0s autopkgtest [14:49:38]: starting date and time: 2024-03-24 14:49:38+0000 0s autopkgtest [14:49:38]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [14:49:38]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.9ihabjsk/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-23,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-23/23~15ea-1 alsa-lib/1.2.11-1build1 at-spi2-core/2.51.90-3 cups/2.4.7-1.2ubuntu1 glib2.0/2.79.3-3ubuntu5 gnutls28/3.8.3-1.1ubuntu2 gtk+3.0/3.24.41-1.1ubuntu3 libpng1.6/1.6.43-3 nettle/3.9.1-2.2 wp2latex/4.4~ds-1build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-big --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos02-s390x-4.secgroup --name adt-noble-s390x-bbmap-20240324-144938-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 283s autopkgtest [14:54:21]: testbed dpkg architecture: s390x 283s autopkgtest [14:54:21]: testbed apt version: 2.7.12 283s autopkgtest [14:54:21]: @@@@@@@@@@@@@@@@@@@@ test bed setup 284s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 285s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [538 kB] 285s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3983 kB] 286s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 286s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 286s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [720 kB] 286s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 286s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 286s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 286s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4199 kB] 287s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 287s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [47.2 kB] 287s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 289s Fetched 9680 kB in 3s (2839 kB/s) 289s Reading package lists... 293s Reading package lists... 294s Building dependency tree... 294s Reading state information... 294s Calculating upgrade... 294s The following packages will be REMOVED: 294s libglib2.0-0 294s The following NEW packages will be installed: 294s libglib2.0-0t64 xdg-user-dirs 294s The following packages will be upgraded: 294s gir1.2-glib-2.0 libglib2.0-data 294s 2 upgraded, 2 newly installed, 1 to remove and 0 not upgraded. 294s Need to get 1811 kB of archives. 294s After this operation, 159 kB of additional disk space will be used. 294s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gir1.2-glib-2.0 s390x 2.79.3-3ubuntu5 [180 kB] 295s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libglib2.0-0t64 s390x 2.79.3-3ubuntu5 [1566 kB] 296s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 296s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x xdg-user-dirs s390x 0.18-1 [18.5 kB] 296s Fetched 1811 kB in 1s (1476 kB/s) 296s (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 ... 52170 files and directories currently installed.) 296s Preparing to unpack .../gir1.2-glib-2.0_2.79.3-3ubuntu5_s390x.deb ... 296s Unpacking gir1.2-glib-2.0:s390x (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 296s dpkg: libglib2.0-0:s390x: dependency problems, but removing anyway as you requested: 296s udisks2 depends on libglib2.0-0 (>= 2.77.0). 296s shared-mime-info depends on libglib2.0-0 (>= 2.75.3). 296s s390-tools depends on libglib2.0-0 (>= 2.77.0). 296s python3-gi depends on libglib2.0-0 (>= 2.77.0). 296s python3-dbus depends on libglib2.0-0 (>= 2.16.0). 296s netplan.io depends on libglib2.0-0 (>= 2.70.0). 296s netplan-generator depends on libglib2.0-0 (>= 2.70.0). 296s libxmlb2:s390x depends on libglib2.0-0 (>= 2.54.0). 296s libvolume-key1:s390x depends on libglib2.0-0 (>= 2.18.0). 296s libudisks2-0:s390x depends on libglib2.0-0 (>= 2.75.3). 296s libqrtr-glib0:s390x depends on libglib2.0-0 (>= 2.56). 296s libqmi-proxy depends on libglib2.0-0 (>= 2.30.0). 296s libqmi-glib5:s390x depends on libglib2.0-0 (>= 2.54.0). 296s libpolkit-gobject-1-0:s390x depends on libglib2.0-0 (>= 2.38.0). 296s libpolkit-agent-1-0:s390x depends on libglib2.0-0 (>= 2.38.0). 296s libnetplan0:s390x depends on libglib2.0-0 (>= 2.75.3). 296s libmm-glib0:s390x depends on libglib2.0-0 (>= 2.62.0). 296s libmbim-proxy depends on libglib2.0-0 (>= 2.56). 296s libmbim-glib4:s390x depends on libglib2.0-0 (>= 2.56). 296s libjson-glib-1.0-0:s390x depends on libglib2.0-0 (>= 2.75.3). 296s libjcat1:s390x depends on libglib2.0-0 (>= 2.75.3). 296s libgusb2:s390x depends on libglib2.0-0 (>= 2.75.3). 296s libgudev-1.0-0:s390x depends on libglib2.0-0 (>= 2.38.0). 296s libgirepository-1.0-1:s390x depends on libglib2.0-0 (>= 2.79.0). 296s libfwupd2:s390x depends on libglib2.0-0 (>= 2.79.0). 296s libblockdev3:s390x depends on libglib2.0-0 (>= 2.42.2). 296s libblockdev-utils3:s390x depends on libglib2.0-0 (>= 2.75.3). 296s libblockdev-swap3:s390x depends on libglib2.0-0 (>= 2.42.2). 296s libblockdev-part3:s390x depends on libglib2.0-0 (>= 2.42.2). 296s libblockdev-nvme3:s390x depends on libglib2.0-0 (>= 2.42.2). 296s libblockdev-mdraid3:s390x depends on libglib2.0-0 (>= 2.42.2). 296s libblockdev-loop3:s390x depends on libglib2.0-0 (>= 2.42.2). 296s libblockdev-fs3:s390x depends on libglib2.0-0 (>= 2.42.2). 296s libblockdev-crypto3:s390x depends on libglib2.0-0 (>= 2.42.2). 296s fwupd depends on libglib2.0-0 (>= 2.79.0). 296s bolt depends on libglib2.0-0 (>= 2.56.0). 296s 296s (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 ... 52170 files and directories currently installed.) 296s Removing libglib2.0-0:s390x (2.79.2-1~ubuntu1) ... 296s Selecting previously unselected package libglib2.0-0t64:s390x. 296s (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 ... 52145 files and directories currently installed.) 296s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_s390x.deb ... 296s libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:s390x.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled... 296s removed '/var/lib/dpkg/info/libglib2.0-0:s390x.postrm' 296s Unpacking libglib2.0-0t64:s390x (2.79.3-3ubuntu5) ... 296s Preparing to unpack .../libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 296s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 296s Selecting previously unselected package xdg-user-dirs. 296s Preparing to unpack .../xdg-user-dirs_0.18-1_s390x.deb ... 296s Unpacking xdg-user-dirs (0.18-1) ... 296s Setting up xdg-user-dirs (0.18-1) ... 296s Setting up libglib2.0-0t64:s390x (2.79.3-3ubuntu5) ... 296s No schema files found: doing nothing. 296s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 296s Setting up gir1.2-glib-2.0:s390x (2.79.3-3ubuntu5) ... 296s Processing triggers for man-db (2.12.0-3) ... 297s Processing triggers for libc-bin (2.39-0ubuntu6) ... 297s Reading package lists... 298s Building dependency tree... 298s Reading state information... 298s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 298s Unknown architecture, assuming PC-style ttyS0 298s sh: Attempting to set up Debian/Ubuntu apt sources automatically 298s sh: Distribution appears to be Ubuntu 300s Reading package lists... 300s Building dependency tree... 300s Reading state information... 300s eatmydata is already the newest version (131-1). 300s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 300s Reading package lists... 300s Building dependency tree... 300s Reading state information... 301s dbus is already the newest version (1.14.10-4ubuntu1). 301s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 301s Reading package lists... 301s Building dependency tree... 301s Reading state information... 301s rng-tools-debian is already the newest version (2.4). 301s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 301s Reading package lists... 301s Building dependency tree... 301s Reading state information... 302s The following packages will be REMOVED: 302s cloud-init* python3-configobj* python3-debconf* 302s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 302s After this operation, 3256 kB disk space will be freed. 302s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 52184 files and directories currently installed.) 302s Removing cloud-init (24.1.2-0ubuntu1) ... 302s Removing python3-configobj (5.0.8-3) ... 302s Removing python3-debconf (1.5.86) ... 302s Processing triggers for man-db (2.12.0-3) ... 303s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 51795 files and directories currently installed.) 303s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 303s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 303s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 303s invoke-rc.d: policy-rc.d denied execution of try-restart. 304s Reading package lists... 304s Building dependency tree... 304s Reading state information... 304s linux-generic is already the newest version (6.8.0-11.11+1). 304s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 305s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 305s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 305s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 307s Reading package lists... 307s Reading package lists... 307s Building dependency tree... 307s Reading state information... 307s Calculating upgrade... 307s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 307s Reading package lists... 308s Building dependency tree... 308s Reading state information... 308s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 308s autopkgtest [14:54:46]: rebooting testbed after setup commands that affected boot 328s autopkgtest [14:55:06]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 331s autopkgtest [14:55:09]: @@@@@@@@@@@@@@@@@@@@ apt-source bbmap 335s Get:1 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (dsc) [2286 B] 335s Get:2 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (tar) [5343 kB] 335s Get:3 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (diff) [25.4 kB] 335s gpgv: Signature made Fri Nov 24 11:00:29 2023 UTC 335s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 335s gpgv: issuer "emollier@debian.org" 335s gpgv: Can't check signature: No public key 335s dpkg-source: warning: cannot verify inline signature for ./bbmap_39.06+dfsg-1.dsc: no acceptable signature found 335s autopkgtest [14:55:13]: testing package bbmap version 39.06+dfsg-1 336s autopkgtest [14:55:14]: build not needed 337s autopkgtest [14:55:15]: test run-unit-test: preparing testbed 345s Reading package lists... 345s Building dependency tree... 345s Reading state information... 345s Starting pkgProblemResolver with broken count: 0 345s Starting 2 pkgProblemResolver with broken count: 0 345s Done 345s The following additional packages will be installed: 345s bbmap bbmap-jni ca-certificates-java fontconfig-config fonts-dejavu-core 345s fonts-dejavu-mono java-common libapache-pom-java libasound2 libasound2-data 345s libavahi-client3 libavahi-common-data libavahi-common3 libcommons-cli-java 345s libcommons-codec-java libcommons-io-java libcommons-parent-java libcups2 345s libfontconfig1 libfreetype6 libgraphite2-3 libharfbuzz0b libjpeg-turbo8 345s libjpeg8 liblcms2-2 liblog4j1.2-java libmpj-java libpcsclite1 345s openjdk-17-jre-headless python-biopython-doc 345s Suggested packages: 345s default-jre libasound2-plugins alsa-utils libcommons-io-java-doc cups-common 345s liblcms2-utils liblog4j1.2-java-doc libmail-java pcscd libnss-mdns 345s fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho 345s fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic 345s Recommended packages: 345s pigz alsa-ucm-conf alsa-topology-conf python3-biopython 345s The following NEW packages will be installed: 345s autopkgtest-satdep bbmap bbmap-jni ca-certificates-java fontconfig-config 345s fonts-dejavu-core fonts-dejavu-mono java-common libapache-pom-java 345s libasound2 libasound2-data libavahi-client3 libavahi-common-data 345s libavahi-common3 libcommons-cli-java libcommons-codec-java 345s libcommons-io-java libcommons-parent-java libcups2 libfontconfig1 345s libfreetype6 libgraphite2-3 libharfbuzz0b libjpeg-turbo8 libjpeg8 liblcms2-2 345s liblog4j1.2-java libmpj-java libpcsclite1 openjdk-17-jre-headless 345s python-biopython-doc 345s 0 upgraded, 31 newly installed, 0 to remove and 0 not upgraded. 345s Need to get 78.1 MB/78.1 MB of archives. 345s After this operation, 226 MB of additional disk space will be used. 345s Get:1 /tmp/autopkgtest.OuPt6z/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [720 B] 346s Get:2 http://ftpmaster.internal/ubuntu noble/universe s390x libcommons-cli-java all 1.6.0-1 [59.9 kB] 346s Get:3 http://ftpmaster.internal/ubuntu noble/universe s390x libapache-pom-java all 29-2 [5284 B] 346s Get:4 http://ftpmaster.internal/ubuntu noble/universe s390x libcommons-parent-java all 56-1 [10.7 kB] 346s Get:5 http://ftpmaster.internal/ubuntu noble/universe s390x libcommons-codec-java all 1.16.0-1 [306 kB] 346s Get:6 http://ftpmaster.internal/ubuntu noble/universe s390x libcommons-io-java all 2.11.0-2 [297 kB] 346s Get:7 http://ftpmaster.internal/ubuntu noble/universe s390x liblog4j1.2-java all 1.2.17-11 [439 kB] 346s Get:8 http://ftpmaster.internal/ubuntu noble/universe s390x libmpj-java all 0.44+dfsg-4 [443 kB] 346s Get:9 http://ftpmaster.internal/ubuntu noble/main s390x ca-certificates-java all 20240118 [11.6 kB] 346s Get:10 http://ftpmaster.internal/ubuntu noble/main s390x java-common all 0.75+exp1 [6798 B] 346s Get:11 http://ftpmaster.internal/ubuntu noble/main s390x libavahi-common-data s390x 0.8-13ubuntu2 [29.5 kB] 346s Get:12 http://ftpmaster.internal/ubuntu noble/main s390x libavahi-common3 s390x 0.8-13ubuntu2 [23.8 kB] 346s Get:13 http://ftpmaster.internal/ubuntu noble/main s390x libavahi-client3 s390x 0.8-13ubuntu2 [26.7 kB] 346s Get:14 http://ftpmaster.internal/ubuntu noble/main s390x libcups2 s390x 2.4.6-0ubuntu3 [277 kB] 346s Get:15 http://ftpmaster.internal/ubuntu noble/main s390x liblcms2-2 s390x 2.14-2 [155 kB] 346s Get:16 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg-turbo8 s390x 2.1.5-2ubuntu1 [128 kB] 347s Get:17 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 347s Get:18 http://ftpmaster.internal/ubuntu noble/main s390x libfreetype6 s390x 2.13.2+dfsg-1 [431 kB] 347s Get:19 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 347s Get:20 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 347s Get:21 http://ftpmaster.internal/ubuntu noble/main s390x fontconfig-config s390x 2.15.0-1ubuntu1 [37.0 kB] 347s Get:22 http://ftpmaster.internal/ubuntu noble/main s390x libfontconfig1 s390x 2.15.0-1ubuntu1 [150 kB] 347s Get:23 http://ftpmaster.internal/ubuntu noble/main s390x libasound2-data all 1.2.10-3build1 [20.7 kB] 347s Get:24 http://ftpmaster.internal/ubuntu noble/main s390x libasound2 s390x 1.2.10-3build1 [414 kB] 347s Get:25 http://ftpmaster.internal/ubuntu noble/main s390x libgraphite2-3 s390x 1.3.14-2 [90.4 kB] 347s Get:26 http://ftpmaster.internal/ubuntu noble/main s390x libharfbuzz0b s390x 8.3.0-2 [515 kB] 347s Get:27 http://ftpmaster.internal/ubuntu noble/main s390x libpcsclite1 s390x 2.0.0-1 [19.9 kB] 347s Get:28 http://ftpmaster.internal/ubuntu noble/main s390x openjdk-17-jre-headless s390x 17.0.10+7-1 [45.7 MB] 350s Get:29 http://ftpmaster.internal/ubuntu noble/universe s390x bbmap all 39.06+dfsg-1 [9768 kB] 350s Get:30 http://ftpmaster.internal/ubuntu noble/universe s390x bbmap-jni s390x 39.06+dfsg-1 [38.7 kB] 350s Get:31 http://ftpmaster.internal/ubuntu noble/universe s390x python-biopython-doc all 1.81+dfsg-3 [17.3 MB] 351s Fetched 78.1 MB in 5s (15.5 MB/s) 351s Selecting previously unselected package libcommons-cli-java. 351s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 51740 files and directories currently installed.) 351s Preparing to unpack .../00-libcommons-cli-java_1.6.0-1_all.deb ... 351s Unpacking libcommons-cli-java (1.6.0-1) ... 351s Selecting previously unselected package libapache-pom-java. 351s Preparing to unpack .../01-libapache-pom-java_29-2_all.deb ... 351s Unpacking libapache-pom-java (29-2) ... 351s Selecting previously unselected package libcommons-parent-java. 351s Preparing to unpack .../02-libcommons-parent-java_56-1_all.deb ... 351s Unpacking libcommons-parent-java (56-1) ... 351s Selecting previously unselected package libcommons-codec-java. 351s Preparing to unpack .../03-libcommons-codec-java_1.16.0-1_all.deb ... 351s Unpacking libcommons-codec-java (1.16.0-1) ... 351s Selecting previously unselected package libcommons-io-java. 351s Preparing to unpack .../04-libcommons-io-java_2.11.0-2_all.deb ... 351s Unpacking libcommons-io-java (2.11.0-2) ... 351s Selecting previously unselected package liblog4j1.2-java. 351s Preparing to unpack .../05-liblog4j1.2-java_1.2.17-11_all.deb ... 351s Unpacking liblog4j1.2-java (1.2.17-11) ... 351s Selecting previously unselected package libmpj-java. 351s Preparing to unpack .../06-libmpj-java_0.44+dfsg-4_all.deb ... 351s Unpacking libmpj-java (0.44+dfsg-4) ... 351s Selecting previously unselected package ca-certificates-java. 351s Preparing to unpack .../07-ca-certificates-java_20240118_all.deb ... 351s Unpacking ca-certificates-java (20240118) ... 351s Selecting previously unselected package java-common. 351s Preparing to unpack .../08-java-common_0.75+exp1_all.deb ... 351s Unpacking java-common (0.75+exp1) ... 351s Selecting previously unselected package libavahi-common-data:s390x. 351s Preparing to unpack .../09-libavahi-common-data_0.8-13ubuntu2_s390x.deb ... 351s Unpacking libavahi-common-data:s390x (0.8-13ubuntu2) ... 351s Selecting previously unselected package libavahi-common3:s390x. 351s Preparing to unpack .../10-libavahi-common3_0.8-13ubuntu2_s390x.deb ... 351s Unpacking libavahi-common3:s390x (0.8-13ubuntu2) ... 351s Selecting previously unselected package libavahi-client3:s390x. 351s Preparing to unpack .../11-libavahi-client3_0.8-13ubuntu2_s390x.deb ... 351s Unpacking libavahi-client3:s390x (0.8-13ubuntu2) ... 351s Selecting previously unselected package libcups2:s390x. 351s Preparing to unpack .../12-libcups2_2.4.6-0ubuntu3_s390x.deb ... 351s Unpacking libcups2:s390x (2.4.6-0ubuntu3) ... 351s Selecting previously unselected package liblcms2-2:s390x. 351s Preparing to unpack .../13-liblcms2-2_2.14-2_s390x.deb ... 351s Unpacking liblcms2-2:s390x (2.14-2) ... 351s Selecting previously unselected package libjpeg-turbo8:s390x. 351s Preparing to unpack .../14-libjpeg-turbo8_2.1.5-2ubuntu1_s390x.deb ... 351s Unpacking libjpeg-turbo8:s390x (2.1.5-2ubuntu1) ... 351s Selecting previously unselected package libjpeg8:s390x. 351s Preparing to unpack .../15-libjpeg8_8c-2ubuntu11_s390x.deb ... 351s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 351s Selecting previously unselected package libfreetype6:s390x. 351s Preparing to unpack .../16-libfreetype6_2.13.2+dfsg-1_s390x.deb ... 351s Unpacking libfreetype6:s390x (2.13.2+dfsg-1) ... 351s Selecting previously unselected package fonts-dejavu-mono. 351s Preparing to unpack .../17-fonts-dejavu-mono_2.37-8_all.deb ... 351s Unpacking fonts-dejavu-mono (2.37-8) ... 351s Selecting previously unselected package fonts-dejavu-core. 351s Preparing to unpack .../18-fonts-dejavu-core_2.37-8_all.deb ... 351s Unpacking fonts-dejavu-core (2.37-8) ... 352s Selecting previously unselected package fontconfig-config. 352s Preparing to unpack .../19-fontconfig-config_2.15.0-1ubuntu1_s390x.deb ... 352s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 352s Selecting previously unselected package libfontconfig1:s390x. 352s Preparing to unpack .../20-libfontconfig1_2.15.0-1ubuntu1_s390x.deb ... 352s Unpacking libfontconfig1:s390x (2.15.0-1ubuntu1) ... 352s Selecting previously unselected package libasound2-data. 352s Preparing to unpack .../21-libasound2-data_1.2.10-3build1_all.deb ... 352s Unpacking libasound2-data (1.2.10-3build1) ... 352s Selecting previously unselected package libasound2:s390x. 352s Preparing to unpack .../22-libasound2_1.2.10-3build1_s390x.deb ... 352s Unpacking libasound2:s390x (1.2.10-3build1) ... 352s Selecting previously unselected package libgraphite2-3:s390x. 352s Preparing to unpack .../23-libgraphite2-3_1.3.14-2_s390x.deb ... 352s Unpacking libgraphite2-3:s390x (1.3.14-2) ... 352s Selecting previously unselected package libharfbuzz0b:s390x. 352s Preparing to unpack .../24-libharfbuzz0b_8.3.0-2_s390x.deb ... 352s Unpacking libharfbuzz0b:s390x (8.3.0-2) ... 352s Selecting previously unselected package libpcsclite1:s390x. 352s Preparing to unpack .../25-libpcsclite1_2.0.0-1_s390x.deb ... 352s Unpacking libpcsclite1:s390x (2.0.0-1) ... 352s Selecting previously unselected package openjdk-17-jre-headless:s390x. 352s Preparing to unpack .../26-openjdk-17-jre-headless_17.0.10+7-1_s390x.deb ... 352s Unpacking openjdk-17-jre-headless:s390x (17.0.10+7-1) ... 353s Selecting previously unselected package bbmap. 353s Preparing to unpack .../27-bbmap_39.06+dfsg-1_all.deb ... 353s Unpacking bbmap (39.06+dfsg-1) ... 353s Selecting previously unselected package bbmap-jni. 353s Preparing to unpack .../28-bbmap-jni_39.06+dfsg-1_s390x.deb ... 353s Unpacking bbmap-jni (39.06+dfsg-1) ... 353s Selecting previously unselected package python-biopython-doc. 353s Preparing to unpack .../29-python-biopython-doc_1.81+dfsg-3_all.deb ... 353s Unpacking python-biopython-doc (1.81+dfsg-3) ... 354s Selecting previously unselected package autopkgtest-satdep. 354s Preparing to unpack .../30-1-autopkgtest-satdep.deb ... 354s Unpacking autopkgtest-satdep (0) ... 354s Setting up libgraphite2-3:s390x (1.3.14-2) ... 354s Setting up liblcms2-2:s390x (2.14-2) ... 354s Setting up java-common (0.75+exp1) ... 354s Setting up libcommons-cli-java (1.6.0-1) ... 354s Setting up liblog4j1.2-java (1.2.17-11) ... 354s Setting up libasound2-data (1.2.10-3build1) ... 354s Setting up libfreetype6:s390x (2.13.2+dfsg-1) ... 354s Setting up libapache-pom-java (29-2) ... 354s Setting up libavahi-common-data:s390x (0.8-13ubuntu2) ... 354s Setting up fonts-dejavu-mono (2.37-8) ... 354s Setting up fonts-dejavu-core (2.37-8) ... 354s Setting up libpcsclite1:s390x (2.0.0-1) ... 354s Setting up libjpeg-turbo8:s390x (2.1.5-2ubuntu1) ... 354s Setting up python-biopython-doc (1.81+dfsg-3) ... 354s Setting up libasound2:s390x (1.2.10-3build1) ... 354s Setting up libharfbuzz0b:s390x (8.3.0-2) ... 354s Setting up bbmap-jni (39.06+dfsg-1) ... 354s Setting up ca-certificates-java (20240118) ... 354s No JRE found. Skipping Java certificates setup. 354s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 354s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 354s Setting up libcommons-parent-java (56-1) ... 354s Setting up libavahi-common3:s390x (0.8-13ubuntu2) ... 354s Setting up libfontconfig1:s390x (2.15.0-1ubuntu1) ... 354s Setting up libcommons-codec-java (1.16.0-1) ... 354s Setting up libavahi-client3:s390x (0.8-13ubuntu2) ... 354s Setting up libcommons-io-java (2.11.0-2) ... 354s Setting up libmpj-java (0.44+dfsg-4) ... 354s Setting up libcups2:s390x (2.4.6-0ubuntu3) ... 354s Setting up openjdk-17-jre-headless:s390x (17.0.10+7-1) ... 354s update-alternatives: using /usr/lib/jvm/java-17-openjdk-s390x/bin/java to provide /usr/bin/java (java) in auto mode 354s update-alternatives: using /usr/lib/jvm/java-17-openjdk-s390x/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 354s update-alternatives: using /usr/lib/jvm/java-17-openjdk-s390x/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 354s update-alternatives: using /usr/lib/jvm/java-17-openjdk-s390x/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 354s update-alternatives: using /usr/lib/jvm/java-17-openjdk-s390x/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 354s Processing triggers for libc-bin (2.39-0ubuntu6) ... 354s Processing triggers for man-db (2.12.0-3) ... 355s Processing triggers for ca-certificates-java (20240118) ... 355s Adding debian:ACCVRAIZ1.pem 355s Adding debian:AC_RAIZ_FNMT-RCM.pem 355s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 355s Adding debian:ANF_Secure_Server_Root_CA.pem 355s Adding debian:Actalis_Authentication_Root_CA.pem 355s Adding debian:AffirmTrust_Commercial.pem 355s Adding debian:AffirmTrust_Networking.pem 355s Adding debian:AffirmTrust_Premium.pem 355s Adding debian:AffirmTrust_Premium_ECC.pem 355s Adding debian:Amazon_Root_CA_1.pem 355s Adding debian:Amazon_Root_CA_2.pem 355s Adding debian:Amazon_Root_CA_3.pem 355s Adding debian:Amazon_Root_CA_4.pem 355s Adding debian:Atos_TrustedRoot_2011.pem 355s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 355s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 355s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 355s Adding debian:BJCA_Global_Root_CA1.pem 355s Adding debian:BJCA_Global_Root_CA2.pem 355s Adding debian:Baltimore_CyberTrust_Root.pem 355s Adding debian:Buypass_Class_2_Root_CA.pem 355s Adding debian:Buypass_Class_3_Root_CA.pem 355s Adding debian:CA_Disig_Root_R2.pem 355s Adding debian:CFCA_EV_ROOT.pem 355s Adding debian:COMODO_Certification_Authority.pem 355s Adding debian:COMODO_ECC_Certification_Authority.pem 355s Adding debian:COMODO_RSA_Certification_Authority.pem 355s Adding debian:Certainly_Root_E1.pem 355s Adding debian:Certainly_Root_R1.pem 355s Adding debian:Certigna.pem 355s Adding debian:Certigna_Root_CA.pem 355s Adding debian:Certum_EC-384_CA.pem 355s Adding debian:Certum_Trusted_Network_CA.pem 355s Adding debian:Certum_Trusted_Network_CA_2.pem 355s Adding debian:Certum_Trusted_Root_CA.pem 355s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 355s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 355s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 355s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 355s Adding debian:Comodo_AAA_Services_root.pem 355s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 355s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 355s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 355s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 355s Adding debian:DigiCert_Assured_ID_Root_CA.pem 355s Adding debian:DigiCert_Assured_ID_Root_G2.pem 355s Adding debian:DigiCert_Assured_ID_Root_G3.pem 355s Adding debian:DigiCert_Global_Root_CA.pem 355s Adding debian:DigiCert_Global_Root_G2.pem 355s Adding debian:DigiCert_Global_Root_G3.pem 355s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 355s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 355s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 355s Adding debian:DigiCert_Trusted_Root_G4.pem 355s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 355s Adding debian:Entrust_Root_Certification_Authority.pem 355s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 355s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 355s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem 355s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 355s Adding debian:GLOBALTRUST_2020.pem 355s Adding debian:GTS_Root_R1.pem 355s Adding debian:GTS_Root_R2.pem 355s Adding debian:GTS_Root_R3.pem 355s Adding debian:GTS_Root_R4.pem 355s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 355s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 355s Adding debian:GlobalSign_Root_CA.pem 355s Adding debian:GlobalSign_Root_CA_-_R3.pem 355s Adding debian:GlobalSign_Root_CA_-_R6.pem 355s Adding debian:GlobalSign_Root_E46.pem 355s Adding debian:GlobalSign_Root_R46.pem 355s Adding debian:Go_Daddy_Class_2_CA.pem 355s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 355s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 355s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 355s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 355s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 355s Adding debian:HiPKI_Root_CA_-_G1.pem 355s Adding debian:Hongkong_Post_Root_CA_3.pem 355s Adding debian:ISRG_Root_X1.pem 355s Adding debian:ISRG_Root_X2.pem 355s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 355s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 355s Adding debian:Izenpe.com.pem 355s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 355s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 355s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 355s Adding debian:NAVER_Global_Root_Certification_Authority.pem 355s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 355s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 355s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 355s Adding debian:QuoVadis_Root_CA_1_G3.pem 355s Adding debian:QuoVadis_Root_CA_2.pem 355s Adding debian:QuoVadis_Root_CA_2_G3.pem 355s Adding debian:QuoVadis_Root_CA_3.pem 355s Adding debian:QuoVadis_Root_CA_3_G3.pem 355s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 355s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 355s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 355s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 355s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 355s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 355s Adding debian:SZAFIR_ROOT_CA2.pem 355s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 355s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 355s Adding debian:SecureSign_RootCA11.pem 355s Adding debian:SecureTrust_CA.pem 355s Adding debian:Secure_Global_CA.pem 355s Adding debian:Security_Communication_ECC_RootCA1.pem 355s Adding debian:Security_Communication_RootCA2.pem 355s Adding debian:Security_Communication_RootCA3.pem 355s Adding debian:Security_Communication_Root_CA.pem 355s Adding debian:Starfield_Class_2_CA.pem 355s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 355s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 355s Adding debian:SwissSign_Gold_CA_-_G2.pem 355s Adding debian:SwissSign_Silver_CA_-_G2.pem 355s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 355s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 355s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 355s Adding debian:TWCA_Global_Root_CA.pem 355s Adding debian:TWCA_Root_Certification_Authority.pem 355s Adding debian:TeliaSonera_Root_CA_v1.pem 355s Adding debian:Telia_Root_CA_v2.pem 355s Adding debian:TrustAsia_Global_Root_CA_G3.pem 355s Adding debian:TrustAsia_Global_Root_CA_G4.pem 355s Adding debian:Trustwave_Global_Certification_Authority.pem 355s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 355s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 355s Adding debian:TunTrust_Root_CA.pem 355s Adding debian:UCA_Extended_Validation_Root.pem 355s Adding debian:UCA_Global_G2_Root.pem 355s Adding debian:USERTrust_ECC_Certification_Authority.pem 355s Adding debian:USERTrust_RSA_Certification_Authority.pem 355s Adding debian:XRamp_Global_CA_Root.pem 355s Adding debian:certSIGN_ROOT_CA.pem 355s Adding debian:certSIGN_Root_CA_G2.pem 355s Adding debian:e-Szigno_Root_CA_2017.pem 355s Adding debian:ePKI_Root_Certification_Authority.pem 355s Adding debian:emSign_ECC_Root_CA_-_C3.pem 355s Adding debian:emSign_ECC_Root_CA_-_G3.pem 355s Adding debian:emSign_Root_CA_-_C1.pem 355s Adding debian:emSign_Root_CA_-_G1.pem 355s Adding debian:vTrus_ECC_Root_CA.pem 355s Adding debian:vTrus_Root_CA.pem 355s done. 355s Setting up bbmap (39.06+dfsg-1) ... 355s Setting up autopkgtest-satdep (0) ... 359s (Reading database ... 54582 files and directories currently installed.) 359s Removing autopkgtest-satdep (0) ... 359s autopkgtest [14:55:37]: test run-unit-test: [----------------------- 360s 360s # bbmap 360s bbmap.sh --version 360s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 360s java -ea -Xmx2845m -Xms2845m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 --version 360s BBMap version 39.06 360s For help, please run the shellscript with no parameters, or look in /docs/. 360s bbmap.sh --help 360s 360s BBMap 360s Written by Brian Bushnell, from Dec. 2010 - present 360s Last modified September 15, 2022 360s 360s Description: Fast and accurate splice-aware read aligner. 360s Please read bbmap/docs/guides/BBMapGuide.txt for more information. 360s 360s To index: bbmap.sh ref= 360s To map: bbmap.sh in= out= 360s To map without writing an index: 360s bbmap.sh ref= in= out= nodisk 360s 360s in=stdin will accept reads from standard in, and out=stdout will write to 360s standard out, but file extensions are still needed to specify the format of the 360s input and output files e.g. in=stdin.fa.gz will read gzipped fasta from 360s standard in; out=stdout.sam.gz will write gzipped sam. 360s 360s Indexing Parameters (required when building the index): 360s nodisk=f Set to true to build index in memory and write nothing 360s to disk except output. 360s ref= Specify the reference sequence. Only do this ONCE, 360s when building the index (unless using 'nodisk'). 360s build=1 If multiple references are indexed in the same directory, 360s each needs a unique numeric ID (unless using 'nodisk'). 360s k=13 Kmer length, range 8-15. Longer is faster but uses 360s more memory. Shorter is more sensitive. 360s If indexing and mapping are done in two steps, K should 360s be specified each time. 360s path=<.> Specify the location to write the index, if you don't 360s want it in the current working directory. 360s usemodulo=f Throw away ~80% of kmers based on remainder modulo a 360s number (reduces RAM by 50% and sensitivity slightly). 360s Should be enabled both when building the index AND 360s when mapping. 360s rebuild=f Force a rebuild of the index (ref= should be set). 360s 360s Input Parameters: 360s build=1 Designate index to use. Corresponds to the number 360s specified when building the index. 360s in= Primary reads input; required parameter. 360s in2= For paired reads in two files. 360s interleaved=auto True forces paired/interleaved input; false forces 360s single-ended mapping. If not specified, interleaved 360s status will be autodetected from read names. 360s fastareadlen=500 Break up FASTA reads longer than this. Max is 500 for 360s BBMap and 6000 for BBMapPacBio. Only works for FASTA 360s input (use 'maxlen' for FASTQ input). The default for 360s bbmap.sh is 500, and for mapPacBio.sh is 6000. 360s unpigz=f Spawn a pigz (parallel gzip) process for faster 360s decompression than using Java. 360s Requires pigz to be installed. 360s touppercase=t (tuc) Convert lowercase letters in reads to upper case 360s (otherwise they will not match the reference). 360s 360s Sampling Parameters: 360s 360s reads=-1 Set to a positive number N to only process the first N 360s reads (or pairs), then quit. -1 means use all reads. 360s samplerate=1 Set to a number from 0 to 1 to randomly select that 360s fraction of reads for mapping. 1 uses all reads. 360s skipreads=0 Set to a number N to skip the first N reads (or pairs), 360s then map the rest. 360s 360s Mapping Parameters: 360s fast=f This flag is a macro which sets other paramters to run 360s faster, at reduced sensitivity. Bad for RNA-seq. 360s slow=f This flag is a macro which sets other paramters to run 360s slower, at greater sensitivity. 'vslow' is even slower. 360s maxindel=16000 Don't look for indels longer than this. Lower is faster. 360s Set to >=100k for RNAseq with long introns like mammals. 360s strictmaxindel=f When enabled, do not allow indels longer than 'maxindel'. 360s By default these are not sought, but may be found anyway. 360s tipsearch=100 Look this far for read-end deletions with anchors 360s shorter than K, using brute force. 360s minid=0.76 Approximate minimum alignment identity to look for. 360s Higher is faster and less sensitive. 360s minhits=1 Minimum number of seed hits required for candidate sites. 360s Higher is faster. 360s local=f Set to true to use local, rather than global, alignments. 360s This will soft-clip ugly ends of poor alignments. 360s perfectmode=f Allow only perfect mappings when set to true (very fast). 360s semiperfectmode=f Allow only perfect and semiperfect (perfect except for 360s N's in the reference) mappings. 360s threads=auto (t) Set to number of threads desired. By default, uses 360s all cores available. 360s ambiguous=best (ambig) Set behavior on ambiguously-mapped reads (with 360s multiple top-scoring mapping locations). 360s best (use the first best site) 360s toss (consider unmapped) 360s random (select one top-scoring site randomly) 360s all (retain all top-scoring sites) 360s samestrandpairs=f (ssp) Specify whether paired reads should map to the 360s same strand or opposite strands. 360s requirecorrectstrand=t (rcs) Forbid pairing of reads without correct strand 360s orientation. Set to false for long-mate-pair libraries. 360s killbadpairs=f (kbp) If a read pair is mapped with an inappropriate 360s insert size or orientation, the read with the lower 360s mapping quality is marked unmapped. 360s pairedonly=f (po) Treat unpaired reads as unmapped. Thus they will 360s be sent to 'outu' but not 'outm'. 360s rcomp=f Reverse complement both reads prior to mapping (for LMP 360s outward-facing libraries). 360s rcompmate=f Reverse complement read2 prior to mapping. 360s pairlen=32000 Set max allowed distance between paired reads. 360s (insert size)=(pairlen)+(read1 length)+(read2 length) 360s rescuedist=1200 Don't try to rescue paired reads if avg. insert size 360s greater than this. Lower is faster. 360s rescuemismatches=32 Maximum mismatches allowed in a rescued read. Lower 360s is faster. 360s averagepairdist=100 (apd) Initial average distance between paired reads. 360s Varies dynamically; does not need to be specified. 360s deterministic=f Run in deterministic mode. In this case it is good 360s to set averagepairdist. BBMap is deterministic 360s without this flag if using single-ended reads, 360s or run singlethreaded. 360s bandwidthratio=0 (bwr) If above zero, restrict alignment band to this 360s fraction of read length. Faster but less accurate. 360s bandwidth=0 (bw) Set the bandwidth directly. 360s fraction of read length. Faster but less accurate. 360s usejni=f (jni) Do alignments faster, in C code. Requires 360s compiling the C code; details are in /jni/README.txt. 360s maxsites2=800 Don't analyze (or print) more than this many alignments 360s per read. 360s ignorefrequentkmers=t (ifk) Discard low-information kmers that occur often. 360s excludefraction=0.03 (ef) Fraction of kmers to ignore. For example, 0.03 360s will ignore the most common 3% of kmers. 360s greedy=t Use a greedy algorithm to discard the least-useful 360s kmers on a per-read basis. 360s kfilter=0 If positive, potential mapping sites must have at 360s least this many consecutive exact matches. 360s 360s 360s Quality and Trimming Parameters: 360s qin=auto Set to 33 or 64 to specify input quality value ASCII 360s offset. 33 is Sanger, 64 is old Solexa. 360s qout=auto Set to 33 or 64 to specify output quality value ASCII 360s offset (only if output format is fastq). 360s qtrim=f Quality-trim ends before mapping. Options are: 360s 'f' (false), 'l' (left), 'r' (right), and 'lr' (both). 360s untrim=f Undo trimming after mapping. Untrimmed bases will be 360s soft-clipped in cigar strings. 360s trimq=6 Trim regions with average quality below this 360s (phred algorithm). 360s mintrimlength=60 (mintl) Don't trim reads to be shorter than this. 360s fakefastaquality=-1 (ffq) Set to a positive number 1-50 to generate fake 360s quality strings for fasta input reads. 360s ignorebadquality=f (ibq) Keep going, rather than crashing, if a read has 360s out-of-range quality values. 360s usequality=t Use quality scores when determining which read kmers 360s to use as seeds. 360s minaveragequality=0 (maq) Do not map reads with average quality below this. 360s maqb=0 If positive, calculate maq from this many initial bases. 360s 360s Output Parameters: 360s out= Write all reads to this file. 360s outu= Write only unmapped reads to this file. Does not 360s include unmapped paired reads with a mapped mate. 360s outm= Write only mapped reads to this file. Includes 360s unmapped paired reads with a mapped mate. 360s mappedonly=f If true, treats 'out' like 'outm'. 360s bamscript= (bs) Write a shell script to that will turn 360s the sam output into a sorted, indexed bam file. 360s ordered=f Set to true to output reads in same order as input. 360s Slower and uses more memory. 360s overwrite=f (ow) Allow process to overwrite existing files. 360s secondary=f Print secondary alignments. 360s sssr=0.95 (secondarysitescoreratio) Print only secondary alignments 360s with score of at least this fraction of primary. 360s ssao=f (secondarysiteasambiguousonly) Only print secondary 360s alignments for ambiguously-mapped reads. 360s maxsites=5 Maximum number of total alignments to print per read. 360s Only relevant when secondary=t. 360s quickmatch=f Generate cigar strings more quickly. 360s trimreaddescriptions=f (trd) Truncate read and ref names at the first whitespace, 360s assuming that the remainder is a comment or description. 360s ziplevel=2 (zl) Compression level for zip or gzip output. 360s pigz=f Spawn a pigz (parallel gzip) process for faster 360s compression than Java. Requires pigz to be installed. 360s machineout=f Set to true to output statistics in machine-friendly 360s 'key=value' format. 360s printunmappedcount=f Print the total number of unmapped reads and bases. 360s If input is paired, the number will be of pairs 360s for which both reads are unmapped. 360s showprogress=0 If positive, print a '.' every X reads. 360s showprogress2=0 If positive, print the number of seconds since the 360s last progress update (instead of a '.'). 360s renamebyinsert=f Renames reads based on their mapped insert size. 360s 360s Bloom-Filtering Parameters (bloomfilter.sh is the standalone version). 360s bloom=f Use a Bloom filter to ignore reads not sharing kmers 360s with the reference. This uses more memory, but speeds 360s mapping when most reads don't match the reference. 360s bloomhashes=2 Number of hash functions. 360s bloomminhits=3 Number of consecutive hits to be considered matched. 360s bloomk=31 Bloom filter kmer length. 360s bloomserial=t Use the serialized Bloom filter for greater loading 360s speed, if available. If not, generate and write one. 360s 360s Post-Filtering Parameters: 360s idfilter=0 Independant of minid; sets exact minimum identity 360s allowed for alignments to be printed. Range 0 to 1. 360s subfilter=-1 Ban alignments with more than this many substitutions. 360s insfilter=-1 Ban alignments with more than this many insertions. 360s delfilter=-1 Ban alignments with more than this many deletions. 360s indelfilter=-1 Ban alignments with more than this many indels. 360s editfilter=-1 Ban alignments with more than this many edits. 360s inslenfilter=-1 Ban alignments with an insertion longer than this. 360s dellenfilter=-1 Ban alignments with a deletion longer than this. 360s nfilter=-1 Ban alignments with more than this many ns. This 360s includes nocall, noref, and off scaffold ends. 360s 360s Sam flags and settings: 360s noheader=f Disable generation of header lines. 360s sam=1.4 Set to 1.4 to write Sam version 1.4 cigar strings, 360s with = and X, or 1.3 to use M. 360s saa=t (secondaryalignmentasterisks) Use asterisks instead of 360s bases for sam secondary alignments. 360s cigar=t Set to 'f' to skip generation of cigar strings (faster). 360s keepnames=f Keep original names of paired reads, rather than 360s ensuring both reads have the same name. 360s intronlen=999999999 Set to a lower number like 10 to change 'D' to 'N' in 360s cigar strings for deletions of at least that length. 360s rgid= Set readgroup ID. All other readgroup fields 360s can be set similarly, with the flag rgXX= 360s If you set a readgroup flag to the word 'filename', 360s e.g. rgid=filename, the input file name will be used. 360s mdtag=f Write MD tags. 360s nhtag=f Write NH tags. 360s xmtag=f Write XM tags (may only work correctly with ambig=all). 360s amtag=f Write AM tags. 360s nmtag=f Write NM tags. 360s xstag=f Set to 'xs=fs', 'xs=ss', or 'xs=us' to write XS tags 360s for RNAseq using firststrand, secondstrand, or 360s unstranded libraries. Needed by Cufflinks. 360s JGI mainly uses 'firststrand'. 360s stoptag=f Write a tag indicating read stop location, prefixed by YS:i: 360s lengthtag=f Write a tag indicating (query,ref) alignment lengths, 360s prefixed by YL:Z: 360s idtag=f Write a tag indicating percent identity, prefixed by YI:f: 360s inserttag=f Write a tag indicating insert size, prefixed by X8:Z: 360s scoretag=f Write a tag indicating BBMap's raw score, prefixed by YR:i: 360s timetag=f Write a tag indicating this read's mapping time, prefixed by X0:i: 360s boundstag=f Write a tag indicating whether either read in the pair 360s goes off the end of the reference, prefixed by XB:Z: 360s notags=f Turn off all optional tags. 360s 360s Histogram and statistics output parameters: 360s scafstats= Statistics on how many reads mapped to which scaffold. 360s refstats= Statistics on how many reads mapped to which reference 360s file; only for BBSplit. 360s sortscafs=t Sort scaffolds or references by read count. 360s bhist= Base composition histogram by position. 360s qhist= Quality histogram by position. 360s aqhist= Histogram of average read quality. 360s bqhist= Quality histogram designed for box plots. 360s lhist= Read length histogram. 360s ihist= Write histogram of insert sizes (for paired reads). 360s ehist= Errors-per-read histogram. 360s qahist= Quality accuracy histogram of error rates versus 360s quality score. 360s indelhist= Indel length histogram. 360s mhist= Histogram of match, sub, del, and ins rates by 360s read location. 360s gchist= Read GC content histogram. 360s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 360s gcpairs=t Use average GC of paired reads. 360s idhist= Histogram of read count versus percent identity. 360s idbins=100 Number idhist bins. Set to 'auto' to use read length. 360s statsfile=stderr Mapping statistics are printed here. 360s 360s Coverage output parameters (these may reduce speed and use more RAM): 360s covstats= Per-scaffold coverage info. 360s rpkm= Per-scaffold RPKM/FPKM counts. 360s covhist= Histogram of # occurrences of each depth level. 360s basecov= Coverage per base location. 360s bincov= Print binned coverage per location (one line per X bases). 360s covbinsize=1000 Set the binsize for binned coverage output. 360s nzo=t Only print scaffolds with nonzero coverage. 360s twocolumn=f Change to true to print only ID and Avg_fold instead of 360s all 6 columns to the 'out=' file. 360s 32bit=f Set to true if you need per-base coverage over 64k. 360s strandedcov=f Track coverage for plus and minus strand independently. 360s startcov=f Only track start positions of reads. 360s secondarycov=t Include coverage of secondary alignments. 360s physcov=f Calculate physical coverage for paired reads. 360s This includes the unsequenced bases. 360s delcoverage=t (delcov) Count bases covered by deletions as covered. 360s True is faster than false. 360s covk=0 If positive, calculate kmer coverage statistics. 360s 360s Java Parameters: 360s -Xmx This will set Java's memory usage, 360s overriding autodetection. 360s -Xmx20g will specify 20 gigs of RAM, and -Xmx800m 360s will specify 800 megs. The max is typically 85% of 360s physical memory. The human genome requires around 24g, 360s or 12g with the 'usemodulo' flag. The index uses 360s roughly 6 bytes per reference base. 360s -eoom This flag will cause the process to exit if an 360s out-of-memory exception occurs. Requires Java 8u92+. 360s -da Disable assertions. 360s 360s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter 360s any problems, or post at: http://seqanswers.com/forums/showthread.php?t=41057 360s 360s bbmap.sh ref=example.fasta 360s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 360s java -ea -Xmx2845m -Xms2845m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta 360s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta] 360s Version 39.06 360s 360s No output file. 360s Writing reference. 360s 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] 360s 360s Set genScaffoldInfo=true 360s Writing chunk 1 360s Set genome to 1 360s 360s Loaded Reference: 0.008 seconds. 360s Loading index for chunk 1-1, build 1 360s No index available; generating from reference genome: /tmp/autopkgtest.OuPt6z/autopkgtest_tmp/ref/index/1/chr1_index_k13_c16_b1.block 361s Indexing threads started for block 0-1 361s Indexing threads finished for block 0-1 362s Generated Index: 1.746 seconds. 362s No reads to process; quitting. 362s 362s Total time: 1.947 seconds. 362s test -d ref 362s bbmap.sh in=misc_dna_as_sanger.fastq out=out.sam 362s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 362s java -ea -Xmx2845m -Xms2845m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 in=misc_dna_as_sanger.fastq out=out.sam 362s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, in=misc_dna_as_sanger.fastq, out=out.sam] 362s Version 39.06 362s 362s Retaining first best site only for ambiguous mappings. 362s Set genome to 1 362s 362s Loaded Reference: 0.019 seconds. 362s Loading index for chunk 1-1, build 1 363s Generated Index: 0.830 seconds. 371s Analyzed Index: 8.076 seconds. 371s Started output stream: 0.033 seconds. 371s Cleared Memory: 0.133 seconds. 372s Processing reads in single-ended mode. 372s Started read stream. 372s Started 4 mapping threads. 372s Detecting finished threads: 0, 1, 2, 3 372s 372s ------------------ Results ------------------ 372s 372s Genome: 1 372s Key Length: 13 372s Max Indel: 16000 372s Minimum Score Ratio: 0.56 372s Mapping Mode: normal 372s Reads Used: 4 (153 bases) 372s 372s Mapping: 0.164 seconds. 372s Reads/sec: 24.35 372s kBases/sec: 0.93 372s 372s 372s Read 1 data: pct reads num reads pct bases num bases 372s 372s mapped: 0.0000% 0 0.0000% 0 372s unambiguous: 0.0000% 0 0.0000% 0 372s ambiguous: 0.0000% 0 0.0000% 0 372s low-Q discards: 25.0000% 1 19.6078% 30 372s 372s perfect best site: 0.0000% 0 0.0000% 0 372s semiperfect site: 0.0000% 0 0.0000% 0 372s 372s Match Rate: NA NA NaN% 0 372s Error Rate: NaN% 0 NaN% 0 372s Sub Rate: NaN% 0 NaN% 0 372s Del Rate: NaN% 0 NaN% 0 372s Ins Rate: NaN% 0 NaN% 0 372s N Rate: NaN% 0 NaN% 0 372s 372s Total time: 9.355 seconds. 372s test -r out.sam 372s bbmap.sh ref=example.fasta in=example.fastq out=out2.sam nodisk 372s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 372s java -ea -Xmx2845m -Xms2845m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta in=example.fastq out=out2.sam nodisk 372s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta, in=example.fastq, out=out2.sam, nodisk] 372s Version 39.06 372s 372s Retaining first best site only for ambiguous mappings. 372s 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] 372s 372s Set genScaffoldInfo=true 372s Set genome to 1 372s 372s Loaded Reference: 0.002 seconds. 372s Loading index for chunk 1-1, build 1 372s Indexing threads started for block 0-1 372s Indexing threads finished for block 0-1 373s Generated Index: 0.508 seconds. 382s Analyzed Index: 9.582 seconds. 382s Started output stream: 0.026 seconds. 382s Cleared Memory: 0.133 seconds. 382s Processing reads in single-ended mode. 382s Started read stream. 382s Started 4 mapping threads. 382s Detecting finished threads: 0, 1, 2, 3 382s 382s ------------------ Results ------------------ 382s 382s Genome: 1 382s Key Length: 13 382s Max Indel: 16000 383s Minimum Score Ratio: 0.56 383s Mapping Mode: normal 383s Reads Used: 3 (75 bases) 383s 383s Mapping: 0.146 seconds. 383s Reads/sec: 20.55 383s kBases/sec: 0.51 383s 383s 383s Read 1 data: pct reads num reads pct bases num bases 383s 383s mapped: 100.0000% 3 100.0000% 75 383s unambiguous: 100.0000% 3 100.0000% 75 383s ambiguous: 0.0000% 0 0.0000% 0 383s low-Q discards: 0.0000% 0 0.0000% 0 383s 383s perfect best site: 100.0000% 3 100.0000% 75 383s semiperfect site: 100.0000% 3 100.0000% 75 383s 383s Match Rate: NA NA 100.0000% 75 383s Error Rate: 0.0000% 0 0.0000% 0 383s Sub Rate: 0.0000% 0 0.0000% 0 383s Del Rate: 0.0000% 0 0.0000% 0 383s Ins Rate: 0.0000% 0 0.0000% 0 383s N Rate: 0.0000% 0 0.0000% 0 383s 383s Total time: 10.530 seconds. 383s test -r out2.sam 383s 383s # bbduk 383s bbduk.sh --version 383s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 383s java -ea -Xmx1422m -Xms1422m -cp /usr/share/java/bbmap.jar jgi.BBDuk --version 383s BBMap version 39.06 383s For help, please run the shellscript with no parameters, or look in /docs/. 383s bbduk.sh --help 383s 383s Written by Brian Bushnell 383s Last modified November 9, 2023 383s 383s Description: Compares reads to the kmers in a reference dataset, optionally 383s allowing an edit distance. Splits the reads into two outputs - those that 383s match the reference, and those that don't. Can also trim (remove) the matching 383s parts of the reads rather than binning the reads. 383s Please read bbmap/docs/guides/BBDukGuide.txt for more information. 383s 383s Usage: bbduk.sh in= out= ref= 383s 383s Input may be stdin or a fasta or fastq file, compressed or uncompressed. 383s If you pipe via stdin/stdout, please include the file type; e.g. for gzipped 383s fasta input, set in=stdin.fa.gz 383s 383s Input parameters: 383s in= Main input. in=stdin.fq will pipe from stdin. 383s in2= Input for 2nd read of pairs in a different file. 383s ref= Comma-delimited list of reference files. 383s In addition to filenames, you may also use the keywords: 383s adapters, artifacts, phix, lambda, pjet, mtst, kapa 383s literal= Comma-delimited list of literal reference sequences. 383s touppercase=f (tuc) Change all bases upper-case. 383s interleaved=auto (int) t/f overrides interleaved autodetection. 383s Must be set mainually when streaming fastq input. 383s qin=auto Input quality offset: 33 (Sanger), 64, or auto. 383s reads=-1 If positive, quit after processing X reads or pairs. 383s copyundefined=f (cu) Process non-AGCT IUPAC reference bases by making all 383s possible unambiguous copies. Intended for short motifs 383s or adapter barcodes, as time/memory use is exponential. 383s samplerate=1 Set lower to only process a fraction of input reads. 383s samref= Optional reference fasta for processing sam files. 383s 383s Output parameters: 383s out= (outnonmatch) Write reads here that do not contain 383s kmers matching the database. 'out=stdout.fq' will pipe 383s to standard out. 383s out2= (outnonmatch2) Use this to write 2nd read of pairs to a 383s different file. 383s outm= (outmatch) Write reads here that fail filters. In default 383s kfilter mode, this means any read with a matching kmer. 383s In any mode, it also includes reads that fail filters such 383s as minlength, mingc, maxgc, entropy, etc. In other words, 383s it includes all reads that do not go to 'out'. 383s outm2= (outmatch2) Use this to write 2nd read of pairs to a 383s different file. 383s outs= (outsingle) Use this to write singleton reads whose mate 383s was trimmed shorter than minlen. 383s stats= Write statistics about which contamininants were detected. 383s refstats= Write statistics on a per-reference-file basis. 383s rpkm= Write RPKM for each reference sequence (for RNA-seq). 383s dump= Dump kmer tables to a file, in fasta format. 383s duk= Write statistics in duk's format. *DEPRECATED* 383s nzo=t Only write statistics about ref sequences with nonzero hits. 383s bbduk.sh in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq \ 383s qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 383s overwrite=t (ow) Grant permission to overwrite files. 383s showspeed=t (ss) 'f' suppresses display of processing speed. 383s ziplevel=2 (zl) Compression level; 1 (min) through 9 (max). 383s fastawrap=70 Length of lines in fasta output. 383s qout=auto Output quality offset: 33 (Sanger), 64, or auto. 383s statscolumns=3 (cols) Number of columns for stats output, 3 or 5. 383s 5 includes base counts. 383s rename=f Rename reads to indicate which sequences they matched. 383s refnames=f Use names of reference files rather than scaffold IDs. 383s trd=f Truncate read and ref names at the first whitespace. 383s ordered=f Set to true to output reads in same order as input. 383s maxbasesout=-1 If positive, quit after writing approximately this many 383s bases to out (outu/outnonmatch). 383s maxbasesoutm=-1 If positive, quit after writing approximately this many 383s bases to outm (outmatch). 383s json=f Print to screen in json format. 383s 383s Histogram output parameters: 383s bhist= Base composition histogram by position. 383s qhist= Quality histogram by position. 383s qchist= Count of bases with each quality value. 383s aqhist= Histogram of average read quality. 383s bqhist= Quality histogram designed for box plots. 383s lhist= Read length histogram. 383s phist= Polymer length histogram. 383s gchist= Read GC content histogram. 383s enthist= Read entropy histogram. 383s ihist= Insert size histogram, for paired reads in mapped sam. 383s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 383s maxhistlen=6000 Set an upper bound for histogram lengths; higher uses 383s more memory. The default is 6000 for some histograms 383s and 80000 for others. 383s 383s Histograms for mapped sam/bam files only: 383s histbefore=t Calculate histograms from reads before processing. 383s ehist= Errors-per-read histogram. 383s qahist= Quality accuracy histogram of error rates versus quality 383s score. 383s indelhist= Indel length histogram. 383s mhist= Histogram of match, sub, del, and ins rates by position. 383s idhist= Histogram of read count versus percent identity. 383s idbins=100 Number idhist bins. Set to 'auto' to use read length. 383s varfile= Ignore substitution errors listed in this file when 383s calculating error rates. Can be generated with 383s CallVariants. 383s vcf= Ignore substitution errors listed in this VCF file 383s when calculating error rates. 383s ignorevcfindels=t Also ignore indels listed in the VCF. 383s 383s Processing parameters: 383s k=27 Kmer length used for finding contaminants. Contaminants 383s shorter than k will not be found. k must be at least 1. 383s rcomp=t Look for reverse-complements of kmers in addition to 383s forward kmers. 383s maskmiddle=t (mm) Treat the middle base of a kmer as a wildcard, to 383s increase sensitivity in the presence of errors. This may 383s also be set to a number, e.g. mm=3, to mask that many bp. 383s The default mm=t corresponds to mm=1 for odd-length kmers 383s and mm=2 for even-length kmers (as of v39.04), while 383s mm=f is always equivalent to mm=0. 383s minkmerhits=1 (mkh) Reads need at least this many matching kmers 383s to be considered as matching the reference. 383s minkmerfraction=0.0 (mkf) A reads needs at least this fraction of its total 383s kmers to hit a ref, in order to be considered a match. 383s If this and minkmerhits are set, the greater is used. 383s mincovfraction=0.0 (mcf) A reads needs at least this fraction of its total 383s bases to be covered by ref kmers to be considered a match. 383s If specified, mcf overrides mkh and mkf. 383s hammingdistance=0 (hdist) Maximum Hamming distance for ref kmers (subs only). 383s Memory use is proportional to (3*K)^hdist. 383s qhdist=0 Hamming distance for query kmers; impacts speed, not memory. 383s editdistance=0 (edist) Maximum edit distance from ref kmers (subs 383s and indels). Memory use is proportional to (8*K)^edist. 383s hammingdistance2=0 (hdist2) Sets hdist for short kmers, when using mink. 383s qhdist2=0 Sets qhdist for short kmers, when using mink. 383s editdistance2=0 (edist2) Sets edist for short kmers, when using mink. 383s forbidn=f (fn) Forbids matching of read kmers containing N. 383s By default, these will match a reference 'A' if 383s hdist>0 or edist>0, to increase sensitivity. 383s removeifeitherbad=t (rieb) Paired reads get sent to 'outmatch' if either is 383s match (or either is trimmed shorter than minlen). 383s Set to false to require both. 383s trimfailures=f Instead of discarding failed reads, trim them to 1bp. 383s This makes the statistics a bit odd. 383s findbestmatch=f (fbm) If multiple matches, associate read with sequence 383s sharing most kmers. Reduces speed. 383s skipr1=f Don't do kmer-based operations on read 1. 383s skipr2=f Don't do kmer-based operations on read 2. 383s ecco=f For overlapping paired reads only. Performs error- 383s correction with BBMerge prior to kmer operations. 383s recalibrate=f (recal) Recalibrate quality scores. Requires calibration 383s matrices generated by CalcTrueQuality. 383s sam= If recalibration is desired, and matrices have not already 383s been generated, BBDuk will create them from the sam file. 383s amino=f Run in amino acid mode. Some features have not been 383s tested, but kmer-matching works fine. Maximum k is 12. 383s 383s Speed and Memory parameters: 383s threads=auto (t) Set number of threads to use; default is number of 383s logical processors. 383s prealloc=f Preallocate memory in table. Allows faster table loading 383s and more efficient memory usage, for a large reference. 383s monitor=f Kill this process if it crashes. monitor=600,0.01 would 383s kill after 600 seconds under 1% usage. 383s minrskip=1 (mns) Force minimal skip interval when indexing reference 383s kmers. 1 means use all, 2 means use every other kmer, etc. 383s maxrskip=1 (mxs) Restrict maximal skip interval when indexing 383s reference kmers. Normally all are used for scaffolds<100kb, 383s but with longer scaffolds, up to maxrskip-1 are skipped. 383s rskip= Set both minrskip and maxrskip to the same value. 383s If not set, rskip will vary based on sequence length. 383s qskip=1 Skip query kmers to increase speed. 1 means use all. 383s speed=0 Ignore this fraction of kmer space (0-15 out of 16) in both 383s reads and reference. Increases speed and reduces memory. 383s Note: Do not use more than one of 'speed', 'qskip', and 'rskip'. 383s 383s Trimming/Filtering/Masking parameters: 383s Note - if ktrim, kmask, and ksplit are unset, the default behavior is kfilter. 383s All kmer processing modes are mutually exclusive. 383s Reads only get sent to 'outm' purely based on kmer matches in kfilter mode. 383s 383s ktrim=f Trim reads to remove bases matching reference kmers, plus 383s all bases to the left or right. 383s Values: 383s f (don't trim), 383s r (trim to the right), 383s l (trim to the left) 383s ktrimtips=0 Set this to a positive number to perform ktrim on both 383s ends, examining only the outermost X bases. 383s kmask= Replace bases matching ref kmers with another symbol. 383s Allows any non-whitespace character, and processes short 383s kmers on both ends if mink is set. 'kmask=lc' will 383s convert masked bases to lowercase. 383s maskfullycovered=f (mfc) Only mask bases that are fully covered by kmers. 383s ksplit=f For single-ended reads only. Reads will be split into 383s pairs around the kmer. If the kmer is at the end of the 383s read, it will be trimmed instead. Singletons will go to 383s out, and pairs will go to outm. Do not use ksplit with 383s other operations such as quality-trimming or filtering. 383s mink=0 Look for shorter kmers at read tips down to this length, 383s when k-trimming or masking. 0 means disabled. Enabling 383s this will disable maskmiddle. 383s qtrim=f Trim read ends to remove bases with quality below trimq. 383s Performed AFTER looking for kmers. Values: 383s rl (trim both ends), 383s f (neither end), 383s r (right end only), 383s l (left end only), 383s w (sliding window). 383s trimq=6 Regions with average quality BELOW this will be trimmed, 383s if qtrim is set to something other than f. Can be a 383s floating-point number like 7.3. 383s trimclip=f Trim soft-clipped bases from sam files. 383s minlength=10 (ml) Reads shorter than this after trimming will be 383s discarded. Pairs will be discarded if both are shorter. 383s mlf=0 (minlengthfraction) Reads shorter than this fraction of 383s original length after trimming will be discarded. 383s maxlength= Reads longer than this after trimming will be discarded. 383s minavgquality=0 (maq) Reads with average quality (after trimming) below 383s this will be discarded. 383s maqb=0 If positive, calculate maq from this many initial bases. 383s minbasequality=0 (mbq) Reads with any base below this quality (after 383s trimming) will be discarded. 383s maxns=-1 If non-negative, reads with more Ns than this 383s (after trimming) will be discarded. 383s mcb=0 (minconsecutivebases) Discard reads without at least 383s this many consecutive called bases. 383s ottm=f (outputtrimmedtomatch) Output reads trimmed to shorter 383s than minlength to outm rather than discarding. 383s tp=0 (trimpad) Trim this much extra around matching kmers. 383s tbo=f (trimbyoverlap) Trim adapters based on where paired 383s reads overlap. 383s strictoverlap=t Adjust sensitivity for trimbyoverlap mode. 383s minoverlap=14 Require this many bases of overlap for detection. 383s mininsert=40 Require insert size of at least this for overlap. 383s Should be reduced to 16 for small RNA sequencing. 383s tpe=f (trimpairsevenly) When kmer right-trimming, trim both 383s reads to the minimum length of either. 383s forcetrimleft=0 (ftl) If positive, trim bases to the left of this position 383s (exclusive, 0-based). 383s forcetrimright=0 (ftr) If positive, trim bases to the right of this position 383s (exclusive, 0-based). 383s forcetrimright2=0 (ftr2) If positive, trim this many bases on the right end. 383s forcetrimmod=0 (ftm) If positive, right-trim length to be equal to zero, 383s modulo this number. 383s restrictleft=0 If positive, only look for kmer matches in the 383s leftmost X bases. 383s restrictright=0 If positive, only look for kmer matches in the 383s rightmost X bases. 383s NOTE: restrictleft and restrictright are mutually exclusive. If trimming 383s both ends is desired, use ktrimtips. 383s mingc=0 Discard reads with GC content below this. 383s maxgc=1 Discard reads with GC content above this. 383s gcpairs=t Use average GC of paired reads. 383s Also affects gchist. 383s tossjunk=f Discard reads with invalid characters as bases. 383s swift=f Trim Swift sequences: Trailing C/T/N R1, leading G/A/N R2. 383s 383s Header-parsing parameters - these require Illumina headers: 383s chastityfilter=f (cf) Discard reads with id containing ' 1:Y:' or ' 2:Y:'. 383s barcodefilter=f Remove reads with unexpected barcodes if barcodes is set, 383s or barcodes containing 'N' otherwise. A barcode must be 383s the last part of the read header. Values: 383s t: Remove reads with bad barcodes. 383s f: Ignore barcodes. 383s crash: Crash upon encountering bad barcodes. 383s barcodes= Comma-delimited list of barcodes or files of barcodes. 383s xmin=-1 If positive, discard reads with a lesser X coordinate. 383s ymin=-1 If positive, discard reads with a lesser Y coordinate. 383s xmax=-1 If positive, discard reads with a greater X coordinate. 383s ymax=-1 If positive, discard reads with a greater Y coordinate. 383s 383s Polymer trimming: 383s trimpolya=0 If greater than 0, trim poly-A or poly-T tails of 383s at least this length on either end of reads. 383s trimpolygleft=0 If greater than 0, trim poly-G prefixes of at least this 383s length on the left end of reads. Does not trim poly-C. 383s trimpolygright=0 If greater than 0, trim poly-G tails of at least this 383s length on the right end of reads. Does not trim poly-C. 383s trimpolyg=0 This sets both left and right at once. 383s filterpolyg=0 If greater than 0, remove reads with a poly-G prefix of 383s at least this length (on the left). 383s Note: there are also equivalent poly-C flags. 383s 383s Polymer tracking: 383s pratio=base,base 'pratio=G,C' will print the ratio of G to C polymers. 383s plen=20 Length of homopolymers to count. 383s 383s Entropy/Complexity parameters: 383s entropy=-1 Set between 0 and 1 to filter reads with entropy below 383s that value. Higher is more stringent. 383s entropywindow=50 Calculate entropy using a sliding window of this length. 383s entropyk=5 Calculate entropy using kmers of this length. 383s minbasefrequency=0 Discard reads with a minimum base frequency below this. 383s entropytrim=f Values: 383s f: (false) Do not entropy-trim. 383s r: (right) Trim low entropy on the right end only. 383s l: (left) Trim low entropy on the left end only. 383s rl: (both) Trim low entropy on both ends. 383s entropymask=f Values: 383s f: (filter) Discard low-entropy sequences. 383s t: (true) Mask low-entropy parts of sequences with N. 383s lc: Change low-entropy parts of sequences to lowercase. 383s entropymark=f Mark each base with its entropy value. This is on a scale 383s of 0-41 and is reported as quality scores, so the output 383s should be fastq or fasta+qual. 383s NOTE: If set, entropytrim overrides entropymask. 383s 383s Cardinality estimation: 383s cardinality=f (loglog) Count unique kmers using the LogLog algorithm. 383s cardinalityout=f (loglogout) Count unique kmers in output reads. 383s loglogk=31 Use this kmer length for counting. 383s loglogbuckets=2048 Use this many buckets for counting. 383s khist= Kmer frequency histogram; plots number of kmers versus 383s kmer depth. This is approximate. 383s khistout= Kmer frequency histogram for output reads. 383s 383s Java Parameters: 383s 383s -Xmx This will set Java's memory usage, overriding autodetection. 383s -Xmx20g will 383s specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 383s The max is typically 85% of physical memory. 383s -eoom This flag will cause the process to exit if an 383s out-of-memory exception occurs. Requires Java 8u92+. 383s -da Disable assertions. 383s 383s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 383s 383s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 383s java -ea -Xmx1422m -Xms1422m -cp /usr/share/java/bbmap.jar jgi.BBDuk in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 383s 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] 383s Version 39.06 383s 383s 0.020 seconds. 383s Initial: 383s Memory: max=1491m, total=1491m, free=1461m, used=30m 383s 383s Input is being processed as paired 383s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 383s Started output streams: 0.013 seconds. 383s Processing time: 0.003 seconds. 383s 383s Input: 8 reads 306 bases. 383s QTrimmed: 0 reads (0.00%) 0 bases (0.00%) 383s Total Removed: 8 reads (100.00%) 306 bases (100.00%) 383s Result: 0 reads (0.00%) 0 bases (0.00%) 383s 383s Time: 0.017 seconds. 383s Reads Processed: 8 0.47k reads/sec 383s Bases Processed: 306 0.02m bases/sec 383s test -r out.fastq.gz 383s 383s # bbnorm 383s bbnorm.sh --version 383s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 383s java -ea -Xmx2845m -Xms2845m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 --version 383s BBMap version 39.06 383s For help, please run the shellscript with no parameters, or look in /docs/. 383s bbnorm.sh --help 383s 383s Written by Brian Bushnell 383s Last modified October 19, 2017 383s 383s Description: Normalizes read depth based on kmer counts. 383s Can also error-correct, bin reads by kmer depth, and generate a kmer depth histogram. 383s However, Tadpole has superior error-correction to BBNorm. 383s Please read bbmap/docs/guides/BBNormGuide.txt for more information. 383s 383s Usage: bbnorm.sh in= out= outt= hist= 383s 383s Input parameters: 383s in=null Primary input. Use in2 for paired reads in a second file 383s in2=null Second input file for paired reads in two files 383s extra=null Additional files to use for input (generating hash table) but not for output 383s fastareadlen=2^31 Break up FASTA reads longer than this. Can be useful when processing scaffolded genomes 383s tablereads=-1 Use at most this many reads when building the hashtable (-1 means all) 383s kmersample=1 Process every nth kmer, and skip the rest 383s readsample=1 Process every nth read, and skip the rest 383s 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. 383s qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto. 383s 383s Output parameters: 383s out= File for normalized or corrected reads. Use out2 for paired reads in a second file 383s outt= (outtoss) File for reads that were excluded from primary output 383s reads=-1 Only process this number of reads, then quit (-1 means all) 383s sampleoutput=t Use sampling on output as well as input (not used if sample rates are 1) 383s keepall=f Set to true to keep all reads (e.g. if you just want error correction). 383s 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. 383s Default is false, to prevent confusion about how there can be 0-count kmers. 383s The reason is that based on the 'minq' and 'minprob' settings, some kmers may be excluded from the bloom filter. 383s tmpdir= This will specify a directory for temp files (only needed for multipass runs). If null, they will be written to the output directory. 383s usetempdir=t Allows enabling/disabling of temporary directory; if disabled, temp files will be written to the output directory. 383s qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input). 383s rename=f Rename reads based on their kmer depth. 383s 383s Hashing parameters: 383s k=31 Kmer length (values under 32 are most efficient, but arbitrarily high values are supported) 383s 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. 383s Large values decrease accuracy for a fixed amount of memory, so use the lowest number you can that will still capture highest-depth kmers. 383s hashes=3 Number of times each kmer is hashed and stored. Higher is slower. 383s Higher is MORE accurate if there is enough memory, and LESS accurate if there is not enough memory. 383s 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. 383s prehashes=2 Number of hashes for prefilter. 383s prefilterbits=2 (pbits) Bits per cell in prefilter. 383s prefiltersize=0.35 Fraction of memory to allocate to prefilter. 383s buildpasses=1 More passes can sometimes increase accuracy by iteratively removing low-depth kmers 383s minq=6 Ignore kmers containing bases with quality below this 383s minprob=0.5 Ignore kmers with overall probability of correctness below this 383s 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. 383s 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. 383s 383s Normalization parameters: 383s fixspikes=f (fs) Do a slower, high-precision bloom filter lookup of kmers that appear to have an abnormally high depth due to collisions. 383s target=100 (tgt) Target normalization depth. NOTE: All depth parameters control kmer depth, not read depth. 383s For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1)) 383s maxdepth=-1 (max) Reads will not be downsampled when below this depth, even if they are above the target depth. 383s mindepth=5 (min) Kmers with depth below this number will not be included when calculating the depth of a read. 383s minkmers=15 (mgkpr) Reads must have at least this many kmers over min depth to be retained. Aka 'mingoodkmersperread'. 383s 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. 383s uselowerdepth=t (uld) For pairs, use the depth of the lower read as the depth proxy. 383s deterministic=t (dr) Generate random numbers deterministically to ensure identical output between multiple runs. May decrease speed with a huge number of threads. 383s passes=2 (p) 1 pass is the basic mode. 2 passes (default) allows greater accuracy, error detection, better contol of output depth. 383s 383s Error detection parameters: 383s hdp=90.0 (highdepthpercentile) Position in sorted kmer depth array used as proxy of a read's high kmer depth. 383s ldp=25.0 (lowdepthpercentile) Position in sorted kmer depth array used as proxy of a read's low kmer depth. 383s tossbadreads=f (tbr) Throw away reads detected as containing errors. 383s requirebothbad=f (rbb) Only toss bad pairs if both reads are bad. 383s 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. 383s highthresh=12 (ht) Threshold for high kmer. A high kmer at this or above are considered non-error. 383s lowthresh=3 (lt) Threshold for low kmer. Kmers at this and below are always considered errors. 383s 383s Error correction parameters: 383s ecc=f Set to true to correct errors. NOTE: Tadpole is now preferred for ecc as it does a better job. 383s ecclimit=3 Correct up to this many errors per read. If more are detected, the read will remain unchanged. 383s errorcorrectratio=140 (ecr) Adjacent kmers with a depth ratio of at least this much between will be classified as an error. 383s echighthresh=22 (echt) Threshold for high kmer. A kmer at this or above may be considered non-error. 383s eclowthresh=2 (eclt) Threshold for low kmer. Kmers at this and below are considered errors. 383s eccmaxqual=127 Do not correct bases with quality above this value. 383s aec=f (aggressiveErrorCorrection) Sets more aggressive values of ecr=100, ecclimit=7, echt=16, eclt=3. 383s cec=f (conservativeErrorCorrection) Sets more conservative values of ecr=180, ecclimit=2, echt=30, eclt=1, sl=4, pl=4. 383s meo=f (markErrorsOnly) Marks errors by reducing quality value of suspected errors; does not correct anything. 383s mue=t (markUncorrectableErrors) Marks errors only on uncorrectable reads; requires 'ecc=t'. 383s overlap=f (ecco) Error correct by read overlap. 383s 383s Depth binning parameters: 383s lowbindepth=10 (lbd) Cutoff for low depth bin. 383s highbindepth=80 (hbd) Cutoff for high depth bin. 383s outlow= Pairs in which both reads have a median below lbd go into this file. 383s outhigh= Pairs in which both reads have a median above hbd go into this file. 383s outmid= All other pairs go into this file. 383s 383s Histogram parameters: 383s hist= Specify a file to write the input kmer depth histogram. 383s histout= Specify a file to write the output kmer depth histogram. 383s histcol=3 (histogramcolumns) Number of histogram columns, 2 or 3. 383s pzc=f (printzerocoverage) Print lines in the histogram with zero coverage. 383s histlen=1048576 Max kmer depth displayed in histogram. Also affects statistics displayed, but does not affect normalization. 383s 383s Peak calling parameters: 383s peaks= Write the peaks to this file. Default is stdout. 383s minHeight=2 (h) Ignore peaks shorter than this. 383s minVolume=5 (v) Ignore peaks with less area than this. 383s minWidth=3 (w) Ignore peaks narrower than this. 383s minPeak=2 (minp) Ignore peaks with an X-value below this. 383s maxPeak=BIG (maxp) Ignore peaks with an X-value above this. 383s maxPeakCount=8 (maxpc) Print up to this many peaks (prioritizing height). 383s 383s Java Parameters: 383s -Xmx This will set Java's memory usage, overriding autodetection. 383s -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 383s The max is typically 85% of physical memory. 383s -eoom This flag will cause the process to exit if an 383s out-of-memory exception occurs. Requires Java 8u92+. 383s -da Disable assertions. 383s 383s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 383s 383s bbnorm.sh in=sanger_full_range_original_sanger.fastq qin=33 \ 383s out=out3.fastq outt=outt.fastq hist=hist.plt 383s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 383s java -ea -Xmx2845m -Xms2845m -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 383s Executing jgi.KmerNormalize [bits=32, in=sanger_full_range_original_sanger.fastq, qin=33, out=out3.fastq, outt=outt.fastq, hist=hist.plt] 383s 383s 383s *********** Pass 1 ********** 383s 383s 383s Settings: 383s threads: 4 383s k: 31 383s deterministic: true 383s toss error reads: false 383s passes: 1 383s bits per cell: 16 383s cells: 1053.69M 383s hashes: 3 383s base min quality: 5 383s kmer min prob: 0.5 383s 383s target depth: 400 383s min depth: 3 383s max depth: 500 383s min good kmers: 15 383s depth percentile: 64.8 383s ignore dupe kmers: true 383s fix spikes: false 383s histogram length: 65536 383s print zero cov: false 383s 385s Made hash table: hashes = 3 mem = 1.96 GB cells = 1053.64M used = 0.000% 385s 385s Estimated unique kmers: 7 385s 385s Table creation time: 1.984 seconds. 385s Started output threads. 385s Started output threads. 385s Table read time: 0.005 seconds. 36.58 kb/sec 385s Total reads in: 2 0.000% Kept 385s Total bases in: 188 0.000% Kept 385s Error reads in: 2 100.000% 385s Error type 1: 2 100.000% 385s Error type 2: 0 0.000% 385s Error type 3: 0 0.000% 385s 385s Wrote histogram to hist.plt 385s Total kmers counted: 128 385s Total unique kmer count: 128 385s Includes forward kmers only. 385s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 385s The most accurate value is the greater of the two. 385s 385s Percent unique: 100.00% 385s Depth average: 1.00 (unique kmers) 385s Depth median: 1 (unique kmers) 385s Depth standard deviation: 0.00 (unique kmers) 385s Corrected depth average: 0.00 385s 385s Depth average: 1.00 (all kmers) 385s Depth median: 1 (all kmers) 385s Depth standard deviation: 0.00 (all kmers) 385s 385s Approx. read depth median: 1.47 385s 385s *********** Pass 2 ********** 385s 385s 385s Settings: 385s threads: 4 385s k: 31 385s deterministic: true 385s toss error reads: false 385s passes: 1 385s bits per cell: 16 385s cells: 1053.69M 385s hashes: 3 385s base min quality: 5 385s kmer min prob: 0.5 385s 385s target depth: 100 385s min depth: 5 385s max depth: 100 385s min good kmers: 15 385s depth percentile: 54.0 385s ignore dupe kmers: true 385s fix spikes: false 385s histogram length: 65536 385s 386s Made hash table: hashes = 3 mem = 1.96 GB cells = 1053.64M used = 0.000% 386s 386s Estimated unique kmers: 0 386s 386s Table creation time: 0.786 seconds. 386s Started output threads. 386s Started output threads. 386s Table read time: 0.002 seconds. 0.00 kb/sec 386s Total reads in: 0 NaN% Kept 386s Total bases in: 0 NaN% Kept 386s Error reads in: 0 NaN% 386s Error type 1: 0 NaN% 386s Error type 2: 0 NaN% 386s Error type 3: 0 NaN% 386s Total kmers counted: 0 386s Total unique kmer count: 0 386s Includes forward kmers only. 386s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 386s The most accurate value is the greater of the two. 386s 386s Percent unique: NaN% 386s Depth average: NaN (unique kmers) 386s Depth median: 0 (unique kmers) 386s Depth standard deviation: NaN (unique kmers) 386s Corrected depth average: NaN 386s 386s Depth average: NaN (all kmers) 386s Depth median: 0 (all kmers) 386s Depth standard deviation: 0.00 (all kmers) 386s 386s Approx. read depth median: NaN 386s 386s Removing temp files. 386s 386s Total time: 2.853 seconds. 0.07 kb/sec 387s test -r out3.fastq 387s test -r outt.fastq 387s test -r hist.plt 387s bbnorm.sh in=illumina_full_range_original_illumina.fastq qin=64 \ 387s out=out4.fastq outt=outt2.fastq hist=hist2.plt 387s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 387s java -ea -Xmx2844m -Xms2844m -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 387s Executing jgi.KmerNormalize [bits=32, in=illumina_full_range_original_illumina.fastq, qin=64, out=out4.fastq, outt=outt2.fastq, hist=hist2.plt] 387s 387s 387s *********** Pass 1 ********** 387s 387s 387s Settings: 387s threads: 4 387s k: 31 387s deterministic: true 387s toss error reads: false 387s passes: 1 387s bits per cell: 16 387s cells: 1052.92M 387s hashes: 3 387s base min quality: 5 387s kmer min prob: 0.5 387s 387s target depth: 400 387s min depth: 3 387s max depth: 500 387s min good kmers: 15 387s depth percentile: 64.8 387s ignore dupe kmers: true 387s fix spikes: false 387s histogram length: 65536 387s print zero cov: false 387s 388s Made hash table: hashes = 3 mem = 1.96 GB cells = 1052.59M used = 0.000% 388s 388s Estimated unique kmers: 7 388s 388s Table creation time: 1.327 seconds. 388s Started output threads. 388s Started output threads. 388s Table read time: 0.007 seconds. 19.23 kb/sec 388s Total reads in: 2 0.000% Kept 388s Total bases in: 126 0.000% Kept 388s Error reads in: 2 100.000% 388s Error type 1: 2 100.000% 388s Error type 2: 0 0.000% 388s Error type 3: 0 0.000% 388s 388s Wrote histogram to hist2.plt 388s Total kmers counted: 66 388s Total unique kmer count: 66 388s Includes forward kmers only. 388s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 388s The most accurate value is the greater of the two. 388s 388s Percent unique: 100.00% 388s Depth average: 1.00 (unique kmers) 388s Depth median: 1 (unique kmers) 388s Depth standard deviation: 0.00 (unique kmers) 388s Corrected depth average: 0.00 388s 388s Depth average: 1.00 (all kmers) 388s Depth median: 1 (all kmers) 388s Depth standard deviation: 0.00 (all kmers) 388s 388s Approx. read depth median: 1.91 388s 388s *********** Pass 2 ********** 388s 388s 388s Settings: 388s threads: 4 388s k: 31 388s deterministic: true 388s toss error reads: false 388s passes: 1 388s bits per cell: 16 388s cells: 1052.92M 388s hashes: 3 388s base min quality: 5 388s kmer min prob: 0.5 388s 388s target depth: 100 388s min depth: 5 388s max depth: 100 388s min good kmers: 15 388s depth percentile: 54.0 388s ignore dupe kmers: true 388s fix spikes: false 388s histogram length: 65536 388s 389s Made hash table: hashes = 3 mem = 1.96 GB cells = 1052.59M used = 0.000% 389s 389s Estimated unique kmers: 0 389s 389s Table creation time: 0.785 seconds. 389s Started output threads. 389s Started output threads. 389s Table read time: 0.001 seconds. 0.00 kb/sec 389s Total reads in: 0 NaN% Kept 389s Total bases in: 0 NaN% Kept 389s Error reads in: 0 NaN% 389s Error type 1: 0 NaN% 389s Error type 2: 0 NaN% 389s Error type 3: 0 NaN% 389s Total kmers counted: 0 389s Total unique kmer count: 0 389s Includes forward kmers only. 389s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 389s The most accurate value is the greater of the two. 389s 389s Percent unique: NaN% 389s Depth average: NaN (unique kmers) 389s Depth median: 0 (unique kmers) 389s Depth standard deviation: NaN (unique kmers) 389s Corrected depth average: NaN 389s 389s Depth average: NaN (all kmers) 389s Depth median: 0 (all kmers) 389s Depth standard deviation: 0.00 (all kmers) 389s 389s Approx. read depth median: NaN 389s 389s Removing temp files. 389s 389s Total time: 2.216 seconds. 0.06 kb/sec 389s test -r out4.fastq 389s test -r outt2.fastq 389s test -r hist2.plt 390s autopkgtest [14:56:08]: test run-unit-test: -----------------------] 390s autopkgtest [14:56:08]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 390s run-unit-test PASS 391s autopkgtest [14:56:09]: @@@@@@@@@@@@@@@@@@@@ summary 391s run-unit-test PASS 404s Creating nova instance adt-noble-s390x-bbmap-20240324-144938-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-s390x-server-20240324.img (UUID e13d5247-1289-46d4-b3a9-3aa9fa45fdc9)...