0s autopkgtest [14:48:18]: starting date and time: 2024-03-24 14:48:18+0000 0s autopkgtest [14:48:18]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [14:48:18]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.yjmje7s0/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-ppc64el-14.secgroup --name adt-noble-ppc64el-bbmap-20240324-144818-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 328s autopkgtest [14:53:46]: testbed dpkg architecture: ppc64el 328s autopkgtest [14:53:46]: testbed apt version: 2.7.12 328s autopkgtest [14:53:46]: @@@@@@@@@@@@@@@@@@@@ test bed setup 329s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 330s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 330s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 330s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [538 kB] 330s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3983 kB] 331s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [728 kB] 331s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 331s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 331s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 331s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4274 kB] 332s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 332s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [61.1 kB] 332s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 335s Fetched 9778 kB in 4s (2667 kB/s) 335s Reading package lists... 338s Reading package lists... 338s Building dependency tree... 338s Reading state information... 339s Calculating upgrade... 339s The following packages will be REMOVED: 339s libglib2.0-0 339s The following NEW packages will be installed: 339s libglib2.0-0t64 xdg-user-dirs 339s The following packages will be upgraded: 339s gir1.2-glib-2.0 libglib2.0-data 339s 2 upgraded, 2 newly installed, 1 to remove and 0 not upgraded. 339s Need to get 2022 kB of archives. 339s After this operation, 204 kB of additional disk space will be used. 339s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gir1.2-glib-2.0 ppc64el 2.79.3-3ubuntu5 [182 kB] 339s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libglib2.0-0t64 ppc64el 2.79.3-3ubuntu5 [1773 kB] 340s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 340s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el xdg-user-dirs ppc64el 0.18-1 [20.0 kB] 340s Fetched 2022 kB in 1s (2029 kB/s) 340s (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 ... 70156 files and directories currently installed.) 340s Preparing to unpack .../gir1.2-glib-2.0_2.79.3-3ubuntu5_ppc64el.deb ... 340s Unpacking gir1.2-glib-2.0:ppc64el (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 340s dpkg: libglib2.0-0:ppc64el: dependency problems, but removing anyway as you requested: 340s udisks2 depends on libglib2.0-0 (>= 2.77.0). 340s shared-mime-info depends on libglib2.0-0 (>= 2.75.3). 340s python3-gi depends on libglib2.0-0 (>= 2.77.0). 340s python3-dbus depends on libglib2.0-0 (>= 2.16.0). 340s netplan.io depends on libglib2.0-0 (>= 2.70.0). 340s netplan-generator depends on libglib2.0-0 (>= 2.70.0). 340s libxmlb2:ppc64el depends on libglib2.0-0 (>= 2.54.0). 340s libvolume-key1:ppc64el depends on libglib2.0-0 (>= 2.18.0). 340s libudisks2-0:ppc64el depends on libglib2.0-0 (>= 2.75.3). 340s libqrtr-glib0:ppc64el depends on libglib2.0-0 (>= 2.56). 340s libqmi-proxy depends on libglib2.0-0 (>= 2.30.0). 340s libqmi-glib5:ppc64el depends on libglib2.0-0 (>= 2.54.0). 340s libpolkit-gobject-1-0:ppc64el depends on libglib2.0-0 (>= 2.38.0). 340s libpolkit-agent-1-0:ppc64el depends on libglib2.0-0 (>= 2.38.0). 340s libnetplan0:ppc64el depends on libglib2.0-0 (>= 2.75.3). 340s libmm-glib0:ppc64el depends on libglib2.0-0 (>= 2.62.0). 340s libmbim-proxy depends on libglib2.0-0 (>= 2.56). 340s libmbim-glib4:ppc64el depends on libglib2.0-0 (>= 2.56). 340s libjson-glib-1.0-0:ppc64el depends on libglib2.0-0 (>= 2.75.3). 340s libjcat1:ppc64el depends on libglib2.0-0 (>= 2.75.3). 340s libgusb2:ppc64el depends on libglib2.0-0 (>= 2.75.3). 340s libgudev-1.0-0:ppc64el depends on libglib2.0-0 (>= 2.38.0). 340s libgirepository-1.0-1:ppc64el depends on libglib2.0-0 (>= 2.79.0). 340s libfwupd2:ppc64el depends on libglib2.0-0 (>= 2.79.0). 340s libblockdev3:ppc64el depends on libglib2.0-0 (>= 2.42.2). 340s libblockdev-utils3:ppc64el depends on libglib2.0-0 (>= 2.75.3). 340s libblockdev-swap3:ppc64el depends on libglib2.0-0 (>= 2.42.2). 340s libblockdev-part3:ppc64el depends on libglib2.0-0 (>= 2.42.2). 340s libblockdev-nvme3:ppc64el depends on libglib2.0-0 (>= 2.42.2). 340s libblockdev-mdraid3:ppc64el depends on libglib2.0-0 (>= 2.42.2). 340s libblockdev-loop3:ppc64el depends on libglib2.0-0 (>= 2.42.2). 340s libblockdev-fs3:ppc64el depends on libglib2.0-0 (>= 2.42.2). 340s libblockdev-crypto3:ppc64el depends on libglib2.0-0 (>= 2.42.2). 340s fwupd depends on libglib2.0-0 (>= 2.79.0). 340s bolt depends on libglib2.0-0 (>= 2.56.0). 340s 340s (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 ... 70156 files and directories currently installed.) 340s Removing libglib2.0-0:ppc64el (2.79.2-1~ubuntu1) ... 340s Selecting previously unselected package libglib2.0-0t64:ppc64el. 340s (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 ... 70131 files and directories currently installed.) 340s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_ppc64el.deb ... 340s libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:ppc64el.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled... 340s removed '/var/lib/dpkg/info/libglib2.0-0:ppc64el.postrm' 340s Unpacking libglib2.0-0t64:ppc64el (2.79.3-3ubuntu5) ... 340s Preparing to unpack .../libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 340s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 340s Selecting previously unselected package xdg-user-dirs. 340s Preparing to unpack .../xdg-user-dirs_0.18-1_ppc64el.deb ... 340s Unpacking xdg-user-dirs (0.18-1) ... 340s Setting up xdg-user-dirs (0.18-1) ... 340s Setting up libglib2.0-0t64:ppc64el (2.79.3-3ubuntu5) ... 340s No schema files found: doing nothing. 340s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 340s Setting up gir1.2-glib-2.0:ppc64el (2.79.3-3ubuntu5) ... 340s Processing triggers for man-db (2.12.0-3) ... 341s Processing triggers for libc-bin (2.39-0ubuntu6) ... 341s Reading package lists... 342s Building dependency tree... 342s Reading state information... 342s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 342s sh: Attempting to set up Debian/Ubuntu apt sources automatically 342s sh: Distribution appears to be Ubuntu 343s Reading package lists... 344s Building dependency tree... 344s Reading state information... 344s eatmydata is already the newest version (131-1). 344s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 344s Reading package lists... 344s Building dependency tree... 344s Reading state information... 344s dbus is already the newest version (1.14.10-4ubuntu1). 344s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 344s Reading package lists... 344s Building dependency tree... 344s Reading state information... 344s rng-tools-debian is already the newest version (2.4). 344s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 345s Reading package lists... 345s Building dependency tree... 345s Reading state information... 345s The following packages will be REMOVED: 345s cloud-init* python3-configobj* python3-debconf* 345s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 345s After this operation, 3256 kB disk space will be freed. 345s (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 ... 70170 files and directories currently installed.) 345s Removing cloud-init (24.1.2-0ubuntu1) ... 346s Removing python3-configobj (5.0.8-3) ... 346s Removing python3-debconf (1.5.86) ... 346s Processing triggers for man-db (2.12.0-3) ... 346s (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 ... 69781 files and directories currently installed.) 346s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 347s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 347s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 347s invoke-rc.d: policy-rc.d denied execution of try-restart. 347s Reading package lists... 347s Building dependency tree... 347s Reading state information... 347s linux-generic is already the newest version (6.8.0-11.11+1). 347s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 348s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 348s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 348s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 351s Reading package lists... 351s Reading package lists... 351s Building dependency tree... 351s Reading state information... 351s Calculating upgrade... 351s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 351s Reading package lists... 352s Building dependency tree... 352s Reading state information... 352s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 352s autopkgtest [14:54:10]: rebooting testbed after setup commands that affected boot 517s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 523s autopkgtest [14:57:01]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 526s autopkgtest [14:57:04]: @@@@@@@@@@@@@@@@@@@@ apt-source bbmap 529s Get:1 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (dsc) [2286 B] 529s Get:2 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (tar) [5343 kB] 529s Get:3 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (diff) [25.4 kB] 529s gpgv: Signature made Fri Nov 24 11:00:29 2023 UTC 529s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 529s gpgv: issuer "emollier@debian.org" 529s gpgv: Can't check signature: No public key 529s dpkg-source: warning: cannot verify inline signature for ./bbmap_39.06+dfsg-1.dsc: no acceptable signature found 530s autopkgtest [14:57:08]: testing package bbmap version 39.06+dfsg-1 530s autopkgtest [14:57:08]: build not needed 532s autopkgtest [14:57:10]: test run-unit-test: preparing testbed 537s Reading package lists... 537s Building dependency tree... 537s Reading state information... 538s Starting pkgProblemResolver with broken count: 0 538s Starting 2 pkgProblemResolver with broken count: 0 538s Done 538s The following additional packages will be installed: 538s bbmap bbmap-jni ca-certificates-java fontconfig-config fonts-dejavu-core 538s fonts-dejavu-mono java-common libapache-pom-java libasound2 libasound2-data 538s libavahi-client3 libavahi-common-data libavahi-common3 libcommons-cli-java 538s libcommons-codec-java libcommons-io-java libcommons-parent-java libcups2 538s libfontconfig1 libgraphite2-3 libharfbuzz0b libjpeg-turbo8 libjpeg8 538s liblcms2-2 liblog4j1.2-java libmpj-java libpcsclite1 openjdk-17-jre-headless 538s python-biopython-doc 538s Suggested packages: 538s default-jre libasound2-plugins alsa-utils libcommons-io-java-doc cups-common 538s liblcms2-utils liblog4j1.2-java-doc libmail-java pcscd libnss-mdns 538s fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho 538s fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic 538s Recommended packages: 538s pigz alsa-ucm-conf alsa-topology-conf python3-biopython 538s The following NEW packages will be installed: 538s autopkgtest-satdep bbmap bbmap-jni ca-certificates-java fontconfig-config 538s fonts-dejavu-core fonts-dejavu-mono java-common libapache-pom-java 538s libasound2 libasound2-data libavahi-client3 libavahi-common-data 538s libavahi-common3 libcommons-cli-java libcommons-codec-java 538s libcommons-io-java libcommons-parent-java libcups2 libfontconfig1 538s libgraphite2-3 libharfbuzz0b libjpeg-turbo8 libjpeg8 liblcms2-2 538s liblog4j1.2-java libmpj-java libpcsclite1 openjdk-17-jre-headless 538s python-biopython-doc 538s 0 upgraded, 30 newly installed, 0 to remove and 0 not upgraded. 538s Need to get 79.6 MB/79.6 MB of archives. 538s After this operation, 240 MB of additional disk space will be used. 538s Get:1 /tmp/autopkgtest.wwK4de/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [724 B] 538s Get:2 http://ftpmaster.internal/ubuntu noble/universe ppc64el libcommons-cli-java all 1.6.0-1 [59.9 kB] 538s Get:3 http://ftpmaster.internal/ubuntu noble/universe ppc64el libapache-pom-java all 29-2 [5284 B] 538s Get:4 http://ftpmaster.internal/ubuntu noble/universe ppc64el libcommons-parent-java all 56-1 [10.7 kB] 538s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el libcommons-codec-java all 1.16.0-1 [306 kB] 539s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el libcommons-io-java all 2.11.0-2 [297 kB] 539s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el liblog4j1.2-java all 1.2.17-11 [439 kB] 539s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el libmpj-java all 0.44+dfsg-4 [443 kB] 539s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el ca-certificates-java all 20240118 [11.6 kB] 539s Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el java-common all 0.75+exp1 [6798 B] 539s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el libavahi-common-data ppc64el 0.8-13ubuntu2 [29.5 kB] 539s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el libavahi-common3 ppc64el 0.8-13ubuntu2 [25.8 kB] 539s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el libavahi-client3 ppc64el 0.8-13ubuntu2 [30.6 kB] 539s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el libcups2 ppc64el 2.4.6-0ubuntu3 [344 kB] 539s Get:15 http://ftpmaster.internal/ubuntu noble/main ppc64el liblcms2-2 ppc64el 2.14-2 [243 kB] 539s Get:16 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu1 [212 kB] 539s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 539s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB] 539s Get:19 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB] 539s Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el fontconfig-config ppc64el 2.15.0-1ubuntu1 [37.0 kB] 539s Get:21 http://ftpmaster.internal/ubuntu noble/main ppc64el libfontconfig1 ppc64el 2.15.0-1ubuntu1 [190 kB] 539s Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el libasound2-data all 1.2.10-3build1 [20.7 kB] 539s Get:23 http://ftpmaster.internal/ubuntu noble/main ppc64el libasound2 ppc64el 1.2.10-3build1 [496 kB] 540s Get:24 http://ftpmaster.internal/ubuntu noble/main ppc64el libgraphite2-3 ppc64el 1.3.14-2 [105 kB] 540s Get:25 http://ftpmaster.internal/ubuntu noble/main ppc64el libharfbuzz0b ppc64el 8.3.0-2 [576 kB] 540s Get:26 http://ftpmaster.internal/ubuntu noble/main ppc64el libpcsclite1 ppc64el 2.0.0-1 [27.9 kB] 540s Get:27 http://ftpmaster.internal/ubuntu noble/main ppc64el openjdk-17-jre-headless ppc64el 17.0.10+7-1 [47.2 MB] 544s Get:28 http://ftpmaster.internal/ubuntu noble/universe ppc64el bbmap all 39.06+dfsg-1 [9768 kB] 544s Get:29 http://ftpmaster.internal/ubuntu noble/universe ppc64el bbmap-jni ppc64el 39.06+dfsg-1 [32.8 kB] 544s Get:30 http://ftpmaster.internal/ubuntu noble/universe ppc64el python-biopython-doc all 1.81+dfsg-3 [17.3 MB] 546s Fetched 79.6 MB in 7s (10.7 MB/s) 546s Selecting previously unselected package libcommons-cli-java. 546s (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 ... 69726 files and directories currently installed.) 546s Preparing to unpack .../00-libcommons-cli-java_1.6.0-1_all.deb ... 546s Unpacking libcommons-cli-java (1.6.0-1) ... 546s Selecting previously unselected package libapache-pom-java. 546s Preparing to unpack .../01-libapache-pom-java_29-2_all.deb ... 546s Unpacking libapache-pom-java (29-2) ... 546s Selecting previously unselected package libcommons-parent-java. 546s Preparing to unpack .../02-libcommons-parent-java_56-1_all.deb ... 546s Unpacking libcommons-parent-java (56-1) ... 546s Selecting previously unselected package libcommons-codec-java. 546s Preparing to unpack .../03-libcommons-codec-java_1.16.0-1_all.deb ... 546s Unpacking libcommons-codec-java (1.16.0-1) ... 546s Selecting previously unselected package libcommons-io-java. 546s Preparing to unpack .../04-libcommons-io-java_2.11.0-2_all.deb ... 546s Unpacking libcommons-io-java (2.11.0-2) ... 546s Selecting previously unselected package liblog4j1.2-java. 546s Preparing to unpack .../05-liblog4j1.2-java_1.2.17-11_all.deb ... 546s Unpacking liblog4j1.2-java (1.2.17-11) ... 546s Selecting previously unselected package libmpj-java. 546s Preparing to unpack .../06-libmpj-java_0.44+dfsg-4_all.deb ... 546s Unpacking libmpj-java (0.44+dfsg-4) ... 546s Selecting previously unselected package ca-certificates-java. 546s Preparing to unpack .../07-ca-certificates-java_20240118_all.deb ... 546s Unpacking ca-certificates-java (20240118) ... 546s Selecting previously unselected package java-common. 546s Preparing to unpack .../08-java-common_0.75+exp1_all.deb ... 546s Unpacking java-common (0.75+exp1) ... 546s Selecting previously unselected package libavahi-common-data:ppc64el. 546s Preparing to unpack .../09-libavahi-common-data_0.8-13ubuntu2_ppc64el.deb ... 546s Unpacking libavahi-common-data:ppc64el (0.8-13ubuntu2) ... 546s Selecting previously unselected package libavahi-common3:ppc64el. 546s Preparing to unpack .../10-libavahi-common3_0.8-13ubuntu2_ppc64el.deb ... 546s Unpacking libavahi-common3:ppc64el (0.8-13ubuntu2) ... 546s Selecting previously unselected package libavahi-client3:ppc64el. 546s Preparing to unpack .../11-libavahi-client3_0.8-13ubuntu2_ppc64el.deb ... 546s Unpacking libavahi-client3:ppc64el (0.8-13ubuntu2) ... 546s Selecting previously unselected package libcups2:ppc64el. 546s Preparing to unpack .../12-libcups2_2.4.6-0ubuntu3_ppc64el.deb ... 546s Unpacking libcups2:ppc64el (2.4.6-0ubuntu3) ... 546s Selecting previously unselected package liblcms2-2:ppc64el. 546s Preparing to unpack .../13-liblcms2-2_2.14-2_ppc64el.deb ... 546s Unpacking liblcms2-2:ppc64el (2.14-2) ... 546s Selecting previously unselected package libjpeg-turbo8:ppc64el. 546s Preparing to unpack .../14-libjpeg-turbo8_2.1.5-2ubuntu1_ppc64el.deb ... 546s Unpacking libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 546s Selecting previously unselected package libjpeg8:ppc64el. 546s Preparing to unpack .../15-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 546s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 546s Selecting previously unselected package fonts-dejavu-mono. 546s Preparing to unpack .../16-fonts-dejavu-mono_2.37-8_all.deb ... 546s Unpacking fonts-dejavu-mono (2.37-8) ... 546s Selecting previously unselected package fonts-dejavu-core. 546s Preparing to unpack .../17-fonts-dejavu-core_2.37-8_all.deb ... 546s Unpacking fonts-dejavu-core (2.37-8) ... 546s Selecting previously unselected package fontconfig-config. 546s Preparing to unpack .../18-fontconfig-config_2.15.0-1ubuntu1_ppc64el.deb ... 546s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 546s Selecting previously unselected package libfontconfig1:ppc64el. 546s Preparing to unpack .../19-libfontconfig1_2.15.0-1ubuntu1_ppc64el.deb ... 546s Unpacking libfontconfig1:ppc64el (2.15.0-1ubuntu1) ... 546s Selecting previously unselected package libasound2-data. 546s Preparing to unpack .../20-libasound2-data_1.2.10-3build1_all.deb ... 546s Unpacking libasound2-data (1.2.10-3build1) ... 546s Selecting previously unselected package libasound2:ppc64el. 546s Preparing to unpack .../21-libasound2_1.2.10-3build1_ppc64el.deb ... 546s Unpacking libasound2:ppc64el (1.2.10-3build1) ... 546s Selecting previously unselected package libgraphite2-3:ppc64el. 546s Preparing to unpack .../22-libgraphite2-3_1.3.14-2_ppc64el.deb ... 546s Unpacking libgraphite2-3:ppc64el (1.3.14-2) ... 546s Selecting previously unselected package libharfbuzz0b:ppc64el. 546s Preparing to unpack .../23-libharfbuzz0b_8.3.0-2_ppc64el.deb ... 546s Unpacking libharfbuzz0b:ppc64el (8.3.0-2) ... 547s Selecting previously unselected package libpcsclite1:ppc64el. 547s Preparing to unpack .../24-libpcsclite1_2.0.0-1_ppc64el.deb ... 547s Unpacking libpcsclite1:ppc64el (2.0.0-1) ... 547s Selecting previously unselected package openjdk-17-jre-headless:ppc64el. 547s Preparing to unpack .../25-openjdk-17-jre-headless_17.0.10+7-1_ppc64el.deb ... 547s Unpacking openjdk-17-jre-headless:ppc64el (17.0.10+7-1) ... 548s Selecting previously unselected package bbmap. 548s Preparing to unpack .../26-bbmap_39.06+dfsg-1_all.deb ... 548s Unpacking bbmap (39.06+dfsg-1) ... 548s Selecting previously unselected package bbmap-jni. 548s Preparing to unpack .../27-bbmap-jni_39.06+dfsg-1_ppc64el.deb ... 548s Unpacking bbmap-jni (39.06+dfsg-1) ... 548s Selecting previously unselected package python-biopython-doc. 548s Preparing to unpack .../28-python-biopython-doc_1.81+dfsg-3_all.deb ... 548s Unpacking python-biopython-doc (1.81+dfsg-3) ... 548s Selecting previously unselected package autopkgtest-satdep. 548s Preparing to unpack .../29-1-autopkgtest-satdep.deb ... 548s Unpacking autopkgtest-satdep (0) ... 548s Setting up libgraphite2-3:ppc64el (1.3.14-2) ... 548s Setting up liblcms2-2:ppc64el (2.14-2) ... 548s Setting up java-common (0.75+exp1) ... 548s Setting up libcommons-cli-java (1.6.0-1) ... 548s Setting up liblog4j1.2-java (1.2.17-11) ... 548s Setting up libasound2-data (1.2.10-3build1) ... 548s Setting up libapache-pom-java (29-2) ... 548s Setting up libavahi-common-data:ppc64el (0.8-13ubuntu2) ... 548s Setting up fonts-dejavu-mono (2.37-8) ... 548s Setting up fonts-dejavu-core (2.37-8) ... 548s Setting up libpcsclite1:ppc64el (2.0.0-1) ... 548s Setting up libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 548s Setting up python-biopython-doc (1.81+dfsg-3) ... 548s Setting up libasound2:ppc64el (1.2.10-3build1) ... 548s Setting up libharfbuzz0b:ppc64el (8.3.0-2) ... 548s Setting up bbmap-jni (39.06+dfsg-1) ... 548s Setting up ca-certificates-java (20240118) ... 548s No JRE found. Skipping Java certificates setup. 548s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 548s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 548s Setting up libcommons-parent-java (56-1) ... 548s Setting up libavahi-common3:ppc64el (0.8-13ubuntu2) ... 548s Setting up libfontconfig1:ppc64el (2.15.0-1ubuntu1) ... 548s Setting up libcommons-codec-java (1.16.0-1) ... 548s Setting up libavahi-client3:ppc64el (0.8-13ubuntu2) ... 548s Setting up libcommons-io-java (2.11.0-2) ... 548s Setting up libmpj-java (0.44+dfsg-4) ... 548s Setting up libcups2:ppc64el (2.4.6-0ubuntu3) ... 548s Setting up openjdk-17-jre-headless:ppc64el (17.0.10+7-1) ... 548s update-alternatives: using /usr/lib/jvm/java-17-openjdk-ppc64el/bin/java to provide /usr/bin/java (java) in auto mode 548s update-alternatives: using /usr/lib/jvm/java-17-openjdk-ppc64el/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 548s update-alternatives: using /usr/lib/jvm/java-17-openjdk-ppc64el/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 548s update-alternatives: using /usr/lib/jvm/java-17-openjdk-ppc64el/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 548s update-alternatives: using /usr/lib/jvm/java-17-openjdk-ppc64el/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 548s Processing triggers for libc-bin (2.39-0ubuntu6) ... 548s Processing triggers for man-db (2.12.0-3) ... 549s Processing triggers for ca-certificates-java (20240118) ... 550s Adding debian:ACCVRAIZ1.pem 550s Adding debian:AC_RAIZ_FNMT-RCM.pem 550s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 550s Adding debian:ANF_Secure_Server_Root_CA.pem 550s Adding debian:Actalis_Authentication_Root_CA.pem 550s Adding debian:AffirmTrust_Commercial.pem 550s Adding debian:AffirmTrust_Networking.pem 550s Adding debian:AffirmTrust_Premium.pem 550s Adding debian:AffirmTrust_Premium_ECC.pem 550s Adding debian:Amazon_Root_CA_1.pem 550s Adding debian:Amazon_Root_CA_2.pem 550s Adding debian:Amazon_Root_CA_3.pem 550s Adding debian:Amazon_Root_CA_4.pem 550s Adding debian:Atos_TrustedRoot_2011.pem 550s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 550s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 550s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 550s Adding debian:BJCA_Global_Root_CA1.pem 550s Adding debian:BJCA_Global_Root_CA2.pem 550s Adding debian:Baltimore_CyberTrust_Root.pem 550s Adding debian:Buypass_Class_2_Root_CA.pem 550s Adding debian:Buypass_Class_3_Root_CA.pem 550s Adding debian:CA_Disig_Root_R2.pem 550s Adding debian:CFCA_EV_ROOT.pem 550s Adding debian:COMODO_Certification_Authority.pem 550s Adding debian:COMODO_ECC_Certification_Authority.pem 550s Adding debian:COMODO_RSA_Certification_Authority.pem 550s Adding debian:Certainly_Root_E1.pem 550s Adding debian:Certainly_Root_R1.pem 550s Adding debian:Certigna.pem 550s Adding debian:Certigna_Root_CA.pem 550s Adding debian:Certum_EC-384_CA.pem 550s Adding debian:Certum_Trusted_Network_CA.pem 550s Adding debian:Certum_Trusted_Network_CA_2.pem 550s Adding debian:Certum_Trusted_Root_CA.pem 550s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 550s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 550s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 550s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 550s Adding debian:Comodo_AAA_Services_root.pem 550s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 550s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 550s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 550s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 550s Adding debian:DigiCert_Assured_ID_Root_CA.pem 550s Adding debian:DigiCert_Assured_ID_Root_G2.pem 550s Adding debian:DigiCert_Assured_ID_Root_G3.pem 550s Adding debian:DigiCert_Global_Root_CA.pem 550s Adding debian:DigiCert_Global_Root_G2.pem 550s Adding debian:DigiCert_Global_Root_G3.pem 550s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 550s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 550s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 550s Adding debian:DigiCert_Trusted_Root_G4.pem 550s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 550s Adding debian:Entrust_Root_Certification_Authority.pem 550s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 550s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 550s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem 550s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 550s Adding debian:GLOBALTRUST_2020.pem 550s Adding debian:GTS_Root_R1.pem 550s Adding debian:GTS_Root_R2.pem 550s Adding debian:GTS_Root_R3.pem 550s Adding debian:GTS_Root_R4.pem 550s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 550s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 550s Adding debian:GlobalSign_Root_CA.pem 550s Adding debian:GlobalSign_Root_CA_-_R3.pem 550s Adding debian:GlobalSign_Root_CA_-_R6.pem 550s Adding debian:GlobalSign_Root_E46.pem 550s Adding debian:GlobalSign_Root_R46.pem 550s Adding debian:Go_Daddy_Class_2_CA.pem 550s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 550s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 550s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 550s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 550s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 550s Adding debian:HiPKI_Root_CA_-_G1.pem 550s Adding debian:Hongkong_Post_Root_CA_3.pem 550s Adding debian:ISRG_Root_X1.pem 550s Adding debian:ISRG_Root_X2.pem 550s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 550s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 550s Adding debian:Izenpe.com.pem 550s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 550s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 550s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 550s Adding debian:NAVER_Global_Root_Certification_Authority.pem 550s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 550s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 550s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 550s Adding debian:QuoVadis_Root_CA_1_G3.pem 550s Adding debian:QuoVadis_Root_CA_2.pem 550s Adding debian:QuoVadis_Root_CA_2_G3.pem 550s Adding debian:QuoVadis_Root_CA_3.pem 550s Adding debian:QuoVadis_Root_CA_3_G3.pem 550s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 550s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 550s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 550s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 550s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 550s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 550s Adding debian:SZAFIR_ROOT_CA2.pem 550s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 550s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 550s Adding debian:SecureSign_RootCA11.pem 550s Adding debian:SecureTrust_CA.pem 550s Adding debian:Secure_Global_CA.pem 550s Adding debian:Security_Communication_ECC_RootCA1.pem 550s Adding debian:Security_Communication_RootCA2.pem 550s Adding debian:Security_Communication_RootCA3.pem 550s Adding debian:Security_Communication_Root_CA.pem 550s Adding debian:Starfield_Class_2_CA.pem 550s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 550s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 550s Adding debian:SwissSign_Gold_CA_-_G2.pem 550s Adding debian:SwissSign_Silver_CA_-_G2.pem 550s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 550s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 550s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 550s Adding debian:TWCA_Global_Root_CA.pem 550s Adding debian:TWCA_Root_Certification_Authority.pem 550s Adding debian:TeliaSonera_Root_CA_v1.pem 550s Adding debian:Telia_Root_CA_v2.pem 550s Adding debian:TrustAsia_Global_Root_CA_G3.pem 550s Adding debian:TrustAsia_Global_Root_CA_G4.pem 550s Adding debian:Trustwave_Global_Certification_Authority.pem 550s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 550s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 550s Adding debian:TunTrust_Root_CA.pem 550s Adding debian:UCA_Extended_Validation_Root.pem 550s Adding debian:UCA_Global_G2_Root.pem 550s Adding debian:USERTrust_ECC_Certification_Authority.pem 550s Adding debian:USERTrust_RSA_Certification_Authority.pem 550s Adding debian:XRamp_Global_CA_Root.pem 550s Adding debian:certSIGN_ROOT_CA.pem 550s Adding debian:certSIGN_Root_CA_G2.pem 550s Adding debian:e-Szigno_Root_CA_2017.pem 550s Adding debian:ePKI_Root_Certification_Authority.pem 550s Adding debian:emSign_ECC_Root_CA_-_C3.pem 550s Adding debian:emSign_ECC_Root_CA_-_G3.pem 550s Adding debian:emSign_Root_CA_-_C1.pem 550s Adding debian:emSign_Root_CA_-_G1.pem 550s Adding debian:vTrus_ECC_Root_CA.pem 550s Adding debian:vTrus_Root_CA.pem 550s done. 550s Setting up bbmap (39.06+dfsg-1) ... 550s Setting up autopkgtest-satdep (0) ... 553s (Reading database ... 72565 files and directories currently installed.) 553s Removing autopkgtest-satdep (0) ... 554s autopkgtest [14:57:32]: test run-unit-test: [----------------------- 554s 554s # bbmap 554s bbmap.sh --version 554s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 554s java -ea -Xmx2636m -Xms2636m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 --version 554s BBMap version 39.06 554s For help, please run the shellscript with no parameters, or look in /docs/. 554s bbmap.sh --help 554s bbmap.sh ref=example.fasta 554s 554s BBMap 554s Written by Brian Bushnell, from Dec. 2010 - present 554s Last modified September 15, 2022 554s 554s Description: Fast and accurate splice-aware read aligner. 554s Please read bbmap/docs/guides/BBMapGuide.txt for more information. 554s 554s To index: bbmap.sh ref= 554s To map: bbmap.sh in= out= 554s To map without writing an index: 554s bbmap.sh ref= in= out= nodisk 554s 554s in=stdin will accept reads from standard in, and out=stdout will write to 554s standard out, but file extensions are still needed to specify the format of the 554s input and output files e.g. in=stdin.fa.gz will read gzipped fasta from 554s standard in; out=stdout.sam.gz will write gzipped sam. 554s 554s Indexing Parameters (required when building the index): 554s nodisk=f Set to true to build index in memory and write nothing 554s to disk except output. 554s ref= Specify the reference sequence. Only do this ONCE, 554s when building the index (unless using 'nodisk'). 554s build=1 If multiple references are indexed in the same directory, 554s each needs a unique numeric ID (unless using 'nodisk'). 554s k=13 Kmer length, range 8-15. Longer is faster but uses 554s more memory. Shorter is more sensitive. 554s If indexing and mapping are done in two steps, K should 554s be specified each time. 554s path=<.> Specify the location to write the index, if you don't 554s want it in the current working directory. 554s usemodulo=f Throw away ~80% of kmers based on remainder modulo a 554s number (reduces RAM by 50% and sensitivity slightly). 554s Should be enabled both when building the index AND 554s when mapping. 554s rebuild=f Force a rebuild of the index (ref= should be set). 554s 554s Input Parameters: 554s build=1 Designate index to use. Corresponds to the number 554s specified when building the index. 554s in= Primary reads input; required parameter. 554s in2= For paired reads in two files. 554s interleaved=auto True forces paired/interleaved input; false forces 554s single-ended mapping. If not specified, interleaved 554s status will be autodetected from read names. 554s fastareadlen=500 Break up FASTA reads longer than this. Max is 500 for 554s BBMap and 6000 for BBMapPacBio. Only works for FASTA 554s input (use 'maxlen' for FASTQ input). The default for 554s bbmap.sh is 500, and for mapPacBio.sh is 6000. 554s unpigz=f Spawn a pigz (parallel gzip) process for faster 554s decompression than using Java. 554s Requires pigz to be installed. 554s touppercase=t (tuc) Convert lowercase letters in reads to upper case 554s (otherwise they will not match the reference). 554s 554s Sampling Parameters: 554s 554s reads=-1 Set to a positive number N to only process the first N 554s reads (or pairs), then quit. -1 means use all reads. 554s samplerate=1 Set to a number from 0 to 1 to randomly select that 554s fraction of reads for mapping. 1 uses all reads. 554s skipreads=0 Set to a number N to skip the first N reads (or pairs), 554s then map the rest. 554s 554s Mapping Parameters: 554s fast=f This flag is a macro which sets other paramters to run 554s faster, at reduced sensitivity. Bad for RNA-seq. 554s slow=f This flag is a macro which sets other paramters to run 554s slower, at greater sensitivity. 'vslow' is even slower. 554s maxindel=16000 Don't look for indels longer than this. Lower is faster. 554s Set to >=100k for RNAseq with long introns like mammals. 554s strictmaxindel=f When enabled, do not allow indels longer than 'maxindel'. 554s By default these are not sought, but may be found anyway. 554s tipsearch=100 Look this far for read-end deletions with anchors 554s shorter than K, using brute force. 554s minid=0.76 Approximate minimum alignment identity to look for. 554s Higher is faster and less sensitive. 554s minhits=1 Minimum number of seed hits required for candidate sites. 554s Higher is faster. 554s local=f Set to true to use local, rather than global, alignments. 554s This will soft-clip ugly ends of poor alignments. 554s perfectmode=f Allow only perfect mappings when set to true (very fast). 554s semiperfectmode=f Allow only perfect and semiperfect (perfect except for 554s N's in the reference) mappings. 554s threads=auto (t) Set to number of threads desired. By default, uses 554s all cores available. 554s ambiguous=best (ambig) Set behavior on ambiguously-mapped reads (with 554s multiple top-scoring mapping locations). 554s best (use the first best site) 554s toss (consider unmapped) 554s random (select one top-scoring site randomly) 554s all (retain all top-scoring sites) 554s samestrandpairs=f (ssp) Specify whether paired reads should map to the 554s same strand or opposite strands. 554s requirecorrectstrand=t (rcs) Forbid pairing of reads without correct strand 554s orientation. Set to false for long-mate-pair libraries. 554s killbadpairs=f (kbp) If a read pair is mapped with an inappropriate 554s insert size or orientation, the read with the lower 554s mapping quality is marked unmapped. 554s pairedonly=f (po) Treat unpaired reads as unmapped. Thus they will 554s be sent to 'outu' but not 'outm'. 554s rcomp=f Reverse complement both reads prior to mapping (for LMP 554s outward-facing libraries). 554s rcompmate=f Reverse complement read2 prior to mapping. 554s pairlen=32000 Set max allowed distance between paired reads. 554s (insert size)=(pairlen)+(read1 length)+(read2 length) 554s rescuedist=1200 Don't try to rescue paired reads if avg. insert size 554s greater than this. Lower is faster. 554s rescuemismatches=32 Maximum mismatches allowed in a rescued read. Lower 554s is faster. 554s averagepairdist=100 (apd) Initial average distance between paired reads. 554s Varies dynamically; does not need to be specified. 554s deterministic=f Run in deterministic mode. In this case it is good 554s to set averagepairdist. BBMap is deterministic 554s without this flag if using single-ended reads, 554s or run singlethreaded. 554s bandwidthratio=0 (bwr) If above zero, restrict alignment band to this 554s fraction of read length. Faster but less accurate. 554s bandwidth=0 (bw) Set the bandwidth directly. 554s fraction of read length. Faster but less accurate. 554s usejni=f (jni) Do alignments faster, in C code. Requires 554s compiling the C code; details are in /jni/README.txt. 554s maxsites2=800 Don't analyze (or print) more than this many alignments 554s per read. 554s ignorefrequentkmers=t (ifk) Discard low-information kmers that occur often. 554s excludefraction=0.03 (ef) Fraction of kmers to ignore. For example, 0.03 554s will ignore the most common 3% of kmers. 554s greedy=t Use a greedy algorithm to discard the least-useful 554s kmers on a per-read basis. 554s kfilter=0 If positive, potential mapping sites must have at 554s least this many consecutive exact matches. 554s 554s 554s Quality and Trimming Parameters: 554s qin=auto Set to 33 or 64 to specify input quality value ASCII 554s offset. 33 is Sanger, 64 is old Solexa. 554s qout=auto Set to 33 or 64 to specify output quality value ASCII 554s offset (only if output format is fastq). 554s qtrim=f Quality-trim ends before mapping. Options are: 554s 'f' (false), 'l' (left), 'r' (right), and 'lr' (both). 554s untrim=f Undo trimming after mapping. Untrimmed bases will be 554s soft-clipped in cigar strings. 554s trimq=6 Trim regions with average quality below this 554s (phred algorithm). 554s mintrimlength=60 (mintl) Don't trim reads to be shorter than this. 554s fakefastaquality=-1 (ffq) Set to a positive number 1-50 to generate fake 554s quality strings for fasta input reads. 554s ignorebadquality=f (ibq) Keep going, rather than crashing, if a read has 554s out-of-range quality values. 554s usequality=t Use quality scores when determining which read kmers 554s to use as seeds. 554s minaveragequality=0 (maq) Do not map reads with average quality below this. 554s maqb=0 If positive, calculate maq from this many initial bases. 554s 554s Output Parameters: 554s out= Write all reads to this file. 554s outu= Write only unmapped reads to this file. Does not 554s include unmapped paired reads with a mapped mate. 554s outm= Write only mapped reads to this file. Includes 554s unmapped paired reads with a mapped mate. 554s mappedonly=f If true, treats 'out' like 'outm'. 554s bamscript= (bs) Write a shell script to that will turn 554s the sam output into a sorted, indexed bam file. 554s ordered=f Set to true to output reads in same order as input. 554s Slower and uses more memory. 554s overwrite=f (ow) Allow process to overwrite existing files. 554s secondary=f Print secondary alignments. 554s sssr=0.95 (secondarysitescoreratio) Print only secondary alignments 554s with score of at least this fraction of primary. 554s ssao=f (secondarysiteasambiguousonly) Only print secondary 554s alignments for ambiguously-mapped reads. 554s maxsites=5 Maximum number of total alignments to print per read. 554s Only relevant when secondary=t. 554s quickmatch=f Generate cigar strings more quickly. 554s trimreaddescriptions=f (trd) Truncate read and ref names at the first whitespace, 554s assuming that the remainder is a comment or description. 554s ziplevel=2 (zl) Compression level for zip or gzip output. 554s pigz=f Spawn a pigz (parallel gzip) process for faster 554s compression than Java. Requires pigz to be installed. 554s machineout=f Set to true to output statistics in machine-friendly 554s 'key=value' format. 554s printunmappedcount=f Print the total number of unmapped reads and bases. 554s If input is paired, the number will be of pairs 554s for which both reads are unmapped. 554s showprogress=0 If positive, print a '.' every X reads. 554s showprogress2=0 If positive, print the number of seconds since the 554s last progress update (instead of a '.'). 554s renamebyinsert=f Renames reads based on their mapped insert size. 554s 554s Bloom-Filtering Parameters (bloomfilter.sh is the standalone version). 554s bloom=f Use a Bloom filter to ignore reads not sharing kmers 554s with the reference. This uses more memory, but speeds 554s mapping when most reads don't match the reference. 554s bloomhashes=2 Number of hash functions. 554s bloomminhits=3 Number of consecutive hits to be considered matched. 554s bloomk=31 Bloom filter kmer length. 554s bloomserial=t Use the serialized Bloom filter for greater loading 554s speed, if available. If not, generate and write one. 554s 554s Post-Filtering Parameters: 554s idfilter=0 Independant of minid; sets exact minimum identity 554s allowed for alignments to be printed. Range 0 to 1. 554s subfilter=-1 Ban alignments with more than this many substitutions. 554s insfilter=-1 Ban alignments with more than this many insertions. 554s delfilter=-1 Ban alignments with more than this many deletions. 554s indelfilter=-1 Ban alignments with more than this many indels. 554s editfilter=-1 Ban alignments with more than this many edits. 554s inslenfilter=-1 Ban alignments with an insertion longer than this. 554s dellenfilter=-1 Ban alignments with a deletion longer than this. 554s nfilter=-1 Ban alignments with more than this many ns. This 554s includes nocall, noref, and off scaffold ends. 554s 554s Sam flags and settings: 554s noheader=f Disable generation of header lines. 554s sam=1.4 Set to 1.4 to write Sam version 1.4 cigar strings, 554s with = and X, or 1.3 to use M. 554s saa=t (secondaryalignmentasterisks) Use asterisks instead of 554s bases for sam secondary alignments. 554s cigar=t Set to 'f' to skip generation of cigar strings (faster). 554s keepnames=f Keep original names of paired reads, rather than 554s ensuring both reads have the same name. 554s intronlen=999999999 Set to a lower number like 10 to change 'D' to 'N' in 554s cigar strings for deletions of at least that length. 554s rgid= Set readgroup ID. All other readgroup fields 554s can be set similarly, with the flag rgXX= 554s If you set a readgroup flag to the word 'filename', 554s e.g. rgid=filename, the input file name will be used. 554s mdtag=f Write MD tags. 554s nhtag=f Write NH tags. 554s xmtag=f Write XM tags (may only work correctly with ambig=all). 554s amtag=f Write AM tags. 554s nmtag=f Write NM tags. 554s xstag=f Set to 'xs=fs', 'xs=ss', or 'xs=us' to write XS tags 554s for RNAseq using firststrand, secondstrand, or 554s unstranded libraries. Needed by Cufflinks. 554s JGI mainly uses 'firststrand'. 554s stoptag=f Write a tag indicating read stop location, prefixed by YS:i: 554s lengthtag=f Write a tag indicating (query,ref) alignment lengths, 554s prefixed by YL:Z: 554s idtag=f Write a tag indicating percent identity, prefixed by YI:f: 554s inserttag=f Write a tag indicating insert size, prefixed by X8:Z: 554s scoretag=f Write a tag indicating BBMap's raw score, prefixed by YR:i: 554s timetag=f Write a tag indicating this read's mapping time, prefixed by X0:i: 554s boundstag=f Write a tag indicating whether either read in the pair 554s goes off the end of the reference, prefixed by XB:Z: 554s notags=f Turn off all optional tags. 554s 554s Histogram and statistics output parameters: 554s scafstats= Statistics on how many reads mapped to which scaffold. 554s refstats= Statistics on how many reads mapped to which reference 554s file; only for BBSplit. 554s sortscafs=t Sort scaffolds or references by read count. 554s bhist= Base composition histogram by position. 554s qhist= Quality histogram by position. 554s aqhist= Histogram of average read quality. 554s bqhist= Quality histogram designed for box plots. 554s lhist= Read length histogram. 554s ihist= Write histogram of insert sizes (for paired reads). 554s ehist= Errors-per-read histogram. 554s qahist= Quality accuracy histogram of error rates versus 554s quality score. 554s indelhist= Indel length histogram. 554s mhist= Histogram of match, sub, del, and ins rates by 554s read location. 554s gchist= Read GC content histogram. 554s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 554s gcpairs=t Use average GC of paired reads. 554s idhist= Histogram of read count versus percent identity. 554s idbins=100 Number idhist bins. Set to 'auto' to use read length. 554s statsfile=stderr Mapping statistics are printed here. 554s 554s Coverage output parameters (these may reduce speed and use more RAM): 554s covstats= Per-scaffold coverage info. 554s rpkm= Per-scaffold RPKM/FPKM counts. 554s covhist= Histogram of # occurrences of each depth level. 554s basecov= Coverage per base location. 554s bincov= Print binned coverage per location (one line per X bases). 554s covbinsize=1000 Set the binsize for binned coverage output. 554s nzo=t Only print scaffolds with nonzero coverage. 554s twocolumn=f Change to true to print only ID and Avg_fold instead of 554s all 6 columns to the 'out=' file. 554s 32bit=f Set to true if you need per-base coverage over 64k. 554s strandedcov=f Track coverage for plus and minus strand independently. 554s startcov=f Only track start positions of reads. 554s secondarycov=t Include coverage of secondary alignments. 554s physcov=f Calculate physical coverage for paired reads. 554s This includes the unsequenced bases. 554s delcoverage=t (delcov) Count bases covered by deletions as covered. 554s True is faster than false. 554s covk=0 If positive, calculate kmer coverage statistics. 554s 554s Java Parameters: 554s -Xmx This will set Java's memory usage, 554s overriding autodetection. 554s -Xmx20g will specify 20 gigs of RAM, and -Xmx800m 554s will specify 800 megs. The max is typically 85% of 554s physical memory. The human genome requires around 24g, 554s or 12g with the 'usemodulo' flag. The index uses 554s roughly 6 bytes per reference base. 554s -eoom This flag will cause the process to exit if an 554s out-of-memory exception occurs. Requires Java 8u92+. 554s -da Disable assertions. 554s 554s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter 554s any problems, or post at: http://seqanswers.com/forums/showthread.php?t=41057 554s 554s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 554s java -ea -Xmx2636m -Xms2636m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta 554s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta] 554s Version 39.06 554s 554s No output file. 554s Writing reference. 554s 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] 554s 554s Set genScaffoldInfo=true 554s Writing chunk 1 554s Set genome to 1 554s 554s Loaded Reference: 0.005 seconds. 554s Loading index for chunk 1-1, build 1 554s No index available; generating from reference genome: /tmp/autopkgtest.wwK4de/autopkgtest_tmp/ref/index/1/chr1_index_k13_c16_b1.block 555s Indexing threads started for block 0-1 555s Indexing threads finished for block 0-1 556s Generated Index: 1.342 seconds. 556s No reads to process; quitting. 556s 556s Total time: 1.486 seconds. 556s test -d ref 556s bbmap.sh in=misc_dna_as_sanger.fastq out=out.sam 556s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 556s java -ea -Xmx2635m -Xms2635m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 in=misc_dna_as_sanger.fastq out=out.sam 556s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, in=misc_dna_as_sanger.fastq, out=out.sam] 556s Version 39.06 556s 556s Retaining first best site only for ambiguous mappings. 556s Set genome to 1 556s 556s Loaded Reference: 0.026 seconds. 556s Loading index for chunk 1-1, build 1 557s Generated Index: 0.497 seconds. 560s Analyzed Index: 3.782 seconds. 560s Started output stream: 0.022 seconds. 560s Cleared Memory: 0.113 seconds. 561s Processing reads in single-ended mode. 561s Started read stream. 561s Started 4 mapping threads. 561s Detecting finished threads: 0, 1, 2, 3 561s 561s ------------------ Results ------------------ 561s 561s Genome: 1 561s Key Length: 13 561s Max Indel: 16000 561s Minimum Score Ratio: 0.56 561s Mapping Mode: normal 561s Reads Used: 4 (153 bases) 561s 561s Mapping: 0.086 seconds. 561s Reads/sec: 46.32 561s kBases/sec: 1.77 561s 561s 561s Read 1 data: pct reads num reads pct bases num bases 561s 561s mapped: 0.0000% 0 0.0000% 0 561s unambiguous: 0.0000% 0 0.0000% 0 561s ambiguous: 0.0000% 0 0.0000% 0 561s low-Q discards: 25.0000% 1 19.6078% 30 561s 561s perfect best site: 0.0000% 0 0.0000% 0 561s semiperfect site: 0.0000% 0 0.0000% 0 561s 561s Match Rate: NA NA NaN% 0 561s Error Rate: NaN% 0 NaN% 0 561s Sub Rate: NaN% 0 NaN% 0 561s Del Rate: NaN% 0 NaN% 0 561s Ins Rate: NaN% 0 NaN% 0 561s N Rate: NaN% 0 NaN% 0 561s 561s Total time: 4.632 seconds. 561s test -r out.sam 561s bbmap.sh ref=example.fasta in=example.fastq out=out2.sam nodisk 561s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 561s java -ea -Xmx2635m -Xms2635m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta in=example.fastq out=out2.sam nodisk 561s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta, in=example.fastq, out=out2.sam, nodisk] 561s Version 39.06 561s 561s Retaining first best site only for ambiguous mappings. 561s 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] 561s 561s Set genScaffoldInfo=true 561s Set genome to 1 561s 561s Loaded Reference: 0.002 seconds. 561s Loading index for chunk 1-1, build 1 561s Indexing threads started for block 0-1 561s Indexing threads finished for block 0-1 561s Generated Index: 0.231 seconds. 565s Analyzed Index: 3.830 seconds. 565s Started output stream: 0.023 seconds. 565s Cleared Memory: 0.111 seconds. 565s Processing reads in single-ended mode. 565s Started read stream. 565s Started 4 mapping threads. 565s Detecting finished threads: 0, 1, 2, 3 565s 565s ------------------ Results ------------------ 565s 565s Genome: 1 565s Key Length: 13 565s Max Indel: 16000 565s Minimum Score Ratio: 0.56 565s Mapping Mode: normal 565s Reads Used: 3 (75 bases) 565s 565s Mapping: 0.058 seconds. 565s Reads/sec: 51.75 565s kBases/sec: 1.29 565s 565s 565s Read 1 data: pct reads num reads pct bases num bases 565s 565s mapped: 100.0000% 3 100.0000% 75 565s unambiguous: 100.0000% 3 100.0000% 75 565s ambiguous: 0.0000% 0 0.0000% 0 565s low-Q discards: 0.0000% 0 0.0000% 0 565s 565s perfect best site: 100.0000% 3 100.0000% 75 565s semiperfect site: 100.0000% 3 100.0000% 75 565s 565s Match Rate: NA NA 100.0000% 75 565s Error Rate: 0.0000% 0 0.0000% 0 565s Sub Rate: 0.0000% 0 0.0000% 0 565s Del Rate: 0.0000% 0 0.0000% 0 565s Ins Rate: 0.0000% 0 0.0000% 0 565s N Rate: 0.0000% 0 0.0000% 0 565s 565s Total time: 4.392 seconds. 565s test -r out2.sam 565s 565s # bbduk 565s bbduk.sh --version 565s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 565s java -ea -Xmx1317m -Xms1317m -cp /usr/share/java/bbmap.jar jgi.BBDuk --version 565s BBMap version 39.06 565s For help, please run the shellscript with no parameters, or look in /docs/. 565s bbduk.sh --help 565s 565s Written by Brian Bushnell 565s Last modified November 9, 2023 565s 565s Description: Compares reads to the kmers in a reference dataset, optionally 565s allowing an edit distance. Splits the reads into two outputs - those that 565s match the reference, and those that don't. Can also trim (remove) the matching 565s parts of the reads rather than binning the reads. 565s Please read bbmap/docs/guides/BBDukGuide.txt for more information. 565s 565s Usage: bbduk.sh in= out= ref= 565s 565s Input may be stdin or a fasta or fastq file, compressed or uncompressed. 565s If you pipe via stdin/stdout, please include the file type; e.g. for gzipped 565s fasta input, set in=stdin.fa.gz 565s 565s Input parameters: 565s in= Main input. in=stdin.fq will pipe from stdin. 565s in2= Input for 2nd read of pairs in a different file. 565s ref= Comma-delimited list of reference files. 565s In addition to filenames, you may also use the keywords: 565s adapters, artifacts, phix, lambda, pjet, mtst, kapa 565s literal= Comma-delimited list of literal reference sequences. 565s touppercase=f (tuc) Change all bases upper-case. 565s interleaved=auto (int) t/f overrides interleaved autodetection. 565s Must be set mainually when streaming fastq input. 565s qin=auto Input quality offset: 33 (Sanger), 64, or auto. 565s reads=-1 If positive, quit after processing X reads or pairs. 565s copyundefined=f (cu) Process non-AGCT IUPAC reference bases by making all 565s possible unambiguous copies. Intended for short motifs 565s or adapter barcodes, as time/memory use is exponential. 565s samplerate=1 Set lower to only process a fraction of input reads. 565s samref= Optional reference fasta for processing sam files. 565s 565s Output parameters: 565s out= (outnonmatch) Write reads here that do not contain 565s kmers matching the database. 'out=stdout.fq' will pipe 565s to standard out. 565s out2= (outnonmatch2) Use this to write 2nd read of pairs to a 565s different file. 565s outm= (outmatch) Write reads here that fail filters. In default 565s kfilter mode, this means any read with a matching kmer. 565s In any mode, it also includes reads that fail filters such 565s as minlength, mingc, maxgc, entropy, etc. In other words, 565s it includes all reads that do not go to 'out'. 565s outm2= (outmatch2) Use this to write 2nd read of pairs to a 565s different file. 565s outs= (outsingle) Use this to write singleton reads whose mate 565s was trimmed shorter than minlen. 565s stats= Write statistics about which contamininants were detected. 565s refstats= Write statistics on a per-reference-file basis. 565s rpkm= Write RPKM for each reference sequence (for RNA-seq). 565s dump= Dump kmer tables to a file, in fasta format. 565s duk= Write statistics in duk's format. *DEPRECATED* 565s nzo=t Only write statistics about ref sequences with nonzero hits. 565s overwrite=t (ow) Grant permission to overwrite files. 565s showspeed=t (ss) 'f' suppresses display of processing speed. 565s ziplevel=2 (zl) Compression level; 1 (min) through 9 (max). 565s fastawrap=70 Length of lines in fasta output. 565s qout=auto Output quality offset: 33 (Sanger), 64, or auto. 565s statscolumns=3 (cols) Number of columns for stats output, 3 or 5. 565s 5 includes base counts. 565s rename=f Rename reads to indicate which sequences they matched. 565s refnames=f Use names of reference files rather than scaffold IDs. 565s trd=f Truncate read and ref names at the first whitespace. 565s ordered=f Set to true to output reads in same order as input. 565s maxbasesout=-1 If positive, quit after writing approximately this many 565s bases to out (outu/outnonmatch). 565s maxbasesoutm=-1 If positive, quit after writing approximately this many 565s bases to outm (outmatch). 565s json=f Print to screen in json format. 565s 565s Histogram output parameters: 565s bhist= Base composition histogram by position. 565s qhist= Quality histogram by position. 565s qchist= Count of bases with each quality value. 565s aqhist= Histogram of average read quality. 565s bqhist= Quality histogram designed for box plots. 565s lhist= Read length histogram. 565s phist= Polymer length histogram. 565s gchist= Read GC content histogram. 565s enthist= Read entropy histogram. 565s ihist= Insert size histogram, for paired reads in mapped sam. 565s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 565s maxhistlen=6000 Set an upper bound for histogram lengths; higher uses 565s more memory. The default is 6000 for some histograms 565s and 80000 for others. 565s 565s Histograms for mapped sam/bam files only: 565s histbefore=t Calculate histograms from reads before processing. 565s ehist= Errors-per-read histogram. 565s qahist= Quality accuracy histogram of error rates versus quality 565s score. 565s indelhist= Indel length histogram. 565s mhist= Histogram of match, sub, del, and ins rates by position. 565s idhist= Histogram of read count versus percent identity. 565s idbins=100 Number idhist bins. Set to 'auto' to use read length. 565s varfile= Ignore substitution errors listed in this file when 565s calculating error rates. Can be generated with 565s CallVariants. 565s vcf= Ignore substitution errors listed in this VCF file 565s when calculating error rates. 565s ignorevcfindels=t Also ignore indels listed in the VCF. 565s 565s Processing parameters: 565s k=27 Kmer length used for finding contaminants. Contaminants 565s shorter than k will not be found. k must be at least 1. 565s rcomp=t Look for reverse-complements of kmers in addition to 565s forward kmers. 565s maskmiddle=t (mm) Treat the middle base of a kmer as a wildcard, to 565s increase sensitivity in the presence of errors. This may 565s also be set to a number, e.g. mm=3, to mask that many bp. 565s The default mm=t corresponds to mm=1 for odd-length kmers 565s and mm=2 for even-length kmers (as of v39.04), while 565s mm=f is always equivalent to mm=0. 565s minkmerhits=1 (mkh) Reads need at least this many matching kmers 565s to be considered as matching the reference. 565s minkmerfraction=0.0 (mkf) A reads needs at least this fraction of its total 565s kmers to hit a ref, in order to be considered a match. 565s If this and minkmerhits are set, the greater is used. 565s mincovfraction=0.0 (mcf) A reads needs at least this fraction of its total 565s bases to be covered by ref kmers to be considered a match. 565s If specified, mcf overrides mkh and mkf. 565s hammingdistance=0 (hdist) Maximum Hamming distance for ref kmers (subs only). 565s Memory use is proportional to (3*K)^hdist. 565s qhdist=0 Hamming distance for query kmers; impacts speed, not memory. 565s editdistance=0 (edist) Maximum edit distance from ref kmers (subs 565s and indels). Memory use is proportional to (8*K)^edist. 565s hammingdistance2=0 (hdist2) Sets hdist for short kmers, when using mink. 565s qhdist2=0 Sets qhdist for short kmers, when using mink. 565s editdistance2=0 (edist2) Sets edist for short kmers, when using mink. 565s forbidn=f (fn) Forbids matching of read kmers containing N. 565s By default, these will match a reference 'A' if 565s hdist>0 or edist>0, to increase sensitivity. 565s removeifeitherbad=t (rieb) Paired reads get sent to 'outmatch' if either is 565s match (or either is trimmed shorter than minlen). 565s Set to false to require both. 565s trimfailures=f Instead of discarding failed reads, trim them to 1bp. 565s This makes the statistics a bit odd. 565s findbestmatch=f (fbm) If multiple matches, associate read with sequence 565s sharing most kmers. Reduces speed. 565s skipr1=f Don't do kmer-based operations on read 1. 565s skipr2=f Don't do kmer-based operations on read 2. 565s ecco=f For overlapping paired reads only. Performs error- 565s correction with BBMerge prior to kmer operations. 565s recalibrate=f (recal) Recalibrate quality scores. Requires calibration 565s matrices generated by CalcTrueQuality. 565s sam= If recalibration is desired, and matrices have not already 565s been generated, BBDuk will create them from the sam file. 565s amino=f Run in amino acid mode. Some features have not been 565s tested, but kmer-matching works fine. Maximum k is 12. 565s 565s Speed and Memory parameters: 565s threads=auto (t) Set number of threads to use; default is number of 565s logical processors. 565s prealloc=f Preallocate memory in table. Allows faster table loading 565s and more efficient memory usage, for a large reference. 565s monitor=f Kill this process if it crashes. monitor=600,0.01 would 565s kill after 600 seconds under 1% usage. 565s minrskip=1 (mns) Force minimal skip interval when indexing reference 565s kmers. 1 means use all, 2 means use every other kmer, etc. 565s maxrskip=1 (mxs) Restrict maximal skip interval when indexing 565s reference kmers. Normally all are used for scaffolds<100kb, 565s but with longer scaffolds, up to maxrskip-1 are skipped. 565s rskip= Set both minrskip and maxrskip to the same value. 565s If not set, rskip will vary based on sequence length. 565s qskip=1 Skip query kmers to increase speed. 1 means use all. 565s speed=0 Ignore this fraction of kmer space (0-15 out of 16) in both 565s reads and reference. Increases speed and reduces memory. 565s Note: Do not use more than one of 'speed', 'qskip', and 'rskip'. 565s 565s Trimming/Filtering/Masking parameters: 565s Note - if ktrim, kmask, and ksplit are unset, the default behavior is kfilter. 565s All kmer processing modes are mutually exclusive. 565s Reads only get sent to 'outm' purely based on kmer matches in kfilter mode. 565s 565s ktrim=f Trim reads to remove bases matching reference kmers, plus 565s all bases to the left or right. 565s Values: 565s f (don't trim), 565s r (trim to the right), 565s l (trim to the left) 565s ktrimtips=0 Set this to a positive number to perform ktrim on both 565s ends, examining only the outermost X bases. 565s kmask= Replace bases matching ref kmers with another symbol. 565s Allows any non-whitespace character, and processes short 565s kmers on both ends if mink is set. 'kmask=lc' will 565s convert masked bases to lowercase. 565s maskfullycovered=f (mfc) Only mask bases that are fully covered by kmers. 565s ksplit=f For single-ended reads only. Reads will be split into 565s pairs around the kmer. If the kmer is at the end of the 565s read, it will be trimmed instead. Singletons will go to 565s out, and pairs will go to outm. Do not use ksplit with 565s other operations such as quality-trimming or filtering. 565s mink=0 Look for shorter kmers at read tips down to this length, 565s when k-trimming or masking. 0 means disabled. Enabling 565s this will disable maskmiddle. 565s qtrim=f Trim read ends to remove bases with quality below trimq. 565s Performed AFTER looking for kmers. Values: 565s rl (trim both ends), 565s f (neither end), 565s r (right end only), 565s l (left end only), 565s w (sliding window). 565s trimq=6 Regions with average quality BELOW this will be trimmed, 565s if qtrim is set to something other than f. Can be a 565s floating-point number like 7.3. 565s trimclip=f Trim soft-clipped bases from sam files. 565s minlength=10 (ml) Reads shorter than this after trimming will be 565s discarded. Pairs will be discarded if both are shorter. 565s mlf=0 (minlengthfraction) Reads shorter than this fraction of 565s original length after trimming will be discarded. 565s maxlength= Reads longer than this after trimming will be discarded. 565s minavgquality=0 (maq) Reads with average quality (after trimming) below 565s this will be discarded. 565s maqb=0 If positive, calculate maq from this many initial bases. 565s minbasequality=0 (mbq) Reads with any base below this quality (after 565s trimming) will be discarded. 565s maxns=-1 If non-negative, reads with more Ns than this 565s (after trimming) will be discarded. 565s mcb=0 (minconsecutivebases) Discard reads without at least 565s this many consecutive called bases. 565s ottm=f (outputtrimmedtomatch) Output reads trimmed to shorter 565s than minlength to outm rather than discarding. 565s tp=0 (trimpad) Trim this much extra around matching kmers. 565s tbo=f (trimbyoverlap) Trim adapters based on where paired 565s reads overlap. 565s strictoverlap=t Adjust sensitivity for trimbyoverlap mode. 565s minoverlap=14 Require this many bases of overlap for detection. 565s mininsert=40 Require insert size of at least this for overlap. 565s Should be reduced to 16 for small RNA sequencing. 565s tpe=f (trimpairsevenly) When kmer right-trimming, trim both 565s reads to the minimum length of either. 565s forcetrimleft=0 (ftl) If positive, trim bases to the left of this position 565s (exclusive, 0-based). 565s forcetrimright=0 (ftr) If positive, trim bases to the right of this position 565s (exclusive, 0-based). 565s forcetrimright2=0 (ftr2) If positive, trim this many bases on the right end. 565s forcetrimmod=0 (ftm) If positive, right-trim length to be equal to zero, 565s modulo this number. 565s restrictleft=0 If positive, only look for kmer matches in the 565s leftmost X bases. 565s restrictright=0 If positive, only look for kmer matches in the 565s rightmost X bases. 565s NOTE: restrictleft and restrictright are mutually exclusive. If trimming 565s both ends is desired, use ktrimtips. 565s mingc=0 Discard reads with GC content below this. 565s maxgc=1 Discard reads with GC content above this. 565s gcpairs=t Use average GC of paired reads. 565s Also affects gchist. 565s tossjunk=f Discard reads with invalid characters as bases. 565s swift=f Trim Swift sequences: Trailing C/T/N R1, leading G/A/N R2. 565s 565s Header-parsing parameters - these require Illumina headers: 565s chastityfilter=f (cf) Discard reads with id containing ' 1:Y:' or ' 2:Y:'. 565s barcodefilter=f Remove reads with unexpected barcodes if barcodes is set, 565s or barcodes containing 'N' otherwise. A barcode must be 565s the last part of the read header. Values: 565s t: Remove reads with bad barcodes. 565s f: Ignore barcodes. 565s crash: Crash upon encountering bad barcodes. 565s barcodes= Comma-delimited list of barcodes or files of barcodes. 565s xmin=-1 If positive, discard reads with a lesser X coordinate. 565s ymin=-1 If positive, discard reads with a lesser Y coordinate. 565s xmax=-1 If positive, discard reads with a greater X coordinate. 565s ymax=-1 If positive, discard reads with a greater Y coordinate. 565s 565s Polymer trimming: 565s trimpolya=0 If greater than 0, trim poly-A or poly-T tails of 565s at least this length on either end of reads. 565s trimpolygleft=0 If greater than 0, trim poly-G prefixes of at least this 565s length on the left end of reads. Does not trim poly-C. 565s trimpolygright=0 If greater than 0, trim poly-G tails of at least this 565s length on the right end of reads. Does not trim poly-C. 565s trimpolyg=0 This sets both left and right at once. 565s filterpolyg=0 If greater than 0, remove reads with a poly-G prefix of 565s at least this length (on the left). 565s Note: there are also equivalent poly-C flags. 565s 565s Polymer tracking: 565s pratio=base,base 'pratio=G,C' will print the ratio of G to C polymers. 565s plen=20 Length of homopolymers to count. 565s 565s Entropy/Complexity parameters: 565s entropy=-1 Set between 0 and 1 to filter reads with entropy below 565s that value. Higher is more stringent. 565s entropywindow=50 Calculate entropy using a sliding window of this length. 565s entropyk=5 Calculate entropy using kmers of this length. 565s minbasefrequency=0 Discard reads with a minimum base frequency below this. 565s entropytrim=f Values: 565s f: (false) Do not entropy-trim. 565s r: (right) Trim low entropy on the right end only. 565s l: (left) Trim low entropy on the left end only. 565s rl: (both) Trim low entropy on both ends. 565s entropymask=f Values: 565s f: (filter) Discard low-entropy sequences. 565s t: (true) Mask low-entropy parts of sequences with N. 565s lc: Change low-entropy parts of sequences to lowercase. 565s entropymark=f Mark each base with its entropy value. This is on a scale 565s of 0-41 and is reported as quality scores, so the output 565s should be fastq or fasta+qual. 565s NOTE: If set, entropytrim overrides entropymask. 565s 565s Cardinality estimation: 565s cardinality=f (loglog) Count unique kmers using the LogLog algorithm. 565s cardinalityout=f (loglogout) Count unique kmers in output reads. 565s loglogk=31 Use this kmer length for counting. 565s loglogbuckets=2048 Use this many buckets for counting. 565s khist= Kmer frequency histogram; plots number of kmers versus 565s kmer depth. This is approximate. 565s khistout= Kmer frequency histogram for output reads. 565s 565s Java Parameters: 565s 565s -Xmx This will set Java's memory usage, overriding autodetection. 565s -Xmx20g will 565s specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 565s The max is typically 85% of physical memory. 565s -eoom This flag will cause the process to exit if an 565s out-of-memory exception occurs. Requires Java 8u92+. 565s -da Disable assertions. 565s 565s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 565s 565s bbduk.sh in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq \ 565s qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 565s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 565s java -ea -Xmx1318m -Xms1318m -cp /usr/share/java/bbmap.jar jgi.BBDuk in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 565s 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] 565s Version 39.06 565s 565s 0.017 seconds. 565s Initial: 565s Memory: max=1409m, total=1409m, free=1379m, used=30m 565s 565s Input is being processed as paired 565s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 565s Started output streams: 0.018 seconds. 565s Processing time: 0.004 seconds. 565s 565s Input: 8 reads 306 bases. 565s QTrimmed: 0 reads (0.00%) 0 bases (0.00%) 565s Total Removed: 8 reads (100.00%) 306 bases (100.00%) 565s Result: 0 reads (0.00%) 0 bases (0.00%) 565s 565s Time: 0.024 seconds. 565s Reads Processed: 8 0.33k reads/sec 565s Bases Processed: 306 0.01m bases/sec 565s test -r out.fastq.gz 565s 565s # bbnorm 565s bbnorm.sh --version 566s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 566s java -ea -Xmx2635m -Xms2635m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 --version 566s BBMap version 39.06 566s For help, please run the shellscript with no parameters, or look in /docs/. 566s bbnorm.sh --help 566s bbnorm.sh in=sanger_full_range_original_sanger.fastq qin=33 \ 566s out=out3.fastq outt=outt.fastq hist=hist.plt 566s 566s Written by Brian Bushnell 566s Last modified October 19, 2017 566s 566s Description: Normalizes read depth based on kmer counts. 566s Can also error-correct, bin reads by kmer depth, and generate a kmer depth histogram. 566s However, Tadpole has superior error-correction to BBNorm. 566s Please read bbmap/docs/guides/BBNormGuide.txt for more information. 566s 566s Usage: bbnorm.sh in= out= outt= hist= 566s 566s Input parameters: 566s in=null Primary input. Use in2 for paired reads in a second file 566s in2=null Second input file for paired reads in two files 566s extra=null Additional files to use for input (generating hash table) but not for output 566s fastareadlen=2^31 Break up FASTA reads longer than this. Can be useful when processing scaffolded genomes 566s tablereads=-1 Use at most this many reads when building the hashtable (-1 means all) 566s kmersample=1 Process every nth kmer, and skip the rest 566s readsample=1 Process every nth read, and skip the rest 566s 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. 566s qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto. 566s 566s Output parameters: 566s out= File for normalized or corrected reads. Use out2 for paired reads in a second file 566s outt= (outtoss) File for reads that were excluded from primary output 566s reads=-1 Only process this number of reads, then quit (-1 means all) 566s sampleoutput=t Use sampling on output as well as input (not used if sample rates are 1) 566s keepall=f Set to true to keep all reads (e.g. if you just want error correction). 566s 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. 566s Default is false, to prevent confusion about how there can be 0-count kmers. 566s The reason is that based on the 'minq' and 'minprob' settings, some kmers may be excluded from the bloom filter. 566s tmpdir= This will specify a directory for temp files (only needed for multipass runs). If null, they will be written to the output directory. 566s usetempdir=t Allows enabling/disabling of temporary directory; if disabled, temp files will be written to the output directory. 566s qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input). 566s rename=f Rename reads based on their kmer depth. 566s 566s Hashing parameters: 566s k=31 Kmer length (values under 32 are most efficient, but arbitrarily high values are supported) 566s 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. 566s Large values decrease accuracy for a fixed amount of memory, so use the lowest number you can that will still capture highest-depth kmers. 566s hashes=3 Number of times each kmer is hashed and stored. Higher is slower. 566s Higher is MORE accurate if there is enough memory, and LESS accurate if there is not enough memory. 566s 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. 566s prehashes=2 Number of hashes for prefilter. 566s prefilterbits=2 (pbits) Bits per cell in prefilter. 566s prefiltersize=0.35 Fraction of memory to allocate to prefilter. 566s buildpasses=1 More passes can sometimes increase accuracy by iteratively removing low-depth kmers 566s minq=6 Ignore kmers containing bases with quality below this 566s minprob=0.5 Ignore kmers with overall probability of correctness below this 566s 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. 566s 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. 566s 566s Normalization parameters: 566s fixspikes=f (fs) Do a slower, high-precision bloom filter lookup of kmers that appear to have an abnormally high depth due to collisions. 566s target=100 (tgt) Target normalization depth. NOTE: All depth parameters control kmer depth, not read depth. 566s For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1)) 566s maxdepth=-1 (max) Reads will not be downsampled when below this depth, even if they are above the target depth. 566s mindepth=5 (min) Kmers with depth below this number will not be included when calculating the depth of a read. 566s minkmers=15 (mgkpr) Reads must have at least this many kmers over min depth to be retained. Aka 'mingoodkmersperread'. 566s 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. 566s uselowerdepth=t (uld) For pairs, use the depth of the lower read as the depth proxy. 566s deterministic=t (dr) Generate random numbers deterministically to ensure identical output between multiple runs. May decrease speed with a huge number of threads. 566s passes=2 (p) 1 pass is the basic mode. 2 passes (default) allows greater accuracy, error detection, better contol of output depth. 566s 566s Error detection parameters: 566s hdp=90.0 (highdepthpercentile) Position in sorted kmer depth array used as proxy of a read's high kmer depth. 566s ldp=25.0 (lowdepthpercentile) Position in sorted kmer depth array used as proxy of a read's low kmer depth. 566s tossbadreads=f (tbr) Throw away reads detected as containing errors. 566s requirebothbad=f (rbb) Only toss bad pairs if both reads are bad. 566s 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. 566s highthresh=12 (ht) Threshold for high kmer. A high kmer at this or above are considered non-error. 566s lowthresh=3 (lt) Threshold for low kmer. Kmers at this and below are always considered errors. 566s 566s Error correction parameters: 566s ecc=f Set to true to correct errors. NOTE: Tadpole is now preferred for ecc as it does a better job. 566s ecclimit=3 Correct up to this many errors per read. If more are detected, the read will remain unchanged. 566s errorcorrectratio=140 (ecr) Adjacent kmers with a depth ratio of at least this much between will be classified as an error. 566s echighthresh=22 (echt) Threshold for high kmer. A kmer at this or above may be considered non-error. 566s eclowthresh=2 (eclt) Threshold for low kmer. Kmers at this and below are considered errors. 566s eccmaxqual=127 Do not correct bases with quality above this value. 566s aec=f (aggressiveErrorCorrection) Sets more aggressive values of ecr=100, ecclimit=7, echt=16, eclt=3. 566s cec=f (conservativeErrorCorrection) Sets more conservative values of ecr=180, ecclimit=2, echt=30, eclt=1, sl=4, pl=4. 566s meo=f (markErrorsOnly) Marks errors by reducing quality value of suspected errors; does not correct anything. 566s mue=t (markUncorrectableErrors) Marks errors only on uncorrectable reads; requires 'ecc=t'. 566s overlap=f (ecco) Error correct by read overlap. 566s 566s Depth binning parameters: 566s lowbindepth=10 (lbd) Cutoff for low depth bin. 566s highbindepth=80 (hbd) Cutoff for high depth bin. 566s outlow= Pairs in which both reads have a median below lbd go into this file. 566s outhigh= Pairs in which both reads have a median above hbd go into this file. 566s outmid= All other pairs go into this file. 566s 566s Histogram parameters: 566s hist= Specify a file to write the input kmer depth histogram. 566s histout= Specify a file to write the output kmer depth histogram. 566s histcol=3 (histogramcolumns) Number of histogram columns, 2 or 3. 566s pzc=f (printzerocoverage) Print lines in the histogram with zero coverage. 566s histlen=1048576 Max kmer depth displayed in histogram. Also affects statistics displayed, but does not affect normalization. 566s 566s Peak calling parameters: 566s peaks= Write the peaks to this file. Default is stdout. 566s minHeight=2 (h) Ignore peaks shorter than this. 566s minVolume=5 (v) Ignore peaks with less area than this. 566s minWidth=3 (w) Ignore peaks narrower than this. 566s minPeak=2 (minp) Ignore peaks with an X-value below this. 566s maxPeak=BIG (maxp) Ignore peaks with an X-value above this. 566s maxPeakCount=8 (maxpc) Print up to this many peaks (prioritizing height). 566s 566s Java Parameters: 566s -Xmx This will set Java's memory usage, overriding autodetection. 566s -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 566s The max is typically 85% of physical memory. 566s -eoom This flag will cause the process to exit if an 566s out-of-memory exception occurs. Requires Java 8u92+. 566s -da Disable assertions. 566s 566s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 566s 566s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 566s java -ea -Xmx2636m -Xms2636m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 in=sanger_full_range_original_sanger.fastq qin=33 out=out3.fastq outt=outt.fastq hist=hist.plt 566s Executing jgi.KmerNormalize [bits=32, in=sanger_full_range_original_sanger.fastq, qin=33, out=out3.fastq, outt=outt.fastq, hist=hist.plt] 566s 566s 566s *********** Pass 1 ********** 566s 566s 566s Settings: 566s threads: 4 566s k: 31 566s deterministic: true 566s toss error reads: false 566s passes: 1 566s bits per cell: 16 566s cells: 980.97M 566s hashes: 3 566s base min quality: 5 566s kmer min prob: 0.5 566s 566s target depth: 400 566s min depth: 3 566s max depth: 500 566s min good kmers: 15 566s depth percentile: 64.8 566s ignore dupe kmers: true 566s fix spikes: false 566s histogram length: 65536 566s print zero cov: false 566s 569s Made hash table: hashes = 3 mem = 1.83 GB cells = 980.47M used = 0.000% 569s 569s Estimated unique kmers: 7 569s 569s Table creation time: 2.705 seconds. 569s Started output threads. 569s Started output threads. 569s Table read time: 0.008 seconds. 24.42 kb/sec 569s Total reads in: 2 0.000% Kept 569s Total bases in: 188 0.000% Kept 569s Error reads in: 2 100.000% 569s Error type 1: 2 100.000% 569s Error type 2: 0 0.000% 569s Error type 3: 0 0.000% 569s 569s Wrote histogram to hist.plt 569s Total kmers counted: 128 569s Total unique kmer count: 128 569s Includes forward kmers only. 569s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 569s The most accurate value is the greater of the two. 569s 569s Percent unique: 100.00% 569s Depth average: 1.00 (unique kmers) 569s Depth median: 1 (unique kmers) 569s Depth standard deviation: 0.00 (unique kmers) 569s Corrected depth average: 0.00 569s 569s Depth average: 1.00 (all kmers) 569s Depth median: 1 (all kmers) 569s Depth standard deviation: 0.00 (all kmers) 569s 569s Approx. read depth median: 1.47 569s 569s *********** Pass 2 ********** 569s 569s 569s Settings: 569s threads: 4 569s k: 31 569s deterministic: true 569s toss error reads: false 569s passes: 1 569s bits per cell: 16 569s cells: 980.97M 569s hashes: 3 569s base min quality: 5 569s kmer min prob: 0.5 569s 569s target depth: 100 569s min depth: 5 569s max depth: 100 569s min good kmers: 15 569s depth percentile: 54.0 569s ignore dupe kmers: true 569s fix spikes: false 569s histogram length: 65536 569s 571s Made hash table: hashes = 3 mem = 1.83 GB cells = 980.47M used = 0.000% 571s 571s Estimated unique kmers: 0 571s 571s Table creation time: 2.590 seconds. 571s Started output threads. 571s Started output threads. 571s Table read time: 0.002 seconds. 0.00 kb/sec 571s Total reads in: 0 NaN% Kept 571s Total bases in: 0 NaN% Kept 571s Error reads in: 0 NaN% 571s Error type 1: 0 NaN% 571s Error type 2: 0 NaN% 571s Error type 3: 0 NaN% 571s Total kmers counted: 0 571s Total unique kmer count: 0 571s Includes forward kmers only. 571s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 571s The most accurate value is the greater of the two. 571s 571s Percent unique: NaN% 571s Depth average: NaN (unique kmers) 571s Depth median: 0 (unique kmers) 571s Depth standard deviation: NaN (unique kmers) 571s Corrected depth average: NaN 571s 571s Depth average: NaN (all kmers) 571s Depth median: 0 (all kmers) 571s Depth standard deviation: 0.00 (all kmers) 571s 571s Approx. read depth median: NaN 571s 571s Removing temp files. 571s 571s Total time: 5.422 seconds. 0.03 kb/sec 571s test -r out3.fastq 571s test -r outt.fastq 571s test -r hist.plt 571s bbnorm.sh in=illumina_full_range_original_illumina.fastq qin=64 \ 571s out=out4.fastq outt=outt2.fastq hist=hist2.plt 571s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 571s java -ea -Xmx2636m -Xms2636m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 in=illumina_full_range_original_illumina.fastq qin=64 out=out4.fastq outt=outt2.fastq hist=hist2.plt 571s Executing jgi.KmerNormalize [bits=32, in=illumina_full_range_original_illumina.fastq, qin=64, out=out4.fastq, outt=outt2.fastq, hist=hist2.plt] 571s 571s 571s *********** Pass 1 ********** 571s 571s 571s Settings: 571s threads: 4 571s k: 31 571s deterministic: true 571s toss error reads: false 571s passes: 1 571s bits per cell: 16 571s cells: 980.97M 571s hashes: 3 571s base min quality: 5 571s kmer min prob: 0.5 571s 571s target depth: 400 571s min depth: 3 571s max depth: 500 571s min good kmers: 15 571s depth percentile: 64.8 571s ignore dupe kmers: true 571s fix spikes: false 571s histogram length: 65536 571s print zero cov: false 571s 574s Made hash table: hashes = 3 mem = 1.83 GB cells = 980.47M used = 0.000% 574s 574s Estimated unique kmers: 7 574s 574s Table creation time: 2.698 seconds. 574s Started output threads. 574s Started output threads. 574s Table read time: 0.006 seconds. 21.36 kb/sec 574s Total reads in: 2 0.000% Kept 574s Total bases in: 126 0.000% Kept 574s Error reads in: 2 100.000% 574s Error type 1: 2 100.000% 574s Error type 2: 0 0.000% 574s Error type 3: 0 0.000% 574s 574s Wrote histogram to hist2.plt 574s Total kmers counted: 66 574s Total unique kmer count: 66 574s Includes forward kmers only. 574s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 574s The most accurate value is the greater of the two. 574s 574s Percent unique: 100.00% 574s Depth average: 1.00 (unique kmers) 574s Depth median: 1 (unique kmers) 574s Depth standard deviation: 0.00 (unique kmers) 574s Corrected depth average: 0.00 574s 574s Depth average: 1.00 (all kmers) 574s Depth median: 1 (all kmers) 574s Depth standard deviation: 0.00 (all kmers) 574s 574s Approx. read depth median: 1.91 574s 574s *********** Pass 2 ********** 574s 574s 574s Settings: 574s threads: 4 574s k: 31 574s deterministic: true 574s toss error reads: false 574s passes: 1 574s bits per cell: 16 574s cells: 980.97M 574s hashes: 3 574s base min quality: 5 574s kmer min prob: 0.5 574s 574s target depth: 100 574s min depth: 5 574s max depth: 100 574s min good kmers: 15 574s depth percentile: 54.0 574s ignore dupe kmers: true 574s fix spikes: false 574s histogram length: 65536 574s 577s Made hash table: hashes = 3 mem = 1.83 GB cells = 980.47M used = 0.000% 577s 577s Estimated unique kmers: 0 577s 577s Table creation time: 2.559 seconds. 577s Started output threads. 577s Started output threads. 577s Table read time: 0.003 seconds. 0.00 kb/sec 577s Total reads in: 0 NaN% Kept 577s Total bases in: 0 NaN% Kept 577s Error reads in: 0 NaN% 577s Error type 1: 0 NaN% 577s Error type 2: 0 NaN% 577s Error type 3: 0 NaN% 577s Total kmers counted: 0 577s Total unique kmer count: 0 577s Includes forward kmers only. 577s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 577s The most accurate value is the greater of the two. 577s 577s Percent unique: NaN% 577s Depth average: NaN (unique kmers) 577s Depth median: 0 (unique kmers) 577s Depth standard deviation: NaN (unique kmers) 577s Corrected depth average: NaN 577s 577s Depth average: NaN (all kmers) 577s Depth median: 0 (all kmers) 577s Depth standard deviation: 0.00 (all kmers) 577s 577s Approx. read depth median: NaN 577s 577s Removing temp files. 577s 577s Total time: 5.385 seconds. 0.02 kb/sec 577s test -r out4.fastq 577s test -r outt2.fastq 577s test -r hist2.plt 577s autopkgtest [14:57:55]: test run-unit-test: -----------------------] 578s autopkgtest [14:57:56]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 578s run-unit-test PASS 578s autopkgtest [14:57:56]: @@@@@@@@@@@@@@@@@@@@ summary 578s run-unit-test PASS 605s Creating nova instance adt-noble-ppc64el-bbmap-20240324-144818-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-ppc64el-server-20240324.img (UUID 456c38b1-f024-4aa9-9fc9-7cea731b220e)...