0s autopkgtest [04:14:31]: starting date and time: 2024-11-02 04:14:31+0000 0s autopkgtest [04:14:31]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [04:14:31]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.n1c9z4fc/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:openjdk-24 --apt-upgrade bbmap --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=openjdk-24/24~22ea-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-big-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-s390x-4.secgroup --name adt-plucky-s390x-bbmap-20241102-041431-juju-7f2275-prod-proposed-migration-environment-15-30748b8f-64ff-477f-9b49-78136f67c94a --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-s390x -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,keyserver.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/ 95s autopkgtest [04:16:06]: testbed dpkg architecture: s390x 95s autopkgtest [04:16:06]: testbed apt version: 2.9.8 95s autopkgtest [04:16:06]: @@@@@@@@@@@@@@@@@@@@ test bed setup 95s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 96s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [2604 kB] 96s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 96s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [41.0 kB] 96s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [172 kB] 96s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [212 kB] 96s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [1849 kB] 96s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [33.3 kB] 97s Fetched 4993 kB in 1s (4391 kB/s) 97s Reading package lists... 99s Reading package lists... 99s Building dependency tree... 99s Reading state information... 99s Calculating upgrade... 99s The following packages will be upgraded: 99s libblockdev-crypto3 libblockdev-fs3 libblockdev-loop3 libblockdev-mdraid3 99s libblockdev-nvme3 libblockdev-part3 libblockdev-swap3 libblockdev-utils3 99s libblockdev3 libevdev2 libftdi1-2 libinih1 libpipeline1 nano 99s python3-lazr.uri 99s 15 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 99s Need to get 611 kB of archives. 99s After this operation, 52.2 kB of additional disk space will be used. 99s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libevdev2 s390x 1.13.3+dfsg-1 [35.9 kB] 99s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libpipeline1 s390x 1.5.8-1 [32.5 kB] 99s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x nano s390x 8.2-1 [298 kB] 99s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x libblockdev-utils3 s390x 3.2.0-2 [19.3 kB] 99s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x libblockdev-crypto3 s390x 3.2.0-2 [23.7 kB] 99s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x libblockdev-fs3 s390x 3.2.0-2 [36.1 kB] 99s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libblockdev-loop3 s390x 3.2.0-2 [7092 B] 99s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libblockdev-mdraid3 s390x 3.2.0-2 [12.8 kB] 99s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libblockdev-nvme3 s390x 3.2.0-2 [18.1 kB] 99s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libblockdev-part3 s390x 3.2.0-2 [15.3 kB] 99s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x libblockdev-swap3 s390x 3.2.0-2 [7704 B] 99s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x libblockdev3 s390x 3.2.0-2 [53.8 kB] 99s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x libftdi1-2 s390x 1.5-7 [29.2 kB] 99s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x libinih1 s390x 58-1ubuntu1 [7602 B] 99s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x python3-lazr.uri all 1.0.6-4 [13.6 kB] 100s Fetched 611 kB in 1s (1114 kB/s) 100s (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 ... 55483 files and directories currently installed.) 100s Preparing to unpack .../00-libevdev2_1.13.3+dfsg-1_s390x.deb ... 100s Unpacking libevdev2:s390x (1.13.3+dfsg-1) over (1.13.2+dfsg-1) ... 100s Preparing to unpack .../01-libpipeline1_1.5.8-1_s390x.deb ... 100s Unpacking libpipeline1:s390x (1.5.8-1) over (1.5.7-2) ... 100s Preparing to unpack .../02-nano_8.2-1_s390x.deb ... 100s Unpacking nano (8.2-1) over (8.1-1) ... 100s Preparing to unpack .../03-libblockdev-utils3_3.2.0-2_s390x.deb ... 100s Unpacking libblockdev-utils3:s390x (3.2.0-2) over (3.1.1-2) ... 100s Preparing to unpack .../04-libblockdev-crypto3_3.2.0-2_s390x.deb ... 100s Unpacking libblockdev-crypto3:s390x (3.2.0-2) over (3.1.1-2) ... 100s Preparing to unpack .../05-libblockdev-fs3_3.2.0-2_s390x.deb ... 100s Unpacking libblockdev-fs3:s390x (3.2.0-2) over (3.1.1-2) ... 100s Preparing to unpack .../06-libblockdev-loop3_3.2.0-2_s390x.deb ... 100s Unpacking libblockdev-loop3:s390x (3.2.0-2) over (3.1.1-2) ... 100s Preparing to unpack .../07-libblockdev-mdraid3_3.2.0-2_s390x.deb ... 100s Unpacking libblockdev-mdraid3:s390x (3.2.0-2) over (3.1.1-2) ... 100s Preparing to unpack .../08-libblockdev-nvme3_3.2.0-2_s390x.deb ... 100s Unpacking libblockdev-nvme3:s390x (3.2.0-2) over (3.1.1-2) ... 100s Preparing to unpack .../09-libblockdev-part3_3.2.0-2_s390x.deb ... 100s Unpacking libblockdev-part3:s390x (3.2.0-2) over (3.1.1-2) ... 100s Preparing to unpack .../10-libblockdev-swap3_3.2.0-2_s390x.deb ... 100s Unpacking libblockdev-swap3:s390x (3.2.0-2) over (3.1.1-2) ... 100s Preparing to unpack .../11-libblockdev3_3.2.0-2_s390x.deb ... 100s Unpacking libblockdev3:s390x (3.2.0-2) over (3.1.1-2) ... 100s Preparing to unpack .../12-libftdi1-2_1.5-7_s390x.deb ... 100s Unpacking libftdi1-2:s390x (1.5-7) over (1.5-6build5) ... 100s Preparing to unpack .../13-libinih1_58-1ubuntu1_s390x.deb ... 100s Unpacking libinih1:s390x (58-1ubuntu1) over (55-1ubuntu2) ... 100s Preparing to unpack .../14-python3-lazr.uri_1.0.6-4_all.deb ... 100s Unpacking python3-lazr.uri (1.0.6-4) over (1.0.6-3) ... 100s Setting up libpipeline1:s390x (1.5.8-1) ... 100s Setting up libinih1:s390x (58-1ubuntu1) ... 100s Setting up python3-lazr.uri (1.0.6-4) ... 100s Setting up libftdi1-2:s390x (1.5-7) ... 100s Setting up libblockdev-utils3:s390x (3.2.0-2) ... 100s Setting up libblockdev-nvme3:s390x (3.2.0-2) ... 100s Setting up nano (8.2-1) ... 100s Setting up libblockdev-fs3:s390x (3.2.0-2) ... 100s Setting up libevdev2:s390x (1.13.3+dfsg-1) ... 100s Setting up libblockdev-mdraid3:s390x (3.2.0-2) ... 100s Setting up libblockdev-crypto3:s390x (3.2.0-2) ... 100s Setting up libblockdev-swap3:s390x (3.2.0-2) ... 100s Setting up libblockdev-loop3:s390x (3.2.0-2) ... 100s Setting up libblockdev3:s390x (3.2.0-2) ... 100s Installing new version of config file /etc/libblockdev/3/conf.d/00-default.cfg ... 100s Setting up libblockdev-part3:s390x (3.2.0-2) ... 100s Processing triggers for libc-bin (2.40-1ubuntu3) ... 100s Processing triggers for man-db (2.12.1-3) ... 101s Processing triggers for install-info (7.1.1-1) ... 101s Reading package lists... 101s Building dependency tree... 101s Reading state information... 101s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 101s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 101s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 102s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 102s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 102s Reading package lists... 102s Reading package lists... 102s Building dependency tree... 102s Reading state information... 103s Calculating upgrade... 103s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 103s Reading package lists... 103s Building dependency tree... 103s Reading state information... 103s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 105s autopkgtest [04:16:16]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 12:49:35 UTC 2024 105s autopkgtest [04:16:16]: @@@@@@@@@@@@@@@@@@@@ apt-source bbmap 107s Get:1 http://ftpmaster.internal/ubuntu plucky/universe bbmap 39.08+dfsg-1 (dsc) [2286 B] 107s Get:2 http://ftpmaster.internal/ubuntu plucky/universe bbmap 39.08+dfsg-1 (tar) [5396 kB] 107s Get:3 http://ftpmaster.internal/ubuntu plucky/universe bbmap 39.08+dfsg-1 (diff) [25.4 kB] 108s gpgv: Signature made Fri Aug 9 08:31:18 2024 UTC 108s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 108s gpgv: issuer "emollier@debian.org" 108s gpgv: Can't check signature: No public key 108s dpkg-source: warning: cannot verify inline signature for ./bbmap_39.08+dfsg-1.dsc: no acceptable signature found 108s autopkgtest [04:16:19]: testing package bbmap version 39.08+dfsg-1 108s autopkgtest [04:16:19]: build not needed 110s autopkgtest [04:16:21]: test run-unit-test: preparing testbed 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s Starting pkgProblemResolver with broken count: 0 111s Starting 2 pkgProblemResolver with broken count: 0 111s Done 112s The following additional packages will be installed: 112s bbmap bbmap-jni ca-certificates-java java-common libapache-pom-java 112s libcommons-cli-java libcommons-codec-java libcommons-io-java 112s libcommons-parent-java libjpeg-turbo8 libjpeg8 liblcms2-2 liblog4j1.2-java 112s libmpj-java libpcsclite1 openjdk-17-jre-headless python-biopython-doc 112s Suggested packages: 112s default-jre liblcms2-utils liblog4j1.2-java-doc libmail-java pcscd 112s libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho 112s fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic 112s Recommended packages: 112s pigz libcups2t64 libfontconfig1 libfreetype6 libharfbuzz0b libasound2t64 112s python3-biopython 112s The following NEW packages will be installed: 112s autopkgtest-satdep bbmap bbmap-jni ca-certificates-java java-common 112s libapache-pom-java libcommons-cli-java libcommons-codec-java 112s libcommons-io-java libcommons-parent-java libjpeg-turbo8 libjpeg8 liblcms2-2 112s liblog4j1.2-java libmpj-java libpcsclite1 openjdk-17-jre-headless 112s python-biopython-doc 112s 0 upgraded, 18 newly installed, 0 to remove and 0 not upgraded. 112s Need to get 75.3 MB/75.3 MB of archives. 112s After this operation, 218 MB of additional disk space will be used. 112s Get:1 /tmp/autopkgtest.bWB1UL/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [720 B] 112s Get:2 http://ftpmaster.internal/ubuntu plucky/universe s390x libcommons-cli-java all 1.6.0-1 [59.9 kB] 112s Get:3 http://ftpmaster.internal/ubuntu plucky/universe s390x libapache-pom-java all 33-2 [5874 B] 112s Get:4 http://ftpmaster.internal/ubuntu plucky/universe s390x libcommons-parent-java all 56-1 [10.7 kB] 112s Get:5 http://ftpmaster.internal/ubuntu plucky/universe s390x libcommons-codec-java all 1.16.0-1 [306 kB] 112s Get:6 http://ftpmaster.internal/ubuntu plucky/universe s390x libcommons-io-java all 2.16.1-1 [451 kB] 112s Get:7 http://ftpmaster.internal/ubuntu plucky/universe s390x liblog4j1.2-java all 1.2.17-11 [439 kB] 112s Get:8 http://ftpmaster.internal/ubuntu plucky/universe s390x libmpj-java all 0.44+dfsg-4 [443 kB] 112s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x ca-certificates-java all 20240118 [11.6 kB] 112s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x java-common all 0.76 [6852 B] 112s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x liblcms2-2 s390x 2.14-2build1 [172 kB] 112s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-turbo8 s390x 2.1.5-2ubuntu2 [150 kB] 112s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 112s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x libpcsclite1 s390x 2.3.0-1 [24.0 kB] 112s Get:15 http://ftpmaster.internal/ubuntu plucky/universe s390x openjdk-17-jre-headless s390x 17.0.13+11-2build1 [45.8 MB] 115s Get:16 http://ftpmaster.internal/ubuntu plucky/universe s390x bbmap all 39.08+dfsg-1 [10.0 MB] 115s Get:17 http://ftpmaster.internal/ubuntu plucky/universe s390x bbmap-jni s390x 39.08+dfsg-1 [38.5 kB] 115s Get:18 http://ftpmaster.internal/ubuntu plucky/universe s390x python-biopython-doc all 1.83+dfsg1-3 [17.4 MB] 116s Fetched 75.3 MB in 4s (19.3 MB/s) 116s Selecting previously unselected package libcommons-cli-java. 116s (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 ... 55483 files and directories currently installed.) 116s Preparing to unpack .../00-libcommons-cli-java_1.6.0-1_all.deb ... 116s Unpacking libcommons-cli-java (1.6.0-1) ... 116s Selecting previously unselected package libapache-pom-java. 116s Preparing to unpack .../01-libapache-pom-java_33-2_all.deb ... 116s Unpacking libapache-pom-java (33-2) ... 116s Selecting previously unselected package libcommons-parent-java. 116s Preparing to unpack .../02-libcommons-parent-java_56-1_all.deb ... 116s Unpacking libcommons-parent-java (56-1) ... 116s Selecting previously unselected package libcommons-codec-java. 116s Preparing to unpack .../03-libcommons-codec-java_1.16.0-1_all.deb ... 116s Unpacking libcommons-codec-java (1.16.0-1) ... 116s Selecting previously unselected package libcommons-io-java. 116s Preparing to unpack .../04-libcommons-io-java_2.16.1-1_all.deb ... 116s Unpacking libcommons-io-java (2.16.1-1) ... 116s Selecting previously unselected package liblog4j1.2-java. 116s Preparing to unpack .../05-liblog4j1.2-java_1.2.17-11_all.deb ... 116s Unpacking liblog4j1.2-java (1.2.17-11) ... 116s Selecting previously unselected package libmpj-java. 116s Preparing to unpack .../06-libmpj-java_0.44+dfsg-4_all.deb ... 116s Unpacking libmpj-java (0.44+dfsg-4) ... 116s Selecting previously unselected package ca-certificates-java. 116s Preparing to unpack .../07-ca-certificates-java_20240118_all.deb ... 116s Unpacking ca-certificates-java (20240118) ... 116s Selecting previously unselected package java-common. 116s Preparing to unpack .../08-java-common_0.76_all.deb ... 116s Unpacking java-common (0.76) ... 116s Selecting previously unselected package liblcms2-2:s390x. 116s Preparing to unpack .../09-liblcms2-2_2.14-2build1_s390x.deb ... 116s Unpacking liblcms2-2:s390x (2.14-2build1) ... 116s Selecting previously unselected package libjpeg-turbo8:s390x. 116s Preparing to unpack .../10-libjpeg-turbo8_2.1.5-2ubuntu2_s390x.deb ... 116s Unpacking libjpeg-turbo8:s390x (2.1.5-2ubuntu2) ... 116s Selecting previously unselected package libjpeg8:s390x. 116s Preparing to unpack .../11-libjpeg8_8c-2ubuntu11_s390x.deb ... 116s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 116s Selecting previously unselected package libpcsclite1:s390x. 116s Preparing to unpack .../12-libpcsclite1_2.3.0-1_s390x.deb ... 116s Unpacking libpcsclite1:s390x (2.3.0-1) ... 116s Selecting previously unselected package openjdk-17-jre-headless:s390x. 116s Preparing to unpack .../13-openjdk-17-jre-headless_17.0.13+11-2build1_s390x.deb ... 116s Unpacking openjdk-17-jre-headless:s390x (17.0.13+11-2build1) ... 117s Selecting previously unselected package bbmap. 117s Preparing to unpack .../14-bbmap_39.08+dfsg-1_all.deb ... 117s Unpacking bbmap (39.08+dfsg-1) ... 117s Selecting previously unselected package bbmap-jni. 117s Preparing to unpack .../15-bbmap-jni_39.08+dfsg-1_s390x.deb ... 117s Unpacking bbmap-jni (39.08+dfsg-1) ... 117s Selecting previously unselected package python-biopython-doc. 117s Preparing to unpack .../16-python-biopython-doc_1.83+dfsg1-3_all.deb ... 117s Unpacking python-biopython-doc (1.83+dfsg1-3) ... 117s Selecting previously unselected package autopkgtest-satdep. 117s Preparing to unpack .../17-1-autopkgtest-satdep.deb ... 117s Unpacking autopkgtest-satdep (0) ... 117s Setting up liblcms2-2:s390x (2.14-2build1) ... 117s Setting up java-common (0.76) ... 117s Setting up libcommons-cli-java (1.6.0-1) ... 117s Setting up liblog4j1.2-java (1.2.17-11) ... 117s Setting up libapache-pom-java (33-2) ... 117s Setting up libpcsclite1:s390x (2.3.0-1) ... 117s Setting up libjpeg-turbo8:s390x (2.1.5-2ubuntu2) ... 117s Setting up python-biopython-doc (1.83+dfsg1-3) ... 117s Setting up bbmap-jni (39.08+dfsg-1) ... 117s Setting up ca-certificates-java (20240118) ... 117s No JRE found. Skipping Java certificates setup. 117s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 117s Setting up libcommons-parent-java (56-1) ... 117s Setting up openjdk-17-jre-headless:s390x (17.0.13+11-2build1) ... 117s update-alternatives: using /usr/lib/jvm/java-17-openjdk-s390x/bin/java to provide /usr/bin/java (java) in auto mode 117s update-alternatives: using /usr/lib/jvm/java-17-openjdk-s390x/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 117s update-alternatives: using /usr/lib/jvm/java-17-openjdk-s390x/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 117s update-alternatives: using /usr/lib/jvm/java-17-openjdk-s390x/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 117s update-alternatives: using /usr/lib/jvm/java-17-openjdk-s390x/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 117s Setting up libcommons-codec-java (1.16.0-1) ... 117s Setting up libcommons-io-java (2.16.1-1) ... 117s Setting up libmpj-java (0.44+dfsg-4) ... 117s Processing triggers for libc-bin (2.40-1ubuntu3) ... 117s Processing triggers for man-db (2.12.1-3) ... 117s Processing triggers for ca-certificates-java (20240118) ... 117s Adding debian:ACCVRAIZ1.pem 117s Adding debian:AC_RAIZ_FNMT-RCM.pem 117s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 117s Adding debian:ANF_Secure_Server_Root_CA.pem 117s Adding debian:Actalis_Authentication_Root_CA.pem 117s Adding debian:AffirmTrust_Commercial.pem 117s Adding debian:AffirmTrust_Networking.pem 117s Adding debian:AffirmTrust_Premium.pem 117s Adding debian:AffirmTrust_Premium_ECC.pem 117s Adding debian:Amazon_Root_CA_1.pem 117s Adding debian:Amazon_Root_CA_2.pem 117s Adding debian:Amazon_Root_CA_3.pem 117s Adding debian:Amazon_Root_CA_4.pem 117s Adding debian:Atos_TrustedRoot_2011.pem 117s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 117s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 117s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 117s Adding debian:BJCA_Global_Root_CA1.pem 117s Adding debian:BJCA_Global_Root_CA2.pem 117s Adding debian:Baltimore_CyberTrust_Root.pem 117s Adding debian:Buypass_Class_2_Root_CA.pem 117s Adding debian:Buypass_Class_3_Root_CA.pem 117s Adding debian:CA_Disig_Root_R2.pem 117s Adding debian:CFCA_EV_ROOT.pem 117s Adding debian:COMODO_Certification_Authority.pem 117s Adding debian:COMODO_ECC_Certification_Authority.pem 117s Adding debian:COMODO_RSA_Certification_Authority.pem 117s Adding debian:Certainly_Root_E1.pem 117s Adding debian:Certainly_Root_R1.pem 117s Adding debian:Certigna.pem 117s Adding debian:Certigna_Root_CA.pem 117s Adding debian:Certum_EC-384_CA.pem 117s Adding debian:Certum_Trusted_Network_CA.pem 117s Adding debian:Certum_Trusted_Network_CA_2.pem 117s Adding debian:Certum_Trusted_Root_CA.pem 117s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 117s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 117s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 117s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 117s Adding debian:Comodo_AAA_Services_root.pem 117s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 117s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 117s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 117s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 117s Adding debian:DigiCert_Assured_ID_Root_CA.pem 117s Adding debian:DigiCert_Assured_ID_Root_G2.pem 117s Adding debian:DigiCert_Assured_ID_Root_G3.pem 117s Adding debian:DigiCert_Global_Root_CA.pem 117s Adding debian:DigiCert_Global_Root_G2.pem 117s Adding debian:DigiCert_Global_Root_G3.pem 117s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 117s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 117s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 117s Adding debian:DigiCert_Trusted_Root_G4.pem 117s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 117s Adding debian:Entrust_Root_Certification_Authority.pem 117s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 117s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 117s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem 117s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 117s Adding debian:GLOBALTRUST_2020.pem 117s Adding debian:GTS_Root_R1.pem 117s Adding debian:GTS_Root_R2.pem 117s Adding debian:GTS_Root_R3.pem 117s Adding debian:GTS_Root_R4.pem 117s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 117s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 117s Adding debian:GlobalSign_Root_CA.pem 117s Adding debian:GlobalSign_Root_CA_-_R3.pem 117s Adding debian:GlobalSign_Root_CA_-_R6.pem 117s Adding debian:GlobalSign_Root_E46.pem 117s Adding debian:GlobalSign_Root_R46.pem 117s Adding debian:Go_Daddy_Class_2_CA.pem 117s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 117s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 117s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 117s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 117s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 117s Adding debian:HiPKI_Root_CA_-_G1.pem 117s Adding debian:Hongkong_Post_Root_CA_3.pem 117s Adding debian:ISRG_Root_X1.pem 117s Adding debian:ISRG_Root_X2.pem 117s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 117s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 117s Adding debian:Izenpe.com.pem 117s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 117s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 117s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 117s Adding debian:NAVER_Global_Root_Certification_Authority.pem 117s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 117s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 117s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 117s Adding debian:QuoVadis_Root_CA_1_G3.pem 117s Adding debian:QuoVadis_Root_CA_2.pem 117s Adding debian:QuoVadis_Root_CA_2_G3.pem 117s Adding debian:QuoVadis_Root_CA_3.pem 117s Adding debian:QuoVadis_Root_CA_3_G3.pem 117s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 117s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 117s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 117s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 117s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 117s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 117s Adding debian:SZAFIR_ROOT_CA2.pem 117s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 117s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 117s Adding debian:SecureSign_RootCA11.pem 117s Adding debian:SecureTrust_CA.pem 117s Adding debian:Secure_Global_CA.pem 117s Adding debian:Security_Communication_ECC_RootCA1.pem 117s Adding debian:Security_Communication_RootCA2.pem 117s Adding debian:Security_Communication_RootCA3.pem 117s Adding debian:Security_Communication_Root_CA.pem 117s Adding debian:Starfield_Class_2_CA.pem 117s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 117s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 117s Adding debian:SwissSign_Gold_CA_-_G2.pem 117s Adding debian:SwissSign_Silver_CA_-_G2.pem 117s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 117s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 117s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 117s Adding debian:TWCA_Global_Root_CA.pem 117s Adding debian:TWCA_Root_Certification_Authority.pem 117s Adding debian:TeliaSonera_Root_CA_v1.pem 117s Adding debian:Telia_Root_CA_v2.pem 117s Adding debian:TrustAsia_Global_Root_CA_G3.pem 117s Adding debian:TrustAsia_Global_Root_CA_G4.pem 117s Adding debian:Trustwave_Global_Certification_Authority.pem 117s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 117s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 117s Adding debian:TunTrust_Root_CA.pem 117s Adding debian:UCA_Extended_Validation_Root.pem 117s Adding debian:UCA_Global_G2_Root.pem 117s Adding debian:USERTrust_ECC_Certification_Authority.pem 117s Adding debian:USERTrust_RSA_Certification_Authority.pem 117s Adding debian:XRamp_Global_CA_Root.pem 117s Adding debian:certSIGN_ROOT_CA.pem 117s Adding debian:certSIGN_Root_CA_G2.pem 117s Adding debian:e-Szigno_Root_CA_2017.pem 117s Adding debian:ePKI_Root_Certification_Authority.pem 117s Adding debian:emSign_ECC_Root_CA_-_C3.pem 117s Adding debian:emSign_ECC_Root_CA_-_G3.pem 117s Adding debian:emSign_Root_CA_-_C1.pem 117s Adding debian:emSign_Root_CA_-_G1.pem 117s Adding debian:vTrus_ECC_Root_CA.pem 117s Adding debian:vTrus_Root_CA.pem 117s done. 117s Setting up bbmap (39.08+dfsg-1) ... 117s Setting up autopkgtest-satdep (0) ... 119s (Reading database ... 58025 files and directories currently installed.) 119s Removing autopkgtest-satdep (0) ... 120s autopkgtest [04:16:31]: test run-unit-test: [----------------------- 120s 120s # bbmap 120s bbmap.sh --version 120s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 120s java -ea -Xmx2822m -Xms2822m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 --version 120s BBTools version 39.08 120s For help, please run the shellscript with no parameters, or look in /docs/. 120s bbmap.sh --help 120s 120s BBMap 120s Written by Brian Bushnell, from Dec. 2010 - present 120s Last modified September 15, 2022 120s 120s Description: Fast and accurate splice-aware read aligner. 120s Please read bbmap/docs/guides/BBMapGuide.txt for more information. 120s 120s To index: bbmap.sh ref= 120s To map: bbmap.sh in= out= 120s To map without writing an index: 120s bbmap.sh ref= in= out= nodisk 120s 120s in=stdin will accept reads from standard in, and out=stdout will write to 120s standard out, but file extensions are still needed to specify the format of the 120s input and output files e.g. in=stdin.fa.gz will read gzipped fasta from 120s standard in; out=stdout.sam.gz will write gzipped sam. 120s 120s Indexing Parameters (required when building the index): 120s nodisk=f Set to true to build index in memory and write nothing 120s to disk except output. 120s ref= Specify the reference sequence. Only do this ONCE, 120s when building the index (unless using 'nodisk'). 120s build=1 If multiple references are indexed in the same directory, 120s each needs a unique numeric ID (unless using 'nodisk'). 120s k=13 Kmer length, range 8-15. Longer is faster but uses 120s more memory. Shorter is more sensitive. 120s If indexing and mapping are done in two steps, K should 120s be specified each time. 120s path=<.> Specify the location to write the index, if you don't 120s want it in the current working directory. 120s usemodulo=f Throw away ~80% of kmers based on remainder modulo a 120s number (reduces RAM by 50% and sensitivity slightly). 120s Should be enabled both when building the index AND 120s when mapping. 120s rebuild=f Force a rebuild of the index (ref= should be set). 120s 120s Input Parameters: 120s build=1 Designate index to use. Corresponds to the number 120s specified when building the index. 120s in= Primary reads input; required parameter. 120s in2= For paired reads in two files. 120s interleaved=auto True forces paired/interleaved input; false forces 120s single-ended mapping. If not specified, interleaved 120s status will be autodetected from read names. 120s fastareadlen=500 Break up FASTA reads longer than this. Max is 500 for 120s BBMap and 6000 for BBMapPacBio. Only works for FASTA 120s input (use 'maxlen' for FASTQ input). The default for 120s bbmap.sh is 500, and for mapPacBio.sh is 6000. 120s unpigz=f Spawn a pigz (parallel gzip) process for faster 120s decompression than using Java. 120s Requires pigz to be installed. 120s touppercase=t (tuc) Convert lowercase letters in reads to upper case 120s (otherwise they will not match the reference). 120s 120s Sampling Parameters: 120s 120s reads=-1 Set to a positive number N to only process the first N 120s reads (or pairs), then quit. -1 means use all reads. 120s samplerate=1 Set to a number from 0 to 1 to randomly select that 120s fraction of reads for mapping. 1 uses all reads. 120s skipreads=0 Set to a number N to skip the first N reads (or pairs), 120s then map the rest. 120s 120s Mapping Parameters: 120s fast=f This flag is a macro which sets other paramters to run 120s faster, at reduced sensitivity. Bad for RNA-seq. 120s slow=f This flag is a macro which sets other paramters to run 120s slower, at greater sensitivity. 'vslow' is even slower. 120s maxindel=16000 Don't look for indels longer than this. Lower is faster. 120s Set to >=100k for RNAseq with long introns like mammals. 120s strictmaxindel=f When enabled, do not allow indels longer than 'maxindel'. 120s By default these are not sought, but may be found anyway. 120s tipsearch=100 Look this far for read-end deletions with anchors 120s shorter than K, using brute force. 120s minid=0.76 Approximate minimum alignment identity to look for. 120s Higher is faster and less sensitive. 120s minhits=1 Minimum number of seed hits required for candidate sites. 120s Higher is faster. 120s local=f Set to true to use local, rather than global, alignments. 120s This will soft-clip ugly ends of poor alignments. 120s perfectmode=f Allow only perfect mappings when set to true (very fast). 120s semiperfectmode=f Allow only perfect and semiperfect (perfect except for 120s N's in the reference) mappings. 120s threads=auto (t) Set to number of threads desired. By default, uses 120s all cores available. 120s ambiguous=best (ambig) Set behavior on ambiguously-mapped reads (with 120s multiple top-scoring mapping locations). 120s best (use the first best site) 120s toss (consider unmapped) 120s random (select one top-scoring site randomly) 120s all (retain all top-scoring sites) 120s samestrandpairs=f (ssp) Specify whether paired reads should map to the 120s same strand or opposite strands. 120s requirecorrectstrand=t (rcs) Forbid pairing of reads without correct strand 120s orientation. Set to false for long-mate-pair libraries. 120s killbadpairs=f (kbp) If a read pair is mapped with an inappropriate 120s insert size or orientation, the read with the lower 120s mapping quality is marked unmapped. 120s pairedonly=f (po) Treat unpaired reads as unmapped. Thus they will 120s be sent to 'outu' but not 'outm'. 120s rcomp=f Reverse complement both reads prior to mapping (for LMP 120s outward-facing libraries). 120s rcompmate=f Reverse complement read2 prior to mapping. 120s pairlen=32000 Set max allowed distance between paired reads. 120s (insert size)=(pairlen)+(read1 length)+(read2 length) 120s rescuedist=1200 Don't try to rescue paired reads if avg. insert size 120s greater than this. Lower is faster. 120s rescuemismatches=32 Maximum mismatches allowed in a rescued read. Lower 120s is faster. 120s averagepairdist=100 (apd) Initial average distance between paired reads. 120s Varies dynamically; does not need to be specified. 120s deterministic=f Run in deterministic mode. In this case it is good 120s to set averagepairdist. BBMap is deterministic 120s without this flag if using single-ended reads, 120s or run singlethreaded. 120s bandwidthratio=0 (bwr) If above zero, restrict alignment band to this 120s fraction of read length. Faster but less accurate. 120s bandwidth=0 (bw) Set the bandwidth directly. 120s fraction of read length. Faster but less accurate. 120s usejni=f (jni) Do alignments faster, in C code. Requires 120s compiling the C code; details are in /jni/README.txt. 120s maxsites2=800 Don't analyze (or print) more than this many alignments 120s per read. 120s ignorefrequentkmers=t (ifk) Discard low-information kmers that occur often. 120s excludefraction=0.03 (ef) Fraction of kmers to ignore. For example, 0.03 120s will ignore the most common 3% of kmers. 120s greedy=t Use a greedy algorithm to discard the least-useful 120s kmers on a per-read basis. 120s kfilter=0 If positive, potential mapping sites must have at 120s least this many consecutive exact matches. 120s 120s 120s Quality and Trimming Parameters: 120s qin=auto Set to 33 or 64 to specify input quality value ASCII 120s offset. 33 is Sanger, 64 is old Solexa. 120s qout=auto Set to 33 or 64 to specify output quality value ASCII 120s offset (only if output format is fastq). 120s qtrim=f Quality-trim ends before mapping. Options are: 120s 'f' (false), 'l' (left), 'r' (right), and 'lr' (both). 120s untrim=f Undo trimming after mapping. Untrimmed bases will be 120s soft-clipped in cigar strings. 120s trimq=6 Trim regions with average quality below this 120s (phred algorithm). 120s mintrimlength=60 (mintl) Don't trim reads to be shorter than this. 120s fakefastaquality=-1 (ffq) Set to a positive number 1-50 to generate fake 120s quality strings for fasta input reads. 120s ignorebadquality=f (ibq) Keep going, rather than crashing, if a read has 120s out-of-range quality values. 120s usequality=t Use quality scores when determining which read kmers 120s to use as seeds. 120s minaveragequality=0 (maq) Do not map reads with average quality below this. 120s maqb=0 If positive, calculate maq from this many initial bases. 120s 120s Output Parameters: 120s out= Write all reads to this file. 120s outu= Write only unmapped reads to this file. Does not 120s include unmapped paired reads with a mapped mate. 120s outm= Write only mapped reads to this file. Includes 120s unmapped paired reads with a mapped mate. 120s mappedonly=f If true, treats 'out' like 'outm'. 120s bamscript= (bs) Write a shell script to that will turn 120s the sam output into a sorted, indexed bam file. 120s ordered=f Set to true to output reads in same order as input. 120s Slower and uses more memory. 120s overwrite=f (ow) Allow process to overwrite existing files. 120s secondary=f Print secondary alignments. 120s sssr=0.95 (secondarysitescoreratio) Print only secondary alignments 120s with score of at least this fraction of primary. 120s ssao=f (secondarysiteasambiguousonly) Only print secondary 120s alignments for ambiguously-mapped reads. 120s maxsites=5 Maximum number of total alignments to print per read. 120s Only relevant when secondary=t. 120s quickmatch=f Generate cigar strings more quickly. 120s trimreaddescriptions=f (trd) Truncate read and ref names at the first whitespace, 120s assuming that the remainder is a comment or description. 120s ziplevel=2 (zl) Compression level for zip or gzip output. 120s pigz=f Spawn a pigz (parallel gzip) process for faster 120s compression than Java. Requires pigz to be installed. 120s machineout=f Set to true to output statistics in machine-friendly 120s 'key=value' format. 120s printunmappedcount=f Print the total number of unmapped reads and bases. 120s If input is paired, the number will be of pairs 120s for which both reads are unmapped. 120s showprogress=0 If positive, print a '.' every X reads. 120s showprogress2=0 If positive, print the number of seconds since the 120s last progress update (instead of a '.'). 120s renamebyinsert=f Renames reads based on their mapped insert size. 120s 120s Bloom-Filtering Parameters (bloomfilter.sh is the standalone version). 120s bloom=f Use a Bloom filter to ignore reads not sharing kmers 120s with the reference. This uses more memory, but speeds 120s mapping when most reads don't match the reference. 120s bloomhashes=2 Number of hash functions. 120s bloomminhits=3 Number of consecutive hits to be considered matched. 120s bloomk=31 Bloom filter kmer length. 120s bloomserial=t Use the serialized Bloom filter for greater loading 120s speed, if available. If not, generate and write one. 120s 120s Post-Filtering Parameters: 120s idfilter=0 Independant of minid; sets exact minimum identity 120s allowed for alignments to be printed. Range 0 to 1. 120s subfilter=-1 Ban alignments with more than this many substitutions. 120s insfilter=-1 Ban alignments with more than this many insertions. 120s delfilter=-1 Ban alignments with more than this many deletions. 120s indelfilter=-1 Ban alignments with more than this many indels. 120s editfilter=-1 Ban alignments with more than this many edits. 120s inslenfilter=-1 Ban alignments with an insertion longer than this. 120s dellenfilter=-1 Ban alignments with a deletion longer than this. 120s nfilter=-1 Ban alignments with more than this many ns. This 120s includes nocall, noref, and off scaffold ends. 120s 120s Sam flags and settings: 120s noheader=f Disable generation of header lines. 120s sam=1.4 Set to 1.4 to write Sam version 1.4 cigar strings, 120s with = and X, or 1.3 to use M. 120s saa=t (secondaryalignmentasterisks) Use asterisks instead of 120s bases for sam secondary alignments. 120s cigar=t Set to 'f' to skip generation of cigar strings (faster). 120s keepnames=f Keep original names of paired reads, rather than 120s ensuring both reads have the same name. 120s intronlen=999999999 Set to a lower number like 10 to change 'D' to 'N' in 120s cigar strings for deletions of at least that length. 120s rgid= Set readgroup ID. All other readgroup fields 120s can be set similarly, with the flag rgXX= 120s If you set a readgroup flag to the word 'filename', 120s e.g. rgid=filename, the input file name will be used. 120s mdtag=f Write MD tags. 120s nhtag=f Write NH tags. 120s xmtag=f Write XM tags (may only work correctly with ambig=all). 120s amtag=f Write AM tags. 120s nmtag=f Write NM tags. 120s xstag=f Set to 'xs=fs', 'xs=ss', or 'xs=us' to write XS tags 120s for RNAseq using firststrand, secondstrand, or 120s unstranded libraries. Needed by Cufflinks. 120s JGI mainly uses 'firststrand'. 120s stoptag=f Write a tag indicating read stop location, prefixed by YS:i: 120s lengthtag=f Write a tag indicating (query,ref) alignment lengths, 120s prefixed by YL:Z: 120s idtag=f Write a tag indicating percent identity, prefixed by YI:f: 120s inserttag=f Write a tag indicating insert size, prefixed by X8:Z: 120s scoretag=f Write a tag indicating BBMap's raw score, prefixed by YR:i: 120s timetag=f Write a tag indicating this read's mapping time, prefixed by X0:i: 120s boundstag=f Write a tag indicating whether either read in the pair 120s goes off the end of the reference, prefixed by XB:Z: 120s notags=f Turn off all optional tags. 120s 120s Histogram and statistics output parameters: 120s scafstats= Statistics on how many reads mapped to which scaffold. 120s refstats= Statistics on how many reads mapped to which reference 120s file; only for BBSplit. 120s sortscafs=t Sort scaffolds or references by read count. 120s bhist= Base composition histogram by position. 120s qhist= Quality histogram by position. 120s aqhist= Histogram of average read quality. 120s bqhist= Quality histogram designed for box plots. 120s lhist= Read length histogram. 120s ihist= Write histogram of insert sizes (for paired reads). 120s ehist= Errors-per-read histogram. 120s qahist= bbmap.sh ref=example.fasta 120s Quality accuracy histogram of error rates versus 120s quality score. 120s indelhist= Indel length histogram. 120s mhist= Histogram of match, sub, del, and ins rates by 120s read location. 120s gchist= Read GC content histogram. 120s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 120s gcpairs=t Use average GC of paired reads. 120s idhist= Histogram of read count versus percent identity. 120s idbins=100 Number idhist bins. Set to 'auto' to use read length. 120s statsfile=stderr Mapping statistics are printed here. 120s 120s Coverage output parameters (these may reduce speed and use more RAM): 120s covstats= Per-scaffold coverage info. 120s rpkm= Per-scaffold RPKM/FPKM counts. 120s covhist= Histogram of # occurrences of each depth level. 120s basecov= Coverage per base location. 120s bincov= Print binned coverage per location (one line per X bases). 120s covbinsize=1000 Set the binsize for binned coverage output. 120s nzo=t Only print scaffolds with nonzero coverage. 120s twocolumn=f Change to true to print only ID and Avg_fold instead of 120s all 6 columns to the 'out=' file. 120s 32bit=f Set to true if you need per-base coverage over 64k. 120s strandedcov=f Track coverage for plus and minus strand independently. 120s startcov=f Only track start positions of reads. 120s secondarycov=t Include coverage of secondary alignments. 120s physcov=f Calculate physical coverage for paired reads. 120s This includes the unsequenced bases. 120s delcoverage=t (delcov) Count bases covered by deletions as covered. 120s True is faster than false. 120s covk=0 If positive, calculate kmer coverage statistics. 120s 120s Java Parameters: 120s -Xmx This will set Java's memory usage, 120s overriding autodetection. 120s -Xmx20g will specify 20 gigs of RAM, and -Xmx800m 120s will specify 800 megs. The max is typically 85% of 120s physical memory. The human genome requires around 24g, 120s or 12g with the 'usemodulo' flag. The index uses 120s roughly 6 bytes per reference base. 120s -eoom This flag will cause the process to exit if an 120s out-of-memory exception occurs. Requires Java 8u92+. 120s -da Disable assertions. 120s 120s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter 120s any problems, or post at: http://seqanswers.com/forums/showthread.php?t=41057 120s 120s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 120s java -ea -Xmx2822m -Xms2822m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta 120s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta] 120s Version 39.08 120s 120s No output file. 120s Writing reference. 120s 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] 120s 120s Set genScaffoldInfo=true 120s Writing chunk 1 120s Set genome to 1 120s 120s Loaded Reference: 0.003 seconds. 120s Loading index for chunk 1-1, build 1 120s No index available; generating from reference genome: /tmp/autopkgtest.bWB1UL/autopkgtest_tmp/ref/index/1/chr1_index_k13_c16_b1.block 120s Indexing threads started for block 0-1 120s Indexing threads finished for block 0-1 121s Generated Index: 1.147 seconds. 121s No reads to process; quitting. 121s 121s Total time: 1.225 seconds. 121s test -d ref 121s bbmap.sh in=misc_dna_as_sanger.fastq out=out.sam 121s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 121s java -ea -Xmx2822m -Xms2822m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 in=misc_dna_as_sanger.fastq out=out.sam 121s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, in=misc_dna_as_sanger.fastq, out=out.sam] 121s Version 39.08 121s 121s Retaining first best site only for ambiguous mappings. 121s Set genome to 1 121s 121s Loaded Reference: 0.012 seconds. 121s Loading index for chunk 1-1, build 1 122s Generated Index: 0.593 seconds. 125s Analyzed Index: 2.640 seconds. 125s Started output stream: 0.013 seconds. 125s Cleared Memory: 0.116 seconds. 125s Processing reads in single-ended mode. 125s Started read stream. 125s Started 4 mapping threads. 125s Detecting finished threads: 0, 1, 2, 3 125s 125s ------------------ Results ------------------ 125s 125s Genome: 1 125s Key Length: 13 125s Max Indel: 16000 125s Minimum Score Ratio: 0.56 125s Mapping Mode: normal 125s Reads Used: 4 (153 bases) 125s 125s Mapping: 0.088 seconds. 125s Reads/sec: 45.62 125s kBases/sec: 1.74 125s 125s 125s Read 1 data: pct reads num reads pct bases num bases 125s 125s mapped: 0.0000% 0 0.0000% 0 125s unambiguous: 0.0000% 0 0.0000% 0 125s ambiguous: 0.0000% 0 0.0000% 0 125s low-Q discards: 25.0000% 1 19.6078% 30 125s 125s perfect best site: 0.0000% 0 0.0000% 0 125s semiperfect site: 0.0000% 0 0.0000% 0 125s 125s Match Rate: NA NA NaN% 0 125s Error Rate: NaN% 0 NaN% 0 125s Sub Rate: NaN% 0 NaN% 0 125s Del Rate: NaN% 0 NaN% 0 125s Ins Rate: NaN% 0 NaN% 0 125s N Rate: NaN% 0 NaN% 0 125s 125s Total time: 3.520 seconds. 125s test -r out.sam 125s bbmap.sh ref=example.fasta in=example.fastq out=out2.sam nodisk 125s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 125s java -ea -Xmx2822m -Xms2822m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta in=example.fastq out=out2.sam nodisk 125s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta, in=example.fastq, out=out2.sam, nodisk] 125s Version 39.08 125s 125s Retaining first best site only for ambiguous mappings. 125s 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] 125s 125s Set genScaffoldInfo=true 125s Set genome to 1 125s 125s Loaded Reference: 0.001 seconds. 125s Loading index for chunk 1-1, build 1 125s Indexing threads started for block 0-1 125s Indexing threads finished for block 0-1 125s Generated Index: 0.288 seconds. 128s Analyzed Index: 2.341 seconds. 128s Started output stream: 0.012 seconds. 128s Cleared Memory: 0.111 seconds. 128s Processing reads in single-ended mode. 128s Started read stream. 128s Started 4 mapping threads. 128s Detecting finished threads: 0, 1, 2, 3 128s 128s ------------------ Results ------------------ 128s 128s Genome: 1 128s Key Length: 13 128s Max Indel: 16000 128s Minimum Score Ratio: 0.56 128s Mapping Mode: normal 128s Reads Used: 3 (75 bases) 128s 128s Mapping: 0.065 seconds. 128s Reads/sec: 46.41 128s kBases/sec: 1.16 128s 128s 128s Read 1 data: pct reads num reads pct bases num bases 128s 128s mapped: 100.0000% 3 100.0000% 75 128s unambiguous: 100.0000% 3 100.0000% 75 128s ambiguous: 0.0000% 0 0.0000% 0 128s low-Q discards: 0.0000% 0 0.0000% 0 128s 128s perfect best site: 100.0000% 3 100.0000% 75 128s semiperfect site: 100.0000% 3 100.0000% 75 128s 128s Match Rate: NA NA 100.0000% 75 128s Error Rate: 0.0000% 0 0.0000% 0 128s Sub Rate: 0.0000% 0 0.0000% 0 128s Del Rate: 0.0000% 0 0.0000% 0 128s Ins Rate: 0.0000% 0 0.0000% 0 128s N Rate: 0.0000% 0 0.0000% 0 128s 128s Total time: 2.892 seconds. 128s test -r out2.sam 128s 128s # bbduk 128s bbduk.sh --version 128s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 128s java -ea -Xmx1411m -Xms1411m -cp /usr/share/java/bbmap.jar jgi.BBDuk --version 128s BBTools version 39.08 128s For help, please run the shellscript with no parameters, or look in /docs/. 128s bbduk.sh --help 128s 128s Written by Brian Bushnell 128s Last modified November 9, 2023 128s 128s Description: Compares reads to the kmers in a reference dataset, optionally 128s allowing an edit distance. Splits the reads into two outputs - those that 128s match the reference, and those that don't. Can also trim (remove) the matching 128s parts of the reads rather than binning the reads. 128s Please read bbmap/docs/guides/BBDukGuide.txt for more information. 128s 128s Usage: bbduk.sh in= out= ref= 128s 128s Input may be stdin or a fasta or fastq file, compressed or uncompressed. 128s If you pipe via stdin/stdout, please include the file type; e.g. for gzipped 128s fasta input, set in=stdin.fa.gz 128s 128s Input parameters: 128s in= Main input. in=stdin.fq will pipe from stdin. 128s in2= Input for 2nd read of pairs in a different file. 128s ref= Comma-delimited list of reference files. 128s In addition to filenames, you may also use the keywords: 128s adapters, artifacts, phix, lambda, pjet, mtst, kapa 128s literal= Comma-delimited list of literal reference sequences. 128s touppercase=f (tuc) Change all bases upper-case. 128s interleaved=auto (int) t/f overrides interleaved autodetection. 128s Must be set mainually when streaming fastq input. 128s qin=auto Input quality offset: 33 (Sanger), 64, or auto. 128s reads=-1 If positive, quit after processing X reads or pairs. 128s copyundefined=f (cu) Process non-AGCT IUPAC reference bases by making all 128s possible unambiguous copies. Intended for short motifs 128s or adapter barcodes, as time/memory use is exponential. 128s samplerate=1 Set lower to only process a fraction of input reads. 128s samref= Optional reference fasta for processing sam files. 128s 128s Output parameters: 128s out= (outnonmatch) Write reads here that do not contain 128s kmers matching the database. 'out=stdout.fq' will pipe 128s to standard out. 128s out2= (outnonmatch2) Use this to write 2nd read of pairs to a 128s different file. 128s outm= (outmatch) Write reads here that fail filters. In default 128s kfilter mode, this means any read with a matching kmer. 128s In any mode, it also includes reads that fail filters such 128s as minlength, mingc, maxgc, entropy, etc. In other words, 128s it includes all reads that do not go to 'out'. 128s outm2= (outmatch2) Use this to write 2nd read of pairs to a 128s different file. 128s outs= (outsingle) Use this to write singleton reads whose mate 128s was trimmed shorter than minlen. 128s stats= Write statistics about which contamininants were detected. 128s refstats= Write statistics on a per-reference-file basis. 128s rpkm= Write RPKM for each reference sequence (for RNA-seq). 128s dump= Dump kmer tables to a file, in fasta format. 128s duk= Write statistics in duk's format. *DEPRECATED* 128s nzo=t Only write statistics about ref sequences with nonzero hits. 128s overwrite=t (ow) Grant permission to overwrite files. 128s showspeed=t (ss) 'f' suppresses display of processing speed. 128s ziplevel=2 (zl) Compression level; 1 (min) through 9 (max). 128s fastawrap=70 Length of lines in fasta output. 128s qout=auto Output quality offset: 33 (Sanger), 64, or auto. 128s statscolumns=3 (cols) Number of columns for stats output, 3 or 5. 128s 5 includes base counts. 128s rename=f Rename reads to indicate which sequences they matched. 128s refnames=f Use names of reference files rather than scaffold IDs. 128s trd=f Truncate read and ref names at the first whitespace. 128s ordered=f Set to true to output reads in same order as input. 128s maxbasesout=-1 If positive, quit after writing approximately this many 128s bases to out (outu/outnonmatch). 128s maxbasesoutm=-1 If positive, quit after writing approximately this many 128s bases to outm (outmatch). 128s json=f Print to screen in json format. 128s 128s Histogram output parameters: 128s bhist= Base composition histogram by position. 128s qhist= Quality histogram by position. 128s qchist= Count of bases with each quality value. 128s aqhist= Histogram of average read quality. 128s bqhist= Quality histogram designed for box plots. 128s lhist= Read length histogram. 128s phist= Polymer length histogram. 128s gchist= Read GC content histogram. 128s enthist= Read entropy histogram. 128s ihist= Insert size histogram, for paired reads in mapped sam. 128s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 128s maxhistlen=6000 Set an upper bound for histogram lengths; higher uses 128s more memory. The default is 6000 for some histograms 128s and 80000 for others. 128s 128s Histograms for mapped sam/bam files only: 128s histbefore=t Calculate histograms from reads before processing. 128s ehist= Errors-per-read histogram. 128s qahist= Quality accuracy histogram of error rates versus quality 128s score. 128s indelhist= Indel length histogram. 128s mhist= Histogram of match, sub, del, and ins rates by position. 128s idhist= Histogram of read count versus percent identity. 128s idbins=100 Number idhist bins. Set to 'auto' to use read length. 128s varfile= Ignore substitution errors listed in this file when 128s calculating error rates. Can be generated with 128s CallVariants. 128s vcf= Ignore substitution errors listed in this VCF file 128s when calculating error rates. 128s ignorevcfindels=t Also ignore indels listed in the VCF. 128s 128s Processing parameters: 128s k=27 Kmer length used for finding contaminants. Contaminants 128s shorter than k will not be found. k must be at least 1. 128s rcomp=t Look for reverse-complements of kmers in addition to 128s forward kmers. 128s maskmiddle=t (mm) Treat the middle base of a kmer as a wildcard, to 128s increase sensitivity in the presence of errors. This may 128s also be set to a number, e.g. mm=3, to mask that many bp. 128s The default mm=t corresponds to mm=1 for odd-length kmers 128s and mm=2 for even-length kmers (as of v39.04), while 128s mm=f is always equivalent to mm=0. 128s minkmerhits=1 (mkh) Reads need at least this many matching kmers 128s to be considered as matching the reference. 128s minkmerfraction=0.0 (mkf) A reads needs at least this fraction of its total 128s kmers to hit a ref, in order to be considered a match. 128s If this and minkmerhits are set, the greater is used. 128s mincovfraction=0.0 (mcf) A reads needs at least this fraction of its total 128s bases to be covered by ref kmers to be considered a match. 128s If specified, mcf overrides mkh and mkf. 128s hammingdistance=0 (hdist) Maximum Hamming distance for ref kmers (subs only). 128s Memory use is proportional to (3*K)^hdist. 128s qhdist=0 Hamming distance for query kmers; impacts speed, not memory. 128s editdistance=0 (edist) Maximum edit distance from ref kmers (subs 128s and indels). Memory use is proportional to (8*K)^edist. 128s hammingdistance2=0 (hdist2) Sets hdist for short kmers, when using mink. 128s qhdist2=0 Sets qhdist for short kmers, when using mink. 128s editdistance2=0 (edist2) Sets edist for short kmers, when using mink. 128s forbidn=f (fn) Forbids matching of read kmers containing N. 128s By default, these will match a reference 'A' if 128s hdist>0 or edist>0, to increase sensitivity. 128s removeifeitherbad=t (rieb) Paired reads get sent to 'outmatch' if either is 128s match (or either is trimmed shorter than minlen). 128s bbduk.sh in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq \ 128s qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 128s Set to false to require both. 128s trimfailures=f Instead of discarding failed reads, trim them to 1bp. 128s This makes the statistics a bit odd. 128s findbestmatch=f (fbm) If multiple matches, associate read with sequence 128s sharing most kmers. Reduces speed. 128s skipr1=f Don't do kmer-based operations on read 1. 128s skipr2=f Don't do kmer-based operations on read 2. 128s ecco=f For overlapping paired reads only. Performs error- 128s correction with BBMerge prior to kmer operations. 128s recalibrate=f (recal) Recalibrate quality scores. Requires calibration 128s matrices generated by CalcTrueQuality. 128s sam= If recalibration is desired, and matrices have not already 128s been generated, BBDuk will create them from the sam file. 128s amino=f Run in amino acid mode. Some features have not been 128s tested, but kmer-matching works fine. Maximum k is 12. 128s 128s Speed and Memory parameters: 128s threads=auto (t) Set number of threads to use; default is number of 128s logical processors. 128s prealloc=f Preallocate memory in table. Allows faster table loading 128s and more efficient memory usage, for a large reference. 128s monitor=f Kill this process if it crashes. monitor=600,0.01 would 128s kill after 600 seconds under 1% usage. 128s minrskip=1 (mns) Force minimal skip interval when indexing reference 128s kmers. 1 means use all, 2 means use every other kmer, etc. 128s maxrskip=1 (mxs) Restrict maximal skip interval when indexing 128s reference kmers. Normally all are used for scaffolds<100kb, 128s but with longer scaffolds, up to maxrskip-1 are skipped. 128s rskip= Set both minrskip and maxrskip to the same value. 128s If not set, rskip will vary based on sequence length. 128s qskip=1 Skip query kmers to increase speed. 1 means use all. 128s speed=0 Ignore this fraction of kmer space (0-15 out of 16) in both 128s reads and reference. Increases speed and reduces memory. 128s Note: Do not use more than one of 'speed', 'qskip', and 'rskip'. 128s 128s Trimming/Filtering/Masking parameters: 128s Note - if ktrim, kmask, and ksplit are unset, the default behavior is kfilter. 128s All kmer processing modes are mutually exclusive. 128s Reads only get sent to 'outm' purely based on kmer matches in kfilter mode. 128s 128s ktrim=f Trim reads to remove bases matching reference kmers, plus 128s all bases to the left or right. 128s Values: 128s f (don't trim), 128s r (trim to the right), 128s l (trim to the left) 128s ktrimtips=0 Set this to a positive number to perform ktrim on both 128s ends, examining only the outermost X bases. 128s kmask= Replace bases matching ref kmers with another symbol. 128s Allows any non-whitespace character, and processes short 128s kmers on both ends if mink is set. 'kmask=lc' will 128s convert masked bases to lowercase. 128s maskfullycovered=f (mfc) Only mask bases that are fully covered by kmers. 128s ksplit=f For single-ended reads only. Reads will be split into 128s pairs around the kmer. If the kmer is at the end of the 128s read, it will be trimmed instead. Singletons will go to 128s out, and pairs will go to outm. Do not use ksplit with 128s other operations such as quality-trimming or filtering. 128s mink=0 Look for shorter kmers at read tips down to this length, 128s when k-trimming or masking. 0 means disabled. Enabling 128s this will disable maskmiddle. 128s qtrim=f Trim read ends to remove bases with quality below trimq. 128s Performed AFTER looking for kmers. Values: 128s rl (trim both ends), 128s f (neither end), 128s r (right end only), 128s l (left end only), 128s w (sliding window). 128s trimq=6 Regions with average quality BELOW this will be trimmed, 128s if qtrim is set to something other than f. Can be a 128s floating-point number like 7.3. 128s trimclip=f Trim soft-clipped bases from sam files. 128s minlength=10 (ml) Reads shorter than this after trimming will be 128s discarded. Pairs will be discarded if both are shorter. 128s mlf=0 (minlengthfraction) Reads shorter than this fraction of 128s original length after trimming will be discarded. 128s maxlength= Reads longer than this after trimming will be discarded. 128s minavgquality=0 (maq) Reads with average quality (after trimming) below 128s this will be discarded. 128s maqb=0 If positive, calculate maq from this many initial bases. 128s minbasequality=0 (mbq) Reads with any base below this quality (after 128s trimming) will be discarded. 128s maxns=-1 If non-negative, reads with more Ns than this 128s (after trimming) will be discarded. 128s mcb=0 (minconsecutivebases) Discard reads without at least 128s this many consecutive called bases. 128s ottm=f (outputtrimmedtomatch) Output reads trimmed to shorter 128s than minlength to outm rather than discarding. 128s tp=0 (trimpad) Trim this much extra around matching kmers. 128s tbo=f (trimbyoverlap) Trim adapters based on where paired 128s reads overlap. 128s strictoverlap=t Adjust sensitivity for trimbyoverlap mode. 128s minoverlap=14 Require this many bases of overlap for detection. 128s mininsert=40 Require insert size of at least this for overlap. 128s Should be reduced to 16 for small RNA sequencing. 128s tpe=f (trimpairsevenly) When kmer right-trimming, trim both 128s reads to the minimum length of either. 128s forcetrimleft=0 (ftl) If positive, trim bases to the left of this position 128s (exclusive, 0-based). 128s forcetrimright=0 (ftr) If positive, trim bases to the right of this position 128s (exclusive, 0-based). 128s forcetrimright2=0 (ftr2) If positive, trim this many bases on the right end. 128s forcetrimmod=0 (ftm) If positive, right-trim length to be equal to zero, 128s modulo this number. 128s restrictleft=0 If positive, only look for kmer matches in the 128s leftmost X bases. 128s restrictright=0 If positive, only look for kmer matches in the 128s rightmost X bases. 128s NOTE: restrictleft and restrictright are mutually exclusive. If trimming 128s both ends is desired, use ktrimtips. 128s mingc=0 Discard reads with GC content below this. 128s maxgc=1 Discard reads with GC content above this. 128s gcpairs=t Use average GC of paired reads. 128s Also affects gchist. 128s tossjunk=f Discard reads with invalid characters as bases. 128s swift=f Trim Swift sequences: Trailing C/T/N R1, leading G/A/N R2. 128s 128s Header-parsing parameters - these require Illumina headers: 128s chastityfilter=f (cf) Discard reads with id containing ' 1:Y:' or ' 2:Y:'. 128s barcodefilter=f Remove reads with unexpected barcodes if barcodes is set, 128s or barcodes containing 'N' otherwise. A barcode must be 128s the last part of the read header. Values: 128s t: Remove reads with bad barcodes. 128s f: Ignore barcodes. 128s crash: Crash upon encountering bad barcodes. 128s barcodes= Comma-delimited list of barcodes or files of barcodes. 128s xmin=-1 If positive, discard reads with a lesser X coordinate. 128s ymin=-1 If positive, discard reads with a lesser Y coordinate. 128s xmax=-1 If positive, discard reads with a greater X coordinate. 128s ymax=-1 If positive, discard reads with a greater Y coordinate. 128s 128s Polymer trimming: 128s trimpolya=0 If greater than 0, trim poly-A or poly-T tails of 128s at least this length on either end of reads. 128s trimpolygleft=0 If greater than 0, trim poly-G prefixes of at least this 128s length on the left end of reads. Does not trim poly-C. 128s trimpolygright=0 If greater than 0, trim poly-G tails of at least this 128s length on the right end of reads. Does not trim poly-C. 128s trimpolyg=0 This sets both left and right at once. 128s filterpolyg=0 If greater than 0, remove reads with a poly-G prefix of 128s at least this length (on the left). 128s Note: there are also equivalent poly-C flags. 128s 128s Polymer tracking: 128s pratio=base,base 'pratio=G,C' will print the ratio of G to C polymers. 128s plen=20 Length of homopolymers to count. 128s 128s Entropy/Complexity parameters: 128s entropy=-1 Set between 0 and 1 to filter reads with entropy below 128s that value. Higher is more stringent. 128s entropywindow=50 Calculate entropy using a sliding window of this length. 128s entropyk=5 Calculate entropy using kmers of this length. 128s minbasefrequency=0 Discard reads with a minimum base frequency below this. 128s entropytrim=f Values: 128s f: (false) Do not entropy-trim. 128s r: (right) Trim low entropy on the right end only. 128s l: (left) Trim low entropy on the left end only. 128s rl: (both) Trim low entropy on both ends. 128s entropymask=f Values: 128s f: (filter) Discard low-entropy sequences. 128s t: (true) Mask low-entropy parts of sequences with N. 128s lc: Change low-entropy parts of sequences to lowercase. 128s entropymark=f Mark each base with its entropy value. This is on a scale 128s of 0-41 and is reported as quality scores, so the output 128s should be fastq or fasta+qual. 128s NOTE: If set, entropytrim overrides entropymask. 128s 128s Cardinality estimation: 128s cardinality=f (loglog) Count unique kmers using the LogLog algorithm. 128s cardinalityout=f (loglogout) Count unique kmers in output reads. 128s loglogk=31 Use this kmer length for counting. 128s loglogbuckets=2048 Use this many buckets for counting. 128s khist= Kmer frequency histogram; plots number of kmers versus 128s kmer depth. This is approximate. 128s khistout= Kmer frequency histogram for output reads. 128s 128s Java Parameters: 128s 128s -Xmx This will set Java's memory usage, overriding autodetection. 128s -Xmx20g will 128s specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 128s The max is typically 85% of physical memory. 128s -eoom This flag will cause the process to exit if an 128s out-of-memory exception occurs. Requires Java 8u92+. 128s -da Disable assertions. 128s 128s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 128s 128s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 128s java -ea -Xmx1411m -Xms1411m -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 128s 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] 128s Version 39.08 128s 128s Changed from ASCII-33 to ASCII-64 on input quality X (Q55) for base A at lines 1 and 3, position 24 while prescanning. 128s Changed from ASCII-33 to ASCII-64 on input quality X (Q55) for base A at lines 1 and 3, position 24 while prescanning. 128s 0.013 seconds. 128s Initial: 128s Memory: max=1480m, total=1480m, free=1450m, used=30m 128s 128s Input is being processed as paired 128s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 128s Started output streams: 0.009 seconds. 128s Processing time: 0.002 seconds. 128s 128s Input: 8 reads 306 bases. 128s QTrimmed: 0 reads (0.00%) 0 bases (0.00%) 128s Total Removed: 8 reads (100.00%) 306 bases (100.00%) 128s Result: 0 reads (0.00%) 0 bases (0.00%) 128s 128s Time: 0.012 seconds. 128s Reads Processed: 8 0.66k reads/sec 128s Bases Processed: 306 0.03m bases/sec 128s test -r out.fastq.gz 128s 128s # bbnorm 128s bbnorm.sh --version 128s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 128s java -ea -Xmx2822m -Xms2822m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 --version 128s BBTools version 39.08 128s For help, please run the shellscript with no parameters, or look in /docs/. 128s bbnorm.sh --help 128s 128s Written by Brian Bushnell 128s Last modified October 19, 2017 128s 128s Description: Normalizes read depth based on kmer counts. 128s Can also error-correct, bin reads by kmer depth, and generate a kmer depth histogram. 128s However, Tadpole has superior error-correction to BBNorm. 128s Please read bbmap/docs/guides/BBNormGuide.txt for more information. 128s 128s Usage: bbnorm.sh in= out= outt= hist= 128s 128s Input parameters: 128s in=null Primary input. Use in2 for paired reads in a second file 128s in2=null Second input file for paired reads in two files 128s extra=null Additional files to use for input (generating hash table) but not for output 128s fastareadlen=2^31 Break up FASTA reads longer than this. Can be useful when processing scaffolded genomes 128s tablereads=-1 Use at most this many reads when building the hashtable (-1 means all) 128s kmersample=1 Process every nth kmer, and skip the rest 128s readsample=1 Process every nth read, and skip the rest 128s 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. 128s qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto. 128s 128s Output parameters: 128s out= File for normalized or corrected reads. Use out2 for paired reads in a second file 128s outt= (outtoss) File for reads that were excluded from primary output 128s reads=-1 Only process this number of reads, then quit (-1 means all) 128s sampleoutput=t Use sampling on output as well as input (not used if sample rates are 1) 128s keepall=f Set to true to keep all reads (e.g. if you just want error correction). 128s 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. 128s Default is false, to prevent confusion about how there can be 0-count kmers. 128s The reason is that based on the 'minq' and 'minprob' settings, some kmers may be excluded from the bloom filter. 128s tmpdir= This will specify a directory for temp files (only needed for multipass runs). If null, they will be written to the output directory. 128s usetempdir=t Allows enabling/disabling of temporary directory; if disabled, temp files will be written to the output directory. 128s qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input). 128s rename=f Rename reads based on their kmer depth. 128s 128s Hashing parameters: 128s k=31 Kmer length (values under 32 are most efficient, but arbitrarily high values are supported) 128s 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. 128s Large values decrease accuracy for a fixed amount of memory, so use the lowest number you can that will still capture highest-depth kmers. 128s hashes=3 Number of times each kmer is hashed and stored. Higher is slower. 128s Higher is MORE accurate if there is enough memory, and LESS accurate if there is not enough memory. 128s 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. 128s prehashes=2 Number of hashes for prefilter. 128s prefilterbits=2 (pbits) Bits per cell in prefilter. 128s prefiltersize=0.35 Fraction of memory to allocate to prefilter. 128s buildpasses=1 More passes can sometimes increase accuracy by iteratively removing low-depth kmers 128s minq=6 Ignore kmers containing bases with quality below this 128s minprob=0.5 Ignore kmers with overall probability of correctness below this 128s bbnorm.sh in=sanger_full_range_original_sanger.fastq qin=33 \ 128s out=out3.fastq outt=outt.fastq hist=hist.plt 128s 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. 128s 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. 128s 128s Normalization parameters: 128s fixspikes=f (fs) Do a slower, high-precision bloom filter lookup of kmers that appear to have an abnormally high depth due to collisions. 128s target=100 (tgt) Target normalization depth. NOTE: All depth parameters control kmer depth, not read depth. 128s For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1)) 128s maxdepth=-1 (max) Reads will not be downsampled when below this depth, even if they are above the target depth. 128s mindepth=5 (min) Kmers with depth below this number will not be included when calculating the depth of a read. 128s minkmers=15 (mgkpr) Reads must have at least this many kmers over min depth to be retained. Aka 'mingoodkmersperread'. 128s 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. 128s uselowerdepth=t (uld) For pairs, use the depth of the lower read as the depth proxy. 128s deterministic=t (dr) Generate random numbers deterministically to ensure identical output between multiple runs. May decrease speed with a huge number of threads. 128s passes=2 (p) 1 pass is the basic mode. 2 passes (default) allows greater accuracy, error detection, better contol of output depth. 128s 128s Error detection parameters: 128s hdp=90.0 (highdepthpercentile) Position in sorted kmer depth array used as proxy of a read's high kmer depth. 128s ldp=25.0 (lowdepthpercentile) Position in sorted kmer depth array used as proxy of a read's low kmer depth. 128s tossbadreads=f (tbr) Throw away reads detected as containing errors. 128s requirebothbad=f (rbb) Only toss bad pairs if both reads are bad. 128s 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. 128s highthresh=12 (ht) Threshold for high kmer. A high kmer at this or above are considered non-error. 128s lowthresh=3 (lt) Threshold for low kmer. Kmers at this and below are always considered errors. 128s 128s Error correction parameters: 128s ecc=f Set to true to correct errors. NOTE: Tadpole is now preferred for ecc as it does a better job. 128s ecclimit=3 Correct up to this many errors per read. If more are detected, the read will remain unchanged. 128s errorcorrectratio=140 (ecr) Adjacent kmers with a depth ratio of at least this much between will be classified as an error. 128s echighthresh=22 (echt) Threshold for high kmer. A kmer at this or above may be considered non-error. 128s eclowthresh=2 (eclt) Threshold for low kmer. Kmers at this and below are considered errors. 128s eccmaxqual=127 Do not correct bases with quality above this value. 128s aec=f (aggressiveErrorCorrection) Sets more aggressive values of ecr=100, ecclimit=7, echt=16, eclt=3. 128s cec=f (conservativeErrorCorrection) Sets more conservative values of ecr=180, ecclimit=2, echt=30, eclt=1, sl=4, pl=4. 128s meo=f (markErrorsOnly) Marks errors by reducing quality value of suspected errors; does not correct anything. 128s mue=t (markUncorrectableErrors) Marks errors only on uncorrectable reads; requires 'ecc=t'. 128s overlap=f (ecco) Error correct by read overlap. 128s 128s Depth binning parameters: 128s lowbindepth=10 (lbd) Cutoff for low depth bin. 128s highbindepth=80 (hbd) Cutoff for high depth bin. 128s outlow= Pairs in which both reads have a median below lbd go into this file. 128s outhigh= Pairs in which both reads have a median above hbd go into this file. 128s outmid= All other pairs go into this file. 128s 128s Histogram parameters: 128s hist= Specify a file to write the input kmer depth histogram. 128s histout= Specify a file to write the output kmer depth histogram. 128s histcol=3 (histogramcolumns) Number of histogram columns, 2 or 3. 128s pzc=f (printzerocoverage) Print lines in the histogram with zero coverage. 128s histlen=1048576 Max kmer depth displayed in histogram. Also affects statistics displayed, but does not affect normalization. 128s 128s Peak calling parameters: 128s peaks= Write the peaks to this file. Default is stdout. 128s minHeight=2 (h) Ignore peaks shorter than this. 128s minVolume=5 (v) Ignore peaks with less area than this. 128s minWidth=3 (w) Ignore peaks narrower than this. 128s minPeak=2 (minp) Ignore peaks with an X-value below this. 128s maxPeak=BIG (maxp) Ignore peaks with an X-value above this. 128s maxPeakCount=8 (maxpc) Print up to this many peaks (prioritizing height). 128s 128s Java Parameters: 128s -Xmx This will set Java's memory usage, overriding autodetection. 128s -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 128s The max is typically 85% of physical memory. 128s -eoom This flag will cause the process to exit if an 128s out-of-memory exception occurs. Requires Java 8u92+. 128s -da Disable assertions. 128s 128s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 128s 128s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 128s java -ea -Xmx2822m -Xms2822m -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 128s Executing jgi.KmerNormalize [bits=32, in=sanger_full_range_original_sanger.fastq, qin=33, out=out3.fastq, outt=outt.fastq, hist=hist.plt] 128s 128s 128s *********** Pass 1 ********** 128s 128s 128s Settings: 128s threads: 4 128s k: 31 128s deterministic: true 128s toss error reads: false 128s passes: 1 128s bits per cell: 16 128s cells: 1044.50M 128s hashes: 3 128s base min quality: 5 128s kmer min prob: 0.5 128s 128s target depth: 400 128s min depth: 3 128s max depth: 500 128s min good kmers: 15 128s depth percentile: 64.8 128s ignore dupe kmers: true 128s fix spikes: false 128s histogram length: 65536 128s print zero cov: false 128s 129s Made hash table: hashes = 3 mem = 1.94 GB cells = 1044.20M used = 0.000% 129s 129s Estimated unique kmers: 4 129s 129s Table creation time: 1.140 seconds. 129s Started output threads. 129s Started output threads. 129s Table read time: 0.004 seconds. 48.44 kb/sec 129s Total reads in: 2 0.000% Kept 129s Total bases in: 188 0.000% Kept 129s Error reads in: 2 100.000% 129s Error type 1: 2 100.000% 129s Error type 2: 0 0.000% 129s Error type 3: 0 0.000% 129s 129s Wrote histogram to hist.plt 130s Total kmers counted: 128 130s Total unique kmer count: 128 130s Includes forward kmers only. 130s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 130s The most accurate value is the greater of the two. 130s 130s Percent unique: 100.00% 130s Depth average: 1.00 (unique kmers) 130s Depth median: 1 (unique kmers) 130s Depth standard deviation: 0.00 (unique kmers) 130s Corrected depth average: 0.00 130s 130s Depth average: 1.00 (all kmers) 130s Depth median: 1 (all kmers) 130s Depth standard deviation: 0.00 (all kmers) 130s 130s Approx. read depth median: 1.47 130s 130s *********** Pass 2 ********** 130s 130s 130s Settings: 130s threads: 4 130s k: 31 130s deterministic: true 130s toss error reads: false 130s passes: 1 130s bits per cell: 16 130s cells: 1044.50M 130s hashes: 3 130s base min quality: 5 130s kmer min prob: 0.5 130s 130s target depth: 100 130s min depth: 5 130s max depth: 100 130s min good kmers: 15 130s depth percentile: 54.0 130s ignore dupe kmers: true 130s fix spikes: false 130s histogram length: 65536 130s 130s Made hash table: hashes = 3 mem = 1.94 GB cells = 1044.20M used = 0.000% 130s 130s Estimated unique kmers: 0 130s 130s Table creation time: 0.401 seconds. 130s Started output threads. 130s Started output threads. 130s Table read time: 0.001 seconds. 0.00 kb/sec 130s Total reads in: 0 NaN% Kept 130s Total bases in: 0 NaN% Kept 130s Error reads in: 0 NaN% 130s Error type 1: 0 NaN% 130s Error type 2: 0 NaN% 130s Error type 3: 0 NaN% 130s Total kmers counted: 0 130s Total unique kmer count: 0 130s Includes forward kmers only. 130s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 130s The most accurate value is the greater of the two. 130s 130s Percent unique: NaN% 130s Depth average: NaN (unique kmers) 130s Depth median: 0 (unique kmers) 130s Depth standard deviation: NaN (unique kmers) 130s Corrected depth average: NaN 130s 130s Depth average: NaN (all kmers) 130s Depth median: 0 (all kmers) 130s Depth standard deviation: 0.00 (all kmers) 130s 130s Approx. read depth median: NaN 130s 130s Removing temp files. 130s 130s Total time: 1.591 seconds. 0.12 kb/sec 130s test -r out3.fastq 130s test -r outt.fastq 130s test -r hist.plt 130s bbnorm.sh in=illumina_full_range_original_illumina.fastq qin=64 \ 130s out=out4.fastq outt=outt2.fastq hist=hist2.plt 130s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 130s java -ea -Xmx2822m -Xms2822m -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 130s Executing jgi.KmerNormalize [bits=32, in=illumina_full_range_original_illumina.fastq, qin=64, out=out4.fastq, outt=outt2.fastq, hist=hist2.plt] 130s 130s 130s *********** Pass 1 ********** 130s 130s 130s Settings: 130s threads: 4 130s k: 31 130s deterministic: true 130s toss error reads: false 130s passes: 1 130s bits per cell: 16 130s cells: 1044.50M 130s hashes: 3 130s base min quality: 5 130s kmer min prob: 0.5 130s 130s target depth: 400 130s min depth: 3 130s max depth: 500 130s min good kmers: 15 130s depth percentile: 64.8 130s ignore dupe kmers: true 130s fix spikes: false 130s histogram length: 65536 130s print zero cov: false 130s 131s Made hash table: hashes = 3 mem = 1.94 GB cells = 1044.20M used = 0.000% 131s 131s Estimated unique kmers: 4 131s 131s Table creation time: 0.686 seconds. 131s Started output threads. 131s Started output threads. 131s Table read time: 0.003 seconds. 42.58 kb/sec 131s Total reads in: 2 0.000% Kept 131s Total bases in: 126 0.000% Kept 131s Error reads in: 2 100.000% 131s Error type 1: 2 100.000% 131s Error type 2: 0 0.000% 131s Error type 3: 0 0.000% 131s 131s Wrote histogram to hist2.plt 131s Total kmers counted: 66 131s Total unique kmer count: 66 131s Includes forward kmers only. 131s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 131s The most accurate value is the greater of the two. 131s 131s Percent unique: 100.00% 131s Depth average: 1.00 (unique kmers) 131s Depth median: 1 (unique kmers) 131s Depth standard deviation: 0.00 (unique kmers) 131s Corrected depth average: 0.00 131s 131s Depth average: 1.00 (all kmers) 131s Depth median: 1 (all kmers) 131s Depth standard deviation: 0.00 (all kmers) 131s 131s Approx. read depth median: 1.91 131s 131s *********** Pass 2 ********** 131s 131s 131s Settings: 131s threads: 4 131s k: 31 131s deterministic: true 131s toss error reads: false 131s passes: 1 131s bits per cell: 16 131s cells: 1044.50M 131s hashes: 3 131s base min quality: 5 131s kmer min prob: 0.5 131s 131s target depth: 100 131s min depth: 5 131s max depth: 100 131s min good kmers: 15 131s depth percentile: 54.0 131s ignore dupe kmers: true 131s fix spikes: false 131s histogram length: 65536 131s 131s Made hash table: hashes = 3 mem = 1.94 GB cells = 1044.20M used = 0.000% 131s 131s Estimated unique kmers: 0 131s 131s Table creation time: 0.364 seconds. 131s Started output threads. 131s Started output threads. 131s Table read time: 0.001 seconds. 0.00 kb/sec 131s Total reads in: 0 NaN% Kept 131s Total bases in: 0 NaN% Kept 131s Error reads in: 0 NaN% 131s Error type 1: 0 NaN% 131s Error type 2: 0 NaN% 131s Error type 3: 0 NaN% 131s Total kmers counted: 0 131s Total unique kmer count: 0 131s Includes forward kmers only. 131s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 131s The most accurate value is the greater of the two. 131s 131s Percent unique: NaN% 131s Depth average: NaN (unique kmers) 131s Depth median: 0 (unique kmers) 131s Depth standard deviation: NaN (unique kmers) 131s Corrected depth average: NaN 131s 131s Depth average: NaN (all kmers) 131s Depth median: 0 (all kmers) 131s Depth standard deviation: 0.00 (all kmers) 131s 131s Approx. read depth median: NaN 131s 131s Removing temp files. 131s 131s Total time: 1.103 seconds. 0.11 kb/sec 131s test -r out4.fastq 131s test -r outt2.fastq 131s test -r hist2.plt 132s autopkgtest [04:16:43]: test run-unit-test: -----------------------] 132s run-unit-test PASS 132s autopkgtest [04:16:43]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 133s autopkgtest [04:16:44]: @@@@@@@@@@@@@@@@@@@@ summary 133s run-unit-test PASS 144s nova [W] Using flock in prodstack6-s390x 144s flock: timeout while waiting to get lock 144s Creating nova instance adt-plucky-s390x-bbmap-20241102-041431-juju-7f2275-prod-proposed-migration-environment-15-30748b8f-64ff-477f-9b49-78136f67c94a from image adt/ubuntu-plucky-s390x-server-20241101.img (UUID efc880a6-ff20-4207-a161-b1113fd9bea7)...