0s autopkgtest [00:43:49]: starting date and time: 2024-03-22 00:43:49+0000 0s autopkgtest [00:43:49]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [00:43:49]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.e8e53psw/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:openjdk-21,src:alsa-lib,src:at-spi2-core,src:cups,src:glib2.0,src:gnutls28,src:gtk+3.0,src:libpng1.6,src:nettle,src:wp2latex --apt-upgrade bbmap --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=openjdk-21/21.0.3~7ea-1 alsa-lib/1.2.11-1build1 at-spi2-core/2.51.90-3 cups/2.4.7-1.2ubuntu1 glib2.0/2.79.3-3ubuntu5 gnutls28/3.8.3-1.1ubuntu2 gtk+3.0/3.24.41-1.1ubuntu3 libpng1.6/1.6.43-3 nettle/3.9.1-2.2 wp2latex/4.4~ds-1build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-big --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-s390x-4.secgroup --name adt-noble-s390x-bbmap-20240322-004349-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 85s autopkgtest [00:45:14]: testbed dpkg architecture: s390x 85s autopkgtest [00:45:14]: testbed apt version: 2.7.12 85s autopkgtest [00:45:14]: @@@@@@@@@@@@@@@@@@@@ test bed setup 86s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 86s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 86s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [53.9 kB] 86s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [494 kB] 86s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3765 kB] 87s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [669 kB] 87s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 87s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 87s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 87s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [3987 kB] 87s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 87s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [45.1 kB] 87s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 90s Fetched 9150 kB in 2s (4089 kB/s) 90s Reading package lists... 92s Reading package lists... 92s Building dependency tree... 92s Reading state information... 93s Calculating upgrade... 93s The following packages will be REMOVED: 93s libglib2.0-0 93s The following NEW packages will be installed: 93s libglib2.0-0t64 xdg-user-dirs 93s The following packages will be upgraded: 93s cloud-init debianutils fonts-ubuntu-console gir1.2-glib-2.0 libglib2.0-data 93s python3-markupsafe 93s 6 upgraded, 2 newly installed, 1 to remove and 0 not upgraded. 93s Need to get 2530 kB of archives. 93s After this operation, 147 kB of additional disk space will be used. 93s Get:1 http://ftpmaster.internal/ubuntu noble/main s390x debianutils s390x 5.17 [90.1 kB] 93s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gir1.2-glib-2.0 s390x 2.79.3-3ubuntu5 [180 kB] 93s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libglib2.0-0t64 s390x 2.79.3-3ubuntu5 [1566 kB] 93s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 93s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x xdg-user-dirs s390x 0.18-1 [18.5 kB] 93s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x fonts-ubuntu-console all 0.869+git20240321-0ubuntu1 [18.7 kB] 93s Get:7 http://ftpmaster.internal/ubuntu noble/main s390x python3-markupsafe s390x 2.1.5-1build1 [12.8 kB] 93s Get:8 http://ftpmaster.internal/ubuntu noble/main s390x cloud-init all 24.1.2-0ubuntu1 [597 kB] 94s Preconfiguring packages ... 94s Fetched 2530 kB in 1s (3949 kB/s) 94s (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 ... 52171 files and directories currently installed.) 94s Preparing to unpack .../debianutils_5.17_s390x.deb ... 94s Unpacking debianutils (5.17) over (5.16) ... 94s Setting up debianutils (5.17) ... 94s (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 ... 52171 files and directories currently installed.) 94s Preparing to unpack .../gir1.2-glib-2.0_2.79.3-3ubuntu5_s390x.deb ... 94s Unpacking gir1.2-glib-2.0:s390x (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 94s dpkg: libglib2.0-0:s390x: dependency problems, but removing anyway as you requested: 94s udisks2 depends on libglib2.0-0 (>= 2.77.0). 94s shared-mime-info depends on libglib2.0-0 (>= 2.75.3). 94s s390-tools depends on libglib2.0-0 (>= 2.77.0). 94s python3-gi depends on libglib2.0-0 (>= 2.77.0). 94s python3-dbus depends on libglib2.0-0 (>= 2.16.0). 94s netplan.io depends on libglib2.0-0 (>= 2.70.0). 94s netplan-generator depends on libglib2.0-0 (>= 2.70.0). 94s libxmlb2:s390x depends on libglib2.0-0 (>= 2.54.0). 94s libvolume-key1:s390x depends on libglib2.0-0 (>= 2.18.0). 94s libudisks2-0:s390x depends on libglib2.0-0 (>= 2.75.3). 94s libqrtr-glib0:s390x depends on libglib2.0-0 (>= 2.56). 94s libqmi-proxy depends on libglib2.0-0 (>= 2.30.0). 94s libqmi-glib5:s390x depends on libglib2.0-0 (>= 2.54.0). 94s libpolkit-gobject-1-0:s390x depends on libglib2.0-0 (>= 2.38.0). 94s libpolkit-agent-1-0:s390x depends on libglib2.0-0 (>= 2.38.0). 94s libnetplan0:s390x depends on libglib2.0-0 (>= 2.75.3). 94s libmm-glib0:s390x depends on libglib2.0-0 (>= 2.62.0). 94s libmbim-proxy depends on libglib2.0-0 (>= 2.56). 94s libmbim-glib4:s390x depends on libglib2.0-0 (>= 2.56). 94s libjson-glib-1.0-0:s390x depends on libglib2.0-0 (>= 2.75.3). 94s libjcat1:s390x depends on libglib2.0-0 (>= 2.75.3). 94s libgusb2:s390x depends on libglib2.0-0 (>= 2.75.3). 94s libgudev-1.0-0:s390x depends on libglib2.0-0 (>= 2.38.0). 94s libgirepository-1.0-1:s390x depends on libglib2.0-0 (>= 2.79.0). 94s libfwupd2:s390x depends on libglib2.0-0 (>= 2.79.0). 94s libblockdev3:s390x depends on libglib2.0-0 (>= 2.42.2). 94s libblockdev-utils3:s390x depends on libglib2.0-0 (>= 2.75.3). 94s libblockdev-swap3:s390x depends on libglib2.0-0 (>= 2.42.2). 94s libblockdev-part3:s390x depends on libglib2.0-0 (>= 2.42.2). 94s libblockdev-nvme3:s390x depends on libglib2.0-0 (>= 2.42.2). 94s libblockdev-mdraid3:s390x depends on libglib2.0-0 (>= 2.42.2). 94s libblockdev-loop3:s390x depends on libglib2.0-0 (>= 2.42.2). 94s libblockdev-fs3:s390x depends on libglib2.0-0 (>= 2.42.2). 94s libblockdev-crypto3:s390x depends on libglib2.0-0 (>= 2.42.2). 94s fwupd depends on libglib2.0-0 (>= 2.79.0). 94s bolt depends on libglib2.0-0 (>= 2.56.0). 94s 94s (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 ... 52171 files and directories currently installed.) 94s Removing libglib2.0-0:s390x (2.79.2-1~ubuntu1) ... 94s Selecting previously unselected package libglib2.0-0t64:s390x. 94s (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 ... 52146 files and directories currently installed.) 94s Preparing to unpack .../0-libglib2.0-0t64_2.79.3-3ubuntu5_s390x.deb ... 94s libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:s390x.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled... 94s removed '/var/lib/dpkg/info/libglib2.0-0:s390x.postrm' 94s Unpacking libglib2.0-0t64:s390x (2.79.3-3ubuntu5) ... 94s Preparing to unpack .../1-libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 94s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 94s Selecting previously unselected package xdg-user-dirs. 94s Preparing to unpack .../2-xdg-user-dirs_0.18-1_s390x.deb ... 94s Unpacking xdg-user-dirs (0.18-1) ... 94s Preparing to unpack .../3-fonts-ubuntu-console_0.869+git20240321-0ubuntu1_all.deb ... 94s Unpacking fonts-ubuntu-console (0.869+git20240321-0ubuntu1) over (0.869-0ubuntu1) ... 94s Preparing to unpack .../4-python3-markupsafe_2.1.5-1build1_s390x.deb ... 94s Unpacking python3-markupsafe (2.1.5-1build1) over (2.1.5-1) ... 94s Preparing to unpack .../5-cloud-init_24.1.2-0ubuntu1_all.deb ... 94s Unpacking cloud-init (24.1.2-0ubuntu1) over (24.1.1-0ubuntu1) ... 95s Setting up fonts-ubuntu-console (0.869+git20240321-0ubuntu1) ... 95s Setting up cloud-init (24.1.2-0ubuntu1) ... 96s Setting up xdg-user-dirs (0.18-1) ... 96s Setting up python3-markupsafe (2.1.5-1build1) ... 96s Setting up libglib2.0-0t64:s390x (2.79.3-3ubuntu5) ... 96s No schema files found: doing nothing. 96s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 96s Setting up gir1.2-glib-2.0:s390x (2.79.3-3ubuntu5) ... 96s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 96s Processing triggers for man-db (2.12.0-3) ... 97s Processing triggers for libc-bin (2.39-0ubuntu2) ... 97s Reading package lists... 97s Building dependency tree... 97s Reading state information... 97s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 98s Unknown architecture, assuming PC-style ttyS0 98s sh: Attempting to set up Debian/Ubuntu apt sources automatically 98s sh: Distribution appears to be Ubuntu 99s Reading package lists... 99s Building dependency tree... 99s Reading state information... 99s eatmydata is already the newest version (131-1). 99s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 99s Reading package lists... 99s Building dependency tree... 99s Reading state information... 99s dbus is already the newest version (1.14.10-4ubuntu1). 99s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 99s Reading package lists... 99s Building dependency tree... 99s Reading state information... 100s rng-tools-debian is already the newest version (2.4). 100s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 100s Reading package lists... 100s Building dependency tree... 100s Reading state information... 100s The following packages will be REMOVED: 100s cloud-init* python3-configobj* python3-debconf* 100s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 100s After this operation, 3256 kB disk space will be freed. 100s (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 ... 52184 files and directories currently installed.) 100s Removing cloud-init (24.1.2-0ubuntu1) ... 100s Removing python3-configobj (5.0.8-3) ... 101s Removing python3-debconf (1.5.86) ... 101s Processing triggers for man-db (2.12.0-3) ... 101s (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 ... 51795 files and directories currently installed.) 101s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 101s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 101s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 101s invoke-rc.d: policy-rc.d denied execution of try-restart. 102s Reading package lists... 102s Building dependency tree... 102s Reading state information... 102s linux-generic is already the newest version (6.8.0-11.11+1). 102s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 102s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 102s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 103s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 104s Reading package lists... 104s Reading package lists... 104s Building dependency tree... 104s Reading state information... 104s Calculating upgrade... 104s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 105s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 105s autopkgtest [00:45:34]: rebooting testbed after setup commands that affected boot 122s autopkgtest [00:45:51]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 124s autopkgtest [00:45:53]: @@@@@@@@@@@@@@@@@@@@ apt-source bbmap 127s Get:1 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (dsc) [2286 B] 127s Get:2 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (tar) [5343 kB] 127s Get:3 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (diff) [25.4 kB] 127s gpgv: Signature made Fri Nov 24 11:00:29 2023 UTC 127s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 127s gpgv: issuer "emollier@debian.org" 127s gpgv: Can't check signature: No public key 127s dpkg-source: warning: cannot verify inline signature for ./bbmap_39.06+dfsg-1.dsc: no acceptable signature found 127s autopkgtest [00:45:56]: testing package bbmap version 39.06+dfsg-1 128s autopkgtest [00:45:57]: build not needed 129s autopkgtest [00:45:58]: test run-unit-test: preparing testbed 136s Reading package lists... 136s Building dependency tree... 136s Reading state information... 136s Starting pkgProblemResolver with broken count: 0 136s Starting 2 pkgProblemResolver with broken count: 0 136s Done 136s The following additional packages will be installed: 136s bbmap bbmap-jni ca-certificates-java fontconfig-config fonts-dejavu-core 136s fonts-dejavu-mono java-common libapache-pom-java libasound2 libasound2-data 136s libavahi-client3 libavahi-common-data libavahi-common3 libcommons-cli-java 136s libcommons-codec-java libcommons-io-java libcommons-parent-java libcups2 136s libfontconfig1 libfreetype6 libgraphite2-3 libharfbuzz0b libjpeg-turbo8 136s libjpeg8 liblcms2-2 liblog4j1.2-java libmpj-java libpcsclite1 136s openjdk-17-jre-headless python-biopython-doc 136s Suggested packages: 136s default-jre libasound2-plugins alsa-utils libcommons-io-java-doc cups-common 136s liblcms2-utils liblog4j1.2-java-doc libmail-java pcscd libnss-mdns 136s fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho 136s fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic 136s Recommended packages: 136s pigz alsa-ucm-conf alsa-topology-conf python3-biopython 136s The following NEW packages will be installed: 136s autopkgtest-satdep bbmap bbmap-jni ca-certificates-java fontconfig-config 136s fonts-dejavu-core fonts-dejavu-mono java-common libapache-pom-java 136s libasound2 libasound2-data libavahi-client3 libavahi-common-data 136s libavahi-common3 libcommons-cli-java libcommons-codec-java 136s libcommons-io-java libcommons-parent-java libcups2 libfontconfig1 136s libfreetype6 libgraphite2-3 libharfbuzz0b libjpeg-turbo8 libjpeg8 liblcms2-2 136s liblog4j1.2-java libmpj-java libpcsclite1 openjdk-17-jre-headless 136s python-biopython-doc 136s 0 upgraded, 31 newly installed, 0 to remove and 0 not upgraded. 136s Need to get 78.1 MB/78.1 MB of archives. 136s After this operation, 226 MB of additional disk space will be used. 136s Get:1 /tmp/autopkgtest.0dfONK/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [724 B] 137s Get:2 http://ftpmaster.internal/ubuntu noble/universe s390x libcommons-cli-java all 1.6.0-1 [59.9 kB] 137s Get:3 http://ftpmaster.internal/ubuntu noble/universe s390x libapache-pom-java all 29-2 [5284 B] 137s Get:4 http://ftpmaster.internal/ubuntu noble/universe s390x libcommons-parent-java all 56-1 [10.7 kB] 137s Get:5 http://ftpmaster.internal/ubuntu noble/universe s390x libcommons-codec-java all 1.16.0-1 [306 kB] 137s Get:6 http://ftpmaster.internal/ubuntu noble/universe s390x libcommons-io-java all 2.11.0-2 [297 kB] 137s Get:7 http://ftpmaster.internal/ubuntu noble/universe s390x liblog4j1.2-java all 1.2.17-11 [439 kB] 137s Get:8 http://ftpmaster.internal/ubuntu noble/universe s390x libmpj-java all 0.44+dfsg-4 [443 kB] 137s Get:9 http://ftpmaster.internal/ubuntu noble/main s390x ca-certificates-java all 20240118 [11.6 kB] 137s Get:10 http://ftpmaster.internal/ubuntu noble/main s390x java-common all 0.75+exp1 [6798 B] 137s Get:11 http://ftpmaster.internal/ubuntu noble/main s390x libavahi-common-data s390x 0.8-13ubuntu2 [29.5 kB] 137s Get:12 http://ftpmaster.internal/ubuntu noble/main s390x libavahi-common3 s390x 0.8-13ubuntu2 [23.8 kB] 137s Get:13 http://ftpmaster.internal/ubuntu noble/main s390x libavahi-client3 s390x 0.8-13ubuntu2 [26.7 kB] 137s Get:14 http://ftpmaster.internal/ubuntu noble/main s390x libcups2 s390x 2.4.6-0ubuntu3 [277 kB] 137s Get:15 http://ftpmaster.internal/ubuntu noble/main s390x liblcms2-2 s390x 2.14-2 [155 kB] 137s Get:16 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg-turbo8 s390x 2.1.5-2ubuntu1 [128 kB] 137s Get:17 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 137s Get:18 http://ftpmaster.internal/ubuntu noble/main s390x libfreetype6 s390x 2.13.2+dfsg-1 [431 kB] 137s Get:19 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 137s Get:20 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 137s Get:21 http://ftpmaster.internal/ubuntu noble/main s390x fontconfig-config s390x 2.15.0-1ubuntu1 [37.0 kB] 137s Get:22 http://ftpmaster.internal/ubuntu noble/main s390x libfontconfig1 s390x 2.15.0-1ubuntu1 [150 kB] 137s Get:23 http://ftpmaster.internal/ubuntu noble/main s390x libasound2-data all 1.2.10-3build1 [20.7 kB] 137s Get:24 http://ftpmaster.internal/ubuntu noble/main s390x libasound2 s390x 1.2.10-3build1 [414 kB] 137s Get:25 http://ftpmaster.internal/ubuntu noble/main s390x libgraphite2-3 s390x 1.3.14-2 [90.4 kB] 137s Get:26 http://ftpmaster.internal/ubuntu noble/main s390x libharfbuzz0b s390x 8.3.0-2 [515 kB] 137s Get:27 http://ftpmaster.internal/ubuntu noble/main s390x libpcsclite1 s390x 2.0.0-1 [19.9 kB] 137s Get:28 http://ftpmaster.internal/ubuntu noble/main s390x openjdk-17-jre-headless s390x 17.0.10+7-1 [45.7 MB] 139s Get:29 http://ftpmaster.internal/ubuntu noble/universe s390x bbmap all 39.06+dfsg-1 [9768 kB] 139s Get:30 http://ftpmaster.internal/ubuntu noble/universe s390x bbmap-jni s390x 39.06+dfsg-1 [38.7 kB] 139s Get:31 http://ftpmaster.internal/ubuntu noble/universe s390x python-biopython-doc all 1.81+dfsg-3 [17.3 MB] 140s Fetched 78.1 MB in 3s (25.6 MB/s) 140s Selecting previously unselected package libcommons-cli-java. 140s (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 ... 51740 files and directories currently installed.) 140s Preparing to unpack .../00-libcommons-cli-java_1.6.0-1_all.deb ... 140s Unpacking libcommons-cli-java (1.6.0-1) ... 140s Selecting previously unselected package libapache-pom-java. 140s Preparing to unpack .../01-libapache-pom-java_29-2_all.deb ... 140s Unpacking libapache-pom-java (29-2) ... 140s Selecting previously unselected package libcommons-parent-java. 140s Preparing to unpack .../02-libcommons-parent-java_56-1_all.deb ... 140s Unpacking libcommons-parent-java (56-1) ... 140s Selecting previously unselected package libcommons-codec-java. 140s Preparing to unpack .../03-libcommons-codec-java_1.16.0-1_all.deb ... 140s Unpacking libcommons-codec-java (1.16.0-1) ... 140s Selecting previously unselected package libcommons-io-java. 140s Preparing to unpack .../04-libcommons-io-java_2.11.0-2_all.deb ... 140s Unpacking libcommons-io-java (2.11.0-2) ... 140s Selecting previously unselected package liblog4j1.2-java. 140s Preparing to unpack .../05-liblog4j1.2-java_1.2.17-11_all.deb ... 140s Unpacking liblog4j1.2-java (1.2.17-11) ... 140s Selecting previously unselected package libmpj-java. 140s Preparing to unpack .../06-libmpj-java_0.44+dfsg-4_all.deb ... 140s Unpacking libmpj-java (0.44+dfsg-4) ... 140s Selecting previously unselected package ca-certificates-java. 140s Preparing to unpack .../07-ca-certificates-java_20240118_all.deb ... 140s Unpacking ca-certificates-java (20240118) ... 140s Selecting previously unselected package java-common. 140s Preparing to unpack .../08-java-common_0.75+exp1_all.deb ... 140s Unpacking java-common (0.75+exp1) ... 140s Selecting previously unselected package libavahi-common-data:s390x. 140s Preparing to unpack .../09-libavahi-common-data_0.8-13ubuntu2_s390x.deb ... 140s Unpacking libavahi-common-data:s390x (0.8-13ubuntu2) ... 140s Selecting previously unselected package libavahi-common3:s390x. 140s Preparing to unpack .../10-libavahi-common3_0.8-13ubuntu2_s390x.deb ... 140s Unpacking libavahi-common3:s390x (0.8-13ubuntu2) ... 140s Selecting previously unselected package libavahi-client3:s390x. 140s Preparing to unpack .../11-libavahi-client3_0.8-13ubuntu2_s390x.deb ... 140s Unpacking libavahi-client3:s390x (0.8-13ubuntu2) ... 140s Selecting previously unselected package libcups2:s390x. 140s Preparing to unpack .../12-libcups2_2.4.6-0ubuntu3_s390x.deb ... 140s Unpacking libcups2:s390x (2.4.6-0ubuntu3) ... 140s Selecting previously unselected package liblcms2-2:s390x. 140s Preparing to unpack .../13-liblcms2-2_2.14-2_s390x.deb ... 140s Unpacking liblcms2-2:s390x (2.14-2) ... 140s Selecting previously unselected package libjpeg-turbo8:s390x. 140s Preparing to unpack .../14-libjpeg-turbo8_2.1.5-2ubuntu1_s390x.deb ... 140s Unpacking libjpeg-turbo8:s390x (2.1.5-2ubuntu1) ... 140s Selecting previously unselected package libjpeg8:s390x. 140s Preparing to unpack .../15-libjpeg8_8c-2ubuntu11_s390x.deb ... 140s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 140s Selecting previously unselected package libfreetype6:s390x. 140s Preparing to unpack .../16-libfreetype6_2.13.2+dfsg-1_s390x.deb ... 140s Unpacking libfreetype6:s390x (2.13.2+dfsg-1) ... 140s Selecting previously unselected package fonts-dejavu-mono. 140s Preparing to unpack .../17-fonts-dejavu-mono_2.37-8_all.deb ... 140s Unpacking fonts-dejavu-mono (2.37-8) ... 140s Selecting previously unselected package fonts-dejavu-core. 140s Preparing to unpack .../18-fonts-dejavu-core_2.37-8_all.deb ... 140s Unpacking fonts-dejavu-core (2.37-8) ... 140s Selecting previously unselected package fontconfig-config. 140s Preparing to unpack .../19-fontconfig-config_2.15.0-1ubuntu1_s390x.deb ... 140s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 140s Selecting previously unselected package libfontconfig1:s390x. 140s Preparing to unpack .../20-libfontconfig1_2.15.0-1ubuntu1_s390x.deb ... 140s Unpacking libfontconfig1:s390x (2.15.0-1ubuntu1) ... 140s Selecting previously unselected package libasound2-data. 140s Preparing to unpack .../21-libasound2-data_1.2.10-3build1_all.deb ... 140s Unpacking libasound2-data (1.2.10-3build1) ... 140s Selecting previously unselected package libasound2:s390x. 140s Preparing to unpack .../22-libasound2_1.2.10-3build1_s390x.deb ... 140s Unpacking libasound2:s390x (1.2.10-3build1) ... 141s Selecting previously unselected package libgraphite2-3:s390x. 141s Preparing to unpack .../23-libgraphite2-3_1.3.14-2_s390x.deb ... 141s Unpacking libgraphite2-3:s390x (1.3.14-2) ... 141s Selecting previously unselected package libharfbuzz0b:s390x. 141s Preparing to unpack .../24-libharfbuzz0b_8.3.0-2_s390x.deb ... 141s Unpacking libharfbuzz0b:s390x (8.3.0-2) ... 141s Selecting previously unselected package libpcsclite1:s390x. 141s Preparing to unpack .../25-libpcsclite1_2.0.0-1_s390x.deb ... 141s Unpacking libpcsclite1:s390x (2.0.0-1) ... 141s Selecting previously unselected package openjdk-17-jre-headless:s390x. 141s Preparing to unpack .../26-openjdk-17-jre-headless_17.0.10+7-1_s390x.deb ... 141s Unpacking openjdk-17-jre-headless:s390x (17.0.10+7-1) ... 142s Selecting previously unselected package bbmap. 142s Preparing to unpack .../27-bbmap_39.06+dfsg-1_all.deb ... 142s Unpacking bbmap (39.06+dfsg-1) ... 142s Selecting previously unselected package bbmap-jni. 142s Preparing to unpack .../28-bbmap-jni_39.06+dfsg-1_s390x.deb ... 142s Unpacking bbmap-jni (39.06+dfsg-1) ... 142s Selecting previously unselected package python-biopython-doc. 142s Preparing to unpack .../29-python-biopython-doc_1.81+dfsg-3_all.deb ... 142s Unpacking python-biopython-doc (1.81+dfsg-3) ... 142s Selecting previously unselected package autopkgtest-satdep. 142s Preparing to unpack .../30-1-autopkgtest-satdep.deb ... 142s Unpacking autopkgtest-satdep (0) ... 142s Setting up libgraphite2-3:s390x (1.3.14-2) ... 142s Setting up liblcms2-2:s390x (2.14-2) ... 142s Setting up java-common (0.75+exp1) ... 142s Setting up libcommons-cli-java (1.6.0-1) ... 142s Setting up liblog4j1.2-java (1.2.17-11) ... 142s Setting up libasound2-data (1.2.10-3build1) ... 142s Setting up libfreetype6:s390x (2.13.2+dfsg-1) ... 142s Setting up libapache-pom-java (29-2) ... 142s Setting up libavahi-common-data:s390x (0.8-13ubuntu2) ... 142s Setting up fonts-dejavu-mono (2.37-8) ... 142s Setting up fonts-dejavu-core (2.37-8) ... 142s Setting up libpcsclite1:s390x (2.0.0-1) ... 142s Setting up libjpeg-turbo8:s390x (2.1.5-2ubuntu1) ... 142s Setting up python-biopython-doc (1.81+dfsg-3) ... 142s Setting up libasound2:s390x (1.2.10-3build1) ... 142s Setting up libharfbuzz0b:s390x (8.3.0-2) ... 142s Setting up bbmap-jni (39.06+dfsg-1) ... 142s Setting up ca-certificates-java (20240118) ... 142s No JRE found. Skipping Java certificates setup. 142s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 142s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 142s Setting up libcommons-parent-java (56-1) ... 142s Setting up libavahi-common3:s390x (0.8-13ubuntu2) ... 142s Setting up libfontconfig1:s390x (2.15.0-1ubuntu1) ... 142s Setting up libcommons-codec-java (1.16.0-1) ... 142s Setting up libavahi-client3:s390x (0.8-13ubuntu2) ... 142s Setting up libcommons-io-java (2.11.0-2) ... 142s Setting up libmpj-java (0.44+dfsg-4) ... 142s Setting up libcups2:s390x (2.4.6-0ubuntu3) ... 142s Setting up openjdk-17-jre-headless:s390x (17.0.10+7-1) ... 142s update-alternatives: using /usr/lib/jvm/java-17-openjdk-s390x/bin/java to provide /usr/bin/java (java) in auto mode 142s update-alternatives: using /usr/lib/jvm/java-17-openjdk-s390x/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 142s update-alternatives: using /usr/lib/jvm/java-17-openjdk-s390x/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 142s update-alternatives: using /usr/lib/jvm/java-17-openjdk-s390x/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 142s update-alternatives: using /usr/lib/jvm/java-17-openjdk-s390x/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 142s Processing triggers for libc-bin (2.39-0ubuntu2) ... 142s Processing triggers for man-db (2.12.0-3) ... 143s Processing triggers for ca-certificates-java (20240118) ... 143s Adding debian:ACCVRAIZ1.pem 143s Adding debian:AC_RAIZ_FNMT-RCM.pem 143s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 143s Adding debian:ANF_Secure_Server_Root_CA.pem 143s Adding debian:Actalis_Authentication_Root_CA.pem 143s Adding debian:AffirmTrust_Commercial.pem 143s Adding debian:AffirmTrust_Networking.pem 143s Adding debian:AffirmTrust_Premium.pem 143s Adding debian:AffirmTrust_Premium_ECC.pem 143s Adding debian:Amazon_Root_CA_1.pem 143s Adding debian:Amazon_Root_CA_2.pem 143s Adding debian:Amazon_Root_CA_3.pem 143s Adding debian:Amazon_Root_CA_4.pem 143s Adding debian:Atos_TrustedRoot_2011.pem 143s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 143s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 143s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 143s Adding debian:BJCA_Global_Root_CA1.pem 143s Adding debian:BJCA_Global_Root_CA2.pem 143s Adding debian:Baltimore_CyberTrust_Root.pem 143s Adding debian:Buypass_Class_2_Root_CA.pem 143s Adding debian:Buypass_Class_3_Root_CA.pem 143s Adding debian:CA_Disig_Root_R2.pem 143s Adding debian:CFCA_EV_ROOT.pem 143s Adding debian:COMODO_Certification_Authority.pem 143s Adding debian:COMODO_ECC_Certification_Authority.pem 143s Adding debian:COMODO_RSA_Certification_Authority.pem 143s Adding debian:Certainly_Root_E1.pem 143s Adding debian:Certainly_Root_R1.pem 143s Adding debian:Certigna.pem 143s Adding debian:Certigna_Root_CA.pem 143s Adding debian:Certum_EC-384_CA.pem 143s Adding debian:Certum_Trusted_Network_CA.pem 143s Adding debian:Certum_Trusted_Network_CA_2.pem 143s Adding debian:Certum_Trusted_Root_CA.pem 143s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 143s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 143s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 143s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 143s Adding debian:Comodo_AAA_Services_root.pem 143s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 143s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 143s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 143s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 143s Adding debian:DigiCert_Assured_ID_Root_CA.pem 143s Adding debian:DigiCert_Assured_ID_Root_G2.pem 143s Adding debian:DigiCert_Assured_ID_Root_G3.pem 143s Adding debian:DigiCert_Global_Root_CA.pem 143s Adding debian:DigiCert_Global_Root_G2.pem 143s Adding debian:DigiCert_Global_Root_G3.pem 143s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 143s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 143s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 143s Adding debian:DigiCert_Trusted_Root_G4.pem 143s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 143s Adding debian:Entrust_Root_Certification_Authority.pem 143s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 143s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 143s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem 143s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 143s Adding debian:GLOBALTRUST_2020.pem 143s Adding debian:GTS_Root_R1.pem 143s Adding debian:GTS_Root_R2.pem 143s Adding debian:GTS_Root_R3.pem 143s Adding debian:GTS_Root_R4.pem 143s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 143s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 143s Adding debian:GlobalSign_Root_CA.pem 143s Adding debian:GlobalSign_Root_CA_-_R3.pem 143s Adding debian:GlobalSign_Root_CA_-_R6.pem 143s Adding debian:GlobalSign_Root_E46.pem 143s Adding debian:GlobalSign_Root_R46.pem 143s Adding debian:Go_Daddy_Class_2_CA.pem 143s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 143s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 143s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 143s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 143s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 143s Adding debian:HiPKI_Root_CA_-_G1.pem 143s Adding debian:Hongkong_Post_Root_CA_3.pem 143s Adding debian:ISRG_Root_X1.pem 143s Adding debian:ISRG_Root_X2.pem 143s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 143s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 143s Adding debian:Izenpe.com.pem 143s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 143s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 143s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 143s Adding debian:NAVER_Global_Root_Certification_Authority.pem 143s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 143s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 143s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 143s Adding debian:QuoVadis_Root_CA_1_G3.pem 143s Adding debian:QuoVadis_Root_CA_2.pem 143s Adding debian:QuoVadis_Root_CA_2_G3.pem 143s Adding debian:QuoVadis_Root_CA_3.pem 143s Adding debian:QuoVadis_Root_CA_3_G3.pem 143s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 143s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 143s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 143s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 143s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 143s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 143s Adding debian:SZAFIR_ROOT_CA2.pem 143s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 143s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 143s Adding debian:SecureSign_RootCA11.pem 143s Adding debian:SecureTrust_CA.pem 143s Adding debian:Secure_Global_CA.pem 143s Adding debian:Security_Communication_ECC_RootCA1.pem 143s Adding debian:Security_Communication_RootCA2.pem 143s Adding debian:Security_Communication_RootCA3.pem 143s Adding debian:Security_Communication_Root_CA.pem 143s Adding debian:Starfield_Class_2_CA.pem 143s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 143s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 143s Adding debian:SwissSign_Gold_CA_-_G2.pem 143s Adding debian:SwissSign_Silver_CA_-_G2.pem 143s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 143s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 143s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 143s Adding debian:TWCA_Global_Root_CA.pem 143s Adding debian:TWCA_Root_Certification_Authority.pem 143s Adding debian:TeliaSonera_Root_CA_v1.pem 143s Adding debian:Telia_Root_CA_v2.pem 143s Adding debian:TrustAsia_Global_Root_CA_G3.pem 143s Adding debian:TrustAsia_Global_Root_CA_G4.pem 143s Adding debian:Trustwave_Global_Certification_Authority.pem 143s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 143s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 143s Adding debian:TunTrust_Root_CA.pem 143s Adding debian:UCA_Extended_Validation_Root.pem 143s Adding debian:UCA_Global_G2_Root.pem 143s Adding debian:USERTrust_ECC_Certification_Authority.pem 143s Adding debian:USERTrust_RSA_Certification_Authority.pem 143s Adding debian:XRamp_Global_CA_Root.pem 143s Adding debian:certSIGN_ROOT_CA.pem 143s Adding debian:certSIGN_Root_CA_G2.pem 143s Adding debian:e-Szigno_Root_CA_2017.pem 143s Adding debian:ePKI_Root_Certification_Authority.pem 143s Adding debian:emSign_ECC_Root_CA_-_C3.pem 143s Adding debian:emSign_ECC_Root_CA_-_G3.pem 143s Adding debian:emSign_Root_CA_-_C1.pem 143s Adding debian:emSign_Root_CA_-_G1.pem 143s Adding debian:vTrus_ECC_Root_CA.pem 143s Adding debian:vTrus_Root_CA.pem 143s done. 143s Setting up bbmap (39.06+dfsg-1) ... 143s Setting up autopkgtest-satdep (0) ... 146s (Reading database ... 54582 files and directories currently installed.) 146s Removing autopkgtest-satdep (0) ... 147s autopkgtest [00:46:16]: test run-unit-test: [----------------------- 147s 147s # bbmap 147s bbmap.sh --version 147s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 147s java -ea -Xmx2844m -Xms2844m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 --version 147s BBMap version 39.06 147s For help, please run the shellscript with no parameters, or look in /docs/. 147s bbmap.sh --help 147s 147s BBMap 147s Written by Brian Bushnell, from Dec. 2010 - present 147s Last modified September 15, 2022 147s 147s Description: Fast and accurate splice-aware read aligner. 147s Please read bbmap/docs/guides/BBMapGuide.txt for more information. 147s 147s To index: bbmap.sh ref= 147s To map: bbmap.sh in= out= 147s To map without writing an index: 147s bbmap.sh ref= in= out= nodisk 147s 147s in=stdin will accept reads from standard in, and out=stdout will write to 147s standard out, but file extensions are still needed to specify the format of the 147s input and output files e.g. in=stdin.fa.gz will read gzipped fasta from 147s standard in; out=stdout.sam.gz will write gzipped sam. 147s 147s Indexing Parameters (required when building the index): 147s nodisk=f Set to true to build index in memory and write nothing 147s to disk except output. 147s ref= Specify the reference sequence. Only do this ONCE, 147s when building the index (unless using 'nodisk'). 147s build=1 If multiple references are indexed in the same directory, 147s each needs a unique numeric ID (unless using 'nodisk'). 147s k=13 Kmer length, range 8-15. Longer is faster but uses 147s more memory. Shorter is more sensitive. 147s If indexing and mapping are done in two steps, K should 147s be specified each time. 147s path=<.> Specify the location to write the index, if you don't 147s want it in the current working directory. 147s usemodulo=f Throw away ~80% of kmers based on remainder modulo a 147s number (reduces RAM by 50% and sensitivity slightly). 147s Should be enabled both when building the index AND 147s when mapping. 147s rebuild=f Force a rebuild of the index (ref= should be set). 147s 147s Input Parameters: 147s build=1 Designate index to use. Corresponds to the number 147s specified when building the index. 147s in= Primary reads input; required parameter. 147s in2= For paired reads in two files. 147s interleaved=auto True forces paired/interleaved input; false forces 147s single-ended mapping. If not specified, interleaved 147s status will be autodetected from read names. 147s fastareadlen=500 Break up FASTA reads longer than this. Max is 500 for 147s BBMap and 6000 for BBMapPacBio. Only works for FASTA 147s input (use 'maxlen' for FASTQ input). The default for 147s bbmap.sh is 500, and for mapPacBio.sh is 6000. 147s unpigz=f Spawn a pigz (parallel gzip) process for faster 147s decompression than using Java. 147s Requires pigz to be installed. 147s touppercase=t (tuc) Convert lowercase letters in reads to upper case 147s (otherwise they will not match the reference). 147s 147s Sampling Parameters: 147s 147s reads=-1 Set to a positive number N to only process the first N 147s reads (or pairs), then quit. -1 means use all reads. 147s samplerate=1 Set to a number from 0 to 1 to randomly select that 147s fraction of reads for mapping. 1 uses all reads. 147s skipreads=0 Set to a number N to skip the first N reads (or pairs), 147s then map the rest. 147s 147s Mapping Parameters: 147s fast=f This flag is a macro which sets other paramters to run 147s faster, at reduced sensitivity. Bad for RNA-seq. 147s slow=f This flag is a macro which sets other paramters to run 147s slower, at greater sensitivity. 'vslow' is even slower. 147s maxindel=16000 Don't look for indels longer than this. Lower is faster. 147s Set to >=100k for RNAseq with long introns like mammals. 147s strictmaxindel=f When enabled, do not allow indels longer than 'maxindel'. 147s By default these are not sought, but may be found anyway. 147s tipsearch=100 Look this far for read-end deletions with anchors 147s shorter than K, using brute force. 147s minid=0.76 Approximate minimum alignment identity to look for. 147s Higher is faster and less sensitive. 147s minhits=1 Minimum number of seed hits required for candidate sites. 147s Higher is faster. 147s local=f Set to true to use local, rather than global, alignments. 147s This will soft-clip ugly ends of poor alignments. 147s perfectmode=f Allow only perfect mappings when set to true (very fast). 147s semiperfectmode=f Allow only perfect and semiperfect (perfect except for 147s N's in the reference) mappings. 147s threads=auto (t) Set to number of threads desired. By default, uses 147s all cores available. 147s ambiguous=best (ambig) Set behavior on ambiguously-mapped reads (with 147s multiple top-scoring mapping locations). 147s best (use the first best site) 147s toss (consider unmapped) 147s random (select one top-scoring site randomly) 147s all (retain all top-scoring sites) 147s samestrandpairs=f (ssp) Specify whether paired reads should map to the 147s same strand or opposite strands. 147s requirecorrectstrand=t (rcs) Forbid pairing of reads without correct strand 147s orientation. Set to false for long-mate-pair libraries. 147s killbadpairs=f (kbp) If a read pair is mapped with an inappropriate 147s insert size or orientation, the read with the lower 147s mapping quality is marked unmapped. 147s pairedonly=f (po) Treat unpaired reads as unmapped. Thus they will 147s be sent to 'outu' but not 'outm'. 147s rcomp=f Reverse complement both reads prior to mapping (for LMP 147s outward-facing libraries). 147s rcompmate=f Reverse complement read2 prior to mapping. 147s pairlen=32000 Set max allowed distance between paired reads. 147s (insert size)=(pairlen)+(read1 length)+(read2 length) 147s rescuedist=1200 Don't try to rescue paired reads if avg. insert size 147s greater than this. Lower is faster. 147s rescuemismatches=32 Maximum mismatches allowed in a rescued read. Lower 147s is faster. 147s averagepairdist=100 (apd) Initial average distance between paired reads. 147s Varies dynamically; does not need to be specified. 147s deterministic=f Run in deterministic mode. In this case it is good 147s to set averagepairdist. BBMap is deterministic 147s without this flag if using single-ended reads, 147s or run singlethreaded. 147s bandwidthratio=0 (bwr) If above zero, restrict alignment band to this 147s fraction of read length. Faster but less accurate. 147s bandwidth=0 (bw) Set the bandwidth directly. 147s fraction of read length. Faster but less accurate. 147s usejni=f (jni) Do alignments faster, in C code. Requires 147s compiling the C code; details are in /jni/README.txt. 147s maxsites2=800 Don't analyze (or print) more than this many alignments 147s per read. 147s ignorefrequentkmers=t (ifk) Discard low-information kmers that occur often. 147s excludefraction=0.03 (ef) Fraction of kmers to ignore. For example, 0.03 147s will ignore the most common 3% of kmers. 147s greedy=t Use a greedy algorithm to discard the least-useful 147s kmers on a per-read basis. 147s kfilter=0 If positive, potential mapping sites must have at 147s least this many consecutive exact matches. 147s 147s 147s Quality and Trimming Parameters: 147s qin=auto Set to 33 or 64 to specify input quality value ASCII 147s offset. 33 is Sanger, 64 is old Solexa. 147s qout=auto Set to 33 or 64 to specify output quality value ASCII 147s offset (only if output format is fastq). 147s qtrim=f Quality-trim ends before mapping. Options are: 147s 'f' (false), 'l' (left), 'r' (right), and 'lr' (both). 147s untrim=f Undo trimming after mapping. Untrimmed bases will be 147s soft-clipped in cigar strings. 147s trimq=6 Trim regions with average quality below this 147s (phred algorithm). 147s mintrimlength=60 (mintl) Don't trim reads to be shorter than this. 147s fakefastaquality=-1 (ffq) Set to a positive number 1-50 to generate fake 147s quality strings for fasta input reads. 147s ignorebadquality=f (ibq) Keep going, rather than crashing, if a read has 147s out-of-range quality values. 147s usequality=t Use quality scores when determining which read kmers 147s to use as seeds. 147s minaveragequality=0 (maq) Do not map reads with average quality below this. 147s maqb=0 If positive, calculate maq from this many initial bases. 147s 147s Output Parameters: 147s out= Write all reads to this file. 147s outu= Write only unmapped reads to this file. Does not 147s include unmapped paired reads with a mapped mate. 147s outm= Write only mapped reads to this file. Includes 147s unmapped paired reads with a mapped mate. 147s mappedonly=f If true, treats 'out' like 'outm'. 147s bamscript= (bs) Write a shell script to that will turn 147s the sam output into a sorted, indexed bam file. 147s ordered=f Set to true to output reads in same order as input. 147s Slower and uses more memory. 147s overwrite=f (ow) Allow process to overwrite existing files. 147s secondary=f Print secondary alignments. 147s sssr=0.95 (secondarysitescoreratio) Print only secondary alignments 147s with score of at least this fraction of primary. 147s ssao=f (secondarysiteasambiguousonly) Only print secondary 147s alignments for ambiguously-mapped reads. 147s maxsites=5 Maximum number of total alignments to print per read. 147s Only relevant when secondary=t. 147s quickmatch=f Generate cigar strings more quickly. 147s trimreaddescriptions=f (trd) Truncate read and ref names at the first whitespace, 147s assuming that the remainder is a comment or description. 147s ziplevel=2 (zl) Compression level for zip or gzip output. 147s pigz=f Spawn a pigz (parallel gzip) process for faster 147s compression than Java. Requires pigz to be installed. 147s machineout=f Set to true to output statistics in machine-friendly 147s 'key=value' format. 147s printunmappedcount=f Print the total number of unmapped reads and bases. 147s If input is paired, the number will be of pairs 147s for which both reads are unmapped. 147s showprogress=0 If positive, print a '.' every X reads. 147s showprogress2=0 If positive, print the number of seconds since the 147s last progress update (instead of a '.'). 147s renamebyinsert=f Renames reads based on their mapped insert size. 147s 147s Bloom-Filtering Parameters (bloomfilter.sh is the standalone version). 147s bloom=f Use a Bloom filter to ignore reads not sharing kmers 147s with the reference. This uses more memory, but speeds 147s mapping when most reads don't match the reference. 147s bloomhashes=2 Number of hash functions. 147s bloomminhits=3 Number of consecutive hits to be considered matched. 147s bloomk=31 Bloom filter kmer length. 147s bloomserial=t Use the serialized Bloom filter for greater loading 147s speed, if available. If not, generate and write one. 147s 147s Post-Filtering Parameters: 147s idfilter=0 Independant of minid; sets exact minimum identity 147s allowed for alignments to be printed. Range 0 to 1. 147s subfilter=-1 Ban alignments with more than this many substitutions. 147s insfilter=-1 Ban alignments with more than this many insertions. 147s delfilter=-1 Ban alignments with more than this many deletions. 147s indelfilter=-1 Ban alignments with more than this many indels. 147s editfilter=-1 Ban alignments with more than this many edits. 147s inslenfilter=-1 Ban alignments with an insertion longer than this. 147s dellenfilter=-1 Ban alignments with a deletion longer than this. 147s nfilter=-1 Ban alignments with more than this many ns. This 147s includes nocall, noref, and off scaffold ends. 147s 147s Sam flags and settings: 147s noheader=f Disable generation of header lines. 147s sam=1.4 Set to 1.4 to write Sam version 1.4 cigar strings, 147s with = and X, or 1.3 to use M. 147s saa=t (secondaryalignmentasterisks) Use asterisks instead of 147s bases for sam secondary alignments. 147s cigar=t Set to 'f' to skip generation of cigar strings (faster). 147s keepnames=f Keep original names of paired reads, rather than 147s ensuring both reads have the same name. 147s intronlen=999999999 Set to a lower number like 10 to change 'D' to 'N' in 147s cigar strings for deletions of at least that length. 147s rgid= Set readgroup ID. All other readgroup fields 147s can be set similarly, with the flag rgXX= 147s If you set a readgroup flag to the word 'filename', 147s e.g. rgid=filename, the input file name will be used. 147s mdtag=f Write MD tags. 147s nhtag=f Write NH tags. 147s xmtag=f Write XM tags (may only work correctly with ambig=all). 147s amtag=f Write AM tags. 147s nmtag=f Write NM tags. 147s xstag=f Set to 'xs=fs', 'xs=ss', or 'xs=us' to write XS tags 147s for RNAseq using firststrand, secondstrand, or 147s unstranded libraries. Needed by Cufflinks. 147s JGI mainly uses 'firststrand'. 147s stoptag=f Write a tag indicating read stop location, prefixed by YS:i: 147s lengthtag=f Write a tag indicating (query,ref) alignment lengths, 147s prefixed by YL:Z: 147s idtag=f Write a tag indicating percent identity, prefixed by YI:f: 147s inserttag=f Write a tag indicating insert size, prefixed by X8:Z: 147s scoretag=f Write a tag indicating BBMap's raw score, prefixed by YR:i: 147s timetag=f Write a tag indicating this read's mapping time, prefixed by X0:i: 147s boundstag=f Write a tag indicating whether either read in the pair 147s goes off the end of the reference, prefixed by XB:Z: 147s notags=f Turn off all optional tags. 147s 147s Histogram and statistics output parameters: 147s scafstats= Statistics on how many reads mapped to which scaffold. 147s refstats= Statistics on how many reads mapped to which reference 147s file; only for BBSplit. 147s sortscafs=t Sort scaffolds or references by read count. 147s bhist= Base composition histogram by position. 147s qhist= Quality histogram by position. 147s aqhist= Histogram of average read quality. 147s bqhist= Quality histogram designed for box plots. 147s lhist= Read length histogram. 147s ihist= Write histogram of insert sizes (for paired reads). 147s ehist= Errors-per-read histogram. 147s qahist= Quality accuracy histogram of error rates versus 147s quality score. 147s indelhist= Indel length histogram. 147s mhist= Histogram of match, sub, del, and ins rates by 147s read location. 147s gchist= Read GC content histogram. 147s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 147s gcpairs=t Use average GC of paired reads. 147s idhist= Histogram of read count versus percent identity. 147s idbins=100 Number idhist bins. Set to 'auto' to use read length. 147s statsfile=stderr Mapping statistics are printed here. 147s 147s Coverage output parameters (these may reduce speed and use more RAM): 147s covstats= Per-scaffold coverage info. 147s rpkm= Per-scaffold RPKM/FPKM counts. 147s covhist= Histogram of # occurrences of each depth level. 147s basecov= Coverage per base location. 147s bincov= Print binned coverage per location (one line per X bases). 147s covbinsize=1000 Set the binsize for binned coverage output. 147s nzo=t Only print scaffolds with nonzero coverage. 147s twocolumn=f Change to true to print only ID and Avg_fold instead of 147s all 6 columns to the 'out=' file. 147s 32bit=f Set to true if you need per-base coverage over 64k. 147s strandedcov=f Track coverage for plus and minus strand independently. 147s startcov=f Only track start positions of reads. 147s secondarycov=t Include coverage of secondary alignments. 147s physcov=f Calculate physical coverage for paired reads. 147s This includes the unsequenced bases. 147s delcoverage=t (delcov) Count bases covered by deletions as covered. 147s True is faster than false. 147s covk=0 If positive, calculate kmer coverage statistics. 147s 147s Java Parameters: 147s -Xmx This will set Java's memory usage, 147s overriding autodetection. 147s -Xmx20g will specify 20 gigs of RAM, and -Xmx800m 147s will specify 800 megs. The max is typically 85% of 147s physical memory. The human genome requires around 24g, 147s or 12g with the 'usemodulo' flag. The index uses 147s roughly 6 bytes per reference base. 147s -eoom This flag will cause the process to exit if an 147s out-of-memory exception occurs. Requires Java 8u92+. 147s -da Disable assertions. 147s 147s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter 147s any problems, or post at: http://seqanswers.com/forums/showthread.php?t=41057 147s 147s bbmap.sh ref=example.fasta 147s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 147s java -ea -Xmx2844m -Xms2844m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta 147s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta] 147s Version 39.06 147s 147s No output file. 147s Writing reference. 147s 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] 147s 147s Set genScaffoldInfo=true 147s Writing chunk 1 147s Set genome to 1 147s 147s Loaded Reference: 0.006 seconds. 147s Loading index for chunk 1-1, build 1 147s No index available; generating from reference genome: /tmp/autopkgtest.0dfONK/autopkgtest_tmp/ref/index/1/chr1_index_k13_c16_b1.block 147s Indexing threads started for block 0-1 147s Indexing threads finished for block 0-1 149s Generated Index: 1.303 seconds. 149s No reads to process; quitting. 149s 149s Total time: 1.426 seconds. 149s test -d ref 149s bbmap.sh in=misc_dna_as_sanger.fastq out=out.sam 149s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 149s java -ea -Xmx2844m -Xms2844m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 in=misc_dna_as_sanger.fastq out=out.sam 149s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, in=misc_dna_as_sanger.fastq, out=out.sam] 149s Version 39.06 149s 149s Retaining first best site only for ambiguous mappings. 149s Set genome to 1 149s 149s Loaded Reference: 0.015 seconds. 149s Loading index for chunk 1-1, build 1 150s Generated Index: 0.764 seconds. 154s Analyzed Index: 4.862 seconds. 154s Started output stream: 0.017 seconds. 155s Cleared Memory: 0.128 seconds. 155s Processing reads in single-ended mode. 155s Started read stream. 155s Started 4 mapping threads. 155s Detecting finished threads: 0, 1, 2, 3 155s 155s ------------------ Results ------------------ 155s 155s Genome: 1 155s Key Length: 13 155s Max Indel: 16000 155s Minimum Score Ratio: 0.56 155s Mapping Mode: normal 155s Reads Used: 4 (153 bases) 155s 155s Mapping: 0.149 seconds. 155s Reads/sec: 26.91 155s kBases/sec: 1.03 155s 155s 155s Read 1 data: pct reads num reads pct bases num bases 155s 155s mapped: 0.0000% 0 0.0000% 0 155s unambiguous: 0.0000% 0 0.0000% 0 155s ambiguous: 0.0000% 0 0.0000% 0 155s low-Q discards: 25.0000% 1 19.6078% 30 155s 155s perfect best site: 0.0000% 0 0.0000% 0 155s semiperfect site: 0.0000% 0 0.0000% 0 155s 155s Match Rate: NA NA NaN% 0 155s Error Rate: NaN% 0 NaN% 0 155s Sub Rate: NaN% 0 NaN% 0 155s Del Rate: NaN% 0 NaN% 0 155s Ins Rate: NaN% 0 NaN% 0 155s N Rate: NaN% 0 NaN% 0 155s 155s Total time: 6.012 seconds. 155s test -r out.sam 155s bbmap.sh ref=example.fasta in=example.fastq out=out2.sam nodisk 155s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 155s java -ea -Xmx2844m -Xms2844m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta in=example.fastq out=out2.sam nodisk 155s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta, in=example.fastq, out=out2.sam, nodisk] 155s Version 39.06 155s 155s Retaining first best site only for ambiguous mappings. 155s 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] 155s 155s Set genScaffoldInfo=true 155s Set genome to 1 155s 155s Loaded Reference: 0.001 seconds. 155s Loading index for chunk 1-1, build 1 155s Indexing threads started for block 0-1 155s Indexing threads finished for block 0-1 155s Generated Index: 0.433 seconds. 159s Analyzed Index: 3.609 seconds. 159s Started output stream: 0.016 seconds. 159s Cleared Memory: 0.119 seconds. 159s Processing reads in single-ended mode. 159s Started read stream. 159s Started 4 mapping threads. 159s Detecting finished threads: 0, 1, 2, 3 159s 159s ------------------ Results ------------------ 159s 159s Genome: 1 159s Key Length: 13 159s Max Indel: 16000 159s Minimum Score Ratio: 0.56 159s Mapping Mode: normal 159s Reads Used: 3 (75 bases) 159s 159s Mapping: 0.128 seconds. 159s Reads/sec: 23.42 159s kBases/sec: 0.59 159s 159s 159s Read 1 data: pct reads num reads pct bases num bases 159s 159s mapped: 100.0000% 3 100.0000% 75 159s unambiguous: 100.0000% 3 100.0000% 75 159s ambiguous: 0.0000% 0 0.0000% 0 159s low-Q discards: 0.0000% 0 0.0000% 0 159s 159s perfect best site: 100.0000% 3 100.0000% 75 159s semiperfect site: 100.0000% 3 100.0000% 75 159s 159s Match Rate: NA NA 100.0000% 75 159s Error Rate: 0.0000% 0 0.0000% 0 159s Sub Rate: 0.0000% 0 0.0000% 0 159s Del Rate: 0.0000% 0 0.0000% 0 159s Ins Rate: 0.0000% 0 0.0000% 0 159s N Rate: 0.0000% 0 0.0000% 0 159s 159s Total time: 4.432 seconds. 159s test -r out2.sam 159s 159s # bbduk 159s bbduk.sh --version 160s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 160s java -ea -Xmx1422m -Xms1422m -cp /usr/share/java/bbmap.jar jgi.BBDuk --version 160s BBMap version 39.06 160s For help, please run the shellscript with no parameters, or look in /docs/. 160s bbduk.sh --help 160s 160s Written by Brian Bushnell 160s Last modified November 9, 2023 160s 160s Description: Compares reads to the kmers in a reference dataset, optionally 160s allowing an edit distance. Splits the reads into two outputs - those that 160s match the reference, and those that don't. Can also trim (remove) the matching 160s parts of the reads rather than binning the reads. 160s Please read bbmap/docs/guides/BBDukGuide.txt for more information. 160s 160s Usage: bbduk.sh in= out= ref= 160s 160s Input may be stdin or a fasta or fastq file, compressed or uncompressed. 160s If you pipe via stdin/stdout, please include the file type; e.g. for gzipped 160s fasta input, set in=stdin.fa.gz 160s 160s Input parameters: 160s in= Main input. in=stdin.fq will pipe from stdin. 160s in2= Input for 2nd read of pairs in a different file. 160s ref= Comma-delimited list of reference files. 160s In addition to filenames, you may also use the keywords: 160s adapters, artifacts, phix, lambda, pjet, mtst, kapa 160s literal= Comma-delimited list of literal reference sequences. 160s touppercase=f (tuc) Change all bases upper-case. 160s interleaved=auto (int) t/f overrides interleaved autodetection. 160s Must be set mainually when streaming fastq input. 160s qin=auto Input quality offset: 33 (Sanger), 64, or auto. 160s reads=-1 If positive, quit after processing X reads or pairs. 160s copyundefined=f (cu) Process non-AGCT IUPAC reference bases by making all 160s possible unambiguous copies. Intended for short motifs 160s or adapter barcodes, as time/memory use is exponential. 160s samplerate=1 Set lower to only process a fraction of input reads. 160s samref= Optional reference fasta for processing sam files. 160s 160s Output parameters: 160s out= (outnonmatch) Write reads here that do not contain 160s kmers matching the database. 'out=stdout.fq' will pipe 160s to standard out. 160s out2= (outnonmatch2) Use this to write 2nd read of pairs to a 160s different file. 160s outm= (outmatch) Write reads here that fail filters. In default 160s kfilter mode, this means any read with a matching kmer. 160s In any mode, it also includes reads that fail filters such 160s as minlength, mingc, maxgc, entropy, etc. In other words, 160s it includes all reads that do not go to 'out'. 160s outm2= (outmatch2) Use this to write 2nd read of pairs to a 160s different file. 160s outs= (outsingle) Use this to write singleton reads whose mate 160s was trimmed shorter than minlen. 160s stats= Write statistics about which contamininants were detected. 160s refstats= Write statistics on a per-reference-file basis. 160s rpkm= Write RPKM for each reference sequence (for RNA-seq). 160s dump= Dump kmer tables to a file, in fasta format. 160s duk= Write statistics in duk's format. *DEPRECATED* 160s nzo=t Only write statistics about ref sequences with nonzero hits. 160s overwrite=t (ow) Grant permission to overwrite files. 160s showspeed=t (ss) 'f' suppresses display of processing speed. 160s ziplevel=2 (zl) Compression level; 1 (min) through 9 (max). 160s fastawrap=70 Length of lines in fasta output. 160s qout=auto Output quality offset: 33 (Sanger), 64, or auto. 160s statscolumns=3 (cols) Number of columns for stats output, 3 or 5. 160s 5 includes base counts. 160s rename=f Rename reads to indicate which sequences they matched. 160s refnames=f Use names of reference files rather than scaffold IDs. 160s trd=f Truncate read and ref names at the first whitespace. 160s ordered=f Set to true to output reads in same order as input. 160s maxbasesout=-1 If positive, quit after writing approximately this many 160s bases to out (outu/outnonmatch). 160s maxbasesoutm=-1 If positive, quit after writing approximately this many 160s bases to outm (outmatch). 160s json=f Print to screen in json format. 160s 160s Histogram output parameters: 160s bhist= Base composition histogram by position. 160s qhist= Quality histogram by position. 160s qchist= Count of bases with each quality value. 160s aqhist= Histogram of average read quality. 160s bqhist= Quality histogram designed for box plots. 160s lhist= Read length histogram. 160s phist= Polymer length histogram. 160s gchist= Read GC content histogram. 160s enthist= Read entropy histogram. 160s ihist= Insert size histogram, for paired reads in mapped sam. 160s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 160s maxhistlen=6000 Set an upper bound for histogram lengths; higher uses 160s more memory. The default is 6000 for some histograms 160s and 80000 for others. 160s 160s Histograms for mapped sam/bam files only: 160s histbefore=t Calculate histograms from reads before processing. 160s ehist= Errors-per-read histogram. 160s qahist= Quality accuracy histogram of error rates versus quality 160s score. 160s indelhist= Indel length histogram. 160s mhist= Histogram of match, sub, del, and ins rates by position. 160s idhist= Histogram of read count versus percent identity. 160s idbins=100 Number idhist bins. Set to 'auto' to use read length. 160s varfile= Ignore substitution errors listed in this file when 160s calculating error rates. Can be generated with 160s CallVariants. 160s vcf= Ignore substitution errors listed in this VCF file 160s when calculating error rates. 160s ignorevcfindels=t Also ignore indels listed in the VCF. 160s 160s Processing parameters: 160s k=27 Kmer length used for finding contaminants. Contaminants 160s shorter than k will not be found. k must be at least 1. 160s rcomp=t Look for reverse-complements of kmers in addition to 160s forward kmers. 160s maskmiddle=t (mm) Treat the middle base of a kmer as a wildcard, to 160s increase sensitivity in the presence of errors. This may 160s also be set to a number, e.g. mm=3, to mask that many bp. 160s The default mm=t corresponds to mm=1 for odd-length kmers 160s and mm=2 for even-length kmers (as of v39.04), while 160s mm=f is always equivalent to mm=0. 160s minkmerhits=1 (mkh) Reads need at least this many matching kmers 160s to be considered as matching the reference. 160s minkmerfraction=0.0 (mkf) A reads needs at least this fraction of its total 160s kmers to hit a ref, in order to be considered a match. 160s If this and minkmerhits are set, the greater is used. 160s mincovfraction=0.0 (mcf) A reads needs at least this fraction of its total 160s bases to be covered by ref kmers to be considered a match. 160s If specified, mcf overrides mkh and mkf. 160s hammingdistance=0 (hdist) Maximum Hamming distance for ref kmers (subs only). 160s Memory use is proportional to (3*K)^hdist. 160s qhdist=0 Hamming distance for query kmers; impacts speed, not memory. 160s editdistance=0 (edist) Maximum edit distance from ref kmers (subs 160s and indels). Memory use is proportional to (8*K)^edist. 160s hammingdistance2=0 (hdist2) Sets hdist for short kmers, when using mink. 160s qhdist2=0 Sets qhdist for short kmers, when using mink. 160s editdistance2=0 (edist2) Sets edist for short kmers, when using mink. 160s forbidn=f (fn) Forbids matching of read kmers containing N. 160s By default, these will match a reference 'A' if 160s hdist>0 or edist>0, to increase sensitivity. 160s removeifeitherbad=t (rieb) Paired reads get sent to 'outmatch' if either is 160s match (or either is trimmed shorter than minlen). 160s Set to false to require both. 160s trimfailures=f Instead of discarding failed reads, trim them to 1bp. 160s This makes the statistics a bit odd. 160s findbestmatch=f (fbm) If multiple matches, associate read with sequence 160s sharing most kmers. Reduces speed. 160s skipr1=f Don't do kmer-based operations on read 1. 160s skipr2=f Don't do kmer-based operations on read 2. 160s ecco=f For overlapping paired reads only. Performs error- 160s correction with BBMerge prior to kmer operations. 160s recalibrate=f (recal) Recalibrate quality scores. Requires calibration 160s matrices generated by CalcTrueQuality. 160s sam= If recalibration is desired, and matrices have not already 160s been generated, BBDuk will create them from the sam file. 160s amino=f Run in amino acid mode. Some features have not been 160s tested, but kmer-matching works fine. Maximum k is 12. 160s 160s Speed and Memory parameters: 160s threads=auto (t) Set number of threads to use; default is number of 160s logical processors. 160s prealloc=f Preallocate memory in table. Allows faster table loading 160s and more efficient memory usage, for a large reference. 160s monitor=f Kill this process if it crashes. monitor=600,0.01 would 160s kill after 600 seconds under 1% usage. 160s minrskip=1 (mns) Force minimal skip interval when indexing reference 160s kmers. 1 means use all, 2 means use every other kmer, etc. 160s maxrskip=1 (mxs) Restrict maximal skip interval when indexing 160s reference kmers. Normally all are used for scaffolds<100kb, 160s but with longer scaffolds, up to maxrskip-1 are skipped. 160s rskip= Set both minrskip and maxrskip to the same value. 160s If not set, rskip will vary based on sequence length. 160s qskip=1 Skip query kmers to increase speed. 1 means use all. 160s speed=0 Ignore this fraction of kmer space (0-15 out of 16) in both 160s reads and reference. Increases speed and reduces memory. 160s Note: Do not use more than one of 'speed', 'qskip', and 'rskip'. 160s 160s Trimming/Filtering/Masking parameters: 160s Note - if ktrim, kmask, and ksplit are unset, the default behavior is kfilter. 160s All kmer processing modes are mutually exclusive. 160s Reads only get sent to 'outm' purely based on kmer matches in kfilter mode. 160s 160s ktrim=f Trim reads to remove bases matching reference kmers, plus 160s all bases to the left or right. 160s Values: 160s f (don't trim), 160s r (trim to the right), 160s l (trim to the left) 160s ktrimtips=0 Set this to a positive number to perform ktrim on both 160s ends, examining only the outermost X bases. 160s kmask= Replace bases matching ref kmers with another symbol. 160s Allows any non-whitespace character, and processes short 160s kmers on both ends if mink is set. 'kmask=lc' will 160s convert masked bases to lowercase. 160s maskfullycovered=f (mfc) Only mask bases that are fully covered by kmers. 160s ksplit=f For single-ended reads only. Reads will be split into 160s pairs around the kmer. If the kmer is at the end of the 160s read, it will be trimmed instead. Singletons will go to 160s out, and pairs will go to outm. Do not use ksplit with 160s other operations such as quality-trimming or filtering. 160s mink=0 Look for shorter kmers at read tips down to this length, 160s when k-trimming or masking. 0 means disabled. Enabling 160s this will disable maskmiddle. 160s qtrim=f Trim read ends to remove bases with quality below trimq. 160s Performed AFTER looking for kmers. Values: 160s rl (trim both ends), 160s f (neither end), 160s r (right end only), 160s l (left end only), 160s w (sliding window). 160s trimq=6 Regions with average quality BELOW this will be trimmed, 160s if qtrim is set to something other than f. Can be a 160s floating-point number like 7.3. 160s trimclip=f Trim soft-clipped bases from sam files. 160s minlength=10 (ml) Reads shorter than this after trimming will be 160s discarded. Pairs will be discarded if both are shorter. 160s mlf=0 (minlengthfraction) Reads shorter than this fraction of 160s original length after trimming will be discarded. 160s maxlength= Reads longer than this after trimming will be discarded. 160s minavgquality=0 (maq) Reads with average quality (after trimming) below 160s this will be discarded. 160s maqb=0 If positive, calculate maq from this many initial bases. 160s minbasequality=0 (mbq) Reads with any base below this quality (after 160s trimming) will be discarded. 160s maxns=-1 If non-negative, reads with more Ns than this 160s (after trimming) will be discarded. 160s mcb=0 (minconsecutivebases) Discard reads without at least 160s this many consecutive called bases. 160s bbduk.sh in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq \ 160s qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 160s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 160s java -ea -Xmx1422m -Xms1422m -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 160s ottm=f (outputtrimmedtomatch) Output reads trimmed to shorter 160s than minlength to outm rather than discarding. 160s tp=0 (trimpad) Trim this much extra around matching kmers. 160s tbo=f (trimbyoverlap) Trim adapters based on where paired 160s reads overlap. 160s strictoverlap=t Adjust sensitivity for trimbyoverlap mode. 160s minoverlap=14 Require this many bases of overlap for detection. 160s mininsert=40 Require insert size of at least this for overlap. 160s Should be reduced to 16 for small RNA sequencing. 160s tpe=f (trimpairsevenly) When kmer right-trimming, trim both 160s reads to the minimum length of either. 160s forcetrimleft=0 (ftl) If positive, trim bases to the left of this position 160s (exclusive, 0-based). 160s forcetrimright=0 (ftr) If positive, trim bases to the right of this position 160s (exclusive, 0-based). 160s forcetrimright2=0 (ftr2) If positive, trim this many bases on the right end. 160s forcetrimmod=0 (ftm) If positive, right-trim length to be equal to zero, 160s modulo this number. 160s restrictleft=0 If positive, only look for kmer matches in the 160s leftmost X bases. 160s restrictright=0 If positive, only look for kmer matches in the 160s rightmost X bases. 160s NOTE: restrictleft and restrictright are mutually exclusive. If trimming 160s both ends is desired, use ktrimtips. 160s mingc=0 Discard reads with GC content below this. 160s maxgc=1 Discard reads with GC content above this. 160s gcpairs=t Use average GC of paired reads. 160s Also affects gchist. 160s tossjunk=f Discard reads with invalid characters as bases. 160s swift=f Trim Swift sequences: Trailing C/T/N R1, leading G/A/N R2. 160s 160s Header-parsing parameters - these require Illumina headers: 160s chastityfilter=f (cf) Discard reads with id containing ' 1:Y:' or ' 2:Y:'. 160s barcodefilter=f Remove reads with unexpected barcodes if barcodes is set, 160s or barcodes containing 'N' otherwise. A barcode must be 160s the last part of the read header. Values: 160s t: Remove reads with bad barcodes. 160s f: Ignore barcodes. 160s crash: Crash upon encountering bad barcodes. 160s barcodes= Comma-delimited list of barcodes or files of barcodes. 160s xmin=-1 If positive, discard reads with a lesser X coordinate. 160s ymin=-1 If positive, discard reads with a lesser Y coordinate. 160s xmax=-1 If positive, discard reads with a greater X coordinate. 160s ymax=-1 If positive, discard reads with a greater Y coordinate. 160s 160s Polymer trimming: 160s trimpolya=0 If greater than 0, trim poly-A or poly-T tails of 160s at least this length on either end of reads. 160s trimpolygleft=0 If greater than 0, trim poly-G prefixes of at least this 160s length on the left end of reads. Does not trim poly-C. 160s trimpolygright=0 If greater than 0, trim poly-G tails of at least this 160s length on the right end of reads. Does not trim poly-C. 160s trimpolyg=0 This sets both left and right at once. 160s filterpolyg=0 If greater than 0, remove reads with a poly-G prefix of 160s at least this length (on the left). 160s Note: there are also equivalent poly-C flags. 160s 160s Polymer tracking: 160s pratio=base,base 'pratio=G,C' will print the ratio of G to C polymers. 160s plen=20 Length of homopolymers to count. 160s 160s Entropy/Complexity parameters: 160s entropy=-1 Set between 0 and 1 to filter reads with entropy below 160s that value. Higher is more stringent. 160s entropywindow=50 Calculate entropy using a sliding window of this length. 160s entropyk=5 Calculate entropy using kmers of this length. 160s minbasefrequency=0 Discard reads with a minimum base frequency below this. 160s entropytrim=f Values: 160s f: (false) Do not entropy-trim. 160s r: (right) Trim low entropy on the right end only. 160s l: (left) Trim low entropy on the left end only. 160s rl: (both) Trim low entropy on both ends. 160s entropymask=f Values: 160s f: (filter) Discard low-entropy sequences. 160s t: (true) Mask low-entropy parts of sequences with N. 160s lc: Change low-entropy parts of sequences to lowercase. 160s entropymark=f Mark each base with its entropy value. This is on a scale 160s of 0-41 and is reported as quality scores, so the output 160s should be fastq or fasta+qual. 160s NOTE: If set, entropytrim overrides entropymask. 160s 160s Cardinality estimation: 160s cardinality=f (loglog) Count unique kmers using the LogLog algorithm. 160s cardinalityout=f (loglogout) Count unique kmers in output reads. 160s loglogk=31 Use this kmer length for counting. 160s loglogbuckets=2048 Use this many buckets for counting. 160s khist= Kmer frequency histogram; plots number of kmers versus 160s kmer depth. This is approximate. 160s khistout= Kmer frequency histogram for output reads. 160s 160s Java Parameters: 160s 160s -Xmx This will set Java's memory usage, overriding autodetection. 160s -Xmx20g will 160s specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 160s The max is typically 85% of physical memory. 160s -eoom This flag will cause the process to exit if an 160s out-of-memory exception occurs. Requires Java 8u92+. 160s -da Disable assertions. 160s 160s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 160s 160s 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] 160s Version 39.06 160s 160s 0.013 seconds. 160s Initial: 160s Memory: max=1491m, total=1491m, free=1461m, used=30m 160s 160s Input is being processed as paired 160s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 160s Started output streams: 0.011 seconds. 160s Processing time: 0.003 seconds. 160s 160s Input: 8 reads 306 bases. 160s QTrimmed: 0 reads (0.00%) 0 bases (0.00%) 160s Total Removed: 8 reads (100.00%) 306 bases (100.00%) 160s Result: 0 reads (0.00%) 0 bases (0.00%) 160s 160s Time: 0.015 seconds. 160s Reads Processed: 8 0.54k reads/sec 160s Bases Processed: 306 0.02m bases/sec 160s test -r out.fastq.gz 160s 160s # bbnorm 160s bbnorm.sh --version 160s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 160s java -ea -Xmx2844m -Xms2844m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 --version 160s BBMap version 39.06 160s For help, please run the shellscript with no parameters, or look in /docs/. 160s bbnorm.sh --help 160s bbnorm.sh in=sanger_full_range_original_sanger.fastq qin=33 \ 160s out=out3.fastq outt=outt.fastq hist=hist.plt 160s 160s Written by Brian Bushnell 160s Last modified October 19, 2017 160s 160s Description: Normalizes read depth based on kmer counts. 160s Can also error-correct, bin reads by kmer depth, and generate a kmer depth histogram. 160s However, Tadpole has superior error-correction to BBNorm. 160s Please read bbmap/docs/guides/BBNormGuide.txt for more information. 160s 160s Usage: bbnorm.sh in= out= outt= hist= 160s 160s Input parameters: 160s in=null Primary input. Use in2 for paired reads in a second file 160s in2=null Second input file for paired reads in two files 160s extra=null Additional files to use for input (generating hash table) but not for output 160s fastareadlen=2^31 Break up FASTA reads longer than this. Can be useful when processing scaffolded genomes 160s tablereads=-1 Use at most this many reads when building the hashtable (-1 means all) 160s kmersample=1 Process every nth kmer, and skip the rest 160s readsample=1 Process every nth read, and skip the rest 160s 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. 160s qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto. 160s 160s Output parameters: 160s out= File for normalized or corrected reads. Use out2 for paired reads in a second file 160s outt= (outtoss) File for reads that were excluded from primary output 160s reads=-1 Only process this number of reads, then quit (-1 means all) 160s sampleoutput=t Use sampling on output as well as input (not used if sample rates are 1) 160s keepall=f Set to true to keep all reads (e.g. if you just want error correction). 160s 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. 160s Default is false, to prevent confusion about how there can be 0-count kmers. 160s The reason is that based on the 'minq' and 'minprob' settings, some kmers may be excluded from the bloom filter. 160s tmpdir= This will specify a directory for temp files (only needed for multipass runs). If null, they will be written to the output directory. 160s usetempdir=t Allows enabling/disabling of temporary directory; if disabled, temp files will be written to the output directory. 160s qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input). 160s rename=f Rename reads based on their kmer depth. 160s 160s Hashing parameters: 160s k=31 Kmer length (values under 32 are most efficient, but arbitrarily high values are supported) 160s 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. 160s Large values decrease accuracy for a fixed amount of memory, so use the lowest number you can that will still capture highest-depth kmers. 160s hashes=3 Number of times each kmer is hashed and stored. Higher is slower. 160s Higher is MORE accurate if there is enough memory, and LESS accurate if there is not enough memory. 160s 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. 160s prehashes=2 Number of hashes for prefilter. 160s prefilterbits=2 (pbits) Bits per cell in prefilter. 160s prefiltersize=0.35 Fraction of memory to allocate to prefilter. 160s buildpasses=1 More passes can sometimes increase accuracy by iteratively removing low-depth kmers 160s minq=6 Ignore kmers containing bases with quality below this 160s minprob=0.5 Ignore kmers with overall probability of correctness below this 160s 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. 160s 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. 160s 160s Normalization parameters: 160s fixspikes=f (fs) Do a slower, high-precision bloom filter lookup of kmers that appear to have an abnormally high depth due to collisions. 160s target=100 (tgt) Target normalization depth. NOTE: All depth parameters control kmer depth, not read depth. 160s For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1)) 160s maxdepth=-1 (max) Reads will not be downsampled when below this depth, even if they are above the target depth. 160s mindepth=5 (min) Kmers with depth below this number will not be included when calculating the depth of a read. 160s minkmers=15 (mgkpr) Reads must have at least this many kmers over min depth to be retained. Aka 'mingoodkmersperread'. 160s 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. 160s uselowerdepth=t (uld) For pairs, use the depth of the lower read as the depth proxy. 160s deterministic=t (dr) Generate random numbers deterministically to ensure identical output between multiple runs. May decrease speed with a huge number of threads. 160s passes=2 (p) 1 pass is the basic mode. 2 passes (default) allows greater accuracy, error detection, better contol of output depth. 160s 160s Error detection parameters: 160s hdp=90.0 (highdepthpercentile) Position in sorted kmer depth array used as proxy of a read's high kmer depth. 160s ldp=25.0 (lowdepthpercentile) Position in sorted kmer depth array used as proxy of a read's low kmer depth. 160s tossbadreads=f (tbr) Throw away reads detected as containing errors. 160s requirebothbad=f (rbb) Only toss bad pairs if both reads are bad. 160s 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. 160s highthresh=12 (ht) Threshold for high kmer. A high kmer at this or above are considered non-error. 160s lowthresh=3 (lt) Threshold for low kmer. Kmers at this and below are always considered errors. 160s 160s Error correction parameters: 160s ecc=f Set to true to correct errors. NOTE: Tadpole is now preferred for ecc as it does a better job. 160s ecclimit=3 Correct up to this many errors per read. If more are detected, the read will remain unchanged. 160s errorcorrectratio=140 (ecr) Adjacent kmers with a depth ratio of at least this much between will be classified as an error. 160s echighthresh=22 (echt) Threshold for high kmer. A kmer at this or above may be considered non-error. 160s eclowthresh=2 (eclt) Threshold for low kmer. Kmers at this and below are considered errors. 160s eccmaxqual=127 Do not correct bases with quality above this value. 160s aec=f (aggressiveErrorCorrection) Sets more aggressive values of ecr=100, ecclimit=7, echt=16, eclt=3. 160s cec=f (conservativeErrorCorrection) Sets more conservative values of ecr=180, ecclimit=2, echt=30, eclt=1, sl=4, pl=4. 160s meo=f (markErrorsOnly) Marks errors by reducing quality value of suspected errors; does not correct anything. 160s mue=t (markUncorrectableErrors) Marks errors only on uncorrectable reads; requires 'ecc=t'. 160s overlap=f (ecco) Error correct by read overlap. 160s 160s Depth binning parameters: 160s lowbindepth=10 (lbd) Cutoff for low depth bin. 160s highbindepth=80 (hbd) Cutoff for high depth bin. 160s outlow= Pairs in which both reads have a median below lbd go into this file. 160s outhigh= Pairs in which both reads have a median above hbd go into this file. 160s outmid= All other pairs go into this file. 160s 160s Histogram parameters: 160s hist= Specify a file to write the input kmer depth histogram. 160s histout= Specify a file to write the output kmer depth histogram. 160s histcol=3 (histogramcolumns) Number of histogram columns, 2 or 3. 160s pzc=f (printzerocoverage) Print lines in the histogram with zero coverage. 160s histlen=1048576 Max kmer depth displayed in histogram. Also affects statistics displayed, but does not affect normalization. 160s 160s Peak calling parameters: 160s peaks= Write the peaks to this file. Default is stdout. 160s minHeight=2 (h) Ignore peaks shorter than this. 160s minVolume=5 (v) Ignore peaks with less area than this. 160s minWidth=3 (w) Ignore peaks narrower than this. 160s minPeak=2 (minp) Ignore peaks with an X-value below this. 160s maxPeak=BIG (maxp) Ignore peaks with an X-value above this. 160s maxPeakCount=8 (maxpc) Print up to this many peaks (prioritizing height). 160s 160s Java Parameters: 160s -Xmx This will set Java's memory usage, overriding autodetection. 160s -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 160s The max is typically 85% of physical memory. 160s -eoom This flag will cause the process to exit if an 160s out-of-memory exception occurs. Requires Java 8u92+. 160s -da Disable assertions. 160s 160s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 160s 160s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 160s java -ea -Xmx2844m -Xms2844m -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 160s Executing jgi.KmerNormalize [bits=32, in=sanger_full_range_original_sanger.fastq, qin=33, out=out3.fastq, outt=outt.fastq, hist=hist.plt] 160s 160s 160s *********** Pass 1 ********** 160s 160s 160s Settings: 160s threads: 4 160s k: 31 160s deterministic: true 160s toss error reads: false 160s passes: 1 160s bits per cell: 16 160s cells: 1052.92M 160s hashes: 3 160s base min quality: 5 160s kmer min prob: 0.5 160s 160s target depth: 400 160s min depth: 3 160s max depth: 500 160s min good kmers: 15 160s depth percentile: 64.8 160s ignore dupe kmers: true 160s fix spikes: false 160s histogram length: 65536 160s print zero cov: false 160s 162s Made hash table: hashes = 3 mem = 1.96 GB cells = 1052.59M used = 0.000% 162s 162s Estimated unique kmers: 7 162s 162s Table creation time: 1.389 seconds. 162s Started output threads. 162s Started output threads. 162s Table read time: 0.006 seconds. 31.43 kb/sec 162s Total reads in: 2 0.000% Kept 162s Total bases in: 188 0.000% Kept 162s Error reads in: 2 100.000% 162s Error type 1: 2 100.000% 162s Error type 2: 0 0.000% 162s Error type 3: 0 0.000% 162s 162s Wrote histogram to hist.plt 162s Total kmers counted: 128 162s Total unique kmer count: 128 162s Includes forward kmers only. 162s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 162s The most accurate value is the greater of the two. 162s 162s Percent unique: 100.00% 162s Depth average: 1.00 (unique kmers) 162s Depth median: 1 (unique kmers) 162s Depth standard deviation: 0.00 (unique kmers) 162s Corrected depth average: 0.00 162s 162s Depth average: 1.00 (all kmers) 162s Depth median: 1 (all kmers) 162s Depth standard deviation: 0.00 (all kmers) 162s 162s Approx. read depth median: 1.47 162s 162s *********** Pass 2 ********** 162s 162s 162s Settings: 162s threads: 4 162s k: 31 162s deterministic: true 162s toss error reads: false 162s passes: 1 162s bits per cell: 16 162s cells: 1052.92M 162s hashes: 3 162s base min quality: 5 162s kmer min prob: 0.5 162s 162s target depth: 100 162s min depth: 5 162s max depth: 100 162s min good kmers: 15 162s depth percentile: 54.0 162s ignore dupe kmers: true 162s fix spikes: false 162s histogram length: 65536 162s 162s Made hash table: hashes = 3 mem = 1.96 GB cells = 1052.59M used = 0.000% 162s 162s Estimated unique kmers: 0 162s 162s Table creation time: 0.596 seconds. 162s Started output threads. 162s Started output threads. 162s Table read time: 0.001 seconds. 0.00 kb/sec 162s Total reads in: 0 NaN% Kept 162s Total bases in: 0 NaN% Kept 162s Error reads in: 0 NaN% 162s Error type 1: 0 NaN% 162s Error type 2: 0 NaN% 162s Error type 3: 0 NaN% 162s Total kmers counted: 0 162s Total unique kmer count: 0 162s Includes forward kmers only. 162s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 162s The most accurate value is the greater of the two. 162s 162s Percent unique: NaN% 162s Depth average: NaN (unique kmers) 162s Depth median: 0 (unique kmers) 162s Depth standard deviation: NaN (unique kmers) 162s Corrected depth average: NaN 162s 162s Depth average: NaN (all kmers) 162s Depth median: 0 (all kmers) 162s Depth standard deviation: 0.00 (all kmers) 162s 162s Approx. read depth median: NaN 162s 162s Removing temp files. 162s 162s Total time: 2.063 seconds. 0.09 kb/sec 163s test -r out3.fastq 163s test -r outt.fastq 163s test -r hist.plt 163s bbnorm.sh in=illumina_full_range_original_illumina.fastq qin=64 \ 163s out=out4.fastq outt=outt2.fastq hist=hist2.plt 163s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 163s java -ea -Xmx2844m -Xms2844m -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 163s Executing jgi.KmerNormalize [bits=32, in=illumina_full_range_original_illumina.fastq, qin=64, out=out4.fastq, outt=outt2.fastq, hist=hist2.plt] 163s 163s 163s *********** Pass 1 ********** 163s 163s 163s Settings: 163s threads: 4 163s k: 31 163s deterministic: true 163s toss error reads: false 163s passes: 1 163s bits per cell: 16 163s cells: 1052.92M 163s hashes: 3 163s base min quality: 5 163s kmer min prob: 0.5 163s 163s target depth: 400 163s min depth: 3 163s max depth: 500 163s min good kmers: 15 163s depth percentile: 64.8 163s ignore dupe kmers: true 163s fix spikes: false 163s histogram length: 65536 163s print zero cov: false 163s 164s Made hash table: hashes = 3 mem = 1.96 GB cells = 1052.59M used = 0.000% 164s 164s Estimated unique kmers: 7 164s 164s Table creation time: 1.066 seconds. 164s Started output threads. 164s Started output threads. 164s Table read time: 0.004 seconds. 35.66 kb/sec 164s Total reads in: 2 0.000% Kept 164s Total bases in: 126 0.000% Kept 164s Error reads in: 2 100.000% 164s Error type 1: 2 100.000% 164s Error type 2: 0 0.000% 164s Error type 3: 0 0.000% 164s 164s Wrote histogram to hist2.plt 164s Total kmers counted: 66 164s Total unique kmer count: 66 164s Includes forward kmers only. 164s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 164s The most accurate value is the greater of the two. 164s 164s Percent unique: 100.00% 164s Depth average: 1.00 (unique kmers) 164s Depth median: 1 (unique kmers) 164s Depth standard deviation: 0.00 (unique kmers) 164s Corrected depth average: 0.00 164s 164s Depth average: 1.00 (all kmers) 164s Depth median: 1 (all kmers) 164s Depth standard deviation: 0.00 (all kmers) 164s 164s Approx. read depth median: 1.91 164s 164s *********** Pass 2 ********** 164s 164s 164s Settings: 164s threads: 4 164s k: 31 164s deterministic: true 164s toss error reads: false 164s passes: 1 164s bits per cell: 16 164s cells: 1052.92M 164s hashes: 3 164s base min quality: 5 164s kmer min prob: 0.5 164s 164s target depth: 100 164s min depth: 5 164s max depth: 100 164s min good kmers: 15 164s depth percentile: 54.0 164s ignore dupe kmers: true 164s fix spikes: false 164s histogram length: 65536 164s 164s Made hash table: hashes = 3 mem = 1.96 GB cells = 1052.59M used = 0.000% 164s 164s Estimated unique kmers: 0 164s 164s Table creation time: 0.520 seconds. 164s Started output threads. 164s Started output threads. 164s Table read time: 0.001 seconds. 0.00 kb/sec 164s Total reads in: 0 NaN% Kept 164s Total bases in: 0 NaN% Kept 164s Error reads in: 0 NaN% 164s Error type 1: 0 NaN% 164s Error type 2: 0 NaN% 164s Error type 3: 0 NaN% 164s Total kmers counted: 0 164s Total unique kmer count: 0 164s Includes forward kmers only. 164s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 164s The most accurate value is the greater of the two. 164s 164s Percent unique: NaN% 164s Depth average: NaN (unique kmers) 164s Depth median: 0 (unique kmers) 164s Depth standard deviation: NaN (unique kmers) 164s Corrected depth average: NaN 164s 164s Depth average: NaN (all kmers) 164s Depth median: 0 (all kmers) 164s Depth standard deviation: 0.00 (all kmers) 164s 164s Approx. read depth median: NaN 164s 164s Removing temp files. 164s 164s Total time: 1.643 seconds. 0.08 kb/sec 165s test -r out4.fastq 165s test -r outt2.fastq 165s test -r hist2.plt 165s autopkgtest [00:46:34]: test run-unit-test: -----------------------] 165s autopkgtest [00:46:34]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 165s run-unit-test PASS 166s autopkgtest [00:46:35]: @@@@@@@@@@@@@@@@@@@@ summary 166s run-unit-test PASS 177s Creating nova instance adt-noble-s390x-bbmap-20240322-004349-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-s390x-server-20240321.img (UUID f7ee8f0f-480f-4014-94f0-3be2a19e259d)...