0s autopkgtest [19:11:49]: starting date and time: 2024-03-21 19:11:49+0000 0s autopkgtest [19:11:49]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [19:11:49]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.0meoz_2j/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-3@bos01-ppc64el-14.secgroup --name adt-noble-ppc64el-bbmap-20240321-191148-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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://us.ports.ubuntu.com/ubuntu-ports/ 778s autopkgtest [19:24:47]: testbed dpkg architecture: ppc64el 778s autopkgtest [19:24:47]: testbed apt version: 2.7.12 778s autopkgtest [19:24:47]: @@@@@@@@@@@@@@@@@@@@ test bed setup 779s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 779s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 779s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 780s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3796 kB] 781s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [53.9 kB] 781s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [670 kB] 781s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 781s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 781s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 781s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4084 kB] 781s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 781s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [58.3 kB] 781s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 784s Fetched 9295 kB in 3s (3139 kB/s) 784s Reading package lists... 787s Reading package lists... 787s Building dependency tree... 787s Reading state information... 787s Calculating upgrade... 787s The following packages will be REMOVED: 787s libglib2.0-0 787s The following NEW packages will be installed: 787s libglib2.0-0t64 xdg-user-dirs 787s The following packages will be upgraded: 787s gir1.2-glib-2.0 libglib2.0-data 787s 2 upgraded, 2 newly installed, 1 to remove and 0 not upgraded. 787s Need to get 2022 kB of archives. 787s After this operation, 204 kB of additional disk space will be used. 787s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gir1.2-glib-2.0 ppc64el 2.79.3-3ubuntu5 [182 kB] 788s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libglib2.0-0t64 ppc64el 2.79.3-3ubuntu5 [1773 kB] 788s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 788s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el xdg-user-dirs ppc64el 0.18-1 [20.0 kB] 789s Fetched 2022 kB in 1s (2292 kB/s) 789s (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 ... 70157 files and directories currently installed.) 789s Preparing to unpack .../gir1.2-glib-2.0_2.79.3-3ubuntu5_ppc64el.deb ... 789s Unpacking gir1.2-glib-2.0:ppc64el (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 789s dpkg: libglib2.0-0:ppc64el: dependency problems, but removing anyway as you requested: 789s udisks2 depends on libglib2.0-0 (>= 2.77.0). 789s shared-mime-info depends on libglib2.0-0 (>= 2.75.3). 789s python3-gi depends on libglib2.0-0 (>= 2.77.0). 789s python3-dbus depends on libglib2.0-0 (>= 2.16.0). 789s netplan.io depends on libglib2.0-0 (>= 2.70.0). 789s netplan-generator depends on libglib2.0-0 (>= 2.70.0). 789s libxmlb2:ppc64el depends on libglib2.0-0 (>= 2.54.0). 789s libvolume-key1:ppc64el depends on libglib2.0-0 (>= 2.18.0). 789s libudisks2-0:ppc64el depends on libglib2.0-0 (>= 2.75.3). 789s libqrtr-glib0:ppc64el depends on libglib2.0-0 (>= 2.56). 789s libqmi-proxy depends on libglib2.0-0 (>= 2.30.0). 789s libqmi-glib5:ppc64el depends on libglib2.0-0 (>= 2.54.0). 789s libpolkit-gobject-1-0:ppc64el depends on libglib2.0-0 (>= 2.38.0). 789s libpolkit-agent-1-0:ppc64el depends on libglib2.0-0 (>= 2.38.0). 789s libnetplan0:ppc64el depends on libglib2.0-0 (>= 2.75.3). 789s libmm-glib0:ppc64el depends on libglib2.0-0 (>= 2.62.0). 789s libmbim-proxy depends on libglib2.0-0 (>= 2.56). 789s libmbim-glib4:ppc64el depends on libglib2.0-0 (>= 2.56). 789s libjson-glib-1.0-0:ppc64el depends on libglib2.0-0 (>= 2.75.3). 789s libjcat1:ppc64el depends on libglib2.0-0 (>= 2.75.3). 789s libgusb2:ppc64el depends on libglib2.0-0 (>= 2.75.3). 789s libgudev-1.0-0:ppc64el depends on libglib2.0-0 (>= 2.38.0). 789s libgirepository-1.0-1:ppc64el depends on libglib2.0-0 (>= 2.79.0). 789s libfwupd2:ppc64el depends on libglib2.0-0 (>= 2.79.0). 789s libblockdev3:ppc64el depends on libglib2.0-0 (>= 2.42.2). 789s libblockdev-utils3:ppc64el depends on libglib2.0-0 (>= 2.75.3). 789s libblockdev-swap3:ppc64el depends on libglib2.0-0 (>= 2.42.2). 789s libblockdev-part3:ppc64el depends on libglib2.0-0 (>= 2.42.2). 789s libblockdev-nvme3:ppc64el depends on libglib2.0-0 (>= 2.42.2). 789s libblockdev-mdraid3:ppc64el depends on libglib2.0-0 (>= 2.42.2). 789s libblockdev-loop3:ppc64el depends on libglib2.0-0 (>= 2.42.2). 789s libblockdev-fs3:ppc64el depends on libglib2.0-0 (>= 2.42.2). 789s libblockdev-crypto3:ppc64el depends on libglib2.0-0 (>= 2.42.2). 789s fwupd depends on libglib2.0-0 (>= 2.79.0). 789s bolt depends on libglib2.0-0 (>= 2.56.0). 789s 789s (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 ... 70157 files and directories currently installed.) 789s Removing libglib2.0-0:ppc64el (2.79.2-1~ubuntu1) ... 789s Selecting previously unselected package libglib2.0-0t64:ppc64el. 789s (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 ... 70132 files and directories currently installed.) 789s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_ppc64el.deb ... 789s libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:ppc64el.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled... 789s removed '/var/lib/dpkg/info/libglib2.0-0:ppc64el.postrm' 789s Unpacking libglib2.0-0t64:ppc64el (2.79.3-3ubuntu5) ... 789s Preparing to unpack .../libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 789s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 789s Selecting previously unselected package xdg-user-dirs. 789s Preparing to unpack .../xdg-user-dirs_0.18-1_ppc64el.deb ... 789s Unpacking xdg-user-dirs (0.18-1) ... 789s Setting up xdg-user-dirs (0.18-1) ... 789s Setting up libglib2.0-0t64:ppc64el (2.79.3-3ubuntu5) ... 789s No schema files found: doing nothing. 789s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 789s Setting up gir1.2-glib-2.0:ppc64el (2.79.3-3ubuntu5) ... 789s Processing triggers for man-db (2.12.0-3) ... 789s Processing triggers for libc-bin (2.39-0ubuntu2) ... 790s Reading package lists... 790s Building dependency tree... 790s Reading state information... 790s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 791s sh: Attempting to set up Debian/Ubuntu apt sources automatically 791s sh: Distribution appears to be Ubuntu 791s Reading package lists... 792s Building dependency tree... 792s Reading state information... 792s eatmydata is already the newest version (131-1). 792s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 792s Reading package lists... 792s Building dependency tree... 792s Reading state information... 792s dbus is already the newest version (1.14.10-4ubuntu1). 792s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 792s Reading package lists... 792s Building dependency tree... 792s Reading state information... 793s rng-tools-debian is already the newest version (2.4). 793s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 793s Reading package lists... 793s Building dependency tree... 793s Reading state information... 793s The following packages will be REMOVED: 793s cloud-init* python3-configobj* python3-debconf* 793s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 793s After this operation, 3252 kB disk space will be freed. 793s (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 ... 70171 files and directories currently installed.) 793s Removing cloud-init (24.1.1-0ubuntu1) ... 794s Removing python3-configobj (5.0.8-3) ... 794s Removing python3-debconf (1.5.86) ... 794s Processing triggers for man-db (2.12.0-3) ... 794s (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 ... 69782 files and directories currently installed.) 794s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 795s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 795s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 795s invoke-rc.d: policy-rc.d denied execution of try-restart. 795s Reading package lists... 795s Building dependency tree... 795s Reading state information... 795s linux-generic is already the newest version (6.8.0-11.11+1). 795s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 796s Get:1 http://ftpmaster.internal/ubuntu noble InRelease [255 kB] 796s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 796s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 796s Get:4 http://ftpmaster.internal/ubuntu noble/main Sources [1373 kB] 797s Get:5 http://ftpmaster.internal/ubuntu noble/universe Sources [19.8 MB] 799s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el Packages [1378 kB] 799s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el Packages [15.4 MB] 800s Get:8 http://ftpmaster.internal/ubuntu noble/multiverse ppc64el Packages [185 kB] 806s Fetched 38.4 MB in 9s (4225 kB/s) 807s Reading package lists... 807s Reading package lists... 807s Building dependency tree... 807s Reading state information... 807s Calculating upgrade... 807s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 807s Reading package lists... 807s Building dependency tree... 807s Reading state information... 808s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 808s autopkgtest [19:25:17]: rebooting testbed after setup commands that affected boot 966s autopkgtest [19:27:55]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 969s autopkgtest [19:27:58]: @@@@@@@@@@@@@@@@@@@@ apt-source bbmap 973s Get:1 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (dsc) [2286 B] 973s Get:2 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (tar) [5343 kB] 973s Get:3 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (diff) [25.4 kB] 973s gpgv: Signature made Fri Nov 24 11:00:29 2023 UTC 973s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 973s gpgv: issuer "emollier@debian.org" 973s gpgv: Can't check signature: No public key 973s dpkg-source: warning: cannot verify inline signature for ./bbmap_39.06+dfsg-1.dsc: no acceptable signature found 974s autopkgtest [19:28:03]: testing package bbmap version 39.06+dfsg-1 975s autopkgtest [19:28:04]: build not needed 977s autopkgtest [19:28:06]: test run-unit-test: preparing testbed 986s Reading package lists... 986s Building dependency tree... 986s Reading state information... 986s Starting pkgProblemResolver with broken count: 0 986s Starting 2 pkgProblemResolver with broken count: 0 986s Done 986s The following additional packages will be installed: 986s bbmap bbmap-jni ca-certificates-java fontconfig-config fonts-dejavu-core 986s fonts-dejavu-mono java-common libapache-pom-java libasound2 libasound2-data 986s libavahi-client3 libavahi-common-data libavahi-common3 libcommons-cli-java 986s libcommons-codec-java libcommons-io-java libcommons-parent-java libcups2 986s libfontconfig1 libgraphite2-3 libharfbuzz0b libjpeg-turbo8 libjpeg8 986s liblcms2-2 liblog4j1.2-java libmpj-java libpcsclite1 openjdk-17-jre-headless 986s python-biopython-doc 986s Suggested packages: 986s default-jre libasound2-plugins alsa-utils libcommons-io-java-doc cups-common 986s liblcms2-utils liblog4j1.2-java-doc libmail-java pcscd libnss-mdns 986s fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho 986s fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic 986s Recommended packages: 986s pigz alsa-ucm-conf alsa-topology-conf python3-biopython 986s The following NEW packages will be installed: 986s autopkgtest-satdep bbmap bbmap-jni ca-certificates-java fontconfig-config 986s fonts-dejavu-core fonts-dejavu-mono java-common libapache-pom-java 986s libasound2 libasound2-data libavahi-client3 libavahi-common-data 986s libavahi-common3 libcommons-cli-java libcommons-codec-java 986s libcommons-io-java libcommons-parent-java libcups2 libfontconfig1 986s libgraphite2-3 libharfbuzz0b libjpeg-turbo8 libjpeg8 liblcms2-2 986s liblog4j1.2-java libmpj-java libpcsclite1 openjdk-17-jre-headless 986s python-biopython-doc 986s 0 upgraded, 30 newly installed, 0 to remove and 0 not upgraded. 986s Need to get 79.6 MB/79.6 MB of archives. 986s After this operation, 240 MB of additional disk space will be used. 986s Get:1 /tmp/autopkgtest.NnA862/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [724 B] 987s Get:2 http://ftpmaster.internal/ubuntu noble/universe ppc64el libcommons-cli-java all 1.6.0-1 [59.9 kB] 987s Get:3 http://ftpmaster.internal/ubuntu noble/universe ppc64el libapache-pom-java all 29-2 [5284 B] 987s Get:4 http://ftpmaster.internal/ubuntu noble/universe ppc64el libcommons-parent-java all 56-1 [10.7 kB] 987s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el libcommons-codec-java all 1.16.0-1 [306 kB] 987s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el libcommons-io-java all 2.11.0-2 [297 kB] 987s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el liblog4j1.2-java all 1.2.17-11 [439 kB] 987s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el libmpj-java all 0.44+dfsg-4 [443 kB] 988s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el ca-certificates-java all 20240118 [11.6 kB] 988s Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el java-common all 0.75+exp1 [6798 B] 988s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el libavahi-common-data ppc64el 0.8-13ubuntu2 [29.5 kB] 988s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el libavahi-common3 ppc64el 0.8-13ubuntu2 [25.8 kB] 988s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el libavahi-client3 ppc64el 0.8-13ubuntu2 [30.6 kB] 988s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el libcups2 ppc64el 2.4.6-0ubuntu3 [344 kB] 988s Get:15 http://ftpmaster.internal/ubuntu noble/main ppc64el liblcms2-2 ppc64el 2.14-2 [243 kB] 988s Get:16 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu1 [212 kB] 988s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 988s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB] 988s Get:19 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB] 988s Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el fontconfig-config ppc64el 2.15.0-1ubuntu1 [37.0 kB] 988s Get:21 http://ftpmaster.internal/ubuntu noble/main ppc64el libfontconfig1 ppc64el 2.15.0-1ubuntu1 [190 kB] 988s Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el libasound2-data all 1.2.10-3build1 [20.7 kB] 988s Get:23 http://ftpmaster.internal/ubuntu noble/main ppc64el libasound2 ppc64el 1.2.10-3build1 [496 kB] 988s Get:24 http://ftpmaster.internal/ubuntu noble/main ppc64el libgraphite2-3 ppc64el 1.3.14-2 [105 kB] 989s Get:25 http://ftpmaster.internal/ubuntu noble/main ppc64el libharfbuzz0b ppc64el 8.3.0-2 [576 kB] 989s Get:26 http://ftpmaster.internal/ubuntu noble/main ppc64el libpcsclite1 ppc64el 2.0.0-1 [27.9 kB] 989s Get:27 http://ftpmaster.internal/ubuntu noble/main ppc64el openjdk-17-jre-headless ppc64el 17.0.10+7-1 [47.2 MB] 993s Get:28 http://ftpmaster.internal/ubuntu noble/universe ppc64el bbmap all 39.06+dfsg-1 [9768 kB] 993s Get:29 http://ftpmaster.internal/ubuntu noble/universe ppc64el bbmap-jni ppc64el 39.06+dfsg-1 [32.8 kB] 993s Get:30 http://ftpmaster.internal/ubuntu noble/universe ppc64el python-biopython-doc all 1.81+dfsg-3 [17.3 MB] 994s Fetched 79.6 MB in 7s (11.3 MB/s) 994s Selecting previously unselected package libcommons-cli-java. 994s (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 ... 69727 files and directories currently installed.) 994s Preparing to unpack .../00-libcommons-cli-java_1.6.0-1_all.deb ... 994s Unpacking libcommons-cli-java (1.6.0-1) ... 994s Selecting previously unselected package libapache-pom-java. 994s Preparing to unpack .../01-libapache-pom-java_29-2_all.deb ... 994s Unpacking libapache-pom-java (29-2) ... 994s Selecting previously unselected package libcommons-parent-java. 994s Preparing to unpack .../02-libcommons-parent-java_56-1_all.deb ... 994s Unpacking libcommons-parent-java (56-1) ... 994s Selecting previously unselected package libcommons-codec-java. 994s Preparing to unpack .../03-libcommons-codec-java_1.16.0-1_all.deb ... 994s Unpacking libcommons-codec-java (1.16.0-1) ... 994s Selecting previously unselected package libcommons-io-java. 994s Preparing to unpack .../04-libcommons-io-java_2.11.0-2_all.deb ... 994s Unpacking libcommons-io-java (2.11.0-2) ... 994s Selecting previously unselected package liblog4j1.2-java. 994s Preparing to unpack .../05-liblog4j1.2-java_1.2.17-11_all.deb ... 994s Unpacking liblog4j1.2-java (1.2.17-11) ... 994s Selecting previously unselected package libmpj-java. 994s Preparing to unpack .../06-libmpj-java_0.44+dfsg-4_all.deb ... 994s Unpacking libmpj-java (0.44+dfsg-4) ... 994s Selecting previously unselected package ca-certificates-java. 994s Preparing to unpack .../07-ca-certificates-java_20240118_all.deb ... 994s Unpacking ca-certificates-java (20240118) ... 994s Selecting previously unselected package java-common. 994s Preparing to unpack .../08-java-common_0.75+exp1_all.deb ... 994s Unpacking java-common (0.75+exp1) ... 994s Selecting previously unselected package libavahi-common-data:ppc64el. 994s Preparing to unpack .../09-libavahi-common-data_0.8-13ubuntu2_ppc64el.deb ... 994s Unpacking libavahi-common-data:ppc64el (0.8-13ubuntu2) ... 994s Selecting previously unselected package libavahi-common3:ppc64el. 994s Preparing to unpack .../10-libavahi-common3_0.8-13ubuntu2_ppc64el.deb ... 994s Unpacking libavahi-common3:ppc64el (0.8-13ubuntu2) ... 994s Selecting previously unselected package libavahi-client3:ppc64el. 994s Preparing to unpack .../11-libavahi-client3_0.8-13ubuntu2_ppc64el.deb ... 994s Unpacking libavahi-client3:ppc64el (0.8-13ubuntu2) ... 994s Selecting previously unselected package libcups2:ppc64el. 994s Preparing to unpack .../12-libcups2_2.4.6-0ubuntu3_ppc64el.deb ... 994s Unpacking libcups2:ppc64el (2.4.6-0ubuntu3) ... 994s Selecting previously unselected package liblcms2-2:ppc64el. 994s Preparing to unpack .../13-liblcms2-2_2.14-2_ppc64el.deb ... 994s Unpacking liblcms2-2:ppc64el (2.14-2) ... 994s Selecting previously unselected package libjpeg-turbo8:ppc64el. 994s Preparing to unpack .../14-libjpeg-turbo8_2.1.5-2ubuntu1_ppc64el.deb ... 994s Unpacking libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 994s Selecting previously unselected package libjpeg8:ppc64el. 994s Preparing to unpack .../15-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 994s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 994s Selecting previously unselected package fonts-dejavu-mono. 994s Preparing to unpack .../16-fonts-dejavu-mono_2.37-8_all.deb ... 994s Unpacking fonts-dejavu-mono (2.37-8) ... 994s Selecting previously unselected package fonts-dejavu-core. 994s Preparing to unpack .../17-fonts-dejavu-core_2.37-8_all.deb ... 994s Unpacking fonts-dejavu-core (2.37-8) ... 994s Selecting previously unselected package fontconfig-config. 994s Preparing to unpack .../18-fontconfig-config_2.15.0-1ubuntu1_ppc64el.deb ... 994s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 994s Selecting previously unselected package libfontconfig1:ppc64el. 994s Preparing to unpack .../19-libfontconfig1_2.15.0-1ubuntu1_ppc64el.deb ... 994s Unpacking libfontconfig1:ppc64el (2.15.0-1ubuntu1) ... 994s Selecting previously unselected package libasound2-data. 994s Preparing to unpack .../20-libasound2-data_1.2.10-3build1_all.deb ... 994s Unpacking libasound2-data (1.2.10-3build1) ... 994s Selecting previously unselected package libasound2:ppc64el. 994s Preparing to unpack .../21-libasound2_1.2.10-3build1_ppc64el.deb ... 994s Unpacking libasound2:ppc64el (1.2.10-3build1) ... 994s Selecting previously unselected package libgraphite2-3:ppc64el. 994s Preparing to unpack .../22-libgraphite2-3_1.3.14-2_ppc64el.deb ... 994s Unpacking libgraphite2-3:ppc64el (1.3.14-2) ... 994s Selecting previously unselected package libharfbuzz0b:ppc64el. 994s Preparing to unpack .../23-libharfbuzz0b_8.3.0-2_ppc64el.deb ... 994s Unpacking libharfbuzz0b:ppc64el (8.3.0-2) ... 994s Selecting previously unselected package libpcsclite1:ppc64el. 994s Preparing to unpack .../24-libpcsclite1_2.0.0-1_ppc64el.deb ... 994s Unpacking libpcsclite1:ppc64el (2.0.0-1) ... 994s Selecting previously unselected package openjdk-17-jre-headless:ppc64el. 994s Preparing to unpack .../25-openjdk-17-jre-headless_17.0.10+7-1_ppc64el.deb ... 994s Unpacking openjdk-17-jre-headless:ppc64el (17.0.10+7-1) ... 995s Selecting previously unselected package bbmap. 995s Preparing to unpack .../26-bbmap_39.06+dfsg-1_all.deb ... 995s Unpacking bbmap (39.06+dfsg-1) ... 995s Selecting previously unselected package bbmap-jni. 995s Preparing to unpack .../27-bbmap-jni_39.06+dfsg-1_ppc64el.deb ... 995s Unpacking bbmap-jni (39.06+dfsg-1) ... 995s Selecting previously unselected package python-biopython-doc. 995s Preparing to unpack .../28-python-biopython-doc_1.81+dfsg-3_all.deb ... 995s Unpacking python-biopython-doc (1.81+dfsg-3) ... 996s Selecting previously unselected package autopkgtest-satdep. 996s Preparing to unpack .../29-1-autopkgtest-satdep.deb ... 996s Unpacking autopkgtest-satdep (0) ... 996s Setting up libgraphite2-3:ppc64el (1.3.14-2) ... 996s Setting up liblcms2-2:ppc64el (2.14-2) ... 996s Setting up java-common (0.75+exp1) ... 996s Setting up libcommons-cli-java (1.6.0-1) ... 996s Setting up liblog4j1.2-java (1.2.17-11) ... 996s Setting up libasound2-data (1.2.10-3build1) ... 996s Setting up libapache-pom-java (29-2) ... 996s Setting up libavahi-common-data:ppc64el (0.8-13ubuntu2) ... 996s Setting up fonts-dejavu-mono (2.37-8) ... 996s Setting up fonts-dejavu-core (2.37-8) ... 996s Setting up libpcsclite1:ppc64el (2.0.0-1) ... 996s Setting up libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 996s Setting up python-biopython-doc (1.81+dfsg-3) ... 996s Setting up libasound2:ppc64el (1.2.10-3build1) ... 996s Setting up libharfbuzz0b:ppc64el (8.3.0-2) ... 996s Setting up bbmap-jni (39.06+dfsg-1) ... 996s Setting up ca-certificates-java (20240118) ... 996s No JRE found. Skipping Java certificates setup. 996s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 996s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 996s Setting up libcommons-parent-java (56-1) ... 996s Setting up libavahi-common3:ppc64el (0.8-13ubuntu2) ... 996s Setting up libfontconfig1:ppc64el (2.15.0-1ubuntu1) ... 996s Setting up libcommons-codec-java (1.16.0-1) ... 996s Setting up libavahi-client3:ppc64el (0.8-13ubuntu2) ... 996s Setting up libcommons-io-java (2.11.0-2) ... 996s Setting up libmpj-java (0.44+dfsg-4) ... 996s Setting up libcups2:ppc64el (2.4.6-0ubuntu3) ... 996s Setting up openjdk-17-jre-headless:ppc64el (17.0.10+7-1) ... 996s update-alternatives: using /usr/lib/jvm/java-17-openjdk-ppc64el/bin/java to provide /usr/bin/java (java) in auto mode 996s update-alternatives: using /usr/lib/jvm/java-17-openjdk-ppc64el/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 996s update-alternatives: using /usr/lib/jvm/java-17-openjdk-ppc64el/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 996s update-alternatives: using /usr/lib/jvm/java-17-openjdk-ppc64el/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 996s update-alternatives: using /usr/lib/jvm/java-17-openjdk-ppc64el/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 996s Processing triggers for libc-bin (2.39-0ubuntu2) ... 996s Processing triggers for man-db (2.12.0-3) ... 997s Processing triggers for ca-certificates-java (20240118) ... 997s Adding debian:ACCVRAIZ1.pem 997s Adding debian:AC_RAIZ_FNMT-RCM.pem 997s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 997s Adding debian:ANF_Secure_Server_Root_CA.pem 997s Adding debian:Actalis_Authentication_Root_CA.pem 997s Adding debian:AffirmTrust_Commercial.pem 997s Adding debian:AffirmTrust_Networking.pem 997s Adding debian:AffirmTrust_Premium.pem 997s Adding debian:AffirmTrust_Premium_ECC.pem 997s Adding debian:Amazon_Root_CA_1.pem 997s Adding debian:Amazon_Root_CA_2.pem 997s Adding debian:Amazon_Root_CA_3.pem 997s Adding debian:Amazon_Root_CA_4.pem 997s Adding debian:Atos_TrustedRoot_2011.pem 997s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 997s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 997s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 997s Adding debian:BJCA_Global_Root_CA1.pem 997s Adding debian:BJCA_Global_Root_CA2.pem 997s Adding debian:Baltimore_CyberTrust_Root.pem 997s Adding debian:Buypass_Class_2_Root_CA.pem 997s Adding debian:Buypass_Class_3_Root_CA.pem 997s Adding debian:CA_Disig_Root_R2.pem 997s Adding debian:CFCA_EV_ROOT.pem 997s Adding debian:COMODO_Certification_Authority.pem 997s Adding debian:COMODO_ECC_Certification_Authority.pem 997s Adding debian:COMODO_RSA_Certification_Authority.pem 997s Adding debian:Certainly_Root_E1.pem 997s Adding debian:Certainly_Root_R1.pem 997s Adding debian:Certigna.pem 997s Adding debian:Certigna_Root_CA.pem 997s Adding debian:Certum_EC-384_CA.pem 997s Adding debian:Certum_Trusted_Network_CA.pem 997s Adding debian:Certum_Trusted_Network_CA_2.pem 997s Adding debian:Certum_Trusted_Root_CA.pem 997s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 997s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 997s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 997s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 997s Adding debian:Comodo_AAA_Services_root.pem 997s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 997s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 997s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 997s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 997s Adding debian:DigiCert_Assured_ID_Root_CA.pem 997s Adding debian:DigiCert_Assured_ID_Root_G2.pem 997s Adding debian:DigiCert_Assured_ID_Root_G3.pem 997s Adding debian:DigiCert_Global_Root_CA.pem 997s Adding debian:DigiCert_Global_Root_G2.pem 997s Adding debian:DigiCert_Global_Root_G3.pem 997s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 997s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 997s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 997s Adding debian:DigiCert_Trusted_Root_G4.pem 997s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 997s Adding debian:Entrust_Root_Certification_Authority.pem 997s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 997s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 997s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem 997s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 997s Adding debian:GLOBALTRUST_2020.pem 997s Adding debian:GTS_Root_R1.pem 997s Adding debian:GTS_Root_R2.pem 997s Adding debian:GTS_Root_R3.pem 997s Adding debian:GTS_Root_R4.pem 997s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 997s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 997s Adding debian:GlobalSign_Root_CA.pem 997s Adding debian:GlobalSign_Root_CA_-_R3.pem 997s Adding debian:GlobalSign_Root_CA_-_R6.pem 997s Adding debian:GlobalSign_Root_E46.pem 997s Adding debian:GlobalSign_Root_R46.pem 997s Adding debian:Go_Daddy_Class_2_CA.pem 997s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 997s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 997s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 997s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 997s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 997s Adding debian:HiPKI_Root_CA_-_G1.pem 997s Adding debian:Hongkong_Post_Root_CA_3.pem 997s Adding debian:ISRG_Root_X1.pem 997s Adding debian:ISRG_Root_X2.pem 997s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 997s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 997s Adding debian:Izenpe.com.pem 997s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 997s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 997s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 997s Adding debian:NAVER_Global_Root_Certification_Authority.pem 997s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 997s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 997s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 997s Adding debian:QuoVadis_Root_CA_1_G3.pem 998s Adding debian:QuoVadis_Root_CA_2.pem 998s Adding debian:QuoVadis_Root_CA_2_G3.pem 998s Adding debian:QuoVadis_Root_CA_3.pem 998s Adding debian:QuoVadis_Root_CA_3_G3.pem 998s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 998s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 998s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 998s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 998s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 998s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 998s Adding debian:SZAFIR_ROOT_CA2.pem 998s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 998s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 998s Adding debian:SecureSign_RootCA11.pem 998s Adding debian:SecureTrust_CA.pem 998s Adding debian:Secure_Global_CA.pem 998s Adding debian:Security_Communication_ECC_RootCA1.pem 998s Adding debian:Security_Communication_RootCA2.pem 998s Adding debian:Security_Communication_RootCA3.pem 998s Adding debian:Security_Communication_Root_CA.pem 998s Adding debian:Starfield_Class_2_CA.pem 998s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 998s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 998s Adding debian:SwissSign_Gold_CA_-_G2.pem 998s Adding debian:SwissSign_Silver_CA_-_G2.pem 998s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 998s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 998s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 998s Adding debian:TWCA_Global_Root_CA.pem 998s Adding debian:TWCA_Root_Certification_Authority.pem 998s Adding debian:TeliaSonera_Root_CA_v1.pem 998s Adding debian:Telia_Root_CA_v2.pem 998s Adding debian:TrustAsia_Global_Root_CA_G3.pem 998s Adding debian:TrustAsia_Global_Root_CA_G4.pem 998s Adding debian:Trustwave_Global_Certification_Authority.pem 998s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 998s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 998s Adding debian:TunTrust_Root_CA.pem 998s Adding debian:UCA_Extended_Validation_Root.pem 998s Adding debian:UCA_Global_G2_Root.pem 998s Adding debian:USERTrust_ECC_Certification_Authority.pem 998s Adding debian:USERTrust_RSA_Certification_Authority.pem 998s Adding debian:XRamp_Global_CA_Root.pem 998s Adding debian:certSIGN_ROOT_CA.pem 998s Adding debian:certSIGN_Root_CA_G2.pem 998s Adding debian:e-Szigno_Root_CA_2017.pem 998s Adding debian:ePKI_Root_Certification_Authority.pem 998s Adding debian:emSign_ECC_Root_CA_-_C3.pem 998s Adding debian:emSign_ECC_Root_CA_-_G3.pem 998s Adding debian:emSign_Root_CA_-_C1.pem 998s Adding debian:emSign_Root_CA_-_G1.pem 998s Adding debian:vTrus_ECC_Root_CA.pem 998s Adding debian:vTrus_Root_CA.pem 998s done. 998s Setting up bbmap (39.06+dfsg-1) ... 998s Setting up autopkgtest-satdep (0) ... 1000s (Reading database ... 72566 files and directories currently installed.) 1000s Removing autopkgtest-satdep (0) ... 1001s autopkgtest [19:28:30]: test run-unit-test: [----------------------- 1001s 1001s # bbmap 1001s bbmap.sh --version 1001s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 1001s java -ea -Xmx2637m -Xms2637m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 --version 1001s BBMap version 39.06 1001s For help, please run the shellscript with no parameters, or look in /docs/. 1001s bbmap.sh --help 1001s bbmap.sh ref=example.fasta 1001s 1001s BBMap 1001s Written by Brian Bushnell, from Dec. 2010 - present 1001s Last modified September 15, 2022 1001s 1001s Description: Fast and accurate splice-aware read aligner. 1001s Please read bbmap/docs/guides/BBMapGuide.txt for more information. 1001s 1001s To index: bbmap.sh ref= 1001s To map: bbmap.sh in= out= 1001s To map without writing an index: 1001s bbmap.sh ref= in= out= nodisk 1001s 1001s in=stdin will accept reads from standard in, and out=stdout will write to 1001s standard out, but file extensions are still needed to specify the format of the 1001s input and output files e.g. in=stdin.fa.gz will read gzipped fasta from 1001s standard in; out=stdout.sam.gz will write gzipped sam. 1001s 1001s Indexing Parameters (required when building the index): 1001s nodisk=f Set to true to build index in memory and write nothing 1001s to disk except output. 1001s ref= Specify the reference sequence. Only do this ONCE, 1001s when building the index (unless using 'nodisk'). 1001s build=1 If multiple references are indexed in the same directory, 1001s each needs a unique numeric ID (unless using 'nodisk'). 1001s k=13 Kmer length, range 8-15. Longer is faster but uses 1001s more memory. Shorter is more sensitive. 1001s If indexing and mapping are done in two steps, K should 1001s be specified each time. 1001s path=<.> Specify the location to write the index, if you don't 1001s want it in the current working directory. 1001s usemodulo=f Throw away ~80% of kmers based on remainder modulo a 1001s number (reduces RAM by 50% and sensitivity slightly). 1001s Should be enabled both when building the index AND 1001s when mapping. 1001s rebuild=f Force a rebuild of the index (ref= should be set). 1001s 1001s Input Parameters: 1001s build=1 Designate index to use. Corresponds to the number 1001s specified when building the index. 1001s in= Primary reads input; required parameter. 1001s in2= For paired reads in two files. 1001s interleaved=auto True forces paired/interleaved input; false forces 1001s single-ended mapping. If not specified, interleaved 1001s status will be autodetected from read names. 1001s fastareadlen=500 Break up FASTA reads longer than this. Max is 500 for 1001s BBMap and 6000 for BBMapPacBio. Only works for FASTA 1001s input (use 'maxlen' for FASTQ input). The default for 1001s bbmap.sh is 500, and for mapPacBio.sh is 6000. 1001s unpigz=f Spawn a pigz (parallel gzip) process for faster 1001s decompression than using Java. 1001s Requires pigz to be installed. 1001s touppercase=t (tuc) Convert lowercase letters in reads to upper case 1001s (otherwise they will not match the reference). 1001s 1001s Sampling Parameters: 1001s 1001s reads=-1 Set to a positive number N to only process the first N 1001s reads (or pairs), then quit. -1 means use all reads. 1001s samplerate=1 Set to a number from 0 to 1 to randomly select that 1001s fraction of reads for mapping. 1 uses all reads. 1001s skipreads=0 Set to a number N to skip the first N reads (or pairs), 1001s then map the rest. 1001s 1001s Mapping Parameters: 1001s fast=f This flag is a macro which sets other paramters to run 1001s faster, at reduced sensitivity. Bad for RNA-seq. 1001s slow=f This flag is a macro which sets other paramters to run 1001s slower, at greater sensitivity. 'vslow' is even slower. 1001s maxindel=16000 Don't look for indels longer than this. Lower is faster. 1001s Set to >=100k for RNAseq with long introns like mammals. 1001s strictmaxindel=f When enabled, do not allow indels longer than 'maxindel'. 1001s By default these are not sought, but may be found anyway. 1001s tipsearch=100 Look this far for read-end deletions with anchors 1001s shorter than K, using brute force. 1001s minid=0.76 Approximate minimum alignment identity to look for. 1001s Higher is faster and less sensitive. 1001s minhits=1 Minimum number of seed hits required for candidate sites. 1001s Higher is faster. 1001s local=f Set to true to use local, rather than global, alignments. 1001s This will soft-clip ugly ends of poor alignments. 1001s perfectmode=f Allow only perfect mappings when set to true (very fast). 1001s semiperfectmode=f Allow only perfect and semiperfect (perfect except for 1001s N's in the reference) mappings. 1001s threads=auto (t) Set to number of threads desired. By default, uses 1001s all cores available. 1001s ambiguous=best (ambig) Set behavior on ambiguously-mapped reads (with 1001s multiple top-scoring mapping locations). 1001s best (use the first best site) 1001s toss (consider unmapped) 1001s random (select one top-scoring site randomly) 1001s all (retain all top-scoring sites) 1001s samestrandpairs=f (ssp) Specify whether paired reads should map to the 1001s same strand or opposite strands. 1001s requirecorrectstrand=t (rcs) Forbid pairing of reads without correct strand 1001s orientation. Set to false for long-mate-pair libraries. 1001s killbadpairs=f (kbp) If a read pair is mapped with an inappropriate 1001s insert size or orientation, the read with the lower 1001s mapping quality is marked unmapped. 1001s pairedonly=f (po) Treat unpaired reads as unmapped. Thus they will 1001s be sent to 'outu' but not 'outm'. 1001s rcomp=f Reverse complement both reads prior to mapping (for LMP 1001s outward-facing libraries). 1001s rcompmate=f Reverse complement read2 prior to mapping. 1001s pairlen=32000 Set max allowed distance between paired reads. 1001s (insert size)=(pairlen)+(read1 length)+(read2 length) 1001s rescuedist=1200 Don't try to rescue paired reads if avg. insert size 1001s greater than this. Lower is faster. 1001s rescuemismatches=32 Maximum mismatches allowed in a rescued read. Lower 1001s is faster. 1001s averagepairdist=100 (apd) Initial average distance between paired reads. 1001s Varies dynamically; does not need to be specified. 1001s deterministic=f Run in deterministic mode. In this case it is good 1001s to set averagepairdist. BBMap is deterministic 1001s without this flag if using single-ended reads, 1001s or run singlethreaded. 1001s bandwidthratio=0 (bwr) If above zero, restrict alignment band to this 1001s fraction of read length. Faster but less accurate. 1001s bandwidth=0 (bw) Set the bandwidth directly. 1001s fraction of read length. Faster but less accurate. 1001s usejni=f (jni) Do alignments faster, in C code. Requires 1001s compiling the C code; details are in /jni/README.txt. 1001s maxsites2=800 Don't analyze (or print) more than this many alignments 1001s per read. 1001s ignorefrequentkmers=t (ifk) Discard low-information kmers that occur often. 1001s excludefraction=0.03 (ef) Fraction of kmers to ignore. For example, 0.03 1001s will ignore the most common 3% of kmers. 1001s greedy=t Use a greedy algorithm to discard the least-useful 1001s kmers on a per-read basis. 1001s kfilter=0 If positive, potential mapping sites must have at 1001s least this many consecutive exact matches. 1001s 1001s 1001s Quality and Trimming Parameters: 1001s qin=auto Set to 33 or 64 to specify input quality value ASCII 1001s offset. 33 is Sanger, 64 is old Solexa. 1001s qout=auto Set to 33 or 64 to specify output quality value ASCII 1001s offset (only if output format is fastq). 1001s qtrim=f Quality-trim ends before mapping. Options are: 1001s 'f' (false), 'l' (left), 'r' (right), and 'lr' (both). 1001s untrim=f Undo trimming after mapping. Untrimmed bases will be 1001s soft-clipped in cigar strings. 1001s trimq=6 Trim regions with average quality below this 1001s (phred algorithm). 1001s mintrimlength=60 (mintl) Don't trim reads to be shorter than this. 1001s fakefastaquality=-1 (ffq) Set to a positive number 1-50 to generate fake 1001s quality strings for fasta input reads. 1001s ignorebadquality=f (ibq) Keep going, rather than crashing, if a read has 1001s out-of-range quality values. 1001s usequality=t Use quality scores when determining which read kmers 1001s to use as seeds. 1001s minaveragequality=0 (maq) Do not map reads with average quality below this. 1001s maqb=0 If positive, calculate maq from this many initial bases. 1001s 1001s Output Parameters: 1001s out= Write all reads to this file. 1001s outu= Write only unmapped reads to this file. Does not 1001s include unmapped paired reads with a mapped mate. 1001s outm= Write only mapped reads to this file. Includes 1001s unmapped paired reads with a mapped mate. 1001s mappedonly=f If true, treats 'out' like 'outm'. 1001s bamscript= (bs) Write a shell script to that will turn 1001s the sam output into a sorted, indexed bam file. 1001s ordered=f Set to true to output reads in same order as input. 1001s Slower and uses more memory. 1001s overwrite=f (ow) Allow process to overwrite existing files. 1001s secondary=f Print secondary alignments. 1001s sssr=0.95 (secondarysitescoreratio) Print only secondary alignments 1001s with score of at least this fraction of primary. 1001s ssao=f (secondarysiteasambiguousonly) Only print secondary 1001s alignments for ambiguously-mapped reads. 1001s maxsites=5 Maximum number of total alignments to print per read. 1001s Only relevant when secondary=t. 1001s quickmatch=f Generate cigar strings more quickly. 1001s trimreaddescriptions=f (trd) Truncate read and ref names at the first whitespace, 1001s assuming that the remainder is a comment or description. 1001s ziplevel=2 (zl) Compression level for zip or gzip output. 1001s pigz=f Spawn a pigz (parallel gzip) process for faster 1001s compression than Java. Requires pigz to be installed. 1001s machineout=f Set to true to output statistics in machine-friendly 1001s 'key=value' format. 1001s printunmappedcount=f Print the total number of unmapped reads and bases. 1001s If input is paired, the number will be of pairs 1001s for which both reads are unmapped. 1001s showprogress=0 If positive, print a '.' every X reads. 1001s showprogress2=0 If positive, print the number of seconds since the 1001s last progress update (instead of a '.'). 1001s renamebyinsert=f Renames reads based on their mapped insert size. 1001s 1001s Bloom-Filtering Parameters (bloomfilter.sh is the standalone version). 1001s bloom=f Use a Bloom filter to ignore reads not sharing kmers 1001s with the reference. This uses more memory, but speeds 1001s mapping when most reads don't match the reference. 1001s bloomhashes=2 Number of hash functions. 1001s bloomminhits=3 Number of consecutive hits to be considered matched. 1001s bloomk=31 Bloom filter kmer length. 1001s bloomserial=t Use the serialized Bloom filter for greater loading 1001s speed, if available. If not, generate and write one. 1001s 1001s Post-Filtering Parameters: 1001s idfilter=0 Independant of minid; sets exact minimum identity 1001s allowed for alignments to be printed. Range 0 to 1. 1001s subfilter=-1 Ban alignments with more than this many substitutions. 1001s insfilter=-1 Ban alignments with more than this many insertions. 1001s delfilter=-1 Ban alignments with more than this many deletions. 1001s indelfilter=-1 Ban alignments with more than this many indels. 1001s editfilter=-1 Ban alignments with more than this many edits. 1001s inslenfilter=-1 Ban alignments with an insertion longer than this. 1001s dellenfilter=-1 Ban alignments with a deletion longer than this. 1001s nfilter=-1 Ban alignments with more than this many ns. This 1001s includes nocall, noref, and off scaffold ends. 1001s 1001s Sam flags and settings: 1001s noheader=f Disable generation of header lines. 1001s sam=1.4 Set to 1.4 to write Sam version 1.4 cigar strings, 1001s with = and X, or 1.3 to use M. 1001s saa=t (secondaryalignmentasterisks) Use asterisks instead of 1001s bases for sam secondary alignments. 1001s cigar=t Set to 'f' to skip generation of cigar strings (faster). 1001s keepnames=f Keep original names of paired reads, rather than 1001s ensuring both reads have the same name. 1001s intronlen=999999999 Set to a lower number like 10 to change 'D' to 'N' in 1001s cigar strings for deletions of at least that length. 1001s rgid= Set readgroup ID. All other readgroup fields 1001s can be set similarly, with the flag rgXX= 1001s If you set a readgroup flag to the word 'filename', 1001s e.g. rgid=filename, the input file name will be used. 1001s mdtag=f Write MD tags. 1001s nhtag=f Write NH tags. 1001s xmtag=f Write XM tags (may only work correctly with ambig=all). 1001s amtag=f Write AM tags. 1001s nmtag=f Write NM tags. 1001s xstag=f Set to 'xs=fs', 'xs=ss', or 'xs=us' to write XS tags 1001s for RNAseq using firststrand, secondstrand, or 1001s unstranded libraries. Needed by Cufflinks. 1001s JGI mainly uses 'firststrand'. 1001s stoptag=f Write a tag indicating read stop location, prefixed by YS:i: 1001s lengthtag=f Write a tag indicating (query,ref) alignment lengths, 1001s prefixed by YL:Z: 1001s idtag=f Write a tag indicating percent identity, prefixed by YI:f: 1001s inserttag=f Write a tag indicating insert size, prefixed by X8:Z: 1001s scoretag=f Write a tag indicating BBMap's raw score, prefixed by YR:i: 1001s timetag=f Write a tag indicating this read's mapping time, prefixed by X0:i: 1001s boundstag=f Write a tag indicating whether either read in the pair 1001s goes off the end of the reference, prefixed by XB:Z: 1001s notags=f Turn off all optional tags. 1001s 1001s Histogram and statistics output parameters: 1001s scafstats= Statistics on how many reads mapped to which scaffold. 1001s refstats= Statistics on how many reads mapped to which reference 1001s file; only for BBSplit. 1001s sortscafs=t Sort scaffolds or references by read count. 1001s bhist= Base composition histogram by position. 1001s qhist= Quality histogram by position. 1001s aqhist= Histogram of average read quality. 1001s bqhist= Quality histogram designed for box plots. 1001s lhist= Read length histogram. 1001s ihist= Write histogram of insert sizes (for paired reads). 1001s ehist= Errors-per-read histogram. 1001s qahist= Quality accuracy histogram of error rates versus 1001s quality score. 1001s indelhist= Indel length histogram. 1001s mhist= Histogram of match, sub, del, and ins rates by 1001s read location. 1001s gchist= Read GC content histogram. 1001s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 1001s gcpairs=t Use average GC of paired reads. 1001s idhist= Histogram of read count versus percent identity. 1001s idbins=100 Number idhist bins. Set to 'auto' to use read length. 1001s statsfile=stderr Mapping statistics are printed here. 1001s 1001s Coverage output parameters (these may reduce speed and use more RAM): 1001s covstats= Per-scaffold coverage info. 1001s rpkm= Per-scaffold RPKM/FPKM counts. 1001s covhist= Histogram of # occurrences of each depth level. 1001s basecov= Coverage per base location. 1001s bincov= Print binned coverage per location (one line per X bases). 1001s covbinsize=1000 Set the binsize for binned coverage output. 1001s nzo=t Only print scaffolds with nonzero coverage. 1001s twocolumn=f Change to true to print only ID and Avg_fold instead of 1001s all 6 columns to the 'out=' file. 1001s 32bit=f Set to true if you need per-base coverage over 64k. 1001s strandedcov=f Track coverage for plus and minus strand independently. 1001s startcov=f Only track start positions of reads. 1001s secondarycov=t Include coverage of secondary alignments. 1001s physcov=f Calculate physical coverage for paired reads. 1001s This includes the unsequenced bases. 1001s delcoverage=t (delcov) Count bases covered by deletions as covered. 1001s True is faster than false. 1001s covk=0 If positive, calculate kmer coverage statistics. 1001s 1001s Java Parameters: 1001s -Xmx This will set Java's memory usage, 1001s overriding autodetection. 1001s -Xmx20g will specify 20 gigs of RAM, and -Xmx800m 1001s will specify 800 megs. The max is typically 85% of 1001s physical memory. The human genome requires around 24g, 1001s or 12g with the 'usemodulo' flag. The index uses 1001s roughly 6 bytes per reference base. 1001s -eoom This flag will cause the process to exit if an 1001s out-of-memory exception occurs. Requires Java 8u92+. 1001s -da Disable assertions. 1001s 1001s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter 1001s any problems, or post at: http://seqanswers.com/forums/showthread.php?t=41057 1001s 1001s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 1001s java -ea -Xmx2636m -Xms2636m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta 1001s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta] 1001s Version 39.06 1001s 1001s No output file. 1001s Writing reference. 1001s 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] 1001s 1001s Set genScaffoldInfo=true 1001s Writing chunk 1 1001s Set genome to 1 1001s 1001s Loaded Reference: 0.012 seconds. 1001s Loading index for chunk 1-1, build 1 1001s No index available; generating from reference genome: /tmp/autopkgtest.NnA862/autopkgtest_tmp/ref/index/1/chr1_index_k13_c16_b1.block 1001s Indexing threads started for block 0-1 1001s Indexing threads finished for block 0-1 1003s Generated Index: 1.218 seconds. 1003s No reads to process; quitting. 1003s 1003s Total time: 1.358 seconds. 1003s test -d ref 1003s bbmap.sh in=misc_dna_as_sanger.fastq out=out.sam 1003s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 1003s java -ea -Xmx2636m -Xms2636m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 in=misc_dna_as_sanger.fastq out=out.sam 1003s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, in=misc_dna_as_sanger.fastq, out=out.sam] 1003s Version 39.06 1003s 1003s Retaining first best site only for ambiguous mappings. 1003s Set genome to 1 1003s 1003s Loaded Reference: 0.023 seconds. 1003s Loading index for chunk 1-1, build 1 1003s Generated Index: 0.453 seconds. 1007s Analyzed Index: 3.626 seconds. 1007s Started output stream: 0.020 seconds. 1007s Cleared Memory: 0.111 seconds. 1007s Processing reads in single-ended mode. 1007s Started read stream. 1007s Started 4 mapping threads. 1007s Detecting finished threads: 0, 1, 2, 3 1007s 1007s ------------------ Results ------------------ 1007s 1007s Genome: 1 1007s Key Length: 13 1007s Max Indel: 16000 1007s Minimum Score Ratio: 0.56 1007s Mapping Mode: normal 1007s Reads Used: 4 (153 bases) 1007s 1007s Mapping: 0.077 seconds. 1007s Reads/sec: 51.86 1007s kBases/sec: 1.98 1007s 1007s 1007s Read 1 data: pct reads num reads pct bases num bases 1007s 1007s mapped: 0.0000% 0 0.0000% 0 1007s unambiguous: 0.0000% 0 0.0000% 0 1007s ambiguous: 0.0000% 0 0.0000% 0 1007s low-Q discards: 25.0000% 1 19.6078% 30 1007s 1007s perfect best site: 0.0000% 0 0.0000% 0 1007s semiperfect site: 0.0000% 0 0.0000% 0 1007s 1007s Match Rate: NA NA NaN% 0 1007s Error Rate: NaN% 0 NaN% 0 1007s Sub Rate: NaN% 0 NaN% 0 1007s Del Rate: NaN% 0 NaN% 0 1007s Ins Rate: NaN% 0 NaN% 0 1007s N Rate: NaN% 0 NaN% 0 1007s 1007s Total time: 4.403 seconds. 1007s test -r out.sam 1007s bbmap.sh ref=example.fasta in=example.fastq out=out2.sam nodisk 1007s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 1007s java -ea -Xmx2636m -Xms2636m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta in=example.fastq out=out2.sam nodisk 1007s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta, in=example.fastq, out=out2.sam, nodisk] 1007s Version 39.06 1007s 1007s Retaining first best site only for ambiguous mappings. 1007s 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] 1007s 1007s Set genScaffoldInfo=true 1007s Set genome to 1 1007s 1007s Loaded Reference: 0.005 seconds. 1007s Loading index for chunk 1-1, build 1 1007s Indexing threads started for block 0-1 1007s Indexing threads finished for block 0-1 1008s Generated Index: 0.210 seconds. 1011s Analyzed Index: 3.604 seconds. 1011s Started output stream: 0.019 seconds. 1011s Cleared Memory: 0.113 seconds. 1011s Processing reads in single-ended mode. 1011s Started read stream. 1011s Started 4 mapping threads. 1011s Detecting finished threads: 0, 1, 2, 3 1011s 1011s ------------------ Results ------------------ 1011s 1011s Genome: 1 1011s Key Length: 13 1011s Max Indel: 16000 1011s Minimum Score Ratio: 0.56 1011s Mapping Mode: normal 1011s Reads Used: 3 (75 bases) 1011s 1011s Mapping: 0.082 seconds. 1011s Reads/sec: 36.45 1011s kBases/sec: 0.91 1011s 1011s 1011s Read 1 data: pct reads num reads pct bases num bases 1011s 1011s mapped: 100.0000% 3 100.0000% 75 1011s unambiguous: 100.0000% 3 100.0000% 75 1011s ambiguous: 0.0000% 0 0.0000% 0 1011s low-Q discards: 0.0000% 0 0.0000% 0 1011s 1011s perfect best site: 100.0000% 3 100.0000% 75 1011s semiperfect site: 100.0000% 3 100.0000% 75 1011s 1011s Match Rate: NA NA 100.0000% 75 1011s Error Rate: 0.0000% 0 0.0000% 0 1011s Sub Rate: 0.0000% 0 0.0000% 0 1011s Del Rate: 0.0000% 0 0.0000% 0 1011s Ins Rate: 0.0000% 0 0.0000% 0 1011s N Rate: 0.0000% 0 0.0000% 0 1011s 1011s Total time: 4.157 seconds. 1011s test -r out2.sam 1011s 1011s # bbduk 1011s bbduk.sh --version 1011s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 1011s java -ea -Xmx1318m -Xms1318m -cp /usr/share/java/bbmap.jar jgi.BBDuk --version 1011s BBMap version 39.06 1011s For help, please run the shellscript with no parameters, or look in /docs/. 1011s bbduk.sh --help 1011s bbduk.sh in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq \ 1011s qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 1011s 1011s Written by Brian Bushnell 1011s Last modified November 9, 2023 1011s 1011s Description: Compares reads to the kmers in a reference dataset, optionally 1011s allowing an edit distance. Splits the reads into two outputs - those that 1011s match the reference, and those that don't. Can also trim (remove) the matching 1011s parts of the reads rather than binning the reads. 1011s Please read bbmap/docs/guides/BBDukGuide.txt for more information. 1011s 1011s Usage: bbduk.sh in= out= ref= 1011s 1011s Input may be stdin or a fasta or fastq file, compressed or uncompressed. 1011s If you pipe via stdin/stdout, please include the file type; e.g. for gzipped 1011s fasta input, set in=stdin.fa.gz 1011s 1011s Input parameters: 1011s in= Main input. in=stdin.fq will pipe from stdin. 1011s in2= Input for 2nd read of pairs in a different file. 1011s ref= Comma-delimited list of reference files. 1011s In addition to filenames, you may also use the keywords: 1011s adapters, artifacts, phix, lambda, pjet, mtst, kapa 1011s literal= Comma-delimited list of literal reference sequences. 1011s touppercase=f (tuc) Change all bases upper-case. 1011s interleaved=auto (int) t/f overrides interleaved autodetection. 1011s Must be set mainually when streaming fastq input. 1011s qin=auto Input quality offset: 33 (Sanger), 64, or auto. 1011s reads=-1 If positive, quit after processing X reads or pairs. 1011s copyundefined=f (cu) Process non-AGCT IUPAC reference bases by making all 1011s possible unambiguous copies. Intended for short motifs 1011s or adapter barcodes, as time/memory use is exponential. 1011s samplerate=1 Set lower to only process a fraction of input reads. 1011s samref= Optional reference fasta for processing sam files. 1011s 1011s Output parameters: 1011s out= (outnonmatch) Write reads here that do not contain 1011s kmers matching the database. 'out=stdout.fq' will pipe 1011s to standard out. 1011s out2= (outnonmatch2) Use this to write 2nd read of pairs to a 1011s different file. 1011s outm= (outmatch) Write reads here that fail filters. In default 1011s kfilter mode, this means any read with a matching kmer. 1011s In any mode, it also includes reads that fail filters such 1011s as minlength, mingc, maxgc, entropy, etc. In other words, 1011s it includes all reads that do not go to 'out'. 1011s outm2= (outmatch2) Use this to write 2nd read of pairs to a 1011s different file. 1011s outs= (outsingle) Use this to write singleton reads whose mate 1011s was trimmed shorter than minlen. 1011s stats= Write statistics about which contamininants were detected. 1011s refstats= Write statistics on a per-reference-file basis. 1011s rpkm= Write RPKM for each reference sequence (for RNA-seq). 1011s dump= Dump kmer tables to a file, in fasta format. 1011s duk= Write statistics in duk's format. *DEPRECATED* 1011s nzo=t Only write statistics about ref sequences with nonzero hits. 1011s overwrite=t (ow) Grant permission to overwrite files. 1011s showspeed=t (ss) 'f' suppresses display of processing speed. 1011s ziplevel=2 (zl) Compression level; 1 (min) through 9 (max). 1011s fastawrap=70 Length of lines in fasta output. 1011s qout=auto Output quality offset: 33 (Sanger), 64, or auto. 1011s statscolumns=3 (cols) Number of columns for stats output, 3 or 5. 1011s 5 includes base counts. 1011s rename=f Rename reads to indicate which sequences they matched. 1011s refnames=f Use names of reference files rather than scaffold IDs. 1011s trd=f Truncate read and ref names at the first whitespace. 1011s ordered=f Set to true to output reads in same order as input. 1011s maxbasesout=-1 If positive, quit after writing approximately this many 1011s bases to out (outu/outnonmatch). 1011s maxbasesoutm=-1 If positive, quit after writing approximately this many 1011s bases to outm (outmatch). 1011s json=f Print to screen in json format. 1011s 1011s Histogram output parameters: 1011s bhist= Base composition histogram by position. 1011s qhist= Quality histogram by position. 1011s qchist= Count of bases with each quality value. 1011s aqhist= Histogram of average read quality. 1011s bqhist= Quality histogram designed for box plots. 1011s lhist= Read length histogram. 1011s phist= Polymer length histogram. 1011s gchist= Read GC content histogram. 1011s enthist= Read entropy histogram. 1011s ihist= Insert size histogram, for paired reads in mapped sam. 1011s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 1011s maxhistlen=6000 Set an upper bound for histogram lengths; higher uses 1011s more memory. The default is 6000 for some histograms 1011s and 80000 for others. 1011s 1011s Histograms for mapped sam/bam files only: 1011s histbefore=t Calculate histograms from reads before processing. 1011s ehist= Errors-per-read histogram. 1011s qahist= Quality accuracy histogram of error rates versus quality 1011s score. 1011s indelhist= Indel length histogram. 1011s mhist= Histogram of match, sub, del, and ins rates by position. 1011s idhist= Histogram of read count versus percent identity. 1011s idbins=100 Number idhist bins. Set to 'auto' to use read length. 1011s varfile= Ignore substitution errors listed in this file when 1011s calculating error rates. Can be generated with 1011s CallVariants. 1011s vcf= Ignore substitution errors listed in this VCF file 1011s when calculating error rates. 1011s ignorevcfindels=t Also ignore indels listed in the VCF. 1011s 1011s Processing parameters: 1011s k=27 Kmer length used for finding contaminants. Contaminants 1011s shorter than k will not be found. k must be at least 1. 1011s rcomp=t Look for reverse-complements of kmers in addition to 1011s forward kmers. 1011s maskmiddle=t (mm) Treat the middle base of a kmer as a wildcard, to 1011s increase sensitivity in the presence of errors. This may 1011s also be set to a number, e.g. mm=3, to mask that many bp. 1011s The default mm=t corresponds to mm=1 for odd-length kmers 1011s and mm=2 for even-length kmers (as of v39.04), while 1011s mm=f is always equivalent to mm=0. 1011s minkmerhits=1 (mkh) Reads need at least this many matching kmers 1011s to be considered as matching the reference. 1011s minkmerfraction=0.0 (mkf) A reads needs at least this fraction of its total 1011s kmers to hit a ref, in order to be considered a match. 1011s If this and minkmerhits are set, the greater is used. 1011s mincovfraction=0.0 (mcf) A reads needs at least this fraction of its total 1011s bases to be covered by ref kmers to be considered a match. 1011s If specified, mcf overrides mkh and mkf. 1011s hammingdistance=0 (hdist) Maximum Hamming distance for ref kmers (subs only). 1011s Memory use is proportional to (3*K)^hdist. 1011s qhdist=0 Hamming distance for query kmers; impacts speed, not memory. 1011s editdistance=0 (edist) Maximum edit distance from ref kmers (subs 1011s and indels). Memory use is proportional to (8*K)^edist. 1011s hammingdistance2=0 (hdist2) Sets hdist for short kmers, when using mink. 1011s qhdist2=0 Sets qhdist for short kmers, when using mink. 1011s editdistance2=0 (edist2) Sets edist for short kmers, when using mink. 1011s forbidn=f (fn) Forbids matching of read kmers containing N. 1011s By default, these will match a reference 'A' if 1011s hdist>0 or edist>0, to increase sensitivity. 1011s removeifeitherbad=t (rieb) Paired reads get sent to 'outmatch' if either is 1011s match (or either is trimmed shorter than minlen). 1011s Set to false to require both. 1011s trimfailures=f Instead of discarding failed reads, trim them to 1bp. 1011s This makes the statistics a bit odd. 1011s findbestmatch=f (fbm) If multiple matches, associate read with sequence 1011s sharing most kmers. Reduces speed. 1011s skipr1=f Don't do kmer-based operations on read 1. 1011s skipr2=f Don't do kmer-based operations on read 2. 1011s ecco=f For overlapping paired reads only. Performs error- 1011s correction with BBMerge prior to kmer operations. 1011s recalibrate=f (recal) Recalibrate quality scores. Requires calibration 1011s matrices generated by CalcTrueQuality. 1011s sam= If recalibration is desired, and matrices have not already 1011s been generated, BBDuk will create them from the sam file. 1011s amino=f Run in amino acid mode. Some features have not been 1011s tested, but kmer-matching works fine. Maximum k is 12. 1011s 1011s Speed and Memory parameters: 1011s threads=auto (t) Set number of threads to use; default is number of 1011s logical processors. 1011s prealloc=f Preallocate memory in table. Allows faster table loading 1011s and more efficient memory usage, for a large reference. 1011s monitor=f Kill this process if it crashes. monitor=600,0.01 would 1011s kill after 600 seconds under 1% usage. 1011s minrskip=1 (mns) Force minimal skip interval when indexing reference 1011s kmers. 1 means use all, 2 means use every other kmer, etc. 1011s maxrskip=1 (mxs) Restrict maximal skip interval when indexing 1011s reference kmers. Normally all are used for scaffolds<100kb, 1011s but with longer scaffolds, up to maxrskip-1 are skipped. 1011s rskip= Set both minrskip and maxrskip to the same value. 1011s If not set, rskip will vary based on sequence length. 1011s qskip=1 Skip query kmers to increase speed. 1 means use all. 1011s speed=0 Ignore this fraction of kmer space (0-15 out of 16) in both 1011s reads and reference. Increases speed and reduces memory. 1011s Note: Do not use more than one of 'speed', 'qskip', and 'rskip'. 1011s 1011s Trimming/Filtering/Masking parameters: 1011s Note - if ktrim, kmask, and ksplit are unset, the default behavior is kfilter. 1011s All kmer processing modes are mutually exclusive. 1011s Reads only get sent to 'outm' purely based on kmer matches in kfilter mode. 1011s 1011s ktrim=f Trim reads to remove bases matching reference kmers, plus 1011s all bases to the left or right. 1011s Values: 1011s f (don't trim), 1011s r (trim to the right), 1011s l (trim to the left) 1011s ktrimtips=0 Set this to a positive number to perform ktrim on both 1011s ends, examining only the outermost X bases. 1011s kmask= Replace bases matching ref kmers with another symbol. 1011s Allows any non-whitespace character, and processes short 1011s kmers on both ends if mink is set. 'kmask=lc' will 1011s convert masked bases to lowercase. 1011s maskfullycovered=f (mfc) Only mask bases that are fully covered by kmers. 1011s ksplit=f For single-ended reads only. Reads will be split into 1011s pairs around the kmer. If the kmer is at the end of the 1011s read, it will be trimmed instead. Singletons will go to 1011s out, and pairs will go to outm. Do not use ksplit with 1011s other operations such as quality-trimming or filtering. 1011s mink=0 Look for shorter kmers at read tips down to this length, 1011s when k-trimming or masking. 0 means disabled. Enabling 1011s this will disable maskmiddle. 1011s qtrim=f Trim read ends to remove bases with quality below trimq. 1011s Performed AFTER looking for kmers. Values: 1011s rl (trim both ends), 1011s f (neither end), 1011s r (right end only), 1011s l (left end only), 1011s w (sliding window). 1011s trimq=6 Regions with average quality BELOW this will be trimmed, 1011s if qtrim is set to something other than f. Can be a 1011s floating-point number like 7.3. 1011s trimclip=f Trim soft-clipped bases from sam files. 1011s minlength=10 (ml) Reads shorter than this after trimming will be 1011s discarded. Pairs will be discarded if both are shorter. 1011s mlf=0 (minlengthfraction) Reads shorter than this fraction of 1011s original length after trimming will be discarded. 1011s maxlength= Reads longer than this after trimming will be discarded. 1011s minavgquality=0 (maq) Reads with average quality (after trimming) below 1011s this will be discarded. 1011s maqb=0 If positive, calculate maq from this many initial bases. 1011s minbasequality=0 (mbq) Reads with any base below this quality (after 1011s trimming) will be discarded. 1011s maxns=-1 If non-negative, reads with more Ns than this 1011s (after trimming) will be discarded. 1011s mcb=0 (minconsecutivebases) Discard reads without at least 1011s this many consecutive called bases. 1011s ottm=f (outputtrimmedtomatch) Output reads trimmed to shorter 1011s than minlength to outm rather than discarding. 1011s tp=0 (trimpad) Trim this much extra around matching kmers. 1011s tbo=f (trimbyoverlap) Trim adapters based on where paired 1011s reads overlap. 1011s strictoverlap=t Adjust sensitivity for trimbyoverlap mode. 1011s minoverlap=14 Require this many bases of overlap for detection. 1011s mininsert=40 Require insert size of at least this for overlap. 1011s Should be reduced to 16 for small RNA sequencing. 1011s tpe=f (trimpairsevenly) When kmer right-trimming, trim both 1011s reads to the minimum length of either. 1011s forcetrimleft=0 (ftl) If positive, trim bases to the left of this position 1011s (exclusive, 0-based). 1011s forcetrimright=0 (ftr) If positive, trim bases to the right of this position 1011s (exclusive, 0-based). 1011s forcetrimright2=0 (ftr2) If positive, trim this many bases on the right end. 1011s forcetrimmod=0 (ftm) If positive, right-trim length to be equal to zero, 1011s modulo this number. 1011s restrictleft=0 If positive, only look for kmer matches in the 1011s leftmost X bases. 1011s restrictright=0 If positive, only look for kmer matches in the 1011s rightmost X bases. 1011s NOTE: restrictleft and restrictright are mutually exclusive. If trimming 1011s both ends is desired, use ktrimtips. 1011s mingc=0 Discard reads with GC content below this. 1011s maxgc=1 Discard reads with GC content above this. 1011s gcpairs=t Use average GC of paired reads. 1011s Also affects gchist. 1011s tossjunk=f Discard reads with invalid characters as bases. 1011s swift=f Trim Swift sequences: Trailing C/T/N R1, leading G/A/N R2. 1011s 1011s Header-parsing parameters - these require Illumina headers: 1011s chastityfilter=f (cf) Discard reads with id containing ' 1:Y:' or ' 2:Y:'. 1011s barcodefilter=f Remove reads with unexpected barcodes if barcodes is set, 1011s or barcodes containing 'N' otherwise. A barcode must be 1011s the last part of the read header. Values: 1011s t: Remove reads with bad barcodes. 1011s f: Ignore barcodes. 1011s crash: Crash upon encountering bad barcodes. 1011s barcodes= Comma-delimited list of barcodes or files of barcodes. 1011s xmin=-1 If positive, discard reads with a lesser X coordinate. 1011s ymin=-1 If positive, discard reads with a lesser Y coordinate. 1011s xmax=-1 If positive, discard reads with a greater X coordinate. 1011s ymax=-1 If positive, discard reads with a greater Y coordinate. 1011s 1011s Polymer trimming: 1011s trimpolya=0 If greater than 0, trim poly-A or poly-T tails of 1011s at least this length on either end of reads. 1011s trimpolygleft=0 If greater than 0, trim poly-G prefixes of at least this 1011s length on the left end of reads. Does not trim poly-C. 1011s trimpolygright=0 If greater than 0, trim poly-G tails of at least this 1011s length on the right end of reads. Does not trim poly-C. 1011s trimpolyg=0 This sets both left and right at once. 1011s filterpolyg=0 If greater than 0, remove reads with a poly-G prefix of 1011s at least this length (on the left). 1011s Note: there are also equivalent poly-C flags. 1011s 1011s Polymer tracking: 1011s pratio=base,base 'pratio=G,C' will print the ratio of G to C polymers. 1011s plen=20 Length of homopolymers to count. 1011s 1011s Entropy/Complexity parameters: 1011s entropy=-1 Set between 0 and 1 to filter reads with entropy below 1011s that value. Higher is more stringent. 1011s entropywindow=50 Calculate entropy using a sliding window of this length. 1011s entropyk=5 Calculate entropy using kmers of this length. 1011s minbasefrequency=0 Discard reads with a minimum base frequency below this. 1011s entropytrim=f Values: 1011s f: (false) Do not entropy-trim. 1011s r: (right) Trim low entropy on the right end only. 1011s l: (left) Trim low entropy on the left end only. 1011s rl: (both) Trim low entropy on both ends. 1011s entropymask=f Values: 1011s f: (filter) Discard low-entropy sequences. 1011s t: (true) Mask low-entropy parts of sequences with N. 1011s lc: Change low-entropy parts of sequences to lowercase. 1011s entropymark=f Mark each base with its entropy value. This is on a scale 1011s of 0-41 and is reported as quality scores, so the output 1011s should be fastq or fasta+qual. 1011s NOTE: If set, entropytrim overrides entropymask. 1011s 1011s Cardinality estimation: 1011s cardinality=f (loglog) Count unique kmers using the LogLog algorithm. 1011s cardinalityout=f (loglogout) Count unique kmers in output reads. 1011s loglogk=31 Use this kmer length for counting. 1011s loglogbuckets=2048 Use this many buckets for counting. 1011s khist= Kmer frequency histogram; plots number of kmers versus 1011s kmer depth. This is approximate. 1011s khistout= Kmer frequency histogram for output reads. 1011s 1011s Java Parameters: 1011s 1011s -Xmx This will set Java's memory usage, overriding autodetection. 1011s -Xmx20g will 1011s specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 1011s The max is typically 85% of physical memory. 1011s -eoom This flag will cause the process to exit if an 1011s out-of-memory exception occurs. Requires Java 8u92+. 1011s -da Disable assertions. 1011s 1011s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 1011s 1012s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 1012s java -ea -Xmx1318m -Xms1318m -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 1012s 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] 1012s Version 39.06 1012s 1012s 0.013 seconds. 1012s Initial: 1012s Memory: max=1409m, total=1409m, free=1379m, used=30m 1012s 1012s Input is being processed as paired 1012s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 1012s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 1012s Started output streams: 0.015 seconds. 1012s Processing time: 0.004 seconds. 1012s 1012s Input: 8 reads 306 bases. 1012s QTrimmed: 0 reads (0.00%) 0 bases (0.00%) 1012s Total Removed: 8 reads (100.00%) 306 bases (100.00%) 1012s Result: 0 reads (0.00%) 0 bases (0.00%) 1012s 1012s Time: 0.021 seconds. 1012s Reads Processed: 8 0.39k reads/sec 1012s Bases Processed: 306 0.01m bases/sec 1012s test -r out.fastq.gz 1012s 1012s # bbnorm 1012s bbnorm.sh --version 1012s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 1012s java -ea -Xmx2636m -Xms2636m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 --version 1012s BBMap version 39.06 1012s For help, please run the shellscript with no parameters, or look in /docs/. 1012s bbnorm.sh --help 1012s bbnorm.sh in=sanger_full_range_original_sanger.fastq qin=33 \ 1012s out=out3.fastq outt=outt.fastq hist=hist.plt 1012s 1012s Written by Brian Bushnell 1012s Last modified October 19, 2017 1012s 1012s Description: Normalizes read depth based on kmer counts. 1012s Can also error-correct, bin reads by kmer depth, and generate a kmer depth histogram. 1012s However, Tadpole has superior error-correction to BBNorm. 1012s Please read bbmap/docs/guides/BBNormGuide.txt for more information. 1012s 1012s Usage: bbnorm.sh in= out= outt= hist= 1012s 1012s Input parameters: 1012s in=null Primary input. Use in2 for paired reads in a second file 1012s in2=null Second input file for paired reads in two files 1012s extra=null Additional files to use for input (generating hash table) but not for output 1012s fastareadlen=2^31 Break up FASTA reads longer than this. Can be useful when processing scaffolded genomes 1012s tablereads=-1 Use at most this many reads when building the hashtable (-1 means all) 1012s kmersample=1 Process every nth kmer, and skip the rest 1012s readsample=1 Process every nth read, and skip the rest 1012s 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. 1012s qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto. 1012s 1012s Output parameters: 1012s out= File for normalized or corrected reads. Use out2 for paired reads in a second file 1012s outt= (outtoss) File for reads that were excluded from primary output 1012s reads=-1 Only process this number of reads, then quit (-1 means all) 1012s sampleoutput=t Use sampling on output as well as input (not used if sample rates are 1) 1012s keepall=f Set to true to keep all reads (e.g. if you just want error correction). 1012s 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. 1012s Default is false, to prevent confusion about how there can be 0-count kmers. 1012s The reason is that based on the 'minq' and 'minprob' settings, some kmers may be excluded from the bloom filter. 1012s tmpdir= This will specify a directory for temp files (only needed for multipass runs). If null, they will be written to the output directory. 1012s usetempdir=t Allows enabling/disabling of temporary directory; if disabled, temp files will be written to the output directory. 1012s qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input). 1012s rename=f Rename reads based on their kmer depth. 1012s 1012s Hashing parameters: 1012s k=31 Kmer length (values under 32 are most efficient, but arbitrarily high values are supported) 1012s 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. 1012s Large values decrease accuracy for a fixed amount of memory, so use the lowest number you can that will still capture highest-depth kmers. 1012s hashes=3 Number of times each kmer is hashed and stored. Higher is slower. 1012s Higher is MORE accurate if there is enough memory, and LESS accurate if there is not enough memory. 1012s 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. 1012s prehashes=2 Number of hashes for prefilter. 1012s prefilterbits=2 (pbits) Bits per cell in prefilter. 1012s prefiltersize=0.35 Fraction of memory to allocate to prefilter. 1012s buildpasses=1 More passes can sometimes increase accuracy by iteratively removing low-depth kmers 1012s minq=6 Ignore kmers containing bases with quality below this 1012s minprob=0.5 Ignore kmers with overall probability of correctness below this 1012s 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. 1012s 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. 1012s 1012s Normalization parameters: 1012s fixspikes=f (fs) Do a slower, high-precision bloom filter lookup of kmers that appear to have an abnormally high depth due to collisions. 1012s target=100 (tgt) Target normalization depth. NOTE: All depth parameters control kmer depth, not read depth. 1012s For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1)) 1012s maxdepth=-1 (max) Reads will not be downsampled when below this depth, even if they are above the target depth. 1012s mindepth=5 (min) Kmers with depth below this number will not be included when calculating the depth of a read. 1012s minkmers=15 (mgkpr) Reads must have at least this many kmers over min depth to be retained. Aka 'mingoodkmersperread'. 1012s 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. 1012s uselowerdepth=t (uld) For pairs, use the depth of the lower read as the depth proxy. 1012s deterministic=t (dr) Generate random numbers deterministically to ensure identical output between multiple runs. May decrease speed with a huge number of threads. 1012s passes=2 (p) 1 pass is the basic mode. 2 passes (default) allows greater accuracy, error detection, better contol of output depth. 1012s 1012s Error detection parameters: 1012s hdp=90.0 (highdepthpercentile) Position in sorted kmer depth array used as proxy of a read's high kmer depth. 1012s ldp=25.0 (lowdepthpercentile) Position in sorted kmer depth array used as proxy of a read's low kmer depth. 1012s tossbadreads=f (tbr) Throw away reads detected as containing errors. 1012s requirebothbad=f (rbb) Only toss bad pairs if both reads are bad. 1012s 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. 1012s highthresh=12 (ht) Threshold for high kmer. A high kmer at this or above are considered non-error. 1012s lowthresh=3 (lt) Threshold for low kmer. Kmers at this and below are always considered errors. 1012s 1012s Error correction parameters: 1012s ecc=f Set to true to correct errors. NOTE: Tadpole is now preferred for ecc as it does a better job. 1012s ecclimit=3 Correct up to this many errors per read. If more are detected, the read will remain unchanged. 1012s errorcorrectratio=140 (ecr) Adjacent kmers with a depth ratio of at least this much between will be classified as an error. 1012s echighthresh=22 (echt) Threshold for high kmer. A kmer at this or above may be considered non-error. 1012s eclowthresh=2 (eclt) Threshold for low kmer. Kmers at this and below are considered errors. 1012s eccmaxqual=127 Do not correct bases with quality above this value. 1012s aec=f (aggressiveErrorCorrection) Sets more aggressive values of ecr=100, ecclimit=7, echt=16, eclt=3. 1012s cec=f (conservativeErrorCorrection) Sets more conservative values of ecr=180, ecclimit=2, echt=30, eclt=1, sl=4, pl=4. 1012s meo=f (markErrorsOnly) Marks errors by reducing quality value of suspected errors; does not correct anything. 1012s mue=t (markUncorrectableErrors) Marks errors only on uncorrectable reads; requires 'ecc=t'. 1012s overlap=f (ecco) Error correct by read overlap. 1012s 1012s Depth binning parameters: 1012s lowbindepth=10 (lbd) Cutoff for low depth bin. 1012s highbindepth=80 (hbd) Cutoff for high depth bin. 1012s outlow= Pairs in which both reads have a median below lbd go into this file. 1012s outhigh= Pairs in which both reads have a median above hbd go into this file. 1012s outmid= All other pairs go into this file. 1012s 1012s Histogram parameters: 1012s hist= Specify a file to write the input kmer depth histogram. 1012s histout= Specify a file to write the output kmer depth histogram. 1012s histcol=3 (histogramcolumns) Number of histogram columns, 2 or 3. 1012s pzc=f (printzerocoverage) Print lines in the histogram with zero coverage. 1012s histlen=1048576 Max kmer depth displayed in histogram. Also affects statistics displayed, but does not affect normalization. 1012s 1012s Peak calling parameters: 1012s peaks= Write the peaks to this file. Default is stdout. 1012s minHeight=2 (h) Ignore peaks shorter than this. 1012s minVolume=5 (v) Ignore peaks with less area than this. 1012s minWidth=3 (w) Ignore peaks narrower than this. 1012s minPeak=2 (minp) Ignore peaks with an X-value below this. 1012s maxPeak=BIG (maxp) Ignore peaks with an X-value above this. 1012s maxPeakCount=8 (maxpc) Print up to this many peaks (prioritizing height). 1012s 1012s Java Parameters: 1012s -Xmx This will set Java's memory usage, overriding autodetection. 1012s -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 1012s The max is typically 85% of physical memory. 1012s -eoom This flag will cause the process to exit if an 1012s out-of-memory exception occurs. Requires Java 8u92+. 1012s -da Disable assertions. 1012s 1012s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 1012s 1012s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 1012s java -ea -Xmx2636m -Xms2636m -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 1012s Executing jgi.KmerNormalize [bits=32, in=sanger_full_range_original_sanger.fastq, qin=33, out=out3.fastq, outt=outt.fastq, hist=hist.plt] 1012s 1012s 1012s *********** Pass 1 ********** 1012s 1012s 1012s Settings: 1012s threads: 4 1012s k: 31 1012s deterministic: true 1012s toss error reads: false 1012s passes: 1 1012s bits per cell: 16 1012s cells: 980.97M 1012s hashes: 3 1012s base min quality: 5 1012s kmer min prob: 0.5 1012s 1012s target depth: 400 1012s min depth: 3 1012s max depth: 500 1012s min good kmers: 15 1012s depth percentile: 64.8 1012s ignore dupe kmers: true 1012s fix spikes: false 1012s histogram length: 65536 1012s print zero cov: false 1012s 1014s Made hash table: hashes = 3 mem = 1.83 GB cells = 980.47M used = 0.000% 1014s 1014s Estimated unique kmers: 7 1014s 1014s Table creation time: 2.437 seconds. 1014s Started output threads. 1014s Started output threads. 1014s Table read time: 0.007 seconds. 26.87 kb/sec 1014s Total reads in: 2 0.000% Kept 1014s Total bases in: 188 0.000% Kept 1014s Error reads in: 2 100.000% 1014s Error type 1: 2 100.000% 1014s Error type 2: 0 0.000% 1014s Error type 3: 0 0.000% 1014s 1014s Wrote histogram to hist.plt 1015s Total kmers counted: 128 1015s Total unique kmer count: 128 1015s Includes forward kmers only. 1015s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 1015s The most accurate value is the greater of the two. 1015s 1015s Percent unique: 100.00% 1015s Depth average: 1.00 (unique kmers) 1015s Depth median: 1 (unique kmers) 1015s Depth standard deviation: 0.00 (unique kmers) 1015s Corrected depth average: 0.00 1015s 1015s Depth average: 1.00 (all kmers) 1015s Depth median: 1 (all kmers) 1015s Depth standard deviation: 0.00 (all kmers) 1015s 1015s Approx. read depth median: 1.47 1015s 1015s *********** Pass 2 ********** 1015s 1015s 1015s Settings: 1015s threads: 4 1015s k: 31 1015s deterministic: true 1015s toss error reads: false 1015s passes: 1 1015s bits per cell: 16 1015s cells: 980.97M 1015s hashes: 3 1015s base min quality: 5 1015s kmer min prob: 0.5 1015s 1015s target depth: 100 1015s min depth: 5 1015s max depth: 100 1015s min good kmers: 15 1015s depth percentile: 54.0 1015s ignore dupe kmers: true 1015s fix spikes: false 1015s histogram length: 65536 1015s 1017s Made hash table: hashes = 3 mem = 1.83 GB cells = 980.47M used = 0.000% 1017s 1017s Estimated unique kmers: 0 1017s 1017s Table creation time: 2.288 seconds. 1017s Started output threads. 1017s Started output threads. 1017s Table read time: 0.002 seconds. 0.00 kb/sec 1017s Total reads in: 0 NaN% Kept 1017s Total bases in: 0 NaN% Kept 1017s Error reads in: 0 NaN% 1017s Error type 1: 0 NaN% 1017s Error type 2: 0 NaN% 1017s Error type 3: 0 NaN% 1017s Total kmers counted: 0 1017s Total unique kmer count: 0 1017s Includes forward kmers only. 1017s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 1017s The most accurate value is the greater of the two. 1017s 1017s Percent unique: NaN% 1017s Depth average: NaN (unique kmers) 1017s Depth median: 0 (unique kmers) 1017s Depth standard deviation: NaN (unique kmers) 1017s Corrected depth average: NaN 1017s 1017s Depth average: NaN (all kmers) 1017s Depth median: 0 (all kmers) 1017s Depth standard deviation: 0.00 (all kmers) 1017s 1017s Approx. read depth median: NaN 1017s 1017s Removing temp files. 1017s 1017s Total time: 4.835 seconds. 0.04 kb/sec 1017s test -r out3.fastq 1017s test -r outt.fastq 1017s test -r hist.plt 1017s bbnorm.sh in=illumina_full_range_original_illumina.fastq qin=64 \ 1017s out=out4.fastq outt=outt2.fastq hist=hist2.plt 1017s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 1017s java -ea -Xmx2636m -Xms2636m -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 1017s Executing jgi.KmerNormalize [bits=32, in=illumina_full_range_original_illumina.fastq, qin=64, out=out4.fastq, outt=outt2.fastq, hist=hist2.plt] 1017s 1017s 1017s *********** Pass 1 ********** 1017s 1017s 1017s Settings: 1017s threads: 4 1017s k: 31 1017s deterministic: true 1017s toss error reads: false 1017s passes: 1 1017s bits per cell: 16 1017s cells: 980.97M 1017s hashes: 3 1017s base min quality: 5 1017s kmer min prob: 0.5 1017s 1017s target depth: 400 1017s min depth: 3 1017s max depth: 500 1017s min good kmers: 15 1017s depth percentile: 64.8 1017s ignore dupe kmers: true 1017s fix spikes: false 1017s histogram length: 65536 1017s print zero cov: false 1017s 1019s Made hash table: hashes = 3 mem = 1.83 GB cells = 980.47M used = 0.000% 1019s 1019s Estimated unique kmers: 7 1019s 1019s Table creation time: 2.400 seconds. 1019s Started output threads. 1019s Started output threads. 1019s Table read time: 0.006 seconds. 20.11 kb/sec 1019s Total reads in: 2 0.000% Kept 1019s Total bases in: 126 0.000% Kept 1019s Error reads in: 2 100.000% 1019s Error type 1: 2 100.000% 1019s Error type 2: 0 0.000% 1019s Error type 3: 0 0.000% 1019s 1019s Wrote histogram to hist2.plt 1019s Total kmers counted: 66 1019s Total unique kmer count: 66 1019s Includes forward kmers only. 1019s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 1019s The most accurate value is the greater of the two. 1019s 1019s Percent unique: 100.00% 1019s Depth average: 1.00 (unique kmers) 1019s Depth median: 1 (unique kmers) 1019s Depth standard deviation: 0.00 (unique kmers) 1019s Corrected depth average: 0.00 1019s 1019s Depth average: 1.00 (all kmers) 1019s Depth median: 1 (all kmers) 1019s Depth standard deviation: 0.00 (all kmers) 1019s 1019s Approx. read depth median: 1.91 1019s 1019s *********** Pass 2 ********** 1019s 1019s 1019s Settings: 1019s threads: 4 1019s k: 31 1019s deterministic: true 1019s toss error reads: false 1019s passes: 1 1019s bits per cell: 16 1019s cells: 980.97M 1019s hashes: 3 1019s base min quality: 5 1019s kmer min prob: 0.5 1019s 1019s target depth: 100 1019s min depth: 5 1019s max depth: 100 1019s min good kmers: 15 1019s depth percentile: 54.0 1019s ignore dupe kmers: true 1019s fix spikes: false 1019s histogram length: 65536 1019s 1022s Made hash table: hashes = 3 mem = 1.83 GB cells = 980.47M used = 0.000% 1022s 1022s Estimated unique kmers: 0 1022s 1022s Table creation time: 2.275 seconds. 1022s Started output threads. 1022s Started output threads. 1022s Table read time: 0.002 seconds. 0.00 kb/sec 1022s Total reads in: 0 NaN% Kept 1022s Total bases in: 0 NaN% Kept 1022s Error reads in: 0 NaN% 1022s Error type 1: 0 NaN% 1022s Error type 2: 0 NaN% 1022s Error type 3: 0 NaN% 1022s Total kmers counted: 0 1022s Total unique kmer count: 0 1022s Includes forward kmers only. 1022s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 1022s The most accurate value is the greater of the two. 1022s 1022s Percent unique: NaN% 1022s Depth average: NaN (unique kmers) 1022s Depth median: 0 (unique kmers) 1022s Depth standard deviation: NaN (unique kmers) 1022s Corrected depth average: NaN 1022s 1022s Depth average: NaN (all kmers) 1022s Depth median: 0 (all kmers) 1022s Depth standard deviation: 0.00 (all kmers) 1022s 1022s Approx. read depth median: NaN 1022s 1022s Removing temp files. 1022s 1022s Total time: 4.784 seconds. 0.03 kb/sec 1022s test -r out4.fastq 1022s test -r outt2.fastq 1022s test -r hist2.plt 1022s autopkgtest [19:28:51]: test run-unit-test: -----------------------] 1023s autopkgtest [19:28:52]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 1023s run-unit-test PASS 1023s autopkgtest [19:28:52]: @@@@@@@@@@@@@@@@@@@@ summary 1023s run-unit-test PASS 1038s Creating nova instance adt-noble-ppc64el-bbmap-20240321-191148-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-ppc64el-server-20240321.img (UUID 024d6af5-fcba-4a84-85f9-01f41e1878d6)...