0s autopkgtest [00:37:51]: starting date and time: 2024-03-22 00:37:51+0000 0s autopkgtest [00:37:51]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [00:37:51]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.7n3dsh_j/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-17,src:alsa-lib,src:at-spi2-core,src:cups,src:glib2.0,src:gnutls28,src:gtk+2.0,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-17/17.0.11~7ea-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+2.0/2.24.33-3.1ubuntu3 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-5.secgroup --name adt-noble-s390x-bbmap-20240322-003751-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/ 117s autopkgtest [00:39:48]: testbed dpkg architecture: s390x 117s autopkgtest [00:39:48]: testbed apt version: 2.7.12 117s autopkgtest [00:39:48]: @@@@@@@@@@@@@@@@@@@@ test bed setup 118s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 119s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [494 kB] 120s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3765 kB] 122s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 122s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [53.9 kB] 122s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [669 kB] 122s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 122s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 122s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 122s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [3987 kB] 123s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 123s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [45.1 kB] 123s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 125s Fetched 9150 kB in 5s (1760 kB/s) 125s Reading package lists... 129s Reading package lists... 130s Building dependency tree... 130s Reading state information... 130s Calculating upgrade... 130s The following packages will be REMOVED: 130s libglib2.0-0 130s The following NEW packages will be installed: 130s libglib2.0-0t64 xdg-user-dirs 130s The following packages will be upgraded: 130s cloud-init debianutils fonts-ubuntu-console gir1.2-glib-2.0 libglib2.0-data 130s python3-markupsafe 131s 6 upgraded, 2 newly installed, 1 to remove and 0 not upgraded. 131s Need to get 2530 kB of archives. 131s After this operation, 147 kB of additional disk space will be used. 131s Get:1 http://ftpmaster.internal/ubuntu noble/main s390x debianutils s390x 5.17 [90.1 kB] 131s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gir1.2-glib-2.0 s390x 2.79.3-3ubuntu5 [180 kB] 131s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libglib2.0-0t64 s390x 2.79.3-3ubuntu5 [1566 kB] 131s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 131s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x xdg-user-dirs s390x 0.18-1 [18.5 kB] 131s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x fonts-ubuntu-console all 0.869+git20240321-0ubuntu1 [18.7 kB] 131s Get:7 http://ftpmaster.internal/ubuntu noble/main s390x python3-markupsafe s390x 2.1.5-1build1 [12.8 kB] 131s Get:8 http://ftpmaster.internal/ubuntu noble/main s390x cloud-init all 24.1.2-0ubuntu1 [597 kB] 132s Preconfiguring packages ... 132s Fetched 2530 kB in 1s (2695 kB/s) 132s (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.) 132s Preparing to unpack .../debianutils_5.17_s390x.deb ... 132s Unpacking debianutils (5.17) over (5.16) ... 132s Setting up debianutils (5.17) ... 132s (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.) 132s Preparing to unpack .../gir1.2-glib-2.0_2.79.3-3ubuntu5_s390x.deb ... 132s Unpacking gir1.2-glib-2.0:s390x (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 132s dpkg: libglib2.0-0:s390x: dependency problems, but removing anyway as you requested: 132s udisks2 depends on libglib2.0-0 (>= 2.77.0). 132s shared-mime-info depends on libglib2.0-0 (>= 2.75.3). 132s s390-tools depends on libglib2.0-0 (>= 2.77.0). 132s python3-gi depends on libglib2.0-0 (>= 2.77.0). 132s python3-dbus depends on libglib2.0-0 (>= 2.16.0). 132s netplan.io depends on libglib2.0-0 (>= 2.70.0). 132s netplan-generator depends on libglib2.0-0 (>= 2.70.0). 132s libxmlb2:s390x depends on libglib2.0-0 (>= 2.54.0). 132s libvolume-key1:s390x depends on libglib2.0-0 (>= 2.18.0). 132s libudisks2-0:s390x depends on libglib2.0-0 (>= 2.75.3). 132s libqrtr-glib0:s390x depends on libglib2.0-0 (>= 2.56). 132s libqmi-proxy depends on libglib2.0-0 (>= 2.30.0). 132s libqmi-glib5:s390x depends on libglib2.0-0 (>= 2.54.0). 132s libpolkit-gobject-1-0:s390x depends on libglib2.0-0 (>= 2.38.0). 132s libpolkit-agent-1-0:s390x depends on libglib2.0-0 (>= 2.38.0). 132s libnetplan0:s390x depends on libglib2.0-0 (>= 2.75.3). 132s libmm-glib0:s390x depends on libglib2.0-0 (>= 2.62.0). 132s libmbim-proxy depends on libglib2.0-0 (>= 2.56). 132s libmbim-glib4:s390x depends on libglib2.0-0 (>= 2.56). 132s libjson-glib-1.0-0:s390x depends on libglib2.0-0 (>= 2.75.3). 132s libjcat1:s390x depends on libglib2.0-0 (>= 2.75.3). 132s libgusb2:s390x depends on libglib2.0-0 (>= 2.75.3). 132s libgudev-1.0-0:s390x depends on libglib2.0-0 (>= 2.38.0). 132s libgirepository-1.0-1:s390x depends on libglib2.0-0 (>= 2.79.0). 132s libfwupd2:s390x depends on libglib2.0-0 (>= 2.79.0). 132s libblockdev3:s390x depends on libglib2.0-0 (>= 2.42.2). 132s libblockdev-utils3:s390x depends on libglib2.0-0 (>= 2.75.3). 132s libblockdev-swap3:s390x depends on libglib2.0-0 (>= 2.42.2). 132s libblockdev-part3:s390x depends on libglib2.0-0 (>= 2.42.2). 132s libblockdev-nvme3:s390x depends on libglib2.0-0 (>= 2.42.2). 132s libblockdev-mdraid3:s390x depends on libglib2.0-0 (>= 2.42.2). 132s libblockdev-loop3:s390x depends on libglib2.0-0 (>= 2.42.2). 132s libblockdev-fs3:s390x depends on libglib2.0-0 (>= 2.42.2). 132s libblockdev-crypto3:s390x depends on libglib2.0-0 (>= 2.42.2). 132s fwupd depends on libglib2.0-0 (>= 2.79.0). 132s bolt depends on libglib2.0-0 (>= 2.56.0). 132s 132s (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.) 132s Removing libglib2.0-0:s390x (2.79.2-1~ubuntu1) ... 132s Selecting previously unselected package libglib2.0-0t64:s390x. 132s (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.) 132s Preparing to unpack .../0-libglib2.0-0t64_2.79.3-3ubuntu5_s390x.deb ... 132s 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... 132s removed '/var/lib/dpkg/info/libglib2.0-0:s390x.postrm' 132s Unpacking libglib2.0-0t64:s390x (2.79.3-3ubuntu5) ... 132s Preparing to unpack .../1-libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 132s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 132s Selecting previously unselected package xdg-user-dirs. 132s Preparing to unpack .../2-xdg-user-dirs_0.18-1_s390x.deb ... 132s Unpacking xdg-user-dirs (0.18-1) ... 132s Preparing to unpack .../3-fonts-ubuntu-console_0.869+git20240321-0ubuntu1_all.deb ... 132s Unpacking fonts-ubuntu-console (0.869+git20240321-0ubuntu1) over (0.869-0ubuntu1) ... 132s Preparing to unpack .../4-python3-markupsafe_2.1.5-1build1_s390x.deb ... 132s Unpacking python3-markupsafe (2.1.5-1build1) over (2.1.5-1) ... 132s Preparing to unpack .../5-cloud-init_24.1.2-0ubuntu1_all.deb ... 133s Unpacking cloud-init (24.1.2-0ubuntu1) over (24.1.1-0ubuntu1) ... 133s Setting up fonts-ubuntu-console (0.869+git20240321-0ubuntu1) ... 133s Setting up cloud-init (24.1.2-0ubuntu1) ... 134s Setting up xdg-user-dirs (0.18-1) ... 134s Setting up python3-markupsafe (2.1.5-1build1) ... 134s Setting up libglib2.0-0t64:s390x (2.79.3-3ubuntu5) ... 134s No schema files found: doing nothing. 134s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 134s Setting up gir1.2-glib-2.0:s390x (2.79.3-3ubuntu5) ... 134s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 135s Processing triggers for man-db (2.12.0-3) ... 136s Processing triggers for libc-bin (2.39-0ubuntu2) ... 136s Reading package lists... 136s Building dependency tree... 136s Reading state information... 137s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 137s Unknown architecture, assuming PC-style ttyS0 137s sh: Attempting to set up Debian/Ubuntu apt sources automatically 137s sh: Distribution appears to be Ubuntu 138s Reading package lists... 138s Building dependency tree... 138s Reading state information... 139s eatmydata is already the newest version (131-1). 139s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 139s Reading package lists... 139s Building dependency tree... 139s Reading state information... 139s dbus is already the newest version (1.14.10-4ubuntu1). 139s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 139s Reading package lists... 139s Building dependency tree... 139s Reading state information... 140s rng-tools-debian is already the newest version (2.4). 140s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 140s Reading package lists... 140s Building dependency tree... 140s Reading state information... 140s The following packages will be REMOVED: 140s cloud-init* python3-configobj* python3-debconf* 141s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 141s After this operation, 3256 kB disk space will be freed. 141s (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.) 141s Removing cloud-init (24.1.2-0ubuntu1) ... 141s Removing python3-configobj (5.0.8-3) ... 142s Removing python3-debconf (1.5.86) ... 142s Processing triggers for man-db (2.12.0-3) ... 142s (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.) 142s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 143s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 143s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 143s invoke-rc.d: policy-rc.d denied execution of try-restart. 143s Reading package lists... 143s Building dependency tree... 143s Reading state information... 144s linux-generic is already the newest version (6.8.0-11.11+1). 144s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 144s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 144s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 144s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 146s Reading package lists... 146s Reading package lists... 146s Building dependency tree... 146s Reading state information... 147s Calculating upgrade... 147s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 147s Reading package lists... 147s Building dependency tree... 147s Reading state information... 147s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 148s autopkgtest [00:40:19]: rebooting testbed after setup commands that affected boot 163s autopkgtest [00:40:34]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 166s autopkgtest [00:40:37]: @@@@@@@@@@@@@@@@@@@@ apt-source bbmap 169s Get:1 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (dsc) [2286 B] 169s Get:2 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (tar) [5343 kB] 169s Get:3 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (diff) [25.4 kB] 169s gpgv: Signature made Fri Nov 24 11:00:29 2023 UTC 169s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 169s gpgv: issuer "emollier@debian.org" 169s gpgv: Can't check signature: No public key 169s dpkg-source: warning: cannot verify inline signature for ./bbmap_39.06+dfsg-1.dsc: no acceptable signature found 170s autopkgtest [00:40:41]: testing package bbmap version 39.06+dfsg-1 170s autopkgtest [00:40:41]: build not needed 171s autopkgtest [00:40:42]: test run-unit-test: preparing testbed 173s Reading package lists... 173s Building dependency tree... 173s Reading state information... 174s Starting pkgProblemResolver with broken count: 0 174s Starting 2 pkgProblemResolver with broken count: 0 174s Done 174s The following additional packages will be installed: 174s bbmap bbmap-jni ca-certificates-java fontconfig-config fonts-dejavu-core 174s fonts-dejavu-mono java-common libapache-pom-java libasound2 libasound2-data 174s libavahi-client3 libavahi-common-data libavahi-common3 libcommons-cli-java 174s libcommons-codec-java libcommons-io-java libcommons-parent-java libcups2 174s libfontconfig1 libfreetype6 libgraphite2-3 libharfbuzz0b libjpeg-turbo8 174s libjpeg8 liblcms2-2 liblog4j1.2-java libmpj-java libpcsclite1 174s openjdk-17-jre-headless python-biopython-doc 174s Suggested packages: 174s default-jre libasound2-plugins alsa-utils libcommons-io-java-doc cups-common 174s liblcms2-utils liblog4j1.2-java-doc libmail-java pcscd libnss-mdns 174s fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho 174s fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic 174s Recommended packages: 174s pigz alsa-ucm-conf alsa-topology-conf python3-biopython 174s The following NEW packages will be installed: 174s autopkgtest-satdep bbmap bbmap-jni ca-certificates-java fontconfig-config 174s fonts-dejavu-core fonts-dejavu-mono java-common libapache-pom-java 174s libasound2 libasound2-data libavahi-client3 libavahi-common-data 174s libavahi-common3 libcommons-cli-java libcommons-codec-java 174s libcommons-io-java libcommons-parent-java libcups2 libfontconfig1 174s libfreetype6 libgraphite2-3 libharfbuzz0b libjpeg-turbo8 libjpeg8 liblcms2-2 174s liblog4j1.2-java libmpj-java libpcsclite1 openjdk-17-jre-headless 174s python-biopython-doc 174s 0 upgraded, 31 newly installed, 0 to remove and 0 not upgraded. 174s Need to get 78.1 MB/78.1 MB of archives. 174s After this operation, 226 MB of additional disk space will be used. 174s Get:1 /tmp/autopkgtest.w2oJl0/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [724 B] 174s Get:2 http://ftpmaster.internal/ubuntu noble/universe s390x libcommons-cli-java all 1.6.0-1 [59.9 kB] 175s Get:3 http://ftpmaster.internal/ubuntu noble/universe s390x libapache-pom-java all 29-2 [5284 B] 175s Get:4 http://ftpmaster.internal/ubuntu noble/universe s390x libcommons-parent-java all 56-1 [10.7 kB] 175s Get:5 http://ftpmaster.internal/ubuntu noble/universe s390x libcommons-codec-java all 1.16.0-1 [306 kB] 175s Get:6 http://ftpmaster.internal/ubuntu noble/universe s390x libcommons-io-java all 2.11.0-2 [297 kB] 175s Get:7 http://ftpmaster.internal/ubuntu noble/universe s390x liblog4j1.2-java all 1.2.17-11 [439 kB] 176s Get:8 http://ftpmaster.internal/ubuntu noble/universe s390x libmpj-java all 0.44+dfsg-4 [443 kB] 176s Get:9 http://ftpmaster.internal/ubuntu noble/main s390x ca-certificates-java all 20240118 [11.6 kB] 176s Get:10 http://ftpmaster.internal/ubuntu noble/main s390x java-common all 0.75+exp1 [6798 B] 176s Get:11 http://ftpmaster.internal/ubuntu noble/main s390x libavahi-common-data s390x 0.8-13ubuntu2 [29.5 kB] 176s Get:12 http://ftpmaster.internal/ubuntu noble/main s390x libavahi-common3 s390x 0.8-13ubuntu2 [23.8 kB] 176s Get:13 http://ftpmaster.internal/ubuntu noble/main s390x libavahi-client3 s390x 0.8-13ubuntu2 [26.7 kB] 176s Get:14 http://ftpmaster.internal/ubuntu noble/main s390x libcups2 s390x 2.4.6-0ubuntu3 [277 kB] 176s Get:15 http://ftpmaster.internal/ubuntu noble/main s390x liblcms2-2 s390x 2.14-2 [155 kB] 176s Get:16 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg-turbo8 s390x 2.1.5-2ubuntu1 [128 kB] 176s Get:17 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 176s Get:18 http://ftpmaster.internal/ubuntu noble/main s390x libfreetype6 s390x 2.13.2+dfsg-1 [431 kB] 176s Get:19 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 177s Get:20 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 177s Get:21 http://ftpmaster.internal/ubuntu noble/main s390x fontconfig-config s390x 2.15.0-1ubuntu1 [37.0 kB] 177s Get:22 http://ftpmaster.internal/ubuntu noble/main s390x libfontconfig1 s390x 2.15.0-1ubuntu1 [150 kB] 177s Get:23 http://ftpmaster.internal/ubuntu noble/main s390x libasound2-data all 1.2.10-3build1 [20.7 kB] 177s Get:24 http://ftpmaster.internal/ubuntu noble/main s390x libasound2 s390x 1.2.10-3build1 [414 kB] 177s Get:25 http://ftpmaster.internal/ubuntu noble/main s390x libgraphite2-3 s390x 1.3.14-2 [90.4 kB] 177s Get:26 http://ftpmaster.internal/ubuntu noble/main s390x libharfbuzz0b s390x 8.3.0-2 [515 kB] 177s Get:27 http://ftpmaster.internal/ubuntu noble/main s390x libpcsclite1 s390x 2.0.0-1 [19.9 kB] 177s Get:28 http://ftpmaster.internal/ubuntu noble/main s390x openjdk-17-jre-headless s390x 17.0.10+7-1 [45.7 MB] 186s Get:29 http://ftpmaster.internal/ubuntu noble/universe s390x bbmap all 39.06+dfsg-1 [9768 kB] 188s Get:30 http://ftpmaster.internal/ubuntu noble/universe s390x bbmap-jni s390x 39.06+dfsg-1 [38.7 kB] 188s Get:31 http://ftpmaster.internal/ubuntu noble/universe s390x python-biopython-doc all 1.81+dfsg-3 [17.3 MB] 191s Fetched 78.1 MB in 16s (4844 kB/s) 191s Selecting previously unselected package libcommons-cli-java. 191s (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.) 191s Preparing to unpack .../00-libcommons-cli-java_1.6.0-1_all.deb ... 191s Unpacking libcommons-cli-java (1.6.0-1) ... 191s Selecting previously unselected package libapache-pom-java. 191s Preparing to unpack .../01-libapache-pom-java_29-2_all.deb ... 191s Unpacking libapache-pom-java (29-2) ... 191s Selecting previously unselected package libcommons-parent-java. 191s Preparing to unpack .../02-libcommons-parent-java_56-1_all.deb ... 191s Unpacking libcommons-parent-java (56-1) ... 191s Selecting previously unselected package libcommons-codec-java. 191s Preparing to unpack .../03-libcommons-codec-java_1.16.0-1_all.deb ... 191s Unpacking libcommons-codec-java (1.16.0-1) ... 191s Selecting previously unselected package libcommons-io-java. 191s Preparing to unpack .../04-libcommons-io-java_2.11.0-2_all.deb ... 191s Unpacking libcommons-io-java (2.11.0-2) ... 191s Selecting previously unselected package liblog4j1.2-java. 191s Preparing to unpack .../05-liblog4j1.2-java_1.2.17-11_all.deb ... 191s Unpacking liblog4j1.2-java (1.2.17-11) ... 191s Selecting previously unselected package libmpj-java. 191s Preparing to unpack .../06-libmpj-java_0.44+dfsg-4_all.deb ... 191s Unpacking libmpj-java (0.44+dfsg-4) ... 191s Selecting previously unselected package ca-certificates-java. 191s Preparing to unpack .../07-ca-certificates-java_20240118_all.deb ... 191s Unpacking ca-certificates-java (20240118) ... 191s Selecting previously unselected package java-common. 191s Preparing to unpack .../08-java-common_0.75+exp1_all.deb ... 191s Unpacking java-common (0.75+exp1) ... 191s Selecting previously unselected package libavahi-common-data:s390x. 191s Preparing to unpack .../09-libavahi-common-data_0.8-13ubuntu2_s390x.deb ... 191s Unpacking libavahi-common-data:s390x (0.8-13ubuntu2) ... 191s Selecting previously unselected package libavahi-common3:s390x. 191s Preparing to unpack .../10-libavahi-common3_0.8-13ubuntu2_s390x.deb ... 191s Unpacking libavahi-common3:s390x (0.8-13ubuntu2) ... 192s Selecting previously unselected package libavahi-client3:s390x. 192s Preparing to unpack .../11-libavahi-client3_0.8-13ubuntu2_s390x.deb ... 192s Unpacking libavahi-client3:s390x (0.8-13ubuntu2) ... 192s Selecting previously unselected package libcups2:s390x. 192s Preparing to unpack .../12-libcups2_2.4.6-0ubuntu3_s390x.deb ... 192s Unpacking libcups2:s390x (2.4.6-0ubuntu3) ... 192s Selecting previously unselected package liblcms2-2:s390x. 192s Preparing to unpack .../13-liblcms2-2_2.14-2_s390x.deb ... 192s Unpacking liblcms2-2:s390x (2.14-2) ... 192s Selecting previously unselected package libjpeg-turbo8:s390x. 192s Preparing to unpack .../14-libjpeg-turbo8_2.1.5-2ubuntu1_s390x.deb ... 192s Unpacking libjpeg-turbo8:s390x (2.1.5-2ubuntu1) ... 192s Selecting previously unselected package libjpeg8:s390x. 192s Preparing to unpack .../15-libjpeg8_8c-2ubuntu11_s390x.deb ... 192s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 192s Selecting previously unselected package libfreetype6:s390x. 192s Preparing to unpack .../16-libfreetype6_2.13.2+dfsg-1_s390x.deb ... 192s Unpacking libfreetype6:s390x (2.13.2+dfsg-1) ... 192s Selecting previously unselected package fonts-dejavu-mono. 192s Preparing to unpack .../17-fonts-dejavu-mono_2.37-8_all.deb ... 192s Unpacking fonts-dejavu-mono (2.37-8) ... 192s Selecting previously unselected package fonts-dejavu-core. 192s Preparing to unpack .../18-fonts-dejavu-core_2.37-8_all.deb ... 192s Unpacking fonts-dejavu-core (2.37-8) ... 192s Selecting previously unselected package fontconfig-config. 192s Preparing to unpack .../19-fontconfig-config_2.15.0-1ubuntu1_s390x.deb ... 192s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 192s Selecting previously unselected package libfontconfig1:s390x. 192s Preparing to unpack .../20-libfontconfig1_2.15.0-1ubuntu1_s390x.deb ... 192s Unpacking libfontconfig1:s390x (2.15.0-1ubuntu1) ... 192s Selecting previously unselected package libasound2-data. 192s Preparing to unpack .../21-libasound2-data_1.2.10-3build1_all.deb ... 192s Unpacking libasound2-data (1.2.10-3build1) ... 192s Selecting previously unselected package libasound2:s390x. 192s Preparing to unpack .../22-libasound2_1.2.10-3build1_s390x.deb ... 192s Unpacking libasound2:s390x (1.2.10-3build1) ... 192s Selecting previously unselected package libgraphite2-3:s390x. 192s Preparing to unpack .../23-libgraphite2-3_1.3.14-2_s390x.deb ... 192s Unpacking libgraphite2-3:s390x (1.3.14-2) ... 192s Selecting previously unselected package libharfbuzz0b:s390x. 192s Preparing to unpack .../24-libharfbuzz0b_8.3.0-2_s390x.deb ... 192s Unpacking libharfbuzz0b:s390x (8.3.0-2) ... 192s Selecting previously unselected package libpcsclite1:s390x. 192s Preparing to unpack .../25-libpcsclite1_2.0.0-1_s390x.deb ... 192s Unpacking libpcsclite1:s390x (2.0.0-1) ... 192s Selecting previously unselected package openjdk-17-jre-headless:s390x. 192s Preparing to unpack .../26-openjdk-17-jre-headless_17.0.10+7-1_s390x.deb ... 192s Unpacking openjdk-17-jre-headless:s390x (17.0.10+7-1) ... 194s Selecting previously unselected package bbmap. 194s Preparing to unpack .../27-bbmap_39.06+dfsg-1_all.deb ... 194s Unpacking bbmap (39.06+dfsg-1) ... 194s Selecting previously unselected package bbmap-jni. 194s Preparing to unpack .../28-bbmap-jni_39.06+dfsg-1_s390x.deb ... 194s Unpacking bbmap-jni (39.06+dfsg-1) ... 194s Selecting previously unselected package python-biopython-doc. 194s Preparing to unpack .../29-python-biopython-doc_1.81+dfsg-3_all.deb ... 194s Unpacking python-biopython-doc (1.81+dfsg-3) ... 195s Selecting previously unselected package autopkgtest-satdep. 195s Preparing to unpack .../30-1-autopkgtest-satdep.deb ... 195s Unpacking autopkgtest-satdep (0) ... 195s Setting up libgraphite2-3:s390x (1.3.14-2) ... 195s Setting up liblcms2-2:s390x (2.14-2) ... 195s Setting up java-common (0.75+exp1) ... 195s Setting up libcommons-cli-java (1.6.0-1) ... 195s Setting up liblog4j1.2-java (1.2.17-11) ... 195s Setting up libasound2-data (1.2.10-3build1) ... 195s Setting up libfreetype6:s390x (2.13.2+dfsg-1) ... 195s Setting up libapache-pom-java (29-2) ... 195s Setting up libavahi-common-data:s390x (0.8-13ubuntu2) ... 195s Setting up fonts-dejavu-mono (2.37-8) ... 195s Setting up fonts-dejavu-core (2.37-8) ... 195s Setting up libpcsclite1:s390x (2.0.0-1) ... 195s Setting up libjpeg-turbo8:s390x (2.1.5-2ubuntu1) ... 195s Setting up python-biopython-doc (1.81+dfsg-3) ... 195s Setting up libasound2:s390x (1.2.10-3build1) ... 195s Setting up libharfbuzz0b:s390x (8.3.0-2) ... 195s Setting up bbmap-jni (39.06+dfsg-1) ... 195s Setting up ca-certificates-java (20240118) ... 195s No JRE found. Skipping Java certificates setup. 195s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 195s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 195s Setting up libcommons-parent-java (56-1) ... 195s Setting up libavahi-common3:s390x (0.8-13ubuntu2) ... 195s Setting up libfontconfig1:s390x (2.15.0-1ubuntu1) ... 195s Setting up libcommons-codec-java (1.16.0-1) ... 195s Setting up libavahi-client3:s390x (0.8-13ubuntu2) ... 195s Setting up libcommons-io-java (2.11.0-2) ... 195s Setting up libmpj-java (0.44+dfsg-4) ... 195s Setting up libcups2:s390x (2.4.6-0ubuntu3) ... 195s Setting up openjdk-17-jre-headless:s390x (17.0.10+7-1) ... 195s update-alternatives: using /usr/lib/jvm/java-17-openjdk-s390x/bin/java to provide /usr/bin/java (java) in auto mode 195s update-alternatives: using /usr/lib/jvm/java-17-openjdk-s390x/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 195s update-alternatives: using /usr/lib/jvm/java-17-openjdk-s390x/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 195s update-alternatives: using /usr/lib/jvm/java-17-openjdk-s390x/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 195s update-alternatives: using /usr/lib/jvm/java-17-openjdk-s390x/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 195s Processing triggers for libc-bin (2.39-0ubuntu2) ... 195s Processing triggers for man-db (2.12.0-3) ... 196s Processing triggers for ca-certificates-java (20240118) ... 197s Adding debian:ACCVRAIZ1.pem 197s Adding debian:AC_RAIZ_FNMT-RCM.pem 197s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 197s Adding debian:ANF_Secure_Server_Root_CA.pem 197s Adding debian:Actalis_Authentication_Root_CA.pem 197s Adding debian:AffirmTrust_Commercial.pem 197s Adding debian:AffirmTrust_Networking.pem 197s Adding debian:AffirmTrust_Premium.pem 197s Adding debian:AffirmTrust_Premium_ECC.pem 197s Adding debian:Amazon_Root_CA_1.pem 197s Adding debian:Amazon_Root_CA_2.pem 197s Adding debian:Amazon_Root_CA_3.pem 197s Adding debian:Amazon_Root_CA_4.pem 197s Adding debian:Atos_TrustedRoot_2011.pem 197s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 197s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 197s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 197s Adding debian:BJCA_Global_Root_CA1.pem 197s Adding debian:BJCA_Global_Root_CA2.pem 197s Adding debian:Baltimore_CyberTrust_Root.pem 197s Adding debian:Buypass_Class_2_Root_CA.pem 197s Adding debian:Buypass_Class_3_Root_CA.pem 197s Adding debian:CA_Disig_Root_R2.pem 197s Adding debian:CFCA_EV_ROOT.pem 197s Adding debian:COMODO_Certification_Authority.pem 197s Adding debian:COMODO_ECC_Certification_Authority.pem 197s Adding debian:COMODO_RSA_Certification_Authority.pem 197s Adding debian:Certainly_Root_E1.pem 197s Adding debian:Certainly_Root_R1.pem 197s Adding debian:Certigna.pem 197s Adding debian:Certigna_Root_CA.pem 197s Adding debian:Certum_EC-384_CA.pem 197s Adding debian:Certum_Trusted_Network_CA.pem 197s Adding debian:Certum_Trusted_Network_CA_2.pem 197s Adding debian:Certum_Trusted_Root_CA.pem 197s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 197s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 197s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 197s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 197s Adding debian:Comodo_AAA_Services_root.pem 197s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 197s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 197s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 197s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 197s Adding debian:DigiCert_Assured_ID_Root_CA.pem 197s Adding debian:DigiCert_Assured_ID_Root_G2.pem 197s Adding debian:DigiCert_Assured_ID_Root_G3.pem 197s Adding debian:DigiCert_Global_Root_CA.pem 197s Adding debian:DigiCert_Global_Root_G2.pem 197s Adding debian:DigiCert_Global_Root_G3.pem 197s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 197s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 197s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 197s Adding debian:DigiCert_Trusted_Root_G4.pem 197s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 197s Adding debian:Entrust_Root_Certification_Authority.pem 197s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 197s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 197s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem 197s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 197s Adding debian:GLOBALTRUST_2020.pem 197s Adding debian:GTS_Root_R1.pem 197s Adding debian:GTS_Root_R2.pem 197s Adding debian:GTS_Root_R3.pem 197s Adding debian:GTS_Root_R4.pem 197s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 197s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 197s Adding debian:GlobalSign_Root_CA.pem 197s Adding debian:GlobalSign_Root_CA_-_R3.pem 197s Adding debian:GlobalSign_Root_CA_-_R6.pem 197s Adding debian:GlobalSign_Root_E46.pem 197s Adding debian:GlobalSign_Root_R46.pem 197s Adding debian:Go_Daddy_Class_2_CA.pem 197s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 197s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 197s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 197s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 197s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 197s Adding debian:HiPKI_Root_CA_-_G1.pem 197s Adding debian:Hongkong_Post_Root_CA_3.pem 197s Adding debian:ISRG_Root_X1.pem 197s Adding debian:ISRG_Root_X2.pem 197s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 197s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 197s Adding debian:Izenpe.com.pem 197s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 197s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 197s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 197s Adding debian:NAVER_Global_Root_Certification_Authority.pem 197s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 197s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 197s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 197s Adding debian:QuoVadis_Root_CA_1_G3.pem 197s Adding debian:QuoVadis_Root_CA_2.pem 197s Adding debian:QuoVadis_Root_CA_2_G3.pem 197s Adding debian:QuoVadis_Root_CA_3.pem 197s Adding debian:QuoVadis_Root_CA_3_G3.pem 197s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 197s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 197s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 197s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 197s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 197s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 197s Adding debian:SZAFIR_ROOT_CA2.pem 197s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 197s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 197s Adding debian:SecureSign_RootCA11.pem 197s Adding debian:SecureTrust_CA.pem 197s Adding debian:Secure_Global_CA.pem 197s Adding debian:Security_Communication_ECC_RootCA1.pem 197s Adding debian:Security_Communication_RootCA2.pem 197s Adding debian:Security_Communication_RootCA3.pem 197s Adding debian:Security_Communication_Root_CA.pem 197s Adding debian:Starfield_Class_2_CA.pem 197s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 197s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 197s Adding debian:SwissSign_Gold_CA_-_G2.pem 197s Adding debian:SwissSign_Silver_CA_-_G2.pem 197s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 197s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 197s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 197s Adding debian:TWCA_Global_Root_CA.pem 197s Adding debian:TWCA_Root_Certification_Authority.pem 197s Adding debian:TeliaSonera_Root_CA_v1.pem 197s Adding debian:Telia_Root_CA_v2.pem 197s Adding debian:TrustAsia_Global_Root_CA_G3.pem 197s Adding debian:TrustAsia_Global_Root_CA_G4.pem 197s Adding debian:Trustwave_Global_Certification_Authority.pem 197s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 197s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 197s Adding debian:TunTrust_Root_CA.pem 197s Adding debian:UCA_Extended_Validation_Root.pem 197s Adding debian:UCA_Global_G2_Root.pem 197s Adding debian:USERTrust_ECC_Certification_Authority.pem 197s Adding debian:USERTrust_RSA_Certification_Authority.pem 197s Adding debian:XRamp_Global_CA_Root.pem 197s Adding debian:certSIGN_ROOT_CA.pem 197s Adding debian:certSIGN_Root_CA_G2.pem 197s Adding debian:e-Szigno_Root_CA_2017.pem 197s Adding debian:ePKI_Root_Certification_Authority.pem 197s Adding debian:emSign_ECC_Root_CA_-_C3.pem 197s Adding debian:emSign_ECC_Root_CA_-_G3.pem 197s Adding debian:emSign_Root_CA_-_C1.pem 197s Adding debian:emSign_Root_CA_-_G1.pem 197s Adding debian:vTrus_ECC_Root_CA.pem 197s Adding debian:vTrus_Root_CA.pem 197s done. 197s Setting up bbmap (39.06+dfsg-1) ... 197s Setting up autopkgtest-satdep (0) ... 201s (Reading database ... 54582 files and directories currently installed.) 201s Removing autopkgtest-satdep (0) ... 201s autopkgtest [00:41:12]: test run-unit-test: [----------------------- 202s 202s # bbmap 202s bbmap.sh --version 202s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 202s java -ea -Xmx2844m -Xms2844m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 --version 202s BBMap version 39.06 202s For help, please run the shellscript with no parameters, or look in /docs/. 202s bbmap.sh --help 202s 202s BBMap 202s Written by Brian Bushnell, from Dec. 2010 - present 202s Last modified September 15, 2022 202s 202s Description: Fast and accurate splice-aware read aligner. 202s Please read bbmap/docs/guides/BBMapGuide.txt for more information. 202s 202s To index: bbmap.sh ref= 202s To map: bbmap.sh in= out= 202s To map without writing an index: 202s bbmap.sh ref= in= out= nodisk 202s 202s in=stdin will accept reads from standard in, and out=stdout will write to 202s standard out, but file extensions are still needed to specify the format of the 202s input and output files e.g. in=stdin.fa.gz will read gzipped fasta from 202s standard in; out=stdout.sam.gz will write gzipped sam. 202s 202s Indexing Parameters (required when building the index): 202s nodisk=f Set to true to build index in memory and write nothing 202s to disk except output. 202s ref= Specify the reference sequence. Only do this ONCE, 202s when building the index (unless using 'nodisk'). 202s build=1 If multiple references are indexed in the same directory, 202s each needs a unique numeric ID (unless using 'nodisk'). 202s k=13 Kmer length, range 8-15. Longer is faster but uses 202s more memory. Shorter is more sensitive. 202s If indexing and mapping are done in two steps, K should 202s be specified each time. 202s path=<.> Specify the location to write the index, if you don't 202s want it in the current working directory. 202s usemodulo=f Throw away ~80% of kmers based on remainder modulo a 202s number (reduces RAM by 50% and sensitivity slightly). 202s Should be enabled both when building the index AND 202s when mapping. 202s rebuild=f Force a rebuild of the index (ref= should be set). 202s 202s Input Parameters: 202s build=1 Designate index to use. Corresponds to the number 202s specified when building the index. 202s in= Primary reads input; required parameter. 202s in2= For paired reads in two files. 202s interleaved=auto True forces paired/interleaved input; false forces 202s single-ended mapping. If not specified, interleaved 202s status will be autodetected from read names. 202s fastareadlen=500 Break up FASTA reads longer than this. Max is 500 for 202s BBMap and 6000 for BBMapPacBio. Only works for FASTA 202s input (use 'maxlen' for FASTQ input). The default for 202s bbmap.sh is 500, and for mapPacBio.sh is 6000. 202s unpigz=f Spawn a pigz (parallel gzip) process for faster 202s decompression than using Java. 202s Requires pigz to be installed. 202s touppercase=t (tuc) Convert lowercase letters in reads to upper case 202s (otherwise they will not match the reference). 202s 202s Sampling Parameters: 202s 202s reads=-1 Set to a positive number N to only process the first N 202s reads (or pairs), then quit. -1 means use all reads. 202s samplerate=1 Set to a number from 0 to 1 to randomly select that 202s fraction of reads for mapping. 1 uses all reads. 202s skipreads=0 Set to a number N to skip the first N reads (or pairs), 202s then map the rest. 202s 202s Mapping Parameters: 202s fast=f This flag is a macro which sets other paramters to run 202s faster, at reduced sensitivity. Bad for RNA-seq. 202s slow=f This flag is a macro which sets other paramters to run 202s slower, at greater sensitivity. 'vslow' is even slower. 202s maxindel=16000 Don't look for indels longer than this. Lower is faster. 202s Set to >=100k for RNAseq with long introns like mammals. 202s strictmaxindel=f When enabled, do not allow indels longer than 'maxindel'. 202s By default these are not sought, but may be found anyway. 202s tipsearch=100 Look this far for read-end deletions with anchors 202s shorter than K, using brute force. 202s minid=0.76 Approximate minimum alignment identity to look for. 202s Higher is faster and less sensitive. 202s minhits=1 Minimum number of seed hits required for candidate sites. 202s Higher is faster. 202s local=f Set to true to use local, rather than global, alignments. 202s This will soft-clip ugly ends of poor alignments. 202s perfectmode=f Allow only perfect mappings when set to true (very fast). 202s semiperfectmode=f Allow only perfect and semiperfect (perfect except for 202s N's in the reference) mappings. 202s threads=auto (t) Set to number of threads desired. By default, uses 202s all cores available. 202s ambiguous=best (ambig) Set behavior on ambiguously-mapped reads (with 202s multiple top-scoring mapping locations). 202s best (use the first best site) 202s toss (consider unmapped) 202s random (select one top-scoring site randomly) 202s all (retain all top-scoring sites) 202s samestrandpairs=f (ssp) Specify whether paired reads should map to the 202s same strand or opposite strands. 202s requirecorrectstrand=t (rcs) Forbid pairing of reads without correct strand 202s orientation. Set to false for long-mate-pair libraries. 202s killbadpairs=f (kbp) If a read pair is mapped with an inappropriate 202s insert size or orientation, the read with the lower 202s mapping quality is marked unmapped. 202s pairedonly=f (po) Treat unpaired reads as unmapped. Thus they will 202s be sent to 'outu' but not 'outm'. 202s rcomp=f Reverse complement both reads prior to mapping (for LMP 202s outward-facing libraries). 202s rcompmate=f Reverse complement read2 prior to mapping. 202s pairlen=32000 Set max allowed distance between paired reads. 202s (insert size)=(pairlen)+(read1 length)+(read2 length) 202s rescuedist=1200 Don't try to rescue paired reads if avg. insert size 202s greater than this. Lower is faster. 202s rescuemismatches=32 Maximum mismatches allowed in a rescued read. Lower 202s is faster. 202s averagepairdist=100 (apd) Initial average distance between paired reads. 202s Varies dynamically; does not need to be specified. 202s deterministic=f Run in deterministic mode. In this case it is good 202s to set averagepairdist. BBMap is deterministic 202s without this flag if using single-ended reads, 202s or run singlethreaded. 202s bandwidthratio=0 (bwr) If above zero, restrict alignment band to this 202s fraction of read length. Faster but less accurate. 202s bandwidth=0 (bw) Set the bandwidth directly. 202s fraction of read length. Faster but less accurate. 202s usejni=f (jni) Do alignments faster, in C code. Requires 202s compiling the C code; details are in /jni/README.txt. 202s maxsites2=800 Don't analyze (or print) more than this many alignments 202s per read. 202s ignorefrequentkmers=t (ifk) Discard low-information kmers that occur often. 202s excludefraction=0.03 (ef) Fraction of kmers to ignore. For example, 0.03 202s will ignore the most common 3% of kmers. 202s greedy=t Use a greedy algorithm to discard the least-useful 202s kmers on a per-read basis. 202s kfilter=0 If positive, potential mapping sites must have at 202s least this many consecutive exact matches. 202s 202s 202s Quality and Trimming Parameters: 202s qin=auto Set to 33 or 64 to specify input quality value ASCII 202s offset. 33 is Sanger, 64 is old Solexa. 202s qout=auto Set to 33 or 64 to specify output quality value ASCII 202s offset (only if output format is fastq). 202s qtrim=f Quality-trim ends before mapping. Options are: 202s 'f' (false), 'l' (left), 'r' (right), and 'lr' (both). 202s untrim=f Undo trimming after mapping. Untrimmed bases will be 202s soft-clipped in cigar strings. 202s trimq=6 Trim regions with average quality below this 202s (phred algorithm). 202s mintrimlength=60 (mintl) Don't trim reads to be shorter than this. 202s fakefastaquality=-1 (ffq) Set to a positive number 1-50 to generate fake 202s quality strings for fasta input reads. 202s ignorebadquality=f (ibq) Keep going, rather than crashing, if a read has 202s out-of-range quality values. 202s usequality=t Use quality scores when determining which read kmers 202s to use as seeds. 202s minaveragequality=0 (maq) Do not map reads with average quality below this. 202s maqb=0 If positive, calculate maq from this many initial bases. 202s 202s Output Parameters: 202s out= Write all reads to this file. 202s outu= Write only unmapped reads to this file. Does not 202s include unmapped paired reads with a mapped mate. 202s outm= Write only mapped reads to this file. Includes 202s unmapped paired reads with a mapped mate. 202s mappedonly=f If true, treats 'out' like 'outm'. 202s bamscript= (bs) Write a shell script to that will turn 202s the sam output into a sorted, indexed bam file. 202s ordered=f Set to true to output reads in same order as input. 202s Slower and uses more memory. 202s overwrite=f (ow) Allow process to overwrite existing files. 202s secondary=f Print secondary alignments. 202s sssr=0.95 (secondarysitescoreratio) Print only secondary alignments 202s with score of at least this fraction of primary. 202s ssao=f (secondarysiteasambiguousonly) Only print secondary 202s alignments for ambiguously-mapped reads. 202s maxsites=5 Maximum number of total alignments to print per read. 202s Only relevant when secondary=t. 202s quickmatch=f Generate cigar strings more quickly. 202s trimreaddescriptions=f (trd) Truncate read and ref names at the first whitespace, 202s assuming that the remainder is a comment or description. 202s ziplevel=2 (zl) Compression level for zip or gzip output. 202s pigz=f Spawn a pigz (parallel gzip) process for faster 202s compression than Java. Requires pigz to be installed. 202s machineout=f Set to true to output statistics in machine-friendly 202s 'key=value' format. 202s printunmappedcount=f Print the total number of unmapped reads and bases. 202s If input is paired, the number will be of pairs 202s for which both reads are unmapped. 202s showprogress=0 If positive, print a '.' every X reads. 202s showprogress2=0 If positive, print the number of seconds since the 202s last progress update (instead of a '.'). 202s renamebyinsert=f Renames reads based on their mapped insert size. 202s 202s Bloom-Filtering Parameters (bloomfilter.sh is the standalone version). 202s bloom=f Use a Bloom filter to ignore reads not sharing kmers 202s with the reference. This uses more memory, but speeds 202s mapping when most reads don't match the reference. 202s bloomhashes=2 Number of hash functions. 202s bloomminhits=3 Number of consecutive hits to be considered matched. 202s bloomk=31 Bloom filter kmer length. 202s bloomserial=t Use the serialized Bloom filter for greater loading 202s speed, if available. If not, generate and write one. 202s 202s Post-Filtering Parameters: 202s idfilter=0 Independant of minid; sets exact minimum identity 202s allowed for alignments to be printed. Range 0 to 1. 202s subfilter=-1 Ban alignments with more than this many substitutions. 202s insfilter=-1 Ban alignments with more than this many insertions. 202s delfilter=-1 Ban alignments with more than this many deletions. 202s indelfilter=-1 Ban alignments with more than this many indels. 202s editfilter=-1 Ban alignments with more than this many edits. 202s inslenfilter=-1 Ban alignments with an insertion longer than this. 202s dellenfilter=-1 Ban alignments with a deletion longer than this. 202s nfilter=-1 Ban alignments with more than this many ns. This 202s includes nocall, noref, and off scaffold ends. 202s 202s Sam flags and settings: 202s noheader=f Disable generation of header lines. 202s sam=1.4 Set to 1.4 to write Sam version 1.4 cigar strings, 202s with = and X, or 1.3 to use M. 202s saa=t (secondaryalignmentasterisks) Use asterisks instead of 202s bases for sam secondary alignments. 202s cigar=t Set to 'f' to skip generation of cigar strings (faster). 202s keepnames=f Keep original names of paired reads, rather than 202s ensuring both reads have the same name. 202s intronlen=999999999 Set to a lower number like 10 to change 'D' to 'N' in 202s cigar strings for deletions of at least that length. 202s rgid= Set readgroup ID. All other readgroup fields 202s can be set similarly, with the flag rgXX= 202s If you set a readgroup flag to the word 'filename', 202s e.g. rgid=filename, the input file name will be used. 202s mdtag=f Write MD tags. 202s nhtag=f Write NH tags. 202s xmtag=f Write XM tags (may only work correctly with ambig=all). 202s amtag=f Write AM tags. 202s nmtag=f Write NM tags. 202s xstag=f Set to 'xs=fs', 'xs=ss', or 'xs=us' to write XS tags 202s for RNAseq using firststrand, secondstrand, or 202s unstranded libraries. Needed by Cufflinks. 202s JGI mainly uses 'firststrand'. 202s stoptag=f Write a tag indicating read stop location, prefixed by YS:i: 202s lengthtag=f Write a tag indicating (query,ref) alignment lengths, 202s prefixed by YL:Z: 202s idtag=f Write a tag indicating percent identity, prefixed by YI:f: 202s inserttag=f Write a tag indicating insert size, prefixed by X8:Z: 202s scoretag=f Write a tag indicating BBMap's raw score, prefixed by YR:i: 202s timetag=f Write a tag indicating this read's mapping time, prefixed by X0:i: 202s boundstag=f Write a tag indicating whether either read in the pair 202s goes off the end of the reference, prefixed by XB:Z: 202s notags=f Turn off all optional tags. 202s 202s Histogram and statistics output parameters: 202s scafstats= Statistics on how many reads mapped to which scaffold. 202s refstats= Statistics on how many reads mapped to which reference 202s file; only for BBSplit. 202s sortscafs=t Sort scaffolds or references by read count. 202s bhist= Base composition histogram by position. 202s qhist= Quality histogram by position. 202s aqhist= Histogram of average read quality. 202s bqhist= Quality histogram designed for box plots. 202s lhist= Read length histogram. 202s ihist= Write histogram of insert sizes (for paired reads). 202s ehist= Errors-per-read histogram. 202s qahist= Quality accuracy histogram of error rates versus 202s quality score. 202s indelhist= Indel length histogram. 202s mhist= Histogram of match, sub, del, and ins rates by 202s read location. 202s gchist= Read GC content histogram. 202s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 202s gcpairs=t Use average GC of paired reads. 202s idhist= Histogram of read count versus percent identity. 202s idbins=100 Number idhist bins. Set to 'auto' to use read length. 202s statsfile=stderr Mapping statistics are printed here. 202s 202s Coverage output parameters (these may reduce speed and use more RAM): 202s covstats= Per-scaffold coverage info. 202s rpkm= Per-scaffold RPKM/FPKM counts. 202s covhist= Histogram of # occurrences of each depth level. 202s basecov= Coverage per base location. 202s bincov= Print binned coverage per location (one line per X bases). 202s covbinsize=1000 Set the binsize for binned coverage output. 202s nzo=t Only print scaffolds with nonzero coverage. 202s twocolumn=f Change to true to print only ID and Avg_fold instead of 202s all 6 columns to the 'out=' file. 202s 32bit=f Set to true if you need per-base coverage over 64k. 202s strandedcov=f Track coverage for plus and minus strand independently. 202s startcov=f Only track start positions of reads. 202s secondarycov=t Include coverage of secondary alignments. 202s physcov=f Calculate physical coverage for paired reads. 202s This includes the unsequenced bases. 202s delcoverage=t (delcov) Count bases covered by deletions as covered. 202s True is faster than false. 202s covk=0 If positive, calculate kmer coverage statistics. 202s 202s Java Parameters: 202s -Xmx This will set Java's memory usage, 202s overriding autodetection. 202s -Xmx20g will specify 20 gigs of RAM, and -Xmx800m 202s will specify 800 megs. The max is typically 85% of 202s physical memory. The human genome requires around 24g, 202s or 12g with the 'usemodulo' flag. The index uses 202s roughly 6 bytes per reference base. 202s -eoom This flag will cause the process to exit if an 202s out-of-memory exception occurs. Requires Java 8u92+. 202s -da Disable assertions. 202s 202s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter 202s any problems, or post at: http://seqanswers.com/forums/showthread.php?t=41057 202s 202s bbmap.sh ref=example.fasta 202s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 202s java -ea -Xmx2845m -Xms2845m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta 202s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta] 202s Version 39.06 202s 202s No output file. 202s Writing reference. 202s 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] 202s 202s Set genScaffoldInfo=true 202s Writing chunk 1 202s Set genome to 1 202s 202s Loaded Reference: 0.010 seconds. 202s Loading index for chunk 1-1, build 1 202s No index available; generating from reference genome: /tmp/autopkgtest.w2oJl0/autopkgtest_tmp/ref/index/1/chr1_index_k13_c16_b1.block 202s Indexing threads started for block 0-1 203s Indexing threads finished for block 0-1 204s Generated Index: 1.832 seconds. 204s No reads to process; quitting. 204s 204s Total time: 1.970 seconds. 204s test -d ref 204s bbmap.sh in=misc_dna_as_sanger.fastq out=out.sam 204s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 204s 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 204s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, in=misc_dna_as_sanger.fastq, out=out.sam] 204s Version 39.06 204s 204s Retaining first best site only for ambiguous mappings. 204s Set genome to 1 204s 204s Loaded Reference: 0.019 seconds. 204s Loading index for chunk 1-1, build 1 205s Generated Index: 1.001 seconds. 214s Analyzed Index: 8.423 seconds. 214s Started output stream: 0.026 seconds. 214s Cleared Memory: 0.134 seconds. 214s Processing reads in single-ended mode. 214s Started read stream. 214s Started 4 mapping threads. 214s Detecting finished threads: 0, 1, 2, 3 214s 214s ------------------ Results ------------------ 214s 214s Genome: 1 214s Key Length: 13 214s Max Indel: 16000 214s Minimum Score Ratio: 0.56 214s Mapping Mode: normal 214s Reads Used: 4 (153 bases) 214s 214s Mapping: 0.157 seconds. 214s Reads/sec: 25.44 214s kBases/sec: 0.97 214s 214s 214s Read 1 data: pct reads num reads pct bases num bases 214s 214s mapped: 0.0000% 0 0.0000% 0 214s unambiguous: 0.0000% 0 0.0000% 0 214s ambiguous: 0.0000% 0 0.0000% 0 214s low-Q discards: 25.0000% 1 19.6078% 30 214s 214s perfect best site: 0.0000% 0 0.0000% 0 214s semiperfect site: 0.0000% 0 0.0000% 0 214s 214s Match Rate: NA NA NaN% 0 214s Error Rate: NaN% 0 NaN% 0 214s Sub Rate: NaN% 0 NaN% 0 214s Del Rate: NaN% 0 NaN% 0 214s Ins Rate: NaN% 0 NaN% 0 214s N Rate: NaN% 0 NaN% 0 214s 214s Total time: 9.850 seconds. 214s test -r out.sam 214s bbmap.sh ref=example.fasta in=example.fastq out=out2.sam nodisk 214s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 214s 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 214s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta, in=example.fastq, out=out2.sam, nodisk] 214s Version 39.06 214s 214s Retaining first best site only for ambiguous mappings. 214s 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] 214s 214s Set genScaffoldInfo=true 214s Set genome to 1 214s 214s Loaded Reference: 0.001 seconds. 214s Loading index for chunk 1-1, build 1 214s Indexing threads started for block 0-1 215s Indexing threads finished for block 0-1 215s Generated Index: 0.408 seconds. 223s Analyzed Index: 8.392 seconds. 223s Started output stream: 0.024 seconds. 223s Cleared Memory: 0.120 seconds. 223s Processing reads in single-ended mode. 223s Started read stream. 223s Started 4 mapping threads. 223s Detecting finished threads: 0, 1, 2, 3 223s 223s ------------------ Results ------------------ 223s 223s Genome: 1 223s Key Length: 13 223s Max Indel: 16000 223s Minimum Score Ratio: 0.56 223s Mapping Mode: normal 223s Reads Used: 3 (75 bases) 223s 223s Mapping: 0.143 seconds. 223s Reads/sec: 20.96 223s kBases/sec: 0.52 223s 223s 223s Read 1 data: pct reads num reads pct bases num bases 223s 223s mapped: 100.0000% 3 100.0000% 75 223s unambiguous: 100.0000% 3 100.0000% 75 223s ambiguous: 0.0000% 0 0.0000% 0 223s low-Q discards: 0.0000% 0 0.0000% 0 223s 223s perfect best site: 100.0000% 3 100.0000% 75 223s semiperfect site: 100.0000% 3 100.0000% 75 223s 223s Match Rate: NA NA 100.0000% 75 223s Error Rate: 0.0000% 0 0.0000% 0 223s Sub Rate: 0.0000% 0 0.0000% 0 223s Del Rate: 0.0000% 0 0.0000% 0 223s Ins Rate: 0.0000% 0 0.0000% 0 223s N Rate: 0.0000% 0 0.0000% 0 223s 223s Total time: 9.191 seconds. 224s test -r out2.sam 224s 224s # bbduk 224s bbduk.sh --version 224s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 224s java -ea -Xmx1422m -Xms1422m -cp /usr/share/java/bbmap.jar jgi.BBDuk --version 224s BBMap version 39.06 224s For help, please run the shellscript with no parameters, or look in /docs/. 224s bbduk.sh --help 224s 224s Written by Brian Bushnell 224s Last modified November 9, 2023 224s 224s Description: Compares reads to the kmers in a reference dataset, optionally 224s allowing an edit distance. Splits the reads into two outputs - those that 224s match the reference, and those that don't. Can also trim (remove) the matching 224s parts of the reads rather than binning the reads. 224s Please read bbmap/docs/guides/BBDukGuide.txt for more information. 224s 224s Usage: bbduk.sh in= out= ref= 224s 224s Input may be stdin or a fasta or fastq file, compressed or uncompressed. 224s If you pipe via stdin/stdout, please include the file type; e.g. for gzipped 224s fasta input, set in=stdin.fa.gz 224s 224s Input parameters: 224s in= Main input. in=stdin.fq will pipe from stdin. 224s in2= Input for 2nd read of pairs in a different file. 224s ref= Comma-delimited list of reference files. 224s In addition to filenames, you may also use the keywords: 224s adapters, artifacts, phix, lambda, pjet, mtst, kapa 224s literal= Comma-delimited list of literal reference sequences. 224s touppercase=f (tuc) Change all bases upper-case. 224s interleaved=auto (int) t/f overrides interleaved autodetection. 224s Must be set mainually when streaming fastq input. 224s qin=auto Input quality offset: 33 (Sanger), 64, or auto. 224s reads=-1 If positive, quit after processing X reads or pairs. 224s copyundefined=f (cu) Process non-AGCT IUPAC reference bases by making all 224s possible unambiguous copies. Intended for short motifs 224s or adapter barcodes, as time/memory use is exponential. 224s samplerate=1 Set lower to only process a fraction of input reads. 224s samref= Optional reference fasta for processing sam files. 224s 224s Output parameters: 224s out= (outnonmatch) Write reads here that do not contain 224s kmers matching the database. 'out=stdout.fq' will pipe 224s to standard out. 224s out2= (outnonmatch2) Use this to write 2nd read of pairs to a 224s different file. 224s outm= (outmatch) Write reads here that fail filters. In default 224s kfilter mode, this means any read with a matching kmer. 224s In any mode, it also includes reads that fail filters such 224s as minlength, mingc, maxgc, entropy, etc. In other words, 224s it includes all reads that do not go to 'out'. 224s outm2= (outmatch2) Use this to write 2nd read of pairs to a 224s different file. 224s outs= (outsingle) Use this to write singleton reads whose mate 224s was trimmed shorter than minlen. 224s stats= Write statistics about which contamininants were detected. 224s refstats= Write statistics on a per-reference-file basis. 224s rpkm= Write RPKM for each reference sequence (for RNA-seq). 224s dump= Dump kmer tables to a file, in fasta format. 224s duk= Write statistics in duk's format. *DEPRECATED* 224s nzo=t Only write statistics about ref sequences with nonzero hits. 224s overwrite=t (ow) Grant permission to overwrite files. 224s showspeed=t (ss) 'f' suppresses display of processing speed. 224s ziplevel=2 (zl) Compression level; 1 (min) through 9 (max). 224s fastawrap=70 Length of lines in fasta output. 224s qout=auto Output quality offset: 33 (Sanger), 64, or auto. 224s statscolumns=3 (cols) Number of columns for stats output, 3 or 5. 224s 5 includes base counts. 224s rename=f Rename reads to indicate which sequences they matched. 224s refnames=f Use names of reference files rather than scaffold IDs. 224s trd=f Truncate read and ref names at the first whitespace. 224s ordered=f Set to true to output reads in same order as input. 224s maxbasesout=-1 If positive, quit after writing approximately this many 224s bases to out (outu/outnonmatch). 224s maxbasesoutm=-1 If positive, quit after writing approximately this many 224s bases to outm (outmatch). 224s json=f Print to screen in json format. 224s 224s Histogram output parameters: 224s bhist= Base composition histogram by position. 224s qhist= Quality histogram by position. 224s qchist= Count of bases with each quality value. 224s aqhist= Histogram of average read quality. 224s bqhist= Quality histogram designed for box plots. 224s lhist= Read length histogram. 224s phist= Polymer length histogram. 224s gchist= Read GC content histogram. 224s enthist= Read entropy histogram. 224s ihist= Insert size histogram, for paired reads in mapped sam. 224s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 224s maxhistlen=6000 Set an upper bound for histogram lengths; higher uses 224s more memory. The default is 6000 for some histograms 224s and 80000 for others. 224s 224s Histograms for mapped sam/bam files only: 224s histbefore=t Calculate histograms from reads before processing. 224s ehist= Errors-per-read histogram. 224s qahist= Quality accuracy histogram of error rates versus quality 224s score. 224s indelhist= Indel length histogram. 224s mhist= Histogram of match, sub, del, and ins rates by position. 224s idhist= Histogram of read count versus percent identity. 224s idbins=100 Number idhist bins. Set to 'auto' to use read length. 224s varfile= Ignore substitution errors listed in this file when 224s calculating error rates. Can be generated with 224s CallVariants. 224s vcf= Ignore substitution errors listed in this VCF file 224s when calculating error rates. 224s ignorevcfindels=t Also ignore indels listed in the VCF. 224s 224s Processing parameters: 224s k=27 Kmer length used for finding contaminants. Contaminants 224s shorter than k will not be found. k must be at least 1. 224s rcomp=t Look for reverse-complements of kmers in addition to 224s forward kmers. 224s maskmiddle=t (mm) Treat the middle base of a kmer as a wildcard, to 224s increase sensitivity in the presence of errors. This may 224s also be set to a number, e.g. mm=3, to mask that many bp. 224s The default mm=t corresponds to mm=1 for odd-length kmers 224s and mm=2 for even-length kmers (as of v39.04), while 224s mm=f is always equivalent to mm=0. 224s minkmerhits=1 (mkh) Reads need at least this many matching kmers 224s to be considered as matching the reference. 224s minkmerfraction=0.0 (mkf) A reads needs at least this fraction of its total 224s kmers to hit a ref, in order to be considered a match. 224s If this and minkmerhits are set, the greater is used. 224s mincovfraction=0.0 (mcf) A reads needs at least this fraction of its total 224s bases to be covered by ref kmers to be considered a match. 224s If specified, mcf overrides mkh and mkf. 224s hammingdistance=0 (hdist) Maximum Hamming distance for ref kmers (subs only). 224s Memory use is proportional to (3*K)^hdist. 224s qhdist=0 Hamming distance for query kmers; impacts speed, not memory. 224s editdistance=0 (edist) Maximum edit distance from ref kmers (subs 224s and indels). Memory use is proportional to (8*K)^edist. 224s hammingdistance2=0 (hdist2) Sets hdist for short kmers, when using mink. 224s qhdist2=0 Sets qhdist for short kmers, when using mink. 224s editdistance2=0 (edist2) Sets edist for short kmers, when using mink. 224s forbidn=f (fn) Forbids matching of read kmers containing N. 224s By default, these will match a reference 'A' if 224s hdist>0 or edist>0, to increase sensitivity. 224s removeifeitherbad=t (rieb) Paired reads get sent to 'outmatch' if either is 224s match (or either is trimmed shorter than minlen). 224s Set to false to require both. 224s trimfailures=f Instead of discarding failed reads, trim them to 1bp. 224s This makes the statistics a bit odd. 224s findbestmatch=f (fbm) If multiple matches, associate read with sequence 224s sharing most kmers. Reduces speed. 224s skipr1=f Don't do kmer-based operations on read 1. 224s skipr2=f Don't do kmer-based operations on read 2. 224s ecco=f For overlapping paired reads only. Performs error- 224s correction with BBMerge prior to kmer operations. 224s recalibrate=f (recal) Recalibrate quality scores. Requires calibration 224s matrices generated by CalcTrueQuality. 224s sam= If recalibration is desired, and matrices have not already 224s been generated, BBDuk will create them from the sam file. 224s amino=f Run in amino acid mode. Some features have not been 224s tested, but kmer-matching works fine. Maximum k is 12. 224s 224s Speed and Memory parameters: 224s threads=auto (t) Set number of threads to use; default is number of 224s logical processors. 224s prealloc=f Preallocate memory in table. Allows faster table loading 224s and more efficient memory usage, for a large reference. 224s monitor=f Kill this process if it crashes. monitor=600,0.01 would 224s kill after 600 seconds under 1% usage. 224s minrskip=1 (mns) Force minimal skip interval when indexing reference 224s kmers. 1 means use all, 2 means use every other kmer, etc. 224s maxrskip=1 (mxs) Restrict maximal skip interval when indexing 224s reference kmers. Normally all are used for scaffolds<100kb, 224s but with longer scaffolds, up to maxrskip-1 are skipped. 224s rskip= Set both minrskip and maxrskip to the same value. 224s If not set, rskip will vary based on sequence length. 224s qskip=1 Skip query kmers to increase speed. 1 means use all. 224s speed=0 Ignore this fraction of kmer space (0-15 out of 16) in both 224s reads and reference. Increases speed and reduces memory. 224s Note: Do not use more than one of 'speed', 'qskip', and 'rskip'. 224s 224s Trimming/Filtering/Masking parameters: 224s Note - if ktrim, kmask, and ksplit are unset, the default behavior is kfilter. 224s All kmer processing modes are mutually exclusive. 224s Reads only get sent to 'outm' purely based on kmer matches in kfilter mode. 224s 224s ktrim=f Trim reads to remove bases matching reference kmers, plus 224s all bases to the left or right. 224s Values: 224s f (don't trim), 224s r (trim to the right), 224s l (trim to the left) 224s ktrimtips=0 Set this to a positive number to perform ktrim on both 224s ends, examining only the outermost X bases. 224s kmask= Replace bases matching ref kmers with another symbol. 224s Allows any non-whitespace character, and processes short 224s kmers on both ends if mink is set. 'kmask=lc' will 224s convert masked bases to lowercase. 224s maskfullycovered=f (mfc) Only mask bases that are fully covered by kmers. 224s ksplit=f For single-ended reads only. Reads will be split into 224s pairs around the kmer. If the kmer is at the end of the 224s read, it will be trimmed instead. Singletons will go to 224s out, and pairs will go to outm. Do not use ksplit with 224s other operations such as quality-trimming or filtering. 224s mink=0 Look for shorter kmers at read tips down to this length, 224s when k-trimming or masking. 0 means disabled. Enabling 224s this will disable maskmiddle. 224s qtrim=f Trim read ends to remove bases with quality below trimq. 224s Performed AFTER looking for kmers. Values: 224s rl (trim both ends), 224s f (neither end), 224s r (right end only), 224s l (left end only), 224s w (sliding window). 224s trimq=6 Regions with average quality BELOW this will be trimmed, 224s if qtrim is set to something other than f. Can be a 224s floating-point number like 7.3. 224s trimclip=f Trim soft-clipped bases from sam files. 224s minlength=10 (ml) Reads shorter than this after trimming will be 224s discarded. Pairs will be discarded if both are shorter. 224s mlf=0 (minlengthfraction) Reads shorter than this fraction of 224s original length after trimming will be discarded. 224s maxlength= Reads longer than this after trimming will be discarded. 224s minavgquality=0 (maq) Reads with average quality (after trimming) below 224s this will be discarded. 224s maqb=0 If positive, calculate maq from this many initial bases. 224s minbasequality=0 (mbq) Reads with any base below this quality (after 224s trimming) will be discarded. 224s maxns=-1 If non-negative, reads with more Ns than this 224s (after trimming) will be discarded. 224s mcb=0 (minconsecutivebases) Discard reads without at least 224s this many consecutive called bases. 224s ottm=f (outputtrimmedtomatch) Output reads trimmed to shorter 224s than minlength to outm rather than discarding. 224s tp=0 (trimpad) Trim this much extra around matching kmers. 224s tbo=f (trimbyoverlap) Trim adapters based on where paired 224s reads overlap. 224s strictoverlap=t Adjust sensitivity for trimbyoverlap mode. 224s minoverlap=14 Require this many bases of overlap for detection. 224s mininsert=40 Require insert size of at least this for overlap. 224s Should be reduced to 16 for small RNA sequencing. 224s tpe=f (trimpairsevenly) When kmer right-trimming, trim both 224s reads to the minimum length of either. 224s forcetrimleft=0 (ftl) If positive, trim bases to the left of this position 224s (exclusive, 0-based). 224s forcetrimright=0 (ftr) If positive, trim bases to the right of this position 224s (exclusive, 0-based). 224s forcetrimright2=0 (ftr2) If positive, trim this many bases on the right end. 224s forcetrimmod=0 (ftm) If positive, right-trim length to be equal to zero, 224s modulo this number. 224s restrictleft=0 If positive, only look for kmer matches in the 224s leftmost X bases. 224s restrictright=0 If positive, only look for kmer matches in the 224s rightmost X bases. 224s NOTE: restrictleft and restrictright are mutually exclusive. If trimming 224s both ends is desired, use ktrimtips. 224s mingc=0 Discard reads with GC content below this. 224s maxgc=1 Discard reads with GC content above this. 224s gcpairs=t Use average GC of paired reads. 224s Also affects gchist. 224s tossjunk=f Discard reads with invalid characters as bases. 224s swift=f Trim Swift sequences: Trailing C/T/N R1, leading G/A/N R2. 224s 224s Header-parsing parameters - these require Illumina headers: 224s chastityfilter=f (cf) Discard reads with id containing ' 1:Y:' or ' 2:Y:'. 224s barcodefilter=f Remove reads with unexpected barcodes if barcodes is set, 224s or barcodes containing 'N' otherwise. A barcode must be 224s the last part of the read header. Values: 224s t: Remove reads with bad barcodes. 224s f: Ignore barcodes. 224s crash: Crash upon encountering bad barcodes. 224s barcodes= Comma-delimited list of barcodes or files of barcodes. 224s xmin=-1 If positive, discard reads with a lesser X coordinate. 224s ymin=-1 If positive, discard reads with a lesser Y coordinate. 224s xmax=-1 If positive, discard reads with a greater X coordinate. 224s ymax=-1 If positive, discard reads with a greater Y coordinate. 224s 224s Polymer trimming: 224s trimpolya=0 If greater than 0, trim poly-A or poly-T tails of 224s at least this length on either end of reads. 224s trimpolygleft=0 If greater than 0, trim poly-G prefixes of at least this 224s length on the left end of reads. Does not trim poly-C. 224s trimpolygright=0 If greater than 0, trim poly-G tails of at least this 224s length on the right end of reads. Does not trim poly-C. 224s trimpolyg=0 This sets both left and right at once. 224s filterpolyg=0 If greater than 0, remove reads with a poly-G prefix of 224s at least this length (on the left). 224s Note: there are also equivalent poly-C flags. 224s 224s Polymer tracking: 224s pratio=base,base 'pratio=G,C' will print the ratio of G to C polymers. 224s plen=20 Length of homopolymers to count. 224s 224s Entropy/Complexity parameters: 224s entropy=-1 Set between 0 and 1 to filter reads with entropy below 224s that value. Higher is more stringent. 224s entropywindow=50 Calculate entropy using a sliding window of this length. 224s entropyk=5 Calculate entropy using kmers of this length. 224s minbasefrequency=0 Discard reads with a minimum base frequency below this. 224s entropytrim=f Values: 224s f: (false) Do not entropy-trim. 224s r: (right) Trim low entropy on the right end only. 224s l: (left) Trim low entropy on the left end only. 224s rl: (both) Trim low entropy on both ends. 224s entropymask=f Values: 224s f: (filter) Discard low-entropy sequences. 224s t: (true) Mask low-entropy parts of sequences with N. 224s lc: Change low-entropy parts of sequences to lowercase. 224s entropymark=f Mark each base with its entropy value. This is on a scale 224s of 0-41 and is reported as quality scores, so the output 224s should be fastq or fasta+qual. 224s NOTE: If set, entropytrim overrides entropymask. 224s 224s Cardinality estimation: 224s cardinality=f (loglog) Count unique kmers using the LogLog algorithm. 224s cardinalityout=f (loglogout) Count unique kmers in output reads. 224s loglogk=31 Use this kmer length for counting. 224s loglogbuckets=2048 Use this many buckets for counting. 224s khist= Kmer frequency histogram; plots number of kmers versus 224s kmer depth. This is approximate. 224s khistout= Kmer frequency histogram for output reads. 224s 224s Java Parameters: 224s 224s -Xmx This will set Java's memory usage, overriding autodetection. 224s -Xmx20g will 224s specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 224s The max is typically 85% of physical memory. 224s -eoom This flag will cause the process to exit if an 224s out-of-memory exception occurs. Requires Java 8u92+. 224s -da Disable assertions. 224s 224s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 224s 224s bbduk.sh in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq \ 224s qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 224s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 224s 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 224s 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] 224s Version 39.06 224s 224s 0.034 seconds. 224s Initial: 224s Memory: max=1491m, total=1491m, free=1460m, used=31m 224s 224s Input is being processed as paired 224s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 224s Started output streams: 0.031 seconds. 224s Processing time: 0.005 seconds. 224s 224s Input: 8 reads 306 bases. 224s QTrimmed: 0 reads (0.00%) 0 bases (0.00%) 224s Total Removed: 8 reads (100.00%) 306 bases (100.00%) 224s Result: 0 reads (0.00%) 0 bases (0.00%) 224s 224s Time: 0.038 seconds. 224s Reads Processed: 8 0.21k reads/sec 224s Bases Processed: 306 0.01m bases/sec 224s test -r out.fastq.gz 224s 224s # bbnorm 224s bbnorm.sh --version 224s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 224s java -ea -Xmx2845m -Xms2845m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 --version 224s BBMap version 39.06 224s For help, please run the shellscript with no parameters, or look in /docs/. 224s bbnorm.sh --help 224s 224s Written by Brian Bushnell 224s Last modified October 19, 2017 224s 224s Description: Normalizes read depth based on kmer counts. 224s Can also error-correct, bin reads by kmer depth, and generate a kmer depth histogram. 224s However, Tadpole has superior error-correction to BBNorm. 224s Please read bbmap/docs/guides/BBNormGuide.txt for more information. 224s 224s Usage: bbnorm.sh in= out= outt= hist= 224s 224s Input parameters: 224s in=null Primary input. Use in2 for paired reads in a second file 224s in2=null Second input file for paired reads in two files 224s extra=null Additional files to use for input (generating hash table) but not for output 224s fastareadlen=2^31 Break up FASTA reads longer than this. Can be useful when processing scaffolded genomes 224s tablereads=-1 Use at most this many reads when building the hashtable (-1 means all) 224s kmersample=1 Process every nth kmer, and skip the rest 224s readsample=1 Process every nth read, and skip the rest 224s 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. 224s qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto. 224s 224s Output parameters: 224s out= File for normalized or corrected reads. Use out2 for paired reads in a second file 224s outt= (outtoss) File for reads that were excluded from primary output 224s reads=-1 Only process this number of reads, then quit (-1 means all) 224s sampleoutput=t Use sampling on output as well as input (not used if sample rates are 1) 224s keepall=f Set to true to keep all reads (e.g. if you just want error correction). 224s 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. 224s Default is false, to prevent confusion about how there can be 0-count kmers. 224s The reason is that based on the 'minq' and 'minprob' settings, some kmers may be excluded from the bloom filter. 224s tmpdir= This will specify a directory for temp files (only needed for multipass runs). If null, they will be written to the output directory. 224s usetempdir=t Allows enabling/disabling of temporary directory; if disabled, temp files will be written to the output directory. 224s qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input). 224s rename=f Rename reads based on their kmer depth. 224s 224s Hashing parameters: 224s k=31 Kmer length (values under 32 are most efficient, but arbitrarily high values are supported) 224s 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. 224s Large values decrease accuracy for a fixed amount of memory, so use the lowest number you can that will still capture highest-depth kmers. 224s hashes=3 Number of times each kmer is hashed and stored. Higher is slower. 224s Higher is MORE accurate if there is enough memory, and LESS accurate if there is not enough memory. 224s 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. 224s prehashes=2 Number of hashes for prefilter. 224s prefilterbits=2 (pbits) Bits per cell in prefilter. 224s prefiltersize=0.35 Fraction of memory to allocate to prefilter. 224s buildpasses=1 More passes can sometimes increase accuracy by iteratively removing low-depth kmers 224s minq=6 Ignore kmers containing bases with quality below this 224s minprob=0.5 Ignore kmers with overall probability of correctness below this 224s 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. 224s 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. 224s 224s Normalization parameters: 224s fixspikes=f (fs) Do a slower, high-precision bloom filter lookup of kmers that appear to have an abnormally high depth due to collisions. 224s target=100 (tgt) Target normalization depth. NOTE: All depth parameters control kmer depth, not read depth. 224s For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1)) 224s maxdepth=-1 (max) Reads will not be downsampled when below this depth, even if they are above the target depth. 224s mindepth=5 (min) Kmers with depth below this number will not be included when calculating the depth of a read. 224s minkmers=15 (mgkpr) Reads must have at least this many kmers over min depth to be retained. Aka 'mingoodkmersperread'. 224s 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. 224s uselowerdepth=t (uld) For pairs, use the depth of the lower read as the depth proxy. 224s deterministic=t (dr) Generate random numbers deterministically to ensure identical output between multiple runs. May decrease speed with a huge number of threads. 224s passes=2 (p) 1 pass is the basic mode. 2 passes (default) allows greater accuracy, error detection, better contol of output depth. 224s 224s Error detection parameters: 224s hdp=90.0 (highdepthpercentile) Position in sorted kmer depth array used as proxy of a read's high kmer depth. 224s ldp=25.0 (lowdepthpercentile) Position in sorted kmer depth array used as proxy of a read's low kmer depth. 224s tossbadreads=f (tbr) Throw away reads detected as containing errors. 224s requirebothbad=f (rbb) Only toss bad pairs if both reads are bad. 224s 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. 224s highthresh=12 (ht) Threshold for high kmer. A high kmer at this or above are considered non-error. 224s lowthresh=3 (lt) Threshold for low kmer. Kmers at this and below are always considered errors. 224s 224s Error correction parameters: 224s ecc=f Set to true to correct errors. NOTE: Tadpole is now preferred for ecc as it does a better job. 224s ecclimit=3 Correct up to this many errors per read. If more are detected, the read will remain unchanged. 224s errorcorrectratio=140 (ecr) Adjacent kmers with a depth ratio of at least this much between will be classified as an error. 224s echighthresh=22 (echt) Threshold for high kmer. A kmer at this or above may be considered non-error. 224s eclowthresh=2 (eclt) Threshold for low kmer. Kmers at this and below are considered errors. 224s eccmaxqual=127 Do not correct bases with quality above this value. 224s aec=f (aggressiveErrorCorrection) Sets more aggressive values of ecr=100, ecclimit=7, echt=16, eclt=3. 224s cec=f (conservativeErrorCorrection) Sets more conservative values of ecr=180, ecclimit=2, echt=30, eclt=1, sl=4, pl=4. 224s meo=f (markErrorsOnly) Marks errors by reducing quality value of suspected errors; does not correct anything. 224s mue=t (markUncorrectableErrors) Marks errors only on uncorrectable reads; requires 'ecc=t'. 224s overlap=f (ecco) Error correct by read overlap. 224s 224s Depth binning parameters: 224s lowbindepth=10 (lbd) Cutoff for low depth bin. 224s highbindepth=80 (hbd) Cutoff for high depth bin. 224s outlow= Pairs in which both reads have a median below lbd go into this file. 224s outhigh= Pairs in which both reads have a median above hbd go into this file. 224s outmid= All other pairs go into this file. 224s 224s Histogram parameters: 224s hist= Specify a file to write the input kmer depth histogram. 224s histout= Specify a file to write the output kmer depth histogram. 224s histcol=3 (histogramcolumns) Number of histogram columns, 2 or 3. 224s pzc=f (printzerocoverage) Print lines in the histogram with zero coverage. 224s histlen=1048576 Max kmer depth displayed in histogram. Also affects statistics displayed, but does not affect normalization. 224s 224s Peak calling parameters: 224s peaks= Write the peaks to this file. Default is stdout. 224s minHeight=2 (h) Ignore peaks shorter than this. 224s minVolume=5 (v) Ignore peaks with less area than this. 224s minWidth=3 (w) Ignore peaks narrower than this. 224s minPeak=2 (minp) Ignore peaks with an X-value below this. 224s maxPeak=BIG (maxp) Ignore peaks with an X-value above this. 224s maxPeakCount=8 (maxpc) Print up to this many peaks (prioritizing height). 224s 224s Java Parameters: 224s -Xmx This will set Java's memory usage, overriding autodetection. 224s -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 224s The max is typically 85% of physical memory. 224s -eoom This flag will cause the process to exit if an 224s out-of-memory exception occurs. Requires Java 8u92+. 224s -da Disable assertions. 224s 224s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 224s 224s bbnorm.sh in=sanger_full_range_original_sanger.fastq qin=33 \ 224s out=out3.fastq outt=outt.fastq hist=hist.plt 224s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 224s 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 224s Executing jgi.KmerNormalize [bits=32, in=sanger_full_range_original_sanger.fastq, qin=33, out=out3.fastq, outt=outt.fastq, hist=hist.plt] 224s 224s 224s *********** Pass 1 ********** 224s 224s 224s Settings: 224s threads: 4 224s k: 31 224s deterministic: true 224s toss error reads: false 224s passes: 1 224s bits per cell: 16 224s cells: 1052.92M 224s hashes: 3 224s base min quality: 5 224s kmer min prob: 0.5 224s 224s target depth: 400 224s min depth: 3 224s max depth: 500 224s min good kmers: 15 224s depth percentile: 64.8 224s ignore dupe kmers: true 224s fix spikes: false 224s histogram length: 65536 224s print zero cov: false 224s 226s Made hash table: hashes = 3 mem = 1.96 GB cells = 1052.59M used = 0.000% 226s 226s Estimated unique kmers: 7 226s 226s Table creation time: 1.948 seconds. 226s Started output threads. 226s Started output threads. 226s Table read time: 0.008 seconds. 22.83 kb/sec 226s Total reads in: 2 0.000% Kept 226s Total bases in: 188 0.000% Kept 226s Error reads in: 2 100.000% 226s Error type 1: 2 100.000% 226s Error type 2: 0 0.000% 226s Error type 3: 0 0.000% 226s 226s Wrote histogram to hist.plt 226s Total kmers counted: 128 227s Total unique kmer count: 128 227s Includes forward kmers only. 227s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 227s The most accurate value is the greater of the two. 227s 227s Percent unique: 100.00% 227s Depth average: 1.00 (unique kmers) 227s Depth median: 1 (unique kmers) 227s Depth standard deviation: 0.00 (unique kmers) 227s Corrected depth average: 0.00 227s 227s Depth average: 1.00 (all kmers) 227s Depth median: 1 (all kmers) 227s Depth standard deviation: 0.00 (all kmers) 227s 227s Approx. read depth median: 1.47 227s 227s *********** Pass 2 ********** 227s 227s 227s Settings: 227s threads: 4 227s k: 31 227s deterministic: true 227s toss error reads: false 227s passes: 1 227s bits per cell: 16 227s cells: 1052.92M 227s hashes: 3 227s base min quality: 5 227s kmer min prob: 0.5 227s 227s target depth: 100 227s min depth: 5 227s max depth: 100 227s min good kmers: 15 227s depth percentile: 54.0 227s ignore dupe kmers: true 227s fix spikes: false 227s histogram length: 65536 227s 227s Made hash table: hashes = 3 mem = 1.96 GB cells = 1052.59M used = 0.000% 227s 227s Estimated unique kmers: 0 227s 227s Table creation time: 0.734 seconds. 227s Started output threads. 227s Started output threads. 227s Table read time: 0.001 seconds. 0.00 kb/sec 227s Total reads in: 0 NaN% Kept 227s Total bases in: 0 NaN% Kept 227s Error reads in: 0 NaN% 227s Error type 1: 0 NaN% 227s Error type 2: 0 NaN% 227s Error type 3: 0 NaN% 227s Total kmers counted: 0 227s Total unique kmer count: 0 227s Includes forward kmers only. 227s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 227s The most accurate value is the greater of the two. 227s 227s Percent unique: NaN% 227s Depth average: NaN (unique kmers) 227s Depth median: 0 (unique kmers) 227s Depth standard deviation: NaN (unique kmers) 227s Corrected depth average: NaN 227s 227s Depth average: NaN (all kmers) 227s Depth median: 0 (all kmers) 227s Depth standard deviation: 0.00 (all kmers) 227s 227s Approx. read depth median: NaN 227s 227s Removing temp files. 227s 227s Total time: 2.800 seconds. 0.07 kb/sec 228s test -r out3.fastq 228s test -r outt.fastq 228s test -r hist.plt 228s bbnorm.sh in=illumina_full_range_original_illumina.fastq qin=64 \ 228s out=out4.fastq outt=outt2.fastq hist=hist2.plt 228s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 228s java -ea -Xmx2845m -Xms2845m -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 228s Executing jgi.KmerNormalize [bits=32, in=illumina_full_range_original_illumina.fastq, qin=64, out=out4.fastq, outt=outt2.fastq, hist=hist2.plt] 228s 228s 228s *********** Pass 1 ********** 228s 228s 228s Settings: 228s threads: 4 228s k: 31 228s deterministic: true 228s toss error reads: false 228s passes: 1 228s bits per cell: 16 228s cells: 1053.69M 228s hashes: 3 228s base min quality: 5 228s kmer min prob: 0.5 228s 228s target depth: 400 228s min depth: 3 228s max depth: 500 228s min good kmers: 15 228s depth percentile: 64.8 228s ignore dupe kmers: true 228s fix spikes: false 228s histogram length: 65536 228s print zero cov: false 228s 230s Made hash table: hashes = 3 mem = 1.96 GB cells = 1053.64M used = 0.000% 230s 230s Estimated unique kmers: 7 230s 230s Table creation time: 1.749 seconds. 230s Started output threads. 230s Started output threads. 230s Table read time: 0.007 seconds. 18.49 kb/sec 230s Total reads in: 2 0.000% Kept 230s Total bases in: 126 0.000% Kept 230s Error reads in: 2 100.000% 230s Error type 1: 2 100.000% 230s Error type 2: 0 0.000% 230s Error type 3: 0 0.000% 230s 230s Wrote histogram to hist2.plt 230s Total kmers counted: 66 230s Total unique kmer count: 66 230s Includes forward kmers only. 230s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 230s The most accurate value is the greater of the two. 230s 230s Percent unique: 100.00% 230s Depth average: 1.00 (unique kmers) 230s Depth median: 1 (unique kmers) 230s Depth standard deviation: 0.00 (unique kmers) 230s Corrected depth average: 0.00 230s 230s Depth average: 1.00 (all kmers) 230s Depth median: 1 (all kmers) 230s Depth standard deviation: 0.00 (all kmers) 230s 230s Approx. read depth median: 1.91 230s 230s *********** Pass 2 ********** 230s 230s 230s Settings: 230s threads: 4 230s k: 31 230s deterministic: true 230s toss error reads: false 230s passes: 1 230s bits per cell: 16 230s cells: 1053.69M 230s hashes: 3 230s base min quality: 5 230s kmer min prob: 0.5 230s 230s target depth: 100 230s min depth: 5 230s max depth: 100 230s min good kmers: 15 230s depth percentile: 54.0 230s ignore dupe kmers: true 230s fix spikes: false 230s histogram length: 65536 230s 230s Made hash table: hashes = 3 mem = 1.96 GB cells = 1053.64M used = 0.000% 230s 230s Estimated unique kmers: 0 230s 230s Table creation time: 0.818 seconds. 230s Started output threads. 230s Started output threads. 230s Table read time: 0.002 seconds. 0.00 kb/sec 230s Total reads in: 0 NaN% Kept 230s Total bases in: 0 NaN% Kept 230s Error reads in: 0 NaN% 230s Error type 1: 0 NaN% 230s Error type 2: 0 NaN% 230s Error type 3: 0 NaN% 230s Total kmers counted: 0 230s Total unique kmer count: 0 230s Includes forward kmers only. 230s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 230s The most accurate value is the greater of the two. 230s 230s Percent unique: NaN% 230s Depth average: NaN (unique kmers) 230s Depth median: 0 (unique kmers) 230s Depth standard deviation: NaN (unique kmers) 230s Corrected depth average: NaN 230s 230s Depth average: NaN (all kmers) 230s Depth median: 0 (all kmers) 230s Depth standard deviation: 0.00 (all kmers) 230s 230s Approx. read depth median: NaN 230s 230s Removing temp files. 230s 230s Total time: 2.696 seconds. 0.05 kb/sec 231s test -r out4.fastq 231s test -r outt2.fastq 231s test -r hist2.plt 231s autopkgtest [00:41:42]: test run-unit-test: -----------------------] 232s run-unit-test PASS 232s autopkgtest [00:41:43]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 232s autopkgtest [00:41:43]: @@@@@@@@@@@@@@@@@@@@ summary 232s run-unit-test PASS 243s Creating nova instance adt-noble-s390x-bbmap-20240322-003751-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-s390x-server-20240321.img (UUID f7ee8f0f-480f-4014-94f0-3be2a19e259d)...