0s autopkgtest [19:24:59]: starting date and time: 2024-03-21 19:24:59+0000 0s autopkgtest [19:24:59]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [19:24:59]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ie6aprzr/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-arm64-15.secgroup --name adt-noble-arm64-bbmap-20240321-192459-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-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/ 118s autopkgtest [19:26:57]: testbed dpkg architecture: arm64 118s autopkgtest [19:26:57]: testbed apt version: 2.7.12 118s autopkgtest [19:26:57]: @@@@@@@@@@@@@@@@@@@@ test bed setup 119s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 119s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3796 kB] 120s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [53.9 kB] 120s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 120s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 120s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [678 kB] 120s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 120s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 120s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 120s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4178 kB] 120s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 120s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [67.4 kB] 120s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 125s Fetched 9438 kB in 2s (4413 kB/s) 125s Reading package lists... 129s Reading package lists... 129s Building dependency tree... 129s Reading state information... 130s Calculating upgrade... 131s The following packages will be REMOVED: 131s libglib2.0-0 131s The following NEW packages will be installed: 131s libglib2.0-0t64 xdg-user-dirs 131s The following packages will be upgraded: 131s gir1.2-glib-2.0 libglib2.0-data 131s 2 upgraded, 2 newly installed, 1 to remove and 0 not upgraded. 131s Need to get 1774 kB of archives. 131s After this operation, 138 kB of additional disk space will be used. 131s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gir1.2-glib-2.0 arm64 2.79.3-3ubuntu5 [182 kB] 131s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-0t64 arm64 2.79.3-3ubuntu5 [1527 kB] 132s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 132s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-user-dirs arm64 0.18-1 [18.1 kB] 132s Fetched 1774 kB in 1s (1775 kB/s) 132s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75912 files and directories currently installed.) 133s Preparing to unpack .../gir1.2-glib-2.0_2.79.3-3ubuntu5_arm64.deb ... 133s Unpacking gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 133s dpkg: libglib2.0-0:arm64: dependency problems, but removing anyway as you requested: 133s udisks2 depends on libglib2.0-0 (>= 2.77.0). 133s shared-mime-info depends on libglib2.0-0 (>= 2.75.3). 133s python3-gi depends on libglib2.0-0 (>= 2.77.0). 133s python3-dbus depends on libglib2.0-0 (>= 2.16.0). 133s netplan.io depends on libglib2.0-0 (>= 2.70.0). 133s netplan-generator depends on libglib2.0-0 (>= 2.70.0). 133s libxmlb2:arm64 depends on libglib2.0-0 (>= 2.54.0). 133s libvolume-key1:arm64 depends on libglib2.0-0 (>= 2.18.0). 133s libudisks2-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 133s libqrtr-glib0:arm64 depends on libglib2.0-0 (>= 2.56). 133s libqmi-proxy depends on libglib2.0-0 (>= 2.30.0). 133s libqmi-glib5:arm64 depends on libglib2.0-0 (>= 2.54.0). 133s libpolkit-gobject-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 133s libpolkit-agent-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 133s libnetplan0:arm64 depends on libglib2.0-0 (>= 2.75.3). 133s libmm-glib0:arm64 depends on libglib2.0-0 (>= 2.62.0). 133s libmbim-proxy depends on libglib2.0-0 (>= 2.56). 133s libmbim-glib4:arm64 depends on libglib2.0-0 (>= 2.56). 133s libjson-glib-1.0-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 133s libjcat1:arm64 depends on libglib2.0-0 (>= 2.75.3). 133s libgusb2:arm64 depends on libglib2.0-0 (>= 2.75.3). 133s libgudev-1.0-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 133s libgirepository-1.0-1:arm64 depends on libglib2.0-0 (>= 2.79.0). 133s libfwupd2:arm64 depends on libglib2.0-0 (>= 2.79.0). 133s libblockdev3:arm64 depends on libglib2.0-0 (>= 2.42.2). 133s libblockdev-utils3:arm64 depends on libglib2.0-0 (>= 2.75.3). 133s libblockdev-swap3:arm64 depends on libglib2.0-0 (>= 2.42.2). 133s libblockdev-part3:arm64 depends on libglib2.0-0 (>= 2.42.2). 133s libblockdev-nvme3:arm64 depends on libglib2.0-0 (>= 2.42.2). 133s libblockdev-mdraid3:arm64 depends on libglib2.0-0 (>= 2.42.2). 133s libblockdev-loop3:arm64 depends on libglib2.0-0 (>= 2.42.2). 133s libblockdev-fs3:arm64 depends on libglib2.0-0 (>= 2.42.2). 133s libblockdev-crypto3:arm64 depends on libglib2.0-0 (>= 2.42.2). 133s fwupd depends on libglib2.0-0 (>= 2.79.0). 133s bolt depends on libglib2.0-0 (>= 2.56.0). 133s 133s (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 ... 75912 files and directories currently installed.) 133s Removing libglib2.0-0:arm64 (2.79.2-1~ubuntu1) ... 133s Selecting previously unselected package libglib2.0-0t64:arm64. 133s (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 ... 75887 files and directories currently installed.) 133s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_arm64.deb ... 133s libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:arm64.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled... 133s removed '/var/lib/dpkg/info/libglib2.0-0:arm64.postrm' 133s Unpacking libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 133s Preparing to unpack .../libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 133s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 133s Selecting previously unselected package xdg-user-dirs. 133s Preparing to unpack .../xdg-user-dirs_0.18-1_arm64.deb ... 133s Unpacking xdg-user-dirs (0.18-1) ... 133s Setting up xdg-user-dirs (0.18-1) ... 133s Setting up libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 133s No schema files found: doing nothing. 133s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 133s Setting up gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) ... 133s Processing triggers for man-db (2.12.0-3) ... 134s Processing triggers for libc-bin (2.39-0ubuntu2) ... 134s Reading package lists... 135s Building dependency tree... 135s Reading state information... 136s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 136s sh: Attempting to set up Debian/Ubuntu apt sources automatically 136s sh: Distribution appears to be Ubuntu 138s Reading package lists... 138s Building dependency tree... 138s Reading state information... 139s eatmydata is already the newest version (131-1). 139s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 139s Reading package lists... 140s Building dependency tree... 140s Reading state information... 141s dbus is already the newest version (1.14.10-4ubuntu1). 141s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 141s Reading package lists... 141s Building dependency tree... 141s Reading state information... 142s rng-tools-debian is already the newest version (2.4). 142s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 142s Reading package lists... 142s Building dependency tree... 142s Reading state information... 143s The following packages will be REMOVED: 143s cloud-init* python3-configobj* python3-debconf* 144s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 144s After this operation, 3252 kB disk space will be freed. 144s (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 ... 75926 files and directories currently installed.) 144s Removing cloud-init (24.1.1-0ubuntu1) ... 145s Removing python3-configobj (5.0.8-3) ... 145s Removing python3-debconf (1.5.86) ... 145s Processing triggers for man-db (2.12.0-3) ... 146s (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 ... 75537 files and directories currently installed.) 146s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 147s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 147s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 147s invoke-rc.d: policy-rc.d denied execution of try-restart. 147s Reading package lists... 147s Building dependency tree... 147s Reading state information... 149s linux-generic is already the newest version (6.8.0-11.11+1). 149s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 149s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 149s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 149s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 153s Reading package lists... 153s Reading package lists... 154s Building dependency tree... 154s Reading state information... 154s Calculating upgrade... 155s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 155s Reading package lists... 155s Building dependency tree... 155s Reading state information... 156s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 157s autopkgtest [19:27:36]: rebooting testbed after setup commands that affected boot 314s autopkgtest [19:30:13]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 317s autopkgtest [19:30:16]: @@@@@@@@@@@@@@@@@@@@ apt-source bbmap 322s Get:1 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (dsc) [2286 B] 322s Get:2 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (tar) [5343 kB] 322s Get:3 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (diff) [25.4 kB] 322s gpgv: Signature made Fri Nov 24 11:00:29 2023 UTC 322s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 322s gpgv: issuer "emollier@debian.org" 322s gpgv: Can't check signature: No public key 322s dpkg-source: warning: cannot verify inline signature for ./bbmap_39.06+dfsg-1.dsc: no acceptable signature found 323s autopkgtest [19:30:22]: testing package bbmap version 39.06+dfsg-1 323s autopkgtest [19:30:22]: build not needed 326s autopkgtest [19:30:25]: test run-unit-test: preparing testbed 337s Reading package lists... 337s Building dependency tree... 337s Reading state information... 338s Starting pkgProblemResolver with broken count: 0 338s Starting 2 pkgProblemResolver with broken count: 0 338s Done 339s The following additional packages will be installed: 339s bbmap bbmap-jni ca-certificates-java fontconfig-config fonts-dejavu-core 339s fonts-dejavu-mono java-common libapache-pom-java libasound2 libasound2-data 339s libavahi-client3 libavahi-common-data libavahi-common3 libcommons-cli-java 339s libcommons-codec-java libcommons-io-java libcommons-parent-java libcups2 339s libfontconfig1 libgraphite2-3 libharfbuzz0b libjpeg-turbo8 libjpeg8 339s liblcms2-2 liblog4j1.2-java libmpj-java libpcsclite1 openjdk-17-jre-headless 339s python-biopython-doc 339s Suggested packages: 339s default-jre libasound2-plugins alsa-utils libcommons-io-java-doc cups-common 339s liblcms2-utils liblog4j1.2-java-doc libmail-java pcscd libnss-mdns 339s fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho 339s fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic 339s Recommended packages: 339s pigz alsa-ucm-conf alsa-topology-conf python3-biopython 339s The following NEW packages will be installed: 339s autopkgtest-satdep bbmap bbmap-jni ca-certificates-java fontconfig-config 339s fonts-dejavu-core fonts-dejavu-mono java-common libapache-pom-java 339s libasound2 libasound2-data libavahi-client3 libavahi-common-data 339s libavahi-common3 libcommons-cli-java libcommons-codec-java 339s libcommons-io-java libcommons-parent-java libcups2 libfontconfig1 339s libgraphite2-3 libharfbuzz0b libjpeg-turbo8 libjpeg8 liblcms2-2 339s liblog4j1.2-java libmpj-java libpcsclite1 openjdk-17-jre-headless 339s python-biopython-doc 340s 0 upgraded, 30 newly installed, 0 to remove and 0 not upgraded. 340s Need to get 79.2 MB/79.2 MB of archives. 340s After this operation, 238 MB of additional disk space will be used. 340s Get:1 /tmp/autopkgtest.Qj93c2/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [720 B] 340s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-cli-java all 1.6.0-1 [59.9 kB] 340s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 libapache-pom-java all 29-2 [5284 B] 340s Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-parent-java all 56-1 [10.7 kB] 340s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-codec-java all 1.16.0-1 [306 kB] 340s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-io-java all 2.11.0-2 [297 kB] 340s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 liblog4j1.2-java all 1.2.17-11 [439 kB] 340s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 libmpj-java all 0.44+dfsg-4 [443 kB] 341s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 ca-certificates-java all 20240118 [11.6 kB] 341s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 java-common all 0.75+exp1 [6798 B] 341s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libavahi-common-data arm64 0.8-13ubuntu2 [29.5 kB] 341s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libavahi-common3 arm64 0.8-13ubuntu2 [23.2 kB] 341s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libavahi-client3 arm64 0.8-13ubuntu2 [27.3 kB] 341s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libcups2 arm64 2.4.6-0ubuntu3 [270 kB] 341s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB] 341s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 341s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 341s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 341s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 341s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 341s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 341s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libasound2-data all 1.2.10-3build1 [20.7 kB] 341s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libasound2 arm64 1.2.10-3build1 [386 kB] 341s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 341s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 342s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libpcsclite1 arm64 2.0.0-1 [21.2 kB] 342s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 openjdk-17-jre-headless arm64 17.0.10+7-1 [47.3 MB] 348s Get:28 http://ftpmaster.internal/ubuntu noble/universe arm64 bbmap all 39.06+dfsg-1 [9768 kB] 350s Get:29 http://ftpmaster.internal/ubuntu noble/universe arm64 bbmap-jni arm64 39.06+dfsg-1 [26.3 kB] 350s Get:30 http://ftpmaster.internal/ubuntu noble/universe arm64 python-biopython-doc all 1.81+dfsg-3 [17.3 MB] 355s Fetched 79.2 MB in 15s (5312 kB/s) 355s Selecting previously unselected package libcommons-cli-java. 355s (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 ... 75482 files and directories currently installed.) 355s Preparing to unpack .../00-libcommons-cli-java_1.6.0-1_all.deb ... 355s Unpacking libcommons-cli-java (1.6.0-1) ... 355s Selecting previously unselected package libapache-pom-java. 355s Preparing to unpack .../01-libapache-pom-java_29-2_all.deb ... 355s Unpacking libapache-pom-java (29-2) ... 355s Selecting previously unselected package libcommons-parent-java. 355s Preparing to unpack .../02-libcommons-parent-java_56-1_all.deb ... 355s Unpacking libcommons-parent-java (56-1) ... 355s Selecting previously unselected package libcommons-codec-java. 355s Preparing to unpack .../03-libcommons-codec-java_1.16.0-1_all.deb ... 355s Unpacking libcommons-codec-java (1.16.0-1) ... 355s Selecting previously unselected package libcommons-io-java. 355s Preparing to unpack .../04-libcommons-io-java_2.11.0-2_all.deb ... 355s Unpacking libcommons-io-java (2.11.0-2) ... 355s Selecting previously unselected package liblog4j1.2-java. 355s Preparing to unpack .../05-liblog4j1.2-java_1.2.17-11_all.deb ... 355s Unpacking liblog4j1.2-java (1.2.17-11) ... 355s Selecting previously unselected package libmpj-java. 356s Preparing to unpack .../06-libmpj-java_0.44+dfsg-4_all.deb ... 356s Unpacking libmpj-java (0.44+dfsg-4) ... 356s Selecting previously unselected package ca-certificates-java. 356s Preparing to unpack .../07-ca-certificates-java_20240118_all.deb ... 356s Unpacking ca-certificates-java (20240118) ... 356s Selecting previously unselected package java-common. 356s Preparing to unpack .../08-java-common_0.75+exp1_all.deb ... 356s Unpacking java-common (0.75+exp1) ... 356s Selecting previously unselected package libavahi-common-data:arm64. 356s Preparing to unpack .../09-libavahi-common-data_0.8-13ubuntu2_arm64.deb ... 356s Unpacking libavahi-common-data:arm64 (0.8-13ubuntu2) ... 356s Selecting previously unselected package libavahi-common3:arm64. 356s Preparing to unpack .../10-libavahi-common3_0.8-13ubuntu2_arm64.deb ... 356s Unpacking libavahi-common3:arm64 (0.8-13ubuntu2) ... 356s Selecting previously unselected package libavahi-client3:arm64. 356s Preparing to unpack .../11-libavahi-client3_0.8-13ubuntu2_arm64.deb ... 356s Unpacking libavahi-client3:arm64 (0.8-13ubuntu2) ... 356s Selecting previously unselected package libcups2:arm64. 356s Preparing to unpack .../12-libcups2_2.4.6-0ubuntu3_arm64.deb ... 356s Unpacking libcups2:arm64 (2.4.6-0ubuntu3) ... 356s Selecting previously unselected package liblcms2-2:arm64. 356s Preparing to unpack .../13-liblcms2-2_2.14-2_arm64.deb ... 356s Unpacking liblcms2-2:arm64 (2.14-2) ... 356s Selecting previously unselected package libjpeg-turbo8:arm64. 356s Preparing to unpack .../14-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 356s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 356s Selecting previously unselected package libjpeg8:arm64. 356s Preparing to unpack .../15-libjpeg8_8c-2ubuntu11_arm64.deb ... 356s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 356s Selecting previously unselected package fonts-dejavu-mono. 356s Preparing to unpack .../16-fonts-dejavu-mono_2.37-8_all.deb ... 356s Unpacking fonts-dejavu-mono (2.37-8) ... 356s Selecting previously unselected package fonts-dejavu-core. 356s Preparing to unpack .../17-fonts-dejavu-core_2.37-8_all.deb ... 356s Unpacking fonts-dejavu-core (2.37-8) ... 356s Selecting previously unselected package fontconfig-config. 356s Preparing to unpack .../18-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 357s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 357s Selecting previously unselected package libfontconfig1:arm64. 357s Preparing to unpack .../19-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 357s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 357s Selecting previously unselected package libasound2-data. 357s Preparing to unpack .../20-libasound2-data_1.2.10-3build1_all.deb ... 357s Unpacking libasound2-data (1.2.10-3build1) ... 357s Selecting previously unselected package libasound2:arm64. 357s Preparing to unpack .../21-libasound2_1.2.10-3build1_arm64.deb ... 357s Unpacking libasound2:arm64 (1.2.10-3build1) ... 357s Selecting previously unselected package libgraphite2-3:arm64. 357s Preparing to unpack .../22-libgraphite2-3_1.3.14-2_arm64.deb ... 357s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 357s Selecting previously unselected package libharfbuzz0b:arm64. 357s Preparing to unpack .../23-libharfbuzz0b_8.3.0-2_arm64.deb ... 357s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 357s Selecting previously unselected package libpcsclite1:arm64. 357s Preparing to unpack .../24-libpcsclite1_2.0.0-1_arm64.deb ... 357s Unpacking libpcsclite1:arm64 (2.0.0-1) ... 357s Selecting previously unselected package openjdk-17-jre-headless:arm64. 357s Preparing to unpack .../25-openjdk-17-jre-headless_17.0.10+7-1_arm64.deb ... 357s Unpacking openjdk-17-jre-headless:arm64 (17.0.10+7-1) ... 358s Selecting previously unselected package bbmap. 358s Preparing to unpack .../26-bbmap_39.06+dfsg-1_all.deb ... 358s Unpacking bbmap (39.06+dfsg-1) ... 359s Selecting previously unselected package bbmap-jni. 359s Preparing to unpack .../27-bbmap-jni_39.06+dfsg-1_arm64.deb ... 359s Unpacking bbmap-jni (39.06+dfsg-1) ... 359s Selecting previously unselected package python-biopython-doc. 359s Preparing to unpack .../28-python-biopython-doc_1.81+dfsg-3_all.deb ... 359s Unpacking python-biopython-doc (1.81+dfsg-3) ... 359s Selecting previously unselected package autopkgtest-satdep. 359s Preparing to unpack .../29-1-autopkgtest-satdep.deb ... 359s Unpacking autopkgtest-satdep (0) ... 359s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 359s Setting up liblcms2-2:arm64 (2.14-2) ... 359s Setting up java-common (0.75+exp1) ... 359s Setting up libcommons-cli-java (1.6.0-1) ... 359s Setting up liblog4j1.2-java (1.2.17-11) ... 359s Setting up libasound2-data (1.2.10-3build1) ... 359s Setting up libapache-pom-java (29-2) ... 359s Setting up libavahi-common-data:arm64 (0.8-13ubuntu2) ... 359s Setting up fonts-dejavu-mono (2.37-8) ... 359s Setting up fonts-dejavu-core (2.37-8) ... 359s Setting up libpcsclite1:arm64 (2.0.0-1) ... 359s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 359s Setting up python-biopython-doc (1.81+dfsg-3) ... 359s Setting up libasound2:arm64 (1.2.10-3build1) ... 359s Setting up libharfbuzz0b:arm64 (8.3.0-2) ... 359s Setting up bbmap-jni (39.06+dfsg-1) ... 359s Setting up ca-certificates-java (20240118) ... 359s No JRE found. Skipping Java certificates setup. 359s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 359s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 360s Setting up libcommons-parent-java (56-1) ... 360s Setting up libavahi-common3:arm64 (0.8-13ubuntu2) ... 360s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 360s Setting up libcommons-codec-java (1.16.0-1) ... 360s Setting up libavahi-client3:arm64 (0.8-13ubuntu2) ... 360s Setting up libcommons-io-java (2.11.0-2) ... 360s Setting up libmpj-java (0.44+dfsg-4) ... 360s Setting up libcups2:arm64 (2.4.6-0ubuntu3) ... 360s Setting up openjdk-17-jre-headless:arm64 (17.0.10+7-1) ... 360s update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode 360s update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 360s update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 360s update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 360s update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 360s Processing triggers for libc-bin (2.39-0ubuntu2) ... 360s Processing triggers for man-db (2.12.0-3) ... 361s Processing triggers for ca-certificates-java (20240118) ... 361s Adding debian:ACCVRAIZ1.pem 361s Adding debian:AC_RAIZ_FNMT-RCM.pem 362s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 362s Adding debian:ANF_Secure_Server_Root_CA.pem 362s Adding debian:Actalis_Authentication_Root_CA.pem 362s Adding debian:AffirmTrust_Commercial.pem 362s Adding debian:AffirmTrust_Networking.pem 362s Adding debian:AffirmTrust_Premium.pem 362s Adding debian:AffirmTrust_Premium_ECC.pem 362s Adding debian:Amazon_Root_CA_1.pem 362s Adding debian:Amazon_Root_CA_2.pem 362s Adding debian:Amazon_Root_CA_3.pem 362s Adding debian:Amazon_Root_CA_4.pem 362s Adding debian:Atos_TrustedRoot_2011.pem 362s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 362s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 362s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 362s Adding debian:BJCA_Global_Root_CA1.pem 362s Adding debian:BJCA_Global_Root_CA2.pem 362s Adding debian:Baltimore_CyberTrust_Root.pem 362s Adding debian:Buypass_Class_2_Root_CA.pem 362s Adding debian:Buypass_Class_3_Root_CA.pem 362s Adding debian:CA_Disig_Root_R2.pem 362s Adding debian:CFCA_EV_ROOT.pem 362s Adding debian:COMODO_Certification_Authority.pem 362s Adding debian:COMODO_ECC_Certification_Authority.pem 362s Adding debian:COMODO_RSA_Certification_Authority.pem 362s Adding debian:Certainly_Root_E1.pem 362s Adding debian:Certainly_Root_R1.pem 362s Adding debian:Certigna.pem 362s Adding debian:Certigna_Root_CA.pem 362s Adding debian:Certum_EC-384_CA.pem 362s Adding debian:Certum_Trusted_Network_CA.pem 362s Adding debian:Certum_Trusted_Network_CA_2.pem 362s Adding debian:Certum_Trusted_Root_CA.pem 362s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 362s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 362s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 362s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 362s Adding debian:Comodo_AAA_Services_root.pem 362s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 362s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 362s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 362s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 362s Adding debian:DigiCert_Assured_ID_Root_CA.pem 362s Adding debian:DigiCert_Assured_ID_Root_G2.pem 362s Adding debian:DigiCert_Assured_ID_Root_G3.pem 362s Adding debian:DigiCert_Global_Root_CA.pem 362s Adding debian:DigiCert_Global_Root_G2.pem 362s Adding debian:DigiCert_Global_Root_G3.pem 362s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 362s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 362s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 362s Adding debian:DigiCert_Trusted_Root_G4.pem 362s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 362s Adding debian:Entrust_Root_Certification_Authority.pem 362s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 362s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 362s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem 362s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 362s Adding debian:GLOBALTRUST_2020.pem 362s Adding debian:GTS_Root_R1.pem 362s Adding debian:GTS_Root_R2.pem 362s Adding debian:GTS_Root_R3.pem 362s Adding debian:GTS_Root_R4.pem 362s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 362s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 362s Adding debian:GlobalSign_Root_CA.pem 362s Adding debian:GlobalSign_Root_CA_-_R3.pem 362s Adding debian:GlobalSign_Root_CA_-_R6.pem 362s Adding debian:GlobalSign_Root_E46.pem 362s Adding debian:GlobalSign_Root_R46.pem 362s Adding debian:Go_Daddy_Class_2_CA.pem 362s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 362s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 362s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 362s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 362s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 362s Adding debian:HiPKI_Root_CA_-_G1.pem 362s Adding debian:Hongkong_Post_Root_CA_3.pem 362s Adding debian:ISRG_Root_X1.pem 362s Adding debian:ISRG_Root_X2.pem 362s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 362s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 362s Adding debian:Izenpe.com.pem 362s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 362s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 362s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 362s Adding debian:NAVER_Global_Root_Certification_Authority.pem 362s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 362s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 362s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 362s Adding debian:QuoVadis_Root_CA_1_G3.pem 362s Adding debian:QuoVadis_Root_CA_2.pem 362s Adding debian:QuoVadis_Root_CA_2_G3.pem 362s Adding debian:QuoVadis_Root_CA_3.pem 362s Adding debian:QuoVadis_Root_CA_3_G3.pem 362s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 362s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 362s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 362s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 362s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 362s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 362s Adding debian:SZAFIR_ROOT_CA2.pem 362s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 362s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 362s Adding debian:SecureSign_RootCA11.pem 362s Adding debian:SecureTrust_CA.pem 362s Adding debian:Secure_Global_CA.pem 362s Adding debian:Security_Communication_ECC_RootCA1.pem 362s Adding debian:Security_Communication_RootCA2.pem 362s Adding debian:Security_Communication_RootCA3.pem 362s Adding debian:Security_Communication_Root_CA.pem 362s Adding debian:Starfield_Class_2_CA.pem 362s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 362s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 362s Adding debian:SwissSign_Gold_CA_-_G2.pem 362s Adding debian:SwissSign_Silver_CA_-_G2.pem 362s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 362s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 362s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 362s Adding debian:TWCA_Global_Root_CA.pem 362s Adding debian:TWCA_Root_Certification_Authority.pem 362s Adding debian:TeliaSonera_Root_CA_v1.pem 362s Adding debian:Telia_Root_CA_v2.pem 362s Adding debian:TrustAsia_Global_Root_CA_G3.pem 362s Adding debian:TrustAsia_Global_Root_CA_G4.pem 362s Adding debian:Trustwave_Global_Certification_Authority.pem 362s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 362s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 362s Adding debian:TunTrust_Root_CA.pem 362s Adding debian:UCA_Extended_Validation_Root.pem 362s Adding debian:UCA_Global_G2_Root.pem 362s Adding debian:USERTrust_ECC_Certification_Authority.pem 362s Adding debian:USERTrust_RSA_Certification_Authority.pem 362s Adding debian:XRamp_Global_CA_Root.pem 362s Adding debian:certSIGN_ROOT_CA.pem 362s Adding debian:certSIGN_Root_CA_G2.pem 362s Adding debian:e-Szigno_Root_CA_2017.pem 362s Adding debian:ePKI_Root_Certification_Authority.pem 362s Adding debian:emSign_ECC_Root_CA_-_C3.pem 362s Adding debian:emSign_ECC_Root_CA_-_G3.pem 362s Adding debian:emSign_Root_CA_-_C1.pem 362s Adding debian:emSign_Root_CA_-_G1.pem 362s Adding debian:vTrus_ECC_Root_CA.pem 362s Adding debian:vTrus_Root_CA.pem 362s done. 362s Setting up bbmap (39.06+dfsg-1) ... 362s Setting up autopkgtest-satdep (0) ... 368s (Reading database ... 78327 files and directories currently installed.) 368s Removing autopkgtest-satdep (0) ... 369s autopkgtest [19:31:08]: test run-unit-test: [----------------------- 369s 369s # bbmap 369s bbmap.sh --version 369s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 369s java -ea -Xmx2799m -Xms2799m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 --version 369s BBMap version 39.06 369s For help, please run the shellscript with no parameters, or look in /docs/. 369s bbmap.sh --help 369s bbmap.sh ref=example.fasta 369s 369s BBMap 369s Written by Brian Bushnell, from Dec. 2010 - present 369s Last modified September 15, 2022 369s 369s Description: Fast and accurate splice-aware read aligner. 369s Please read bbmap/docs/guides/BBMapGuide.txt for more information. 369s 369s To index: bbmap.sh ref= 369s To map: bbmap.sh in= out= 369s To map without writing an index: 369s bbmap.sh ref= in= out= nodisk 369s 369s in=stdin will accept reads from standard in, and out=stdout will write to 369s standard out, but file extensions are still needed to specify the format of the 369s input and output files e.g. in=stdin.fa.gz will read gzipped fasta from 369s standard in; out=stdout.sam.gz will write gzipped sam. 369s 369s Indexing Parameters (required when building the index): 369s nodisk=f Set to true to build index in memory and write nothing 369s to disk except output. 369s ref= Specify the reference sequence. Only do this ONCE, 369s when building the index (unless using 'nodisk'). 369s build=1 If multiple references are indexed in the same directory, 369s each needs a unique numeric ID (unless using 'nodisk'). 369s k=13 Kmer length, range 8-15. Longer is faster but uses 369s more memory. Shorter is more sensitive. 369s If indexing and mapping are done in two steps, K should 369s be specified each time. 369s path=<.> Specify the location to write the index, if you don't 369s want it in the current working directory. 369s usemodulo=f Throw away ~80% of kmers based on remainder modulo a 369s number (reduces RAM by 50% and sensitivity slightly). 369s Should be enabled both when building the index AND 369s when mapping. 369s rebuild=f Force a rebuild of the index (ref= should be set). 369s 369s Input Parameters: 369s build=1 Designate index to use. Corresponds to the number 369s specified when building the index. 369s in= Primary reads input; required parameter. 369s in2= For paired reads in two files. 369s interleaved=auto True forces paired/interleaved input; false forces 369s single-ended mapping. If not specified, interleaved 369s status will be autodetected from read names. 369s fastareadlen=500 Break up FASTA reads longer than this. Max is 500 for 369s BBMap and 6000 for BBMapPacBio. Only works for FASTA 369s input (use 'maxlen' for FASTQ input). The default for 369s bbmap.sh is 500, and for mapPacBio.sh is 6000. 369s unpigz=f Spawn a pigz (parallel gzip) process for faster 369s decompression than using Java. 369s Requires pigz to be installed. 369s touppercase=t (tuc) Convert lowercase letters in reads to upper case 369s (otherwise they will not match the reference). 369s 369s Sampling Parameters: 369s 369s reads=-1 Set to a positive number N to only process the first N 369s reads (or pairs), then quit. -1 means use all reads. 369s samplerate=1 Set to a number from 0 to 1 to randomly select that 369s fraction of reads for mapping. 1 uses all reads. 369s skipreads=0 Set to a number N to skip the first N reads (or pairs), 369s then map the rest. 369s 369s Mapping Parameters: 369s fast=f This flag is a macro which sets other paramters to run 369s faster, at reduced sensitivity. Bad for RNA-seq. 369s slow=f This flag is a macro which sets other paramters to run 369s slower, at greater sensitivity. 'vslow' is even slower. 369s maxindel=16000 Don't look for indels longer than this. Lower is faster. 369s Set to >=100k for RNAseq with long introns like mammals. 369s strictmaxindel=f When enabled, do not allow indels longer than 'maxindel'. 369s By default these are not sought, but may be found anyway. 369s tipsearch=100 Look this far for read-end deletions with anchors 369s shorter than K, using brute force. 369s minid=0.76 Approximate minimum alignment identity to look for. 369s Higher is faster and less sensitive. 369s minhits=1 Minimum number of seed hits required for candidate sites. 369s Higher is faster. 369s local=f Set to true to use local, rather than global, alignments. 369s This will soft-clip ugly ends of poor alignments. 369s perfectmode=f Allow only perfect mappings when set to true (very fast). 369s semiperfectmode=f Allow only perfect and semiperfect (perfect except for 369s N's in the reference) mappings. 369s threads=auto (t) Set to number of threads desired. By default, uses 369s all cores available. 369s ambiguous=best (ambig) Set behavior on ambiguously-mapped reads (with 369s multiple top-scoring mapping locations). 369s best (use the first best site) 369s toss (consider unmapped) 369s random (select one top-scoring site randomly) 369s all (retain all top-scoring sites) 369s samestrandpairs=f (ssp) Specify whether paired reads should map to the 369s same strand or opposite strands. 369s requirecorrectstrand=t (rcs) Forbid pairing of reads without correct strand 369s orientation. Set to false for long-mate-pair libraries. 369s killbadpairs=f (kbp) If a read pair is mapped with an inappropriate 369s insert size or orientation, the read with the lower 369s mapping quality is marked unmapped. 369s pairedonly=f (po) Treat unpaired reads as unmapped. Thus they will 369s be sent to 'outu' but not 'outm'. 369s rcomp=f Reverse complement both reads prior to mapping (for LMP 369s outward-facing libraries). 369s rcompmate=f Reverse complement read2 prior to mapping. 369s pairlen=32000 Set max allowed distance between paired reads. 369s (insert size)=(pairlen)+(read1 length)+(read2 length) 369s rescuedist=1200 Don't try to rescue paired reads if avg. insert size 369s greater than this. Lower is faster. 369s rescuemismatches=32 Maximum mismatches allowed in a rescued read. Lower 369s is faster. 369s averagepairdist=100 (apd) Initial average distance between paired reads. 369s Varies dynamically; does not need to be specified. 369s deterministic=f Run in deterministic mode. In this case it is good 369s to set averagepairdist. BBMap is deterministic 369s without this flag if using single-ended reads, 369s or run singlethreaded. 369s bandwidthratio=0 (bwr) If above zero, restrict alignment band to this 369s fraction of read length. Faster but less accurate. 369s bandwidth=0 (bw) Set the bandwidth directly. 369s fraction of read length. Faster but less accurate. 369s usejni=f (jni) Do alignments faster, in C code. Requires 369s compiling the C code; details are in /jni/README.txt. 369s maxsites2=800 Don't analyze (or print) more than this many alignments 369s per read. 369s ignorefrequentkmers=t (ifk) Discard low-information kmers that occur often. 369s excludefraction=0.03 (ef) Fraction of kmers to ignore. For example, 0.03 369s will ignore the most common 3% of kmers. 369s greedy=t Use a greedy algorithm to discard the least-useful 369s kmers on a per-read basis. 369s kfilter=0 If positive, potential mapping sites must have at 369s least this many consecutive exact matches. 369s 369s 369s Quality and Trimming Parameters: 369s qin=auto Set to 33 or 64 to specify input quality value ASCII 369s offset. 33 is Sanger, 64 is old Solexa. 369s qout=auto Set to 33 or 64 to specify output quality value ASCII 369s offset (only if output format is fastq). 369s qtrim=f Quality-trim ends before mapping. Options are: 369s 'f' (false), 'l' (left), 'r' (right), and 'lr' (both). 369s untrim=f Undo trimming after mapping. Untrimmed bases will be 369s soft-clipped in cigar strings. 369s trimq=6 Trim regions with average quality below this 369s (phred algorithm). 369s mintrimlength=60 (mintl) Don't trim reads to be shorter than this. 369s fakefastaquality=-1 (ffq) Set to a positive number 1-50 to generate fake 369s quality strings for fasta input reads. 369s ignorebadquality=f (ibq) Keep going, rather than crashing, if a read has 369s out-of-range quality values. 369s usequality=t Use quality scores when determining which read kmers 369s to use as seeds. 369s minaveragequality=0 (maq) Do not map reads with average quality below this. 369s maqb=0 If positive, calculate maq from this many initial bases. 369s 369s Output Parameters: 369s out= Write all reads to this file. 369s outu= Write only unmapped reads to this file. Does not 369s include unmapped paired reads with a mapped mate. 369s outm= Write only mapped reads to this file. Includes 369s unmapped paired reads with a mapped mate. 369s mappedonly=f If true, treats 'out' like 'outm'. 369s bamscript= (bs) Write a shell script to that will turn 369s the sam output into a sorted, indexed bam file. 369s ordered=f Set to true to output reads in same order as input. 369s Slower and uses more memory. 369s overwrite=f (ow) Allow process to overwrite existing files. 369s secondary=f Print secondary alignments. 369s sssr=0.95 (secondarysitescoreratio) Print only secondary alignments 369s with score of at least this fraction of primary. 369s ssao=f (secondarysiteasambiguousonly) Only print secondary 369s alignments for ambiguously-mapped reads. 369s maxsites=5 Maximum number of total alignments to print per read. 369s Only relevant when secondary=t. 369s quickmatch=f Generate cigar strings more quickly. 369s trimreaddescriptions=f (trd) Truncate read and ref names at the first whitespace, 369s assuming that the remainder is a comment or description. 369s ziplevel=2 (zl) Compression level for zip or gzip output. 369s pigz=f Spawn a pigz (parallel gzip) process for faster 369s compression than Java. Requires pigz to be installed. 369s machineout=f Set to true to output statistics in machine-friendly 369s 'key=value' format. 369s printunmappedcount=f Print the total number of unmapped reads and bases. 369s If input is paired, the number will be of pairs 369s for which both reads are unmapped. 369s showprogress=0 If positive, print a '.' every X reads. 369s showprogress2=0 If positive, print the number of seconds since the 369s last progress update (instead of a '.'). 369s renamebyinsert=f Renames reads based on their mapped insert size. 369s 369s Bloom-Filtering Parameters (bloomfilter.sh is the standalone version). 369s bloom=f Use a Bloom filter to ignore reads not sharing kmers 369s with the reference. This uses more memory, but speeds 369s mapping when most reads don't match the reference. 369s bloomhashes=2 Number of hash functions. 369s bloomminhits=3 Number of consecutive hits to be considered matched. 369s bloomk=31 Bloom filter kmer length. 369s bloomserial=t Use the serialized Bloom filter for greater loading 369s speed, if available. If not, generate and write one. 369s 369s Post-Filtering Parameters: 369s idfilter=0 Independant of minid; sets exact minimum identity 369s allowed for alignments to be printed. Range 0 to 1. 369s subfilter=-1 Ban alignments with more than this many substitutions. 369s insfilter=-1 Ban alignments with more than this many insertions. 369s delfilter=-1 Ban alignments with more than this many deletions. 369s indelfilter=-1 Ban alignments with more than this many indels. 369s editfilter=-1 Ban alignments with more than this many edits. 369s inslenfilter=-1 Ban alignments with an insertion longer than this. 369s dellenfilter=-1 Ban alignments with a deletion longer than this. 369s nfilter=-1 Ban alignments with more than this many ns. This 369s includes nocall, noref, and off scaffold ends. 369s 369s Sam flags and settings: 369s noheader=f Disable generation of header lines. 369s sam=1.4 Set to 1.4 to write Sam version 1.4 cigar strings, 369s with = and X, or 1.3 to use M. 369s saa=t (secondaryalignmentasterisks) Use asterisks instead of 369s bases for sam secondary alignments. 369s cigar=t Set to 'f' to skip generation of cigar strings (faster). 369s keepnames=f Keep original names of paired reads, rather than 369s ensuring both reads have the same name. 369s intronlen=999999999 Set to a lower number like 10 to change 'D' to 'N' in 369s cigar strings for deletions of at least that length. 369s rgid= Set readgroup ID. All other readgroup fields 369s can be set similarly, with the flag rgXX= 369s If you set a readgroup flag to the word 'filename', 369s e.g. rgid=filename, the input file name will be used. 369s mdtag=f Write MD tags. 369s nhtag=f Write NH tags. 369s xmtag=f Write XM tags (may only work correctly with ambig=all). 369s amtag=f Write AM tags. 369s nmtag=f Write NM tags. 369s xstag=f Set to 'xs=fs', 'xs=ss', or 'xs=us' to write XS tags 369s for RNAseq using firststrand, secondstrand, or 369s unstranded libraries. Needed by Cufflinks. 369s JGI mainly uses 'firststrand'. 369s stoptag=f Write a tag indicating read stop location, prefixed by YS:i: 369s lengthtag=f Write a tag indicating (query,ref) alignment lengths, 369s prefixed by YL:Z: 369s idtag=f Write a tag indicating percent identity, prefixed by YI:f: 369s inserttag=f Write a tag indicating insert size, prefixed by X8:Z: 369s scoretag=f Write a tag indicating BBMap's raw score, prefixed by YR:i: 369s timetag=f Write a tag indicating this read's mapping time, prefixed by X0:i: 369s boundstag=f Write a tag indicating whether either read in the pair 369s goes off the end of the reference, prefixed by XB:Z: 369s notags=f Turn off all optional tags. 369s 369s Histogram and statistics output parameters: 369s scafstats= Statistics on how many reads mapped to which scaffold. 369s refstats= Statistics on how many reads mapped to which reference 369s file; only for BBSplit. 369s sortscafs=t Sort scaffolds or references by read count. 369s bhist= Base composition histogram by position. 369s qhist= Quality histogram by position. 369s aqhist= Histogram of average read quality. 369s bqhist= Quality histogram designed for box plots. 369s lhist= Read length histogram. 369s ihist= Write histogram of insert sizes (for paired reads). 369s ehist= Errors-per-read histogram. 369s qahist= Quality accuracy histogram of error rates versus 369s quality score. 369s indelhist= Indel length histogram. 369s mhist= Histogram of match, sub, del, and ins rates by 369s read location. 369s gchist= Read GC content histogram. 369s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 369s gcpairs=t Use average GC of paired reads. 369s idhist= Histogram of read count versus percent identity. 369s idbins=100 Number idhist bins. Set to 'auto' to use read length. 369s statsfile=stderr Mapping statistics are printed here. 369s 369s Coverage output parameters (these may reduce speed and use more RAM): 369s covstats= Per-scaffold coverage info. 369s rpkm= Per-scaffold RPKM/FPKM counts. 369s covhist= Histogram of # occurrences of each depth level. 369s basecov= Coverage per base location. 369s bincov= Print binned coverage per location (one line per X bases). 369s covbinsize=1000 Set the binsize for binned coverage output. 369s nzo=t Only print scaffolds with nonzero coverage. 369s twocolumn=f Change to true to print only ID and Avg_fold instead of 369s all 6 columns to the 'out=' file. 369s 32bit=f Set to true if you need per-base coverage over 64k. 369s strandedcov=f Track coverage for plus and minus strand independently. 369s startcov=f Only track start positions of reads. 369s secondarycov=t Include coverage of secondary alignments. 369s physcov=f Calculate physical coverage for paired reads. 369s This includes the unsequenced bases. 369s delcoverage=t (delcov) Count bases covered by deletions as covered. 369s True is faster than false. 369s covk=0 If positive, calculate kmer coverage statistics. 369s 369s Java Parameters: 369s -Xmx This will set Java's memory usage, 369s overriding autodetection. 369s -Xmx20g will specify 20 gigs of RAM, and -Xmx800m 369s will specify 800 megs. The max is typically 85% of 369s physical memory. The human genome requires around 24g, 369s or 12g with the 'usemodulo' flag. The index uses 369s roughly 6 bytes per reference base. 369s -eoom This flag will cause the process to exit if an 369s out-of-memory exception occurs. Requires Java 8u92+. 369s -da Disable assertions. 369s 369s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter 369s any problems, or post at: http://seqanswers.com/forums/showthread.php?t=41057 369s 369s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 369s java -ea -Xmx2799m -Xms2799m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta 370s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta] 370s Version 39.06 370s 370s No output file. 370s Writing reference. 370s 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] 370s 370s Set genScaffoldInfo=true 370s Writing chunk 1 370s Set genome to 1 370s 370s Loaded Reference: 0.009 seconds. 370s Loading index for chunk 1-1, build 1 370s No index available; generating from reference genome: /tmp/autopkgtest.Qj93c2/autopkgtest_tmp/ref/index/1/chr1_index_k13_c16_b1.block 370s Indexing threads started for block 0-1 370s Indexing threads finished for block 0-1 372s Generated Index: 2.092 seconds. 372s No reads to process; quitting. 372s 372s Total time: 2.351 seconds. 372s test -d ref 372s bbmap.sh in=misc_dna_as_sanger.fastq out=out.sam 372s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 372s java -ea -Xmx2799m -Xms2799m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 in=misc_dna_as_sanger.fastq out=out.sam 372s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, in=misc_dna_as_sanger.fastq, out=out.sam] 372s Version 39.06 372s 372s Retaining first best site only for ambiguous mappings. 372s Set genome to 1 372s 372s Loaded Reference: 0.054 seconds. 372s Loading index for chunk 1-1, build 1 373s Generated Index: 0.724 seconds. 380s Analyzed Index: 6.796 seconds. 380s Started output stream: 0.043 seconds. 380s Cleared Memory: 0.120 seconds. 380s Processing reads in single-ended mode. 380s Started read stream. 380s Started 4 mapping threads. 380s Detecting finished threads: 0, 1, 2, 3 380s 380s ------------------ Results ------------------ 380s 380s Genome: 1 380s Key Length: 13 380s Max Indel: 16000 380s Minimum Score Ratio: 0.56 380s Mapping Mode: normal 380s Reads Used: 4 (153 bases) 380s 380s Mapping: 0.182 seconds. 380s Reads/sec: 21.99 380s kBases/sec: 0.84 380s 380s 380s Read 1 data: pct reads num reads pct bases num bases 380s 380s mapped: 0.0000% 0 0.0000% 0 380s unambiguous: 0.0000% 0 0.0000% 0 380s ambiguous: 0.0000% 0 0.0000% 0 380s low-Q discards: 25.0000% 1 19.6078% 30 380s 380s perfect best site: 0.0000% 0 0.0000% 0 380s semiperfect site: 0.0000% 0 0.0000% 0 380s 380s Match Rate: NA NA NaN% 0 380s Error Rate: NaN% 0 NaN% 0 380s Sub Rate: NaN% 0 NaN% 0 380s Del Rate: NaN% 0 NaN% 0 380s Ins Rate: NaN% 0 NaN% 0 380s N Rate: NaN% 0 NaN% 0 380s 380s Total time: 8.117 seconds. 380s test -r out.sam 380s bbmap.sh ref=example.fasta in=example.fastq out=out2.sam nodisk 380s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 380s java -ea -Xmx2799m -Xms2799m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta in=example.fastq out=out2.sam nodisk 381s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta, in=example.fastq, out=out2.sam, nodisk] 381s Version 39.06 381s 381s Retaining first best site only for ambiguous mappings. 381s 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] 381s 381s Set genScaffoldInfo=true 381s Set genome to 1 381s 381s Loaded Reference: 0.003 seconds. 381s Loading index for chunk 1-1, build 1 381s Indexing threads started for block 0-1 381s Indexing threads finished for block 0-1 381s Generated Index: 0.321 seconds. 388s Analyzed Index: 6.691 seconds. 388s Started output stream: 0.044 seconds. 388s Cleared Memory: 0.120 seconds. 388s Processing reads in single-ended mode. 388s Started read stream. 388s Started 4 mapping threads. 388s Detecting finished threads: 0, 1, 2, 3 388s 388s ------------------ Results ------------------ 388s 388s Genome: 1 388s Key Length: 13 388s Max Indel: 16000 388s Minimum Score Ratio: 0.56 388s Mapping Mode: normal 388s Reads Used: 3 (75 bases) 388s 388s Mapping: 0.173 seconds. 388s Reads/sec: 17.30 388s kBases/sec: 0.43 388s 388s 388s Read 1 data: pct reads num reads pct bases num bases 388s 388s mapped: 100.0000% 3 100.0000% 75 388s unambiguous: 100.0000% 3 100.0000% 75 388s ambiguous: 0.0000% 0 0.0000% 0 388s low-Q discards: 0.0000% 0 0.0000% 0 388s 388s perfect best site: 100.0000% 3 100.0000% 75 388s semiperfect site: 100.0000% 3 100.0000% 75 388s 388s Match Rate: NA NA 100.0000% 75 388s Error Rate: 0.0000% 0 0.0000% 0 388s Sub Rate: 0.0000% 0 0.0000% 0 388s Del Rate: 0.0000% 0 0.0000% 0 388s Ins Rate: 0.0000% 0 0.0000% 0 388s N Rate: 0.0000% 0 0.0000% 0 388s 388s Total time: 7.595 seconds. 388s test -r out2.sam 388s 388s # bbduk 388s bbduk.sh --version 388s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 388s java -ea -Xmx1399m -Xms1399m -cp /usr/share/java/bbmap.jar jgi.BBDuk --version 388s BBMap version 39.06 388s For help, please run the shellscript with no parameters, or look in /docs/. 388s bbduk.sh --help 388s 388s Written by Brian Bushnell 388s Last modified November 9, 2023 388s 388s Description: Compares reads to the kmers in a reference dataset, optionally 388s allowing an edit distance. Splits the reads into two outputs - those that 388s match the reference, and those that don't. Can also trim (remove) the matching 388s parts of the reads rather than binning the reads. 388s Please read bbmap/docs/guides/BBDukGuide.txt for more information. 388s 388s Usage: bbduk.sh in= out= ref= 388s 388s Input may be stdin or a fasta or fastq file, compressed or uncompressed. 388s If you pipe via stdin/stdout, please include the file type; e.g. for gzipped 388s fasta input, set in=stdin.fa.gz 388s 388s Input parameters: 388s in= Main input. in=stdin.fq will pipe from stdin. 388s in2= Input for 2nd read of pairs in a different file. 388s ref= Comma-delimited list of reference files. 388s In addition to filenames, you may also use the keywords: 388s adapters, artifacts, phix, lambda, pjet, mtst, kapa 388s literal= Comma-delimited list of literal reference sequences. 388s touppercase=f (tuc) Change all bases upper-case. 388s interleaved=auto (int) t/f overrides interleaved autodetection. 388s Must be set mainually when streaming fastq input. 388s qin=auto Input quality offset: 33 (Sanger), 64, or auto. 388s reads=-1 If positive, quit after processing X reads or pairs. 388s copyundefined=f (cu) Process non-AGCT IUPAC reference bases by making all 388s possible unambiguous copies. Intended for short motifs 388s or adapter barcodes, as time/memory use is exponential. 388s samplerate=1 Set lower to only process a fraction of input reads. 388s samref= Optional reference fasta for processing sam files. 388s 388s Output parameters: 388s out= (outnonmatch) Write reads here that do not contain 388s kmers matching the database. 'out=stdout.fq' will pipe 388s to standard out. 388s out2= (outnonmatch2) Use this to write 2nd read of pairs to a 388s different file. 388s outm= (outmatch) Write reads here that fail filters. In default 388s kfilter mode, this means any read with a matching kmer. 388s In any mode, it also includes reads that fail filters such 388s as minlength, mingc, maxgc, entropy, etc. In other words, 388s it includes all reads that do not go to 'out'. 388s outm2= (outmatch2) Use this to write 2nd read of pairs to a 388s different file. 388s outs= (outsingle) Use this to write singleton reads whose mate 388s was trimmed shorter than minlen. 388s stats= Write statistics about which contamininants were detected. 388s refstats= Write statistics on a per-reference-file basis. 388s rpkm= Write RPKM for each reference sequence (for RNA-seq). 388s dump= Dump kmer tables to a file, in fasta format. 388s duk= Write statistics in duk's format. *DEPRECATED* 388s nzo=t Only write statistics about ref sequences with nonzero hits. 388s overwrite=t (ow) Grant permission to overwrite files. 388s showspeed=t (ss) 'f' suppresses display of processing speed. 388s ziplevel=2 (zl) Compression level; 1 (min) through 9 (max). 388s fastawrap=70 Length of lines in fasta output. 388s qout=auto Output quality offset: 33 (Sanger), 64, or auto. 388s statscolumns=3 (cols) Number of columns for stats output, 3 or 5. 388s 5 includes base counts. 388s rename=f Rename reads to indicate which sequences they matched. 388s refnames=f Use names of reference files rather than scaffold IDs. 388s trd=f Truncate read and ref names at the first whitespace. 388s ordered=f Set to true to output reads in same order as input. 388s maxbasesout=-1 If positive, quit after writing approximately this many 388s bases to out (outu/outnonmatch). 388s maxbasesoutm=-1 If positive, quit after writing approximately this many 388s bases to outm (outmatch). 388s json=f Print to screen in json format. 388s 388s Histogram output parameters: 388s bhist= Base composition histogram by position. 388s qhist= Quality histogram by position. 388s qchist= Count of bases with each quality value. 388s aqhist= Histogram of average read quality. 388s bqhist= Quality histogram designed for box plots. 388s lhist= Read length histogram. 388s phist= Polymer length histogram. 388s gchist= Read GC content histogram. 388s enthist= Read entropy histogram. 388s ihist= Insert size histogram, for paired reads in mapped sam. 388s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 388s maxhistlen=6000 Set an upper bound for histogram lengths; higher uses 388s more memory. The default is 6000 for some histograms 388s and 80000 for others. 388s 388s Histograms for mapped sam/bam files only: 388s histbefore=t Calculate histograms from reads before processing. 388s ehist= Errors-per-read histogram. 388s qahist= Quality accuracy histogram of error rates versus quality 388s score. 388s indelhist= Indel length histogram. 388s mhist= Histogram of match, sub, del, and ins rates by position. 388s idhist= Histogram of read count versus percent identity. 388s idbins=100 Number idhist bins. Set to 'auto' to use read length. 388s varfile= Ignore substitution errors listed in this file when 388s calculating error rates. Can be generated with 388s CallVariants. 388s vcf= Ignore substitution errors listed in this VCF file 388s when calculating error rates. 388s ignorevcfindels=t Also ignore indels listed in the VCF. 388s 388s Processing parameters: 388s k=27 Kmer length used for finding contaminants. Contaminants 388s shorter than k will not be found. k must be at least 1. 388s rcomp=t Look for reverse-complements of kmers in addition to 388s forward kmers. 388s maskmiddle=t (mm) Treat the middle base of a kmer as a wildcard, to 388s increase sensitivity in the presence of errors. This may 388s also be set to a number, e.g. mm=3, to mask that many bp. 388s The default mm=t corresponds to mm=1 for odd-length kmers 388s and mm=2 for even-length kmers (as of v39.04), while 388s mm=f is always equivalent to mm=0. 388s minkmerhits=1 (mkh) Reads need at least this many matching kmers 388s to be considered as matching the reference. 388s minkmerfraction=0.0 (mkf) A reads needs at least this fraction of its total 388s kmers to hit a ref, in order to be considered a match. 388s If this and minkmerhits are set, the greater is used. 388s mincovfraction=0.0 (mcf) A reads needs at least this fraction of its total 388s bases to be covered by ref kmers to be considered a match. 388s If specified, mcf overrides mkh and mkf. 388s hammingdistance=0 (hdist) Maximum Hamming distance for ref kmers (subs only). 388s Memory use is proportional to (3*K)^hdist. 388s qhdist=0 Hamming distance for query kmers; impacts speed, not memory. 388s editdistance=0 (edist) Maximum edit distance from ref kmers (subs 388s and indels). Memory use is proportional to (8*K)^edist. 388s hammingdistance2=0 (hdist2) Sets hdist for short kmers, when using mink. 388s qhdist2=0 Sets qhdist for short kmers, when using mink. 388s editdistance2=0 (edist2) Sets edist for short kmers, when using mink. 388s forbidn=f (fn) Forbids matching of read kmers containing N. 388s By default, these will match a reference 'A' if 388s hdist>0 or edist>0, to increase sensitivity. 388s removeifeitherbad=t (rieb) Paired reads get sent to 'outmatch' if either is 388s match (or either is trimmed shorter than minlen). 388s Set to false to require both. 388s trimfailures=f Instead of discarding failed reads, trim them to 1bp. 388s This makes the statistics a bit odd. 388s findbestmatch=f (fbm) If multiple matches, associate read with sequence 388s sharing most kmers. Reduces speed. 388s skipr1=f Don't do kmer-based operations on read 1. 388s skipr2=f Don't do kmer-based operations on read 2. 388s ecco=f For overlapping paired reads only. Performs error- 388s correction with BBMerge prior to kmer operations. 388s recalibrate=f (recal) Recalibrate quality scores. Requires calibration 388s matrices generated by CalcTrueQuality. 388s sam= If recalibration is desired, and matrices have not already 388s been generated, BBDuk will create them from the sam file. 388s amino=f Run in amino acid mode. Some features have not been 388s tested, but kmer-matching works fine. Maximum k is 12. 388s 388s Speed and Memory parameters: 388s threads=auto (t) Set number of threads to use; default is number of 388s logical processors. 388s prealloc=f Preallocate memory in table. Allows faster table loading 388s and more efficient memory usage, for a large reference. 388s monitor=f Kill this process if it crashes. monitor=600,0.01 would 388s kill after 600 seconds under 1% usage. 388s minrskip=1 (mns) Force minimal skip interval when indexing reference 388s kmers. 1 means use all, 2 means use every other kmer, etc. 388s maxrskip=1 (mxs) Restrict maximal skip interval when indexing 388s reference kmers. Normally all are used for scaffolds<100kb, 388s but with longer scaffolds, up to maxrskip-1 are skipped. 388s rskip= Set both minrskip and maxrskip to the same value. 388s If not set, rskip will vary based on sequence length. 388s qskip=1 Skip query kmers to increase speed. 1 means use all. 388s speed=0 Ignore this fraction of kmer space (0-15 out of 16) in both 388s reads and reference. Increases speed and reduces memory. 388s Note: Do not use more than one of 'speed', 'qskip', and 'rskip'. 388s 388s Trimming/Filtering/Masking parameters: 388s Note - if ktrim, kmask, and ksplit are unset, the default behavior is kfilter. 388s All kmer processing modes are mutually exclusive. 388s Reads only get sent to 'outm' purely based on kmer matches in kfilter mode. 388s 388s ktrim=f Trim reads to remove bases matching reference kmers, plus 388s all bases to the left or right. 388s Values: 388s f (don't trim), 388s r (trim to the right), 388s l (trim to the left) 388s ktrimtips=0 Set this to a positive number to perform ktrim on both 388s ends, examining only the outermost X bases. 388s kmask= Replace bases matching ref kmers with another symbol. 388s Allows any non-whitespace character, and processes short 388s kmers on both ends if mink is set. 'kmask=lc' will 388s convert masked bases to lowercase. 388s maskfullycovered=f (mfc) Only mask bases that are fully covered by kmers. 388s ksplit=f For single-ended reads only. Reads will be split into 388s pairs around the kmer. If the kmer is at the end of the 388s read, it will be trimmed instead. Singletons will go to 388s out, and pairs will go to outm. Do not use ksplit with 388s other operations such as quality-trimming or filtering. 388s mink=0 Look for shorter kmers at read tips down to this length, 388s when k-trimming or masking. 0 means disabled. Enabling 388s this will disable maskmiddle. 388s qtrim=f Trim read ends to remove bases with quality below trimq. 388s Performed AFTER looking for kmers. Values: 388s rl (trim both ends), 388s f (neither end), 388s r (right end only), 388s l (left end only), 388s w (sliding window). 388s trimq=6 Regions with average quality BELOW this will be trimmed, 388s if qtrim is set to something other than f. Can be a 388s floating-point number like 7.3. 388s trimclip=f Trim soft-clipped bases from sam files. 388s minlength=10 (ml) Reads shorter than this after trimming will be 388s discarded. Pairs will be discarded if both are shorter. 388s mlf=0 (minlengthfraction) Reads shorter than this fraction of 388s original length after trimming will be discarded. 388s maxlength= Reads longer than this after trimming will be discarded. 388s minavgquality=0 (maq) Reads with average quality (after trimming) below 388s this will be discarded. 388s maqb=0 If positive, calculate maq from this many initial bases. 388s minbasequality=0 (mbq) Reads with any base below this quality (after 388s trimming) will be discarded. 388s maxns=-1 If non-negative, reads with more Ns than this 388s (after trimming) will be discarded. 388s mcb=0 (minconsecutivebases) Discard reads without at least 388s this many consecutive called bases. 388s ottm=f (outputtrimmedtomatch) Output reads trimmed to shorter 388s than minlength to outm rather than discarding. 388s tp=0 (trimpad) Trim this much extra around matching kmers. 388s tbo=f (trimbyoverlap) Trim adapters based on where paired 388s reads overlap. 388s strictoverlap=t Adjust sensitivity for trimbyoverlap mode. 388s minoverlap=14 Require this many bases of overlap for detection. 388s mininsert=40 Require insert size of at least this for overlap. 388s Should be reduced to 16 for small RNA sequencing. 388s tpe=f (trimpairsevenly) When kmer right-trimming, trim both 388s reads to the minimum length of either. 388s forcetrimleft=0 (ftl) If positive, trim bases to the left of this position 388s (exclusive, 0-based). 388s forcetrimright=0 (ftr) If positive, trim bases to the right of this position 388s (exclusive, 0-based). 388s forcetrimright2=0 (ftr2) If positive, trim this many bases on the right end. 388s forcetrimmod=0 (ftm) If positive, right-trim length to be equal to zero, 388s modulo this number. 388s restrictleft=0 If positive, only look for kmer matches in the 388s leftmost X bases. 388s restrictright=0 If positive, only look for kmer matches in the 388s rightmost X bases. 388s NOTE: restrictleft and restrictright are mutually exclusive. If trimming 388s both ends is desired, use ktrimtips. 388s mingc=0 Discard reads with GC content below this. 388s maxgc=1 Discard reads with GC content above this. 388s gcpairs=t Use average GC of paired reads. 388s Also affects gchist. 388s tossjunk=f Discard reads with invalid characters as bases. 388s swift=f Trim Swift sequences: Trailing C/T/N R1, leading G/A/N R2. 388s 388s Header-parsing parameters - these require Illumina headers: 388s chastityfilter=f (cf) Discard reads with id containing ' 1:Y:' or ' 2:Y:'. 388s barcodefilter=f Remove reads with unexpected barcodes if barcodes is set, 388s or barcodes containing 'N' otherwise. A barcode must be 388s the last part of the read header. Values: 388s t: Remove reads with bad barcodes. 388s f: Ignore barcodes. 388s crash: Crash upon encountering bad barcodes. 388s barcodes= Comma-delimited list of barcodes or files of barcodes. 388s xmin=-1 If positive, discard reads with a lesser X coordinate. 388s ymin=-1 If positive, discard reads with a lesser Y coordinate. 388s xmax=-1 If positive, discard reads with a greater X coordinate. 388s ymax=-1 If positive, discard reads with a greater Y coordinate. 388s 388s Polymer trimming: 388s trimpolya=0 If greater than 0, trim poly-A or poly-T tails of 388s at least this length on either end of reads. 388s trimpolygleft=0 If greater than 0, trim poly-G prefixes of at least this 388s length on the left end of reads. Does not trim poly-C. 388s trimpolygright=0 If greater than 0, trim poly-G tails of at least this 388s length on the right end of reads. Does not trim poly-C. 388s trimpolyg=0 This sets both left and right at once. 388s filterpolyg=0 If greater than 0, remove reads with a poly-G prefix of 388s at least this length (on the left). 388s Note: there are also equivalent poly-C flags. 388s 388s Polymer tracking: 388s pratio=base,base 'pratio=G,C' will print the ratio of G to C polymers. 388s plen=20 Length of homopolymers to count. 388s 388s Entropy/Complexity parameters: 388s entropy=-1 Set between 0 and 1 to filter reads with entropy below 388s that value. Higher is more stringent. 388s entropywindow=50 Calculate entropy using a sliding window of this length. 388s entropyk=5 Calculate entropy using kmers of this length. 388s minbasefrequency=0 Discard reads with a minimum base frequency below this. 388s entropytrim=f Values: 388s f: (false) Do not entropy-trim. 388s r: (right) Trim low entropy on the right end only. 388s l: (left) Trim low entropy on the left end only. 388s rl: (both) Trim low entropy on both ends. 388s entropymask=f Values: 388s f: (filter) Discard low-entropy sequences. 388s t: (true) Mask low-entropy parts of sequences with N. 388s lc: Change low-entropy parts of sequences to lowercase. 388s entropymark=f Mark each base with its entropy value. This is on a scale 388s of 0-41 and is reported as quality scores, so the output 388s should be fastq or fasta+qual. 388s NOTE: If set, entropytrim overrides entropymask. 388s 388s Cardinality estimation: 388s cardinality=f (loglog) Count unique kmers using the LogLog algorithm. 388s cardinalityout=f (loglogout) Count unique kmers in output reads. 388s loglogk=31 Use this kmer length for counting. 388s loglogbuckets=2048 Use this many buckets for counting. 388s khist= Kmer frequency histogram; plots number of kmers versus 388s kmer depth. This is approximate. 388s khistout= Kmer frequency histogram for output reads. 388s 388s Java Parameters: 388s 388s -Xmx This will set Java's memory usage, overriding autodetection. 388s -Xmx20g will 388s specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 388s The max is typically 85% of physical memory. 388s -eoom This flag will cause the process to exit if an 388s out-of-memory exception occurs. Requires Java 8u92+. 388s -da Disable assertions. 388s 388s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 388s 388s bbduk.sh in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq \ 388s qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 389s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 389s java -ea -Xmx1399m -Xms1399m -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 389s 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] 389s Version 39.06 389s 389s 0.031 seconds. 389s Initial: 389s Memory: max=1468m, total=1468m, free=1437m, used=31m 389s 389s Input is being processed as paired 389s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 389s Started output streams: 0.032 seconds. 389s Processing time: 0.007 seconds. 389s 389s Input: 8 reads 306 bases. 389s QTrimmed: 0 reads (0.00%) 0 bases (0.00%) 389s Total Removed: 8 reads (100.00%) 306 bases (100.00%) 389s Result: 0 reads (0.00%) 0 bases (0.00%) 389s 389s Time: 0.043 seconds. 389s Reads Processed: 8 0.18k reads/sec 389s Bases Processed: 306 0.01m bases/sec 389s test -r out.fastq.gz 389s 389s # bbnorm 389s bbnorm.sh --version 389s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 389s java -ea -Xmx2799m -Xms2799m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 --version 389s BBMap version 39.06 389s For help, please run the shellscript with no parameters, or look in /docs/. 389s bbnorm.sh --help 389s bbnorm.sh in=sanger_full_range_original_sanger.fastq qin=33 \ 389s out=out3.fastq outt=outt.fastq hist=hist.plt 389s 389s Written by Brian Bushnell 389s Last modified October 19, 2017 389s 389s Description: Normalizes read depth based on kmer counts. 389s Can also error-correct, bin reads by kmer depth, and generate a kmer depth histogram. 389s However, Tadpole has superior error-correction to BBNorm. 389s Please read bbmap/docs/guides/BBNormGuide.txt for more information. 389s 389s Usage: bbnorm.sh in= out= outt= hist= 389s 389s Input parameters: 389s in=null Primary input. Use in2 for paired reads in a second file 389s in2=null Second input file for paired reads in two files 389s extra=null Additional files to use for input (generating hash table) but not for output 389s fastareadlen=2^31 Break up FASTA reads longer than this. Can be useful when processing scaffolded genomes 389s tablereads=-1 Use at most this many reads when building the hashtable (-1 means all) 389s kmersample=1 Process every nth kmer, and skip the rest 389s readsample=1 Process every nth read, and skip the rest 389s 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. 389s qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto. 389s 389s Output parameters: 389s out= File for normalized or corrected reads. Use out2 for paired reads in a second file 389s outt= (outtoss) File for reads that were excluded from primary output 389s reads=-1 Only process this number of reads, then quit (-1 means all) 389s sampleoutput=t Use sampling on output as well as input (not used if sample rates are 1) 389s keepall=f Set to true to keep all reads (e.g. if you just want error correction). 389s 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. 389s Default is false, to prevent confusion about how there can be 0-count kmers. 389s The reason is that based on the 'minq' and 'minprob' settings, some kmers may be excluded from the bloom filter. 389s tmpdir= This will specify a directory for temp files (only needed for multipass runs). If null, they will be written to the output directory. 389s usetempdir=t Allows enabling/disabling of temporary directory; if disabled, temp files will be written to the output directory. 389s qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input). 389s rename=f Rename reads based on their kmer depth. 389s 389s Hashing parameters: 389s k=31 Kmer length (values under 32 are most efficient, but arbitrarily high values are supported) 389s 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. 389s Large values decrease accuracy for a fixed amount of memory, so use the lowest number you can that will still capture highest-depth kmers. 389s hashes=3 Number of times each kmer is hashed and stored. Higher is slower. 389s Higher is MORE accurate if there is enough memory, and LESS accurate if there is not enough memory. 389s 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. 389s prehashes=2 Number of hashes for prefilter. 389s prefilterbits=2 (pbits) Bits per cell in prefilter. 389s prefiltersize=0.35 Fraction of memory to allocate to prefilter. 389s buildpasses=1 More passes can sometimes increase accuracy by iteratively removing low-depth kmers 389s minq=6 Ignore kmers containing bases with quality below this 389s minprob=0.5 Ignore kmers with overall probability of correctness below this 389s 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. 389s 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. 389s 389s Normalization parameters: 389s fixspikes=f (fs) Do a slower, high-precision bloom filter lookup of kmers that appear to have an abnormally high depth due to collisions. 389s target=100 (tgt) Target normalization depth. NOTE: All depth parameters control kmer depth, not read depth. 389s For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1)) 389s maxdepth=-1 (max) Reads will not be downsampled when below this depth, even if they are above the target depth. 389s mindepth=5 (min) Kmers with depth below this number will not be included when calculating the depth of a read. 389s minkmers=15 (mgkpr) Reads must have at least this many kmers over min depth to be retained. Aka 'mingoodkmersperread'. 389s 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. 389s uselowerdepth=t (uld) For pairs, use the depth of the lower read as the depth proxy. 389s deterministic=t (dr) Generate random numbers deterministically to ensure identical output between multiple runs. May decrease speed with a huge number of threads. 389s passes=2 (p) 1 pass is the basic mode. 2 passes (default) allows greater accuracy, error detection, better contol of output depth. 389s 389s Error detection parameters: 389s hdp=90.0 (highdepthpercentile) Position in sorted kmer depth array used as proxy of a read's high kmer depth. 389s ldp=25.0 (lowdepthpercentile) Position in sorted kmer depth array used as proxy of a read's low kmer depth. 389s tossbadreads=f (tbr) Throw away reads detected as containing errors. 389s requirebothbad=f (rbb) Only toss bad pairs if both reads are bad. 389s 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. 389s highthresh=12 (ht) Threshold for high kmer. A high kmer at this or above are considered non-error. 389s lowthresh=3 (lt) Threshold for low kmer. Kmers at this and below are always considered errors. 389s 389s Error correction parameters: 389s ecc=f Set to true to correct errors. NOTE: Tadpole is now preferred for ecc as it does a better job. 389s ecclimit=3 Correct up to this many errors per read. If more are detected, the read will remain unchanged. 389s errorcorrectratio=140 (ecr) Adjacent kmers with a depth ratio of at least this much between will be classified as an error. 389s echighthresh=22 (echt) Threshold for high kmer. A kmer at this or above may be considered non-error. 389s eclowthresh=2 (eclt) Threshold for low kmer. Kmers at this and below are considered errors. 389s eccmaxqual=127 Do not correct bases with quality above this value. 389s aec=f (aggressiveErrorCorrection) Sets more aggressive values of ecr=100, ecclimit=7, echt=16, eclt=3. 389s cec=f (conservativeErrorCorrection) Sets more conservative values of ecr=180, ecclimit=2, echt=30, eclt=1, sl=4, pl=4. 389s meo=f (markErrorsOnly) Marks errors by reducing quality value of suspected errors; does not correct anything. 389s mue=t (markUncorrectableErrors) Marks errors only on uncorrectable reads; requires 'ecc=t'. 389s overlap=f (ecco) Error correct by read overlap. 389s 389s Depth binning parameters: 389s lowbindepth=10 (lbd) Cutoff for low depth bin. 389s highbindepth=80 (hbd) Cutoff for high depth bin. 389s outlow= Pairs in which both reads have a median below lbd go into this file. 389s outhigh= Pairs in which both reads have a median above hbd go into this file. 389s outmid= All other pairs go into this file. 389s 389s Histogram parameters: 389s hist= Specify a file to write the input kmer depth histogram. 389s histout= Specify a file to write the output kmer depth histogram. 389s histcol=3 (histogramcolumns) Number of histogram columns, 2 or 3. 389s pzc=f (printzerocoverage) Print lines in the histogram with zero coverage. 389s histlen=1048576 Max kmer depth displayed in histogram. Also affects statistics displayed, but does not affect normalization. 389s 389s Peak calling parameters: 389s peaks= Write the peaks to this file. Default is stdout. 389s minHeight=2 (h) Ignore peaks shorter than this. 389s minVolume=5 (v) Ignore peaks with less area than this. 389s minWidth=3 (w) Ignore peaks narrower than this. 389s minPeak=2 (minp) Ignore peaks with an X-value below this. 389s maxPeak=BIG (maxp) Ignore peaks with an X-value above this. 389s maxPeakCount=8 (maxpc) Print up to this many peaks (prioritizing height). 389s 389s Java Parameters: 389s -Xmx This will set Java's memory usage, overriding autodetection. 389s -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 389s The max is typically 85% of physical memory. 389s -eoom This flag will cause the process to exit if an 389s out-of-memory exception occurs. Requires Java 8u92+. 389s -da Disable assertions. 389s 389s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 389s 389s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 389s java -ea -Xmx2799m -Xms2799m -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 390s Executing jgi.KmerNormalize [bits=32, in=sanger_full_range_original_sanger.fastq, qin=33, out=out3.fastq, outt=outt.fastq, hist=hist.plt] 390s 390s 390s *********** Pass 1 ********** 390s 390s 390s Settings: 390s threads: 4 390s k: 31 390s deterministic: true 390s toss error reads: false 390s passes: 1 390s bits per cell: 16 390s cells: 1036.08M 390s hashes: 3 390s base min quality: 5 390s kmer min prob: 0.5 390s 390s target depth: 400 390s min depth: 3 390s max depth: 500 390s min good kmers: 15 390s depth percentile: 64.8 390s ignore dupe kmers: true 390s fix spikes: false 390s histogram length: 65536 390s print zero cov: false 390s 391s Made hash table: hashes = 3 mem = 1.93 GB cells = 1035.89M used = 0.000% 391s 391s Estimated unique kmers: 7 391s 391s Table creation time: 1.760 seconds. 391s Started output threads. 391s Started output threads. 391s Table read time: 0.012 seconds. 15.83 kb/sec 391s Total reads in: 2 0.000% Kept 391s Total bases in: 188 0.000% Kept 391s Error reads in: 2 100.000% 391s Error type 1: 2 100.000% 391s Error type 2: 0 0.000% 391s Error type 3: 0 0.000% 391s 391s Wrote histogram to hist.plt 391s Total kmers counted: 128 391s Total unique kmer count: 128 391s Includes forward kmers only. 391s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 391s The most accurate value is the greater of the two. 391s 391s Percent unique: 100.00% 391s Depth average: 1.00 (unique kmers) 391s Depth median: 1 (unique kmers) 391s Depth standard deviation: 0.00 (unique kmers) 391s Corrected depth average: 0.00 391s 391s Depth average: 1.00 (all kmers) 391s Depth median: 1 (all kmers) 391s Depth standard deviation: 0.00 (all kmers) 391s 391s Approx. read depth median: 1.47 391s 391s *********** Pass 2 ********** 391s 391s 391s Settings: 391s threads: 4 391s k: 31 391s deterministic: true 391s toss error reads: false 391s passes: 1 391s bits per cell: 16 391s cells: 1036.08M 391s hashes: 3 391s base min quality: 5 391s kmer min prob: 0.5 391s 391s target depth: 100 391s min depth: 5 391s max depth: 100 391s min good kmers: 15 391s depth percentile: 54.0 391s ignore dupe kmers: true 391s fix spikes: false 391s histogram length: 65536 391s 393s Made hash table: hashes = 3 mem = 1.93 GB cells = 1035.89M used = 0.000% 393s 393s Estimated unique kmers: 0 393s 393s Table creation time: 1.138 seconds. 393s Started output threads. 393s Started output threads. 393s Table read time: 0.003 seconds. 0.00 kb/sec 393s Total reads in: 0 NaN% Kept 393s Total bases in: 0 NaN% Kept 393s Error reads in: 0 NaN% 393s Error type 1: 0 NaN% 393s Error type 2: 0 NaN% 393s Error type 3: 0 NaN% 393s Total kmers counted: 0 393s Total unique kmer count: 0 393s Includes forward kmers only. 393s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 393s The most accurate value is the greater of the two. 393s 393s Percent unique: NaN% 393s Depth average: NaN (unique kmers) 393s Depth median: 0 (unique kmers) 393s Depth standard deviation: NaN (unique kmers) 393s Corrected depth average: NaN 393s 393s Depth average: NaN (all kmers) 393s Depth median: 0 (all kmers) 393s Depth standard deviation: 0.00 (all kmers) 393s 393s Approx. read depth median: NaN 393s 393s Removing temp files. 393s 393s Total time: 3.072 seconds. 0.06 kb/sec 393s test -r out3.fastq 393s test -r outt.fastq 393s test -r hist.plt 393s bbnorm.sh in=illumina_full_range_original_illumina.fastq qin=64 \ 393s out=out4.fastq outt=outt2.fastq hist=hist2.plt 393s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 393s java -ea -Xmx2799m -Xms2799m -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 393s Executing jgi.KmerNormalize [bits=32, in=illumina_full_range_original_illumina.fastq, qin=64, out=out4.fastq, outt=outt2.fastq, hist=hist2.plt] 393s 393s 393s *********** Pass 1 ********** 393s 393s 393s Settings: 393s threads: 4 393s k: 31 393s deterministic: true 393s toss error reads: false 393s passes: 1 393s bits per cell: 16 393s cells: 1036.08M 393s hashes: 3 393s base min quality: 5 393s kmer min prob: 0.5 393s 393s target depth: 400 393s min depth: 3 393s max depth: 500 393s min good kmers: 15 393s depth percentile: 64.8 393s ignore dupe kmers: true 393s fix spikes: false 393s histogram length: 65536 393s print zero cov: false 393s 395s Made hash table: hashes = 3 mem = 1.93 GB cells = 1035.89M used = 0.000% 395s 395s Estimated unique kmers: 7 395s 395s Table creation time: 1.696 seconds. 395s Started output threads. 395s Started output threads. 395s Table read time: 0.010 seconds. 12.53 kb/sec 395s Total reads in: 2 0.000% Kept 395s Total bases in: 126 0.000% Kept 395s Error reads in: 2 100.000% 395s Error type 1: 2 100.000% 395s Error type 2: 0 0.000% 395s Error type 3: 0 0.000% 395s 395s Wrote histogram to hist2.plt 395s Total kmers counted: 66 395s Total unique kmer count: 66 395s Includes forward kmers only. 395s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 395s The most accurate value is the greater of the two. 395s 395s Percent unique: 100.00% 395s Depth average: 1.00 (unique kmers) 395s Depth median: 1 (unique kmers) 395s Depth standard deviation: 0.00 (unique kmers) 395s Corrected depth average: 0.00 395s 395s Depth average: 1.00 (all kmers) 395s Depth median: 1 (all kmers) 395s Depth standard deviation: 0.00 (all kmers) 395s 395s Approx. read depth median: 1.91 395s 395s *********** Pass 2 ********** 395s 395s 395s Settings: 395s threads: 4 395s k: 31 395s deterministic: true 395s toss error reads: false 395s passes: 1 395s bits per cell: 16 395s cells: 1036.08M 395s hashes: 3 395s base min quality: 5 395s kmer min prob: 0.5 395s 395s target depth: 100 395s min depth: 5 395s max depth: 100 395s min good kmers: 15 395s depth percentile: 54.0 395s ignore dupe kmers: true 395s fix spikes: false 395s histogram length: 65536 395s 396s Made hash table: hashes = 3 mem = 1.93 GB cells = 1035.89M used = 0.000% 396s 396s Estimated unique kmers: 0 396s 396s Table creation time: 1.121 seconds. 396s Started output threads. 396s Started output threads. 396s Table read time: 0.003 seconds. 0.00 kb/sec 396s Total reads in: 0 NaN% Kept 396s Total bases in: 0 NaN% Kept 396s Error reads in: 0 NaN% 396s Error type 1: 0 NaN% 396s Error type 2: 0 NaN% 396s Error type 3: 0 NaN% 396s Total kmers counted: 0 396s Total unique kmer count: 0 396s Includes forward kmers only. 396s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 396s The most accurate value is the greater of the two. 396s 396s Percent unique: NaN% 396s Depth average: NaN (unique kmers) 396s Depth median: 0 (unique kmers) 396s Depth standard deviation: NaN (unique kmers) 396s Corrected depth average: NaN 396s 396s Depth average: NaN (all kmers) 396s Depth median: 0 (all kmers) 396s Depth standard deviation: 0.00 (all kmers) 396s 396s Approx. read depth median: NaN 396s 396s Removing temp files. 396s 396s Total time: 2.995 seconds. 0.04 kb/sec 396s test -r out4.fastq 396s test -r outt2.fastq 396s test -r hist2.plt 397s autopkgtest [19:31:36]: test run-unit-test: -----------------------] 397s autopkgtest [19:31:36]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 397s run-unit-test PASS 398s autopkgtest [19:31:37]: @@@@@@@@@@@@@@@@@@@@ summary 398s run-unit-test PASS 421s Creating nova instance adt-noble-arm64-bbmap-20240321-192459-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240321.img (UUID be08c705-4b33-4c09-862a-ed756e66178f)...