0s autopkgtest [12:03:16]: starting date and time: 2024-03-19 12:03:16+0000 0s autopkgtest [12:03:16]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [12:03:16]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.oborlof1/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@bos03-arm64-6.secgroup --name adt-noble-arm64-bbmap-20240319-120316-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 128s autopkgtest [12:05:24]: testbed dpkg architecture: arm64 128s autopkgtest [12:05:24]: testbed apt version: 2.7.12 128s autopkgtest [12:05:24]: @@@@@@@@@@@@@@@@@@@@ test bed setup 128s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 129s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [53.7 kB] 129s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3768 kB] 130s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 130s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [486 kB] 130s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [659 kB] 130s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 130s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 130s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 130s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4142 kB] 130s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 130s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [56.7 kB] 130s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 133s Fetched 9334 kB in 3s (3339 kB/s) 133s Reading package lists... 137s Reading package lists... 137s Building dependency tree... 137s Reading state information... 138s Calculating upgrade... 138s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 138s Reading package lists... 139s Building dependency tree... 139s Reading state information... 140s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 141s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 141s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 141s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 141s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 142s Reading package lists... 143s Reading package lists... 143s Building dependency tree... 143s Reading state information... 143s Calculating upgrade... 144s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 144s Reading package lists... 144s Building dependency tree... 144s Reading state information... 145s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 148s autopkgtest [12:05:44]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 148s autopkgtest [12:05:44]: @@@@@@@@@@@@@@@@@@@@ apt-source bbmap 152s Get:1 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (dsc) [2286 B] 152s Get:2 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (tar) [5343 kB] 152s Get:3 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (diff) [25.4 kB] 152s gpgv: Signature made Fri Nov 24 11:00:29 2023 UTC 152s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 152s gpgv: issuer "emollier@debian.org" 152s gpgv: Can't check signature: No public key 152s dpkg-source: warning: cannot verify inline signature for ./bbmap_39.06+dfsg-1.dsc: no acceptable signature found 154s autopkgtest [12:05:50]: testing package bbmap version 39.06+dfsg-1 154s autopkgtest [12:05:50]: build not needed 155s autopkgtest [12:05:51]: test run-unit-test: preparing testbed 162s Reading package lists... 162s Building dependency tree... 162s Reading state information... 163s Starting pkgProblemResolver with broken count: 0 163s Starting 2 pkgProblemResolver with broken count: 0 163s Done 164s The following additional packages will be installed: 164s bbmap bbmap-jni ca-certificates-java fontconfig-config fonts-dejavu-core 164s fonts-dejavu-mono java-common libapache-pom-java libasound2 libasound2-data 164s libavahi-client3 libavahi-common-data libavahi-common3 libcommons-cli-java 164s libcommons-codec-java libcommons-io-java libcommons-parent-java libcups2 164s libfontconfig1 libgraphite2-3 libharfbuzz0b libjpeg-turbo8 libjpeg8 164s liblcms2-2 liblog4j1.2-java libmpj-java libpcsclite1 openjdk-17-jre-headless 164s python-biopython-doc 164s Suggested packages: 164s default-jre libasound2-plugins alsa-utils libcommons-io-java-doc cups-common 164s liblcms2-utils liblog4j1.2-java-doc libmail-java pcscd libnss-mdns 164s fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho 164s fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic 164s Recommended packages: 164s pigz alsa-ucm-conf alsa-topology-conf python3-biopython 164s The following NEW packages will be installed: 164s autopkgtest-satdep bbmap bbmap-jni ca-certificates-java fontconfig-config 164s fonts-dejavu-core fonts-dejavu-mono java-common libapache-pom-java 164s libasound2 libasound2-data libavahi-client3 libavahi-common-data 164s libavahi-common3 libcommons-cli-java libcommons-codec-java 164s libcommons-io-java libcommons-parent-java libcups2 libfontconfig1 164s libgraphite2-3 libharfbuzz0b libjpeg-turbo8 libjpeg8 liblcms2-2 164s liblog4j1.2-java libmpj-java libpcsclite1 openjdk-17-jre-headless 164s python-biopython-doc 164s 0 upgraded, 30 newly installed, 0 to remove and 0 not upgraded. 164s Need to get 79.2 MB/79.2 MB of archives. 164s After this operation, 238 MB of additional disk space will be used. 164s Get:1 /tmp/autopkgtest.QEL1Rz/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [720 B] 164s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-cli-java all 1.6.0-1 [59.9 kB] 164s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 libapache-pom-java all 29-2 [5284 B] 164s Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-parent-java all 56-1 [10.7 kB] 164s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-codec-java all 1.16.0-1 [306 kB] 164s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-io-java all 2.11.0-2 [297 kB] 164s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 liblog4j1.2-java all 1.2.17-11 [439 kB] 164s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 libmpj-java all 0.44+dfsg-4 [443 kB] 164s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 ca-certificates-java all 20240118 [11.6 kB] 164s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 java-common all 0.75+exp1 [6798 B] 164s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libavahi-common-data arm64 0.8-13ubuntu2 [29.5 kB] 164s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libavahi-common3 arm64 0.8-13ubuntu2 [23.2 kB] 164s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libavahi-client3 arm64 0.8-13ubuntu2 [27.3 kB] 164s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libcups2 arm64 2.4.6-0ubuntu3 [270 kB] 164s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB] 164s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 164s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 164s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 164s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 164s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 164s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 164s Get:22 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libasound2-data all 1.2.11-1build1 [21.0 kB] 164s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libasound2 arm64 1.2.10-3build1 [386 kB] 164s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 164s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 164s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libpcsclite1 arm64 2.0.0-1 [21.2 kB] 164s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 openjdk-17-jre-headless arm64 17.0.10+7-1 [47.3 MB] 166s Get:28 http://ftpmaster.internal/ubuntu noble/universe arm64 bbmap all 39.06+dfsg-1 [9768 kB] 167s Get:29 http://ftpmaster.internal/ubuntu noble/universe arm64 bbmap-jni arm64 39.06+dfsg-1 [26.3 kB] 167s Get:30 http://ftpmaster.internal/ubuntu noble/universe arm64 python-biopython-doc all 1.81+dfsg-3 [17.3 MB] 168s Fetched 79.2 MB in 3s (23.8 MB/s) 168s Selecting previously unselected package libcommons-cli-java. 168s (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 ... 74758 files and directories currently installed.) 168s Preparing to unpack .../00-libcommons-cli-java_1.6.0-1_all.deb ... 168s Unpacking libcommons-cli-java (1.6.0-1) ... 168s Selecting previously unselected package libapache-pom-java. 168s Preparing to unpack .../01-libapache-pom-java_29-2_all.deb ... 168s Unpacking libapache-pom-java (29-2) ... 168s Selecting previously unselected package libcommons-parent-java. 168s Preparing to unpack .../02-libcommons-parent-java_56-1_all.deb ... 168s Unpacking libcommons-parent-java (56-1) ... 168s Selecting previously unselected package libcommons-codec-java. 168s Preparing to unpack .../03-libcommons-codec-java_1.16.0-1_all.deb ... 168s Unpacking libcommons-codec-java (1.16.0-1) ... 168s Selecting previously unselected package libcommons-io-java. 168s Preparing to unpack .../04-libcommons-io-java_2.11.0-2_all.deb ... 168s Unpacking libcommons-io-java (2.11.0-2) ... 168s Selecting previously unselected package liblog4j1.2-java. 168s Preparing to unpack .../05-liblog4j1.2-java_1.2.17-11_all.deb ... 168s Unpacking liblog4j1.2-java (1.2.17-11) ... 168s Selecting previously unselected package libmpj-java. 168s Preparing to unpack .../06-libmpj-java_0.44+dfsg-4_all.deb ... 168s Unpacking libmpj-java (0.44+dfsg-4) ... 168s Selecting previously unselected package ca-certificates-java. 168s Preparing to unpack .../07-ca-certificates-java_20240118_all.deb ... 168s Unpacking ca-certificates-java (20240118) ... 168s Selecting previously unselected package java-common. 168s Preparing to unpack .../08-java-common_0.75+exp1_all.deb ... 168s Unpacking java-common (0.75+exp1) ... 168s Selecting previously unselected package libavahi-common-data:arm64. 168s Preparing to unpack .../09-libavahi-common-data_0.8-13ubuntu2_arm64.deb ... 168s Unpacking libavahi-common-data:arm64 (0.8-13ubuntu2) ... 168s Selecting previously unselected package libavahi-common3:arm64. 168s Preparing to unpack .../10-libavahi-common3_0.8-13ubuntu2_arm64.deb ... 168s Unpacking libavahi-common3:arm64 (0.8-13ubuntu2) ... 168s Selecting previously unselected package libavahi-client3:arm64. 168s Preparing to unpack .../11-libavahi-client3_0.8-13ubuntu2_arm64.deb ... 168s Unpacking libavahi-client3:arm64 (0.8-13ubuntu2) ... 168s Selecting previously unselected package libcups2:arm64. 168s Preparing to unpack .../12-libcups2_2.4.6-0ubuntu3_arm64.deb ... 168s Unpacking libcups2:arm64 (2.4.6-0ubuntu3) ... 169s Selecting previously unselected package liblcms2-2:arm64. 169s Preparing to unpack .../13-liblcms2-2_2.14-2_arm64.deb ... 169s Unpacking liblcms2-2:arm64 (2.14-2) ... 169s Selecting previously unselected package libjpeg-turbo8:arm64. 169s Preparing to unpack .../14-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 169s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 169s Selecting previously unselected package libjpeg8:arm64. 169s Preparing to unpack .../15-libjpeg8_8c-2ubuntu11_arm64.deb ... 169s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 169s Selecting previously unselected package fonts-dejavu-mono. 169s Preparing to unpack .../16-fonts-dejavu-mono_2.37-8_all.deb ... 169s Unpacking fonts-dejavu-mono (2.37-8) ... 169s Selecting previously unselected package fonts-dejavu-core. 169s Preparing to unpack .../17-fonts-dejavu-core_2.37-8_all.deb ... 169s Unpacking fonts-dejavu-core (2.37-8) ... 169s Selecting previously unselected package fontconfig-config. 169s Preparing to unpack .../18-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 169s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 169s Selecting previously unselected package libfontconfig1:arm64. 169s Preparing to unpack .../19-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 169s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 169s Selecting previously unselected package libasound2-data. 169s Preparing to unpack .../20-libasound2-data_1.2.11-1build1_all.deb ... 169s Unpacking libasound2-data (1.2.11-1build1) ... 169s Selecting previously unselected package libasound2:arm64. 169s Preparing to unpack .../21-libasound2_1.2.10-3build1_arm64.deb ... 169s Unpacking libasound2:arm64 (1.2.10-3build1) ... 169s Selecting previously unselected package libgraphite2-3:arm64. 169s Preparing to unpack .../22-libgraphite2-3_1.3.14-2_arm64.deb ... 169s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 169s Selecting previously unselected package libharfbuzz0b:arm64. 169s Preparing to unpack .../23-libharfbuzz0b_8.3.0-2_arm64.deb ... 169s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 169s Selecting previously unselected package libpcsclite1:arm64. 169s Preparing to unpack .../24-libpcsclite1_2.0.0-1_arm64.deb ... 169s Unpacking libpcsclite1:arm64 (2.0.0-1) ... 169s Selecting previously unselected package openjdk-17-jre-headless:arm64. 169s Preparing to unpack .../25-openjdk-17-jre-headless_17.0.10+7-1_arm64.deb ... 169s Unpacking openjdk-17-jre-headless:arm64 (17.0.10+7-1) ... 171s Selecting previously unselected package bbmap. 171s Preparing to unpack .../26-bbmap_39.06+dfsg-1_all.deb ... 171s Unpacking bbmap (39.06+dfsg-1) ... 171s Selecting previously unselected package bbmap-jni. 171s Preparing to unpack .../27-bbmap-jni_39.06+dfsg-1_arm64.deb ... 171s Unpacking bbmap-jni (39.06+dfsg-1) ... 171s Selecting previously unselected package python-biopython-doc. 171s Preparing to unpack .../28-python-biopython-doc_1.81+dfsg-3_all.deb ... 171s Unpacking python-biopython-doc (1.81+dfsg-3) ... 171s Selecting previously unselected package autopkgtest-satdep. 171s Preparing to unpack .../29-1-autopkgtest-satdep.deb ... 171s Unpacking autopkgtest-satdep (0) ... 171s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 171s Setting up liblcms2-2:arm64 (2.14-2) ... 171s Setting up java-common (0.75+exp1) ... 171s Setting up libcommons-cli-java (1.6.0-1) ... 171s Setting up liblog4j1.2-java (1.2.17-11) ... 171s Setting up libasound2-data (1.2.11-1build1) ... 171s Setting up libapache-pom-java (29-2) ... 171s Setting up libavahi-common-data:arm64 (0.8-13ubuntu2) ... 171s Setting up fonts-dejavu-mono (2.37-8) ... 171s Setting up fonts-dejavu-core (2.37-8) ... 171s Setting up libpcsclite1:arm64 (2.0.0-1) ... 171s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 171s Setting up python-biopython-doc (1.81+dfsg-3) ... 171s Setting up libasound2:arm64 (1.2.10-3build1) ... 171s Setting up libharfbuzz0b:arm64 (8.3.0-2) ... 171s Setting up bbmap-jni (39.06+dfsg-1) ... 171s Setting up ca-certificates-java (20240118) ... 171s No JRE found. Skipping Java certificates setup. 171s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 171s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 172s Setting up libcommons-parent-java (56-1) ... 172s Setting up libavahi-common3:arm64 (0.8-13ubuntu2) ... 172s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 172s Setting up libcommons-codec-java (1.16.0-1) ... 172s Setting up libavahi-client3:arm64 (0.8-13ubuntu2) ... 172s Setting up libcommons-io-java (2.11.0-2) ... 172s Setting up libmpj-java (0.44+dfsg-4) ... 172s Setting up libcups2:arm64 (2.4.6-0ubuntu3) ... 172s Setting up openjdk-17-jre-headless:arm64 (17.0.10+7-1) ... 172s update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode 172s update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 172s update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 172s update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 172s update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 172s Processing triggers for libc-bin (2.39-0ubuntu2) ... 172s Processing triggers for man-db (2.12.0-3) ... 173s Processing triggers for ca-certificates-java (20240118) ... 174s Adding debian:ACCVRAIZ1.pem 174s Adding debian:AC_RAIZ_FNMT-RCM.pem 174s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 174s Adding debian:ANF_Secure_Server_Root_CA.pem 174s Adding debian:Actalis_Authentication_Root_CA.pem 174s Adding debian:AffirmTrust_Commercial.pem 174s Adding debian:AffirmTrust_Networking.pem 174s Adding debian:AffirmTrust_Premium.pem 174s Adding debian:AffirmTrust_Premium_ECC.pem 174s Adding debian:Amazon_Root_CA_1.pem 174s Adding debian:Amazon_Root_CA_2.pem 174s Adding debian:Amazon_Root_CA_3.pem 174s Adding debian:Amazon_Root_CA_4.pem 174s Adding debian:Atos_TrustedRoot_2011.pem 174s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 174s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 174s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 174s Adding debian:BJCA_Global_Root_CA1.pem 174s Adding debian:BJCA_Global_Root_CA2.pem 174s Adding debian:Baltimore_CyberTrust_Root.pem 174s Adding debian:Buypass_Class_2_Root_CA.pem 174s Adding debian:Buypass_Class_3_Root_CA.pem 174s Adding debian:CA_Disig_Root_R2.pem 174s Adding debian:CFCA_EV_ROOT.pem 174s Adding debian:COMODO_Certification_Authority.pem 174s Adding debian:COMODO_ECC_Certification_Authority.pem 174s Adding debian:COMODO_RSA_Certification_Authority.pem 174s Adding debian:Certainly_Root_E1.pem 174s Adding debian:Certainly_Root_R1.pem 174s Adding debian:Certigna.pem 174s Adding debian:Certigna_Root_CA.pem 174s Adding debian:Certum_EC-384_CA.pem 174s Adding debian:Certum_Trusted_Network_CA.pem 174s Adding debian:Certum_Trusted_Network_CA_2.pem 174s Adding debian:Certum_Trusted_Root_CA.pem 174s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 174s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 174s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 174s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 174s Adding debian:Comodo_AAA_Services_root.pem 174s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 174s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 174s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 174s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 174s Adding debian:DigiCert_Assured_ID_Root_CA.pem 174s Adding debian:DigiCert_Assured_ID_Root_G2.pem 174s Adding debian:DigiCert_Assured_ID_Root_G3.pem 174s Adding debian:DigiCert_Global_Root_CA.pem 174s Adding debian:DigiCert_Global_Root_G2.pem 174s Adding debian:DigiCert_Global_Root_G3.pem 174s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 174s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 174s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 174s Adding debian:DigiCert_Trusted_Root_G4.pem 174s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 174s Adding debian:Entrust_Root_Certification_Authority.pem 174s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 174s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 174s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem 174s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 174s Adding debian:GLOBALTRUST_2020.pem 174s Adding debian:GTS_Root_R1.pem 174s Adding debian:GTS_Root_R2.pem 174s Adding debian:GTS_Root_R3.pem 174s Adding debian:GTS_Root_R4.pem 174s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 174s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 174s Adding debian:GlobalSign_Root_CA.pem 174s Adding debian:GlobalSign_Root_CA_-_R3.pem 174s Adding debian:GlobalSign_Root_CA_-_R6.pem 174s Adding debian:GlobalSign_Root_E46.pem 174s Adding debian:GlobalSign_Root_R46.pem 174s Adding debian:Go_Daddy_Class_2_CA.pem 174s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 174s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 174s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 174s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 174s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 174s Adding debian:HiPKI_Root_CA_-_G1.pem 174s Adding debian:Hongkong_Post_Root_CA_3.pem 174s Adding debian:ISRG_Root_X1.pem 174s Adding debian:ISRG_Root_X2.pem 174s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 174s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 174s Adding debian:Izenpe.com.pem 174s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 174s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 174s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 174s Adding debian:NAVER_Global_Root_Certification_Authority.pem 174s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 174s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 174s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 174s Adding debian:QuoVadis_Root_CA_1_G3.pem 174s Adding debian:QuoVadis_Root_CA_2.pem 174s Adding debian:QuoVadis_Root_CA_2_G3.pem 174s Adding debian:QuoVadis_Root_CA_3.pem 174s Adding debian:QuoVadis_Root_CA_3_G3.pem 174s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 174s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 174s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 174s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 174s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 174s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 174s Adding debian:SZAFIR_ROOT_CA2.pem 174s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 174s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 174s Adding debian:SecureSign_RootCA11.pem 174s Adding debian:SecureTrust_CA.pem 174s Adding debian:Secure_Global_CA.pem 174s Adding debian:Security_Communication_ECC_RootCA1.pem 174s Adding debian:Security_Communication_RootCA2.pem 174s Adding debian:Security_Communication_RootCA3.pem 174s Adding debian:Security_Communication_Root_CA.pem 174s Adding debian:Starfield_Class_2_CA.pem 174s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 174s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 174s Adding debian:SwissSign_Gold_CA_-_G2.pem 174s Adding debian:SwissSign_Silver_CA_-_G2.pem 174s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 174s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 174s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 174s Adding debian:TWCA_Global_Root_CA.pem 174s Adding debian:TWCA_Root_Certification_Authority.pem 174s Adding debian:TeliaSonera_Root_CA_v1.pem 174s Adding debian:Telia_Root_CA_v2.pem 174s Adding debian:TrustAsia_Global_Root_CA_G3.pem 174s Adding debian:TrustAsia_Global_Root_CA_G4.pem 174s Adding debian:Trustwave_Global_Certification_Authority.pem 174s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 174s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 174s Adding debian:TunTrust_Root_CA.pem 174s Adding debian:UCA_Extended_Validation_Root.pem 174s Adding debian:UCA_Global_G2_Root.pem 174s Adding debian:USERTrust_ECC_Certification_Authority.pem 174s Adding debian:USERTrust_RSA_Certification_Authority.pem 174s Adding debian:XRamp_Global_CA_Root.pem 174s Adding debian:certSIGN_ROOT_CA.pem 174s Adding debian:certSIGN_Root_CA_G2.pem 174s Adding debian:e-Szigno_Root_CA_2017.pem 174s Adding debian:ePKI_Root_Certification_Authority.pem 174s Adding debian:emSign_ECC_Root_CA_-_C3.pem 174s Adding debian:emSign_ECC_Root_CA_-_G3.pem 174s Adding debian:emSign_Root_CA_-_C1.pem 174s Adding debian:emSign_Root_CA_-_G1.pem 174s Adding debian:vTrus_ECC_Root_CA.pem 174s Adding debian:vTrus_Root_CA.pem 175s done. 175s Setting up bbmap (39.06+dfsg-1) ... 175s Setting up autopkgtest-satdep (0) ... 179s (Reading database ... 77603 files and directories currently installed.) 179s Removing autopkgtest-satdep (0) ... 180s autopkgtest [12:06:16]: test run-unit-test: [----------------------- 181s 181s # bbmap 181s bbmap.sh --version 181s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 181s java -ea -Xmx2756m -Xms2756m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 --version 182s BBMap version 39.06 182s For help, please run the shellscript with no parameters, or look in /docs/. 182s bbmap.sh --help 183s 183s BBMap 183s Written by Brian Bushnell, from Dec. 2010 - present 183s Last modified September 15, 2022 183s 183s Description: Fast and accurate splice-aware read aligner. 183s Please read bbmap/docs/guides/BBMapGuide.txt for more information. 183s 183s To index: bbmap.sh ref= 183s To map: bbmap.sh in= out= 183s To map without writing an index: 183s bbmap.sh ref= in= out= nodisk 183s 183s in=stdin will accept reads from standard in, and out=stdout will write to 183s standard out, but file extensions are still needed to specify the format of the 183s input and output files e.g. in=stdin.fa.gz will read gzipped fasta from 183s standard in; out=stdout.sam.gz will write gzipped sam. 183s 183s Indexing Parameters (required when building the index): 183s nodisk=f Set to true to build index in memory and write nothing 183s to disk except output. 183s ref= Specify the reference sequence. Only do this ONCE, 183s when building the index (unless using 'nodisk'). 183s build=1 If multiple references are indexed in the same directory, 183s each needs a unique numeric ID (unless using 'nodisk'). 183s k=13 Kmer length, range 8-15. Longer is faster but uses 183s more memory. Shorter is more sensitive. 183s If indexing and mapping are done in two steps, K should 183s be specified each time. 183s path=<.> Specify the location to write the index, if you don't 183s want it in the current working directory. 183s usemodulo=f Throw away ~80% of kmers based on remainder modulo a 183s number (reduces RAM by 50% and sensitivity slightly). 183s Should be enabled both when building the index AND 183s when mapping. 183s rebuild=f Force a rebuild of the index (ref= should be set). 183s 183s Input Parameters: 183s build=1 Designate index to use. Corresponds to the number 183s specified when building the index. 183s in= Primary reads input; required parameter. 183s in2= For paired reads in two files. 183s interleaved=auto True forces paired/interleaved input; false forces 183s single-ended mapping. If not specified, interleaved 183s status will be autodetected from read names. 183s fastareadlen=500 Break up FASTA reads longer than this. Max is 500 for 183s BBMap and 6000 for BBMapPacBio. Only works for FASTA 183s input (use 'maxlen' for FASTQ input). The default for 183s bbmap.sh is 500, and for mapPacBio.sh is 6000. 183s unpigz=f Spawn a pigz (parallel gzip) process for faster 183s decompression than using Java. 183s Requires pigz to be installed. 183s touppercase=t (tuc) Convert lowercase letters in reads to upper case 183s (otherwise they will not match the reference). 183s 183s Sampling Parameters: 183s 183s reads=-1 Set to a positive number N to only process the first N 183s reads (or pairs), then quit. -1 means use all reads. 183s samplerate=1 Set to a number from 0 to 1 to randomly select that 183s fraction of reads for mapping. 1 uses all reads. 183s skipreads=0 Set to a number N to skip the first N reads (or pairs), 183s then map the rest. 183s 183s Mapping Parameters: 183s fast=f This flag is a macro which sets other paramters to run 183s faster, at reduced sensitivity. Bad for RNA-seq. 183s slow=f This flag is a macro which sets other paramters to run 183s slower, at greater sensitivity. 'vslow' is even slower. 183s maxindel=16000 Don't look for indels longer than this. Lower is faster. 183s Set to >=100k for RNAseq with long introns like mammals. 183s strictmaxindel=f When enabled, do not allow indels longer than 'maxindel'. 183s By default these are not sought, but may be found anyway. 183s tipsearch=100 Look this far for read-end deletions with anchors 183s shorter than K, using brute force. 183s minid=0.76 Approximate minimum alignment identity to look for. 183s Higher is faster and less sensitive. 183s minhits=1 Minimum number of seed hits required for candidate sites. 183s Higher is faster. 183s local=f Set to true to use local, rather than global, alignments. 183s This will soft-clip ugly ends of poor alignments. 183s perfectmode=f Allow only perfect mappings when set to true (very fast). 183s semiperfectmode=f Allow only perfect and semiperfect (perfect except for 183s N's in the reference) mappings. 183s threads=auto (t) Set to number of threads desired. By default, uses 183s all cores available. 183s ambiguous=best (ambig) Set behavior on ambiguously-mapped reads (with 183s multiple top-scoring mapping locations). 183s best (use the first best site) 183s toss (consider unmapped) 183s random (select one top-scoring site randomly) 183s all (retain all top-scoring sites) 183s samestrandpairs=f (ssp) Specify whether paired reads should map to the 183s same strand or opposite strands. 183s requirecorrectstrand=t (rcs) Forbid pairing of reads without correct strand 183s orientation. Set to false for long-mate-pair libraries. 183s killbadpairs=f (kbp) If a read pair is mapped with an inappropriate 183s insert size or orientation, the read with the lower 183s mapping quality is marked unmapped. 183s pairedonly=f (po) Treat unpaired reads as unmapped. Thus they will 183s be sent to 'outu' but not 'outm'. 183s rcomp=f Reverse complement both reads prior to mapping (for LMP 183s outward-facing libraries). 183s rcompmate=f Reverse complement read2 prior to mapping. 183s pairlen=32000 Set max allowed distance between paired reads. 183s (insert size)=(pairlen)+(read1 length)+(read2 length) 183s rescuedist=1200 Don't try to rescue paired reads if avg. insert size 183s greater than this. Lower is faster. 183s rescuemismatches=32 Maximum mismatches allowed in a rescued read. Lower 183s is faster. 183s averagepairdist=100 (apd) Initial average distance between paired reads. 183s Varies dynamically; does not need to be specified. 183s deterministic=f Run in deterministic mode. In this case it is good 183s to set averagepairdist. BBMap is deterministic 183s without this flag if using single-ended reads, 183s or run singlethreaded. 183s bandwidthratio=0 (bwr) If above zero, restrict alignment band to this 183s fraction of read length. Faster but less accurate. 183s bandwidth=0 (bw) Set the bandwidth directly. 183s fraction of read length. Faster but less accurate. 183s usejni=f (jni) Do alignments faster, in C code. Requires 183s compiling the C code; details are in /jni/README.txt. 183s maxsites2=800 Don't analyze (or print) more than this many alignments 183s per read. 183s ignorefrequentkmers=t (ifk) Discard low-information kmers that occur often. 183s excludefraction=0.03 (ef) Fraction of kmers to ignore. For example, 0.03 183s will ignore the most common 3% of kmers. 183s greedy=t Use a greedy algorithm to discard the least-useful 183s kmers on a per-read basis. 183s kfilter=0 If positive, potential mapping sites must have at 183s least this many consecutive exact matches. 183s 183s 183s Quality and Trimming Parameters: 183s qin=auto Set to 33 or 64 to specify input quality value ASCII 183s offset. 33 is Sanger, 64 is old Solexa. 183s qout=auto Set to 33 or 64 to specify output quality value ASCII 183s offset (only if output format is fastq). 183s qtrim=f Quality-trim ends before mapping. Options are: 183s 'f' (false), 'l' (left), 'r' (right), and 'lr' (both). 183s untrim=f Undo trimming after mapping. Untrimmed bases will be 183s soft-clipped in cigar strings. 183s trimq=6 Trim regions with average quality below this 183s (phred algorithm). 183s mintrimlength=60 (mintl) Don't trim reads to be shorter than this. 183s fakefastaquality=-1 (ffq) Set to a positive number 1-50 to generate fake 183s quality strings for fasta input reads. 183s ignorebadquality=f (ibq) Keep going, rather than crashing, if a read has 183s out-of-range quality values. 183s usequality=t Use quality scores when determining which read kmers 183s to use as seeds. 183s minaveragequality=0 (maq) Do not map reads with average quality below this. 183s maqb=0 If positive, calculate maq from this many initial bases. 183s 183s Output Parameters: 183s out= Write all reads to this file. 183s outu= Write only unmapped reads to this file. Does not 183s include unmapped paired reads with a mapped mate. 183s outm= Write only mapped reads to this file. Includes 183s unmapped paired reads with a mapped mate. 183s mappedonly=f If true, treats 'out' like 'outm'. 183s bamscript= (bs) Write a shell script to that will turn 183s the sam output into a sorted, indexed bam file. 183s ordered=f Set to true to output reads in same order as input. 183s Slower and uses more memory. 183s overwrite=f (ow) Allow process to overwrite existing files. 183s secondary=f Print secondary alignments. 183s sssr=0.95 (secondarysitescoreratio) Print only secondary alignments 183s with score of at least this fraction of primary. 183s ssao=f (secondarysiteasambiguousonly) Only print secondary 183s alignments for ambiguously-mapped reads. 183s maxsites=5 Maximum number of total alignments to print per read. 183s Only relevant when secondary=t. 183s quickmatch=f Generate cigar strings more quickly. 183s trimreaddescriptions=f (trd) Truncate read and ref names at the first whitespace, 183s assuming that the remainder is a comment or description. 183s ziplevel=2 (zl) Compression level for zip or gzip output. 183s pigz=f Spawn a pigz (parallel gzip) process for faster 183s compression than Java. Requires pigz to be installed. 183s machineout=f Set to true to output statistics in machine-friendly 183s 'key=value' format. 183s printunmappedcount=f Print the total number of unmapped reads and bases. 183s If input is paired, the number will be of pairs 183s for which both reads are unmapped. 183s showprogress=0 If positive, print a '.' every X reads. 183s showprogress2=0 If positive, print the number of seconds since the 183s last progress update (instead of a '.'). 183s renamebyinsert=f Renames reads based on their mapped insert size. 183s 183s Bloom-Filtering Parameters (bloomfilter.sh is the standalone version). 183s bloom=f Use a Bloom filter to ignore reads not sharing kmers 183s with the reference. This uses more memory, but speeds 183s mapping when most reads don't match the reference. 183s bloomhashes=2 Number of hash functions. 183s bloomminhits=3 Number of consecutive hits to be considered matched. 183s bloomk=31 Bloom filter kmer length. 183s bloomserial=t Use the serialized Bloom filter for greater loading 183s speed, if available. If not, generate and write one. 183s 183s Post-Filtering Parameters: 183s idfilter=0 Independant of minid; sets exact minimum identity 183s allowed for alignments to be printed. Range 0 to 1. 183s subfilter=-1 Ban alignments with more than this many substitutions. 183s insfilter=-1 Ban alignments with more than this many insertions. 183s delfilter=-1 Ban alignments with more than this many deletions. 183s indelfilter=-1 Ban alignments with more than this many indels. 183s editfilter=-1 Ban alignments with more than this many edits. 183s inslenfilter=-1 Ban alignments with an insertion longer than this. 183s dellenfilter=-1 Ban alignments with a deletion longer than this. 183s nfilter=-1 Ban alignments with more than this many ns. This 183s includes nocall, noref, and off scaffold ends. 183s 183s Sam flags and settings: 183s noheader=f Disable generation of header lines. 183s sam=1.4 Set to 1.4 to write Sam version 1.4 cigar strings, 183s with = and X, or 1.3 to use M. 183s saa=t (secondaryalignmentasterisks) Use asterisks instead of 183s bases for sam secondary alignments. 183s cigar=t Set to 'f' to skip generation of cigar strings (faster). 183s keepnames=f Keep original names of paired reads, rather than 183s ensuring both reads have the same name. 183s intronlen=999999999 Set to a lower number like 10 to change 'D' to 'N' in 183s cigar strings for deletions of at least that length. 183s rgid= Set readgroup ID. All other readgroup fields 183s can be set similarly, with the flag rgXX= 183s If you set a readgroup flag to the word 'filename', 183s e.g. rgid=filename, the input file name will be used. 183s mdtag=f Write MD tags. 183s nhtag=f Write NH tags. 183s xmtag=f Write XM tags (may only work correctly with ambig=all). 183s amtag=f Write AM tags. 183s nmtag=f Write NM tags. 183s xstag=f Set to 'xs=fs', 'xs=ss', or 'xs=us' to write XS tags 183s for RNAseq using firststrand, secondstrand, or 183s unstranded libraries. Needed by Cufflinks. 183s JGI mainly uses 'firststrand'. 183s stoptag=f Write a tag indicating read stop location, prefixed by YS:i: 183s lengthtag=f Write a tag indicating (query,ref) alignment lengths, 183s prefixed by YL:Z: 183s idtag=f Write a tag indicating percent identity, prefixed by YI:f: 183s inserttag=f Write a tag indicating insert size, prefixed by X8:Z: 183s scoretag=f Write a tag indicating BBMap's raw score, prefixed by YR:i: 183s timetag=f Write a tag indicating this read's mapping time, prefixed by X0:i: 183s boundstag=f Write a tag indicating whether either read in the pair 183s goes off the end of the reference, prefixed by XB:Z: 183s notags=f Turn off all optional tags. 183s 183s Histogram and statistics output parameters: 183s scafstats= Statistics on how many reads mapped to which scaffold. 183s refstats= Statistics on how many reads mapped to which reference 183s file; only for BBSplit. 183s sortscafs=t Sort scaffolds or references by read count. 183s bhist= Base composition histogram by position. 183s qhist= Quality histogram by position. 183s aqhist= Histogram of average read quality. 183s bqhist= Quality histogram designed for box plots. 183s lhist= Read length histogram. 183s ihist= Write histogram of insert sizes (for paired reads). 183s ehist= Errors-per-read histogram. 183s qahist= Quality accuracy histogram of error rates versus 183s quality score. 183s indelhist= Indel length histogram. 183s mhist= Histogram of match, sub, del, and ins rates by 183s read location. 183s gchist= Read GC content histogram. 183s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 183s gcpairs=t Use average GC of paired reads. 183s idhist= Histogram of read count versus percent identity. 183s idbins=100 Number idhist bins. Set to 'auto' to use read length. 183s statsfile=stderr Mapping statistics are printed here. 183s 183s Coverage output parameters (these may reduce speed and use more RAM): 183s covstats= Per-scaffold coverage info. 183s rpkm= Per-scaffold RPKM/FPKM counts. 183s covhist= Histogram of # occurrences of each depth level. 183s basecov= Coverage per base location. 183s bincov= Print binned coverage per location (one line per X bases). 183s covbinsize=1000 Set the binsize for binned coverage output. 183s nzo=t Only print scaffolds with nonzero coverage. 183s twocolumn=f Change to true to print only ID and Avg_fold instead of 183s all 6 columns to the 'out=' file. 183s 32bit=f Set to true if you need per-base coverage over 64k. 183s strandedcov=f Track coverage for plus and minus strand independently. 183s startcov=f Only track start positions of reads. 183s secondarycov=t Include coverage of secondary alignments. 183s physcov=f Calculate physical coverage for paired reads. 183s This includes the unsequenced bases. 183s delcoverage=t (delcov) Count bases covered by deletions as covered. 183s True is faster than false. 183s covk=0 If positive, calculate kmer coverage statistics. 183s 183s Java Parameters: 183s -Xmx This will set Java's memory usage, 183s overriding autodetection. 183s -Xmx20g will specify 20 gigs of RAM, and -Xmx800m 183s will specify 800 megs. The max is typically 85% of 183s physical memory. The human genome requires around 24g, 183s or 12g with the 'usemodulo' flag. The index uses 183s roughly 6 bytes per reference base. 183s -eoom This flag will cause the process to exit if an 183s out-of-memory exception occurs. Requires Java 8u92+. 183s -da Disable assertions. 183s 183s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter 183s any problems, or post at: http://seqanswers.com/forums/showthread.php?t=41057 183s 183s bbmap.sh ref=example.fasta 183s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 183s java -ea -Xmx2756m -Xms2756m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta 183s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta] 183s Version 39.06 183s 183s No output file. 183s Writing reference. 183s 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] 183s 183s Set genScaffoldInfo=true 183s Writing chunk 1 183s Set genome to 1 183s 183s Loaded Reference: 0.037 seconds. 183s Loading index for chunk 1-1, build 1 183s No index available; generating from reference genome: /tmp/autopkgtest.QEL1Rz/autopkgtest_tmp/ref/index/1/chr1_index_k13_c16_b1.block 183s Indexing threads started for block 0-1 183s Indexing threads finished for block 0-1 184s Generated Index: 0.945 seconds. 184s No reads to process; quitting. 184s 184s Total time: 1.317 seconds. 184s test -d ref 184s bbmap.sh in=misc_dna_as_sanger.fastq out=out.sam 184s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 184s java -ea -Xmx2756m -Xms2756m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 in=misc_dna_as_sanger.fastq out=out.sam 184s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, in=misc_dna_as_sanger.fastq, out=out.sam] 184s Version 39.06 184s 184s Retaining first best site only for ambiguous mappings. 184s Set genome to 1 184s 184s Loaded Reference: 0.031 seconds. 184s Loading index for chunk 1-1, build 1 185s Generated Index: 0.382 seconds. 188s Analyzed Index: 3.139 seconds. 188s Started output stream: 0.024 seconds. 188s Cleared Memory: 0.114 seconds. 188s Processing reads in single-ended mode. 188s Started read stream. 188s Started 4 mapping threads. 188s Detecting finished threads: 0, 1, 2, 3 188s 188s ------------------ Results ------------------ 188s 188s Genome: 1 188s Key Length: 13 188s Max Indel: 16000 188s Minimum Score Ratio: 0.56 188s Mapping Mode: normal 188s Reads Used: 4 (153 bases) 188s 188s Mapping: 0.071 seconds. 188s Reads/sec: 56.70 188s kBases/sec: 2.17 188s 188s 188s Read 1 data: pct reads num reads pct bases num bases 188s 188s mapped: 0.0000% 0 0.0000% 0 188s unambiguous: 0.0000% 0 0.0000% 0 188s ambiguous: 0.0000% 0 0.0000% 0 188s low-Q discards: 25.0000% 1 19.6078% 30 188s 188s perfect best site: 0.0000% 0 0.0000% 0 188s semiperfect site: 0.0000% 0 0.0000% 0 188s 188s Match Rate: NA NA NaN% 0 188s Error Rate: NaN% 0 NaN% 0 188s Sub Rate: NaN% 0 NaN% 0 188s Del Rate: NaN% 0 NaN% 0 188s Ins Rate: NaN% 0 NaN% 0 188s N Rate: NaN% 0 NaN% 0 188s 188s Total time: 3.897 seconds. 188s test -r out.sam 188s bbmap.sh ref=example.fasta in=example.fastq out=out2.sam nodisk 188s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 188s java -ea -Xmx2756m -Xms2756m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta in=example.fastq out=out2.sam nodisk 188s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta, in=example.fastq, out=out2.sam, nodisk] 188s Version 39.06 188s 188s Retaining first best site only for ambiguous mappings. 188s 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] 188s 188s Set genScaffoldInfo=true 188s Set genome to 1 188s 188s Loaded Reference: 0.002 seconds. 188s Loading index for chunk 1-1, build 1 188s Indexing threads started for block 0-1 188s Indexing threads finished for block 0-1 189s Generated Index: 0.221 seconds. 192s Analyzed Index: 3.038 seconds. 192s Started output stream: 0.045 seconds. 192s Cleared Memory: 0.114 seconds. 192s Processing reads in single-ended mode. 192s Started read stream. 192s Started 4 mapping threads. 192s Detecting finished threads: 0, 1, 2, 3 192s 192s ------------------ Results ------------------ 192s 192s Genome: 1 192s Key Length: 13 192s Max Indel: 16000 192s Minimum Score Ratio: 0.56 192s Mapping Mode: normal 192s Reads Used: 3 (75 bases) 192s 192s Mapping: 0.172 seconds. 192s Reads/sec: 17.43 192s kBases/sec: 0.44 192s 192s 192s Read 1 data: pct reads num reads pct bases num bases 192s 192s mapped: 100.0000% 3 100.0000% 75 192s unambiguous: 100.0000% 3 100.0000% 75 192s ambiguous: 0.0000% 0 0.0000% 0 192s low-Q discards: 0.0000% 0 0.0000% 0 192s 192s perfect best site: 100.0000% 3 100.0000% 75 192s semiperfect site: 100.0000% 3 100.0000% 75 192s 192s Match Rate: NA NA 100.0000% 75 192s Error Rate: 0.0000% 0 0.0000% 0 192s Sub Rate: 0.0000% 0 0.0000% 0 192s Del Rate: 0.0000% 0 0.0000% 0 192s Ins Rate: 0.0000% 0 0.0000% 0 192s N Rate: 0.0000% 0 0.0000% 0 192s 192s Total time: 3.849 seconds. 192s test -r out2.sam 192s 192s # bbduk 192s bbduk.sh --version 192s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 192s java -ea -Xmx1378m -Xms1378m -cp /usr/share/java/bbmap.jar jgi.BBDuk --version 193s BBMap version 39.06 193s For help, please run the shellscript with no parameters, or look in /docs/. 193s bbduk.sh --help 193s bbduk.sh in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq \ 193s qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 193s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 193s 193s Written by Brian Bushnell 193s Last modified November 9, 2023 193s 193s Description: Compares reads to the kmers in a reference dataset, optionally 193s allowing an edit distance. Splits the reads into two outputs - those that 193s match the reference, and those that don't. Can also trim (remove) the matching 193s parts of the reads rather than binning the reads. 193s Please read bbmap/docs/guides/BBDukGuide.txt for more information. 193s 193s Usage: bbduk.sh in= out= ref= 193s 193s Input may be stdin or a fasta or fastq file, compressed or uncompressed. 193s If you pipe via stdin/stdout, please include the file type; e.g. for gzipped 193s fasta input, set in=stdin.fa.gz 193s 193s Input parameters: 193s in= Main input. in=stdin.fq will pipe from stdin. 193s in2= Input for 2nd read of pairs in a different file. 193s ref= Comma-delimited list of reference files. 193s In addition to filenames, you may also use the keywords: 193s adapters, artifacts, phix, lambda, pjet, mtst, kapa 193s literal= Comma-delimited list of literal reference sequences. 193s touppercase=f (tuc) Change all bases upper-case. 193s interleaved=auto (int) t/f overrides interleaved autodetection. 193s Must be set mainually when streaming fastq input. 193s qin=auto Input quality offset: 33 (Sanger), 64, or auto. 193s reads=-1 If positive, quit after processing X reads or pairs. 193s copyundefined=f (cu) Process non-AGCT IUPAC reference bases by making all 193s possible unambiguous copies. Intended for short motifs 193s or adapter barcodes, as time/memory use is exponential. 193s samplerate=1 Set lower to only process a fraction of input reads. 193s samref= Optional reference fasta for processing sam files. 193s 193s Output parameters: 193s out= (outnonmatch) Write reads here that do not contain 193s kmers matching the database. 'out=stdout.fq' will pipe 193s to standard out. 193s out2= (outnonmatch2) Use this to write 2nd read of pairs to a 193s different file. 193s outm= (outmatch) Write reads here that fail filters. In default 193s kfilter mode, this means any read with a matching kmer. 193s In any mode, it also includes reads that fail filters such 193s as minlength, mingc, maxgc, entropy, etc. In other words, 193s it includes all reads that do not go to 'out'. 193s outm2= (outmatch2) Use this to write 2nd read of pairs to a 193s different file. 193s outs= (outsingle) Use this to write singleton reads whose mate 193s was trimmed shorter than minlen. 193s stats= Write statistics about which contamininants were detected. 193s refstats= Write statistics on a per-reference-file basis. 193s rpkm= Write RPKM for each reference sequence (for RNA-seq). 193s dump= Dump kmer tables to a file, in fasta format. 193s duk= Write statistics in duk's format. *DEPRECATED* 193s nzo=t Only write statistics about ref sequences with nonzero hits. 193s overwrite=t (ow) Grant permission to overwrite files. 193s showspeed=t (ss) 'f' suppresses display of processing speed. 193s ziplevel=2 (zl) Compression level; 1 (min) through 9 (max). 193s fastawrap=70 Length of lines in fasta output. 193s qout=auto Output quality offset: 33 (Sanger), 64, or auto. 193s statscolumns=3 (cols) Number of columns for stats output, 3 or 5. 193s 5 includes base counts. 193s rename=f Rename reads to indicate which sequences they matched. 193s refnames=f Use names of reference files rather than scaffold IDs. 193s trd=f Truncate read and ref names at the first whitespace. 193s ordered=f Set to true to output reads in same order as input. 193s maxbasesout=-1 If positive, quit after writing approximately this many 193s bases to out (outu/outnonmatch). 193s maxbasesoutm=-1 If positive, quit after writing approximately this many 193s bases to outm (outmatch). 193s json=f Print to screen in json format. 193s 193s Histogram output parameters: 193s bhist= Base composition histogram by position. 193s qhist= Quality histogram by position. 193s qchist= Count of bases with each quality value. 193s aqhist= Histogram of average read quality. 193s bqhist= Quality histogram designed for box plots. 193s lhist= Read length histogram. 193s phist= Polymer length histogram. 193s gchist= Read GC content histogram. 193s enthist= Read entropy histogram. 193s ihist= Insert size histogram, for paired reads in mapped sam. 193s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 193s maxhistlen=6000 Set an upper bound for histogram lengths; higher uses 193s more memory. The default is 6000 for some histograms 193s and 80000 for others. 193s 193s Histograms for mapped sam/bam files only: 193s histbefore=t Calculate histograms from reads before processing. 193s ehist= Errors-per-read histogram. 193s qahist= Quality accuracy histogram of error rates versus quality 193s score. 193s indelhist= Indel length histogram. 193s mhist= Histogram of match, sub, del, and ins rates by position. 193s idhist= Histogram of read count versus percent identity. 193s idbins=100 Number idhist bins. Set to 'auto' to use read length. 193s varfile= Ignore substitution errors listed in this file when 193s calculating error rates. Can be generated with 193s CallVariants. 193s vcf= Ignore substitution errors listed in this VCF file 193s when calculating error rates. 193s ignorevcfindels=t Also ignore indels listed in the VCF. 193s 193s Processing parameters: 193s k=27 Kmer length used for finding contaminants. Contaminants 193s shorter than k will not be found. k must be at least 1. 193s rcomp=t Look for reverse-complements of kmers in addition to 193s forward kmers. 193s maskmiddle=t (mm) Treat the middle base of a kmer as a wildcard, to 193s increase sensitivity in the presence of errors. This may 193s also be set to a number, e.g. mm=3, to mask that many bp. 193s The default mm=t corresponds to mm=1 for odd-length kmers 193s and mm=2 for even-length kmers (as of v39.04), while 193s mm=f is always equivalent to mm=0. 193s minkmerhits=1 (mkh) Reads need at least this many matching kmers 193s to be considered as matching the reference. 193s minkmerfraction=0.0 (mkf) A reads needs at least this fraction of its total 193s kmers to hit a ref, in order to be considered a match. 193s If this and minkmerhits are set, the greater is used. 193s mincovfraction=0.0 (mcf) A reads needs at least this fraction of its total 193s bases to be covered by ref kmers to be considered a match. 193s If specified, mcf overrides mkh and mkf. 193s hammingdistance=0 (hdist) Maximum Hamming distance for ref kmers (subs only). 193s Memory use is proportional to (3*K)^hdist. 193s qhdist=0 Hamming distance for query kmers; impacts speed, not memory. 193s editdistance=0 (edist) Maximum edit distance from ref kmers (subs 193s and indels). Memory use is proportional to (8*K)^edist. 193s hammingdistance2=0 (hdist2) Sets hdist for short kmers, when using mink. 193s qhdist2=0 Sets qhdist for short kmers, when using mink. 193s editdistance2=0 (edist2) Sets edist for short kmers, when using mink. 193s forbidn=f (fn) Forbids matching of read kmers containing N. 193s By default, these will match a reference 'A' if 193s hdist>0 or edist>0, to increase sensitivity. 193s removeifeitherbad=t (rieb) Paired reads get sent to 'outmatch' if either is 193s match (or either is trimmed shorter than minlen). 193s Set to false to require both. 193s trimfailures=f Instead of discarding failed reads, trim them to 1bp. 193s This makes the statistics a bit odd. 193s findbestmatch=f (fbm) If multiple matches, associate read with sequence 193s sharing most kmers. Reduces speed. 193s skipr1=f Don't do kmer-based operations on read 1. 193s skipr2=f Don't do kmer-based operations on read 2. 193s ecco=f For overlapping paired reads only. Performs error- 193s correction with BBMerge prior to kmer operations. 193s recalibrate=f (recal) Recalibrate quality scores. Requires calibration 193s matrices generated by CalcTrueQuality. 193s sam= If recalibration is desired, and matrices have not already 193s been generated, BBDuk will create them from the sam file. 193s amino=f Run in amino acid mode. Some features have not been 193s tested, but kmer-matching works fine. Maximum k is 12. 193s 193s Speed and Memory parameters: 193s threads=auto (t) Set number of threads to use; default is number of 193s logical processors. 193s prealloc=f Preallocate memory in table. Allows faster table loading 193s and more efficient memory usage, for a large reference. 193s monitor=f Kill this process if it crashes. monitor=600,0.01 would 193s kill after 600 seconds under 1% usage. 193s minrskip=1 (mns) Force minimal skip interval when indexing reference 193s kmers. 1 means use all, 2 means use every other kmer, etc. 193s maxrskip=1 (mxs) Restrict maximal skip interval when indexing 193s reference kmers. Normally all are used for scaffolds<100kb, 193s but with longer scaffolds, up to maxrskip-1 are skipped. 193s rskip= Set both minrskip and maxrskip to the same value. 193s If not set, rskip will vary based on sequence length. 193s qskip=1 Skip query kmers to increase speed. 1 means use all. 193s speed=0 Ignore this fraction of kmer space (0-15 out of 16) in both 193s reads and reference. Increases speed and reduces memory. 193s Note: Do not use more than one of 'speed', 'qskip', and 'rskip'. 193s 193s Trimming/Filtering/Masking parameters: 193s Note - if ktrim, kmask, and ksplit are unset, the default behavior is kfilter. 193s All kmer processing modes are mutually exclusive. 193s Reads only get sent to 'outm' purely based on kmer matches in kfilter mode. 193s 193s ktrim=f Trim reads to remove bases matching reference kmers, plus 193s all bases to the left or right. 193s Values: 193s f (don't trim), 193s r (trim to the right), 193s l (trim to the left) 193s ktrimtips=0 Set this to a positive number to perform ktrim on both 193s ends, examining only the outermost X bases. 193s kmask= Replace bases matching ref kmers with another symbol. 193s Allows any non-whitespace character, and processes short 193s kmers on both ends if mink is set. 'kmask=lc' will 193s convert masked bases to lowercase. 193s maskfullycovered=f (mfc) Only mask bases that are fully covered by kmers. 193s ksplit=f For single-ended reads only. Reads will be split into 193s pairs around the kmer. If the kmer is at the end of the 193s read, it will be trimmed instead. Singletons will go to 193s out, and pairs will go to outm. Do not use ksplit with 193s other operations such as quality-trimming or filtering. 193s mink=0 Look for shorter kmers at read tips down to this length, 193s when k-trimming or masking. 0 means disabled. Enabling 193s this will disable maskmiddle. 193s qtrim=f Trim read ends to remove bases with quality below trimq. 193s Performed AFTER looking for kmers. Values: 193s rl (trim both ends), 193s f (neither end), 193s r (right end only), 193s l (left end only), 193s w (sliding window). 193s trimq=6 Regions with average quality BELOW this will be trimmed, 193s if qtrim is set to something other than f. Can be a 193s floating-point number like 7.3. 193s trimclip=f Trim soft-clipped bases from sam files. 193s minlength=10 (ml) Reads shorter than this after trimming will be 193s discarded. Pairs will be discarded if both are shorter. 193s mlf=0 (minlengthfraction) Reads shorter than this fraction of 193s original length after trimming will be discarded. 193s maxlength= Reads longer than this after trimming will be discarded. 193s minavgquality=0 (maq) Reads with average quality (after trimming) below 193s this will be discarded. 193s maqb=0 If positive, calculate maq from this many initial bases. 193s minbasequality=0 (mbq) Reads with any base below this quality (after 193s trimming) will be discarded. 193s maxns=-1 If non-negative, reads with more Ns than this 193s (after trimming) will be discarded. 193s mcb=0 (minconsecutivebases) Discard reads without at least 193s this many consecutive called bases. 193s ottm=f (outputtrimmedtomatch) Output reads trimmed to shorter 193s than minlength to outm rather than discarding. 193s tp=0 (trimpad) Trim this much extra around matching kmers. 193s tbo=f (trimbyoverlap) Trim adapters based on where paired 193s reads overlap. 193s strictoverlap=t Adjust sensitivity for trimbyoverlap mode. 193s minoverlap=14 Require this many bases of overlap for detection. 193s mininsert=40 Require insert size of at least this for overlap. 193s Should be reduced to 16 for small RNA sequencing. 193s tpe=f (trimpairsevenly) When kmer right-trimming, trim both 193s reads to the minimum length of either. 193s forcetrimleft=0 (ftl) If positive, trim bases to the left of this position 193s (exclusive, 0-based). 193s forcetrimright=0 (ftr) If positive, trim bases to the right of this position 193s (exclusive, 0-based). 193s forcetrimright2=0 (ftr2) If positive, trim this many bases on the right end. 193s forcetrimmod=0 (ftm) If positive, right-trim length to be equal to zero, 193s modulo this number. 193s restrictleft=0 If positive, only look for kmer matches in the 193s leftmost X bases. 193s restrictright=0 If positive, only look for kmer matches in the 193s rightmost X bases. 193s NOTE: restrictleft and restrictright are mutually exclusive. If trimming 193s both ends is desired, use ktrimtips. 193s mingc=0 Discard reads with GC content below this. 193s maxgc=1 Discard reads with GC content above this. 193s gcpairs=t Use average GC of paired reads. 193s Also affects gchist. 193s tossjunk=f Discard reads with invalid characters as bases. 193s swift=f Trim Swift sequences: Trailing C/T/N R1, leading G/A/N R2. 193s 193s Header-parsing parameters - these require Illumina headers: 193s chastityfilter=f (cf) Discard reads with id containing ' 1:Y:' or ' 2:Y:'. 193s barcodefilter=f Remove reads with unexpected barcodes if barcodes is set, 193s or barcodes containing 'N' otherwise. A barcode must be 193s the last part of the read header. Values: 193s t: Remove reads with bad barcodes. 193s f: Ignore barcodes. 193s crash: Crash upon encountering bad barcodes. 193s barcodes= Comma-delimited list of barcodes or files of barcodes. 193s xmin=-1 If positive, discard reads with a lesser X coordinate. 193s ymin=-1 If positive, discard reads with a lesser Y coordinate. 193s xmax=-1 If positive, discard reads with a greater X coordinate. 193s ymax=-1 If positive, discard reads with a greater Y coordinate. 193s 193s Polymer trimming: 193s trimpolya=0 If greater than 0, trim poly-A or poly-T tails of 193s at least this length on either end of reads. 193s trimpolygleft=0 If greater than 0, trim poly-G prefixes of at least this 193s length on the left end of reads. Does not trim poly-C. 193s trimpolygright=0 If greater than 0, trim poly-G tails of at least this 193s length on the right end of reads. Does not trim poly-C. 193s trimpolyg=0 This sets both left and right at once. 193s filterpolyg=0 If greater than 0, remove reads with a poly-G prefix of 193s at least this length (on the left). 193s Note: there are also equivalent poly-C flags. 193s 193s Polymer tracking: 193s pratio=base,base 'pratio=G,C' will print the ratio of G to C polymers. 193s plen=20 Length of homopolymers to count. 193s 193s Entropy/Complexity parameters: 193s entropy=-1 Set between 0 and 1 to filter reads with entropy below 193s that value. Higher is more stringent. 193s entropywindow=50 Calculate entropy using a sliding window of this length. 193s entropyk=5 Calculate entropy using kmers of this length. 193s minbasefrequency=0 Discard reads with a minimum base frequency below this. 193s entropytrim=f Values: 193s f: (false) Do not entropy-trim. 193s r: (right) Trim low entropy on the right end only. 193s l: (left) Trim low entropy on the left end only. 193s rl: (both) Trim low entropy on both ends. 193s entropymask=f Values: 193s f: (filter) Discard low-entropy sequences. 193s t: (true) Mask low-entropy parts of sequences with N. 193s lc: Change low-entropy parts of sequences to lowercase. 193s entropymark=f Mark each base with its entropy value. This is on a scale 193s of 0-41 and is reported as quality scores, so the output 193s should be fastq or fasta+qual. 193s NOTE: If set, entropytrim overrides entropymask. 193s 193s Cardinality estimation: 193s cardinality=f (loglog) Count unique kmers using the LogLog algorithm. 193s cardinalityout=f (loglogout) Count unique kmers in output reads. 193s loglogk=31 Use this kmer length for counting. 193s loglogbuckets=2048 Use this many buckets for counting. 193s khist= Kmer frequency histogram; plots number of kmers versus 193s kmer depth. This is approximate. 193s khistout= Kmer frequency histogram for output reads. 193s 193s Java Parameters: 193s 193s -Xmx This will set Java's memory usage, overriding autodetection. 193s -Xmx20g will 193s specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 193s The max is typically 85% of physical memory. 193s -eoom This flag will cause the process to exit if an 193s out-of-memory exception occurs. Requires Java 8u92+. 193s -da Disable assertions. 193s 193s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 193s 193s java -ea -Xmx1378m -Xms1378m -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 193s 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] 193s Version 39.06 193s 193s 0.038 seconds. 193s Initial: 193s Memory: max=1444m, total=1444m, free=1414m, used=30m 193s 193s Input is being processed as paired 193s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 193s Started output streams: 0.031 seconds. 193s Processing time: 0.004 seconds. 193s 193s Input: 8 reads 306 bases. 193s QTrimmed: 0 reads (0.00%) 0 bases (0.00%) 193s Total Removed: 8 reads (100.00%) 306 bases (100.00%) 193s Result: 0 reads (0.00%) 0 bases (0.00%) 193s 193s Time: 0.037 seconds. 193s Reads Processed: 8 0.21k reads/sec 193s Bases Processed: 306 0.01m bases/sec 193s test -r out.fastq.gz 193s 193s # bbnorm 193s bbnorm.sh --version 193s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 193s java -ea -Xmx2756m -Xms2756m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 --version 194s BBMap version 39.06 194s For help, please run the shellscript with no parameters, or look in /docs/. 194s bbnorm.sh --help 194s 194s Written by Brian Bushnell 194s Last modified October 19, 2017 194s 194s Description: Normalizes read depth based on kmer counts. 194s Can also error-correct, bin reads by kmer depth, and generate a kmer depth histogram. 194s However, Tadpole has superior error-correction to BBNorm. 194s Please read bbmap/docs/guides/BBNormGuide.txt for more information. 194s 194s Usage: bbnorm.sh in= out= outt= hist= 194s 194s Input parameters: 194s in=null Primary input. Use in2 for paired reads in a second file 194s in2=null Second input file for paired reads in two files 194s extra=null Additional files to use for input (generating hash table) but not for output 194s fastareadlen=2^31 Break up FASTA reads longer than this. Can be useful when processing scaffolded genomes 194s tablereads=-1 Use at most this many reads when building the hashtable (-1 means all) 194s kmersample=1 Process every nth kmer, and skip the rest 194s readsample=1 Process every nth read, and skip the rest 194s 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. 194s qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto. 194s 194s Output parameters: 194s out= File for normalized or corrected reads. Use out2 for paired reads in a second file 194s outt= (outtoss) File for reads that were excluded from primary output 194s reads=-1 Only process this number of reads, then quit (-1 means all) 194s sampleoutput=t Use sampling on output as well as input (not used if sample rates are 1) 194s keepall=f Set to true to keep all reads (e.g. if you just want error correction). 194s 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. 194s Default is false, to prevent confusion about how there can be 0-count kmers. 194s The reason is that based on the 'minq' and 'minprob' settings, some kmers may be excluded from the bloom filter. 194s tmpdir= This will specify a directory for temp files (only needed for multipass runs). If null, they will be written to the output directory. 194s usetempdir=t Allows enabling/disabling of temporary directory; if disabled, temp files will be written to the output directory. 194s qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input). 194s rename=f Rename reads based on their kmer depth. 194s 194s Hashing parameters: 194s k=31 Kmer length (values under 32 are most efficient, but arbitrarily high values are supported) 194s 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. 194s Large values decrease accuracy for a fixed amount of memory, so use the lowest number you can that will still capture highest-depth kmers. 194s hashes=3 Number of times each kmer is hashed and stored. Higher is slower. 194s Higher is MORE accurate if there is enough memory, and LESS accurate if there is not enough memory. 194s 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. 194s prehashes=2 Number of hashes for prefilter. 194s prefilterbits=2 (pbits) Bits per cell in prefilter. 194s prefiltersize=0.35 Fraction of memory to allocate to prefilter. 194s buildpasses=1 More passes can sometimes increase accuracy by iteratively removing low-depth kmers 194s minq=6 Ignore kmers containing bases with quality below this 194s minprob=0.5 Ignore kmers with overall probability of correctness below this 194s 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. 194s 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. 194s 194s Normalization parameters: 194s fixspikes=f (fs) Do a slower, high-precision bloom filter lookup of kmers that appear to have an abnormally high depth due to collisions. 194s target=100 (tgt) Target normalization depth. NOTE: All depth parameters control kmer depth, not read depth. 194s For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1)) 194s maxdepth=-1 (max) Reads will not be downsampled when below this depth, even if they are above the target depth. 194s mindepth=5 (min) Kmers with depth below this number will not be included when calculating the depth of a read. 194s minkmers=15 (mgkpr) Reads must have at least this many kmers over min depth to be retained. Aka 'mingoodkmersperread'. 194s 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. 194s uselowerdepth=t (uld) For pairs, use the depth of the lower read as the depth proxy. 194s deterministic=t (dr) Generate random numbers deterministically to ensure identical output between multiple runs. May decrease speed with a huge number of threads. 194s passes=2 (p) 1 pass is the basic mode. 2 passes (default) allows greater accuracy, error detection, better contol of output depth. 194s 194s Error detection parameters: 194s hdp=90.0 (highdepthpercentile) Position in sorted kmer depth array used as proxy of a read's high kmer depth. 194s ldp=25.0 (lowdepthpercentile) Position in sorted kmer depth array used as proxy of a read's low kmer depth. 194s tossbadreads=f (tbr) Throw away reads detected as containing errors. 194s requirebothbad=f (rbb) Only toss bad pairs if both reads are bad. 194s 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. 194s highthresh=12 (ht) Threshold for high kmer. A high kmer at this or above are considered non-error. 194s lowthresh=3 (lt) Threshold for low kmer. Kmers at this and below are always considered errors. 194s 194s Error correction parameters: 194s ecc=f Set to true to correct errors. NOTE: Tadpole is now preferred for ecc as it does a better job. 194s ecclimit=3 Correct up to this many errors per read. If more are detected, the read will remain unchanged. 194s errorcorrectratio=140 (ecr) Adjacent kmers with a depth ratio of at least this much between will be classified as an error. 194s echighthresh=22 (echt) Threshold for high kmer. A kmer at this or above may be considered non-error. 194s eclowthresh=2 (eclt) Threshold for low kmer. Kmers at this and below are considered errors. 194s eccmaxqual=127 Do not correct bases with quality above this value. 194s aec=f (aggressiveErrorCorrection) Sets more aggressive values of ecr=100, ecclimit=7, echt=16, eclt=3. 194s cec=f (conservativeErrorCorrection) Sets more conservative values of ecr=180, ecclimit=2, echt=30, eclt=1, sl=4, pl=4. 194s meo=f (markErrorsOnly) Marks errors by reducing quality value of suspected errors; does not correct anything. 194s mue=t (markUncorrectableErrors) Marks errors only on uncorrectable reads; requires 'ecc=t'. 194s overlap=f (ecco) Error correct by read overlap. 194s 194s Depth binning parameters: 194s lowbindepth=10 (lbd) Cutoff for low depth bin. 194s highbindepth=80 (hbd) Cutoff for high depth bin. 194s outlow= Pairs in which both reads have a median below lbd go into this file. 194s outhigh= Pairs in which both reads have a median above hbd go into this file. 194s outmid= All other pairs go into this file. 194s 194s Histogram parameters: 194s hist= Specify a file to write the input kmer depth histogram. 194s histout= Specify a file to write the output kmer depth histogram. 194s histcol=3 (histogramcolumns) Number of histogram columns, 2 or 3. 194s pzc=f (printzerocoverage) Print lines in the histogram with zero coverage. 194s histlen=1048576 Max kmer depth displayed in histogram. Also affe bbnorm.sh in=sanger_full_range_original_sanger.fastq qin=33 \ 194s out=out3.fastq outt=outt.fastq hist=hist.plt 194s cts statistics displayed, but does not affect normalization. 194s 194s Peak calling parameters: 194s peaks= Write the peaks to this file. Default is stdout. 194s minHeight=2 (h) Ignore peaks shorter than this. 194s minVolume=5 (v) Ignore peaks with less area than this. 194s minWidth=3 (w) Ignore peaks narrower than this. 194s minPeak=2 (minp) Ignore peaks with an X-value below this. 194s maxPeak=BIG (maxp) Ignore peaks with an X-value above this. 194s maxPeakCount=8 (maxpc) Print up to this many peaks (prioritizing height). 194s 194s Java Parameters: 194s -Xmx This will set Java's memory usage, overriding autodetection. 194s -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 194s The max is typically 85% of physical memory. 194s -eoom This flag will cause the process to exit if an 194s out-of-memory exception occurs. Requires Java 8u92+. 194s -da Disable assertions. 194s 194s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 194s 194s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 194s java -ea -Xmx2756m -Xms2756m -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 194s Executing jgi.KmerNormalize [bits=32, in=sanger_full_range_original_sanger.fastq, qin=33, out=out3.fastq, outt=outt.fastq, hist=hist.plt] 194s 194s 194s *********** Pass 1 ********** 194s 194s 194s Settings: 194s threads: 4 194s k: 31 194s deterministic: true 194s toss error reads: false 194s passes: 1 194s bits per cell: 16 194s cells: 1019.24M 194s hashes: 3 194s base min quality: 5 194s kmer min prob: 0.5 194s 194s target depth: 400 194s min depth: 3 194s max depth: 500 194s min good kmers: 15 194s depth percentile: 64.8 194s ignore dupe kmers: true 194s fix spikes: false 194s histogram length: 65536 194s print zero cov: false 194s 195s Made hash table: hashes = 3 mem = 1.90 GB cells = 1018.43M used = 0.000% 195s 195s Estimated unique kmers: 7 195s 195s Table creation time: 1.339 seconds. 195s Started output threads. 195s Started output threads. 195s Table read time: 0.027 seconds. 7.06 kb/sec 195s Total reads in: 2 0.000% Kept 195s Total bases in: 188 0.000% Kept 195s Error reads in: 2 100.000% 195s Error type 1: 2 100.000% 195s Error type 2: 0 0.000% 195s Error type 3: 0 0.000% 195s 195s Wrote histogram to hist.plt 195s Total kmers counted: 128 195s Total unique kmer count: 128 195s Includes forward kmers only. 195s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 195s The most accurate value is the greater of the two. 195s 195s Percent unique: 100.00% 195s Depth average: 1.00 (unique kmers) 195s Depth median: 1 (unique kmers) 195s Depth standard deviation: 0.00 (unique kmers) 195s Corrected depth average: 0.00 195s 195s Depth average: 1.00 (all kmers) 195s Depth median: 1 (all kmers) 195s Depth standard deviation: 0.00 (all kmers) 195s 195s Approx. read depth median: 1.47 195s 195s *********** Pass 2 ********** 195s 195s 195s Settings: 195s threads: 4 195s k: 31 195s deterministic: true 195s toss error reads: false 195s passes: 1 195s bits per cell: 16 195s cells: 1019.24M 195s hashes: 3 195s base min quality: 5 195s kmer min prob: 0.5 195s 195s target depth: 100 195s min depth: 5 195s max depth: 100 195s min good kmers: 15 195s depth percentile: 54.0 195s ignore dupe kmers: true 195s fix spikes: false 195s histogram length: 65536 195s 196s Made hash table: hashes = 3 mem = 1.90 GB cells = 1018.43M used = 0.000% 196s 196s Estimated unique kmers: 0 196s 196s Table creation time: 0.276 seconds. 196s Started output threads. 196s Started output threads. 196s Table read time: 0.001 seconds. 0.00 kb/sec 196s Total reads in: 0 NaN% Kept 196s Total bases in: 0 NaN% Kept 196s Error reads in: 0 NaN% 196s Error type 1: 0 NaN% 196s Error type 2: 0 NaN% 196s Error type 3: 0 NaN% 196s Total kmers counted: 0 196s Total unique kmer count: 0 196s Includes forward kmers only. 196s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 196s The most accurate value is the greater of the two. 196s 196s Percent unique: NaN% 196s Depth average: NaN (unique kmers) 196s Depth median: 0 (unique kmers) 196s Depth standard deviation: NaN (unique kmers) 196s Corrected depth average: NaN 196s 196s Depth average: NaN (all kmers) 196s Depth median: 0 (all kmers) 196s Depth standard deviation: 0.00 (all kmers) 196s 196s Approx. read depth median: NaN 196s 196s Removing temp files. 196s 196s Total time: 1.749 seconds. 0.11 kb/sec 196s test -r out3.fastq 196s test -r outt.fastq 196s test -r hist.plt 196s bbnorm.sh in=illumina_full_range_original_illumina.fastq qin=64 \ 196s out=out4.fastq outt=outt2.fastq hist=hist2.plt 196s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 196s java -ea -Xmx2756m -Xms2756m -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 196s Executing jgi.KmerNormalize [bits=32, in=illumina_full_range_original_illumina.fastq, qin=64, out=out4.fastq, outt=outt2.fastq, hist=hist2.plt] 196s 196s 196s *********** Pass 1 ********** 196s 196s 196s Settings: 196s threads: 4 196s k: 31 196s deterministic: true 196s toss error reads: false 196s passes: 1 196s bits per cell: 16 196s cells: 1019.24M 196s hashes: 3 196s base min quality: 5 196s kmer min prob: 0.5 196s 196s target depth: 400 196s min depth: 3 196s max depth: 500 196s min good kmers: 15 196s depth percentile: 64.8 196s ignore dupe kmers: true 196s fix spikes: false 196s histogram length: 65536 196s print zero cov: false 196s 197s Made hash table: hashes = 3 mem = 1.90 GB cells = 1018.43M used = 0.000% 197s 197s Estimated unique kmers: 7 197s 197s Table creation time: 0.827 seconds. 197s Started output threads. 197s Started output threads. 197s Table read time: 0.075 seconds. 1.67 kb/sec 197s Total reads in: 2 0.000% Kept 197s Total bases in: 126 0.000% Kept 197s Error reads in: 2 100.000% 197s Error type 1: 2 100.000% 197s Error type 2: 0 0.000% 197s Error type 3: 0 0.000% 197s 197s Wrote histogram to hist2.plt 197s Total kmers counted: 66 197s Total unique kmer count: 66 197s Includes forward kmers only. 197s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 197s The most accurate value is the greater of the two. 197s 197s Percent unique: 100.00% 197s Depth average: 1.00 (unique kmers) 197s Depth median: 1 (unique kmers) 197s Depth standard deviation: 0.00 (unique kmers) 197s Corrected depth average: 0.00 197s 197s Depth average: 1.00 (all kmers) 197s Depth median: 1 (all kmers) 197s Depth standard deviation: 0.00 (all kmers) 197s 197s Approx. read depth median: 1.91 197s 197s *********** Pass 2 ********** 197s 197s 197s Settings: 197s threads: 4 197s k: 31 197s deterministic: true 197s toss error reads: false 197s passes: 1 197s bits per cell: 16 197s cells: 1019.24M 197s hashes: 3 197s base min quality: 5 197s kmer min prob: 0.5 197s 197s target depth: 100 197s min depth: 5 197s max depth: 100 197s min good kmers: 15 197s depth percentile: 54.0 197s ignore dupe kmers: true 197s fix spikes: false 197s histogram length: 65536 197s 197s Made hash table: hashes = 3 mem = 1.90 GB cells = 1018.43M used = 0.000% 197s 197s Estimated unique kmers: 0 197s 197s Table creation time: 0.277 seconds. 197s Started output threads. 197s Started output threads. 197s Table read time: 0.001 seconds. 0.00 kb/sec 197s Total reads in: 0 NaN% Kept 197s Total bases in: 0 NaN% Kept 197s Error reads in: 0 NaN% 197s Error type 1: 0 NaN% 197s Error type 2: 0 NaN% 197s Error type 3: 0 NaN% 197s Total kmers counted: 0 197s Total unique kmer count: 0 197s Includes forward kmers only. 197s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 197s The most accurate value is the greater of the two. 197s 197s Percent unique: NaN% 197s Depth average: NaN (unique kmers) 197s Depth median: 0 (unique kmers) 197s Depth standard deviation: NaN (unique kmers) 197s Corrected depth average: NaN 197s 197s Depth average: NaN (all kmers) 197s Depth median: 0 (all kmers) 197s Depth standard deviation: 0.00 (all kmers) 197s 197s Approx. read depth median: NaN 197s 197s Removing temp files. 197s 197s Total time: 1.270 seconds. 0.10 kb/sec 197s test -r out4.fastq 197s test -r outt2.fastq 197s test -r hist2.plt 198s autopkgtest [12:06:34]: test run-unit-test: -----------------------] 198s autopkgtest [12:06:34]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 198s run-unit-test PASS 199s autopkgtest [12:06:35]: @@@@@@@@@@@@@@@@@@@@ summary 199s run-unit-test PASS 211s Creating nova instance adt-noble-arm64-bbmap-20240319-120316-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240319.img (UUID 821fd622-e452-4ae8-b5c8-959e73b1612a)...