0s autopkgtest [12:31:30]: starting date and time: 2024-03-19 12:31:30+0000 0s autopkgtest [12:31:30]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [12:31:30]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.fzhdu3ee/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:openjdk-8,src:alsa-lib,src:libpng1.6,src:wp2latex --apt-upgrade bbmap --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=openjdk-8/8u402-ga-2ubuntu6 alsa-lib/1.2.11-1build1 libpng1.6/1.6.43-3 wp2latex/4.4~ds-1build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-big --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos01-ppc64el-10.secgroup --name adt-noble-ppc64el-bbmap-20240319-123130-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://us.ports.ubuntu.com/ubuntu-ports/ 186s autopkgtest [12:34:36]: testbed dpkg architecture: ppc64el 186s autopkgtest [12:34:36]: testbed apt version: 2.7.12 186s autopkgtest [12:34:36]: @@@@@@@@@@@@@@@@@@@@ test bed setup 188s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 188s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3777 kB] 189s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [487 kB] 189s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 189s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [53.7 kB] 189s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [651 kB] 189s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 189s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 189s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 189s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4049 kB] 189s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 189s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [48.5 kB] 189s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 193s Fetched 9203 kB in 3s (3304 kB/s) 193s Reading package lists... 196s Reading package lists... 196s Building dependency tree... 196s Reading state information... 197s Calculating upgrade... 197s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 197s Reading package lists... 197s Building dependency tree... 197s Reading state information... 198s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 198s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 198s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 198s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 198s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 200s Reading package lists... 200s Reading package lists... 200s Building dependency tree... 200s Reading state information... 201s Calculating upgrade... 201s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 201s Reading package lists... 201s Building dependency tree... 201s Reading state information... 201s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 205s autopkgtest [12:34:55]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 205s autopkgtest [12:34:55]: @@@@@@@@@@@@@@@@@@@@ apt-source bbmap 208s Get:1 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (dsc) [2286 B] 208s Get:2 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (tar) [5343 kB] 208s Get:3 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (diff) [25.4 kB] 208s gpgv: Signature made Fri Nov 24 11:00:29 2023 UTC 208s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 208s gpgv: issuer "emollier@debian.org" 208s gpgv: Can't check signature: No public key 208s dpkg-source: warning: cannot verify inline signature for ./bbmap_39.06+dfsg-1.dsc: no acceptable signature found 209s autopkgtest [12:34:59]: testing package bbmap version 39.06+dfsg-1 209s autopkgtest [12:34:59]: build not needed 213s autopkgtest [12:35:03]: test run-unit-test: preparing testbed 214s Reading package lists... 215s Building dependency tree... 215s Reading state information... 215s Starting pkgProblemResolver with broken count: 0 215s Starting 2 pkgProblemResolver with broken count: 0 215s Done 215s The following additional packages will be installed: 215s bbmap bbmap-jni ca-certificates-java fontconfig-config fonts-dejavu-core 215s fonts-dejavu-mono java-common libapache-pom-java libasound2 libasound2-data 215s libavahi-client3 libavahi-common-data libavahi-common3 libcommons-cli-java 215s libcommons-codec-java libcommons-io-java libcommons-parent-java libcups2 215s libfontconfig1 libgraphite2-3 libharfbuzz0b libjpeg-turbo8 libjpeg8 215s liblcms2-2 liblog4j1.2-java libmpj-java libpcsclite1 openjdk-17-jre-headless 215s python-biopython-doc 215s Suggested packages: 215s default-jre libasound2-plugins alsa-utils libcommons-io-java-doc cups-common 215s liblcms2-utils liblog4j1.2-java-doc libmail-java pcscd libnss-mdns 215s fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho 215s fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic 215s Recommended packages: 215s pigz alsa-ucm-conf alsa-topology-conf python3-biopython 215s The following NEW packages will be installed: 215s autopkgtest-satdep bbmap bbmap-jni ca-certificates-java fontconfig-config 215s fonts-dejavu-core fonts-dejavu-mono java-common libapache-pom-java 215s libasound2 libasound2-data libavahi-client3 libavahi-common-data 215s libavahi-common3 libcommons-cli-java libcommons-codec-java 215s libcommons-io-java libcommons-parent-java libcups2 libfontconfig1 215s libgraphite2-3 libharfbuzz0b libjpeg-turbo8 libjpeg8 liblcms2-2 215s liblog4j1.2-java libmpj-java libpcsclite1 openjdk-17-jre-headless 215s python-biopython-doc 215s 0 upgraded, 30 newly installed, 0 to remove and 0 not upgraded. 215s Need to get 79.6 MB/79.6 MB of archives. 215s After this operation, 240 MB of additional disk space will be used. 215s Get:1 /tmp/autopkgtest.KSTWlk/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [724 B] 215s Get:2 http://ftpmaster.internal/ubuntu noble/universe ppc64el libcommons-cli-java all 1.6.0-1 [59.9 kB] 216s Get:3 http://ftpmaster.internal/ubuntu noble/universe ppc64el libapache-pom-java all 29-2 [5284 B] 216s Get:4 http://ftpmaster.internal/ubuntu noble/universe ppc64el libcommons-parent-java all 56-1 [10.7 kB] 216s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el libcommons-codec-java all 1.16.0-1 [306 kB] 216s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el libcommons-io-java all 2.11.0-2 [297 kB] 216s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el liblog4j1.2-java all 1.2.17-11 [439 kB] 216s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el libmpj-java all 0.44+dfsg-4 [443 kB] 216s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el ca-certificates-java all 20240118 [11.6 kB] 216s Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el java-common all 0.75+exp1 [6798 B] 216s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el libavahi-common-data ppc64el 0.8-13ubuntu2 [29.5 kB] 216s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el libavahi-common3 ppc64el 0.8-13ubuntu2 [25.8 kB] 216s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el libavahi-client3 ppc64el 0.8-13ubuntu2 [30.6 kB] 216s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el libcups2 ppc64el 2.4.6-0ubuntu3 [344 kB] 216s Get:15 http://ftpmaster.internal/ubuntu noble/main ppc64el liblcms2-2 ppc64el 2.14-2 [243 kB] 216s Get:16 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu1 [212 kB] 216s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 216s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB] 216s Get:19 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB] 216s Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el fontconfig-config ppc64el 2.15.0-1ubuntu1 [37.0 kB] 216s Get:21 http://ftpmaster.internal/ubuntu noble/main ppc64el libfontconfig1 ppc64el 2.15.0-1ubuntu1 [190 kB] 216s Get:22 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libasound2-data all 1.2.11-1build1 [21.0 kB] 216s Get:23 http://ftpmaster.internal/ubuntu noble/main ppc64el libasound2 ppc64el 1.2.10-3build1 [496 kB] 216s Get:24 http://ftpmaster.internal/ubuntu noble/main ppc64el libgraphite2-3 ppc64el 1.3.14-2 [105 kB] 216s Get:25 http://ftpmaster.internal/ubuntu noble/main ppc64el libharfbuzz0b ppc64el 8.3.0-2 [576 kB] 216s Get:26 http://ftpmaster.internal/ubuntu noble/main ppc64el libpcsclite1 ppc64el 2.0.0-1 [27.9 kB] 216s Get:27 http://ftpmaster.internal/ubuntu noble/main ppc64el openjdk-17-jre-headless ppc64el 17.0.10+7-1 [47.2 MB] 218s Get:28 http://ftpmaster.internal/ubuntu noble/universe ppc64el bbmap all 39.06+dfsg-1 [9768 kB] 219s Get:29 http://ftpmaster.internal/ubuntu noble/universe ppc64el bbmap-jni ppc64el 39.06+dfsg-1 [32.8 kB] 219s Get:30 http://ftpmaster.internal/ubuntu noble/universe ppc64el python-biopython-doc all 1.81+dfsg-3 [17.3 MB] 220s Fetched 79.6 MB in 4s (20.3 MB/s) 220s Selecting previously unselected package libcommons-cli-java. 220s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70095 files and directories currently installed.) 220s Preparing to unpack .../00-libcommons-cli-java_1.6.0-1_all.deb ... 220s Unpacking libcommons-cli-java (1.6.0-1) ... 220s Selecting previously unselected package libapache-pom-java. 220s Preparing to unpack .../01-libapache-pom-java_29-2_all.deb ... 220s Unpacking libapache-pom-java (29-2) ... 220s Selecting previously unselected package libcommons-parent-java. 220s Preparing to unpack .../02-libcommons-parent-java_56-1_all.deb ... 220s Unpacking libcommons-parent-java (56-1) ... 220s Selecting previously unselected package libcommons-codec-java. 220s Preparing to unpack .../03-libcommons-codec-java_1.16.0-1_all.deb ... 220s Unpacking libcommons-codec-java (1.16.0-1) ... 220s Selecting previously unselected package libcommons-io-java. 220s Preparing to unpack .../04-libcommons-io-java_2.11.0-2_all.deb ... 220s Unpacking libcommons-io-java (2.11.0-2) ... 220s Selecting previously unselected package liblog4j1.2-java. 220s Preparing to unpack .../05-liblog4j1.2-java_1.2.17-11_all.deb ... 220s Unpacking liblog4j1.2-java (1.2.17-11) ... 220s Selecting previously unselected package libmpj-java. 220s Preparing to unpack .../06-libmpj-java_0.44+dfsg-4_all.deb ... 220s Unpacking libmpj-java (0.44+dfsg-4) ... 220s Selecting previously unselected package ca-certificates-java. 220s Preparing to unpack .../07-ca-certificates-java_20240118_all.deb ... 220s Unpacking ca-certificates-java (20240118) ... 220s Selecting previously unselected package java-common. 220s Preparing to unpack .../08-java-common_0.75+exp1_all.deb ... 220s Unpacking java-common (0.75+exp1) ... 220s Selecting previously unselected package libavahi-common-data:ppc64el. 220s Preparing to unpack .../09-libavahi-common-data_0.8-13ubuntu2_ppc64el.deb ... 220s Unpacking libavahi-common-data:ppc64el (0.8-13ubuntu2) ... 220s Selecting previously unselected package libavahi-common3:ppc64el. 220s Preparing to unpack .../10-libavahi-common3_0.8-13ubuntu2_ppc64el.deb ... 220s Unpacking libavahi-common3:ppc64el (0.8-13ubuntu2) ... 220s Selecting previously unselected package libavahi-client3:ppc64el. 220s Preparing to unpack .../11-libavahi-client3_0.8-13ubuntu2_ppc64el.deb ... 220s Unpacking libavahi-client3:ppc64el (0.8-13ubuntu2) ... 220s Selecting previously unselected package libcups2:ppc64el. 220s Preparing to unpack .../12-libcups2_2.4.6-0ubuntu3_ppc64el.deb ... 220s Unpacking libcups2:ppc64el (2.4.6-0ubuntu3) ... 220s Selecting previously unselected package liblcms2-2:ppc64el. 220s Preparing to unpack .../13-liblcms2-2_2.14-2_ppc64el.deb ... 220s Unpacking liblcms2-2:ppc64el (2.14-2) ... 220s Selecting previously unselected package libjpeg-turbo8:ppc64el. 220s Preparing to unpack .../14-libjpeg-turbo8_2.1.5-2ubuntu1_ppc64el.deb ... 220s Unpacking libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 220s Selecting previously unselected package libjpeg8:ppc64el. 220s Preparing to unpack .../15-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 220s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 220s Selecting previously unselected package fonts-dejavu-mono. 220s Preparing to unpack .../16-fonts-dejavu-mono_2.37-8_all.deb ... 220s Unpacking fonts-dejavu-mono (2.37-8) ... 221s Selecting previously unselected package fonts-dejavu-core. 221s Preparing to unpack .../17-fonts-dejavu-core_2.37-8_all.deb ... 221s Unpacking fonts-dejavu-core (2.37-8) ... 221s Selecting previously unselected package fontconfig-config. 221s Preparing to unpack .../18-fontconfig-config_2.15.0-1ubuntu1_ppc64el.deb ... 221s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 221s Selecting previously unselected package libfontconfig1:ppc64el. 221s Preparing to unpack .../19-libfontconfig1_2.15.0-1ubuntu1_ppc64el.deb ... 221s Unpacking libfontconfig1:ppc64el (2.15.0-1ubuntu1) ... 221s Selecting previously unselected package libasound2-data. 221s Preparing to unpack .../20-libasound2-data_1.2.11-1build1_all.deb ... 221s Unpacking libasound2-data (1.2.11-1build1) ... 221s Selecting previously unselected package libasound2:ppc64el. 221s Preparing to unpack .../21-libasound2_1.2.10-3build1_ppc64el.deb ... 221s Unpacking libasound2:ppc64el (1.2.10-3build1) ... 221s Selecting previously unselected package libgraphite2-3:ppc64el. 221s Preparing to unpack .../22-libgraphite2-3_1.3.14-2_ppc64el.deb ... 221s Unpacking libgraphite2-3:ppc64el (1.3.14-2) ... 221s Selecting previously unselected package libharfbuzz0b:ppc64el. 221s Preparing to unpack .../23-libharfbuzz0b_8.3.0-2_ppc64el.deb ... 221s Unpacking libharfbuzz0b:ppc64el (8.3.0-2) ... 221s Selecting previously unselected package libpcsclite1:ppc64el. 221s Preparing to unpack .../24-libpcsclite1_2.0.0-1_ppc64el.deb ... 221s Unpacking libpcsclite1:ppc64el (2.0.0-1) ... 221s Selecting previously unselected package openjdk-17-jre-headless:ppc64el. 221s Preparing to unpack .../25-openjdk-17-jre-headless_17.0.10+7-1_ppc64el.deb ... 221s Unpacking openjdk-17-jre-headless:ppc64el (17.0.10+7-1) ... 222s Selecting previously unselected package bbmap. 222s Preparing to unpack .../26-bbmap_39.06+dfsg-1_all.deb ... 222s Unpacking bbmap (39.06+dfsg-1) ... 223s Selecting previously unselected package bbmap-jni. 223s Preparing to unpack .../27-bbmap-jni_39.06+dfsg-1_ppc64el.deb ... 223s Unpacking bbmap-jni (39.06+dfsg-1) ... 223s Selecting previously unselected package python-biopython-doc. 223s Preparing to unpack .../28-python-biopython-doc_1.81+dfsg-3_all.deb ... 223s Unpacking python-biopython-doc (1.81+dfsg-3) ... 223s Selecting previously unselected package autopkgtest-satdep. 223s Preparing to unpack .../29-1-autopkgtest-satdep.deb ... 223s Unpacking autopkgtest-satdep (0) ... 223s Setting up libgraphite2-3:ppc64el (1.3.14-2) ... 223s Setting up liblcms2-2:ppc64el (2.14-2) ... 223s Setting up java-common (0.75+exp1) ... 223s Setting up libcommons-cli-java (1.6.0-1) ... 223s Setting up liblog4j1.2-java (1.2.17-11) ... 223s Setting up libasound2-data (1.2.11-1build1) ... 223s Setting up libapache-pom-java (29-2) ... 223s Setting up libavahi-common-data:ppc64el (0.8-13ubuntu2) ... 223s Setting up fonts-dejavu-mono (2.37-8) ... 223s Setting up fonts-dejavu-core (2.37-8) ... 223s Setting up libpcsclite1:ppc64el (2.0.0-1) ... 223s Setting up libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 223s Setting up python-biopython-doc (1.81+dfsg-3) ... 223s Setting up libasound2:ppc64el (1.2.10-3build1) ... 223s Setting up libharfbuzz0b:ppc64el (8.3.0-2) ... 223s Setting up bbmap-jni (39.06+dfsg-1) ... 223s Setting up ca-certificates-java (20240118) ... 223s No JRE found. Skipping Java certificates setup. 223s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 223s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 223s Setting up libcommons-parent-java (56-1) ... 223s Setting up libavahi-common3:ppc64el (0.8-13ubuntu2) ... 223s Setting up libfontconfig1:ppc64el (2.15.0-1ubuntu1) ... 223s Setting up libcommons-codec-java (1.16.0-1) ... 223s Setting up libavahi-client3:ppc64el (0.8-13ubuntu2) ... 223s Setting up libcommons-io-java (2.11.0-2) ... 223s Setting up libmpj-java (0.44+dfsg-4) ... 223s Setting up libcups2:ppc64el (2.4.6-0ubuntu3) ... 223s Setting up openjdk-17-jre-headless:ppc64el (17.0.10+7-1) ... 223s update-alternatives: using /usr/lib/jvm/java-17-openjdk-ppc64el/bin/java to provide /usr/bin/java (java) in auto mode 223s update-alternatives: using /usr/lib/jvm/java-17-openjdk-ppc64el/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 223s update-alternatives: using /usr/lib/jvm/java-17-openjdk-ppc64el/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 223s update-alternatives: using /usr/lib/jvm/java-17-openjdk-ppc64el/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 223s update-alternatives: using /usr/lib/jvm/java-17-openjdk-ppc64el/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 223s Processing triggers for libc-bin (2.39-0ubuntu2) ... 223s Processing triggers for man-db (2.12.0-3) ... 225s Processing triggers for ca-certificates-java (20240118) ... 226s Adding debian:ACCVRAIZ1.pem 226s Adding debian:AC_RAIZ_FNMT-RCM.pem 226s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 226s Adding debian:ANF_Secure_Server_Root_CA.pem 226s Adding debian:Actalis_Authentication_Root_CA.pem 226s Adding debian:AffirmTrust_Commercial.pem 226s Adding debian:AffirmTrust_Networking.pem 226s Adding debian:AffirmTrust_Premium.pem 226s Adding debian:AffirmTrust_Premium_ECC.pem 226s Adding debian:Amazon_Root_CA_1.pem 226s Adding debian:Amazon_Root_CA_2.pem 226s Adding debian:Amazon_Root_CA_3.pem 226s Adding debian:Amazon_Root_CA_4.pem 226s Adding debian:Atos_TrustedRoot_2011.pem 226s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 226s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 226s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 226s Adding debian:BJCA_Global_Root_CA1.pem 226s Adding debian:BJCA_Global_Root_CA2.pem 226s Adding debian:Baltimore_CyberTrust_Root.pem 226s Adding debian:Buypass_Class_2_Root_CA.pem 226s Adding debian:Buypass_Class_3_Root_CA.pem 226s Adding debian:CA_Disig_Root_R2.pem 226s Adding debian:CFCA_EV_ROOT.pem 226s Adding debian:COMODO_Certification_Authority.pem 226s Adding debian:COMODO_ECC_Certification_Authority.pem 226s Adding debian:COMODO_RSA_Certification_Authority.pem 226s Adding debian:Certainly_Root_E1.pem 226s Adding debian:Certainly_Root_R1.pem 226s Adding debian:Certigna.pem 226s Adding debian:Certigna_Root_CA.pem 226s Adding debian:Certum_EC-384_CA.pem 226s Adding debian:Certum_Trusted_Network_CA.pem 226s Adding debian:Certum_Trusted_Network_CA_2.pem 226s Adding debian:Certum_Trusted_Root_CA.pem 226s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 226s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 226s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 226s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 226s Adding debian:Comodo_AAA_Services_root.pem 226s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 226s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 226s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 226s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 226s Adding debian:DigiCert_Assured_ID_Root_CA.pem 226s Adding debian:DigiCert_Assured_ID_Root_G2.pem 226s Adding debian:DigiCert_Assured_ID_Root_G3.pem 226s Adding debian:DigiCert_Global_Root_CA.pem 226s Adding debian:DigiCert_Global_Root_G2.pem 226s Adding debian:DigiCert_Global_Root_G3.pem 226s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 226s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 226s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 226s Adding debian:DigiCert_Trusted_Root_G4.pem 226s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 226s Adding debian:Entrust_Root_Certification_Authority.pem 226s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 226s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 226s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem 226s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 226s Adding debian:GLOBALTRUST_2020.pem 226s Adding debian:GTS_Root_R1.pem 226s Adding debian:GTS_Root_R2.pem 226s Adding debian:GTS_Root_R3.pem 226s Adding debian:GTS_Root_R4.pem 226s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 226s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 226s Adding debian:GlobalSign_Root_CA.pem 226s Adding debian:GlobalSign_Root_CA_-_R3.pem 226s Adding debian:GlobalSign_Root_CA_-_R6.pem 226s Adding debian:GlobalSign_Root_E46.pem 226s Adding debian:GlobalSign_Root_R46.pem 226s Adding debian:Go_Daddy_Class_2_CA.pem 226s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 226s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 226s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 226s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 226s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 226s Adding debian:HiPKI_Root_CA_-_G1.pem 226s Adding debian:Hongkong_Post_Root_CA_3.pem 226s Adding debian:ISRG_Root_X1.pem 226s Adding debian:ISRG_Root_X2.pem 226s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 226s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 226s Adding debian:Izenpe.com.pem 226s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 226s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 226s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 226s Adding debian:NAVER_Global_Root_Certification_Authority.pem 226s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 226s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 226s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 226s Adding debian:QuoVadis_Root_CA_1_G3.pem 226s Adding debian:QuoVadis_Root_CA_2.pem 226s Adding debian:QuoVadis_Root_CA_2_G3.pem 226s Adding debian:QuoVadis_Root_CA_3.pem 226s Adding debian:QuoVadis_Root_CA_3_G3.pem 226s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 226s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 226s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 226s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 226s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 226s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 226s Adding debian:SZAFIR_ROOT_CA2.pem 226s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 226s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 226s Adding debian:SecureSign_RootCA11.pem 226s Adding debian:SecureTrust_CA.pem 226s Adding debian:Secure_Global_CA.pem 226s Adding debian:Security_Communication_ECC_RootCA1.pem 226s Adding debian:Security_Communication_RootCA2.pem 226s Adding debian:Security_Communication_RootCA3.pem 226s Adding debian:Security_Communication_Root_CA.pem 226s Adding debian:Starfield_Class_2_CA.pem 226s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 226s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 226s Adding debian:SwissSign_Gold_CA_-_G2.pem 226s Adding debian:SwissSign_Silver_CA_-_G2.pem 226s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 226s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 226s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 226s Adding debian:TWCA_Global_Root_CA.pem 226s Adding debian:TWCA_Root_Certification_Authority.pem 226s Adding debian:TeliaSonera_Root_CA_v1.pem 226s Adding debian:Telia_Root_CA_v2.pem 226s Adding debian:TrustAsia_Global_Root_CA_G3.pem 226s Adding debian:TrustAsia_Global_Root_CA_G4.pem 226s Adding debian:Trustwave_Global_Certification_Authority.pem 226s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 226s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 226s Adding debian:TunTrust_Root_CA.pem 226s Adding debian:UCA_Extended_Validation_Root.pem 226s Adding debian:UCA_Global_G2_Root.pem 226s Adding debian:USERTrust_ECC_Certification_Authority.pem 226s Adding debian:USERTrust_RSA_Certification_Authority.pem 226s Adding debian:XRamp_Global_CA_Root.pem 226s Adding debian:certSIGN_ROOT_CA.pem 226s Adding debian:certSIGN_Root_CA_G2.pem 226s Adding debian:e-Szigno_Root_CA_2017.pem 226s Adding debian:ePKI_Root_Certification_Authority.pem 226s Adding debian:emSign_ECC_Root_CA_-_C3.pem 226s Adding debian:emSign_ECC_Root_CA_-_G3.pem 226s Adding debian:emSign_Root_CA_-_C1.pem 226s Adding debian:emSign_Root_CA_-_G1.pem 226s Adding debian:vTrus_ECC_Root_CA.pem 226s Adding debian:vTrus_Root_CA.pem 226s done. 226s Setting up bbmap (39.06+dfsg-1) ... 226s Setting up autopkgtest-satdep (0) ... 230s (Reading database ... 72934 files and directories currently installed.) 230s Removing autopkgtest-satdep (0) ... 231s autopkgtest [12:35:21]: test run-unit-test: [----------------------- 231s 231s # bbmap 231s bbmap.sh --version 231s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 231s java -ea -Xmx2635m -Xms2635m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 --version 231s BBMap version 39.06 231s For help, please run the shellscript with no parameters, or look in /docs/. 231s bbmap.sh --help 231s bbmap.sh ref=example.fasta 231s 231s BBMap 231s Written by Brian Bushnell, from Dec. 2010 - present 231s Last modified September 15, 2022 231s 231s Description: Fast and accurate splice-aware read aligner. 231s Please read bbmap/docs/guides/BBMapGuide.txt for more information. 231s 231s To index: bbmap.sh ref= 231s To map: bbmap.sh in= out= 231s To map without writing an index: 231s bbmap.sh ref= in= out= nodisk 231s 231s in=stdin will accept reads from standard in, and out=stdout will write to 231s standard out, but file extensions are still needed to specify the format of the 231s input and output files e.g. in=stdin.fa.gz will read gzipped fasta from 231s standard in; out=stdout.sam.gz will write gzipped sam. 231s 231s Indexing Parameters (required when building the index): 231s nodisk=f Set to true to build index in memory and write nothing 231s to disk except output. 231s ref= Specify the reference sequence. Only do this ONCE, 231s when building the index (unless using 'nodisk'). 231s build=1 If multiple references are indexed in the same directory, 231s each needs a unique numeric ID (unless using 'nodisk'). 231s k=13 Kmer length, range 8-15. Longer is faster but uses 231s more memory. Shorter is more sensitive. 231s If indexing and mapping are done in two steps, K should 231s be specified each time. 231s path=<.> Specify the location to write the index, if you don't 231s want it in the current working directory. 231s usemodulo=f Throw away ~80% of kmers based on remainder modulo a 231s number (reduces RAM by 50% and sensitivity slightly). 231s Should be enabled both when building the index AND 231s when mapping. 231s rebuild=f Force a rebuild of the index (ref= should be set). 231s 231s Input Parameters: 231s build=1 Designate index to use. Corresponds to the number 231s specified when building the index. 231s in= Primary reads input; required parameter. 231s in2= For paired reads in two files. 231s interleaved=auto True forces paired/interleaved input; false forces 231s single-ended mapping. If not specified, interleaved 231s status will be autodetected from read names. 231s fastareadlen=500 Break up FASTA reads longer than this. Max is 500 for 231s BBMap and 6000 for BBMapPacBio. Only works for FASTA 231s input (use 'maxlen' for FASTQ input). The default for 231s bbmap.sh is 500, and for mapPacBio.sh is 6000. 231s unpigz=f Spawn a pigz (parallel gzip) process for faster 231s decompression than using Java. 231s Requires pigz to be installed. 231s touppercase=t (tuc) Convert lowercase letters in reads to upper case 231s (otherwise they will not match the reference). 231s 231s Sampling Parameters: 231s 231s reads=-1 Set to a positive number N to only process the first N 231s reads (or pairs), then quit. -1 means use all reads. 231s samplerate=1 Set to a number from 0 to 1 to randomly select that 231s fraction of reads for mapping. 1 uses all reads. 231s skipreads=0 Set to a number N to skip the first N reads (or pairs), 231s then map the rest. 231s 231s Mapping Parameters: 231s fast=f This flag is a macro which sets other paramters to run 231s faster, at reduced sensitivity. Bad for RNA-seq. 231s slow=f This flag is a macro which sets other paramters to run 231s slower, at greater sensitivity. 'vslow' is even slower. 231s maxindel=16000 Don't look for indels longer than this. Lower is faster. 231s Set to >=100k for RNAseq with long introns like mammals. 231s strictmaxindel=f When enabled, do not allow indels longer than 'maxindel'. 231s By default these are not sought, but may be found anyway. 231s tipsearch=100 Look this far for read-end deletions with anchors 231s shorter than K, using brute force. 231s minid=0.76 Approximate minimum alignment identity to look for. 231s Higher is faster and less sensitive. 231s minhits=1 Minimum number of seed hits required for candidate sites. 231s Higher is faster. 231s local=f Set to true to use local, rather than global, alignments. 231s This will soft-clip ugly ends of poor alignments. 231s perfectmode=f Allow only perfect mappings when set to true (very fast). 231s semiperfectmode=f Allow only perfect and semiperfect (perfect except for 231s N's in the reference) mappings. 231s threads=auto (t) Set to number of threads desired. By default, uses 231s all cores available. 231s ambiguous=best (ambig) Set behavior on ambiguously-mapped reads (with 231s multiple top-scoring mapping locations). 231s best (use the first best site) 231s toss (consider unmapped) 231s random (select one top-scoring site randomly) 231s all (retain all top-scoring sites) 231s samestrandpairs=f (ssp) Specify whether paired reads should map to the 231s same strand or opposite strands. 231s requirecorrectstrand=t (rcs) Forbid pairing of reads without correct strand 231s orientation. Set to false for long-mate-pair libraries. 231s killbadpairs=f (kbp) If a read pair is mapped with an inappropriate 231s insert size or orientation, the read with the lower 231s mapping quality is marked unmapped. 231s pairedonly=f (po) Treat unpaired reads as unmapped. Thus they will 231s be sent to 'outu' but not 'outm'. 231s rcomp=f Reverse complement both reads prior to mapping (for LMP 231s outward-facing libraries). 231s rcompmate=f Reverse complement read2 prior to mapping. 231s pairlen=32000 Set max allowed distance between paired reads. 231s (insert size)=(pairlen)+(read1 length)+(read2 length) 231s rescuedist=1200 Don't try to rescue paired reads if avg. insert size 231s greater than this. Lower is faster. 231s rescuemismatches=32 Maximum mismatches allowed in a rescued read. Lower 231s is faster. 231s averagepairdist=100 (apd) Initial average distance between paired reads. 231s Varies dynamically; does not need to be specified. 231s deterministic=f Run in deterministic mode. In this case it is good 231s to set averagepairdist. BBMap is deterministic 231s without this flag if using single-ended reads, 231s or run singlethreaded. 231s bandwidthratio=0 (bwr) If above zero, restrict alignment band to this 231s fraction of read length. Faster but less accurate. 231s bandwidth=0 (bw) Set the bandwidth directly. 231s fraction of read length. Faster but less accurate. 231s usejni=f (jni) Do alignments faster, in C code. Requires 231s compiling the C code; details are in /jni/README.txt. 231s maxsites2=800 Don't analyze (or print) more than this many alignments 231s per read. 231s ignorefrequentkmers=t (ifk) Discard low-information kmers that occur often. 231s excludefraction=0.03 (ef) Fraction of kmers to ignore. For example, 0.03 231s will ignore the most common 3% of kmers. 231s greedy=t Use a greedy algorithm to discard the least-useful 231s kmers on a per-read basis. 231s kfilter=0 If positive, potential mapping sites must have at 231s least this many consecutive exact matches. 231s 231s 231s Quality and Trimming Parameters: 231s qin=auto Set to 33 or 64 to specify input quality value ASCII 231s offset. 33 is Sanger, 64 is old Solexa. 231s qout=auto Set to 33 or 64 to specify output quality value ASCII 231s offset (only if output format is fastq). 231s qtrim=f Quality-trim ends before mapping. Options are: 231s 'f' (false), 'l' (left), 'r' (right), and 'lr' (both). 231s untrim=f Undo trimming after mapping. Untrimmed bases will be 231s soft-clipped in cigar strings. 231s trimq=6 Trim regions with average quality below this 231s (phred algorithm). 231s mintrimlength=60 (mintl) Don't trim reads to be shorter than this. 231s fakefastaquality=-1 (ffq) Set to a positive number 1-50 to generate fake 231s quality strings for fasta input reads. 231s ignorebadquality=f (ibq) Keep going, rather than crashing, if a read has 231s out-of-range quality values. 231s usequality=t Use quality scores when determining which read kmers 231s to use as seeds. 231s minaveragequality=0 (maq) Do not map reads with average quality below this. 231s maqb=0 If positive, calculate maq from this many initial bases. 231s 231s Output Parameters: 231s out= Write all reads to this file. 231s outu= Write only unmapped reads to this file. Does not 231s include unmapped paired reads with a mapped mate. 231s outm= Write only mapped reads to this file. Includes 231s unmapped paired reads with a mapped mate. 231s mappedonly=f If true, treats 'out' like 'outm'. 231s bamscript= (bs) Write a shell script to that will turn 231s the sam output into a sorted, indexed bam file. 231s ordered=f Set to true to output reads in same order as input. 231s Slower and uses more memory. 231s overwrite=f (ow) Allow process to overwrite existing files. 231s secondary=f Print secondary alignments. 231s sssr=0.95 (secondarysitescoreratio) Print only secondary alignments 231s with score of at least this fraction of primary. 231s ssao=f (secondarysiteasambiguousonly) Only print secondary 231s alignments for ambiguously-mapped reads. 231s maxsites=5 Maximum number of total alignments to print per read. 231s Only relevant when secondary=t. 231s quickmatch=f Generate cigar strings more quickly. 231s trimreaddescriptions=f (trd) Truncate read and ref names at the first whitespace, 231s assuming that the remainder is a comment or description. 231s ziplevel=2 (zl) Compression level for zip or gzip output. 231s pigz=f Spawn a pigz (parallel gzip) process for faster 231s compression than Java. Requires pigz to be installed. 231s machineout=f Set to true to output statistics in machine-friendly 231s 'key=value' format. 231s printunmappedcount=f Print the total number of unmapped reads and bases. 231s If input is paired, the number will be of pairs 231s for which both reads are unmapped. 231s showprogress=0 If positive, print a '.' every X reads. 231s showprogress2=0 If positive, print the number of seconds since the 231s last progress update (instead of a '.'). 231s renamebyinsert=f Renames reads based on their mapped insert size. 231s 231s Bloom-Filtering Parameters (bloomfilter.sh is the standalone version). 231s bloom=f Use a Bloom filter to ignore reads not sharing kmers 231s with the reference. This uses more memory, but speeds 231s mapping when most reads don't match the reference. 231s bloomhashes=2 Number of hash functions. 231s bloomminhits=3 Number of consecutive hits to be considered matched. 231s bloomk=31 Bloom filter kmer length. 231s bloomserial=t Use the serialized Bloom filter for greater loading 231s speed, if available. If not, generate and write one. 231s 231s Post-Filtering Parameters: 231s idfilter=0 Independant of minid; sets exact minimum identity 231s allowed for alignments to be printed. Range 0 to 1. 231s subfilter=-1 Ban alignments with more than this many substitutions. 231s insfilter=-1 Ban alignments with more than this many insertions. 231s delfilter=-1 Ban alignments with more than this many deletions. 231s indelfilter=-1 Ban alignments with more than this many indels. 231s editfilter=-1 Ban alignments with more than this many edits. 231s inslenfilter=-1 Ban alignments with an insertion longer than this. 231s dellenfilter=-1 Ban alignments with a deletion longer than this. 231s nfilter=-1 Ban alignments with more than this many ns. This 231s includes nocall, noref, and off scaffold ends. 231s 231s Sam flags and settings: 231s noheader=f Disable generation of header lines. 231s sam=1.4 Set to 1.4 to write Sam version 1.4 cigar strings, 231s with = and X, or 1.3 to use M. 231s saa=t (secondaryalignmentasterisks) Use asterisks instead of 231s bases for sam secondary alignments. 231s cigar=t Set to 'f' to skip generation of cigar strings (faster). 231s keepnames=f Keep original names of paired reads, rather than 231s ensuring both reads have the same name. 231s intronlen=999999999 Set to a lower number like 10 to change 'D' to 'N' in 231s cigar strings for deletions of at least that length. 231s rgid= Set readgroup ID. All other readgroup fields 231s can be set similarly, with the flag rgXX= 231s If you set a readgroup flag to the word 'filename', 231s e.g. rgid=filename, the input file name will be used. 231s mdtag=f Write MD tags. 231s nhtag=f Write NH tags. 231s xmtag=f Write XM tags (may only work correctly with ambig=all). 231s amtag=f Write AM tags. 231s nmtag=f Write NM tags. 231s xstag=f Set to 'xs=fs', 'xs=ss', or 'xs=us' to write XS tags 231s for RNAseq using firststrand, secondstrand, or 231s unstranded libraries. Needed by Cufflinks. 231s JGI mainly uses 'firststrand'. 231s stoptag=f Write a tag indicating read stop location, prefixed by YS:i: 231s lengthtag=f Write a tag indicating (query,ref) alignment lengths, 231s prefixed by YL:Z: 231s idtag=f Write a tag indicating percent identity, prefixed by YI:f: 231s inserttag=f Write a tag indicating insert size, prefixed by X8:Z: 231s scoretag=f Write a tag indicating BBMap's raw score, prefixed by YR:i: 231s timetag=f Write a tag indicating this read's mapping time, prefixed by X0:i: 231s boundstag=f Write a tag indicating whether either read in the pair 231s goes off the end of the reference, prefixed by XB:Z: 231s notags=f Turn off all optional tags. 231s 231s Histogram and statistics output parameters: 231s scafstats= Statistics on how many reads mapped to which scaffold. 231s refstats= Statistics on how many reads mapped to which reference 231s file; only for BBSplit. 231s sortscafs=t Sort scaffolds or references by read count. 231s bhist= Base composition histogram by position. 231s qhist= Quality histogram by position. 231s aqhist= Histogram of average read quality. 231s bqhist= Quality histogram designed for box plots. 231s lhist= Read length histogram. 231s ihist= Write histogram of insert sizes (for paired reads). 231s ehist= Errors-per-read histogram. 231s qahist= Quality accuracy histogram of error rates versus 231s quality score. 231s indelhist= Indel length histogram. 231s mhist= Histogram of match, sub, del, and ins rates by 231s read location. 231s gchist= Read GC content histogram. 231s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 231s gcpairs=t Use average GC of paired reads. 231s idhist= Histogram of read count versus percent identity. 231s idbins=100 Number idhist bins. Set to 'auto' to use read length. 231s statsfile=stderr Mapping statistics are printed here. 231s 231s Coverage output parameters (these may reduce speed and use more RAM): 231s covstats= Per-scaffold coverage info. 231s rpkm= Per-scaffold RPKM/FPKM counts. 231s covhist= Histogram of # occurrences of each depth level. 231s basecov= Coverage per base location. 231s bincov= Print binned coverage per location (one line per X bases). 231s covbinsize=1000 Set the binsize for binned coverage output. 231s nzo=t Only print scaffolds with nonzero coverage. 231s twocolumn=f Change to true to print only ID and Avg_fold instead of 231s all 6 columns to the 'out=' file. 231s 32bit=f Set to true if you need per-base coverage over 64k. 231s strandedcov=f Track coverage for plus and minus strand independently. 231s startcov=f Only track start positions of reads. 231s secondarycov=t Include coverage of secondary alignments. 231s physcov=f Calculate physical coverage for paired reads. 231s This includes the unsequenced bases. 231s delcoverage=t (delcov) Count bases covered by deletions as covered. 231s True is faster than false. 231s covk=0 If positive, calculate kmer coverage statistics. 231s 231s Java Parameters: 231s -Xmx This will set Java's memory usage, 231s overriding autodetection. 231s -Xmx20g will specify 20 gigs of RAM, and -Xmx800m 231s will specify 800 megs. The max is typically 85% of 231s physical memory. The human genome requires around 24g, 231s or 12g with the 'usemodulo' flag. The index uses 231s roughly 6 bytes per reference base. 231s -eoom This flag will cause the process to exit if an 231s out-of-memory exception occurs. Requires Java 8u92+. 231s -da Disable assertions. 231s 231s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter 231s any problems, or post at: http://seqanswers.com/forums/showthread.php?t=41057 231s 231s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 231s java -ea -Xmx2635m -Xms2635m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta 231s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta] 231s Version 39.06 231s 232s No output file. 232s Writing reference. 232s 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] 232s 232s Set genScaffoldInfo=true 232s Writing chunk 1 232s Set genome to 1 232s 232s Loaded Reference: 0.008 seconds. 232s Loading index for chunk 1-1, build 1 232s No index available; generating from reference genome: /tmp/autopkgtest.KSTWlk/autopkgtest_tmp/ref/index/1/chr1_index_k13_c16_b1.block 232s Indexing threads started for block 0-1 232s Indexing threads finished for block 0-1 233s Generated Index: 1.341 seconds. 233s No reads to process; quitting. 233s 233s Total time: 1.600 seconds. 233s test -d ref 233s bbmap.sh in=misc_dna_as_sanger.fastq out=out.sam 233s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 233s 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 233s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, in=misc_dna_as_sanger.fastq, out=out.sam] 233s Version 39.06 233s 233s Retaining first best site only for ambiguous mappings. 233s Set genome to 1 233s 233s Loaded Reference: 0.041 seconds. 233s Loading index for chunk 1-1, build 1 234s Generated Index: 0.524 seconds. 241s Analyzed Index: 7.512 seconds. 241s Started output stream: 0.034 seconds. 242s Cleared Memory: 0.129 seconds. 242s Processing reads in single-ended mode. 242s Started read stream. 242s Started 4 mapping threads. 242s Detecting finished threads: 0, 1, 2, 3 242s 242s ------------------ Results ------------------ 242s 242s Genome: 1 242s Key Length: 13 242s Max Indel: 16000 242s Minimum Score Ratio: 0.56 242s Mapping Mode: normal 242s Reads Used: 4 (153 bases) 242s 242s Mapping: 0.115 seconds. 242s Reads/sec: 34.85 242s kBases/sec: 1.33 242s 242s 242s Read 1 data: pct reads num reads pct bases num bases 242s 242s mapped: 0.0000% 0 0.0000% 0 242s unambiguous: 0.0000% 0 0.0000% 0 242s ambiguous: 0.0000% 0 0.0000% 0 242s low-Q discards: 25.0000% 1 19.6078% 30 242s 242s perfect best site: 0.0000% 0 0.0000% 0 242s semiperfect site: 0.0000% 0 0.0000% 0 242s 242s Match Rate: NA NA NaN% 0 242s Error Rate: NaN% 0 NaN% 0 242s Sub Rate: NaN% 0 NaN% 0 242s Del Rate: NaN% 0 NaN% 0 242s Ins Rate: NaN% 0 NaN% 0 242s N Rate: NaN% 0 NaN% 0 242s 242s Total time: 8.472 seconds. 242s test -r out.sam 242s bbmap.sh ref=example.fasta in=example.fastq out=out2.sam nodisk 242s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 242s 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 242s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta, in=example.fastq, out=out2.sam, nodisk] 242s Version 39.06 242s 242s Retaining first best site only for ambiguous mappings. 242s 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] 242s 242s Set genScaffoldInfo=true 242s Set genome to 1 242s 242s Loaded Reference: 0.002 seconds. 242s Loading index for chunk 1-1, build 1 242s Indexing threads started for block 0-1 242s Indexing threads finished for block 0-1 242s Generated Index: 0.294 seconds. 246s Analyzed Index: 3.827 seconds. 246s Started output stream: 0.028 seconds. 246s Cleared Memory: 0.121 seconds. 246s Processing reads in single-ended mode. 246s Started read stream. 246s Started 4 mapping threads. 246s Detecting finished threads: 0, 1, 2, 3 246s 246s ------------------ Results ------------------ 246s 246s Genome: 1 246s Key Length: 13 246s Max Indel: 16000 246s Minimum Score Ratio: 0.56 246s Mapping Mode: normal 246s Reads Used: 3 (75 bases) 246s 246s Mapping: 0.092 seconds. 246s Reads/sec: 32.58 246s kBases/sec: 0.81 246s 246s 246s Read 1 data: pct reads num reads pct bases num bases 246s 246s mapped: 100.0000% 3 100.0000% 75 246s unambiguous: 100.0000% 3 100.0000% 75 246s ambiguous: 0.0000% 0 0.0000% 0 246s low-Q discards: 0.0000% 0 0.0000% 0 246s 246s perfect best site: 100.0000% 3 100.0000% 75 246s semiperfect site: 100.0000% 3 100.0000% 75 246s 246s Match Rate: NA NA 100.0000% 75 246s Error Rate: 0.0000% 0 0.0000% 0 246s Sub Rate: 0.0000% 0 0.0000% 0 246s Del Rate: 0.0000% 0 0.0000% 0 246s Ins Rate: 0.0000% 0 0.0000% 0 246s N Rate: 0.0000% 0 0.0000% 0 246s 246s Total time: 4.513 seconds. 246s test -r out2.sam 246s 246s # bbduk 246s bbduk.sh --version 246s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 246s java -ea -Xmx1318m -Xms1318m -cp /usr/share/java/bbmap.jar jgi.BBDuk --version 246s BBMap version 39.06 246s For help, please run the shellscript with no parameters, or look in /docs/. 246s bbduk.sh --help 246s bbduk.sh in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq \ 246s qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 246s 246s Written by Brian Bushnell 246s Last modified November 9, 2023 246s 246s Description: Compares reads to the kmers in a reference dataset, optionally 246s allowing an edit distance. Splits the reads into two outputs - those that 246s match the reference, and those that don't. Can also trim (remove) the matching 246s parts of the reads rather than binning the reads. 246s Please read bbmap/docs/guides/BBDukGuide.txt for more information. 246s 246s Usage: bbduk.sh in= out= ref= 246s 246s Input may be stdin or a fasta or fastq file, compressed or uncompressed. 246s If you pipe via stdin/stdout, please include the file type; e.g. for gzipped 246s fasta input, set in=stdin.fa.gz 246s 246s Input parameters: 246s in= Main input. in=stdin.fq will pipe from stdin. 246s in2= Input for 2nd read of pairs in a different file. 246s ref= Comma-delimited list of reference files. 246s In addition to filenames, you may also use the keywords: 246s adapters, artifacts, phix, lambda, pjet, mtst, kapa 246s literal= Comma-delimited list of literal reference sequences. 246s touppercase=f (tuc) Change all bases upper-case. 246s interleaved=auto (int) t/f overrides interleaved autodetection. 246s Must be set mainually when streaming fastq input. 246s qin=auto Input quality offset: 33 (Sanger), 64, or auto. 246s reads=-1 If positive, quit after processing X reads or pairs. 246s copyundefined=f (cu) Process non-AGCT IUPAC reference bases by making all 246s possible unambiguous copies. Intended for short motifs 246s or adapter barcodes, as time/memory use is exponential. 246s samplerate=1 Set lower to only process a fraction of input reads. 246s samref= Optional reference fasta for processing sam files. 246s 246s Output parameters: 246s out= (outnonmatch) Write reads here that do not contain 246s kmers matching the database. 'out=stdout.fq' will pipe 246s to standard out. 246s out2= (outnonmatch2) Use this to write 2nd read of pairs to a 246s different file. 246s outm= (outmatch) Write reads here that fail filters. In default 246s kfilter mode, this means any read with a matching kmer. 246s In any mode, it also includes reads that fail filters such 246s as minlength, mingc, maxgc, entropy, etc. In other words, 246s it includes all reads that do not go to 'out'. 246s outm2= (outmatch2) Use this to write 2nd read of pairs to a 246s different file. 246s outs= (outsingle) Use this to write singleton reads whose mate 246s was trimmed shorter than minlen. 246s stats= Write statistics about which contamininants were detected. 246s refstats= Write statistics on a per-reference-file basis. 246s rpkm= Write RPKM for each reference sequence (for RNA-seq). 246s dump= Dump kmer tables to a file, in fasta format. 246s duk= Write statistics in duk's format. *DEPRECATED* 246s nzo=t Only write statistics about ref sequences with nonzero hits. 246s overwrite=t (ow) Grant permission to overwrite files. 246s showspeed=t (ss) 'f' suppresses display of processing speed. 246s ziplevel=2 (zl) Compression level; 1 (min) through 9 (max). 246s fastawrap=70 Length of lines in fasta output. 246s qout=auto Output quality offset: 33 (Sanger), 64, or auto. 246s statscolumns=3 (cols) Number of columns for stats output, 3 or 5. 246s 5 includes base counts. 246s rename=f Rename reads to indicate which sequences they matched. 246s refnames=f Use names of reference files rather than scaffold IDs. 246s trd=f Truncate read and ref names at the first whitespace. 246s ordered=f Set to true to output reads in same order as input. 246s maxbasesout=-1 If positive, quit after writing approximately this many 246s bases to out (outu/outnonmatch). 246s maxbasesoutm=-1 If positive, quit after writing approximately this many 246s bases to outm (outmatch). 246s json=f Print to screen in json format. 246s 246s Histogram output parameters: 246s bhist= Base composition histogram by position. 246s qhist= Quality histogram by position. 246s qchist= Count of bases with each quality value. 246s aqhist= Histogram of average read quality. 246s bqhist= Quality histogram designed for box plots. 246s lhist= Read length histogram. 246s phist= Polymer length histogram. 246s gchist= Read GC content histogram. 246s enthist= Read entropy histogram. 246s ihist= Insert size histogram, for paired reads in mapped sam. 246s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 246s maxhistlen=6000 Set an upper bound for histogram lengths; higher uses 246s more memory. The default is 6000 for some histograms 246s and 80000 for others. 246s 246s Histograms for mapped sam/bam files only: 246s histbefore=t Calculate histograms from reads before processing. 246s ehist= Errors-per-read histogram. 246s qahist= Quality accuracy histogram of error rates versus quality 246s score. 246s indelhist= Indel length histogram. 246s mhist= Histogram of match, sub, del, and ins rates by position. 246s idhist= Histogram of read count versus percent identity. 246s idbins=100 Number idhist bins. Set to 'auto' to use read length. 246s varfile= Ignore substitution errors listed in this file when 246s calculating error rates. Can be generated with 246s CallVariants. 246s vcf= Ignore substitution errors listed in this VCF file 246s when calculating error rates. 246s ignorevcfindels=t Also ignore indels listed in the VCF. 246s 246s Processing parameters: 246s k=27 Kmer length used for finding contaminants. Contaminants 246s shorter than k will not be found. k must be at least 1. 246s rcomp=t Look for reverse-complements of kmers in addition to 246s forward kmers. 246s maskmiddle=t (mm) Treat the middle base of a kmer as a wildcard, to 246s increase sensitivity in the presence of errors. This may 246s also be set to a number, e.g. mm=3, to mask that many bp. 246s The default mm=t corresponds to mm=1 for odd-length kmers 246s and mm=2 for even-length kmers (as of v39.04), while 246s mm=f is always equivalent to mm=0. 246s minkmerhits=1 (mkh) Reads need at least this many matching kmers 246s to be considered as matching the reference. 246s minkmerfraction=0.0 (mkf) A reads needs at least this fraction of its total 246s kmers to hit a ref, in order to be considered a match. 246s If this and minkmerhits are set, the greater is used. 246s mincovfraction=0.0 (mcf) A reads needs at least this fraction of its total 246s bases to be covered by ref kmers to be considered a match. 246s If specified, mcf overrides mkh and mkf. 246s hammingdistance=0 (hdist) Maximum Hamming distance for ref kmers (subs only). 246s Memory use is proportional to (3*K)^hdist. 246s qhdist=0 Hamming distance for query kmers; impacts speed, not memory. 246s editdistance=0 (edist) Maximum edit distance from ref kmers (subs 246s and indels). Memory use is proportional to (8*K)^edist. 246s hammingdistance2=0 (hdist2) Sets hdist for short kmers, when using mink. 246s qhdist2=0 Sets qhdist for short kmers, when using mink. 246s editdistance2=0 (edist2) Sets edist for short kmers, when using mink. 246s forbidn=f (fn) Forbids matching of read kmers containing N. 246s By default, these will match a reference 'A' if 246s hdist>0 or edist>0, to increase sensitivity. 246s removeifeitherbad=t (rieb) Paired reads get sent to 'outmatch' if either is 246s match (or either is trimmed shorter than minlen). 246s Set to false to require both. 246s trimfailures=f Instead of discarding failed reads, trim them to 1bp. 246s This makes the statistics a bit odd. 246s findbestmatch=f (fbm) If multiple matches, associate read with sequence 246s sharing most kmers. Reduces speed. 246s skipr1=f Don't do kmer-based operations on read 1. 246s skipr2=f Don't do kmer-based operations on read 2. 246s ecco=f For overlapping paired reads only. Performs error- 246s correction with BBMerge prior to kmer operations. 246s recalibrate=f (recal) Recalibrate quality scores. Requires calibration 246s matrices generated by CalcTrueQuality. 246s sam= If recalibration is desired, and matrices have not already 246s been generated, BBDuk will create them from the sam file. 246s amino=f Run in amino acid mode. Some features have not been 246s tested, but kmer-matching works fine. Maximum k is 12. 246s 246s Speed and Memory parameters: 246s threads=auto (t) Set number of threads to use; default is number of 246s logical processors. 246s prealloc=f Preallocate memory in table. Allows faster table loading 246s and more efficient memory usage, for a large reference. 246s monitor=f Kill this process if it crashes. monitor=600,0.01 would 246s kill after 600 seconds under 1% usage. 246s minrskip=1 (mns) Force minimal skip interval when indexing reference 246s kmers. 1 means use all, 2 means use every other kmer, etc. 246s maxrskip=1 (mxs) Restrict maximal skip interval when indexing 246s reference kmers. Normally all are used for scaffolds<100kb, 246s but with longer scaffolds, up to maxrskip-1 are skipped. 246s rskip= Set both minrskip and maxrskip to the same value. 246s If not set, rskip will vary based on sequence length. 246s qskip=1 Skip query kmers to increase speed. 1 means use all. 246s speed=0 Ignore this fraction of kmer space (0-15 out of 16) in both 246s reads and reference. Increases speed and reduces memory. 246s Note: Do not use more than one of 'speed', 'qskip', and 'rskip'. 246s 246s Trimming/Filtering/Masking parameters: 246s Note - if ktrim, kmask, and ksplit are unset, the default behavior is kfilter. 246s All kmer processing modes are mutually exclusive. 246s Reads only get sent to 'outm' purely based on kmer matches in kfilter mode. 246s 246s ktrim=f Trim reads to remove bases matching reference kmers, plus 246s all bases to the left or right. 246s Values: 246s f (don't trim), 246s r (trim to the right), 246s l (trim to the left) 246s ktrimtips=0 Set this to a positive number to perform ktrim on both 246s ends, examining only the outermost X bases. 246s kmask= Replace bases matching ref kmers with another symbol. 246s Allows any non-whitespace character, and processes short 246s kmers on both ends if mink is set. 'kmask=lc' will 246s convert masked bases to lowercase. 246s maskfullycovered=f (mfc) Only mask bases that are fully covered by kmers. 246s ksplit=f For single-ended reads only. Reads will be split into 246s pairs around the kmer. If the kmer is at the end of the 246s read, it will be trimmed instead. Singletons will go to 246s out, and pairs will go to outm. Do not use ksplit with 246s other operations such as quality-trimming or filtering. 246s mink=0 Look for shorter kmers at read tips down to this length, 246s when k-trimming or masking. 0 means disabled. Enabling 246s this will disable maskmiddle. 246s qtrim=f Trim read ends to remove bases with quality below trimq. 246s Performed AFTER looking for kmers. Values: 246s rl (trim both ends), 246s f (neither end), 246s r (right end only), 246s l (left end only), 246s w (sliding window). 246s trimq=6 Regions with average quality BELOW this will be trimmed, 246s if qtrim is set to something other than f. Can be a 246s floating-point number like 7.3. 246s trimclip=f Trim soft-clipped bases from sam files. 246s minlength=10 (ml) Reads shorter than this after trimming will be 246s discarded. Pairs will be discarded if both are shorter. 246s mlf=0 (minlengthfraction) Reads shorter than this fraction of 246s original length after trimming will be discarded. 246s maxlength= Reads longer than this after trimming will be discarded. 246s minavgquality=0 (maq) Reads with average quality (after trimming) below 246s this will be discarded. 246s maqb=0 If positive, calculate maq from this many initial bases. 246s minbasequality=0 (mbq) Reads with any base below this quality (after 246s trimming) will be discarded. 246s maxns=-1 If non-negative, reads with more Ns than this 246s (after trimming) will be discarded. 246s mcb=0 (minconsecutivebases) Discard reads without at least 246s this many consecutive called bases. 246s ottm=f (outputtrimmedtomatch) Output reads trimmed to shorter 246s than minlength to outm rather than discarding. 246s tp=0 (trimpad) Trim this much extra around matching kmers. 246s tbo=f (trimbyoverlap) Trim adapters based on where paired 246s reads overlap. 246s strictoverlap=t Adjust sensitivity for trimbyoverlap mode. 246s minoverlap=14 Require this many bases of overlap for detection. 246s mininsert=40 Require insert size of at least this for overlap. 246s Should be reduced to 16 for small RNA sequencing. 246s tpe=f (trimpairsevenly) When kmer right-trimming, trim both 246s reads to the minimum length of either. 246s forcetrimleft=0 (ftl) If positive, trim bases to the left of this position 246s (exclusive, 0-based). 246s forcetrimright=0 (ftr) If positive, trim bases to the right of this position 246s (exclusive, 0-based). 246s forcetrimright2=0 (ftr2) If positive, trim this many bases on the right end. 246s forcetrimmod=0 (ftm) If positive, right-trim length to be equal to zero, 246s modulo this number. 246s restrictleft=0 If positive, only look for kmer matches in the 246s leftmost X bases. 246s restrictright=0 If positive, only look for kmer matches in the 246s rightmost X bases. 246s NOTE: restrictleft and restrictright are mutually exclusive. If trimming 246s both ends is desired, use ktrimtips. 246s mingc=0 Discard reads with GC content below this. 246s maxgc=1 Discard reads with GC content above this. 246s gcpairs=t Use average GC of paired reads. 246s Also affects gchist. 246s tossjunk=f Discard reads with invalid characters as bases. 246s swift=f Trim Swift sequences: Trailing C/T/N R1, leading G/A/N R2. 246s 246s Header-parsing parameters - these require Illumina headers: 246s chastityfilter=f (cf) Discard reads with id containing ' 1:Y:' or ' 2:Y:'. 246s barcodefilter=f Remove reads with unexpected barcodes if barcodes is set, 246s or barcodes containing 'N' otherwise. A barcode must be 246s the last part of the read header. Values: 246s t: Remove reads with bad barcodes. 246s f: Ignore barcodes. 246s crash: Crash upon encountering bad barcodes. 246s barcodes= Comma-delimited list of barcodes or files of barcodes. 246s xmin=-1 If positive, discard reads with a lesser X coordinate. 246s ymin=-1 If positive, discard reads with a lesser Y coordinate. 246s xmax=-1 If positive, discard reads with a greater X coordinate. 246s ymax=-1 If positive, discard reads with a greater Y coordinate. 246s 246s Polymer trimming: 246s trimpolya=0 If greater than 0, trim poly-A or poly-T tails of 246s at least this length on either end of reads. 246s trimpolygleft=0 If greater than 0, trim poly-G prefixes of at least this 246s length on the left end of reads. Does not trim poly-C. 246s trimpolygright=0 If greater than 0, trim poly-G tails of at least this 246s length on the right end of reads. Does not trim poly-C. 246s trimpolyg=0 This sets both left and right at once. 246s filterpolyg=0 If greater than 0, remove reads with a poly-G prefix of 246s at least this length (on the left). 246s Note: there are also equivalent poly-C flags. 246s 246s Polymer tracking: 246s pratio=base,base 'pratio=G,C' will print the ratio of G to C polymers. 246s plen=20 Length of homopolymers to count. 246s 246s Entropy/Complexity parameters: 246s entropy=-1 Set between 0 and 1 to filter reads with entropy below 246s that value. Higher is more stringent. 246s entropywindow=50 Calculate entropy using a sliding window of this length. 246s entropyk=5 Calculate entropy using kmers of this length. 246s minbasefrequency=0 Discard reads with a minimum base frequency below this. 246s entropytrim=f Values: 246s f: (false) Do not entropy-trim. 246s r: (right) Trim low entropy on the right end only. 246s l: (left) Trim low entropy on the left end only. 246s rl: (both) Trim low entropy on both ends. 246s entropymask=f Values: 246s f: (filter) Discard low-entropy sequences. 246s t: (true) Mask low-entropy parts of sequences with N. 246s lc: Change low-entropy parts of sequences to lowercase. 246s entropymark=f Mark each base with its entropy value. This is on a scale 246s of 0-41 and is reported as quality scores, so the output 246s should be fastq or fasta+qual. 246s NOTE: If set, entropytrim overrides entropymask. 246s 246s Cardinality estimation: 246s cardinality=f (loglog) Count unique kmers using the LogLog algorithm. 246s cardinalityout=f (loglogout) Count unique kmers in output reads. 246s loglogk=31 Use this kmer length for counting. 246s loglogbuckets=2048 Use this many buckets for counting. 246s khist= Kmer frequency histogram; plots number of kmers versus 246s kmer depth. This is approximate. 246s khistout= Kmer frequency histogram for output reads. 246s 246s Java Parameters: 246s 246s -Xmx This will set Java's memory usage, overriding autodetection. 246s -Xmx20g will 246s specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 246s The max is typically 85% of physical memory. 246s -eoom This flag will cause the process to exit if an 246s out-of-memory exception occurs. Requires Java 8u92+. 246s -da Disable assertions. 246s 246s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 246s 247s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 247s java -ea -Xmx1317m -Xms1317m -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 247s 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] 247s Version 39.06 247s 247s 0.025 seconds. 247s Initial: 247s Memory: max=1409m, total=1409m, free=1379m, used=30m 247s 247s Input is being processed as paired 247s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 247s Started output streams: 0.034 seconds. 247s Processing time: 0.013 seconds. 247s 247s Input: 8 reads 306 bases. 247s QTrimmed: 0 reads (0.00%) 0 bases (0.00%) 247s Total Removed: 8 reads (100.00%) 306 bases (100.00%) 247s Result: 0 reads (0.00%) 0 bases (0.00%) 247s 247s Time: 0.050 seconds. 247s Reads Processed: 8 0.16k reads/sec 247s Bases Processed: 306 0.01m bases/sec 247s test -r out.fastq.gz 247s 247s # bbnorm 247s bbnorm.sh --version 247s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 247s java -ea -Xmx2635m -Xms2635m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 --version 247s BBMap version 39.06 247s For help, please run the shellscript with no parameters, or look in /docs/. 247s bbnorm.sh --help 247s 247s Written by Brian Bushnell 247s Last modified October 19, 2017 247s 247s Description: Normalizes read depth based on kmer counts. 247s Can also error-correct, bin reads by kmer depth, and generate a kmer depth histogram. 247s However, Tadpole has superior error-correction to BBNorm. 247s Please read bbmap/docs/guides/BBNormGuide.txt for more information. 247s 247s Usage: bbnorm.sh in= out= outt= hist= 247s 247s Input parameters: 247s in=null Primary input. Use in2 for paired reads in a second file 247s in2=null Second input file for paired reads in two files 247s extra=null Additional files to use for input (generating hash table) but not for output 247s fastareadlen=2^31 Break up FASTA reads longer than this. Can be useful when processing scaffolded genomes 247s tablereads=-1 Use at most this many reads when building the hashtable (-1 means all) 247s kmersample=1 Process every nth kmer, and skip the rest 247s readsample=1 Process every nth read, and skip the rest 247s 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. 247s qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto. 247s 247s Output parameters: 247s out= File for normalized or corrected reads. Use out2 for paired reads in a second file 247s outt= (outtoss) File for reads that were excluded from primary output 247s reads=-1 Only process this number of reads, then quit (-1 means all) 247s sampleoutput=t Use sampling on output as well as input (not used if sample rates are 1) 247s keepall=f Set to true to keep all reads (e.g. if you just want error correction). 247s 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. 247s Default is false, to prevent confusion about how there can be 0-count kmers. 247s The reason is that based on the 'minq' and 'minprob' settings, some kmers may be excluded from the bloom filter. 247s tmpdir= This will specify a directory for temp files (only needed for multipass runs). If null, they will be written to the output directory. 247s usetempdir=t Allows enabling/disabling of temporary directory; if disabled, temp files will be written to the output directory. 247s qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input). 247s rename=f Rename reads based on their kmer depth. 247s 247s Hashing parameters: 247s k=31 Kmer length (values under 32 are most efficient, but arbitrarily high values are supported) 247s 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. 247s Large values decrease accuracy for a fixed amount of memory, so use the lowest number you can that will still capture highest-depth kmers. 247s hashes=3 Number of times each kmer is hashed and stored. Higher is slower. 247s Higher is MORE accurate if there is enough memory, and LESS accurate if there is not enough memory. 247s 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. 247s prehashes=2 Number of hashes for prefilter. 247s prefilterbits=2 (pbits) Bits per cell in prefilter. 247s prefiltersize=0.35 Fraction of memory to allocate to prefilter. 247s buildpasses=1 More passes can sometimes increase accuracy by iteratively removing low-depth kmers 247s minq=6 Ignore kmers containing bases with quality below this 247s minprob=0.5 Ignore kmers with overall probability of correctness below this 247s 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. 247s 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. 247s 247s Normalization parameters: 247s fixspikes=f (fs) Do a slower, high-precision bloom filter lookup of kmers that appear to have an abnormally high depth due to collisions. 247s target=100 (tgt) Target normalization depth. NOTE: All depth parameters control kmer depth, not read depth. 247s For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1)) 247s maxdepth=-1 (max) Reads will not be downsampled when below this depth, even if they are above the target depth. 247s mindepth=5 (min) Kmers with depth below this number will not be included when calculating the depth of a read. 247s minkmers=15 (mgkpr) Reads must have at least this many kmers over min depth to be retained. Aka 'mingoodkmersperread'. 247s 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. 247s uselowerdepth=t (uld) For pairs, use the depth of the lower read as the depth proxy. 247s deterministic=t (dr) Generate random numbers deterministically to ensure identical output between multiple runs. May decrease speed with a huge number of threads. 247s passes=2 (p) 1 pass is the basic mode. 2 passes (default) allows greater accuracy, error detection, better contol of output depth. 247s 247s Error detection parameters: 247s hdp=90.0 (highdepthpercentile) Position in sorted kmer depth array used as proxy of a read's high kmer depth. 247s ldp=25.0 (lowdepthpercentile) Position in sorted kmer depth array used as proxy of a read's low kmer depth. 247s tossbadreads=f (tbr) Throw away reads detected as containing errors. 247s requirebothbad=f (rbb) Only toss bad pairs if both reads are bad. 247s 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. 247s highthresh=12 (ht) Threshold for high kmer. A high kmer at this or above are considered non-error. 247s lowthresh=3 (lt) Threshold for low kmer. Kmers at this and below are always considered errors. 247s 247s Error correction parameters: 247s ecc=f Set to true to correct errors. NOTE: Tadpole is now preferred for ecc as it does a better job. 247s ecclimit=3 Correct up to this many errors per read. If more are detected, the read will remain unchanged. 247s errorcorrectratio=140 (ecr) Adjacent kmers with a depth ratio of at least this much between will be classified as an error. 247s echighthresh=22 (echt) Threshold for high kmer. A kmer at this or above may be considered non-error. 247s eclowthresh=2 (eclt) Threshold for low kmer. Kmers at this and below are considered errors. 247s eccmaxqual=127 Do not correct bases with quality above this value. 247s aec=f (aggressiveErrorCorrection) Sets more aggressive values of ecr=100, ecclimit=7, echt=16, eclt=3. 247s cec=f (conservativeErrorCorrection) Sets more conservative values of ecr=180, ecclimit=2, echt=30, eclt=1, sl=4, pl=4. 247s meo=f (markErrorsOnly) Marks errors by reducing quality value of suspected errors; does not correct anything. 247s mue=t (markUncorrectableErrors) Marks errors only on uncorrectable reads; requires 'ecc=t'. 247s overlap=f (ecco) Error correct by read overlap. 247s 247s Depth binning parameters: 247s lowbindepth=10 (lbd) Cutoff for low depth bin. 247s highbindepth=80 (hbd) Cutoff for high depth bin. 247s outlow= Pairs in which both reads have a median below lbd go into this file. 247s outhigh= Pairs in which both reads have a median above hbd go into this file. 247s outmid= All other pairs go into this file. 247s 247s Histogram parameters: 247s hist= Specify a file to write the input kmer depth histogram. 247s histout= Specify a file to write the output kmer depth histogram. 247s histcol=3 (histogramcolumns) Number of histogram columns, 2 or 3. 247s pzc=f (printzerocoverage) Print lines in the histogram with zero coverage. 247s histlen=1048576 Max kmer depth displayed in histogram. Also affects statistics displayed, but does not affect normalization. 247s 247s Peak calling parameters: 247s peaks= Write the peaks to this file. Default is stdout. 247s minHeight=2 (h) Ignore peaks shorter than this. 247s minVolume=5 (v) Ignore peaks with less area than this. 247s minWidth=3 (w) Ignore peaks narrower than this. 247s minPeak=2 (minp) Ignore peaks with an X-value below this. 247s maxPeak=BIG (maxp) Ignore peaks with an X-value above this. 247s maxPeakCount=8 (maxpc) Print up to this many peaks (prioritizing height). 247s 247s Java Parameters: 247s -Xmx This will set Java's memory usage, overriding autodetection. 247s -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 247s The max is typically 85% of physical memory. 247s -eoom This flag will cause the process to exit if an 247s out-of-memory exception occurs. Requires Java 8u92+. 247s -da Disable assertions. 247s 247s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 247s 247s bbnorm.sh in=sanger_full_range_original_sanger.fastq qin=33 \ 247s out=out3.fastq outt=outt.fastq hist=hist.plt 247s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 247s java -ea -Xmx2635m -Xms2635m -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 247s Executing jgi.KmerNormalize [bits=32, in=sanger_full_range_original_sanger.fastq, qin=33, out=out3.fastq, outt=outt.fastq, hist=hist.plt] 247s 247s 247s *********** Pass 1 ********** 247s 247s 247s Settings: 247s threads: 4 247s k: 31 247s deterministic: true 247s toss error reads: false 247s passes: 1 247s bits per cell: 16 247s cells: 980.97M 247s hashes: 3 247s base min quality: 5 247s kmer min prob: 0.5 247s 247s target depth: 400 247s min depth: 3 247s max depth: 500 247s min good kmers: 15 247s depth percentile: 64.8 247s ignore dupe kmers: true 247s fix spikes: false 247s histogram length: 65536 247s print zero cov: false 247s 250s Made hash table: hashes = 3 mem = 1.83 GB cells = 980.47M used = 0.000% 250s 250s Estimated unique kmers: 7 250s 250s Table creation time: 2.611 seconds. 250s Started output threads. 250s Started output threads. 250s Table read time: 0.009 seconds. 21.25 kb/sec 250s Total reads in: 2 0.000% Kept 250s Total bases in: 188 0.000% Kept 250s Error reads in: 2 100.000% 250s Error type 1: 2 100.000% 250s Error type 2: 0 0.000% 250s Error type 3: 0 0.000% 250s 250s Wrote histogram to hist.plt 250s Total kmers counted: 128 250s Total unique kmer count: 128 250s Includes forward kmers only. 250s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 250s The most accurate value is the greater of the two. 250s 250s Percent unique: 100.00% 250s Depth average: 1.00 (unique kmers) 250s Depth median: 1 (unique kmers) 250s Depth standard deviation: 0.00 (unique kmers) 250s Corrected depth average: 0.00 250s 250s Depth average: 1.00 (all kmers) 250s Depth median: 1 (all kmers) 250s Depth standard deviation: 0.00 (all kmers) 250s 250s Approx. read depth median: 1.47 250s 250s *********** Pass 2 ********** 250s 250s 250s Settings: 250s threads: 4 250s k: 31 250s deterministic: true 250s toss error reads: false 250s passes: 1 250s bits per cell: 16 250s cells: 980.97M 250s hashes: 3 250s base min quality: 5 250s kmer min prob: 0.5 250s 250s target depth: 100 250s min depth: 5 250s max depth: 100 250s min good kmers: 15 250s depth percentile: 54.0 250s ignore dupe kmers: true 250s fix spikes: false 250s histogram length: 65536 250s 253s Made hash table: hashes = 3 mem = 1.83 GB cells = 980.47M used = 0.000% 253s 253s Estimated unique kmers: 0 253s 253s Table creation time: 2.581 seconds. 253s Started output threads. 253s Started output threads. 253s Table read time: 0.002 seconds. 0.00 kb/sec 253s Total reads in: 0 NaN% Kept 253s Total bases in: 0 NaN% Kept 253s Error reads in: 0 NaN% 253s Error type 1: 0 NaN% 253s Error type 2: 0 NaN% 253s Error type 3: 0 NaN% 253s Total kmers counted: 0 253s Total unique kmer count: 0 253s Includes forward kmers only. 253s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 253s The most accurate value is the greater of the two. 253s 253s Percent unique: NaN% 253s Depth average: NaN (unique kmers) 253s Depth median: 0 (unique kmers) 253s Depth standard deviation: NaN (unique kmers) 253s Corrected depth average: NaN 253s 253s Depth average: NaN (all kmers) 253s Depth median: 0 (all kmers) 253s Depth standard deviation: 0.00 (all kmers) 253s 253s Approx. read depth median: NaN 253s 253s Removing temp files. 253s 253s Total time: 5.338 seconds. 0.04 kb/sec 253s test -r out3.fastq 253s test -r outt.fastq 253s test -r hist.plt 253s bbnorm.sh in=illumina_full_range_original_illumina.fastq qin=64 \ 253s out=out4.fastq outt=outt2.fastq hist=hist2.plt 253s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 253s java -ea -Xmx2635m -Xms2635m -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 253s Executing jgi.KmerNormalize [bits=32, in=illumina_full_range_original_illumina.fastq, qin=64, out=out4.fastq, outt=outt2.fastq, hist=hist2.plt] 253s 253s 253s *********** Pass 1 ********** 253s 253s 253s Settings: 253s threads: 4 253s k: 31 253s deterministic: true 253s toss error reads: false 253s passes: 1 253s bits per cell: 16 253s cells: 980.97M 253s hashes: 3 253s base min quality: 5 253s kmer min prob: 0.5 253s 253s target depth: 400 253s min depth: 3 253s max depth: 500 253s min good kmers: 15 253s depth percentile: 64.8 253s ignore dupe kmers: true 253s fix spikes: false 253s histogram length: 65536 253s print zero cov: false 253s 256s Made hash table: hashes = 3 mem = 1.83 GB cells = 980.47M used = 0.000% 256s 256s Estimated unique kmers: 7 256s 256s Table creation time: 2.633 seconds. 256s Started output threads. 256s Started output threads. 256s Table read time: 0.014 seconds. 9.16 kb/sec 256s Total reads in: 2 0.000% Kept 256s Total bases in: 126 0.000% Kept 256s Error reads in: 2 100.000% 256s Error type 1: 2 100.000% 256s Error type 2: 0 0.000% 256s Error type 3: 0 0.000% 256s 256s Wrote histogram to hist2.plt 256s Total kmers counted: 66 256s Total unique kmer count: 66 256s Includes forward kmers only. 256s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 256s The most accurate value is the greater of the two. 256s 256s Percent unique: 100.00% 256s Depth average: 1.00 (unique kmers) 256s Depth median: 1 (unique kmers) 256s Depth standard deviation: 0.00 (unique kmers) 256s Corrected depth average: 0.00 256s 256s Depth average: 1.00 (all kmers) 256s Depth median: 1 (all kmers) 256s Depth standard deviation: 0.00 (all kmers) 256s 256s Approx. read depth median: 1.91 256s 256s *********** Pass 2 ********** 256s 256s 256s Settings: 256s threads: 4 256s k: 31 256s deterministic: true 256s toss error reads: false 256s passes: 1 256s bits per cell: 16 256s cells: 980.97M 256s hashes: 3 256s base min quality: 5 256s kmer min prob: 0.5 256s 256s target depth: 100 256s min depth: 5 256s max depth: 100 256s min good kmers: 15 256s depth percentile: 54.0 256s ignore dupe kmers: true 256s fix spikes: false 256s histogram length: 65536 256s 258s Made hash table: hashes = 3 mem = 1.83 GB cells = 980.47M used = 0.000% 258s 258s Estimated unique kmers: 0 258s 258s Table creation time: 2.490 seconds. 258s Started output threads. 258s Started output threads. 258s Table read time: 0.003 seconds. 0.00 kb/sec 258s Total reads in: 0 NaN% Kept 258s Total bases in: 0 NaN% Kept 258s Error reads in: 0 NaN% 258s Error type 1: 0 NaN% 258s Error type 2: 0 NaN% 258s Error type 3: 0 NaN% 258s Total kmers counted: 0 258s Total unique kmer count: 0 258s Includes forward kmers only. 258s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 258s The most accurate value is the greater of the two. 258s 258s Percent unique: NaN% 258s Depth average: NaN (unique kmers) 258s Depth median: 0 (unique kmers) 258s Depth standard deviation: NaN (unique kmers) 258s Corrected depth average: NaN 258s 258s Depth average: NaN (all kmers) 258s Depth median: 0 (all kmers) 258s Depth standard deviation: 0.00 (all kmers) 258s 258s Approx. read depth median: NaN 258s 258s Removing temp files. 258s 258s Total time: 5.275 seconds. 0.02 kb/sec 258s test -r out4.fastq 258s test -r outt2.fastq 258s test -r hist2.plt 258s autopkgtest [12:35:48]: test run-unit-test: -----------------------] 259s run-unit-test PASS 259s autopkgtest [12:35:49]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 259s autopkgtest [12:35:49]: @@@@@@@@@@@@@@@@@@@@ summary 259s run-unit-test PASS 274s Creating nova instance adt-noble-ppc64el-bbmap-20240319-123130-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240319.img (UUID 9d87beed-6c32-481f-958d-7469e26317f3)...