of average read quality. 179s bqhist= Quality histogram designed for box plots. 179s lhist= Read length histogram. 179s ihist= Write histogram of insert sizes (for paired reads). 179s ehist= Errors-per-read histogram. 179s qahist= Quality accuracy histogram of error rates versus 179s quality score. 179s indelhist= Indel length histogram. 179s mhist= Histogram of match, sub, del, and ins rates by 179s read location. 179s gchist= Read GC content histogram. 179s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 179s gcpairs=t Use average GC of paired reads. 179s idhist= Histogram of read count versus percent identity. 179s idbins=100 Number idhist bins. Set to 'auto' to use read length. 179s statsfile=stderr Mapping statistics are printed here. 179s 179s Coverage output parameters (these may reduce speed and use more RAM): 179s covstats= Per-scaffold coverage info. 179s rpkm= Per-scaffold RPKM/FPKM counts. 179s covhist= Histogram of # occurrences of each depth level. 179s basecov= Coverage per base location. 179s bincov= Print binned coverage per location (one line per X bases). 179s covbinsize=1000 Set the binsize for binned coverage output. 179s nzo=t Only print scaffolds with nonzero coverage. 179s twocolumn=f Change to true to print only ID and Avg_fold instead of 179s all 6 columns to the 'out=' file. 179s 32bit=f Set to true if you need per-base coverage over 64k. 179s strandedcov=f Track coverage for plus and minus strand independently. 179s startcov=f Only track start positions of reads. 179s secondarycov=t Include coverage of secondary alignments. 179s physcov=f Calculate physical coverage for paired reads. 179s This includes the unsequenced bases. 179s delcoverage=t (delcov) Count bases covered by deletions as covered. 179s True is faster than false. 179s covk=0 If positive, calculate kmer coverage statistics. 179s 179s Java Parameters: 179s -Xmx This will set Java's memory usage, 179s overriding autodetection. 179s -Xmx20g will specify 20 gigs of RAM, and -Xmx800m 179s will specify 800 megs. The max is typically 85% of 179s physical memory. The human genome requires around 24g, 179s or 12g with the 'usemodulo' flag. The index uses 179s roughly 6 bytes per reference base. 179s -eoom This flag will cause the process to exit if an 179s out-of-memory exception occurs. Requires Java 8u92+. 179s -da Disable assertions. 179s 179s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter 179s any problems, or post at: http://seqanswers.com/forums/showthread.php?t=41057 179s 179s java -ea -Xmx2200m -Xms2200m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta 179s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta] 179s Version 39.20 179s 179s No output file. 179s Writing reference. 179s 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] 179s 179s Set genScaffoldInfo=true 179s Writing chunk 1 179s Set genome to 1 179s 179s Loaded Reference: 0.007 seconds. 179s Loading index for chunk 1-1, build 1 179s No index available; generating from reference genome: /tmp/autopkgtest.KBjjPG/autopkgtest_tmp/ref/index/1/chr1_index_k13_c16_b1.block 179s Indexing threads started for block 0-1 179s Indexing threads finished for block 0-1 181s Generated Index: 1.568 seconds. 181s No reads to process; quitting. 181s 181s Total time: 1.791 seconds. 181s test -d ref 181s bbmap.sh in=misc_dna_as_sanger.fastq out=out.sam 181s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 181s 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 181s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, in=misc_dna_as_sanger.fastq, out=out.sam] 181s Version 39.20 181s 181s Retaining first best site only for ambiguous mappings. 181s Set genome to 1 181s 181s Loaded Reference: 0.046 seconds. 181s Loading index for chunk 1-1, build 1 182s Generated Index: 0.776 seconds. 185s Analyzed Index: 3.560 seconds. 185s Started output stream: 0.035 seconds. 185s Cleared Memory: 0.113 seconds. 186s Processing reads in single-ended mode. 186s Started read stream. 186s Started 8 mapping threads. 186s Detecting finished threads: 0, 1, 2, 3, 4, 5, 6, 7 186s 186s ------------------ Results ------------------ 186s 186s Genome: 1 186s Key Length: 13 186s Max Indel: 16000 186s Minimum Score Ratio: 0.56 186s Mapping Mode: normal 186s Reads Used: 4 (153 bases) 186s 186s Mapping: 0.147 seconds. 186s Reads/sec: 27.13 186s kBases/sec: 1.04 186s 186s 186s Read 1 data: pct reads num reads pct bases num bases 186s 186s mapped: 0.0000% 0 0.0000% 0 186s unambiguous: 0.0000% 0 0.0000% 0 186s ambiguous: 0.0000% 0 0.0000% 0 186s low-Q discards: 25.0000% 1 19.6078% 30 186s 186s perfect best site: 0.0000% 0 0.0000% 0 186s semiperfect site: 0.0000% 0 0.0000% 0 186s 186s Match Rate: NA NA NaN% 0 186s Error Rate: NaN% 0 NaN% 0 186s Sub Rate: NaN% 0 NaN% 0 186s Del Rate: NaN% 0 NaN% 0 186s Ins Rate: NaN% 0 NaN% 0 186s N Rate: NaN% 0 NaN% 0 186s 186s Total time: 4.887 seconds. 186s test -r out.sam 186s bbmap.sh ref=example.fasta in=example.fastq out=out2.sam nodisk 186s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 186s 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 186s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta, in=example.fastq, out=out2.sam, nodisk] 186s Version 39.20 186s 186s Retaining first best site only for ambiguous mappings. 186s 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] 186s 186s Set genScaffoldInfo=true 186s Set genome to 1 186s 186s Loaded Reference: 0.002 seconds. 186s Loading index for chunk 1-1, build 1 186s Indexing threads started for block 0-1 186s Indexing threads finished for block 0-1 186s Generated Index: 0.231 seconds. 190s Analyzed Index: 3.661 seconds. 190s Started output stream: 0.035 seconds. 190s Cleared Memory: 0.114 seconds. 190s Processing reads in single-ended mode. 190s Started read stream. 190s Started 8 mapping threads. 190s Detecting finished threads: 0, 1, 2, 3, 4, 5, 6, 7 190s 190s ------------------ Results ------------------ 190s 190s Genome: 1 190s Key Length: 13 190s Max Indel: 16000 190s Minimum Score Ratio: 0.56 190s Mapping Mode: normal 190s Reads Used: 3 (75 bases) 190s 190s Mapping: 0.156 seconds. 190s Reads/sec: 19.29 190s kBases/sec: 0.48 190s 190s 190s Read 1 data: pct reads num reads pct bases num bases 190s 190s mapped: 100.0000% 3 100.0000% 75 190s unambiguous: 100.0000% 3 100.0000% 75 190s ambiguous: 0.0000% 0 0.0000% 0 190s low-Q discards: 0.0000% 0 0.0000% 0 190s 190s perfect best site: 100.0000% 3 100.0000% 75 190s semiperfect site: 100.0000% 3 100.0000% 75 190s 190s Match Rate: NA NA 100.0000% 75 190s Error Rate: 0.0000% 0 0.0000% 0 190s Sub Rate: 0.0000% 0 0.0000% 0 190s Del Rate: 0.0000% 0 0.0000% 0 190s Ins Rate: 0.0000% 0 0.0000% 0 190s N Rate: 0.0000% 0 0.0000% 0 190s 190s Total time: 4.408 seconds. 190s test -r out2.sam 190s 190s # bbduk 190s bbduk.sh --version 190s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 190s java -ea -Xmx2200m -Xms2200m -cp /usr/share/java/bbmap.jar jgi.BBDuk --version 191s BBTools version 39.20 191s For help, please run the shellscript with no parameters, or look in /docs/. 191s bbduk.sh --help 191s 191s Written by Brian Bushnell 191s Last modified November 18, 2024 191s 191s Description: Compares reads to the kmers in a reference dataset, optionally 191s allowing an edit distance. Splits the reads into two outputs - those that 191s match the reference, and those that don't. Can also trim (remove) the matching 191s parts of the reads rather than binning the reads. 191s Please read bbmap/docs/guides/BBDukGuide.txt for more information. 191s 191s Usage: bbduk.sh in= out= ref= 191s 191s Input may be stdin or a fasta or fastq file, compressed or uncompressed. 191s If you pipe via stdin/stdout, please include the file type; e.g. for gzipped 191s fasta input, set in=stdin.fa.gz 191s 191s Input parameters: 191s in= Main input. in=stdin.fq will pipe from stdin. 191s in2= Input for 2nd read of pairs in a different file. 191s ref= Comma-delimited list of reference files. 191s In addition to filenames, you may also use the keywords: 191s adapters, artifacts, phix, lambda, pjet, mtst, kapa 191s literal= Comma-delimited list of literal reference sequences. 191s Polymers are also allowed with the 'poly' prefix; 191s for example, 'literal=ATGGT,polyGC' will add both ATGGT 191s and GCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGC - 32+ of them, 191s enough replicates to ensure that all kmers are present. 191s touppercase=f (tuc) Change all bases upper-case. 191s interleaved=auto (int) t/f overrides interleaved autodetection. 191s Must be set mainually when streaming fastq input. 191s qin=auto Input quality offset: 33 (Sanger), 64, or auto. 191s reads=-1 If positive, quit after processing X reads or pairs. 191s copyundefined=f (cu) Process non-AGCT IUPAC reference bases by making all 191s possible unambiguous copies. Intended for short motifs 191s or adapter barcodes, as time/memory use is exponential. 191s samplerate=1 Set lower to only process a fraction of input reads. 191s samref= Optional reference fasta for processing sam files. 191s 191s Output parameters: 191s out= (outnonmatch) Write reads here that do not contain 191s kmers matching the database. 'out=stdout.fq' will pipe 191s to standard out. 191s out2= (outnonmatch2) Use this to write 2nd read of pairs to a 191s different file. 191s outm= (outmatch) Write reads here that fail filters. In default 191s kfilter mode, this means any read with a matching kmer. 191s In any mode, it also includes reads that fail filters such 191s as minlength, mingc, maxgc, entropy, etc. In other words, 191s it includes all reads that do not go to 'out'. 191s outm2= (outmatch2) Use this to write 2nd read of pairs to a 191s different file. 191s outs= (outsingle) Use this to write singleton reads whose mate 191s was trimmed shorter than minlen. 191s stats= Write statistics about which contamininants were detected. 191s refstats= Write statistics on a per-reference-file basis. 191s rpkm= Write RPKM for each reference sequence (for RNA-seq). 191s dump= Dump kmer tables to a file, in fasta format. 191s duk= Write statistics in duk's format. *DEPRECATED* 191s nzo=t Only write statistics about ref sequences with nonzero hits. 191s overwrite=t (ow) Grant permission to overwrite files. 191s showspeed=t (ss) 'f' suppresses display of processing speed. 191s ziplevel=2 (zl) Compression level; 1 (min) through 9 (max). 191s fastawrap=70 Length of lines in fasta output. 191s qout=auto Output quality offset: 33 (Sanger), 64, or auto. 191s statscolumns=3 (cols) Number of columns for stats output, 3 or 5. 191s 5 includes base counts. 191s rename=f Rename reads to indicate which sequences they matched. 191s refnames=f Use names of reference files rather than scaffold IDs. 191s trd=f Truncate read and ref names at the first whitespace. 191s ordered=f Set to true to output reads in same order as input. 191s maxbasesout=-1 If positive, quit after writing approximately this many 191s bases to out (outu/outnonmatch). 191s maxbasesoutm=-1 If positive, quit after writing approximately this many 191s bases to outm (outmatch). 191s json=f Print to screen in json format. 191s 191s Histogram output parameters: 191s bhist= Base composition histogram by position. 191s qhist= Quality histogram by position. 191s qchist= Count of bases with each quality value. 191s aqhist= Histogram of average read quality. 191s bqhist= Quality histogram designed for box plots. 191s lhist= Read length histogram. 191s phist= Polymer length histogram. 191s gchist= Read GC content histogram. 191s enthist= Read entropy histogram. 191s ihist= Insert size histogram, for paired reads in mapped sam. 191s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 191s maxhistlen=6000 Set an upper bound for histogram lengths; higher uses 191s more memory. The default is 6000 for some histograms 191s and 80000 for others. 191s 191s Histograms for mapped sam/bam files only: 191s histbefore=t Calculate histograms from reads before processing. 191s ehist= Errors-per-read histogram. 191s qahist= Quality accuracy histogram of error rates versus quality 191s score. 191s indelhist= Indel length histogram. 191s mhist= Histogram of match, sub, del, and ins rates by position. 191s idhist= Histogram of read count versus percent identity. 191s idbins=100 Number idhist bins. Set to 'auto' to use read length. 191s varfile= Ignore substitution errors listed in this file when 191s calculating error rates. Can be generated with 191s CallVariants. 191s vcf= Ignore substitution errors listed in this VCF file 191s when calculating error rates. 191s ignorevcfindels=t Also ignore indels listed in the VCF. 191s 191s Processing parameters: 191s k=27 Kmer length used for finding contaminants. Contaminants 191s shorter than k will not be found. k must be at least 1. 191s rcomp=t Look for reverse-complements of kmers in addition to 191s forward kmers. 191s maskmiddle=t (mm) Treat the middle base of a kmer as a wildcard, to 191s increase sensitivity in the presence of errors. This may 191s also be set to a number, e.g. mm=3, to mask that many bp. 191s The default mm=t corresponds to mm=1 for odd-length kmers 191s and mm=2 for even-length kmers (as of v39.04), while 191s mm=f is always equivalent to mm=0. 191s minkmerhits=1 (mkh) Reads need at least this many matching kmers 191s to be considered as matching the reference. 191s minkmerfraction=0.0 (mkf) A reads needs at least this fraction of its total 191s kmers to hit a ref, in order to be considered a match. 191s If this and minkmerhits are set, the greater is used. 191s mincovfraction=0.0 (mcf) A reads needs at least this fraction of its total 191s bases to be covered by ref kmers to be considered a match. 191s If specified, mcf overrides mkh and mkf. 191s hammingdistance=0 (hdist) Maximum Hamming distance for ref kmers (subs only). 191s Memory use is proportional to (3*K)^hdist. 191s qhdist=0 Hamming distance for query kmers; impacts speed, not memory. 191s editdistance=0 (edist) Maximum edit distance from ref kmers (subs 191s and indels). Memory use is proportional to (8*K)^edist. 191s hammingdistance2=0 (hdist2) Sets hdist for short kmers, when using mink. 191s qhdist2=0 Sets qhdist for short kmers, when using mink. 191s editdistance2=0 (edist2) Sets edist for short kmers, when using mink. 191s forbidn=f (fn) Forbids matching of read kmers containing N. 191s By default, these will mat bbduk.sh in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq \ 191s qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 191s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 191s ch a reference 'A' if 191s hdist>0 or edist>0, to increase sensitivity. 191s removeifeitherbad=t (rieb) Paired reads get sent to 'outmatch' if either is 191s match (or either is trimmed shorter than minlen). 191s Set to false to require both. 191s trimfailures=f Instead of discarding failed reads, trim them to 1bp. 191s This makes the statistics a bit odd. 191s findbestmatch=f (fbm) If multiple matches, associate read with sequence 191s sharing most kmers. Reduces speed. 191s skipr1=f Don't do kmer-based operations on read 1. 191s skipr2=f Don't do kmer-based operations on read 2. 191s ecco=f For overlapping paired reads only. Performs error- 191s correction with BBMerge prior to kmer operations. 191s recalibrate=f (recal) Recalibrate quality scores. Requires calibration 191s matrices generated by CalcTrueQuality. 191s sam= If recalibration is desired, and matrices have not already 191s been generated, BBDuk will create them from the sam file. 191s amino=f Run in amino acid mode. Some features have not been 191s tested, but kmer-matching works fine. Maximum k is 12. 191s 191s Speed and Memory parameters: 191s threads=auto (t) Set number of threads to use; default is number of 191s logical processors. 191s prealloc=f Preallocate memory in table. Allows faster table loading 191s and more efficient memory usage, for a large reference. 191s monitor=f Kill this process if it crashes. monitor=600,0.01 would 191s kill after 600 seconds under 1% usage. 191s minrskip=1 (mns) Force minimal skip interval when indexing reference 191s kmers. 1 means use all, 2 means use every other kmer, etc. 191s maxrskip=1 (mxs) Restrict maximal skip interval when indexing 191s reference kmers. Normally all are used for scaffolds<100kb, 191s but with longer scaffolds, up to maxrskip-1 are skipped. 191s rskip= Set both minrskip and maxrskip to the same value. 191s If not set, rskip will vary based on sequence length. 191s qskip=1 Skip query kmers to increase speed. 1 means use all. 191s speed=0 Ignore this fraction of kmer space (0-15 out of 16) in both 191s reads and reference. Increases speed and reduces memory. 191s Note: Do not use more than one of 'speed', 'qskip', and 'rskip'. 191s 191s Trimming/Filtering/Masking parameters: 191s Note - if ktrim, kmask, and ksplit are unset, the default behavior is kfilter. 191s All kmer processing modes are mutually exclusive. 191s Reads only get sent to 'outm' purely based on kmer matches in kfilter mode. 191s 191s ktrim=f Trim reads to remove bases matching reference kmers, plus 191s all bases to the left or right. 191s Values: 191s f (don't trim), 191s r (trim to the right), 191s l (trim to the left) 191s ktrimtips=0 Set this to a positive number to perform ktrim on both 191s ends, examining only the outermost X bases. 191s kmask= Replace bases matching ref kmers with another symbol. 191s Allows any non-whitespace character, and processes short 191s kmers on both ends if mink is set. 'kmask=lc' will 191s convert masked bases to lowercase. 191s maskfullycovered=f (mfc) Only mask bases that are fully covered by kmers. 191s ksplit=f For single-ended reads only. Reads will be split into 191s pairs around the kmer. If the kmer is at the end of the 191s read, it will be trimmed instead. Singletons will go to 191s out, and pairs will go to outm. Do not use ksplit with 191s other operations such as quality-trimming or filtering. 191s mink=0 Look for shorter kmers at read tips down to this length, 191s when k-trimming or masking. 0 means disabled. Enabling 191s this will disable maskmiddle. 191s qtrim=f Trim read ends to remove bases with quality below trimq. 191s Performed AFTER looking for kmers. Values: 191s rl (trim both ends), 191s f (neither end), 191s r (right end only), 191s l (left end only), 191s w (sliding window). 191s trimq=6 Regions with average quality BELOW this will be trimmed, 191s if qtrim is set to something other than f. Can be a 191s floating-point number like 7.3. 191s quantize Bin quality scores to reduce file size. quantize=2 will 191s eliminate all odd quality scores, while quantize=0,10,37 191s will only allow qualty scores of 0, 10, or 37. 191s trimclip=f Trim soft-clipped bases from sam files. 191s minlength=10 (ml) Reads shorter than this after trimming will be 191s discarded. Pairs will be discarded if both are shorter. 191s mlf=0 (minlengthfraction) Reads shorter than this fraction of 191s original length after trimming will be discarded. 191s maxlength= Reads longer than this after trimming will be discarded. 191s minavgquality=0 (maq) Reads with average quality (after trimming) below 191s this will be discarded. 191s maqb=0 If positive, calculate maq from this many initial bases. 191s minbasequality=0 (mbq) Reads with any base below this quality (after 191s trimming) will be discarded. 191s maxns=-1 If non-negative, reads with more Ns than this 191s (after trimming) will be discarded. 191s mcb=0 (minconsecutivebases) Discard reads without at least 191s this many consecutive called bases. 191s ottm=f (outputtrimmedtomatch) Output reads trimmed to shorter 191s than minlength to outm rather than discarding. 191s tp=0 (trimpad) Trim this much extra around matching kmers. 191s tbo=f (trimbyoverlap) Trim adapters based on where paired 191s reads overlap. 191s strictoverlap=t Adjust sensitivity for trimbyoverlap mode. 191s minoverlap=14 Require this many bases of overlap for detection. 191s mininsert=40 Require insert size of at least this for overlap. 191s Should be reduced to 16 for small RNA sequencing. 191s tpe=f (trimpairsevenly) When kmer right-trimming, trim both 191s reads to the minimum length of either. 191s forcetrimleft=0 (ftl) If positive, trim bases to the left of this position 191s (exclusive, 0-based). 191s forcetrimright=0 (ftr) If positive, trim bases to the right of this position 191s (exclusive, 0-based). 191s forcetrimright2=0 (ftr2) If positive, trim this many bases on the right end. 191s forcetrimmod=0 (ftm) If positive, right-trim length to be equal to zero, 191s modulo this number. 191s restrictleft=0 If positive, only look for kmer matches in the 191s leftmost X bases. 191s restrictright=0 If positive, only look for kmer matches in the 191s rightmost X bases. 191s NOTE: restrictleft and restrictright are mutually exclusive. If trimming 191s both ends is desired, use ktrimtips. 191s mingc=0 Discard reads with GC content below this. 191s maxgc=1 Discard reads with GC content above this. 191s gcpairs=t Use average GC of paired reads. 191s Also affects gchist. 191s tossjunk=f Discard reads with invalid characters as bases. 191s swift=f Trim Swift sequences: Trailing C/T/N R1, leading G/A/N R2. 191s 191s Header-parsing parameters - these require Illumina headers: 191s chastityfilter=f (cf) Discard reads with id containing ' 1:Y:' or ' 2:Y:'. 191s barcodefilter=f Remove reads with unexpected barcodes if barcodes is set, 191s or barcodes containing 'N' otherwise. A barcode must be 191s the last part of the read header. Values: 191s t: Remove reads with bad barcodes. 191s f: Ignore barcodes. 191s crash: Crash upon encountering bad barcodes. 191s barcodes= Comma-delimited list of barcodes or files of barcodes. 191s xmin=-1 If positive, discard reads with a lesser X coordinate. 191s ymin=-1 If positive, discard reads with a lesser Y coordinate. 191s xmax=-1 If positive, discard reads with a greater X coordinate. 191s ymax=-1 If positive, discard reads with a greater Y coordinate. 191s 191s Polymer trimming: 191s trimpolya=0 If greater than 0, trim poly-A or poly-T tails of 191s at least this length on either end of reads. 191s trimpolygleft=0 If greater than 0, trim poly-G prefixes of at least this 191s length on the left end of reads. Does not trim poly-C. 191s trimpolygright=0 If greater than 0, trim poly-G tails of at least this 191s length on the right end of reads. Does not trim poly-C. 191s trimpolyg=0 This sets both left and right at once. 191s filterpolyg=0 If greater than 0, remove reads with a poly-G prefix of 191s at least this length (on the left). 191s Note: there are also equivalent poly-C flags. 191s 191s Polymer tracking: 191s pratio=base,base 'pratio=G,C' will print the ratio of G to C polymers. 191s plen=20 Length of homopolymers to count. 191s 191s Entropy/Complexity parameters: 191s entropy=-1 Set between 0 and 1 to filter reads with entropy below 191s that value. Higher is more stringent. 191s entropywindow=50 Calculate entropy using a sliding window of this length. 191s entropyk=5 Calculate entropy using kmers of this length. 191s minbasefrequency=0 Discard reads with a minimum base frequency below this. 191s entropytrim=f Values: 191s f: (false) Do not entropy-trim. 191s r: (right) Trim low entropy on the right end only. 191s l: (left) Trim low entropy on the left end only. 191s rl: (both) Trim low entropy on both ends. 191s entropymask=f Values: 191s f: (filter) Discard low-entropy sequences. 191s t: (true) Mask low-entropy parts of sequences with N. 191s lc: Change low-entropy parts of sequences to lowercase. 191s entropymark=f Mark each base with its entropy value. This is on a scale 191s of 0-41 and is reported as quality scores, so the output 191s should be fastq or fasta+qual. 191s NOTE: If set, entropytrim overrides entropymask. 191s 191s Cardinality estimation: 191s cardinality=f (loglog) Count unique kmers using the LogLog algorithm. 191s cardinalityout=f (loglogout) Count unique kmers in output reads. 191s loglogk=31 Use this kmer length for counting. 191s loglogbuckets=2048 Use this many buckets for counting. 191s khist= Kmer frequency histogram; plots number of kmers versus 191s kmer depth. This is approximate. 191s khistout= Kmer frequency histogram for output reads. 191s 191s Side Channel: 191s sideout= Output for aligned reads. 191s sideref=phix Reference for side-channel alignment; must be a single 191s sequence and virtually repeat-free at selected k. 191s sidek1=17 Kmer length for seeding alignment to reference. 191s sidek2=13 Kmer length for seeding alignment of unaligned reads 191s with an aligned mate. 191s sideminid1=0.66 Minimum identity to accept individual alignments. 191s sideminid2=0.58 Minimum identity for aligning reads with aligned mates. 191s sidemm1=1 Middle mask length for sidek1. 191s sidemm2=1 Middle mask length for sidek2. 191s Note: The side channel is a special additional output that allows alignment 191s to a secondary reference while also doing trimming. Alignment does not affect 191s whether reads go to the normal outputs (out, outm). The main purpose is to 191s simplify pipelines that need trimmed, aligned phiX reads for recalibration. 191s 191s 191s Java Parameters: 191s 191s -Xmx This will set Java's memory usage, overriding autodetection. 191s -Xmx20g will 191s specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 191s The max is typically 85% of physical memory. 191s -eoom This flag will cause the process to exit if an 191s out-of-memory exception occurs. Requires Java 8u92+. 191s -da Disable assertions. 191s 191s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 191s 191s 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 191s 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] 191s Version 39.20 191s 191s Changed from ASCII-33 to ASCII-64 on input quality X (Q55) for base A at lines 1 and 3, position 24 while prescanning. 191s Changed from ASCII-33 to ASCII-64 on input quality X (Q55) for base A at lines 1 and 3, position 24 while prescanning. 191s Allocating kmer table: 0.022 seconds. 191s Initial: 191s Memory: max=2306m, total=2306m, free=2285m, used=21m 191s 191s Input is being processed as paired 191s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 191s Started output streams: 0.025 seconds. 191s Processing time: 0.005 seconds. 191s 191s Input: 8 reads 306 bases. 191s QTrimmed: 0 reads (0.00%) 0 bases (0.00%) 191s Total Removed: 8 reads (100.00%) 306 bases (100.00%) 191s Result: 0 reads (0.00%) 0 bases (0.00%) 191s 191s Time: 0.032 seconds. 191s Reads Processed: 8 0.25k reads/sec 191s Bases Processed: 306 0.01m bases/sec 191s test -r out.fastq.gz 191s 191s # bbnorm 191s bbnorm.sh --version 191s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 191s java -ea -Xmx2200m -Xms2200m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 --version 191s BBTools version 39.20 191s For help, please run the shellscript with no parameters, or look in /docs/. 191s bbnorm.sh --help 191s 191s Written by Brian Bushnell 191s Last modified October 19, 2017 191s 191s Description: Normalizes read depth based on kmer counts. 191s Can also error-correct, bin reads by kmer depth, and generate a kmer depth histogram. 191s However, Tadpole has superior error-correction to BBNorm. 191s Please read bbmap/docs/guides/BBNormGuide.txt for more information. 191s 191s Usage: bbnorm.sh in= out= outt= hist= 191s 191s Input parameters: 191s in=null Primary input. Use in2 for paired reads in a second file 191s in2=null Second input file for paired reads in two files 191s extra=null Additional files to use for input (generating hash table) but not for output 191s fastareadlen=2^31 Break up FASTA reads longer than this. Can be useful when processing scaffolded genomes 191s tablereads=-1 Use at most this many reads when building the hashtable (-1 means all) 191s kmersample=1 Process every nth kmer, and skip the rest 191s readsample=1 Process every nth read, and skip the rest 191s 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. 191s qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto. 191s 191s Output parameters: 191s out= File for normalized or corrected reads. Use out2 for paired reads in a second file 191s outt= (outtoss) File for reads that were excluded from primary output 191s reads=-1 Only process this number of reads, then quit (-1 means all) 191s sampleoutput=t Use sampling on output as well as input (not used if sample rates are 1) 191s keepall=f Set to true to keep all reads (e.g. if you just want error correction). 191s 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. 191s Default is false, to prevent confusion about how there can be 0-count kmers. 191s The reason is that based on the 'minq' and 'minprob' settings, some kmers may be excluded from the bloom filter. 191s tmpdir= This will specify a directory for temp files (only needed for multipass runs). If null, they will be written to the output directory. 191s usetempdir=t Allows enabling/disabling of temporary directory; if disabled, temp files will be written to the output directory. 191s qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input). 191s rename=f Rename reads based on their kmer depth. 191s 191s Hashing parameters: 191s k=31 Kmer length (values under 32 are most efficient, but arbitrarily high values are supported) 191s 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. 191s Large values decrease accuracy for a fixed amount of memory, so use the lowest number you can that will still capture highest-depth kmers. 191s hashes=3 Number of times each kmer is hashed and stored. Higher is slower. 191s Higher is MORE accurate if there is enough memory, and LESS accurate if there is not enough memory. 191s 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. 191s prehashes=2 Number of hashes for prefilter. 191s prefilterbits=2 (pbits) Bits per cell in prefilter. 191s prefiltersize=0.35 Fraction of memory to allocate to prefilter. 191s buildpasses=1 More passes can sometimes increase accuracy by iteratively removing low-depth kmers 191s minq=6 Ignore kmers containing bases with quality below this 191s minprob=0.5 Ignore kmers with overall probability of correctness below this 191s 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. 191s 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. 191s 191s Normalization parameters: 191s fixspikes=f (fs) Do a slower, high-precision bloom filter lookup of kmers that appear to have an abnormally high depth due to collisions. 191s target=100 (tgt) Target normalization depth. NOTE: All depth parameters control kmer depth, not read depth. 191s For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1)) 191s maxdepth=-1 (max) Reads will not be downsampled when below this depth, even if they are above the target depth. 191s mindepth=5 (min) Kmers with depth below this number will not be included when calculating the depth of a read. 191s minkmers=15 (mgkpr) Reads must have at least this many kmers over min depth to be retained. Aka 'mingoodkmersperread'. 191s 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. 191s uselowerdepth=t (uld) For pairs, use the depth of the lower read as the depth proxy. 191s deterministic=t (dr) Generate random numbers deterministically to ensure identical output between multiple runs. May decrease speed with a huge number of threads. 191s passes=2 (p) 1 pass is the basic mode. 2 passes (default) allows greater accuracy, error detection, better contol of output depth. 191s 191s Error detection parameters: 191s hdp=90.0 (highdepthpercentile) Position in sorted kmer depth array used as proxy of a read's high kmer depth. 191s ldp=25.0 (lowdepthpercentile) Position in sorted kmer depth array used as proxy of a read's low kmer depth. 191s tossbadreads=f (tbr) Throw away reads detected as containing errors. 191s requirebothbad=f (rbb) Only toss bad pairs if both reads are bad. 191s 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. 191s highthresh=12 (ht) Threshold for high kmer. A high kmer at this or above are considered non-error. 191s lowthresh=3 (lt) Threshold for low kmer. Kmers at this and below are always considered errors. 191s 191s Error correction parameters: 191s ecc=f Set to true to correct errors. NOTE: Tadpole is now preferred for ecc as it does a better job. 191s ecclimit=3 Correct up to this many errors per read. If more are detected, the read will remain unchanged. 191s errorcorrectratio=140 (ecr) Adjacent kmers with a depth ratio of at least this much between will be classified as an error. 191s echighthresh=22 (echt) Threshold for high kmer. A kmer at this or above may be considered non-error. 191s eclowthresh=2 (eclt) Threshold for low kmer. Kmers at this and below are considered errors. 191s eccmaxqual=127 Do not correct bases with quality above this value. 191s aec=f (aggressiveErrorCorrection) Sets more aggressive values of ecr=100, ecclimit=7, echt=16, eclt=3. 191s cec=f (conservativeErrorCorrection) Sets more conservative values of ecr=180, ecclimit=2, echt=30, eclt=1, sl=4, pl=4. 191s meo=f (markErrorsOnly) Marks errors by reducing quality value of suspected errors; does not correct anything. 191s mue=t (markUncorrectableErrors) Marks errors only on uncorrectable reads; requires 'ecc=t'. 191s overlap=f (ecco) Error correct by read overlap. 191s 191s Depth binning parameters: 191s lowbindepth=10 (lbd) Cutoff for low depth bin. 191s highbindepth=80 (hbd) Cutoff for high depth bin. 191s outlow= Pairs in which both reads have a median below lbd go into this file. 191s outhigh= Pairs in which both reads have a median above hbd go into this file. 191s outmid= All other pairs go into this file. 191s 191s Histogram parameters: 191s hist= Specify a file to write the input kmer depth histogram. 191s histout= Specify a file to write the output kmer depth histogram. 191s histcol=3 (histogramcolumns) Number of histogram columns, 2 or 3. 191s pzc=f (printzerocoverage) Print lines in the histogram with zero coverage. 191s histlen=1048576 Max kmer depth displayed in histogram. Also affects statistics displayed, but does not affect normalization. 191s 191s Peak calling parameters: 191s peaks= Write the peaks to this file. Default is stdout. 191s minHeight=2 (h) Ignore peaks shorter than this. 191s minVolume=5 (v) Ignore peaks with less area than this. 191s minWidth=3 (w) Ignore peaks narrower than this. 191s minPeak=2 (minp) Ignore peaks with an X-value below this. 191s maxPeak=BIG (maxp) Ignore peaks with an X-value above this. 191s maxPeakCount=8 (maxpc) Print up to this many peaks (prioritizing height). 191s 191s Java Parameters: 191s -Xmx This will set Java's memory usage, overriding autodetection. 191s -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 191s The max is typically 85% of physical memory. 191s -eoom This flag will cause the process to exit if an 191s out-of-memory exception occurs. Requires Java 8u92+. 191s -da Disable assertions. 191s 191s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 191s 191s bbnorm.sh in=sanger_full_range_original_sanger.fastq qin=33 \ 191s out=out3.fastq outt=outt.fastq hist=hist.plt 191s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 191s 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 191s Executing jgi.KmerNormalize [bits=32, in=sanger_full_range_original_sanger.fastq, qin=33, out=out3.fastq, outt=outt.fastq, hist=hist.plt] 191s 191s 191s *********** Pass 1 ********** 191s 191s 191s Settings: 191s threads: 8 191s k: 31 191s deterministic: true 191s toss error reads: false 191s passes: 1 191s bits per cell: 16 191s cells: 806.44M 191s hashes: 3 191s base min quality: 5 191s kmer min prob: 0.5 191s 191s target depth: 400 191s min depth: 3 191s max depth: 500 191s min good kmers: 15 191s depth percentile: 64.8 191s ignore dupe kmers: true 191s fix spikes: false 191s histogram length: 65536 191s print zero cov: false 191s 192s Made hash table: hashes = 3 mem = 1.50 GB cells = 806.41M used = 0.000% 192s 192s Estimated unique kmers: 4 192s 192s Table creation time: 0.659 seconds. 192s Started output threads. 192s Started output threads. 192s Table read time: 0.015 seconds. 12.43 kb/sec 192s Total reads in: 2 0.000% Kept 192s Total bases in: 188 0.000% Kept 192s Error reads in: 2 100.000% 192s Error type 1: 2 100.000% 192s Error type 2: 0 0.000% 192s Error type 3: 0 0.000% 192s 192s Wrote histogram to hist.plt 192s Total kmers counted: 128 192s Total unique kmer count: 128 192s Includes forward kmers only. 192s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 192s The most accurate value is the greater of the two. 192s 192s Percent unique: 100.00% 192s Depth average: 1.00 (unique kmers) 192s Depth median: 1 (unique kmers) 192s Depth standard deviation: 0.00 (unique kmers) 192s Corrected depth average: 0.00 192s 192s Depth average: 1.00 (all kmers) 192s Depth median: 1 (all kmers) 192s Depth standard deviation: 0.00 (all kmers) 192s 192s Approx. read depth median: 1.47 192s 192s *********** Pass 2 ********** 192s 192s 192s Settings: 192s threads: 8 192s k: 31 192s deterministic: true 192s toss error reads: false 192s passes: 1 192s bits per cell: 16 192s cells: 806.44M 192s hashes: 3 192s base min quality: 5 192s kmer min prob: 0.5 192s 192s target depth: 100 192s min depth: 5 192s max depth: 100 192s min good kmers: 15 192s depth percentile: 54.0 192s ignore dupe kmers: true 192s fix spikes: false 192s histogram length: 65536 192s 193s Made hash table: hashes = 3 mem = 1.50 GB cells = 806.41M used = 0.000% 193s 193s Estimated unique kmers: 0 193s 193s Table creation time: 0.343 seconds. 193s Started output threads. 193s Started output threads. 193s Table read time: 0.003 seconds. 0.00 kb/sec 193s Total reads in: 0 NaN% Kept 193s Total bases in: 0 NaN% Kept 193s Error reads in: 0 NaN% 193s Error type 1: 0 NaN% 193s Error type 2: 0 NaN% 193s Error type 3: 0 NaN% 193s Total kmers counted: 0 193s Total unique kmer count: 0 193s Includes forward kmers only. 193s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 193s The most accurate value is the greater of the two. 193s 193s Percent unique: NaN% 193s Depth average: NaN (unique kmers) 193s Depth median: 0 (unique kmers) 193s Depth standard deviation: NaN (unique kmers) 193s Corrected depth average: NaN 193s 193s Depth average: NaN (all kmers) 193s Depth median: 0 (all kmers) 193s Depth standard deviation: 0.00 (all kmers) 193s 193s Approx. read depth median: NaN 193s 193s Removing temp files. 193s 193s Total time: 1.115 seconds. 0.17 kb/sec 193s test -r out3.fastq 193s test -r outt.fastq 193s test -r hist.plt 193s bbnorm.sh in=illumina_full_range_original_illumina.fastq qin=64 \ 193s out=out4.fastq outt=outt2.fastq hist=hist2.plt 193s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 193s 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 193s Executing jgi.KmerNormalize [bits=32, in=illumina_full_range_original_illumina.fastq, qin=64, out=out4.fastq, outt=outt2.fastq, hist=hist2.plt] 193s 193s 193s *********** Pass 1 ********** 193s 193s 193s Settings: 193s threads: 8 193s k: 31 193s deterministic: true 193s toss error reads: false 193s passes: 1 193s bits per cell: 16 193s cells: 806.44M 193s hashes: 3 193s base min quality: 5 193s kmer min prob: 0.5 193s 193s target depth: 400 193s min depth: 3 193s max depth: 500 193s min good kmers: 15 193s depth percentile: 64.8 193s ignore dupe kmers: true 193s fix spikes: false 193s histogram length: 65536 193s print zero cov: false 193s 194s Made hash table: hashes = 3 mem = 1.50 GB cells = 806.41M used = 0.000% 194s 194s Estimated unique kmers: 4 194s 194s Table creation time: 0.717 seconds. 194s Started output threads. 194s Started output threads. 194s Table read time: 0.011 seconds. 11.32 kb/sec 194s Total reads in: 2 0.000% Kept 194s Total bases in: 126 0.000% Kept 194s Error reads in: 2 100.000% 194s Error type 1: 2 100.000% 194s Error type 2: 0 0.000% 194s Error type 3: 0 0.000% 194s 194s Wrote histogram to hist2.plt 194s Total kmers counted: 66 194s Total unique kmer count: 66 194s Includes forward kmers only. 194s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 194s The most accurate value is the greater of the two. 194s 194s Percent unique: 100.00% 194s Depth average: 1.00 (unique kmers) 194s Depth median: 1 (unique kmers) 194s Depth standard deviation: 0.00 (unique kmers) 194s Corrected depth average: 0.00 194s 194s Depth average: 1.00 (all kmers) 194s Depth median: 1 (all kmers) 194s Depth standard deviation: 0.00 (all kmers) 194s 194s Approx. read depth median: 1.91 194s 194s *********** Pass 2 ********** 194s 194s 194s Settings: 194s threads: 8 194s k: 31 194s deterministic: true 194s toss error reads: false 194s passes: 1 194s bits per cell: 16 194s cells: 806.44M 194s hashes: 3 194s base min quality: 5 194s kmer min prob: 0.5 194s 194s target depth: 100 194s min depth: 5 194s max depth: 100 194s min good kmers: 15 194s depth percentile: 54.0 194s ignore dupe kmers: true 194s fix spikes: false 194s histogram length: 65536 194s 194s Made hash table: hashes = 3 mem = 1.50 GB cells = 806.41M used = 0.000% 194s 194s Estimated unique kmers: 0 194s 194s Table creation time: 0.409 seconds. 194s Started output threads. 194s Started output threads. 194s Table read time: 0.003 seconds. 0.00 kb/sec 194s Total reads in: 0 NaN% Kept 194s Total bases in: 0 NaN% Kept 194s Error reads in: 0 NaN% 194s Error type 1: 0 NaN% 194s Error type 2: 0 NaN% 194s Error type 3: 0 NaN% 194s Total kmers counted: 0 194s Total unique kmer count: 0 194s Includes forward kmers only. 194s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 194s The most accurate value is the greater of the two. 194s 194s Percent unique: NaN% 194s Depth average: NaN (unique kmers) 194s Depth median: 0 (unique kmers) 194s Depth standard deviation: NaN (unique kmers) 194s Corrected depth average: NaN 194s 194s Depth average: NaN (all kmers) 194s Depth median: 0 (all kmers) 194s Depth standard deviation: 0.00 (all kmers) 194s 194s Approx. read depth median: NaN 194s 194s Removing temp files. 194s 194s Total time: 1.224 seconds. 0.10 kb/sec 194s test -r out4.fastq 194s test -r outt2.fastq 194s test -r hist2.plt 195s autopkgtest [18:13:04]: test run-unit-test: -----------------------] 199s autopkgtest [18:13:08]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 199s run-unit-test PASS 202s autopkgtest [18:13:11]: @@@@@@@@@@@@@@@@@@@@ summary 202s run-unit-test PASS