0s autopkgtest [19:54:15]: starting date and time: 2024-03-21 19:54:15+0000 0s autopkgtest [19:54:15]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [19:54:15]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.fbl5kk6c/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-22,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-22/22+36-1 alsa-lib/1.2.11-1build1 at-spi2-core/2.51.90-3 cups/2.4.7-1.2ubuntu1 glib2.0/2.79.3-3ubuntu5 gnutls28/3.8.3-1.1ubuntu2 gtk+3.0/3.24.41-1.1ubuntu3 libpng1.6/1.6.43-3 nettle/3.9.1-2.2 wp2latex/4.4~ds-1build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-big --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-ppc64el-11.secgroup --name adt-noble-ppc64el-bbmap-20240321-195414-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 103s autopkgtest [19:55:58]: testbed dpkg architecture: ppc64el 104s autopkgtest [19:55:59]: testbed apt version: 2.7.12 104s autopkgtest [19:55:59]: @@@@@@@@@@@@@@@@@@@@ test bed setup 105s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 105s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [53.9 kB] 105s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 106s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3796 kB] 108s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 108s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [670 kB] 108s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 108s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 108s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 108s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4084 kB] 109s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 109s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [58.3 kB] 109s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 111s Fetched 9295 kB in 4s (2076 kB/s) 111s Reading package lists... 114s Reading package lists... 115s Building dependency tree... 115s Reading state information... 115s Calculating upgrade... 115s The following packages will be REMOVED: 115s libglib2.0-0 115s The following NEW packages will be installed: 115s libglib2.0-0t64 xdg-user-dirs 115s The following packages will be upgraded: 115s debianutils gir1.2-glib-2.0 libglib2.0-data linux-firmware 115s 4 upgraded, 2 newly installed, 1 to remove and 0 not upgraded. 115s Need to get 478 MB of archives. 115s After this operation, 5928 kB of additional disk space will be used. 115s Get:1 http://ftpmaster.internal/ubuntu noble/main ppc64el debianutils ppc64el 5.17 [90.4 kB] 116s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gir1.2-glib-2.0 ppc64el 2.79.3-3ubuntu5 [182 kB] 116s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libglib2.0-0t64 ppc64el 2.79.3-3ubuntu5 [1773 kB] 116s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 116s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el xdg-user-dirs ppc64el 0.18-1 [20.0 kB] 116s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el linux-firmware ppc64el 20240318.git3b128b60-0ubuntu1 [475 MB] 301s Fetched 478 MB in 3min 6s (2571 kB/s) 301s (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 ... 70095 files and directories currently installed.) 301s Preparing to unpack .../debianutils_5.17_ppc64el.deb ... 301s Unpacking debianutils (5.17) over (5.16) ... 301s Setting up debianutils (5.17) ... 301s (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 ... 70095 files and directories currently installed.) 301s Preparing to unpack .../gir1.2-glib-2.0_2.79.3-3ubuntu5_ppc64el.deb ... 301s Unpacking gir1.2-glib-2.0:ppc64el (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 301s dpkg: libglib2.0-0:ppc64el: dependency problems, but removing anyway as you requested: 301s udisks2 depends on libglib2.0-0 (>= 2.77.0). 301s shared-mime-info depends on libglib2.0-0 (>= 2.75.3). 301s python3-gi depends on libglib2.0-0 (>= 2.77.0). 301s python3-dbus depends on libglib2.0-0 (>= 2.16.0). 301s netplan.io depends on libglib2.0-0 (>= 2.70.0). 301s netplan-generator depends on libglib2.0-0 (>= 2.70.0). 301s libxmlb2:ppc64el depends on libglib2.0-0 (>= 2.54.0). 301s libvolume-key1:ppc64el depends on libglib2.0-0 (>= 2.18.0). 301s libudisks2-0:ppc64el depends on libglib2.0-0 (>= 2.75.3). 301s libqrtr-glib0:ppc64el depends on libglib2.0-0 (>= 2.56). 301s libqmi-proxy depends on libglib2.0-0 (>= 2.30.0). 301s libqmi-glib5:ppc64el depends on libglib2.0-0 (>= 2.54.0). 301s libpolkit-gobject-1-0:ppc64el depends on libglib2.0-0 (>= 2.38.0). 301s libpolkit-agent-1-0:ppc64el depends on libglib2.0-0 (>= 2.38.0). 301s libnetplan0:ppc64el depends on libglib2.0-0 (>= 2.75.3). 301s libmm-glib0:ppc64el depends on libglib2.0-0 (>= 2.62.0). 301s libmbim-proxy depends on libglib2.0-0 (>= 2.56). 301s libmbim-glib4:ppc64el depends on libglib2.0-0 (>= 2.56). 301s libjson-glib-1.0-0:ppc64el depends on libglib2.0-0 (>= 2.75.3). 301s libjcat1:ppc64el depends on libglib2.0-0 (>= 2.75.3). 301s libgusb2:ppc64el depends on libglib2.0-0 (>= 2.75.3). 301s libgudev-1.0-0:ppc64el depends on libglib2.0-0 (>= 2.38.0). 301s libgirepository-1.0-1:ppc64el depends on libglib2.0-0 (>= 2.79.0). 301s libfwupd2:ppc64el depends on libglib2.0-0 (>= 2.79.0). 301s libblockdev3:ppc64el depends on libglib2.0-0 (>= 2.42.2). 301s libblockdev-utils3:ppc64el depends on libglib2.0-0 (>= 2.75.3). 301s libblockdev-swap3:ppc64el depends on libglib2.0-0 (>= 2.42.2). 301s libblockdev-part3:ppc64el depends on libglib2.0-0 (>= 2.42.2). 301s libblockdev-nvme3:ppc64el depends on libglib2.0-0 (>= 2.42.2). 301s libblockdev-mdraid3:ppc64el depends on libglib2.0-0 (>= 2.42.2). 301s libblockdev-loop3:ppc64el depends on libglib2.0-0 (>= 2.42.2). 301s libblockdev-fs3:ppc64el depends on libglib2.0-0 (>= 2.42.2). 301s libblockdev-crypto3:ppc64el depends on libglib2.0-0 (>= 2.42.2). 301s fwupd depends on libglib2.0-0 (>= 2.79.0). 301s bolt depends on libglib2.0-0 (>= 2.56.0). 301s 301s (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 ... 70095 files and directories currently installed.) 301s Removing libglib2.0-0:ppc64el (2.79.2-1~ubuntu1) ... 301s Selecting previously unselected package libglib2.0-0t64:ppc64el. 301s (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 ... 70070 files and directories currently installed.) 301s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_ppc64el.deb ... 301s libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:ppc64el.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled... 301s removed '/var/lib/dpkg/info/libglib2.0-0:ppc64el.postrm' 301s Unpacking libglib2.0-0t64:ppc64el (2.79.3-3ubuntu5) ... 301s Preparing to unpack .../libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 301s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 301s Selecting previously unselected package xdg-user-dirs. 301s Preparing to unpack .../xdg-user-dirs_0.18-1_ppc64el.deb ... 301s Unpacking xdg-user-dirs (0.18-1) ... 301s Preparing to unpack .../linux-firmware_20240318.git3b128b60-0ubuntu1_ppc64el.deb ... 301s Unpacking linux-firmware (20240318.git3b128b60-0ubuntu1) over (20240202.git36777504-0ubuntu1) ... 304s Setting up xdg-user-dirs (0.18-1) ... 304s Setting up linux-firmware (20240318.git3b128b60-0ubuntu1) ... 304s Setting up libglib2.0-0t64:ppc64el (2.79.3-3ubuntu5) ... 304s No schema files found: doing nothing. 305s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 305s Setting up gir1.2-glib-2.0:ppc64el (2.79.3-3ubuntu5) ... 305s Processing triggers for man-db (2.12.0-3) ... 306s Processing triggers for libc-bin (2.39-0ubuntu2) ... 306s Processing triggers for initramfs-tools (0.142ubuntu20) ... 306s update-initramfs: Generating /boot/initrd.img-6.8.0-11-generic 306s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 312s Reading package lists... 313s Building dependency tree... 313s Reading state information... 313s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 314s sh: Attempting to set up Debian/Ubuntu apt sources automatically 314s sh: Distribution appears to be Ubuntu 315s Reading package lists... 315s Building dependency tree... 315s Reading state information... 315s eatmydata is already the newest version (131-1). 315s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 315s Reading package lists... 315s Building dependency tree... 315s Reading state information... 315s dbus is already the newest version (1.14.10-4ubuntu1). 315s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 315s Reading package lists... 316s Building dependency tree... 316s Reading state information... 316s rng-tools-debian is already the newest version (2.4). 316s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 316s Reading package lists... 316s Building dependency tree... 316s Reading state information... 316s The following packages will be REMOVED: 316s cloud-init* python3-configobj* python3-debconf* 316s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 316s After this operation, 3252 kB disk space will be freed. 317s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70171 files and directories currently installed.) 317s Removing cloud-init (24.1.1-0ubuntu1) ... 317s Removing python3-configobj (5.0.8-3) ... 317s Removing python3-debconf (1.5.86) ... 317s Processing triggers for man-db (2.12.0-3) ... 317s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 69782 files and directories currently installed.) 318s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 318s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 318s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 318s invoke-rc.d: policy-rc.d denied execution of try-restart. 318s Reading package lists... 318s Building dependency tree... 318s Reading state information... 318s linux-generic is already the newest version (6.8.0-11.11+1). 318s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 319s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 319s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 319s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 321s Reading package lists... 321s Reading package lists... 322s Building dependency tree... 322s Reading state information... 322s Calculating upgrade... 322s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 322s Reading package lists... 322s Building dependency tree... 322s Reading state information... 322s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 323s autopkgtest [19:59:38]: rebooting testbed after setup commands that affected boot 489s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 497s autopkgtest [20:02:32]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 500s autopkgtest [20:02:35]: @@@@@@@@@@@@@@@@@@@@ apt-source bbmap 506s Get:1 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (dsc) [2286 B] 506s Get:2 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (tar) [5343 kB] 506s Get:3 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (diff) [25.4 kB] 506s gpgv: Signature made Fri Nov 24 11:00:29 2023 UTC 506s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 506s gpgv: issuer "emollier@debian.org" 506s gpgv: Can't check signature: No public key 506s dpkg-source: warning: cannot verify inline signature for ./bbmap_39.06+dfsg-1.dsc: no acceptable signature found 506s autopkgtest [20:02:41]: testing package bbmap version 39.06+dfsg-1 507s autopkgtest [20:02:42]: build not needed 518s autopkgtest [20:02:53]: test run-unit-test: preparing testbed 532s Reading package lists... 533s Building dependency tree... 533s Reading state information... 533s Starting pkgProblemResolver with broken count: 0 533s Starting 2 pkgProblemResolver with broken count: 0 533s Done 533s The following additional packages will be installed: 533s bbmap bbmap-jni ca-certificates-java fontconfig-config fonts-dejavu-core 533s fonts-dejavu-mono java-common libapache-pom-java libasound2 libasound2-data 533s libavahi-client3 libavahi-common-data libavahi-common3 libcommons-cli-java 533s libcommons-codec-java libcommons-io-java libcommons-parent-java libcups2 533s libfontconfig1 libgraphite2-3 libharfbuzz0b libjpeg-turbo8 libjpeg8 533s liblcms2-2 liblog4j1.2-java libmpj-java libpcsclite1 openjdk-17-jre-headless 533s python-biopython-doc 533s Suggested packages: 533s default-jre libasound2-plugins alsa-utils libcommons-io-java-doc cups-common 533s liblcms2-utils liblog4j1.2-java-doc libmail-java pcscd libnss-mdns 533s fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho 533s fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic 533s Recommended packages: 533s pigz alsa-ucm-conf alsa-topology-conf python3-biopython 533s The following NEW packages will be installed: 533s autopkgtest-satdep bbmap bbmap-jni ca-certificates-java fontconfig-config 533s fonts-dejavu-core fonts-dejavu-mono java-common libapache-pom-java 533s libasound2 libasound2-data libavahi-client3 libavahi-common-data 533s libavahi-common3 libcommons-cli-java libcommons-codec-java 533s libcommons-io-java libcommons-parent-java libcups2 libfontconfig1 533s libgraphite2-3 libharfbuzz0b libjpeg-turbo8 libjpeg8 liblcms2-2 533s liblog4j1.2-java libmpj-java libpcsclite1 openjdk-17-jre-headless 533s python-biopython-doc 533s 0 upgraded, 30 newly installed, 0 to remove and 0 not upgraded. 533s Need to get 79.6 MB/79.6 MB of archives. 533s After this operation, 240 MB of additional disk space will be used. 533s Get:1 /tmp/autopkgtest.L6srLX/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [720 B] 533s Get:2 http://ftpmaster.internal/ubuntu noble/universe ppc64el libcommons-cli-java all 1.6.0-1 [59.9 kB] 534s Get:3 http://ftpmaster.internal/ubuntu noble/universe ppc64el libapache-pom-java all 29-2 [5284 B] 534s Get:4 http://ftpmaster.internal/ubuntu noble/universe ppc64el libcommons-parent-java all 56-1 [10.7 kB] 534s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el libcommons-codec-java all 1.16.0-1 [306 kB] 534s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el libcommons-io-java all 2.11.0-2 [297 kB] 534s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el liblog4j1.2-java all 1.2.17-11 [439 kB] 534s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el libmpj-java all 0.44+dfsg-4 [443 kB] 535s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el ca-certificates-java all 20240118 [11.6 kB] 535s Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el java-common all 0.75+exp1 [6798 B] 535s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el libavahi-common-data ppc64el 0.8-13ubuntu2 [29.5 kB] 535s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el libavahi-common3 ppc64el 0.8-13ubuntu2 [25.8 kB] 535s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el libavahi-client3 ppc64el 0.8-13ubuntu2 [30.6 kB] 535s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el libcups2 ppc64el 2.4.6-0ubuntu3 [344 kB] 535s Get:15 http://ftpmaster.internal/ubuntu noble/main ppc64el liblcms2-2 ppc64el 2.14-2 [243 kB] 535s Get:16 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu1 [212 kB] 535s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 535s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB] 536s Get:19 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB] 536s Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el fontconfig-config ppc64el 2.15.0-1ubuntu1 [37.0 kB] 536s Get:21 http://ftpmaster.internal/ubuntu noble/main ppc64el libfontconfig1 ppc64el 2.15.0-1ubuntu1 [190 kB] 536s Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el libasound2-data all 1.2.10-3build1 [20.7 kB] 536s Get:23 http://ftpmaster.internal/ubuntu noble/main ppc64el libasound2 ppc64el 1.2.10-3build1 [496 kB] 537s Get:24 http://ftpmaster.internal/ubuntu noble/main ppc64el libgraphite2-3 ppc64el 1.3.14-2 [105 kB] 537s Get:25 http://ftpmaster.internal/ubuntu noble/main ppc64el libharfbuzz0b ppc64el 8.3.0-2 [576 kB] 537s Get:26 http://ftpmaster.internal/ubuntu noble/main ppc64el libpcsclite1 ppc64el 2.0.0-1 [27.9 kB] 537s Get:27 http://ftpmaster.internal/ubuntu noble/main ppc64el openjdk-17-jre-headless ppc64el 17.0.10+7-1 [47.2 MB] 598s Get:28 http://ftpmaster.internal/ubuntu noble/universe ppc64el bbmap all 39.06+dfsg-1 [9768 kB] 612s Get:29 http://ftpmaster.internal/ubuntu noble/universe ppc64el bbmap-jni ppc64el 39.06+dfsg-1 [32.8 kB] 612s Get:30 http://ftpmaster.internal/ubuntu noble/universe ppc64el python-biopython-doc all 1.81+dfsg-3 [17.3 MB] 636s Fetched 79.6 MB in 1min 43s (776 kB/s) 636s Selecting previously unselected package libcommons-cli-java. 636s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 69727 files and directories currently installed.) 636s Preparing to unpack .../00-libcommons-cli-java_1.6.0-1_all.deb ... 636s Unpacking libcommons-cli-java (1.6.0-1) ... 636s Selecting previously unselected package libapache-pom-java. 636s Preparing to unpack .../01-libapache-pom-java_29-2_all.deb ... 636s Unpacking libapache-pom-java (29-2) ... 636s Selecting previously unselected package libcommons-parent-java. 636s Preparing to unpack .../02-libcommons-parent-java_56-1_all.deb ... 636s Unpacking libcommons-parent-java (56-1) ... 636s Selecting previously unselected package libcommons-codec-java. 636s Preparing to unpack .../03-libcommons-codec-java_1.16.0-1_all.deb ... 636s Unpacking libcommons-codec-java (1.16.0-1) ... 636s Selecting previously unselected package libcommons-io-java. 636s Preparing to unpack .../04-libcommons-io-java_2.11.0-2_all.deb ... 636s Unpacking libcommons-io-java (2.11.0-2) ... 636s Selecting previously unselected package liblog4j1.2-java. 636s Preparing to unpack .../05-liblog4j1.2-java_1.2.17-11_all.deb ... 636s Unpacking liblog4j1.2-java (1.2.17-11) ... 636s Selecting previously unselected package libmpj-java. 636s Preparing to unpack .../06-libmpj-java_0.44+dfsg-4_all.deb ... 636s Unpacking libmpj-java (0.44+dfsg-4) ... 636s Selecting previously unselected package ca-certificates-java. 636s Preparing to unpack .../07-ca-certificates-java_20240118_all.deb ... 636s Unpacking ca-certificates-java (20240118) ... 636s Selecting previously unselected package java-common. 636s Preparing to unpack .../08-java-common_0.75+exp1_all.deb ... 636s Unpacking java-common (0.75+exp1) ... 636s Selecting previously unselected package libavahi-common-data:ppc64el. 636s Preparing to unpack .../09-libavahi-common-data_0.8-13ubuntu2_ppc64el.deb ... 636s Unpacking libavahi-common-data:ppc64el (0.8-13ubuntu2) ... 636s Selecting previously unselected package libavahi-common3:ppc64el. 636s Preparing to unpack .../10-libavahi-common3_0.8-13ubuntu2_ppc64el.deb ... 636s Unpacking libavahi-common3:ppc64el (0.8-13ubuntu2) ... 636s Selecting previously unselected package libavahi-client3:ppc64el. 636s Preparing to unpack .../11-libavahi-client3_0.8-13ubuntu2_ppc64el.deb ... 636s Unpacking libavahi-client3:ppc64el (0.8-13ubuntu2) ... 636s Selecting previously unselected package libcups2:ppc64el. 636s Preparing to unpack .../12-libcups2_2.4.6-0ubuntu3_ppc64el.deb ... 636s Unpacking libcups2:ppc64el (2.4.6-0ubuntu3) ... 636s Selecting previously unselected package liblcms2-2:ppc64el. 636s Preparing to unpack .../13-liblcms2-2_2.14-2_ppc64el.deb ... 636s Unpacking liblcms2-2:ppc64el (2.14-2) ... 636s Selecting previously unselected package libjpeg-turbo8:ppc64el. 636s Preparing to unpack .../14-libjpeg-turbo8_2.1.5-2ubuntu1_ppc64el.deb ... 636s Unpacking libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 636s Selecting previously unselected package libjpeg8:ppc64el. 636s Preparing to unpack .../15-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 636s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 636s Selecting previously unselected package fonts-dejavu-mono. 636s Preparing to unpack .../16-fonts-dejavu-mono_2.37-8_all.deb ... 636s Unpacking fonts-dejavu-mono (2.37-8) ... 636s Selecting previously unselected package fonts-dejavu-core. 636s Preparing to unpack .../17-fonts-dejavu-core_2.37-8_all.deb ... 636s Unpacking fonts-dejavu-core (2.37-8) ... 636s Selecting previously unselected package fontconfig-config. 636s Preparing to unpack .../18-fontconfig-config_2.15.0-1ubuntu1_ppc64el.deb ... 636s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 637s Selecting previously unselected package libfontconfig1:ppc64el. 637s Preparing to unpack .../19-libfontconfig1_2.15.0-1ubuntu1_ppc64el.deb ... 637s Unpacking libfontconfig1:ppc64el (2.15.0-1ubuntu1) ... 637s Selecting previously unselected package libasound2-data. 637s Preparing to unpack .../20-libasound2-data_1.2.10-3build1_all.deb ... 637s Unpacking libasound2-data (1.2.10-3build1) ... 637s Selecting previously unselected package libasound2:ppc64el. 637s Preparing to unpack .../21-libasound2_1.2.10-3build1_ppc64el.deb ... 637s Unpacking libasound2:ppc64el (1.2.10-3build1) ... 637s Selecting previously unselected package libgraphite2-3:ppc64el. 637s Preparing to unpack .../22-libgraphite2-3_1.3.14-2_ppc64el.deb ... 637s Unpacking libgraphite2-3:ppc64el (1.3.14-2) ... 637s Selecting previously unselected package libharfbuzz0b:ppc64el. 637s Preparing to unpack .../23-libharfbuzz0b_8.3.0-2_ppc64el.deb ... 637s Unpacking libharfbuzz0b:ppc64el (8.3.0-2) ... 637s Selecting previously unselected package libpcsclite1:ppc64el. 637s Preparing to unpack .../24-libpcsclite1_2.0.0-1_ppc64el.deb ... 637s Unpacking libpcsclite1:ppc64el (2.0.0-1) ... 637s Selecting previously unselected package openjdk-17-jre-headless:ppc64el. 637s Preparing to unpack .../25-openjdk-17-jre-headless_17.0.10+7-1_ppc64el.deb ... 637s Unpacking openjdk-17-jre-headless:ppc64el (17.0.10+7-1) ... 637s Selecting previously unselected package bbmap. 637s Preparing to unpack .../26-bbmap_39.06+dfsg-1_all.deb ... 637s Unpacking bbmap (39.06+dfsg-1) ... 638s Selecting previously unselected package bbmap-jni. 638s Preparing to unpack .../27-bbmap-jni_39.06+dfsg-1_ppc64el.deb ... 638s Unpacking bbmap-jni (39.06+dfsg-1) ... 638s Selecting previously unselected package python-biopython-doc. 638s Preparing to unpack .../28-python-biopython-doc_1.81+dfsg-3_all.deb ... 638s Unpacking python-biopython-doc (1.81+dfsg-3) ... 638s Selecting previously unselected package autopkgtest-satdep. 638s Preparing to unpack .../29-1-autopkgtest-satdep.deb ... 638s Unpacking autopkgtest-satdep (0) ... 638s Setting up libgraphite2-3:ppc64el (1.3.14-2) ... 638s Setting up liblcms2-2:ppc64el (2.14-2) ... 638s Setting up java-common (0.75+exp1) ... 638s Setting up libcommons-cli-java (1.6.0-1) ... 638s Setting up liblog4j1.2-java (1.2.17-11) ... 638s Setting up libasound2-data (1.2.10-3build1) ... 638s Setting up libapache-pom-java (29-2) ... 638s Setting up libavahi-common-data:ppc64el (0.8-13ubuntu2) ... 638s Setting up fonts-dejavu-mono (2.37-8) ... 638s Setting up fonts-dejavu-core (2.37-8) ... 638s Setting up libpcsclite1:ppc64el (2.0.0-1) ... 638s Setting up libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 638s Setting up python-biopython-doc (1.81+dfsg-3) ... 638s Setting up libasound2:ppc64el (1.2.10-3build1) ... 638s Setting up libharfbuzz0b:ppc64el (8.3.0-2) ... 638s Setting up bbmap-jni (39.06+dfsg-1) ... 638s Setting up ca-certificates-java (20240118) ... 638s No JRE found. Skipping Java certificates setup. 638s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 638s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 638s Setting up libcommons-parent-java (56-1) ... 638s Setting up libavahi-common3:ppc64el (0.8-13ubuntu2) ... 638s Setting up libfontconfig1:ppc64el (2.15.0-1ubuntu1) ... 638s Setting up libcommons-codec-java (1.16.0-1) ... 638s Setting up libavahi-client3:ppc64el (0.8-13ubuntu2) ... 638s Setting up libcommons-io-java (2.11.0-2) ... 638s Setting up libmpj-java (0.44+dfsg-4) ... 638s Setting up libcups2:ppc64el (2.4.6-0ubuntu3) ... 638s Setting up openjdk-17-jre-headless:ppc64el (17.0.10+7-1) ... 638s update-alternatives: using /usr/lib/jvm/java-17-openjdk-ppc64el/bin/java to provide /usr/bin/java (java) in auto mode 638s update-alternatives: using /usr/lib/jvm/java-17-openjdk-ppc64el/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 638s update-alternatives: using /usr/lib/jvm/java-17-openjdk-ppc64el/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 638s update-alternatives: using /usr/lib/jvm/java-17-openjdk-ppc64el/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 638s update-alternatives: using /usr/lib/jvm/java-17-openjdk-ppc64el/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 638s Processing triggers for libc-bin (2.39-0ubuntu2) ... 638s Processing triggers for man-db (2.12.0-3) ... 639s Processing triggers for ca-certificates-java (20240118) ... 640s Adding debian:ACCVRAIZ1.pem 640s Adding debian:AC_RAIZ_FNMT-RCM.pem 640s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 640s Adding debian:ANF_Secure_Server_Root_CA.pem 640s Adding debian:Actalis_Authentication_Root_CA.pem 640s Adding debian:AffirmTrust_Commercial.pem 640s Adding debian:AffirmTrust_Networking.pem 640s Adding debian:AffirmTrust_Premium.pem 640s Adding debian:AffirmTrust_Premium_ECC.pem 640s Adding debian:Amazon_Root_CA_1.pem 640s Adding debian:Amazon_Root_CA_2.pem 640s Adding debian:Amazon_Root_CA_3.pem 640s Adding debian:Amazon_Root_CA_4.pem 640s Adding debian:Atos_TrustedRoot_2011.pem 640s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 640s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 640s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 640s Adding debian:BJCA_Global_Root_CA1.pem 640s Adding debian:BJCA_Global_Root_CA2.pem 640s Adding debian:Baltimore_CyberTrust_Root.pem 640s Adding debian:Buypass_Class_2_Root_CA.pem 640s Adding debian:Buypass_Class_3_Root_CA.pem 640s Adding debian:CA_Disig_Root_R2.pem 640s Adding debian:CFCA_EV_ROOT.pem 640s Adding debian:COMODO_Certification_Authority.pem 640s Adding debian:COMODO_ECC_Certification_Authority.pem 640s Adding debian:COMODO_RSA_Certification_Authority.pem 640s Adding debian:Certainly_Root_E1.pem 640s Adding debian:Certainly_Root_R1.pem 640s Adding debian:Certigna.pem 640s Adding debian:Certigna_Root_CA.pem 640s Adding debian:Certum_EC-384_CA.pem 640s Adding debian:Certum_Trusted_Network_CA.pem 640s Adding debian:Certum_Trusted_Network_CA_2.pem 640s Adding debian:Certum_Trusted_Root_CA.pem 640s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 640s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 640s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 640s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 640s Adding debian:Comodo_AAA_Services_root.pem 640s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 640s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 640s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 640s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 640s Adding debian:DigiCert_Assured_ID_Root_CA.pem 640s Adding debian:DigiCert_Assured_ID_Root_G2.pem 640s Adding debian:DigiCert_Assured_ID_Root_G3.pem 640s Adding debian:DigiCert_Global_Root_CA.pem 640s Adding debian:DigiCert_Global_Root_G2.pem 640s Adding debian:DigiCert_Global_Root_G3.pem 640s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 640s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 640s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 640s Adding debian:DigiCert_Trusted_Root_G4.pem 640s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 640s Adding debian:Entrust_Root_Certification_Authority.pem 640s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 640s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 640s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem 640s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 640s Adding debian:GLOBALTRUST_2020.pem 640s Adding debian:GTS_Root_R1.pem 640s Adding debian:GTS_Root_R2.pem 640s Adding debian:GTS_Root_R3.pem 640s Adding debian:GTS_Root_R4.pem 640s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 640s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 640s Adding debian:GlobalSign_Root_CA.pem 640s Adding debian:GlobalSign_Root_CA_-_R3.pem 640s Adding debian:GlobalSign_Root_CA_-_R6.pem 640s Adding debian:GlobalSign_Root_E46.pem 640s Adding debian:GlobalSign_Root_R46.pem 640s Adding debian:Go_Daddy_Class_2_CA.pem 640s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 640s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 640s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 640s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 640s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 640s Adding debian:HiPKI_Root_CA_-_G1.pem 640s Adding debian:Hongkong_Post_Root_CA_3.pem 640s Adding debian:ISRG_Root_X1.pem 640s Adding debian:ISRG_Root_X2.pem 640s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 640s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 640s Adding debian:Izenpe.com.pem 640s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 640s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 640s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 640s Adding debian:NAVER_Global_Root_Certification_Authority.pem 640s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 640s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 640s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 640s Adding debian:QuoVadis_Root_CA_1_G3.pem 640s Adding debian:QuoVadis_Root_CA_2.pem 640s Adding debian:QuoVadis_Root_CA_2_G3.pem 640s Adding debian:QuoVadis_Root_CA_3.pem 640s Adding debian:QuoVadis_Root_CA_3_G3.pem 640s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 640s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 640s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 640s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 640s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 640s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 640s Adding debian:SZAFIR_ROOT_CA2.pem 640s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 640s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 640s Adding debian:SecureSign_RootCA11.pem 640s Adding debian:SecureTrust_CA.pem 640s Adding debian:Secure_Global_CA.pem 640s Adding debian:Security_Communication_ECC_RootCA1.pem 640s Adding debian:Security_Communication_RootCA2.pem 640s Adding debian:Security_Communication_RootCA3.pem 640s Adding debian:Security_Communication_Root_CA.pem 640s Adding debian:Starfield_Class_2_CA.pem 640s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 640s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 640s Adding debian:SwissSign_Gold_CA_-_G2.pem 640s Adding debian:SwissSign_Silver_CA_-_G2.pem 640s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 640s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 640s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 640s Adding debian:TWCA_Global_Root_CA.pem 640s Adding debian:TWCA_Root_Certification_Authority.pem 640s Adding debian:TeliaSonera_Root_CA_v1.pem 640s Adding debian:Telia_Root_CA_v2.pem 640s Adding debian:TrustAsia_Global_Root_CA_G3.pem 640s Adding debian:TrustAsia_Global_Root_CA_G4.pem 640s Adding debian:Trustwave_Global_Certification_Authority.pem 640s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 640s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 640s Adding debian:TunTrust_Root_CA.pem 640s Adding debian:UCA_Extended_Validation_Root.pem 640s Adding debian:UCA_Global_G2_Root.pem 640s Adding debian:USERTrust_ECC_Certification_Authority.pem 640s Adding debian:USERTrust_RSA_Certification_Authority.pem 640s Adding debian:XRamp_Global_CA_Root.pem 640s Adding debian:certSIGN_ROOT_CA.pem 640s Adding debian:certSIGN_Root_CA_G2.pem 640s Adding debian:e-Szigno_Root_CA_2017.pem 640s Adding debian:ePKI_Root_Certification_Authority.pem 640s Adding debian:emSign_ECC_Root_CA_-_C3.pem 640s Adding debian:emSign_ECC_Root_CA_-_G3.pem 640s Adding debian:emSign_Root_CA_-_C1.pem 640s Adding debian:emSign_Root_CA_-_G1.pem 640s Adding debian:vTrus_ECC_Root_CA.pem 640s Adding debian:vTrus_Root_CA.pem 640s done. 640s Setting up bbmap (39.06+dfsg-1) ... 640s Setting up autopkgtest-satdep (0) ... 643s (Reading database ... 72566 files and directories currently installed.) 643s Removing autopkgtest-satdep (0) ... 644s autopkgtest [20:04:59]: test run-unit-test: [----------------------- 644s 644s # bbmap 644s bbmap.sh --version 644s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 644s java -ea -Xmx2637m -Xms2637m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 --version 644s BBMap version 39.06 644s For help, please run the shellscript with no parameters, or look in /docs/. 644s bbmap.sh --help 644s bbmap.sh ref=example.fasta 644s 644s BBMap 644s Written by Brian Bushnell, from Dec. 2010 - present 644s Last modified September 15, 2022 644s 644s Description: Fast and accurate splice-aware read aligner. 644s Please read bbmap/docs/guides/BBMapGuide.txt for more information. 644s 644s To index: bbmap.sh ref= 644s To map: bbmap.sh in= out= 644s To map without writing an index: 644s bbmap.sh ref= in= out= nodisk 644s 644s in=stdin will accept reads from standard in, and out=stdout will write to 644s standard out, but file extensions are still needed to specify the format of the 644s input and output files e.g. in=stdin.fa.gz will read gzipped fasta from 644s standard in; out=stdout.sam.gz will write gzipped sam. 644s 644s Indexing Parameters (required when building the index): 644s nodisk=f Set to true to build index in memory and write nothing 644s to disk except output. 644s ref= Specify the reference sequence. Only do this ONCE, 644s when building the index (unless using 'nodisk'). 644s build=1 If multiple references are indexed in the same directory, 644s each needs a unique numeric ID (unless using 'nodisk'). 644s k=13 Kmer length, range 8-15. Longer is faster but uses 644s more memory. Shorter is more sensitive. 644s If indexing and mapping are done in two steps, K should 644s be specified each time. 644s path=<.> Specify the location to write the index, if you don't 644s want it in the current working directory. 644s usemodulo=f Throw away ~80% of kmers based on remainder modulo a 644s number (reduces RAM by 50% and sensitivity slightly). 644s Should be enabled both when building the index AND 644s when mapping. 644s rebuild=f Force a rebuild of the index (ref= should be set). 644s 644s Input Parameters: 644s build=1 Designate index to use. Corresponds to the number 644s specified when building the index. 644s in= Primary reads input; required parameter. 644s in2= For paired reads in two files. 644s interleaved=auto True forces paired/interleaved input; false forces 644s single-ended mapping. If not specified, interleaved 644s status will be autodetected from read names. 644s fastareadlen=500 Break up FASTA reads longer than this. Max is 500 for 644s BBMap and 6000 for BBMapPacBio. Only works for FASTA 644s input (use 'maxlen' for FASTQ input). The default for 644s bbmap.sh is 500, and for mapPacBio.sh is 6000. 644s unpigz=f Spawn a pigz (parallel gzip) process for faster 644s decompression than using Java. 644s Requires pigz to be installed. 644s touppercase=t (tuc) Convert lowercase letters in reads to upper case 644s (otherwise they will not match the reference). 644s 644s Sampling Parameters: 644s 644s reads=-1 Set to a positive number N to only process the first N 644s reads (or pairs), then quit. -1 means use all reads. 644s samplerate=1 Set to a number from 0 to 1 to randomly select that 644s fraction of reads for mapping. 1 uses all reads. 644s skipreads=0 Set to a number N to skip the first N reads (or pairs), 644s then map the rest. 644s 644s Mapping Parameters: 644s fast=f This flag is a macro which sets other paramters to run 644s faster, at reduced sensitivity. Bad for RNA-seq. 644s slow=f This flag is a macro which sets other paramters to run 644s slower, at greater sensitivity. 'vslow' is even slower. 644s maxindel=16000 Don't look for indels longer than this. Lower is faster. 644s Set to >=100k for RNAseq with long introns like mammals. 644s strictmaxindel=f When enabled, do not allow indels longer than 'maxindel'. 644s By default these are not sought, but may be found anyway. 644s tipsearch=100 Look this far for read-end deletions with anchors 644s shorter than K, using brute force. 644s minid=0.76 Approximate minimum alignment identity to look for. 644s Higher is faster and less sensitive. 644s minhits=1 Minimum number of seed hits required for candidate sites. 644s Higher is faster. 644s local=f Set to true to use local, rather than global, alignments. 644s This will soft-clip ugly ends of poor alignments. 644s perfectmode=f Allow only perfect mappings when set to true (very fast). 644s semiperfectmode=f Allow only perfect and semiperfect (perfect except for 644s N's in the reference) mappings. 644s threads=auto (t) Set to number of threads desired. By default, uses 644s all cores available. 644s ambiguous=best (ambig) Set behavior on ambiguously-mapped reads (with 644s multiple top-scoring mapping locations). 644s best (use the first best site) 644s toss (consider unmapped) 644s random (select one top-scoring site randomly) 644s all (retain all top-scoring sites) 644s samestrandpairs=f (ssp) Specify whether paired reads should map to the 644s same strand or opposite strands. 644s requirecorrectstrand=t (rcs) Forbid pairing of reads without correct strand 644s orientation. Set to false for long-mate-pair libraries. 644s killbadpairs=f (kbp) If a read pair is mapped with an inappropriate 644s insert size or orientation, the read with the lower 644s mapping quality is marked unmapped. 644s pairedonly=f (po) Treat unpaired reads as unmapped. Thus they will 644s be sent to 'outu' but not 'outm'. 644s rcomp=f Reverse complement both reads prior to mapping (for LMP 644s outward-facing libraries). 644s rcompmate=f Reverse complement read2 prior to mapping. 644s pairlen=32000 Set max allowed distance between paired reads. 644s (insert size)=(pairlen)+(read1 length)+(read2 length) 644s rescuedist=1200 Don't try to rescue paired reads if avg. insert size 644s greater than this. Lower is faster. 644s rescuemismatches=32 Maximum mismatches allowed in a rescued read. Lower 644s is faster. 644s averagepairdist=100 (apd) Initial average distance between paired reads. 644s Varies dynamically; does not need to be specified. 644s deterministic=f Run in deterministic mode. In this case it is good 644s to set averagepairdist. BBMap is deterministic 644s without this flag if using single-ended reads, 644s or run singlethreaded. 644s bandwidthratio=0 (bwr) If above zero, restrict alignment band to this 644s fraction of read length. Faster but less accurate. 644s bandwidth=0 (bw) Set the bandwidth directly. 644s fraction of read length. Faster but less accurate. 644s usejni=f (jni) Do alignments faster, in C code. Requires 644s compiling the C code; details are in /jni/README.txt. 644s maxsites2=800 Don't analyze (or print) more than this many alignments 644s per read. 644s ignorefrequentkmers=t (ifk) Discard low-information kmers that occur often. 644s excludefraction=0.03 (ef) Fraction of kmers to ignore. For example, 0.03 644s will ignore the most common 3% of kmers. 644s greedy=t Use a greedy algorithm to discard the least-useful 644s kmers on a per-read basis. 644s kfilter=0 If positive, potential mapping sites must have at 644s least this many consecutive exact matches. 644s 644s 644s Quality and Trimming Parameters: 644s qin=auto Set to 33 or 64 to specify input quality value ASCII 644s offset. 33 is Sanger, 64 is old Solexa. 644s qout=auto Set to 33 or 64 to specify output quality value ASCII 644s offset (only if output format is fastq). 644s qtrim=f Quality-trim ends before mapping. Options are: 644s 'f' (false), 'l' (left), 'r' (right), and 'lr' (both). 644s untrim=f Undo trimming after mapping. Untrimmed bases will be 644s soft-clipped in cigar strings. 644s trimq=6 Trim regions with average quality below this 644s (phred algorithm). 644s mintrimlength=60 (mintl) Don't trim reads to be shorter than this. 644s fakefastaquality=-1 (ffq) Set to a positive number 1-50 to generate fake 644s quality strings for fasta input reads. 644s ignorebadquality=f (ibq) Keep going, rather than crashing, if a read has 644s out-of-range quality values. 644s usequality=t Use quality scores when determining which read kmers 644s to use as seeds. 644s minaveragequality=0 (maq) Do not map reads with average quality below this. 644s maqb=0 If positive, calculate maq from this many initial bases. 644s 644s Output Parameters: 644s out= Write all reads to this file. 644s outu= Write only unmapped reads to this file. Does not 644s include unmapped paired reads with a mapped mate. 644s outm= Write only mapped reads to this file. Includes 644s unmapped paired reads with a mapped mate. 644s mappedonly=f If true, treats 'out' like 'outm'. 644s bamscript= (bs) Write a shell script to that will turn 644s the sam output into a sorted, indexed bam file. 644s ordered=f Set to true to output reads in same order as input. 644s Slower and uses more memory. 644s overwrite=f (ow) Allow process to overwrite existing files. 644s secondary=f Print secondary alignments. 644s sssr=0.95 (secondarysitescoreratio) Print only secondary alignments 644s with score of at least this fraction of primary. 644s ssao=f (secondarysiteasambiguousonly) Only print secondary 644s alignments for ambiguously-mapped reads. 644s maxsites=5 Maximum number of total alignments to print per read. 644s Only relevant when secondary=t. 644s quickmatch=f Generate cigar strings more quickly. 644s trimreaddescriptions=f (trd) Truncate read and ref names at the first whitespace, 644s assuming that the remainder is a comment or description. 644s ziplevel=2 (zl) Compression level for zip or gzip output. 644s pigz=f Spawn a pigz (parallel gzip) process for faster 644s compression than Java. Requires pigz to be installed. 644s machineout=f Set to true to output statistics in machine-friendly 644s 'key=value' format. 644s printunmappedcount=f Print the total number of unmapped reads and bases. 644s If input is paired, the number will be of pairs 644s for which both reads are unmapped. 644s showprogress=0 If positive, print a '.' every X reads. 644s showprogress2=0 If positive, print the number of seconds since the 644s last progress update (instead of a '.'). 644s renamebyinsert=f Renames reads based on their mapped insert size. 644s 644s Bloom-Filtering Parameters (bloomfilter.sh is the standalone version). 644s bloom=f Use a Bloom filter to ignore reads not sharing kmers 644s with the reference. This uses more memory, but speeds 644s mapping when most reads don't match the reference. 644s bloomhashes=2 Number of hash functions. 644s bloomminhits=3 Number of consecutive hits to be considered matched. 644s bloomk=31 Bloom filter kmer length. 644s bloomserial=t Use the serialized Bloom filter for greater loading 644s speed, if available. If not, generate and write one. 644s 644s Post-Filtering Parameters: 644s idfilter=0 Independant of minid; sets exact minimum identity 644s allowed for alignments to be printed. Range 0 to 1. 644s subfilter=-1 Ban alignments with more than this many substitutions. 644s insfilter=-1 Ban alignments with more than this many insertions. 644s delfilter=-1 Ban alignments with more than this many deletions. 644s indelfilter=-1 Ban alignments with more than this many indels. 644s editfilter=-1 Ban alignments with more than this many edits. 644s inslenfilter=-1 Ban alignments with an insertion longer than this. 644s dellenfilter=-1 Ban alignments with a deletion longer than this. 644s nfilter=-1 Ban alignments with more than this many ns. This 644s includes nocall, noref, and off scaffold ends. 644s 644s Sam flags and settings: 644s noheader=f Disable generation of header lines. 644s sam=1.4 Set to 1.4 to write Sam version 1.4 cigar strings, 644s with = and X, or 1.3 to use M. 644s saa=t (secondaryalignmentasterisks) Use asterisks instead of 644s bases for sam secondary alignments. 644s cigar=t Set to 'f' to skip generation of cigar strings (faster). 644s keepnames=f Keep original names of paired reads, rather than 644s ensuring both reads have the same name. 644s intronlen=999999999 Set to a lower number like 10 to change 'D' to 'N' in 644s cigar strings for deletions of at least that length. 644s rgid= Set readgroup ID. All other readgroup fields 644s can be set similarly, with the flag rgXX= 644s If you set a readgroup flag to the word 'filename', 644s e.g. rgid=filename, the input file name will be used. 644s mdtag=f Write MD tags. 644s nhtag=f Write NH tags. 644s xmtag=f Write XM tags (may only work correctly with ambig=all). 644s amtag=f Write AM tags. 644s nmtag=f Write NM tags. 644s xstag=f Set to 'xs=fs', 'xs=ss', or 'xs=us' to write XS tags 644s for RNAseq using firststrand, secondstrand, or 644s unstranded libraries. Needed by Cufflinks. 644s JGI mainly uses 'firststrand'. 644s stoptag=f Write a tag indicating read stop location, prefixed by YS:i: 644s lengthtag=f Write a tag indicating (query,ref) alignment lengths, 644s prefixed by YL:Z: 644s idtag=f Write a tag indicating percent identity, prefixed by YI:f: 644s inserttag=f Write a tag indicating insert size, prefixed by X8:Z: 644s scoretag=f Write a tag indicating BBMap's raw score, prefixed by YR:i: 644s timetag=f Write a tag indicating this read's mapping time, prefixed by X0:i: 644s boundstag=f Write a tag indicating whether either read in the pair 644s goes off the end of the reference, prefixed by XB:Z: 644s notags=f Turn off all optional tags. 644s 644s Histogram and statistics output parameters: 644s scafstats= Statistics on how many reads mapped to which scaffold. 644s refstats= Statistics on how many reads mapped to which reference 644s file; only for BBSplit. 644s sortscafs=t Sort scaffolds or references by read count. 644s bhist= Base composition histogram by position. 644s qhist= Quality histogram by position. 644s aqhist= Histogram of average read quality. 644s bqhist= Quality histogram designed for box plots. 644s lhist= Read length histogram. 644s ihist= Write histogram of insert sizes (for paired reads). 644s ehist= Errors-per-read histogram. 644s qahist= Quality accuracy histogram of error rates versus 644s quality score. 644s indelhist= Indel length histogram. 644s mhist= Histogram of match, sub, del, and ins rates by 644s read location. 644s gchist= Read GC content histogram. 644s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 644s gcpairs=t Use average GC of paired reads. 644s idhist= Histogram of read count versus percent identity. 644s idbins=100 Number idhist bins. Set to 'auto' to use read length. 644s statsfile=stderr Mapping statistics are printed here. 644s 644s Coverage output parameters (these may reduce speed and use more RAM): 644s covstats= Per-scaffold coverage info. 644s rpkm= Per-scaffold RPKM/FPKM counts. 644s covhist= Histogram of # occurrences of each depth level. 644s basecov= Coverage per base location. 644s bincov= Print binned coverage per location (one line per X bases). 644s covbinsize=1000 Set the binsize for binned coverage output. 644s nzo=t Only print scaffolds with nonzero coverage. 644s twocolumn=f Change to true to print only ID and Avg_fold instead of 644s all 6 columns to the 'out=' file. 644s 32bit=f Set to true if you need per-base coverage over 64k. 644s strandedcov=f Track coverage for plus and minus strand independently. 644s startcov=f Only track start positions of reads. 644s secondarycov=t Include coverage of secondary alignments. 644s physcov=f Calculate physical coverage for paired reads. 644s This includes the unsequenced bases. 644s delcoverage=t (delcov) Count bases covered by deletions as covered. 644s True is faster than false. 644s covk=0 If positive, calculate kmer coverage statistics. 644s 644s Java Parameters: 644s -Xmx This will set Java's memory usage, 644s overriding autodetection. 644s -Xmx20g will specify 20 gigs of RAM, and -Xmx800m 644s will specify 800 megs. The max is typically 85% of 644s physical memory. The human genome requires around 24g, 644s or 12g with the 'usemodulo' flag. The index uses 644s roughly 6 bytes per reference base. 644s -eoom This flag will cause the process to exit if an 644s out-of-memory exception occurs. Requires Java 8u92+. 644s -da Disable assertions. 644s 644s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter 644s any problems, or post at: http://seqanswers.com/forums/showthread.php?t=41057 644s 644s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 644s java -ea -Xmx2638m -Xms2638m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta 644s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta] 644s Version 39.06 644s 644s No output file. 644s Writing reference. 644s 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] 644s 644s Set genScaffoldInfo=true 644s Writing chunk 1 644s Set genome to 1 644s 644s Loaded Reference: 0.005 seconds. 644s Loading index for chunk 1-1, build 1 644s No index available; generating from reference genome: /tmp/autopkgtest.L6srLX/autopkgtest_tmp/ref/index/1/chr1_index_k13_c16_b1.block 644s Indexing threads started for block 0-1 645s Indexing threads finished for block 0-1 646s Generated Index: 1.207 seconds. 646s No reads to process; quitting. 646s 646s Total time: 1.341 seconds. 646s test -d ref 646s bbmap.sh in=misc_dna_as_sanger.fastq out=out.sam 646s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 646s java -ea -Xmx2637m -Xms2637m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 in=misc_dna_as_sanger.fastq out=out.sam 646s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, in=misc_dna_as_sanger.fastq, out=out.sam] 646s Version 39.06 646s 646s Retaining first best site only for ambiguous mappings. 646s Set genome to 1 646s 646s Loaded Reference: 0.026 seconds. 646s Loading index for chunk 1-1, build 1 646s Generated Index: 0.478 seconds. 653s Analyzed Index: 6.399 seconds. 653s Started output stream: 0.021 seconds. 653s Cleared Memory: 0.114 seconds. 653s Processing reads in single-ended mode. 653s Started read stream. 653s Started 4 mapping threads. 653s Detecting finished threads: 0, 1, 2, 3 653s 653s ------------------ Results ------------------ 653s 653s Genome: 1 653s Key Length: 13 653s Max Indel: 16000 653s Minimum Score Ratio: 0.56 653s Mapping Mode: normal 653s Reads Used: 4 (153 bases) 653s 653s Mapping: 0.082 seconds. 653s Reads/sec: 49.08 653s kBases/sec: 1.88 653s 653s 653s Read 1 data: pct reads num reads pct bases num bases 653s 653s mapped: 0.0000% 0 0.0000% 0 653s unambiguous: 0.0000% 0 0.0000% 0 653s ambiguous: 0.0000% 0 0.0000% 0 653s low-Q discards: 25.0000% 1 19.6078% 30 653s 653s perfect best site: 0.0000% 0 0.0000% 0 653s semiperfect site: 0.0000% 0 0.0000% 0 653s 653s Match Rate: NA NA NaN% 0 653s Error Rate: NaN% 0 NaN% 0 653s Sub Rate: NaN% 0 NaN% 0 653s Del Rate: NaN% 0 NaN% 0 653s Ins Rate: NaN% 0 NaN% 0 653s N Rate: NaN% 0 NaN% 0 653s 653s Total time: 7.222 seconds. 653s test -r out.sam 653s bbmap.sh ref=example.fasta in=example.fastq out=out2.sam nodisk 653s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 653s java -ea -Xmx2638m -Xms2638m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta in=example.fastq out=out2.sam nodisk 653s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta, in=example.fastq, out=out2.sam, nodisk] 653s Version 39.06 653s 653s Retaining first best site only for ambiguous mappings. 653s 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] 653s 653s Set genScaffoldInfo=true 653s Set genome to 1 653s 653s Loaded Reference: 0.002 seconds. 653s Loading index for chunk 1-1, build 1 653s Indexing threads started for block 0-1 653s Indexing threads finished for block 0-1 654s Generated Index: 0.222 seconds. 659s Analyzed Index: 5.612 seconds. 659s Started output stream: 0.021 seconds. 659s Cleared Memory: 0.117 seconds. 659s Processing reads in single-ended mode. 659s Started read stream. 659s Started 4 mapping threads. 659s Detecting finished threads: 0, 1, 2, 3 659s 659s ------------------ Results ------------------ 659s 659s Genome: 1 659s Key Length: 13 659s Max Indel: 16000 659s Minimum Score Ratio: 0.56 659s Mapping Mode: normal 659s Reads Used: 3 (75 bases) 659s 659s Mapping: 0.087 seconds. 659s Reads/sec: 34.39 659s kBases/sec: 0.86 659s 659s 659s Read 1 data: pct reads num reads pct bases num bases 659s 659s mapped: 100.0000% 3 100.0000% 75 659s unambiguous: 100.0000% 3 100.0000% 75 659s ambiguous: 0.0000% 0 0.0000% 0 659s low-Q discards: 0.0000% 0 0.0000% 0 659s 659s perfect best site: 100.0000% 3 100.0000% 75 659s semiperfect site: 100.0000% 3 100.0000% 75 659s 659s Match Rate: NA NA 100.0000% 75 659s Error Rate: 0.0000% 0 0.0000% 0 659s Sub Rate: 0.0000% 0 0.0000% 0 659s Del Rate: 0.0000% 0 0.0000% 0 659s Ins Rate: 0.0000% 0 0.0000% 0 659s N Rate: 0.0000% 0 0.0000% 0 659s 659s Total time: 6.204 seconds. 659s test -r out2.sam 659s 659s # bbduk 659s bbduk.sh --version 659s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 659s java -ea -Xmx1319m -Xms1319m -cp /usr/share/java/bbmap.jar jgi.BBDuk --version 659s BBMap version 39.06 659s For help, please run the shellscript with no parameters, or look in /docs/. 659s bbduk.sh --help 659s bbduk.sh in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq \ 659s qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 659s 659s Written by Brian Bushnell 659s Last modified November 9, 2023 659s 659s Description: Compares reads to the kmers in a reference dataset, optionally 659s allowing an edit distance. Splits the reads into two outputs - those that 659s match the reference, and those that don't. Can also trim (remove) the matching 659s parts of the reads rather than binning the reads. 659s Please read bbmap/docs/guides/BBDukGuide.txt for more information. 659s 659s Usage: bbduk.sh in= out= ref= 659s 659s Input may be stdin or a fasta or fastq file, compressed or uncompressed. 659s If you pipe via stdin/stdout, please include the file type; e.g. for gzipped 659s fasta input, set in=stdin.fa.gz 659s 659s Input parameters: 659s in= Main input. in=stdin.fq will pipe from stdin. 659s in2= Input for 2nd read of pairs in a different file. 659s ref= Comma-delimited list of reference files. 659s In addition to filenames, you may also use the keywords: 659s adapters, artifacts, phix, lambda, pjet, mtst, kapa 659s literal= Comma-delimited list of literal reference sequences. 659s touppercase=f (tuc) Change all bases upper-case. 659s interleaved=auto (int) t/f overrides interleaved autodetection. 659s Must be set mainually when streaming fastq input. 659s qin=auto Input quality offset: 33 (Sanger), 64, or auto. 659s reads=-1 If positive, quit after processing X reads or pairs. 659s copyundefined=f (cu) Process non-AGCT IUPAC reference bases by making all 659s possible unambiguous copies. Intended for short motifs 659s or adapter barcodes, as time/memory use is exponential. 659s samplerate=1 Set lower to only process a fraction of input reads. 659s samref= Optional reference fasta for processing sam files. 659s 659s Output parameters: 659s out= (outnonmatch) Write reads here that do not contain 659s kmers matching the database. 'out=stdout.fq' will pipe 659s to standard out. 659s out2= (outnonmatch2) Use this to write 2nd read of pairs to a 659s different file. 659s outm= (outmatch) Write reads here that fail filters. In default 659s kfilter mode, this means any read with a matching kmer. 659s In any mode, it also includes reads that fail filters such 659s as minlength, mingc, maxgc, entropy, etc. In other words, 659s it includes all reads that do not go to 'out'. 659s outm2= (outmatch2) Use this to write 2nd read of pairs to a 659s different file. 659s outs= (outsingle) Use this to write singleton reads whose mate 659s was trimmed shorter than minlen. 659s stats= Write statistics about which contamininants were detected. 659s refstats= Write statistics on a per-reference-file basis. 659s rpkm= Write RPKM for each reference sequence (for RNA-seq). 659s dump= Dump kmer tables to a file, in fasta format. 659s duk= Write statistics in duk's format. *DEPRECATED* 659s nzo=t Only write statistics about ref sequences with nonzero hits. 659s overwrite=t (ow) Grant permission to overwrite files. 659s showspeed=t (ss) 'f' suppresses display of processing speed. 659s ziplevel=2 (zl) Compression level; 1 (min) through 9 (max). 659s fastawrap=70 Length of lines in fasta output. 659s qout=auto Output quality offset: 33 (Sanger), 64, or auto. 659s statscolumns=3 (cols) Number of columns for stats output, 3 or 5. 659s 5 includes base counts. 659s rename=f Rename reads to indicate which sequences they matched. 659s refnames=f Use names of reference files rather than scaffold IDs. 659s trd=f Truncate read and ref names at the first whitespace. 659s ordered=f Set to true to output reads in same order as input. 659s maxbasesout=-1 If positive, quit after writing approximately this many 659s bases to out (outu/outnonmatch). 659s maxbasesoutm=-1 If positive, quit after writing approximately this many 659s bases to outm (outmatch). 659s json=f Print to screen in json format. 659s 659s Histogram output parameters: 659s bhist= Base composition histogram by position. 659s qhist= Quality histogram by position. 659s qchist= Count of bases with each quality value. 659s aqhist= Histogram of average read quality. 659s bqhist= Quality histogram designed for box plots. 659s lhist= Read length histogram. 659s phist= Polymer length histogram. 659s gchist= Read GC content histogram. 659s enthist= Read entropy histogram. 659s ihist= Insert size histogram, for paired reads in mapped sam. 659s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 659s maxhistlen=6000 Set an upper bound for histogram lengths; higher uses 659s more memory. The default is 6000 for some histograms 659s and 80000 for others. 659s 659s Histograms for mapped sam/bam files only: 659s histbefore=t Calculate histograms from reads before processing. 659s ehist= Errors-per-read histogram. 659s qahist= Quality accuracy histogram of error rates versus quality 659s score. 659s indelhist= Indel length histogram. 659s mhist= Histogram of match, sub, del, and ins rates by position. 659s idhist= Histogram of read count versus percent identity. 659s idbins=100 Number idhist bins. Set to 'auto' to use read length. 659s varfile= Ignore substitution errors listed in this file when 659s calculating error rates. Can be generated with 659s CallVariants. 659s vcf= Ignore substitution errors listed in this VCF file 659s when calculating error rates. 659s ignorevcfindels=t Also ignore indels listed in the VCF. 659s 659s Processing parameters: 659s k=27 Kmer length used for finding contaminants. Contaminants 659s shorter than k will not be found. k must be at least 1. 659s rcomp=t Look for reverse-complements of kmers in addition to 659s forward kmers. 659s maskmiddle=t (mm) Treat the middle base of a kmer as a wildcard, to 659s increase sensitivity in the presence of errors. This may 659s also be set to a number, e.g. mm=3, to mask that many bp. 659s The default mm=t corresponds to mm=1 for odd-length kmers 659s and mm=2 for even-length kmers (as of v39.04), while 659s mm=f is always equivalent to mm=0. 659s minkmerhits=1 (mkh) Reads need at least this many matching kmers 659s to be considered as matching the reference. 659s minkmerfraction=0.0 (mkf) A reads needs at least this fraction of its total 659s kmers to hit a ref, in order to be considered a match. 659s If this and minkmerhits are set, the greater is used. 659s mincovfraction=0.0 (mcf) A reads needs at least this fraction of its total 659s bases to be covered by ref kmers to be considered a match. 659s If specified, mcf overrides mkh and mkf. 659s hammingdistance=0 (hdist) Maximum Hamming distance for ref kmers (subs only). 659s Memory use is proportional to (3*K)^hdist. 659s qhdist=0 Hamming distance for query kmers; impacts speed, not memory. 659s editdistance=0 (edist) Maximum edit distance from ref kmers (subs 659s and indels). Memory use is proportional to (8*K)^edist. 659s hammingdistance2=0 (hdist2) Sets hdist for short kmers, when using mink. 659s qhdist2=0 Sets qhdist for short kmers, when using mink. 659s editdistance2=0 (edist2) Sets edist for short kmers, when using mink. 659s forbidn=f (fn) Forbids matching of read kmers containing N. 659s By default, these will match a reference 'A' if 659s hdist>0 or edist>0, to increase sensitivity. 659s removeifeitherbad=t (rieb) Paired reads get sent to 'outmatch' if either is 659s match (or either is trimmed shorter than minlen). 659s Set to false to require both. 659s trimfailures=f Instead of discarding failed reads, trim them to 1bp. 659s This makes the statistics a bit odd. 659s findbestmatch=f (fbm) If multiple matches, associate read with sequence 659s sharing most kmers. Reduces speed. 659s skipr1=f Don't do kmer-based operations on read 1. 659s skipr2=f Don't do kmer-based operations on read 2. 659s ecco=f For overlapping paired reads only. Performs error- 659s correction with BBMerge prior to kmer operations. 659s recalibrate=f (recal) Recalibrate quality scores. Requires calibration 659s matrices generated by CalcTrueQuality. 659s sam= If recalibration is desired, and matrices have not already 659s been generated, BBDuk will create them from the sam file. 659s amino=f Run in amino acid mode. Some features have not been 659s tested, but kmer-matching works fine. Maximum k is 12. 659s 659s Speed and Memory parameters: 659s threads=auto (t) Set number of threads to use; default is number of 659s logical processors. 659s prealloc=f Preallocate memory in table. Allows faster table loading 659s and more efficient memory usage, for a large reference. 659s monitor=f Kill this process if it crashes. monitor=600,0.01 would 659s kill after 600 seconds under 1% usage. 659s minrskip=1 (mns) Force minimal skip interval when indexing reference 659s kmers. 1 means use all, 2 means use every other kmer, etc. 659s maxrskip=1 (mxs) Restrict maximal skip interval when indexing 659s reference kmers. Normally all are used for scaffolds<100kb, 659s but with longer scaffolds, up to maxrskip-1 are skipped. 659s rskip= Set both minrskip and maxrskip to the same value. 659s If not set, rskip will vary based on sequence length. 659s qskip=1 Skip query kmers to increase speed. 1 means use all. 659s speed=0 Ignore this fraction of kmer space (0-15 out of 16) in both 659s reads and reference. Increases speed and reduces memory. 659s Note: Do not use more than one of 'speed', 'qskip', and 'rskip'. 659s 659s Trimming/Filtering/Masking parameters: 659s Note - if ktrim, kmask, and ksplit are unset, the default behavior is kfilter. 659s All kmer processing modes are mutually exclusive. 659s Reads only get sent to 'outm' purely based on kmer matches in kfilter mode. 659s 659s ktrim=f Trim reads to remove bases matching reference kmers, plus 659s all bases to the left or right. 659s Values: 659s f (don't trim), 659s r (trim to the right), 659s l (trim to the left) 659s ktrimtips=0 Set this to a positive number to perform ktrim on both 659s ends, examining only the outermost X bases. 659s kmask= Replace bases matching ref kmers with another symbol. 659s Allows any non-whitespace character, and processes short 659s kmers on both ends if mink is set. 'kmask=lc' will 659s convert masked bases to lowercase. 659s maskfullycovered=f (mfc) Only mask bases that are fully covered by kmers. 659s ksplit=f For single-ended reads only. Reads will be split into 659s pairs around the kmer. If the kmer is at the end of the 659s read, it will be trimmed instead. Singletons will go to 659s out, and pairs will go to outm. Do not use ksplit with 659s other operations such as quality-trimming or filtering. 659s mink=0 Look for shorter kmers at read tips down to this length, 659s when k-trimming or masking. 0 means disabled. Enabling 659s this will disable maskmiddle. 659s qtrim=f Trim read ends to remove bases with quality below trimq. 659s Performed AFTER looking for kmers. Values: 659s rl (trim both ends), 659s f (neither end), 659s r (right end only), 659s l (left end only), 659s w (sliding window). 659s trimq=6 Regions with average quality BELOW this will be trimmed, 659s if qtrim is set to something other than f. Can be a 659s floating-point number like 7.3. 659s trimclip=f Trim soft-clipped bases from sam files. 659s minlength=10 (ml) Reads shorter than this after trimming will be 659s discarded. Pairs will be discarded if both are shorter. 659s mlf=0 (minlengthfraction) Reads shorter than this fraction of 659s original length after trimming will be discarded. 659s maxlength= Reads longer than this after trimming will be discarded. 659s minavgquality=0 (maq) Reads with average quality (after trimming) below 659s this will be discarded. 659s maqb=0 If positive, calculate maq from this many initial bases. 659s minbasequality=0 (mbq) Reads with any base below this quality (after 659s trimming) will be discarded. 659s maxns=-1 If non-negative, reads with more Ns than this 659s (after trimming) will be discarded. 659s mcb=0 (minconsecutivebases) Discard reads without at least 659s this many consecutive called bases. 659s ottm=f (outputtrimmedtomatch) Output reads trimmed to shorter 659s than minlength to outm rather than discarding. 659s tp=0 (trimpad) Trim this much extra around matching kmers. 659s tbo=f (trimbyoverlap) Trim adapters based on where paired 659s reads overlap. 659s strictoverlap=t Adjust sensitivity for trimbyoverlap mode. 659s minoverlap=14 Require this many bases of overlap for detection. 659s mininsert=40 Require insert size of at least this for overlap. 659s Should be reduced to 16 for small RNA sequencing. 659s tpe=f (trimpairsevenly) When kmer right-trimming, trim both 659s reads to the minimum length of either. 659s forcetrimleft=0 (ftl) If positive, trim bases to the left of this position 659s (exclusive, 0-based). 659s forcetrimright=0 (ftr) If positive, trim bases to the right of this position 659s (exclusive, 0-based). 659s forcetrimright2=0 (ftr2) If positive, trim this many bases on the right end. 659s forcetrimmod=0 (ftm) If positive, right-trim length to be equal to zero, 659s modulo this number. 659s restrictleft=0 If positive, only look for kmer matches in the 659s leftmost X bases. 659s restrictright=0 If positive, only look for kmer matches in the 659s rightmost X bases. 659s NOTE: restrictleft and restrictright are mutually exclusive. If trimming 659s both ends is desired, use ktrimtips. 659s mingc=0 Discard reads with GC content below this. 659s maxgc=1 Discard reads with GC content above this. 659s gcpairs=t Use average GC of paired reads. 659s Also affects gchist. 659s tossjunk=f Discard reads with invalid characters as bases. 659s swift=f Trim Swift sequences: Trailing C/T/N R1, leading G/A/N R2. 659s 659s Header-parsing parameters - these require Illumina headers: 659s chastityfilter=f (cf) Discard reads with id containing ' 1:Y:' or ' 2:Y:'. 659s barcodefilter=f Remove reads with unexpected barcodes if barcodes is set, 659s or barcodes containing 'N' otherwise. A barcode must be 659s the last part of the read header. Values: 659s t: Remove reads with bad barcodes. 659s f: Ignore barcodes. 659s crash: Crash upon encountering bad barcodes. 659s barcodes= Comma-delimited list of barcodes or files of barcodes. 659s xmin=-1 If positive, discard reads with a lesser X coordinate. 659s ymin=-1 If positive, discard reads with a lesser Y coordinate. 659s xmax=-1 If positive, discard reads with a greater X coordinate. 659s ymax=-1 If positive, discard reads with a greater Y coordinate. 659s 659s Polymer trimming: 659s trimpolya=0 If greater than 0, trim poly-A or poly-T tails of 659s at least this length on either end of reads. 659s trimpolygleft=0 If greater than 0, trim poly-G prefixes of at least this 659s length on the left end of reads. Does not trim poly-C. 659s trimpolygright=0 If greater than 0, trim poly-G tails of at least this 659s length on the right end of reads. Does not trim poly-C. 659s trimpolyg=0 This sets both left and right at once. 659s filterpolyg=0 If greater than 0, remove reads with a poly-G prefix of 659s at least this length (on the left). 659s Note: there are also equivalent poly-C flags. 659s 659s Polymer tracking: 659s pratio=base,base 'pratio=G,C' will print the ratio of G to C polymers. 659s plen=20 Length of homopolymers to count. 659s 659s Entropy/Complexity parameters: 659s entropy=-1 Set between 0 and 1 to filter reads with entropy below 659s that value. Higher is more stringent. 659s entropywindow=50 Calculate entropy using a sliding window of this length. 659s entropyk=5 Calculate entropy using kmers of this length. 659s minbasefrequency=0 Discard reads with a minimum base frequency below this. 659s entropytrim=f Values: 659s f: (false) Do not entropy-trim. 659s r: (right) Trim low entropy on the right end only. 659s l: (left) Trim low entropy on the left end only. 659s rl: (both) Trim low entropy on both ends. 659s entropymask=f Values: 659s f: (filter) Discard low-entropy sequences. 659s t: (true) Mask low-entropy parts of sequences with N. 659s lc: Change low-entropy parts of sequences to lowercase. 659s entropymark=f Mark each base with its entropy value. This is on a scale 659s of 0-41 and is reported as quality scores, so the output 659s should be fastq or fasta+qual. 659s NOTE: If set, entropytrim overrides entropymask. 659s 659s Cardinality estimation: 659s cardinality=f (loglog) Count unique kmers using the LogLog algorithm. 659s cardinalityout=f (loglogout) Count unique kmers in output reads. 659s loglogk=31 Use this kmer length for counting. 659s loglogbuckets=2048 Use this many buckets for counting. 659s khist= Kmer frequency histogram; plots number of kmers versus 659s kmer depth. This is approximate. 659s khistout= Kmer frequency histogram for output reads. 659s 659s Java Parameters: 659s 659s -Xmx This will set Java's memory usage, overriding autodetection. 659s -Xmx20g will 659s specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 659s The max is typically 85% of physical memory. 659s -eoom This flag will cause the process to exit if an 659s out-of-memory exception occurs. Requires Java 8u92+. 659s -da Disable assertions. 659s 659s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 659s 660s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 660s java -ea -Xmx1319m -Xms1319m -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 660s 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] 660s Version 39.06 660s 660s 0.013 seconds. 660s Initial: 660s Memory: max=1409m, total=1409m, free=1379m, used=30m 660s 660s Input is being processed as paired 660s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 660s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 660s Started output streams: 0.016 seconds. 660s Processing time: 0.004 seconds. 660s 660s Input: 8 reads 306 bases. 660s QTrimmed: 0 reads (0.00%) 0 bases (0.00%) 660s Total Removed: 8 reads (100.00%) 306 bases (100.00%) 660s Result: 0 reads (0.00%) 0 bases (0.00%) 660s 660s Time: 0.023 seconds. 660s Reads Processed: 8 0.35k reads/sec 660s Bases Processed: 306 0.01m bases/sec 660s test -r out.fastq.gz 660s 660s # bbnorm 660s bbnorm.sh --version 660s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 660s java -ea -Xmx2638m -Xms2638m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 --version 660s BBMap version 39.06 660s For help, please run the shellscript with no parameters, or look in /docs/. 660s bbnorm.sh --help 660s 660s Written by Brian Bushnell 660s Last modified October 19, 2017 660s 660s Description: Normalizes read depth based on kmer counts. 660s Can also error-correct, bin reads by kmer depth, and generate a kmer depth histogram. 660s However, Tadpole has superior error-correction to BBNorm. 660s Please read bbmap/docs/guides/BBNormGuide.txt for more information. 660s 660s Usage: bbnorm.sh in= out= outt= hist= 660s 660s Input parameters: 660s in=null Primary input. Use in2 for paired reads in a second file 660s in2=null Second input file for paired reads in two files 660s extra=null Additional files to use for input (generating hash table) but not for output 660s fastareadlen=2^31 Break up FASTA reads longer than this. Can be useful when processing scaffolded genomes 660s tablereads=-1 Use at most this many reads when building the hashtable (-1 means all) 660s kmersample=1 Process every nth kmer, and skip the rest 660s readsample=1 Process every nth read, and skip the rest 660s 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. 660s qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto. 660s 660s Output parameters: 660s out= File for normalized or corrected reads. Use out2 for paired reads in a second file 660s outt= (outtoss) File for reads that were excluded from primary output 660s reads=-1 Only process this number of reads, then quit (-1 means all) 660s sampleoutput=t Use sampling on output as well as input (not used if sample rates are 1) 660s keepall=f Set to true to keep all reads (e.g. if you just want error correction). 660s 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. 660s Default is false, to prevent confusion about how there can be 0-count kmers. 660s The reason is that based on the 'minq' and 'minprob' settings, some kmers may be excluded from the bloom filter. 660s tmpdir= This will specify a directory for temp files (only needed for multipass runs). If null, they will be written to the output directory. 660s usetempdir=t Allows enabling/disabling of temporary directory; if disabled, temp files will be written to the output directory. 660s qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input). 660s rename=f Rename reads based on their kmer depth. 660s 660s Hashing parameters: 660s k=31 Kmer length (values under 32 are most efficient, but arbitrarily high values are supported) 660s 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. 660s Large values decrease accuracy for a fixed amount of memory, so use the lowest number you can that will still capture highest-depth kmers. 660s hashes=3 Number of times each kmer is hashed and stored. Higher is slower. 660s Higher is MORE accurate if there is enough memory, and LESS accurate if there is not enough memory. 660s 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. 660s prehashes=2 Number of hashes for prefilter. 660s prefilterbits=2 (pbits) Bits per cell in prefilter. 660s prefiltersize=0.35 Fraction of memory to allocate to prefilter. 660s buildpasses=1 More passes can sometimes increase accuracy by iteratively removing low-depth kmers 660s minq=6 Ignore kmers containing bases with quality below this 660s minprob=0.5 Ignore kmers with overall probability of correctness below this 660s 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. 660s 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. 660s 660s Normalization parameters: 660s fixspikes=f (fs) Do a slower, high-precision bloom filter lookup of kmers that appear to have an abnormally high depth due to collisions. 660s target=100 (tgt) Target normalization depth. NOTE: All depth parameters control kmer depth, not read depth. 660s For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1)) 660s maxdepth=-1 (max) Reads will not be downsampled when below this depth, even if they are above the target depth. 660s mindepth=5 (min) Kmers with depth below this number will not be included when calculating the depth of a read. 660s minkmers=15 (mgkpr) Reads must have at least this many kmers over min depth to be retained. Aka 'mingoodkmersperread'. 660s 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. 660s uselowerdepth=t (uld) For pairs, use the depth of the lower read as the depth proxy. 660s deterministic=t (dr) Generate random numbers deterministically to ensure identical output between multiple runs. May decrease speed with a huge number of threads. 660s passes=2 (p) 1 pass is the basic mode. 2 passes (default) allows greater accuracy, error detection, better contol of output depth. 660s 660s Error detection parameters: 660s hdp=90.0 (highdepthpercentile) Position in sorted kmer depth array used as proxy of a read's high kmer depth. 660s ldp=25.0 (lowdepthpercentile) Position in sorted kmer depth array used as proxy of a read's low kmer depth. 660s tossbadreads=f (tbr) Throw away reads detected as containing errors. 660s requirebothbad=f (rbb) Only toss bad pairs if both reads are bad. 660s 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. 660s highthresh=12 (ht) Threshold for high kmer. A high kmer at this or above are considered non-error. 660s lowthresh=3 (lt) Threshold for low kmer. Kmers at this and below are always considered errors. 660s 660s Error correction parameters: 660s ecc=f Set to true to correct errors. NOTE: Tadpole is now preferred for ecc as it does a better job. 660s ecclimit=3 Correct up to this many errors per read. If more are detected, the read will remain unchanged. 660s errorcorrectratio=140 (ecr) Adjacent kmers with a depth ratio of at least this much between will be classified as an error. 660s echighthresh=22 (echt) Threshold for high kmer. A kmer at this or above may be considered non-error. 660s eclowthresh=2 (eclt) Threshold for low kmer. Kmers at this and below are considered errors. 660s eccmaxqual=127 Do not correct bases with quality above this value. 660s aec=f (aggressiveErrorCorrection) Sets more aggressive values of ecr=100, ecclimit=7, echt=16, eclt=3. 660s cec=f (conservativeErrorCorrection) Sets more conservative values of ecr=180, ecclimit=2, echt=30, eclt=1, sl=4, pl=4. 660s meo=f (markErrorsOnly) Marks errors by reducing quality value of suspected errors; does not correct anything. 660s mue=t (markUncorrectableErrors) Marks errors only on uncorrectable reads; requires 'ecc=t'. 660s overlap=f (ecco) Error correct by read overlap. 660s 660s Depth binning parameters: 660s lowbindepth=10 (lbd) Cutoff for low depth bin. 660s highbindepth=80 (hbd) Cutoff for high depth bin. 660s outlow= Pairs in which both reads have a median below lbd go into this file. 660s outhigh= Pairs in which both reads have a median above hbd go into this file. 660s outmid= All other pairs go into this file. 660s 660s Histogram parameters: 660s hist= Specify a file to write the input kmer depth histogram. 660s histout= Specify a file to write the output kmer depth histogram. 660s histcol=3 (histogramcolumns) Number of histogram columns, 2 or 3. 660s pzc=f (printzerocoverage) Print lines in the histogram with zero coverage. 660s histlen=1048576 Max kmer depth displayed in histogram. Also affe bbnorm.sh in=sanger_full_range_original_sanger.fastq qin=33 \ 660s out=out3.fastq outt=outt.fastq hist=hist.plt 660s cts statistics displayed, but does not affect normalization. 660s 660s Peak calling parameters: 660s peaks= Write the peaks to this file. Default is stdout. 660s minHeight=2 (h) Ignore peaks shorter than this. 660s minVolume=5 (v) Ignore peaks with less area than this. 660s minWidth=3 (w) Ignore peaks narrower than this. 660s minPeak=2 (minp) Ignore peaks with an X-value below this. 660s maxPeak=BIG (maxp) Ignore peaks with an X-value above this. 660s maxPeakCount=8 (maxpc) Print up to this many peaks (prioritizing height). 660s 660s Java Parameters: 660s -Xmx This will set Java's memory usage, overriding autodetection. 660s -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 660s The max is typically 85% of physical memory. 660s -eoom This flag will cause the process to exit if an 660s out-of-memory exception occurs. Requires Java 8u92+. 660s -da Disable assertions. 660s 660s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 660s 660s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 660s java -ea -Xmx2638m -Xms2638m -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 660s Executing jgi.KmerNormalize [bits=32, in=sanger_full_range_original_sanger.fastq, qin=33, out=out3.fastq, outt=outt.fastq, hist=hist.plt] 660s 660s 660s *********** Pass 1 ********** 660s 660s 660s Settings: 660s threads: 4 660s k: 31 660s deterministic: true 660s toss error reads: false 660s passes: 1 660s bits per cell: 16 660s cells: 980.97M 660s hashes: 3 660s base min quality: 5 660s kmer min prob: 0.5 660s 660s target depth: 400 660s min depth: 3 660s max depth: 500 660s min good kmers: 15 660s depth percentile: 64.8 660s ignore dupe kmers: true 660s fix spikes: false 660s histogram length: 65536 660s print zero cov: false 660s 663s Made hash table: hashes = 3 mem = 1.83 GB cells = 980.47M used = 0.000% 663s 663s Estimated unique kmers: 7 663s 663s Table creation time: 2.569 seconds. 663s Started output threads. 663s Started output threads. 663s Table read time: 0.009 seconds. 20.88 kb/sec 663s Total reads in: 2 0.000% Kept 663s Total bases in: 188 0.000% Kept 663s Error reads in: 2 100.000% 663s Error type 1: 2 100.000% 663s Error type 2: 0 0.000% 663s Error type 3: 0 0.000% 663s 663s Wrote histogram to hist.plt 663s Total kmers counted: 128 663s Total unique kmer count: 128 663s Includes forward kmers only. 663s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 663s The most accurate value is the greater of the two. 663s 663s Percent unique: 100.00% 663s Depth average: 1.00 (unique kmers) 663s Depth median: 1 (unique kmers) 663s Depth standard deviation: 0.00 (unique kmers) 663s Corrected depth average: 0.00 663s 663s Depth average: 1.00 (all kmers) 663s Depth median: 1 (all kmers) 663s Depth standard deviation: 0.00 (all kmers) 663s 663s Approx. read depth median: 1.47 663s 663s *********** Pass 2 ********** 663s 663s 663s Settings: 663s threads: 4 663s k: 31 663s deterministic: true 663s toss error reads: false 663s passes: 1 663s bits per cell: 16 663s cells: 980.97M 663s hashes: 3 663s base min quality: 5 663s kmer min prob: 0.5 663s 663s target depth: 100 663s min depth: 5 663s max depth: 100 663s min good kmers: 15 663s depth percentile: 54.0 663s ignore dupe kmers: true 663s fix spikes: false 663s histogram length: 65536 663s 665s Made hash table: hashes = 3 mem = 1.83 GB cells = 980.47M used = 0.000% 665s 665s Estimated unique kmers: 0 665s 665s Table creation time: 2.337 seconds. 665s Started output threads. 665s Started output threads. 665s Table read time: 0.002 seconds. 0.00 kb/sec 665s Total reads in: 0 NaN% Kept 665s Total bases in: 0 NaN% Kept 665s Error reads in: 0 NaN% 665s Error type 1: 0 NaN% 666s Error type 2: 0 NaN% 666s Error type 3: 0 NaN% 666s Total kmers counted: 0 666s Total unique kmer count: 0 666s Includes forward kmers only. 666s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 666s The most accurate value is the greater of the two. 666s 666s Percent unique: NaN% 666s Depth average: NaN (unique kmers) 666s Depth median: 0 (unique kmers) 666s Depth standard deviation: NaN (unique kmers) 666s Corrected depth average: NaN 666s 666s Depth average: NaN (all kmers) 666s Depth median: 0 (all kmers) 666s Depth standard deviation: 0.00 (all kmers) 666s 666s Approx. read depth median: NaN 666s 666s Removing temp files. 666s 666s Total time: 5.022 seconds. 0.04 kb/sec 666s test -r out3.fastq 666s test -r outt.fastq 666s test -r hist.plt 666s bbnorm.sh in=illumina_full_range_original_illumina.fastq qin=64 \ 666s out=out4.fastq outt=outt2.fastq hist=hist2.plt 666s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 666s java -ea -Xmx2638m -Xms2638m -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 666s Executing jgi.KmerNormalize [bits=32, in=illumina_full_range_original_illumina.fastq, qin=64, out=out4.fastq, outt=outt2.fastq, hist=hist2.plt] 666s 666s 666s *********** Pass 1 ********** 666s 666s 666s Settings: 666s threads: 4 666s k: 31 666s deterministic: true 666s toss error reads: false 666s passes: 1 666s bits per cell: 16 666s cells: 980.97M 666s hashes: 3 666s base min quality: 5 666s kmer min prob: 0.5 666s 666s target depth: 400 666s min depth: 3 666s max depth: 500 666s min good kmers: 15 666s depth percentile: 64.8 666s ignore dupe kmers: true 666s fix spikes: false 666s histogram length: 65536 666s print zero cov: false 666s 668s Made hash table: hashes = 3 mem = 1.83 GB cells = 980.47M used = 0.000% 668s 668s Estimated unique kmers: 7 668s 668s Table creation time: 2.432 seconds. 668s Started output threads. 668s Started output threads. 668s Table read time: 0.007 seconds. 17.35 kb/sec 668s Total reads in: 2 0.000% Kept 668s Total bases in: 126 0.000% Kept 668s Error reads in: 2 100.000% 668s Error type 1: 2 100.000% 668s Error type 2: 0 0.000% 668s Error type 3: 0 0.000% 668s 668s Wrote histogram to hist2.plt 668s Total kmers counted: 66 668s Total unique kmer count: 66 668s Includes forward kmers only. 668s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 668s The most accurate value is the greater of the two. 668s 668s Percent unique: 100.00% 668s Depth average: 1.00 (unique kmers) 668s Depth median: 1 (unique kmers) 668s Depth standard deviation: 0.00 (unique kmers) 668s Corrected depth average: 0.00 668s 668s Depth average: 1.00 (all kmers) 668s Depth median: 1 (all kmers) 668s Depth standard deviation: 0.00 (all kmers) 668s 668s Approx. read depth median: 1.91 668s 668s *********** Pass 2 ********** 668s 668s 668s Settings: 668s threads: 4 668s k: 31 668s deterministic: true 668s toss error reads: false 668s passes: 1 668s bits per cell: 16 668s cells: 980.97M 668s hashes: 3 668s base min quality: 5 668s kmer min prob: 0.5 668s 668s target depth: 100 668s min depth: 5 668s max depth: 100 668s min good kmers: 15 668s depth percentile: 54.0 668s ignore dupe kmers: true 668s fix spikes: false 668s histogram length: 65536 668s 670s Made hash table: hashes = 3 mem = 1.83 GB cells = 980.47M used = 0.000% 670s 670s Estimated unique kmers: 0 670s 670s Table creation time: 2.297 seconds. 670s Started output threads. 670s Started output threads. 670s Table read time: 0.002 seconds. 0.00 kb/sec 670s Total reads in: 0 NaN% Kept 670s Total bases in: 0 NaN% Kept 670s Error reads in: 0 NaN% 670s Error type 1: 0 NaN% 670s Error type 2: 0 NaN% 670s Error type 3: 0 NaN% 670s Total kmers counted: 0 670s Total unique kmer count: 0 670s Includes forward kmers only. 670s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 670s The most accurate value is the greater of the two. 670s 670s Percent unique: NaN% 670s Depth average: NaN (unique kmers) 670s Depth median: 0 (unique kmers) 670s Depth standard deviation: NaN (unique kmers) 670s Corrected depth average: NaN 670s 670s Depth average: NaN (all kmers) 670s Depth median: 0 (all kmers) 670s Depth standard deviation: 0.00 (all kmers) 670s 670s Approx. read depth median: NaN 670s 670s Removing temp files. 670s 670s Total time: 4.854 seconds. 0.03 kb/sec 670s test -r out4.fastq 670s test -r outt2.fastq 670s test -r hist2.plt 670s autopkgtest [20:05:25]: test run-unit-test: -----------------------] 671s autopkgtest [20:05:26]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 671s run-unit-test PASS 672s autopkgtest [20:05:27]: @@@@@@@@@@@@@@@@@@@@ summary 672s run-unit-test PASS 684s Creating nova instance adt-noble-ppc64el-bbmap-20240321-195414-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240321.img (UUID f9947641-425a-45c2-937a-6db4500fbfac)...