0s autopkgtest [16:03:06]: starting date and time: 2024-03-21 16:03:06+0000 0s autopkgtest [16:03:06]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [16:03:06]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.yielqp7u/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:openjdk-21,src:alsa-lib,src:at-spi2-core,src:cups,src:glib2.0,src:gnutls28,src:gtk+3.0,src:libpng1.6,src:nettle,src:wp2latex --apt-upgrade bbmap --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=openjdk-21/21.0.3~7ea-1 alsa-lib/1.2.11-1build1 at-spi2-core/2.51.90-3 cups/2.4.7-1.2ubuntu1 glib2.0/2.79.3-3ubuntu5 gnutls28/3.8.3-1.1ubuntu2 gtk+3.0/3.24.41-1.1ubuntu3 libpng1.6/1.6.43-3 nettle/3.9.1-2.2 wp2latex/4.4~ds-1build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-big --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos01-ppc64el-5.secgroup --name adt-noble-ppc64el-bbmap-20240321-160306-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/ 206s autopkgtest [16:06:32]: testbed dpkg architecture: ppc64el 206s autopkgtest [16:06:32]: testbed apt version: 2.7.12 206s autopkgtest [16:06:32]: @@@@@@@@@@@@@@@@@@@@ test bed setup 207s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 207s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [53.9 kB] 207s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [495 kB] 207s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3757 kB] 208s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 208s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [668 kB] 208s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 208s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 208s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 208s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4078 kB] 209s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 209s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [58.3 kB] 209s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 212s Fetched 9248 kB in 3s (2720 kB/s) 213s Reading package lists... 216s Reading package lists... 216s Building dependency tree... 216s Reading state information... 216s Calculating upgrade... 216s The following packages will be REMOVED: 216s libglib2.0-0 216s The following NEW packages will be installed: 216s libglib2.0-0t64 xdg-user-dirs 216s The following packages will be upgraded: 216s gir1.2-glib-2.0 libglib2.0-data 216s 2 upgraded, 2 newly installed, 1 to remove and 0 not upgraded. 216s Need to get 2022 kB of archives. 216s After this operation, 204 kB of additional disk space will be used. 216s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gir1.2-glib-2.0 ppc64el 2.79.3-3ubuntu5 [182 kB] 217s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libglib2.0-0t64 ppc64el 2.79.3-3ubuntu5 [1773 kB] 217s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 217s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el xdg-user-dirs ppc64el 0.18-1 [20.0 kB] 217s Fetched 2022 kB in 1s (2310 kB/s) 217s (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.) 217s Preparing to unpack .../gir1.2-glib-2.0_2.79.3-3ubuntu5_ppc64el.deb ... 217s Unpacking gir1.2-glib-2.0:ppc64el (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 218s dpkg: libglib2.0-0:ppc64el: dependency problems, but removing anyway as you requested: 218s udisks2 depends on libglib2.0-0 (>= 2.77.0). 218s shared-mime-info depends on libglib2.0-0 (>= 2.75.3). 218s python3-gi depends on libglib2.0-0 (>= 2.77.0). 218s python3-dbus depends on libglib2.0-0 (>= 2.16.0). 218s netplan.io depends on libglib2.0-0 (>= 2.70.0). 218s netplan-generator depends on libglib2.0-0 (>= 2.70.0). 218s libxmlb2:ppc64el depends on libglib2.0-0 (>= 2.54.0). 218s libvolume-key1:ppc64el depends on libglib2.0-0 (>= 2.18.0). 218s libudisks2-0:ppc64el depends on libglib2.0-0 (>= 2.75.3). 218s libqrtr-glib0:ppc64el depends on libglib2.0-0 (>= 2.56). 218s libqmi-proxy depends on libglib2.0-0 (>= 2.30.0). 218s libqmi-glib5:ppc64el depends on libglib2.0-0 (>= 2.54.0). 218s libpolkit-gobject-1-0:ppc64el depends on libglib2.0-0 (>= 2.38.0). 218s libpolkit-agent-1-0:ppc64el depends on libglib2.0-0 (>= 2.38.0). 218s libnetplan0:ppc64el depends on libglib2.0-0 (>= 2.75.3). 218s libmm-glib0:ppc64el depends on libglib2.0-0 (>= 2.62.0). 218s libmbim-proxy depends on libglib2.0-0 (>= 2.56). 218s libmbim-glib4:ppc64el depends on libglib2.0-0 (>= 2.56). 218s libjson-glib-1.0-0:ppc64el depends on libglib2.0-0 (>= 2.75.3). 218s libjcat1:ppc64el depends on libglib2.0-0 (>= 2.75.3). 218s libgusb2:ppc64el depends on libglib2.0-0 (>= 2.75.3). 218s libgudev-1.0-0:ppc64el depends on libglib2.0-0 (>= 2.38.0). 218s libgirepository-1.0-1:ppc64el depends on libglib2.0-0 (>= 2.79.0). 218s libfwupd2:ppc64el depends on libglib2.0-0 (>= 2.79.0). 218s libblockdev3:ppc64el depends on libglib2.0-0 (>= 2.42.2). 218s libblockdev-utils3:ppc64el depends on libglib2.0-0 (>= 2.75.3). 218s libblockdev-swap3:ppc64el depends on libglib2.0-0 (>= 2.42.2). 218s libblockdev-part3:ppc64el depends on libglib2.0-0 (>= 2.42.2). 218s libblockdev-nvme3:ppc64el depends on libglib2.0-0 (>= 2.42.2). 218s libblockdev-mdraid3:ppc64el depends on libglib2.0-0 (>= 2.42.2). 218s libblockdev-loop3:ppc64el depends on libglib2.0-0 (>= 2.42.2). 218s libblockdev-fs3:ppc64el depends on libglib2.0-0 (>= 2.42.2). 218s libblockdev-crypto3:ppc64el depends on libglib2.0-0 (>= 2.42.2). 218s fwupd depends on libglib2.0-0 (>= 2.79.0). 218s bolt depends on libglib2.0-0 (>= 2.56.0). 218s 218s (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.) 218s Removing libglib2.0-0:ppc64el (2.79.2-1~ubuntu1) ... 218s Selecting previously unselected package libglib2.0-0t64:ppc64el. 218s (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.) 218s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_ppc64el.deb ... 218s 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... 218s removed '/var/lib/dpkg/info/libglib2.0-0:ppc64el.postrm' 218s Unpacking libglib2.0-0t64:ppc64el (2.79.3-3ubuntu5) ... 218s Preparing to unpack .../libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 218s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 218s Selecting previously unselected package xdg-user-dirs. 218s Preparing to unpack .../xdg-user-dirs_0.18-1_ppc64el.deb ... 218s Unpacking xdg-user-dirs (0.18-1) ... 218s Setting up xdg-user-dirs (0.18-1) ... 218s Setting up libglib2.0-0t64:ppc64el (2.79.3-3ubuntu5) ... 218s No schema files found: doing nothing. 218s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 218s Setting up gir1.2-glib-2.0:ppc64el (2.79.3-3ubuntu5) ... 218s Processing triggers for man-db (2.12.0-3) ... 218s Processing triggers for libc-bin (2.39-0ubuntu2) ... 219s Reading package lists... 219s Building dependency tree... 219s Reading state information... 219s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 220s sh: Attempting to set up Debian/Ubuntu apt sources automatically 220s sh: Distribution appears to be Ubuntu 221s Reading package lists... 221s Building dependency tree... 221s Reading state information... 221s eatmydata is already the newest version (131-1). 221s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 221s Reading package lists... 221s Building dependency tree... 221s Reading state information... 221s dbus is already the newest version (1.14.10-4ubuntu1). 221s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 221s Reading package lists... 222s Building dependency tree... 222s Reading state information... 222s rng-tools-debian is already the newest version (2.4). 222s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 222s Reading package lists... 222s Building dependency tree... 222s Reading state information... 222s The following packages will be REMOVED: 222s cloud-init* python3-configobj* python3-debconf* 222s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 222s After this operation, 3252 kB disk space will be freed. 222s (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.) 223s Removing cloud-init (24.1.1-0ubuntu1) ... 223s Removing python3-configobj (5.0.8-3) ... 223s Removing python3-debconf (1.5.86) ... 223s Processing triggers for man-db (2.12.0-3) ... 224s (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.) 224s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 225s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 225s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 225s invoke-rc.d: policy-rc.d denied execution of try-restart. 225s Reading package lists... 225s Building dependency tree... 225s Reading state information... 225s linux-generic is already the newest version (6.8.0-11.11+1). 225s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 226s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 226s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 226s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 229s Reading package lists... 229s Reading package lists... 229s Building dependency tree... 229s Reading state information... 230s Calculating upgrade... 230s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 230s Reading package lists... 230s Building dependency tree... 230s Reading state information... 230s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 230s autopkgtest [16:06:56]: rebooting testbed after setup commands that affected boot 374s autopkgtest [16:09:20]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 377s autopkgtest [16:09:23]: @@@@@@@@@@@@@@@@@@@@ apt-source bbmap 380s Get:1 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (dsc) [2286 B] 380s Get:2 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (tar) [5343 kB] 380s Get:3 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (diff) [25.4 kB] 380s gpgv: Signature made Fri Nov 24 11:00:29 2023 UTC 380s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 380s gpgv: issuer "emollier@debian.org" 380s gpgv: Can't check signature: No public key 380s dpkg-source: warning: cannot verify inline signature for ./bbmap_39.06+dfsg-1.dsc: no acceptable signature found 381s autopkgtest [16:09:27]: testing package bbmap version 39.06+dfsg-1 381s autopkgtest [16:09:27]: build not needed 383s autopkgtest [16:09:29]: test run-unit-test: preparing testbed 393s Reading package lists... 393s Building dependency tree... 393s Reading state information... 393s Starting pkgProblemResolver with broken count: 0 393s Starting 2 pkgProblemResolver with broken count: 0 393s Done 393s The following additional packages will be installed: 393s bbmap bbmap-jni ca-certificates-java fontconfig-config fonts-dejavu-core 393s fonts-dejavu-mono java-common libapache-pom-java libasound2 libasound2-data 393s libavahi-client3 libavahi-common-data libavahi-common3 libcommons-cli-java 393s libcommons-codec-java libcommons-io-java libcommons-parent-java libcups2 393s libfontconfig1 libgraphite2-3 libharfbuzz0b libjpeg-turbo8 libjpeg8 393s liblcms2-2 liblog4j1.2-java libmpj-java libpcsclite1 openjdk-17-jre-headless 393s python-biopython-doc 393s Suggested packages: 393s default-jre libasound2-plugins alsa-utils libcommons-io-java-doc cups-common 393s liblcms2-utils liblog4j1.2-java-doc libmail-java pcscd libnss-mdns 393s fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho 393s fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic 393s Recommended packages: 393s pigz alsa-ucm-conf alsa-topology-conf python3-biopython 393s The following NEW packages will be installed: 393s autopkgtest-satdep bbmap bbmap-jni ca-certificates-java fontconfig-config 393s fonts-dejavu-core fonts-dejavu-mono java-common libapache-pom-java 393s libasound2 libasound2-data libavahi-client3 libavahi-common-data 393s libavahi-common3 libcommons-cli-java libcommons-codec-java 393s libcommons-io-java libcommons-parent-java libcups2 libfontconfig1 393s libgraphite2-3 libharfbuzz0b libjpeg-turbo8 libjpeg8 liblcms2-2 393s liblog4j1.2-java libmpj-java libpcsclite1 openjdk-17-jre-headless 393s python-biopython-doc 393s 0 upgraded, 30 newly installed, 0 to remove and 0 not upgraded. 393s Need to get 79.6 MB/79.6 MB of archives. 393s After this operation, 240 MB of additional disk space will be used. 393s Get:1 /tmp/autopkgtest.FIUvSP/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [724 B] 394s Get:2 http://ftpmaster.internal/ubuntu noble/universe ppc64el libcommons-cli-java all 1.6.0-1 [59.9 kB] 394s Get:3 http://ftpmaster.internal/ubuntu noble/universe ppc64el libapache-pom-java all 29-2 [5284 B] 394s Get:4 http://ftpmaster.internal/ubuntu noble/universe ppc64el libcommons-parent-java all 56-1 [10.7 kB] 395s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el libcommons-codec-java all 1.16.0-1 [306 kB] 396s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el libcommons-io-java all 2.11.0-2 [297 kB] 397s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el liblog4j1.2-java all 1.2.17-11 [439 kB] 398s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el libmpj-java all 0.44+dfsg-4 [443 kB] 399s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el ca-certificates-java all 20240118 [11.6 kB] 399s Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el java-common all 0.75+exp1 [6798 B] 399s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el libavahi-common-data ppc64el 0.8-13ubuntu2 [29.5 kB] 399s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el libavahi-common3 ppc64el 0.8-13ubuntu2 [25.8 kB] 399s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el libavahi-client3 ppc64el 0.8-13ubuntu2 [30.6 kB] 399s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el libcups2 ppc64el 2.4.6-0ubuntu3 [344 kB] 399s Get:15 http://ftpmaster.internal/ubuntu noble/main ppc64el liblcms2-2 ppc64el 2.14-2 [243 kB] 400s Get:16 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu1 [212 kB] 400s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 400s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB] 401s Get:19 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB] 401s Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el fontconfig-config ppc64el 2.15.0-1ubuntu1 [37.0 kB] 401s Get:21 http://ftpmaster.internal/ubuntu noble/main ppc64el libfontconfig1 ppc64el 2.15.0-1ubuntu1 [190 kB] 402s Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el libasound2-data all 1.2.10-3build1 [20.7 kB] 402s Get:23 http://ftpmaster.internal/ubuntu noble/main ppc64el libasound2 ppc64el 1.2.10-3build1 [496 kB] 402s Get:24 http://ftpmaster.internal/ubuntu noble/main ppc64el libgraphite2-3 ppc64el 1.3.14-2 [105 kB] 402s Get:25 http://ftpmaster.internal/ubuntu noble/main ppc64el libharfbuzz0b ppc64el 8.3.0-2 [576 kB] 402s Get:26 http://ftpmaster.internal/ubuntu noble/main ppc64el libpcsclite1 ppc64el 2.0.0-1 [27.9 kB] 402s Get:27 http://ftpmaster.internal/ubuntu noble/main ppc64el openjdk-17-jre-headless ppc64el 17.0.10+7-1 [47.2 MB] 415s Get:28 http://ftpmaster.internal/ubuntu noble/universe ppc64el bbmap all 39.06+dfsg-1 [9768 kB] 417s Get:29 http://ftpmaster.internal/ubuntu noble/universe ppc64el bbmap-jni ppc64el 39.06+dfsg-1 [32.8 kB] 417s Get:30 http://ftpmaster.internal/ubuntu noble/universe ppc64el python-biopython-doc all 1.81+dfsg-3 [17.3 MB] 423s Fetched 79.6 MB in 29s (2723 kB/s) 423s Selecting previously unselected package libcommons-cli-java. 423s (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.) 423s Preparing to unpack .../00-libcommons-cli-java_1.6.0-1_all.deb ... 423s Unpacking libcommons-cli-java (1.6.0-1) ... 423s Selecting previously unselected package libapache-pom-java. 423s Preparing to unpack .../01-libapache-pom-java_29-2_all.deb ... 423s Unpacking libapache-pom-java (29-2) ... 423s Selecting previously unselected package libcommons-parent-java. 423s Preparing to unpack .../02-libcommons-parent-java_56-1_all.deb ... 423s Unpacking libcommons-parent-java (56-1) ... 423s Selecting previously unselected package libcommons-codec-java. 423s Preparing to unpack .../03-libcommons-codec-java_1.16.0-1_all.deb ... 423s Unpacking libcommons-codec-java (1.16.0-1) ... 423s Selecting previously unselected package libcommons-io-java. 423s Preparing to unpack .../04-libcommons-io-java_2.11.0-2_all.deb ... 423s Unpacking libcommons-io-java (2.11.0-2) ... 423s Selecting previously unselected package liblog4j1.2-java. 423s Preparing to unpack .../05-liblog4j1.2-java_1.2.17-11_all.deb ... 423s Unpacking liblog4j1.2-java (1.2.17-11) ... 423s Selecting previously unselected package libmpj-java. 423s Preparing to unpack .../06-libmpj-java_0.44+dfsg-4_all.deb ... 423s Unpacking libmpj-java (0.44+dfsg-4) ... 423s Selecting previously unselected package ca-certificates-java. 423s Preparing to unpack .../07-ca-certificates-java_20240118_all.deb ... 423s Unpacking ca-certificates-java (20240118) ... 423s Selecting previously unselected package java-common. 423s Preparing to unpack .../08-java-common_0.75+exp1_all.deb ... 423s Unpacking java-common (0.75+exp1) ... 423s Selecting previously unselected package libavahi-common-data:ppc64el. 423s Preparing to unpack .../09-libavahi-common-data_0.8-13ubuntu2_ppc64el.deb ... 423s Unpacking libavahi-common-data:ppc64el (0.8-13ubuntu2) ... 423s Selecting previously unselected package libavahi-common3:ppc64el. 423s Preparing to unpack .../10-libavahi-common3_0.8-13ubuntu2_ppc64el.deb ... 423s Unpacking libavahi-common3:ppc64el (0.8-13ubuntu2) ... 423s Selecting previously unselected package libavahi-client3:ppc64el. 424s Preparing to unpack .../11-libavahi-client3_0.8-13ubuntu2_ppc64el.deb ... 424s Unpacking libavahi-client3:ppc64el (0.8-13ubuntu2) ... 424s Selecting previously unselected package libcups2:ppc64el. 424s Preparing to unpack .../12-libcups2_2.4.6-0ubuntu3_ppc64el.deb ... 424s Unpacking libcups2:ppc64el (2.4.6-0ubuntu3) ... 424s Selecting previously unselected package liblcms2-2:ppc64el. 424s Preparing to unpack .../13-liblcms2-2_2.14-2_ppc64el.deb ... 424s Unpacking liblcms2-2:ppc64el (2.14-2) ... 424s Selecting previously unselected package libjpeg-turbo8:ppc64el. 424s Preparing to unpack .../14-libjpeg-turbo8_2.1.5-2ubuntu1_ppc64el.deb ... 424s Unpacking libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 424s Selecting previously unselected package libjpeg8:ppc64el. 424s Preparing to unpack .../15-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 424s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 424s Selecting previously unselected package fonts-dejavu-mono. 424s Preparing to unpack .../16-fonts-dejavu-mono_2.37-8_all.deb ... 424s Unpacking fonts-dejavu-mono (2.37-8) ... 424s Selecting previously unselected package fonts-dejavu-core. 424s Preparing to unpack .../17-fonts-dejavu-core_2.37-8_all.deb ... 424s Unpacking fonts-dejavu-core (2.37-8) ... 424s Selecting previously unselected package fontconfig-config. 424s Preparing to unpack .../18-fontconfig-config_2.15.0-1ubuntu1_ppc64el.deb ... 424s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 424s Selecting previously unselected package libfontconfig1:ppc64el. 424s Preparing to unpack .../19-libfontconfig1_2.15.0-1ubuntu1_ppc64el.deb ... 424s Unpacking libfontconfig1:ppc64el (2.15.0-1ubuntu1) ... 424s Selecting previously unselected package libasound2-data. 424s Preparing to unpack .../20-libasound2-data_1.2.10-3build1_all.deb ... 424s Unpacking libasound2-data (1.2.10-3build1) ... 424s Selecting previously unselected package libasound2:ppc64el. 424s Preparing to unpack .../21-libasound2_1.2.10-3build1_ppc64el.deb ... 424s Unpacking libasound2:ppc64el (1.2.10-3build1) ... 424s Selecting previously unselected package libgraphite2-3:ppc64el. 424s Preparing to unpack .../22-libgraphite2-3_1.3.14-2_ppc64el.deb ... 424s Unpacking libgraphite2-3:ppc64el (1.3.14-2) ... 424s Selecting previously unselected package libharfbuzz0b:ppc64el. 424s Preparing to unpack .../23-libharfbuzz0b_8.3.0-2_ppc64el.deb ... 424s Unpacking libharfbuzz0b:ppc64el (8.3.0-2) ... 424s Selecting previously unselected package libpcsclite1:ppc64el. 424s Preparing to unpack .../24-libpcsclite1_2.0.0-1_ppc64el.deb ... 424s Unpacking libpcsclite1:ppc64el (2.0.0-1) ... 424s Selecting previously unselected package openjdk-17-jre-headless:ppc64el. 424s Preparing to unpack .../25-openjdk-17-jre-headless_17.0.10+7-1_ppc64el.deb ... 424s Unpacking openjdk-17-jre-headless:ppc64el (17.0.10+7-1) ... 425s Selecting previously unselected package bbmap. 425s Preparing to unpack .../26-bbmap_39.06+dfsg-1_all.deb ... 425s Unpacking bbmap (39.06+dfsg-1) ... 425s Selecting previously unselected package bbmap-jni. 425s Preparing to unpack .../27-bbmap-jni_39.06+dfsg-1_ppc64el.deb ... 425s Unpacking bbmap-jni (39.06+dfsg-1) ... 425s Selecting previously unselected package python-biopython-doc. 425s Preparing to unpack .../28-python-biopython-doc_1.81+dfsg-3_all.deb ... 425s Unpacking python-biopython-doc (1.81+dfsg-3) ... 426s Selecting previously unselected package autopkgtest-satdep. 426s Preparing to unpack .../29-1-autopkgtest-satdep.deb ... 426s Unpacking autopkgtest-satdep (0) ... 426s Setting up libgraphite2-3:ppc64el (1.3.14-2) ... 426s Setting up liblcms2-2:ppc64el (2.14-2) ... 426s Setting up java-common (0.75+exp1) ... 426s Setting up libcommons-cli-java (1.6.0-1) ... 426s Setting up liblog4j1.2-java (1.2.17-11) ... 426s Setting up libasound2-data (1.2.10-3build1) ... 426s Setting up libapache-pom-java (29-2) ... 426s Setting up libavahi-common-data:ppc64el (0.8-13ubuntu2) ... 426s Setting up fonts-dejavu-mono (2.37-8) ... 426s Setting up fonts-dejavu-core (2.37-8) ... 426s Setting up libpcsclite1:ppc64el (2.0.0-1) ... 426s Setting up libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 426s Setting up python-biopython-doc (1.81+dfsg-3) ... 426s Setting up libasound2:ppc64el (1.2.10-3build1) ... 426s Setting up libharfbuzz0b:ppc64el (8.3.0-2) ... 426s Setting up bbmap-jni (39.06+dfsg-1) ... 426s Setting up ca-certificates-java (20240118) ... 426s No JRE found. Skipping Java certificates setup. 426s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 426s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 426s Setting up libcommons-parent-java (56-1) ... 426s Setting up libavahi-common3:ppc64el (0.8-13ubuntu2) ... 426s Setting up libfontconfig1:ppc64el (2.15.0-1ubuntu1) ... 426s Setting up libcommons-codec-java (1.16.0-1) ... 426s Setting up libavahi-client3:ppc64el (0.8-13ubuntu2) ... 426s Setting up libcommons-io-java (2.11.0-2) ... 426s Setting up libmpj-java (0.44+dfsg-4) ... 426s Setting up libcups2:ppc64el (2.4.6-0ubuntu3) ... 426s Setting up openjdk-17-jre-headless:ppc64el (17.0.10+7-1) ... 426s update-alternatives: using /usr/lib/jvm/java-17-openjdk-ppc64el/bin/java to provide /usr/bin/java (java) in auto mode 426s update-alternatives: using /usr/lib/jvm/java-17-openjdk-ppc64el/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 426s update-alternatives: using /usr/lib/jvm/java-17-openjdk-ppc64el/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 426s update-alternatives: using /usr/lib/jvm/java-17-openjdk-ppc64el/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 426s update-alternatives: using /usr/lib/jvm/java-17-openjdk-ppc64el/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 426s Processing triggers for libc-bin (2.39-0ubuntu2) ... 426s Processing triggers for man-db (2.12.0-3) ... 427s Processing triggers for ca-certificates-java (20240118) ... 428s Adding debian:ACCVRAIZ1.pem 428s Adding debian:AC_RAIZ_FNMT-RCM.pem 428s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 428s Adding debian:ANF_Secure_Server_Root_CA.pem 428s Adding debian:Actalis_Authentication_Root_CA.pem 428s Adding debian:AffirmTrust_Commercial.pem 428s Adding debian:AffirmTrust_Networking.pem 428s Adding debian:AffirmTrust_Premium.pem 428s Adding debian:AffirmTrust_Premium_ECC.pem 428s Adding debian:Amazon_Root_CA_1.pem 428s Adding debian:Amazon_Root_CA_2.pem 428s Adding debian:Amazon_Root_CA_3.pem 428s Adding debian:Amazon_Root_CA_4.pem 428s Adding debian:Atos_TrustedRoot_2011.pem 428s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 428s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 428s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 428s Adding debian:BJCA_Global_Root_CA1.pem 428s Adding debian:BJCA_Global_Root_CA2.pem 428s Adding debian:Baltimore_CyberTrust_Root.pem 428s Adding debian:Buypass_Class_2_Root_CA.pem 428s Adding debian:Buypass_Class_3_Root_CA.pem 428s Adding debian:CA_Disig_Root_R2.pem 428s Adding debian:CFCA_EV_ROOT.pem 428s Adding debian:COMODO_Certification_Authority.pem 428s Adding debian:COMODO_ECC_Certification_Authority.pem 428s Adding debian:COMODO_RSA_Certification_Authority.pem 428s Adding debian:Certainly_Root_E1.pem 428s Adding debian:Certainly_Root_R1.pem 428s Adding debian:Certigna.pem 428s Adding debian:Certigna_Root_CA.pem 428s Adding debian:Certum_EC-384_CA.pem 428s Adding debian:Certum_Trusted_Network_CA.pem 428s Adding debian:Certum_Trusted_Network_CA_2.pem 428s Adding debian:Certum_Trusted_Root_CA.pem 428s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 428s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 428s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 428s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 428s Adding debian:Comodo_AAA_Services_root.pem 428s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 428s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 428s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 428s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 428s Adding debian:DigiCert_Assured_ID_Root_CA.pem 428s Adding debian:DigiCert_Assured_ID_Root_G2.pem 428s Adding debian:DigiCert_Assured_ID_Root_G3.pem 428s Adding debian:DigiCert_Global_Root_CA.pem 428s Adding debian:DigiCert_Global_Root_G2.pem 428s Adding debian:DigiCert_Global_Root_G3.pem 428s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 428s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 428s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 428s Adding debian:DigiCert_Trusted_Root_G4.pem 428s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 428s Adding debian:Entrust_Root_Certification_Authority.pem 428s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 428s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 428s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem 428s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 428s Adding debian:GLOBALTRUST_2020.pem 428s Adding debian:GTS_Root_R1.pem 428s Adding debian:GTS_Root_R2.pem 428s Adding debian:GTS_Root_R3.pem 428s Adding debian:GTS_Root_R4.pem 428s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 428s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 428s Adding debian:GlobalSign_Root_CA.pem 428s Adding debian:GlobalSign_Root_CA_-_R3.pem 428s Adding debian:GlobalSign_Root_CA_-_R6.pem 428s Adding debian:GlobalSign_Root_E46.pem 428s Adding debian:GlobalSign_Root_R46.pem 428s Adding debian:Go_Daddy_Class_2_CA.pem 428s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 428s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 428s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 428s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 428s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 428s Adding debian:HiPKI_Root_CA_-_G1.pem 428s Adding debian:Hongkong_Post_Root_CA_3.pem 428s Adding debian:ISRG_Root_X1.pem 428s Adding debian:ISRG_Root_X2.pem 428s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 428s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 428s Adding debian:Izenpe.com.pem 428s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 428s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 428s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 428s Adding debian:NAVER_Global_Root_Certification_Authority.pem 428s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 428s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 428s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 428s Adding debian:QuoVadis_Root_CA_1_G3.pem 428s Adding debian:QuoVadis_Root_CA_2.pem 428s Adding debian:QuoVadis_Root_CA_2_G3.pem 428s Adding debian:QuoVadis_Root_CA_3.pem 428s Adding debian:QuoVadis_Root_CA_3_G3.pem 428s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 428s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 428s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 428s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 428s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 428s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 428s Adding debian:SZAFIR_ROOT_CA2.pem 428s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 428s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 428s Adding debian:SecureSign_RootCA11.pem 428s Adding debian:SecureTrust_CA.pem 428s Adding debian:Secure_Global_CA.pem 428s Adding debian:Security_Communication_ECC_RootCA1.pem 428s Adding debian:Security_Communication_RootCA2.pem 428s Adding debian:Security_Communication_RootCA3.pem 428s Adding debian:Security_Communication_Root_CA.pem 428s Adding debian:Starfield_Class_2_CA.pem 428s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 428s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 428s Adding debian:SwissSign_Gold_CA_-_G2.pem 428s Adding debian:SwissSign_Silver_CA_-_G2.pem 428s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 428s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 428s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 428s Adding debian:TWCA_Global_Root_CA.pem 428s Adding debian:TWCA_Root_Certification_Authority.pem 428s Adding debian:TeliaSonera_Root_CA_v1.pem 428s Adding debian:Telia_Root_CA_v2.pem 428s Adding debian:TrustAsia_Global_Root_CA_G3.pem 428s Adding debian:TrustAsia_Global_Root_CA_G4.pem 428s Adding debian:Trustwave_Global_Certification_Authority.pem 428s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 428s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 428s Adding debian:TunTrust_Root_CA.pem 428s Adding debian:UCA_Extended_Validation_Root.pem 428s Adding debian:UCA_Global_G2_Root.pem 428s Adding debian:USERTrust_ECC_Certification_Authority.pem 428s Adding debian:USERTrust_RSA_Certification_Authority.pem 428s Adding debian:XRamp_Global_CA_Root.pem 428s Adding debian:certSIGN_ROOT_CA.pem 428s Adding debian:certSIGN_Root_CA_G2.pem 428s Adding debian:e-Szigno_Root_CA_2017.pem 428s Adding debian:ePKI_Root_Certification_Authority.pem 428s Adding debian:emSign_ECC_Root_CA_-_C3.pem 428s Adding debian:emSign_ECC_Root_CA_-_G3.pem 428s Adding debian:emSign_Root_CA_-_C1.pem 428s Adding debian:emSign_Root_CA_-_G1.pem 428s Adding debian:vTrus_ECC_Root_CA.pem 428s Adding debian:vTrus_Root_CA.pem 428s done. 428s Setting up bbmap (39.06+dfsg-1) ... 428s Setting up autopkgtest-satdep (0) ... 431s (Reading database ... 72566 files and directories currently installed.) 431s Removing autopkgtest-satdep (0) ... 432s autopkgtest [16:10:18]: test run-unit-test: [----------------------- 432s 432s # bbmap 432s bbmap.sh --version 432s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 432s java -ea -Xmx2637m -Xms2637m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 --version 432s BBMap version 39.06 432s For help, please run the shellscript with no parameters, or look in /docs/. 432s bbmap.sh --help 432s 432s BBMap 432s Written by Brian Bushnell, from Dec. 2010 - present 432s Last modified September 15, 2022 432s 432s Description: Fast and accurate splice-aware read aligner. 432s Please read bbmap/docs/guides/BBMapGuide.txt for more information. 432s 432s To index: bbmap.sh ref= 432s To map: bbmap.sh in= out= 432s To map without writing an index: 432s bbmap.sh ref= in= out= nodisk 432s 432s in=stdin will accept reads from standard in, and out=stdout will write to 432s standard out, but file extensions are still needed to specify the format of the 432s input and output files e.g. in=stdin.fa.gz will read gzipped fasta from 432s standard in; out=stdout.sam.gz will write gzipped sam. 432s 432s Indexing Parameters (required when building the index): 432s nodisk=f Set to true to build index in memory and write nothing 432s to disk except output. 432s ref= Specify the reference sequence. Only do this ONCE, 432s when building the index (unless using 'nodisk'). 432s build=1 If multiple references are indexed in the same directory, 432s each needs a unique numeric ID (unless using 'nodisk'). 432s k=13 Kmer length, range 8-15. Longer is faster but uses 432s more memory. Shorter is more sensitive. 432s If indexing and mapping are done in two steps, K should 432s be specified each time. 432s path=<.> Specify the location to write the index, if you don't 432s want it in the current working directory. 432s usemodulo=f Throw away ~80% of kmers based on remainder modulo a 432s number (reduces RAM by 50% and sensitivity slightly). 432s Should be enabled both when building the index AND 432s when mapping. 432s rebuild=f Force a rebuild of the index (ref= should be set). 432s 432s Input Parameters: 432s build=1 Designate index to use. Corresponds to the number 432s specified when building the index. 432s in= Primary reads input; required parameter. 432s in2= For paired reads in two files. 432s interleaved=auto True forces paired/interleaved input; false forces 432s single-ended mapping. If not specified, interleaved 432s status will be autodetected from read names. 432s fastareadlen=500 Break up FASTA reads longer than this. Max is 500 for 432s BBMap and 6000 for BBMapPacBio. Only works for FASTA 432s input (use 'maxlen' for FASTQ input). The default for 432s bbmap.sh is 500, and for mapPacBio.sh is 6000. 432s unpigz=f Spawn a pigz (parallel gzip) process for faster 432s decompression than using Java. 432s Requires pigz to be installed. 432s touppercase=t (tuc) Convert lowercase letters in reads to upper case 432s (otherwise they will not match the reference). 432s 432s Sampling Parameters: 432s 432s reads=-1 Set to a positive number N to only process the first N 432s reads (or pairs), then quit. -1 means use all reads. 432s samplerate=1 Set to a number from 0 to 1 to randomly select that 432s fraction of reads for mapping. 1 uses all reads. 432s skipreads=0 Set to a number N to skip the first N reads (or pairs), 432s then map the rest. 432s 432s Mapping Parameters: 432s fast=f This flag is a macro which sets other paramters to run 432s faster, at reduced sensitivity. Bad for RNA-seq. 432s slow=f This flag is a macro which sets other paramters to run 432s slower, at greater sensitivity. 'vslow' is even slower. 432s maxindel=16000 Don't look for indels longer than this. Lower is faster. 432s Set to >=100k for RNAseq with long introns like mammals. 432s strictmaxindel=f When enabled, do not allow indels longer than 'maxindel'. 432s By default these are not sought, but may be found anyway. 432s tipsearch=100 Look this far for read-end deletions with anchors 432s shorter than K, using brute force. 432s minid=0.76 Approximate minimum alignment identity to look for. 432s Higher is faster and less sensitive. 432s minhits=1 Minimum number of seed hits required for candidate sites. 432s Higher is faster. 432s local=f Set to true to use local, rather than global, alignments. 432s This will soft-clip ugly ends of poor alignments. 432s perfectmode=f Allow only perfect mappings when set to true (very fast). 432s semiperfectmode=f Allow only perfect and semiperfect (perfect except for 432s N's in the reference) mappings. 432s threads=auto (t) Set to number of threads desired. By default, uses 432s all cores available. 432s ambiguous=best (ambig) Set behavior on ambiguously-mapped reads (with 432s multiple top-scoring mapping locations). 432s best (use the first best site) 432s toss (consider unmapped) 432s random (select one top-scoring site randomly) 432s all (retain all top-scoring sites) 432s samestrandpairs=f (ssp) Specify whether paired reads should map to the 432s same strand or opposite strands. 432s requirecorrectstrand=t (rcs) Forbid pairing of reads without correct strand 432s orientation. Set to false for long-mate-pair libraries. 432s killbadpairs=f (kbp) If a read pair is mapped with an inappropriate 432s insert size or orientation, the read with the lower 432s mapping quality is marked unmapped. 432s pairedonly=f (po) Treat unpaired reads as unmapped. Thus they will 432s be sent to 'outu' but not 'outm'. 432s rcomp=f Reverse complement both reads prior to mapping (for LMP 432s outward-facing libraries). 432s rcompmate=f Reverse complement read2 prior to mapping. 432s pairlen=32000 Set max allowed distance between paired reads. 432s (insert size)=(pairlen)+(read1 length)+(read2 length) 432s rescuedist=1200 Don't try to rescue paired reads if avg. insert size 432s greater than this. Lower is faster. 432s rescuemismatches=32 Maximum mismatches allowed in a rescued read. Lower 432s is faster. 432s averagepairdist=100 (apd) Initial average distance between paired reads. 432s Varies dynamically; does not need to be specified. 432s deterministic=f Run in deterministic mode. In this case it is good 432s to set averagepairdist. BBMap is deterministic 432s without this flag if using single-ended reads, 432s or run singlethreaded. 432s bandwidthratio=0 (bwr) If above zero, restrict alignment band to this 432s fraction of read length. Faster but less accurate. 432s bandwidth=0 (bw) Set the bandwidth directly. 432s fraction of read length. Faster but less accurate. 432s usejni=f (jni) Do alignments faster, in C code. Requires 432s compiling the C code; details are in /jni/README.txt. 432s maxsites2=800 Don't analyze (or print) more than this many alignments 432s per read. 432s ignorefrequentkmers=t (ifk) Discard low-information kmers that occur often. 432s excludefraction=0.03 (ef) Fraction of kmers to ignore. For example, 0.03 432s will ignore the most common 3% of kmers. 432s greedy=t Use a greedy algorithm to discard the least-useful 432s kmers on a per-read basis. 432s kfilter=0 If positive, potential mapping sites must have at 432s least this many consecutive exact matches. 432s 432s 432s Quality and Trimming Parameters: 432s qin=auto Set to 33 or 64 to specify input quality value ASCII 432s offset. 33 is Sanger, 64 is old Solexa. 432s qout=auto Set to 33 or 64 to specify output quality value ASCII 432s offset (only if output format is fastq). 432s qtrim=f Quality-trim ends before mapping. Options are: 432s 'f' (false), 'l' (left), 'r' (right), and 'lr' (both). 432s untrim=f Undo trimming after mapping. Untrimmed bases will be 432s soft-clipped in cigar strings. 432s trimq=6 Trim regions with average quality below this 432s (phred algorithm). 432s mintrimlength=60 (mintl) Don't trim reads to be shorter than this. 432s fakefastaquality=-1 (ffq) Set to a positive number 1-50 to generate fake 432s quality strings for fasta input reads. 432s ignorebadquality=f (ibq) Keep going, rather than crashing, if a read has 432s out-of-range quality values. 432s usequality=t Use quality scores when determining which read kmers 432s to use as seeds. 432s minaveragequality=0 (maq) Do not map reads with average quality below this. 432s maqb=0 If positive, calculate maq from this many initial bases. 432s 432s Output Parameters: 432s out= Write all reads to this file. 432s outu= Write only unmapped reads to this file. Does not 432s include unmapped paired reads with a mapped mate. 432s outm= Write only mapped reads to this file. Includes 432s unmapped paired reads with a mapped mate. 432s mappedonly=f If true, treats 'out' like 'outm'. 432s bamscript= (bs) Write a shell script to that will turn 432s the sam output into a sorted, indexed bam file. 432s ordered=f Set to true to output reads in same order as input. 432s Slower and uses more memory. 432s overwrite=f (ow) Allow process to overwrite existing files. 432s secondary=f Print secondary alignments. 432s sssr=0.95 (secondarysitescoreratio) Print only secondary alignments 432s with score of at least this fraction of primary. 432s ssao=f (secondarysiteasambiguousonly) Only print secondary 432s alignments for ambiguously-mapped reads. 432s maxsites=5 Maximum number of total alignments to print per read. 432s Only relevant when secondary=t. 432s quickmatch=f Generate cigar strings more quickly. 432s trimreaddescriptions=f (trd) Truncate read and ref names at the first whitespace, 432s assuming that the remainder is a comment or description. 432s ziplevel=2 (zl) Compression level for zip or gzip output. 432s pigz=f Spawn a pigz (parallel gzip) process for faster 432s compression than Java. Requires pigz to be installed. 432s machineout=f Set to true to output statistics in machine-friendly 432s 'key=value' format. 432s printunmappedcount=f Print the total number of unmapped reads and bases. 432s If input is paired, the number will be of pairs 432s for which both reads are unmapped. 432s showprogress=0 If positive, print a '.' every X reads. 432s showprogress2=0 If positive, print the number of seconds since the 432s last progress update (instead of a '.'). 432s renamebyinsert=f Renames reads based on their mapped insert size. 432s 432s Bloom-Filtering Parameters (bloomfilter.sh is the standalone version). 432s bloom=f Use a Bloom filter to ignore reads not sharing kmers 432s with the reference. This uses more memory, but speeds 432s mapping when most reads don't match the reference. 432s bloomhashes=2 Number of hash functions. 432s bloomminhits=3 Number of consecutive hits to be considered matched. 432s bloomk=31 Bloom filter kmer length. 432s bloomserial=t Use the serialized Bloom filter for greater loading 432s speed, if available. If not, generate and write one. 432s 432s Post-Filtering Parameters: 432s idfilter=0 Independant of minid; sets exact minimum identity 432s allowed for alignments to be printed. Range 0 to 1. 432s subfilter=-1 Ban alignments with more than this many substitutions. 432s insfilter=-1 Ban alignments with more than this many insertions. 432s delfilter=-1 Ban alignments with more than this many deletions. 432s indelfilter=-1 Ban alignments with more than this many indels. 432s editfilter=-1 Ban alignments with more than this many edits. 432s inslenfilter=-1 Ban alignments with an insertion longer than this. 432s dellenfilter=-1 Ban alignments with a deletion longer than this. 432s nfilter=-1 Ban alignments with more than this many ns. This 432s includes nocall, noref, and off scaffold ends. 432s 432s Sam flags and settings: 432s noheader=f Disable generation of header lines. 432s sam=1.4 Set to 1.4 to write Sam version 1.4 cigar strings, 432s with = and X, or 1.3 to use M. 432s saa=t (secondaryalignmentasterisks) Use asterisks instead of 432s bases for sam secondary alignments. 432s cigar=t Set to 'f' to skip generation of cigar strings (faster). 432s keepnames=f Keep original names of paired reads, rather than 432s ensuring both reads have the same name. 432s intronlen=999999999 Set to a lower number like 10 to change 'D' to 'N' in 432s cigar strings for deletions of at least that length. 432s rgid= Set readgroup ID. All other readgroup fields 432s can be set similarly, with the flag rgXX= 432s If you set a readgroup flag to the word 'filename', 432s e.g. rgid=filename, the input file name will be used. 432s mdtag=f Write MD tags. 432s nhtag=f Write NH tags. 432s xmtag=f Write XM tags (may only work correctly with ambig=all). 432s amtag=f Write AM tags. 432s nmtag=f Write NM tags. 432s xstag=f Set to 'xs=fs', 'xs=ss', or 'xs=us' to write XS tags 432s for RNAseq using firststrand, secondstrand, or 432s unstranded libraries. Needed by Cufflinks. 432s JGI mainly uses 'firststrand'. 432s stoptag=f Write a tag indicating read stop location, prefixed by YS:i: 432s lengthtag=f Write a tag indicating (query,ref) alignment lengths, 432s prefixed by YL:Z: 432s idtag=f Write a tag indicating percent identity, prefixed by YI:f: 432s inserttag=f Write a tag indicating insert size, prefixed by X8:Z: 432s scoretag=f Write a tag indicating BBMap's raw score, prefixed by YR:i: 432s timetag=f Write a tag indicating this read's mapping time, prefixed by X0:i: 432s boundstag=f Write a tag indicating whether either read in the pair 432s goes off the end of the reference, prefixed by XB:Z: 432s notags=f Turn off all optional tags. 432s 432s Histogram and statistics output parameters: 432s scafstats= Statistics on how many reads mapped to which scaffold. 432s refstats= Statistics on how many reads mapped to which reference 432s file; only for BBSplit. 432s sortscafs=t Sort scaffolds or references by read count. 432s bhist= Base composition histogram by position. 432s qhist= Quality histogram by position. 432s aqhist= Histogram of average read quality. 432s bqhist= Quality histogram designed for box plots. 432s lhist= Read length histogram. 432s ihist= Write histogram of insert sizes (for paired reads). 432s ehist= Errors-per-read histogram. 432s qahist= bbmap.sh ref=example.fasta 432s Quality accuracy histogram of error rates versus 432s quality score. 432s indelhist= Indel length histogram. 432s mhist= Histogram of match, sub, del, and ins rates by 432s read location. 432s gchist= Read GC content histogram. 432s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 432s gcpairs=t Use average GC of paired reads. 432s idhist= Histogram of read count versus percent identity. 432s idbins=100 Number idhist bins. Set to 'auto' to use read length. 432s statsfile=stderr Mapping statistics are printed here. 432s 432s Coverage output parameters (these may reduce speed and use more RAM): 432s covstats= Per-scaffold coverage info. 432s rpkm= Per-scaffold RPKM/FPKM counts. 432s covhist= Histogram of # occurrences of each depth level. 432s basecov= Coverage per base location. 432s bincov= Print binned coverage per location (one line per X bases). 432s covbinsize=1000 Set the binsize for binned coverage output. 432s nzo=t Only print scaffolds with nonzero coverage. 432s twocolumn=f Change to true to print only ID and Avg_fold instead of 432s all 6 columns to the 'out=' file. 432s 32bit=f Set to true if you need per-base coverage over 64k. 432s strandedcov=f Track coverage for plus and minus strand independently. 432s startcov=f Only track start positions of reads. 432s secondarycov=t Include coverage of secondary alignments. 432s physcov=f Calculate physical coverage for paired reads. 432s This includes the unsequenced bases. 432s delcoverage=t (delcov) Count bases covered by deletions as covered. 432s True is faster than false. 432s covk=0 If positive, calculate kmer coverage statistics. 432s 432s Java Parameters: 432s -Xmx This will set Java's memory usage, 432s overriding autodetection. 432s -Xmx20g will specify 20 gigs of RAM, and -Xmx800m 432s will specify 800 megs. The max is typically 85% of 432s physical memory. The human genome requires around 24g, 432s or 12g with the 'usemodulo' flag. The index uses 432s roughly 6 bytes per reference base. 432s -eoom This flag will cause the process to exit if an 432s out-of-memory exception occurs. Requires Java 8u92+. 432s -da Disable assertions. 432s 432s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter 432s any problems, or post at: http://seqanswers.com/forums/showthread.php?t=41057 432s 433s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 433s java -ea -Xmx2636m -Xms2636m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta 433s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta] 433s Version 39.06 433s 433s No output file. 433s Writing reference. 433s 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] 433s 433s Set genScaffoldInfo=true 433s Writing chunk 1 433s Set genome to 1 433s 433s Loaded Reference: 0.007 seconds. 433s Loading index for chunk 1-1, build 1 433s No index available; generating from reference genome: /tmp/autopkgtest.FIUvSP/autopkgtest_tmp/ref/index/1/chr1_index_k13_c16_b1.block 433s Indexing threads started for block 0-1 433s Indexing threads finished for block 0-1 434s Generated Index: 1.421 seconds. 434s No reads to process; quitting. 434s 434s Total time: 1.612 seconds. 434s test -d ref 434s bbmap.sh in=misc_dna_as_sanger.fastq out=out.sam 434s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 434s java -ea -Xmx2637m -Xms2637m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 in=misc_dna_as_sanger.fastq out=out.sam 435s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, in=misc_dna_as_sanger.fastq, out=out.sam] 435s Version 39.06 435s 435s Retaining first best site only for ambiguous mappings. 435s Set genome to 1 435s 435s Loaded Reference: 0.045 seconds. 435s Loading index for chunk 1-1, build 1 435s Generated Index: 0.556 seconds. 439s Analyzed Index: 4.209 seconds. 440s Started output stream: 0.047 seconds. 440s Cleared Memory: 0.132 seconds. 440s Processing reads in single-ended mode. 440s Started read stream. 440s Started 4 mapping threads. 440s Detecting finished threads: 0, 1, 2, 3 440s 440s ------------------ Results ------------------ 440s 440s Genome: 1 440s Key Length: 13 440s Max Indel: 16000 440s Minimum Score Ratio: 0.56 440s Mapping Mode: normal 440s Reads Used: 4 (153 bases) 440s 440s Mapping: 0.127 seconds. 440s Reads/sec: 31.44 440s kBases/sec: 1.20 440s 440s 440s Read 1 data: pct reads num reads pct bases num bases 440s 440s mapped: 0.0000% 0 0.0000% 0 440s unambiguous: 0.0000% 0 0.0000% 0 440s ambiguous: 0.0000% 0 0.0000% 0 440s low-Q discards: 25.0000% 1 19.6078% 30 440s 440s perfect best site: 0.0000% 0 0.0000% 0 440s semiperfect site: 0.0000% 0 0.0000% 0 440s 440s Match Rate: NA NA NaN% 0 440s Error Rate: NaN% 0 NaN% 0 440s Sub Rate: NaN% 0 NaN% 0 440s Del Rate: NaN% 0 NaN% 0 440s Ins Rate: NaN% 0 NaN% 0 440s N Rate: NaN% 0 NaN% 0 440s 440s Total time: 5.293 seconds. 440s test -r out.sam 440s bbmap.sh ref=example.fasta in=example.fastq out=out2.sam nodisk 440s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 440s java -ea -Xmx2637m -Xms2637m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta in=example.fastq out=out2.sam nodisk 440s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta, in=example.fastq, out=out2.sam, nodisk] 440s Version 39.06 440s 440s Retaining first best site only for ambiguous mappings. 440s 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] 440s 440s Set genScaffoldInfo=true 440s Set genome to 1 440s 440s Loaded Reference: 0.002 seconds. 440s Loading index for chunk 1-1, build 1 440s Indexing threads started for block 0-1 440s Indexing threads finished for block 0-1 440s Generated Index: 0.239 seconds. 444s Analyzed Index: 3.969 seconds. 444s Started output stream: 0.031 seconds. 445s Cleared Memory: 0.130 seconds. 445s Processing reads in single-ended mode. 445s Started read stream. 445s Started 4 mapping threads. 445s Detecting finished threads: 0, 1, 2, 3 445s 445s ------------------ Results ------------------ 445s 445s Genome: 1 445s Key Length: 13 445s Max Indel: 16000 445s Minimum Score Ratio: 0.56 445s Mapping Mode: normal 445s Reads Used: 3 (75 bases) 445s 445s Mapping: 0.108 seconds. 445s Reads/sec: 27.76 445s kBases/sec: 0.69 445s 445s 445s Read 1 data: pct reads num reads pct bases num bases 445s 445s mapped: 100.0000% 3 100.0000% 75 445s unambiguous: 100.0000% 3 100.0000% 75 445s ambiguous: 0.0000% 0 0.0000% 0 445s low-Q discards: 0.0000% 0 0.0000% 0 445s 445s perfect best site: 100.0000% 3 100.0000% 75 445s semiperfect site: 100.0000% 3 100.0000% 75 445s 445s Match Rate: NA NA 100.0000% 75 445s Error Rate: 0.0000% 0 0.0000% 0 445s Sub Rate: 0.0000% 0 0.0000% 0 445s Del Rate: 0.0000% 0 0.0000% 0 445s Ins Rate: 0.0000% 0 0.0000% 0 445s N Rate: 0.0000% 0 0.0000% 0 445s 445s Total time: 4.672 seconds. 445s test -r out2.sam 445s 445s # bbduk 445s bbduk.sh --version 445s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 445s java -ea -Xmx1318m -Xms1318m -cp /usr/share/java/bbmap.jar jgi.BBDuk --version 445s BBMap version 39.06 445s For help, please run the shellscript with no parameters, or look in /docs/. 445s bbduk.sh --help 445s 445s Written by Brian Bushnell 445s Last modified November 9, 2023 445s 445s Description: Compares reads to the kmers in a reference dataset, optionally 445s allowing an edit distance. Splits the reads into two outputs - those that 445s match the reference, and those that don't. Can also trim (remove) the matching 445s parts of the reads rather than binning the reads. 445s Please read bbmap/docs/guides/BBDukGuide.txt for more information. 445s 445s Usage: bbduk.sh in= out= ref= 445s 445s Input may be stdin or a fasta or fastq file, compressed or uncompressed. 445s If you pipe via stdin/stdout, please include the file type; e.g. for gzipped 445s fasta input, set in=stdin.fa.gz 445s 445s Input parameters: 445s in= Main input. in=stdin.fq will pipe from stdin. 445s in2= Input for 2nd read of pairs in a different file. 445s ref= Comma-delimited list of reference files. 445s In addition to filenames, you may also use the keywords: 445s adapters, artifacts, phix, lambda, pjet, mtst, kapa 445s literal= Comma-delimited list of literal reference sequences. 445s touppercase=f (tuc) Change all bases upper-case. 445s interleaved=auto (int) t/f overrides interleaved autodetection. 445s Must be set mainually when streaming fastq input. 445s qin=auto Input quality offset: 33 (Sanger), 64, or auto. 445s reads=-1 If positive, quit after processing X reads or pairs. 445s copyundefined=f (cu) Process non-AGCT IUPAC reference bases by making all 445s possible unambiguous copies. Intended for short motifs 445s or adapter barcodes, as time/memory use is exponential. 445s samplerate=1 Set lower to only process a fraction of input reads. 445s samref= Optional reference fasta for processing sam files. 445s 445s Output parameters: 445s out= (outnonmatch) Write reads here that do not contain 445s kmers matching the database. 'out=stdout.fq' will pipe 445s to standard out. 445s out2= (outnonmatch2) Use this to write 2nd read of pairs to a 445s different file. 445s outm= (outmatch) Write reads here that fail filters. In default 445s kfilter mode, this means any read with a matching kmer. 445s In any mode, it also includes reads that fail filters such 445s as minlength, mingc, maxgc, entropy, etc. In other words, 445s it includes all reads that do not go to 'out'. 445s outm2= (outmatch2) Use this to write 2nd read of pairs to a 445s different file. 445s outs= (outsingle) Use this to write singleton reads whose mate 445s was trimmed shorter than minlen. 445s stats= Write statistics about which contamininants were detected. 445s refstats= Write statistics on a per-reference-file basis. 445s rpkm= Write RPKM for each reference sequence (for RNA-seq). 445s dump= Dump kmer tables to a file, in fasta format. 445s duk= Write statistics in duk's format. *DEPRECATED* 445s nzo=t Only write statistics about ref sequences with nonzero hits. 445s overwrite=t (ow) Grant permission to overwrite files. 445s showspeed=t (ss) 'f' suppresses display of processing speed. 445s ziplevel=2 (zl) Compression level; 1 (min) through 9 (max). 445s fastawrap=70 Length of lines in fasta output. 445s qout=auto Output quality offset: 33 (Sanger), 64, or auto. 445s statscolumns=3 (cols) Number of columns for stats output, 3 or 5. 445s 5 includes base counts. 445s rename=f Rename reads to indicate which sequences they matched. 445s refnames=f Use names of reference files rather than scaffold IDs. 445s trd=f Truncate read and ref names at the first whitespace. 445s ordered=f Set to true to output reads in same order as input. 445s maxbasesout=-1 If positive, quit after writing approximately this many 445s bases to out (outu/outnonmatch). 445s maxbasesoutm=-1 If positive, quit after writing approximately this many 445s bases to outm (outmatch). 445s json=f Print to screen in json format. 445s 445s Histogram output parameters: 445s bhist= Base composition histogram by position. 445s qhist= Quality histogram by position. 445s qchist= Count of bases with each quality value. 445s aqhist= Histogram of average read quality. 445s bqhist= Quality histogram designed for box plots. 445s lhist= Read length histogram. 445s phist= Polymer length histogram. 445s gchist= Read GC content histogram. 445s enthist= Read entropy histogram. 445s ihist= Insert size histogram, for paired reads in mapped sam. 445s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 445s maxhistlen=6000 Set an upper bound for histogram lengths; higher uses 445s more memory. The default is 6000 for some histograms 445s and 80000 for others. 445s 445s Histograms for mapped sam/bam files only: 445s histbefore=t Calculate histograms from reads before processing. 445s ehist= Errors-per-read histogram. 445s qahist= Quality accuracy histogram of error rates versus quality 445s score. 445s indelhist= Indel length histogram. 445s mhist= Histogram of match, sub, del, and ins rates by position. 445s idhist= Histogram of read count versus percent identity. 445s idbins=100 Number idhist bins. Set to 'auto' to use read length. 445s varfile= Ignore substitution errors listed in this file when 445s calculating error rates. Can be generated with 445s CallVariants. 445s vcf= Ignore substitution errors listed in this VCF file 445s when calculating error rates. 445s ignorevcfindels=t Also ignore indels listed in the VCF. 445s 445s Processing parameters: 445s k=27 Kmer length used for finding contaminants. Contaminants 445s shorter than k will not be found. k must be at least 1. 445s rcomp=t Look for reverse-complements of kmers in addition to 445s forward kmers. 445s maskmiddle=t (mm) Treat the middle base of a kmer as a wildcard, to 445s increase sensitivity in the presence of errors. This may 445s also be set to a number, e.g. mm=3, to mask that many bp. 445s The default mm=t corresponds to mm=1 for odd-length kmers 445s and mm=2 for even-length kmers (as of v39.04), while 445s mm=f is always equivalent to mm=0. 445s minkmerhits=1 (mkh) Reads need at least this many matching kmers 445s to be considered as matching the reference. 445s minkmerfraction=0.0 (mkf) A reads needs at least this fraction of its total 445s kmers to hit a ref, in order to be considered a match. 445s If this and minkmerhits are set, the greater is used. 445s mincovfraction=0.0 (mcf) A reads needs at least this fraction of its total 445s bases to be covered by ref kmers to be considered a match. 445s If specified, mcf overrides mkh and mkf. 445s hammingdistance=0 (hdist) Maximum Hamming distance for ref kmers (subs only). 445s Memory use is proportional to (3*K)^hdist. 445s qhdist=0 Hamming distance for query kmers; impacts speed, not memory. 445s editdistance=0 (edist) Maximum edit distance from ref kmers (subs 445s and indels). Memory use is proportional to (8*K)^edist. 445s hammingdistance2=0 (hdist2) Sets hdist for short kmers, when using mink. 445s qhdist2=0 Sets qhdist for short kmers, when using mink. 445s editdistance2=0 (edist2) Sets edist for short kmers, when using mink. 445s forbidn=f (fn) Forbids matching of read kmers containing N. 445s By default, these will match a reference 'A' if 445s hdist>0 or edist>0, to increase sensitivity. 445s removeifeitherbad=t (rieb) Paired reads get sent to 'outmatch' if either is 445s match (or either is trimmed shorter than minlen). 445s Set to false to require both. 445s trimfailures=f Instead of discarding failed reads, trim them to 1bp. 445s This makes the statistics a bit odd. 445s findbestmatch=f (fbm) If multiple matches, associate read with sequence 445s sharing most kmers. Reduces speed. 445s skipr1=f Don't do kmer-based operations on read 1. 445s skipr2=f Don't do kmer-based operations on read 2. 445s ecco=f For overlapping paired reads only. Performs error- 445s correction with BBMerge prior to kmer operations. 445s recalibrate=f (recal) Recalibrate quality scores. Requires calibration 445s matrices generated by CalcTrueQuality. 445s sam= If recalibration is desired, and matrices have not already 445s been generated, BBDuk will create them from the sam file. 445s amino=f Run in amino acid mode. Some features have not been 445s tested, but kmer-matching works fine. Maximum k is 12. 445s 445s Speed and Memory parameters: 445s threads=auto (t) Set number of threads to use; default is number of 445s logical processors. 445s prealloc=f Preallocate memory in table. Allows faster table loading 445s and more efficient memory usage, for a large reference. 445s monitor=f Kill this process if it crashes. monitor=600,0.01 would 445s kill after 600 seconds under 1% usage. 445s minrskip=1 (mns) Force minimal skip interval when indexing reference 445s kmers. 1 means use all, 2 means use every other kmer, etc. 445s maxrskip=1 (mxs) Restrict maximal skip interval when indexing 445s reference kmers. Normally all are used for scaffolds<100kb, 445s but with longer scaffolds, up to maxrskip-1 are skipped. 445s rskip= Set both minrskip and maxrskip to the same value. 445s If not set, rskip will vary based on sequence length. 445s qskip=1 Skip query kmers to increase speed. 1 means use all. 445s speed=0 Ignore this fraction of kmer space (0-15 out of 16) in both 445s reads and reference. Increases speed and reduces memory. 445s Note: Do not use more than one of 'speed', 'qskip', and 'rskip'. 445s 445s Trimming/Filtering/Masking parameters: 445s Note - if ktrim, kmask, and ksplit are unset, the default behavior is kfilter. 445s All kmer processing modes are mutually exclusive. 445s Reads only get sent to 'outm' purely based on kmer matches in kfilter mode. 445s 445s ktrim=f Trim reads to remove bases matching reference kmers, plus 445s all bases to the left or right. 445s Values: 445s f (don't trim), 445s r (trim to the right), 445s l (trim to the left) 445s ktrimtips=0 Set this to a positive number to perform ktrim on both 445s ends, examining only the outermost X bases. 445s kmask= Replace bases matching ref kmers with another symbol. 445s Allows any non-whitespace character, and processes short 445s kmers on both ends if mink is set. 'kmask=lc' will 445s convert masked bases to lowercase. 445s maskfullycovered=f (mfc) Only mask bases that are fully covered by kmers. 445s ksplit=f For single-ended reads only. Reads will be split into 445s pairs around the kmer. If the kmer is at the end of the 445s read, it will be trimmed instead. Singletons will go to 445s out, and pairs will go to outm. Do not use ksplit with 445s other operations such as quality-trimming or filtering. 445s mink=0 Look for shorter kmers at read tips down to this length, 445s when k-trimming or masking. 0 means disabled. Enabling 445s this will disable maskmiddle. 445s qtrim=f Trim read ends to remove bases with quality below trimq. 445s Performed AFTER looking for kmers. Values: 445s rl (trim both ends), 445s bbduk.sh in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq \ 445s qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 445s f (neither end), 445s r (right end only), 445s l (left end only), 445s w (sliding window). 445s trimq=6 Regions with average quality BELOW this will be trimmed, 445s if qtrim is set to something other than f. Can be a 445s floating-point number like 7.3. 445s trimclip=f Trim soft-clipped bases from sam files. 445s minlength=10 (ml) Reads shorter than this after trimming will be 445s discarded. Pairs will be discarded if both are shorter. 445s mlf=0 (minlengthfraction) Reads shorter than this fraction of 445s original length after trimming will be discarded. 445s maxlength= Reads longer than this after trimming will be discarded. 445s minavgquality=0 (maq) Reads with average quality (after trimming) below 445s this will be discarded. 445s maqb=0 If positive, calculate maq from this many initial bases. 445s minbasequality=0 (mbq) Reads with any base below this quality (after 445s trimming) will be discarded. 445s maxns=-1 If non-negative, reads with more Ns than this 445s (after trimming) will be discarded. 445s mcb=0 (minconsecutivebases) Discard reads without at least 445s this many consecutive called bases. 445s ottm=f (outputtrimmedtomatch) Output reads trimmed to shorter 445s than minlength to outm rather than discarding. 445s tp=0 (trimpad) Trim this much extra around matching kmers. 445s tbo=f (trimbyoverlap) Trim adapters based on where paired 445s reads overlap. 445s strictoverlap=t Adjust sensitivity for trimbyoverlap mode. 445s minoverlap=14 Require this many bases of overlap for detection. 445s mininsert=40 Require insert size of at least this for overlap. 445s Should be reduced to 16 for small RNA sequencing. 445s tpe=f (trimpairsevenly) When kmer right-trimming, trim both 445s reads to the minimum length of either. 445s forcetrimleft=0 (ftl) If positive, trim bases to the left of this position 445s (exclusive, 0-based). 445s forcetrimright=0 (ftr) If positive, trim bases to the right of this position 445s (exclusive, 0-based). 445s forcetrimright2=0 (ftr2) If positive, trim this many bases on the right end. 445s forcetrimmod=0 (ftm) If positive, right-trim length to be equal to zero, 445s modulo this number. 445s restrictleft=0 If positive, only look for kmer matches in the 445s leftmost X bases. 445s restrictright=0 If positive, only look for kmer matches in the 445s rightmost X bases. 445s NOTE: restrictleft and restrictright are mutually exclusive. If trimming 445s both ends is desired, use ktrimtips. 445s mingc=0 Discard reads with GC content below this. 445s maxgc=1 Discard reads with GC content above this. 445s gcpairs=t Use average GC of paired reads. 445s Also affects gchist. 445s tossjunk=f Discard reads with invalid characters as bases. 445s swift=f Trim Swift sequences: Trailing C/T/N R1, leading G/A/N R2. 445s 445s Header-parsing parameters - these require Illumina headers: 445s chastityfilter=f (cf) Discard reads with id containing ' 1:Y:' or ' 2:Y:'. 445s barcodefilter=f Remove reads with unexpected barcodes if barcodes is set, 445s or barcodes containing 'N' otherwise. A barcode must be 445s the last part of the read header. Values: 445s t: Remove reads with bad barcodes. 445s f: Ignore barcodes. 445s crash: Crash upon encountering bad barcodes. 445s barcodes= Comma-delimited list of barcodes or files of barcodes. 445s xmin=-1 If positive, discard reads with a lesser X coordinate. 445s ymin=-1 If positive, discard reads with a lesser Y coordinate. 445s xmax=-1 If positive, discard reads with a greater X coordinate. 445s ymax=-1 If positive, discard reads with a greater Y coordinate. 445s 445s Polymer trimming: 445s trimpolya=0 If greater than 0, trim poly-A or poly-T tails of 445s at least this length on either end of reads. 445s trimpolygleft=0 If greater than 0, trim poly-G prefixes of at least this 445s length on the left end of reads. Does not trim poly-C. 445s trimpolygright=0 If greater than 0, trim poly-G tails of at least this 445s length on the right end of reads. Does not trim poly-C. 445s trimpolyg=0 This sets both left and right at once. 445s filterpolyg=0 If greater than 0, remove reads with a poly-G prefix of 445s at least this length (on the left). 445s Note: there are also equivalent poly-C flags. 445s 445s Polymer tracking: 445s pratio=base,base 'pratio=G,C' will print the ratio of G to C polymers. 445s plen=20 Length of homopolymers to count. 445s 445s Entropy/Complexity parameters: 445s entropy=-1 Set between 0 and 1 to filter reads with entropy below 445s that value. Higher is more stringent. 445s entropywindow=50 Calculate entropy using a sliding window of this length. 445s entropyk=5 Calculate entropy using kmers of this length. 445s minbasefrequency=0 Discard reads with a minimum base frequency below this. 445s entropytrim=f Values: 445s f: (false) Do not entropy-trim. 445s r: (right) Trim low entropy on the right end only. 445s l: (left) Trim low entropy on the left end only. 445s rl: (both) Trim low entropy on both ends. 445s entropymask=f Values: 445s f: (filter) Discard low-entropy sequences. 445s t: (true) Mask low-entropy parts of sequences with N. 445s lc: Change low-entropy parts of sequences to lowercase. 445s entropymark=f Mark each base with its entropy value. This is on a scale 445s of 0-41 and is reported as quality scores, so the output 445s should be fastq or fasta+qual. 445s NOTE: If set, entropytrim overrides entropymask. 445s 445s Cardinality estimation: 445s cardinality=f (loglog) Count unique kmers using the LogLog algorithm. 445s cardinalityout=f (loglogout) Count unique kmers in output reads. 445s loglogk=31 Use this kmer length for counting. 445s loglogbuckets=2048 Use this many buckets for counting. 445s khist= Kmer frequency histogram; plots number of kmers versus 445s kmer depth. This is approximate. 445s khistout= Kmer frequency histogram for output reads. 445s 445s Java Parameters: 445s 445s -Xmx This will set Java's memory usage, overriding autodetection. 445s -Xmx20g will 445s specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 445s The max is typically 85% of physical memory. 445s -eoom This flag will cause the process to exit if an 445s out-of-memory exception occurs. Requires Java 8u92+. 445s -da Disable assertions. 445s 445s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 445s 445s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 445s 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 445s 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] 445s Version 39.06 445s 445s 0.033 seconds. 445s Initial: 445s Memory: max=1409m, total=1409m, free=1379m, used=30m 445s 445s Input is being processed as paired 445s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 445s Started output streams: 0.042 seconds. 445s Processing time: 0.015 seconds. 445s 445s Input: 8 reads 306 bases. 445s QTrimmed: 0 reads (0.00%) 0 bases (0.00%) 445s Total Removed: 8 reads (100.00%) 306 bases (100.00%) 445s Result: 0 reads (0.00%) 0 bases (0.00%) 445s 445s Time: 0.058 seconds. 445s Reads Processed: 8 0.14k reads/sec 445s Bases Processed: 306 0.01m bases/sec 445s test -r out.fastq.gz 445s 445s # bbnorm 445s bbnorm.sh --version 446s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 446s java -ea -Xmx2636m -Xms2636m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 --version 446s BBMap version 39.06 446s For help, please run the shellscript with no parameters, or look in /docs/. 446s bbnorm.sh --help 446s 446s Written by Brian Bushnell 446s Last modified October 19, 2017 446s 446s Description: Normalizes read depth based on kmer counts. 446s Can also error-correct, bin reads by kmer depth, and generate a kmer depth histogram. 446s However, Tadpole has superior error-correction to BBNorm. 446s Please read bbmap/docs/guides/BBNormGuide.txt for more information. 446s 446s Usage: bbnorm.sh in= out= outt= hist= 446s 446s Input parameters: 446s in=null Primary input. Use in2 for paired reads in a second file 446s in2=null Second input file for paired reads in two files 446s extra=null Additional files to use for input (generating hash table) but not for output 446s fastareadlen=2^31 Break up FASTA reads longer than this. Can be useful when processing scaffolded genomes 446s tablereads=-1 Use at most this many reads when building the hashtable (-1 means all) 446s kmersample=1 Process every nth kmer, and skip the rest 446s readsample=1 Process every nth read, and skip the rest 446s 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. 446s qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto. 446s 446s Output parameters: 446s out= File for normalized or corrected reads. Use out2 for paired reads in a second file 446s outt= (outtoss) File for reads that were excluded from primary output 446s reads=-1 Only process this number of reads, then quit (-1 means all) 446s sampleoutput=t Use sampling on output as well as input (not used if sample rates are 1) 446s keepall=f Set to true to keep all reads (e.g. if you just want error correction). 446s 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. 446s Default is false, to prevent confusion about how there can be 0-count kmers. 446s The reason is that based on the 'minq' and 'minprob' settings, some kmers may be excluded from the bloom filter. 446s tmpdir= This will specify a directory for temp files (only needed for multipass runs). If null, they will be written to the output directory. 446s usetempdir=t Allows enabling/disabling of temporary directory; if disabled, temp files will be written to the output directory. 446s qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input). 446s rename=f Rename reads based on their kmer depth. 446s 446s Hashing parameters: 446s k=31 Kmer length (values under 32 are most efficient, but arbitrarily high values are supported) 446s 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. 446s Large values decrease accuracy for a fixed amount of memory, so use the lowest number you can that will still capture highest-depth kmers. 446s hashes=3 Number of times each kmer is hashed and stored. Higher is slower. 446s Higher is MORE accurate if there is enough memory, and LESS accurate if there is not enough memory. 446s 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. 446s prehashes=2 Number of hashes for prefilter. 446s prefilterbits=2 (pbits) Bits per cell in prefilter. 446s prefiltersize=0.35 Fraction of memory to allocate to prefilter. 446s buildpasses=1 More passes can sometimes increase accuracy by iteratively removing low-depth kmers 446s minq=6 Ignore kmers containing bases with quality below this 446s minprob=0.5 Ignore kmers with overall probability of correctness below this 446s 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. 446s 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. 446s 446s Normalization parameters: 446s fixspikes=f (fs) Do a slower, high-precision bloom filter lookup of kmers that appear to have an abnormally high depth due to collisions. 446s target=100 (tgt) Target normalization depth. NOTE: All depth parameters control kmer depth, not read depth. 446s For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1)) 446s maxdepth=-1 (max) Reads will not be downsampled when below this depth, even if they are above the target depth. 446s mindepth=5 (min) Kmers with depth below this number will not be included when calculating the depth of a read. 446s minkmers=15 (mgkpr) Reads must have at least this many kmers over min depth to be retained. Aka 'mingoodkmersperread'. 446s 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. 446s uselowerdepth=t (uld) For pairs, use the depth of the lower read as the depth proxy. 446s deterministic=t (dr) Generate random numbers deterministically to ensure identical output between multiple runs. May decrease speed with a huge number of threads. 446s passes=2 (p) 1 pass is the basic mode. 2 passes (default) allows greater accuracy, error detection, better contol of output depth. 446s 446s Error detection parameters: 446s hdp=90.0 (highdepthpercentile) Position in sorted kmer depth array used as proxy of a read's high kmer depth. 446s ldp=25.0 (lowdepthpercentile) Position in sorted kmer depth array used as proxy of a read's low kmer depth. 446s tossbadreads=f (tbr) Throw away reads detected as containing errors. 446s requirebothbad=f (rbb) Only toss bad pairs if both reads are bad. 446s 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. 446s highthresh=12 (ht) Threshold for high kmer. A high kmer at this or above are considered non-error. 446s lowthresh=3 (lt) Threshold for low kmer. Kmers at this and below are always considered errors. 446s 446s Error correction parameters: 446s ecc=f Set to true to correct errors. NOTE: Tadpole is now preferred for ecc as it does a better job. 446s ecclimit=3 Correct up to this many errors per read. If more are detected, the read will remain unchanged. 446s errorcorrectratio=140 (ecr) Adjacent kmers with a depth ratio of at least this much between will be classified as an error. 446s echighthresh=22 (echt) Threshold for high kmer. A kmer at this or above may be considered non-error. 446s eclowthresh=2 (eclt) Threshold for low kmer. Kmers at this and below are considered errors. 446s eccmaxqual=127 Do not correct bases with quality above this value. 446s aec=f (aggressiveErrorCorrection) Sets more aggressive values of ecr=100, ecclimit=7, echt=16, eclt=3. 446s cec=f (conservativeErrorCorrection) Sets more conservative values of ecr=180, ecclimit=2, echt=30, eclt=1, sl=4, pl=4. 446s meo=f (markErrorsOnly) Marks errors by reducing quality value of suspected errors; does not correct anything. 446s mue=t (markUncorrectableErrors) Marks errors only on uncorrectable reads; requires 'ecc=t'. 446s overlap=f (ecco) Error correct by read overlap. 446s 446s Depth binning parameters: 446s lowbindepth=10 (lbd) Cutoff for low depth bin. 446s highbindepth=80 (hbd) Cutoff for high depth bin. 446s outlow= Pairs in which both reads have a median below lbd go into this file. 446s outhigh= Pairs in which both reads have a median above hbd go into this file. 446s outmid= All other pairs go into this file. 446s 446s Histogram parameters: 446s hist= Specify a file to write the input kmer depth histogram. 446s histout= Specify a file to write the output kmer depth histogram. 446s histcol=3 (histogramcolumns) Number of histogram columns, 2 or 3. 446s pzc=f (printzerocoverage) Print lines in the histogram with zero coverage. 446s histlen=1048576 Max kmer depth displayed in histogram. Also affects statistics displayed, but does not affect normalization. 446s 446s Peak calling parameters: 446s peaks= Write the peaks to this file. Default is stdout. 446s minHeight=2 (h) Ignore peaks shorter than this. 446s minVolume=5 (v) Ignore peaks with less area than this. 446s minWidth=3 (w) Ignore peaks narrower than this. 446s minPeak=2 (minp) Ignore peaks with an X-value below this. 446s maxPeak=BIG (maxp) Ignore peaks with an X-value above this. 446s maxPeakCount=8 (maxpc) Print up to this many peaks (prioritizing height). 446s 446s Java Parameters: 446s -Xmx This will set Java's memory usage, overriding autodetection. 446s -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 446s The max is typically 85% of physical memory. 446s -eoom This flag will cause the process to exit if an 446s out-of-memory exception occurs. Requires Java 8u92+. 446s -da Disable assertions. 446s 446s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 446s 446s bbnorm.sh in=sanger_full_range_original_sanger.fastq qin=33 \ 446s out=out3.fastq outt=outt.fastq hist=hist.plt 446s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 446s 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 446s Executing jgi.KmerNormalize [bits=32, in=sanger_full_range_original_sanger.fastq, qin=33, out=out3.fastq, outt=outt.fastq, hist=hist.plt] 446s 446s 446s *********** Pass 1 ********** 446s 446s 446s Settings: 446s threads: 4 446s k: 31 446s deterministic: true 446s toss error reads: false 446s passes: 1 446s bits per cell: 16 446s cells: 980.97M 446s hashes: 3 446s base min quality: 5 446s kmer min prob: 0.5 446s 446s target depth: 400 446s min depth: 3 446s max depth: 500 446s min good kmers: 15 446s depth percentile: 64.8 446s ignore dupe kmers: true 446s fix spikes: false 446s histogram length: 65536 446s print zero cov: false 446s 450s Made hash table: hashes = 3 mem = 1.83 GB cells = 980.47M used = 0.000% 450s 450s Estimated unique kmers: 7 450s 450s Table creation time: 3.376 seconds. 450s Started output threads. 450s Started output threads. 450s Table read time: 0.008 seconds. 22.20 kb/sec 450s Total reads in: 2 0.000% Kept 450s Total bases in: 188 0.000% Kept 450s Error reads in: 2 100.000% 450s Error type 1: 2 100.000% 450s Error type 2: 0 0.000% 450s Error type 3: 0 0.000% 450s 450s Wrote histogram to hist.plt 450s Total kmers counted: 128 450s Total unique kmer count: 128 450s Includes forward kmers only. 450s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 450s The most accurate value is the greater of the two. 450s 450s Percent unique: 100.00% 450s Depth average: 1.00 (unique kmers) 450s Depth median: 1 (unique kmers) 450s Depth standard deviation: 0.00 (unique kmers) 450s Corrected depth average: 0.00 450s 450s Depth average: 1.00 (all kmers) 450s Depth median: 1 (all kmers) 450s Depth standard deviation: 0.00 (all kmers) 450s 450s Approx. read depth median: 1.47 450s 450s *********** Pass 2 ********** 450s 450s 450s Settings: 450s threads: 4 450s k: 31 450s deterministic: true 450s toss error reads: false 450s passes: 1 450s bits per cell: 16 450s cells: 980.97M 450s hashes: 3 450s base min quality: 5 450s kmer min prob: 0.5 450s 450s target depth: 100 450s min depth: 5 450s max depth: 100 450s min good kmers: 15 450s depth percentile: 54.0 450s ignore dupe kmers: true 450s fix spikes: false 450s histogram length: 65536 450s 453s Made hash table: hashes = 3 mem = 1.83 GB cells = 980.47M used = 0.000% 453s 453s Estimated unique kmers: 0 453s 453s Table creation time: 2.874 seconds. 453s Started output threads. 453s Started output threads. 453s Table read time: 0.003 seconds. 0.00 kb/sec 453s Total reads in: 0 NaN% Kept 453s Total bases in: 0 NaN% Kept 453s Error reads in: 0 NaN% 453s Error type 1: 0 NaN% 453s Error type 2: 0 NaN% 453s Error type 3: 0 NaN% 453s Total kmers counted: 0 453s Total unique kmer count: 0 453s Includes forward kmers only. 453s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 453s The most accurate value is the greater of the two. 453s 453s Percent unique: NaN% 453s Depth average: NaN (unique kmers) 453s Depth median: 0 (unique kmers) 453s Depth standard deviation: NaN (unique kmers) 453s Corrected depth average: NaN 453s 453s Depth average: NaN (all kmers) 453s Depth median: 0 (all kmers) 453s Depth standard deviation: 0.00 (all kmers) 453s 453s Approx. read depth median: NaN 453s 453s Removing temp files. 453s 453s Total time: 6.429 seconds. 0.03 kb/sec 453s test -r out3.fastq 453s test -r outt.fastq 453s test -r hist.plt 453s bbnorm.sh in=illumina_full_range_original_illumina.fastq qin=64 \ 453s out=out4.fastq outt=outt2.fastq hist=hist2.plt 453s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 453s 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 453s Executing jgi.KmerNormalize [bits=32, in=illumina_full_range_original_illumina.fastq, qin=64, out=out4.fastq, outt=outt2.fastq, hist=hist2.plt] 453s 453s 453s *********** Pass 1 ********** 453s 453s 453s Settings: 453s threads: 4 453s k: 31 453s deterministic: true 453s toss error reads: false 453s passes: 1 453s bits per cell: 16 453s cells: 980.97M 453s hashes: 3 453s base min quality: 5 453s kmer min prob: 0.5 453s 453s target depth: 400 453s min depth: 3 453s max depth: 500 453s min good kmers: 15 453s depth percentile: 64.8 453s ignore dupe kmers: true 453s fix spikes: false 453s histogram length: 65536 453s print zero cov: false 453s 456s Made hash table: hashes = 3 mem = 1.83 GB cells = 980.47M used = 0.000% 456s 456s Estimated unique kmers: 7 456s 456s Table creation time: 3.014 seconds. 456s Started output threads. 456s Started output threads. 456s Table read time: 0.012 seconds. 10.48 kb/sec 456s Total reads in: 2 0.000% Kept 456s Total bases in: 126 0.000% Kept 456s Error reads in: 2 100.000% 456s Error type 1: 2 100.000% 456s Error type 2: 0 0.000% 456s Error type 3: 0 0.000% 456s 456s Wrote histogram to hist2.plt 456s Total kmers counted: 66 456s Total unique kmer count: 66 456s Includes forward kmers only. 456s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 456s The most accurate value is the greater of the two. 456s 456s Percent unique: 100.00% 456s Depth average: 1.00 (unique kmers) 456s Depth median: 1 (unique kmers) 456s Depth standard deviation: 0.00 (unique kmers) 456s Corrected depth average: 0.00 456s 456s Depth average: 1.00 (all kmers) 456s Depth median: 1 (all kmers) 456s Depth standard deviation: 0.00 (all kmers) 456s 456s Approx. read depth median: 1.91 456s 456s *********** Pass 2 ********** 456s 456s 456s Settings: 456s threads: 4 456s k: 31 456s deterministic: true 456s toss error reads: false 456s passes: 1 456s bits per cell: 16 456s cells: 980.97M 456s hashes: 3 456s base min quality: 5 456s kmer min prob: 0.5 456s 456s target depth: 100 456s min depth: 5 456s max depth: 100 456s min good kmers: 15 456s depth percentile: 54.0 456s ignore dupe kmers: true 456s fix spikes: false 456s histogram length: 65536 456s 459s Made hash table: hashes = 3 mem = 1.83 GB cells = 980.47M used = 0.000% 459s 459s Estimated unique kmers: 0 459s 459s Table creation time: 2.931 seconds. 459s Started output threads. 459s Started output threads. 459s Table read time: 0.007 seconds. 0.00 kb/sec 459s Total reads in: 0 NaN% Kept 459s Total bases in: 0 NaN% Kept 459s Error reads in: 0 NaN% 459s Error type 1: 0 NaN% 459s Error type 2: 0 NaN% 459s Error type 3: 0 NaN% 459s Total kmers counted: 0 459s Total unique kmer count: 0 459s Includes forward kmers only. 459s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 459s The most accurate value is the greater of the two. 459s 459s Percent unique: NaN% 459s Depth average: NaN (unique kmers) 459s Depth median: 0 (unique kmers) 459s Depth standard deviation: NaN (unique kmers) 459s Corrected depth average: NaN 459s 459s Depth average: NaN (all kmers) 459s Depth median: 0 (all kmers) 459s Depth standard deviation: 0.00 (all kmers) 459s 459s Approx. read depth median: NaN 459s 459s Removing temp files. 459s 459s Total time: 6.162 seconds. 0.02 kb/sec 459s test -r out4.fastq 459s test -r outt2.fastq 459s test -r hist2.plt 459s autopkgtest [16:10:45]: test run-unit-test: -----------------------] 460s autopkgtest [16:10:46]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 460s run-unit-test PASS 460s autopkgtest [16:10:46]: @@@@@@@@@@@@@@@@@@@@ summary 460s run-unit-test PASS 560s Creating nova instance adt-noble-ppc64el-bbmap-20240321-160306-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-ppc64el-server-20240321.img (UUID 024d6af5-fcba-4a84-85f9-01f41e1878d6)...