0s autopkgtest [02:50:37]: starting date and time: 2024-11-02 02:50:37+0000 0s autopkgtest [02:50:37]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [02:50:37]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.vxzn3t0s/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-32.secgroup --name adt-plucky-arm64-bbmap-20241102-025037-juju-7f2275-prod-proposed-migration-environment-2-9268fbf3-0ea2-4a39-bdf1-054c51c50d05 --image adt/ubuntu-plucky-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,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/ 72s autopkgtest [02:51:49]: testbed dpkg architecture: arm64 72s autopkgtest [02:51:49]: testbed apt version: 2.9.8 72s autopkgtest [02:51:49]: @@@@@@@@@@@@@@@@@@@@ test bed setup 73s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 73s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [2614 kB] 74s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 74s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [41.0 kB] 74s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [178 kB] 74s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [233 kB] 74s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 74s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [1917 kB] 74s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [34.6 kB] 74s Fetched 5149 kB in 1s (4110 kB/s) 74s Reading package lists... 77s Reading package lists... 77s Building dependency tree... 77s Reading state information... 78s Calculating upgrade... 79s The following packages will be upgraded: 79s libblockdev-crypto3 libblockdev-fs3 libblockdev-loop3 libblockdev-mdraid3 79s libblockdev-nvme3 libblockdev-part3 libblockdev-swap3 libblockdev-utils3 79s libblockdev3 libevdev2 libftdi1-2 libinih1 libpipeline1 nano 79s python3-lazr.uri 79s 15 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 79s Need to get 594 kB of archives. 79s After this operation, 19.5 kB of additional disk space will be used. 79s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libevdev2 arm64 1.13.3+dfsg-1 [36.0 kB] 79s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libpipeline1 arm64 1.5.8-1 [30.6 kB] 79s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 nano arm64 8.2-1 [289 kB] 79s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libblockdev-utils3 arm64 3.2.0-2 [18.8 kB] 79s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libblockdev-crypto3 arm64 3.2.0-2 [22.6 kB] 79s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libblockdev-fs3 arm64 3.2.0-2 [35.8 kB] 79s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libblockdev-loop3 arm64 3.2.0-2 [7276 B] 79s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libblockdev-mdraid3 arm64 3.2.0-2 [12.8 kB] 79s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libblockdev-nvme3 arm64 3.2.0-2 [17.2 kB] 79s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libblockdev-part3 arm64 3.2.0-2 [14.9 kB] 79s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libblockdev-swap3 arm64 3.2.0-2 [7832 B] 79s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libblockdev3 arm64 3.2.0-2 [52.4 kB] 79s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libftdi1-2 arm64 1.5-7 [28.4 kB] 79s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libinih1 arm64 58-1ubuntu1 [7412 B] 79s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lazr.uri all 1.0.6-4 [13.6 kB] 80s Fetched 594 kB in 1s (1097 kB/s) 80s (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 ... 79705 files and directories currently installed.) 80s Preparing to unpack .../00-libevdev2_1.13.3+dfsg-1_arm64.deb ... 80s Unpacking libevdev2:arm64 (1.13.3+dfsg-1) over (1.13.2+dfsg-1) ... 80s Preparing to unpack .../01-libpipeline1_1.5.8-1_arm64.deb ... 80s Unpacking libpipeline1:arm64 (1.5.8-1) over (1.5.7-2) ... 80s Preparing to unpack .../02-nano_8.2-1_arm64.deb ... 80s Unpacking nano (8.2-1) over (8.1-1) ... 80s Preparing to unpack .../03-libblockdev-utils3_3.2.0-2_arm64.deb ... 80s Unpacking libblockdev-utils3:arm64 (3.2.0-2) over (3.1.1-2) ... 81s Preparing to unpack .../04-libblockdev-crypto3_3.2.0-2_arm64.deb ... 81s Unpacking libblockdev-crypto3:arm64 (3.2.0-2) over (3.1.1-2) ... 81s Preparing to unpack .../05-libblockdev-fs3_3.2.0-2_arm64.deb ... 81s Unpacking libblockdev-fs3:arm64 (3.2.0-2) over (3.1.1-2) ... 81s Preparing to unpack .../06-libblockdev-loop3_3.2.0-2_arm64.deb ... 81s Unpacking libblockdev-loop3:arm64 (3.2.0-2) over (3.1.1-2) ... 81s Preparing to unpack .../07-libblockdev-mdraid3_3.2.0-2_arm64.deb ... 81s Unpacking libblockdev-mdraid3:arm64 (3.2.0-2) over (3.1.1-2) ... 81s Preparing to unpack .../08-libblockdev-nvme3_3.2.0-2_arm64.deb ... 81s Unpacking libblockdev-nvme3:arm64 (3.2.0-2) over (3.1.1-2) ... 81s Preparing to unpack .../09-libblockdev-part3_3.2.0-2_arm64.deb ... 81s Unpacking libblockdev-part3:arm64 (3.2.0-2) over (3.1.1-2) ... 81s Preparing to unpack .../10-libblockdev-swap3_3.2.0-2_arm64.deb ... 81s Unpacking libblockdev-swap3:arm64 (3.2.0-2) over (3.1.1-2) ... 81s Preparing to unpack .../11-libblockdev3_3.2.0-2_arm64.deb ... 81s Unpacking libblockdev3:arm64 (3.2.0-2) over (3.1.1-2) ... 81s Preparing to unpack .../12-libftdi1-2_1.5-7_arm64.deb ... 81s Unpacking libftdi1-2:arm64 (1.5-7) over (1.5-6build5) ... 81s Preparing to unpack .../13-libinih1_58-1ubuntu1_arm64.deb ... 81s Unpacking libinih1:arm64 (58-1ubuntu1) over (55-1ubuntu2) ... 81s Preparing to unpack .../14-python3-lazr.uri_1.0.6-4_all.deb ... 81s Unpacking python3-lazr.uri (1.0.6-4) over (1.0.6-3) ... 81s Setting up libpipeline1:arm64 (1.5.8-1) ... 81s Setting up libinih1:arm64 (58-1ubuntu1) ... 81s Setting up python3-lazr.uri (1.0.6-4) ... 81s Setting up libftdi1-2:arm64 (1.5-7) ... 81s Setting up libblockdev-utils3:arm64 (3.2.0-2) ... 81s Setting up libblockdev-nvme3:arm64 (3.2.0-2) ... 81s Setting up nano (8.2-1) ... 82s Setting up libblockdev-fs3:arm64 (3.2.0-2) ... 82s Setting up libevdev2:arm64 (1.13.3+dfsg-1) ... 82s Setting up libblockdev-mdraid3:arm64 (3.2.0-2) ... 82s Setting up libblockdev-crypto3:arm64 (3.2.0-2) ... 82s Setting up libblockdev-swap3:arm64 (3.2.0-2) ... 82s Setting up libblockdev-loop3:arm64 (3.2.0-2) ... 82s Setting up libblockdev3:arm64 (3.2.0-2) ... 82s Installing new version of config file /etc/libblockdev/3/conf.d/00-default.cfg ... 82s Setting up libblockdev-part3:arm64 (3.2.0-2) ... 82s Processing triggers for libc-bin (2.40-1ubuntu3) ... 82s Processing triggers for man-db (2.12.1-3) ... 83s Processing triggers for install-info (7.1.1-1) ... 83s Reading package lists... 83s Building dependency tree... 83s Reading state information... 84s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 84s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 84s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 84s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 85s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 86s Reading package lists... 86s Reading package lists... 86s Building dependency tree... 86s Reading state information... 87s Calculating upgrade... 87s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 87s Reading package lists... 88s Building dependency tree... 88s Reading state information... 89s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 92s autopkgtest [02:52:09]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 92s autopkgtest [02:52:09]: @@@@@@@@@@@@@@@@@@@@ apt-source bbmap 96s Get:1 http://ftpmaster.internal/ubuntu plucky/universe bbmap 39.08+dfsg-1 (dsc) [2286 B] 96s Get:2 http://ftpmaster.internal/ubuntu plucky/universe bbmap 39.08+dfsg-1 (tar) [5396 kB] 96s Get:3 http://ftpmaster.internal/ubuntu plucky/universe bbmap 39.08+dfsg-1 (diff) [25.4 kB] 96s gpgv: Signature made Fri Aug 9 08:31:18 2024 UTC 96s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 96s gpgv: issuer "emollier@debian.org" 96s gpgv: Can't check signature: No public key 96s dpkg-source: warning: cannot verify inline signature for ./bbmap_39.08+dfsg-1.dsc: no acceptable signature found 96s autopkgtest [02:52:13]: testing package bbmap version 39.08+dfsg-1 97s autopkgtest [02:52:14]: build not needed 109s autopkgtest [02:52:26]: test run-unit-test: preparing testbed 110s Reading package lists... 110s Building dependency tree... 110s 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 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 113s 0 upgraded, 18 newly installed, 0 to remove and 0 not upgraded. 113s Need to get 77.0 MB/77.0 MB of archives. 113s After this operation, 231 MB of additional disk space will be used. 113s Get:1 /tmp/autopkgtest.ZXzt4p/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [720 B] 113s Get:2 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcommons-cli-java all 1.6.0-1 [59.9 kB] 113s Get:3 http://ftpmaster.internal/ubuntu plucky/universe arm64 libapache-pom-java all 33-2 [5874 B] 113s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcommons-parent-java all 56-1 [10.7 kB] 113s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcommons-codec-java all 1.16.0-1 [306 kB] 113s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcommons-io-java all 2.16.1-1 [451 kB] 113s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblog4j1.2-java all 1.2.17-11 [439 kB] 113s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmpj-java all 0.44+dfsg-4 [443 kB] 113s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 ca-certificates-java all 20240118 [11.6 kB] 113s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 java-common all 0.76 [6852 B] 113s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.14-2build1 [161 kB] 113s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu2 [163 kB] 113s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 113s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcsclite1 arm64 2.3.0-1 [24.4 kB] 113s Get:15 http://ftpmaster.internal/ubuntu plucky/universe arm64 openjdk-17-jre-headless arm64 17.0.13+11-2build1 [47.4 MB] 115s Get:16 http://ftpmaster.internal/ubuntu plucky/universe arm64 bbmap all 39.08+dfsg-1 [10.0 MB] 115s Get:17 http://ftpmaster.internal/ubuntu plucky/universe arm64 bbmap-jni arm64 39.08+dfsg-1 [28.6 kB] 115s Get:18 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-biopython-doc all 1.83+dfsg1-3 [17.4 MB] 116s Fetched 77.0 MB in 3s (23.9 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 ... 79705 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) ... 117s Selecting previously unselected package liblog4j1.2-java. 117s Preparing to unpack .../05-liblog4j1.2-java_1.2.17-11_all.deb ... 117s Unpacking liblog4j1.2-java (1.2.17-11) ... 117s Selecting previously unselected package libmpj-java. 117s Preparing to unpack .../06-libmpj-java_0.44+dfsg-4_all.deb ... 117s Unpacking libmpj-java (0.44+dfsg-4) ... 117s Selecting previously unselected package ca-certificates-java. 117s Preparing to unpack .../07-ca-certificates-java_20240118_all.deb ... 117s Unpacking ca-certificates-java (20240118) ... 117s Selecting previously unselected package java-common. 117s Preparing to unpack .../08-java-common_0.76_all.deb ... 117s Unpacking java-common (0.76) ... 117s Selecting previously unselected package liblcms2-2:arm64. 117s Preparing to unpack .../09-liblcms2-2_2.14-2build1_arm64.deb ... 117s Unpacking liblcms2-2:arm64 (2.14-2build1) ... 117s Selecting previously unselected package libjpeg-turbo8:arm64. 117s Preparing to unpack .../10-libjpeg-turbo8_2.1.5-2ubuntu2_arm64.deb ... 117s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 117s Selecting previously unselected package libjpeg8:arm64. 117s Preparing to unpack .../11-libjpeg8_8c-2ubuntu11_arm64.deb ... 117s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 117s Selecting previously unselected package libpcsclite1:arm64. 117s Preparing to unpack .../12-libpcsclite1_2.3.0-1_arm64.deb ... 117s Unpacking libpcsclite1:arm64 (2.3.0-1) ... 117s Selecting previously unselected package openjdk-17-jre-headless:arm64. 117s Preparing to unpack .../13-openjdk-17-jre-headless_17.0.13+11-2build1_arm64.deb ... 117s Unpacking openjdk-17-jre-headless:arm64 (17.0.13+11-2build1) ... 118s Selecting previously unselected package bbmap. 118s Preparing to unpack .../14-bbmap_39.08+dfsg-1_all.deb ... 118s Unpacking bbmap (39.08+dfsg-1) ... 118s Selecting previously unselected package bbmap-jni. 118s Preparing to unpack .../15-bbmap-jni_39.08+dfsg-1_arm64.deb ... 118s Unpacking bbmap-jni (39.08+dfsg-1) ... 118s Selecting previously unselected package python-biopython-doc. 118s Preparing to unpack .../16-python-biopython-doc_1.83+dfsg1-3_all.deb ... 118s Unpacking python-biopython-doc (1.83+dfsg1-3) ... 119s Selecting previously unselected package autopkgtest-satdep. 119s Preparing to unpack .../17-1-autopkgtest-satdep.deb ... 119s Unpacking autopkgtest-satdep (0) ... 119s Setting up liblcms2-2:arm64 (2.14-2build1) ... 119s Setting up java-common (0.76) ... 119s Setting up libcommons-cli-java (1.6.0-1) ... 119s Setting up liblog4j1.2-java (1.2.17-11) ... 119s Setting up libapache-pom-java (33-2) ... 119s Setting up libpcsclite1:arm64 (2.3.0-1) ... 119s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 119s Setting up python-biopython-doc (1.83+dfsg1-3) ... 119s Setting up bbmap-jni (39.08+dfsg-1) ... 119s Setting up ca-certificates-java (20240118) ... 119s No JRE found. Skipping Java certificates setup. 119s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 119s Setting up libcommons-parent-java (56-1) ... 119s Setting up openjdk-17-jre-headless:arm64 (17.0.13+11-2build1) ... 119s update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode 119s update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 119s update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 119s update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 119s update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 119s Setting up libcommons-codec-java (1.16.0-1) ... 119s Setting up libcommons-io-java (2.16.1-1) ... 119s Setting up libmpj-java (0.44+dfsg-4) ... 119s Processing triggers for libc-bin (2.40-1ubuntu3) ... 119s Processing triggers for man-db (2.12.1-3) ... 120s Processing triggers for ca-certificates-java (20240118) ... 120s Adding debian:ACCVRAIZ1.pem 120s Adding debian:AC_RAIZ_FNMT-RCM.pem 120s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 120s Adding debian:ANF_Secure_Server_Root_CA.pem 121s Adding debian:Actalis_Authentication_Root_CA.pem 121s Adding debian:AffirmTrust_Commercial.pem 121s Adding debian:AffirmTrust_Networking.pem 121s Adding debian:AffirmTrust_Premium.pem 121s Adding debian:AffirmTrust_Premium_ECC.pem 121s Adding debian:Amazon_Root_CA_1.pem 121s Adding debian:Amazon_Root_CA_2.pem 121s Adding debian:Amazon_Root_CA_3.pem 121s Adding debian:Amazon_Root_CA_4.pem 121s Adding debian:Atos_TrustedRoot_2011.pem 121s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 121s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 121s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 121s Adding debian:BJCA_Global_Root_CA1.pem 121s Adding debian:BJCA_Global_Root_CA2.pem 121s Adding debian:Baltimore_CyberTrust_Root.pem 121s Adding debian:Buypass_Class_2_Root_CA.pem 121s Adding debian:Buypass_Class_3_Root_CA.pem 121s Adding debian:CA_Disig_Root_R2.pem 121s Adding debian:CFCA_EV_ROOT.pem 121s Adding debian:COMODO_Certification_Authority.pem 121s Adding debian:COMODO_ECC_Certification_Authority.pem 121s Adding debian:COMODO_RSA_Certification_Authority.pem 121s Adding debian:Certainly_Root_E1.pem 121s Adding debian:Certainly_Root_R1.pem 121s Adding debian:Certigna.pem 121s Adding debian:Certigna_Root_CA.pem 121s Adding debian:Certum_EC-384_CA.pem 121s Adding debian:Certum_Trusted_Network_CA.pem 121s Adding debian:Certum_Trusted_Network_CA_2.pem 121s Adding debian:Certum_Trusted_Root_CA.pem 121s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 121s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 121s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 121s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 121s Adding debian:Comodo_AAA_Services_root.pem 121s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 121s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 121s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 121s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 121s Adding debian:DigiCert_Assured_ID_Root_CA.pem 121s Adding debian:DigiCert_Assured_ID_Root_G2.pem 121s Adding debian:DigiCert_Assured_ID_Root_G3.pem 121s Adding debian:DigiCert_Global_Root_CA.pem 121s Adding debian:DigiCert_Global_Root_G2.pem 121s Adding debian:DigiCert_Global_Root_G3.pem 121s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 121s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 121s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 121s Adding debian:DigiCert_Trusted_Root_G4.pem 121s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 121s Adding debian:Entrust_Root_Certification_Authority.pem 121s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 121s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 121s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem 121s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 121s Adding debian:GLOBALTRUST_2020.pem 121s Adding debian:GTS_Root_R1.pem 121s Adding debian:GTS_Root_R2.pem 121s Adding debian:GTS_Root_R3.pem 121s Adding debian:GTS_Root_R4.pem 121s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 121s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 121s Adding debian:GlobalSign_Root_CA.pem 121s Adding debian:GlobalSign_Root_CA_-_R3.pem 121s Adding debian:GlobalSign_Root_CA_-_R6.pem 121s Adding debian:GlobalSign_Root_E46.pem 121s Adding debian:GlobalSign_Root_R46.pem 121s Adding debian:Go_Daddy_Class_2_CA.pem 121s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 121s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 121s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 121s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 121s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 121s Adding debian:HiPKI_Root_CA_-_G1.pem 121s Adding debian:Hongkong_Post_Root_CA_3.pem 121s Adding debian:ISRG_Root_X1.pem 121s Adding debian:ISRG_Root_X2.pem 121s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 121s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 121s Adding debian:Izenpe.com.pem 121s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 121s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 121s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 121s Adding debian:NAVER_Global_Root_Certification_Authority.pem 121s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 121s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 121s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 121s Adding debian:QuoVadis_Root_CA_1_G3.pem 121s Adding debian:QuoVadis_Root_CA_2.pem 121s Adding debian:QuoVadis_Root_CA_2_G3.pem 121s Adding debian:QuoVadis_Root_CA_3.pem 121s Adding debian:QuoVadis_Root_CA_3_G3.pem 121s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 121s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 121s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 121s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 121s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 121s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 121s Adding debian:SZAFIR_ROOT_CA2.pem 121s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 121s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 121s Adding debian:SecureSign_RootCA11.pem 121s Adding debian:SecureTrust_CA.pem 121s Adding debian:Secure_Global_CA.pem 121s Adding debian:Security_Communication_ECC_RootCA1.pem 121s Adding debian:Security_Communication_RootCA2.pem 121s Adding debian:Security_Communication_RootCA3.pem 121s Adding debian:Security_Communication_Root_CA.pem 121s Adding debian:Starfield_Class_2_CA.pem 121s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 121s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 121s Adding debian:SwissSign_Gold_CA_-_G2.pem 121s Adding debian:SwissSign_Silver_CA_-_G2.pem 121s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 121s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 121s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 121s Adding debian:TWCA_Global_Root_CA.pem 121s Adding debian:TWCA_Root_Certification_Authority.pem 121s Adding debian:TeliaSonera_Root_CA_v1.pem 121s Adding debian:Telia_Root_CA_v2.pem 121s Adding debian:TrustAsia_Global_Root_CA_G3.pem 121s Adding debian:TrustAsia_Global_Root_CA_G4.pem 121s Adding debian:Trustwave_Global_Certification_Authority.pem 121s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 121s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 121s Adding debian:TunTrust_Root_CA.pem 121s Adding debian:UCA_Extended_Validation_Root.pem 121s Adding debian:UCA_Global_G2_Root.pem 121s Adding debian:USERTrust_ECC_Certification_Authority.pem 121s Adding debian:USERTrust_RSA_Certification_Authority.pem 121s Adding debian:XRamp_Global_CA_Root.pem 121s Adding debian:certSIGN_ROOT_CA.pem 121s Adding debian:certSIGN_Root_CA_G2.pem 121s Adding debian:e-Szigno_Root_CA_2017.pem 121s Adding debian:ePKI_Root_Certification_Authority.pem 121s Adding debian:emSign_ECC_Root_CA_-_C3.pem 121s Adding debian:emSign_ECC_Root_CA_-_G3.pem 121s Adding debian:emSign_Root_CA_-_C1.pem 121s Adding debian:emSign_Root_CA_-_G1.pem 121s Adding debian:vTrus_ECC_Root_CA.pem 121s Adding debian:vTrus_Root_CA.pem 121s done. 121s Setting up bbmap (39.08+dfsg-1) ... 121s Setting up autopkgtest-satdep (0) ... 125s (Reading database ... 82256 files and directories currently installed.) 125s Removing autopkgtest-satdep (0) ... 126s autopkgtest [02:52:43]: test run-unit-test: [----------------------- 127s 127s # bbmap 127s bbmap.sh --version 127s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 127s java -ea -Xmx2759m -Xms2759m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 --version 127s BBTools version 39.08 127s For help, please run the shellscript with no parameters, or look in /docs/. 127s bbmap.sh --help 127s 127s BBMap 127s Written by Brian Bushnell, from Dec. 2010 - present 127s Last modified September 15, 2022 127s 127s Description: Fast and accurate splice-aware read aligner. 127s Please read bbmap/docs/guides/BBMapGuide.txt for more information. 127s 127s To index: bbmap.sh ref= 127s To map: bbmap.sh in= out= 127s To map without writing an index: 127s bbmap.sh ref= in= out= nodisk 127s 127s in=stdin will accept reads from standard in, and out=stdout will write to 127s standard out, but file extensions are still needed to specify the format of the 127s input and output files e.g. in=stdin.fa.gz will read gzipped fasta from 127s standard in; out=stdout.sam.gz will write gzipped sam. 127s 127s Indexing Parameters (required when building the index): 127s nodisk=f Set to true to build index in memory and write nothing 127s to disk except output. 127s ref= Specify the reference sequence. Only do this ONCE, 127s when building the index (unless using 'nodisk'). 127s build=1 If multiple references are indexed in the same directory, 127s each needs a unique numeric ID (unless using 'nodisk'). 127s k=13 Kmer length, range 8-15. Longer is faster but uses 127s more memory. Shorter is more sensitive. 127s If indexing and mapping are done in two steps, K should 127s be specified each time. 127s path=<.> Specify the location to write the index, if you don't 127s want it in the current working directory. 127s usemodulo=f Throw away ~80% of kmers based on remainder modulo a 127s number (reduces RAM by 50% and sensitivity slightly). 127s Should be enabled both when building the index AND 127s when mapping. 127s rebuild=f Force a rebuild of the index (ref= should be set). 127s 127s Input Parameters: 127s build=1 Designate index to use. Corresponds to the number 127s specified when building the index. 127s in= Primary reads input; required parameter. 127s in2= For paired reads in two files. 127s interleaved=auto True forces paired/interleaved input; false forces 127s single-ended mapping. If not specified, interleaved 127s status will be autodetected from read names. 127s fastareadlen=500 Break up FASTA reads longer than this. Max is 500 for 127s BBMap and 6000 for BBMapPacBio. Only works for FASTA 127s input (use 'maxlen' for FASTQ input). The default for 127s bbmap.sh is 500, and for mapPacBio.sh is 6000. 127s unpigz=f Spawn a pigz (parallel gzip) process for faster 127s decompression than using Java. 127s Requires pigz to be installed. 127s touppercase=t (tuc) Convert lowercase letters in reads to upper case 127s (otherwise they will not match the reference). 127s 127s Sampling Parameters: 127s 127s reads=-1 Set to a positive number N to only process the first N 127s reads (or pairs), then quit. -1 means use all reads. 127s samplerate=1 Set to a number from 0 to 1 to randomly select that 127s fraction of reads for mapping. 1 uses all reads. 127s skipreads=0 Set to a number N to skip the first N reads (or pairs), 127s then map the rest. 127s 127s Mapping Parameters: 127s fast=f This flag is a macro which sets other paramters to run 127s faster, at reduced sensitivity. Bad for RNA-seq. 127s slow=f This flag is a macro which sets other paramters to run 127s slower, at greater sensitivity. 'vslow' is even slower. 127s maxindel=16000 Don't look for indels longer than this. Lower is faster. 127s Set to >=100k for RNAseq with long introns like mammals. 127s strictmaxindel=f When enabled, do not allow indels longer than 'maxindel'. 127s By default these are not sought, but may be found anyway. 127s tipsearch=100 Look this far for read-end deletions with anchors 127s shorter than K, using brute force. 127s minid=0.76 Approximate minimum alignment identity to look for. 127s Higher is faster and less sensitive. 127s minhits=1 Minimum number of seed hits required for candidate sites. 127s Higher is faster. 127s local=f Set to true to use local, rather than global, alignments. 127s This will soft-clip ugly ends of poor alignments. 127s perfectmode=f Allow only perfect mappings when set to true (very fast). 127s semiperfectmode=f Allow only perfect and semiperfect (perfect except for 127s N's in the reference) mappings. 127s threads=auto (t) Set to number of threads desired. By default, uses 127s all cores available. 127s ambiguous=best (ambig) Set behavior on ambiguously-mapped reads (with 127s multiple top-scoring mapping locations). 127s best (use the first best site) 127s toss (consider unmapped) 127s random (select one top-scoring site randomly) 127s all (retain all top-scoring sites) 127s samestrandpairs=f (ssp) Specify whether paired reads should map to the 127s same strand or opposite strands. 127s requirecorrectstrand=t (rcs) Forbid pairing of reads without correct strand 127s orientation. Set to false for long-mate-pair libraries. 127s killbadpairs=f (kbp) If a read pair is mapped with an inappropriate 127s insert size or orientation, the read with the lower 127s mapping quality is marked unmapped. 127s pairedonly=f (po) Treat unpaired reads as unmapped. Thus they will 127s be sent to 'outu' but not 'outm'. 127s rcomp=f Reverse complement both reads prior to mapping (for LMP 127s outward-facing libraries). 127s rcompmate=f Reverse complement read2 prior to mapping. 127s pairlen=32000 Set max allowed distance between paired reads. 127s (insert size)=(pairlen)+(read1 length)+(read2 length) 127s rescuedist=1200 Don't try to rescue paired reads if avg. insert size 127s greater than this. Lower is faster. 127s rescuemismatches=32 Maximum mismatches allowed in a rescued read. Lower 127s is faster. 127s averagepairdist=100 (apd) Initial average distance between paired reads. 127s Varies dynamically; does not need to be specified. 127s deterministic=f Run in deterministic mode. In this case it is good 127s to set averagepairdist. BBMap is deterministic 127s without this flag if using single-ended reads, 127s or run singlethreaded. 127s bandwidthratio=0 (bwr) If above zero, restrict alignment band to this 127s fraction of read length. Faster but less accurate. 127s bandwidth=0 (bw) Set the bandwidth directly. 127s fraction of read length. Faster but less accurate. 127s usejni=f (jni) Do alignments faster, in C code. Requires 127s compiling the C code; details are in /jni/README.txt. 127s maxsites2=800 Don't analyze (or print) more than this many alignments 127s per read. 127s ignorefrequentkmers=t (ifk) Discard low-information kmers that occur often. 127s excludefraction=0.03 (ef) Fraction of kmers to ignore. For example, 0.03 127s will ignore the most common 3% of kmers. 127s greedy=t Use a greedy algorithm to discard the least-useful 127s kmers on a per-read basis. 127s kfilter=0 If positive, potential mapping sites must have at 127s least this many consecutive exact matches. 127s 127s 127s Quality and Trimming Parameters: 127s qin=auto Set to 33 or 64 to specify input quality value ASCII 127s offset. 33 is Sanger, 64 is old Solexa. 127s qout=auto Set to 33 or 64 to specify output quality value ASCII 127s offset (only if output format is fastq). 127s qtrim=f Quality-trim ends before mapping. Options are: 127s 'f' (false), 'l' (left), 'r' (right), and 'lr' (both). 127s untrim=f Undo trimming after mapping. Untrimmed bases will be 127s soft-clipped in cigar strings. 127s trimq=6 Trim regions with average quality below this 127s (phred algorithm). 127s mintrimlength=60 (mintl) Don't trim reads to be shorter than this. 127s fakefastaquality=-1 (ffq) Set to a positive number 1-50 to generate fake 127s quality strings for fasta input reads. 127s ignorebadquality=f (ibq) Keep going, rather than crashing, if a read has 127s out-of-range quality values. 127s usequality=t Use quality scores when determining which read kmers 127s to use as seeds. 127s minaveragequality=0 (maq) Do not map reads with average quality below this. 127s maqb=0 If positive, calculate maq from this many initial bases. 127s 127s Output Parameters: 127s out= Write all reads to this file. 127s outu= Write only unmapped reads to this file. Does not 127s include unmapped paired reads with a mapped mate. 127s outm= Write only mapped reads to this file. Includes 127s unmapped paired reads with a mapped mate. 127s mappedonly=f If true, treats 'out' like 'outm'. 127s bamscript= (bs) Write a shell script to that will turn 127s the sam output into a sorted, indexed bam file. 127s ordered=f Set to true to output reads in same order as input. 127s Slower and uses more memory. 127s overwrite=f (ow) Allow process to overwrite existing files. 127s secondary=f Print secondary alignments. 127s sssr=0.95 (secondarysitescoreratio) Print only secondary alignments 127s with score of at least this fraction of primary. 127s ssao=f (secondarysiteasambiguousonly) Only print secondary 127s alignments for ambiguously-mapped reads. 127s maxsites=5 Maximum number of total alignments to print per read. 127s Only relevant when secondary=t. 127s quickmatch=f Generate cigar strings more quickly. 127s trimreaddescriptions=f (trd) Truncate read and ref names at the first whitespace, 127s assuming that the remainder is a comment or description. 127s ziplevel=2 (zl) Compression level for zip or gzip output. 127s pigz=f Spawn a pigz (parallel gzip) process for faster 127s compression than Java. Requires pigz to be installed. 127s machineout=f Set to true to output statistics in machine-friendly 127s 'key=value' format. 127s printunmappedcount=f Print the total number of unmapped reads and bases. 127s If input is paired, the number will be of pairs 127s for which both reads are unmapped. 127s showprogress=0 If positive, print a '.' every X reads. 127s showprogress2=0 If positive, print the number of seconds since the 127s last progress update (instead of a '.'). 127s renamebyinsert=f Renames reads based on their mapped insert size. 127s 127s Bloom-Filtering Parameters (bloomfilter.sh is the standalone version). 127s bloom=f Use a Bloom filter to ignore reads not sharing kmers 127s with the reference. This uses more memory, but speeds 127s mapping when most reads don't match the reference. 127s bloomhashes=2 Number of hash functions. 127s bloomminhits=3 Number of consecutive hits to be considered matched. 127s bloomk=31 Bloom filter kmer length. 127s bloomserial=t Use the serialized Bloom filter for greater loading 127s speed, if available. If not, generate and write one. 127s 127s Post-Filtering Parameters: 127s idfilter=0 Independant of minid; sets exact minimum identity 127s allowed for alignments to be printed. Range 0 to 1. 127s subfilter=-1 Ban alignments with more than this many substitutions. 127s insfilter=-1 Ban alignments with more than this many insertions. 127s delfilter=-1 Ban alignments with more than this many deletions. 127s indelfilter=-1 Ban alignments with more than this many indels. 127s editfilter=-1 Ban alignments with more than this many edits. 127s inslenfilter=-1 Ban alignments with an insertion longer than this. 127s dellenfilter=-1 Ban alignments with a deletion longer than this. 127s nfilter=-1 Ban alignments with more than this many ns. This 127s includes nocall, noref, and off scaffold ends. 127s 127s Sam flags and settings: 127s noheader=f Disable generation of header lines. 127s sam=1.4 Set to 1.4 to write Sam version 1.4 cigar strings, 127s with = and X, or 1.3 to use M. 127s saa=t (secondaryalignmentasterisks) Use asterisks instead of 127s bases for sam secondary alignments. 127s cigar=t Set to 'f' to skip generation of cigar strings (faster). 127s keepnames=f Keep original names of paired reads, rather than 127s ensuring both reads have the same name. 127s intronlen=999999999 Set to a lower number like 10 to change 'D' to 'N' in 127s cigar strings for deletions of at least that length. 127s rgid= Set readgroup ID. All other readgroup fields 127s can be set similarly, with the flag rgXX= 127s If you set a readgroup flag to the word 'filename', 127s e.g. rgid=filename, the input file name will be used. 127s mdtag=f Write MD tags. 127s nhtag=f Write NH tags. 127s xmtag=f Write XM tags (may only work correctly with ambig=all). 127s amtag=f Write AM tags. 127s nmtag=f Write NM tags. 127s xstag=f Set to 'xs=fs', 'xs=ss', or 'xs=us' to write XS tags 127s for RNAseq using firststrand, secondstrand, or 127s unstranded libraries. Needed by Cufflinks. 127s JGI mainly uses 'firststrand'. 127s stoptag=f Write a tag indicating read stop location, prefixed by YS:i: 127s lengthtag=f Write a tag indicating (query,ref) alignment lengths, 127s prefixed by YL:Z: 127s idtag=f Write a tag indicating percent identity, prefixed by YI:f: 127s inserttag=f Write a tag indicating insert size, prefixed by X8:Z: 127s scoretag=f Write a tag indicating BBMap's raw score, prefixed by YR:i: 127s timetag=f Write a tag indicating this read's mapping time, prefixed by X0:i: 127s boundstag=f Write a tag indicating whether either read in the pair 127s goes off the end of the reference, prefixed by XB:Z: 127s notags=f Turn off all optional tags. 127s 127s Histogram and statistics output parameters: 127s scafstats= Statistics on how many reads mapped to which scaffold. 127s refstats= Statistics on how many reads mapped to which reference 127s file; only for BBSplit. 127s sortscafs=t Sort scaffolds or references by read count. 127s bhist= Base composition histogram by position. 127s qhist= Quality histogram by position. 127s aqhist= Histogram of average read quality. 127s bqhist= Quality histogram designed for box plots. 127s lhist= Read length histogram. 127s ihist= Write histogram of insert sizes (for paired reads). 127s ehist= Errors-per-read histogram. 127s qahist= Quality accuracy histogram of error rates versus 127s quality score. 127s indelhist= Indel length histogram. 127s mhist= Histogram of match, sub, del, and ins rates by 127s read location. 127s gchist= Read GC content histogram. 127s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 127s gcpairs=t Use average GC of paired reads. 127s idhist= Histogram of read count versus percent identity. 127s idbins=100 Number idhist bins. Set to 'auto' to use read length. 127s statsfile=stderr Mapping statistics are printed here. 127s 127s Coverage output parameters (these may reduce speed and use more RAM): 127s covstats= Per-scaffold coverage info. 127s rpkm= Per-scaffold RPKM/FPKM counts. 127s covhist= Histogram of # occurrences of each depth level. 127s basecov= Coverage per base location. 127s bincov= Print binned coverage per location (one line per X bases). 127s covbinsize=1000 Set the binsize for binned coverage output. 127s nzo=t Only print scaffolds with nonzero coverage. 127s twocolumn=f Change to true to print only ID and Avg_fold instead of 127s all 6 columns to the 'out=' file. 127s 32bit=f Set to true if you need per-base coverage over 64k. 127s strandedcov=f Track coverage for plus and minus strand independently. 127s startcov=f Only track start positions of reads. 127s secondarycov=t Include coverage of secondary alignments. 127s physcov=f Calculate physical coverage for paired reads. 127s This includes the unsequenced bases. 127s delcoverage=t (delcov) Count bases covered by deletions as covered. 127s True is faster than false. 127s covk=0 If positive, calculate kmer coverage statistics. 127s 127s Java Parameters: 127s -Xmx This will set Java's memory usage, 127s overriding autodetection. 127s -Xmx20g will specify 20 gigs of RAM, and -Xmx800m 127s will specify 800 megs. The max is typically 85% of 127s physical memory. The human genome requires around 24g, 127s or 12g with the 'usemodulo' flag. The index uses 127s roughly 6 bytes per reference base. 127s -eoom This flag will cause the process to exit if an 127s out-of-memory exception occurs. Requires Java 8u92+. 127s -da Disable assertions. 127s 127s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter 127s any problems, or post at: http://seqanswers.com/forums/showthread.php?t=41057 127s 127s bbmap.sh ref=example.fasta 127s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 127s java -ea -Xmx2759m -Xms2759m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta 127s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta] 127s Version 39.08 127s 127s No output file. 127s Writing reference. 127s 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] 127s 127s Set genScaffoldInfo=true 127s Writing chunk 1 127s Set genome to 1 127s 127s Loaded Reference: 0.009 seconds. 127s Loading index for chunk 1-1, build 1 127s No index available; generating from reference genome: /tmp/autopkgtest.ZXzt4p/autopkgtest_tmp/ref/index/1/chr1_index_k13_c16_b1.block 127s Indexing threads started for block 0-1 128s Indexing threads finished for block 0-1 128s Generated Index: 0.998 seconds. 128s No reads to process; quitting. 128s 128s Total time: 1.204 seconds. 128s test -d ref 128s bbmap.sh in=misc_dna_as_sanger.fastq out=out.sam 128s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 129s java -ea -Xmx2759m -Xms2759m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 in=misc_dna_as_sanger.fastq out=out.sam 129s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, in=misc_dna_as_sanger.fastq, out=out.sam] 129s Version 39.08 129s 129s Retaining first best site only for ambiguous mappings. 129s Set genome to 1 129s 129s Loaded Reference: 0.044 seconds. 129s Loading index for chunk 1-1, build 1 129s Generated Index: 0.389 seconds. 132s Analyzed Index: 3.282 seconds. 132s Started output stream: 0.042 seconds. 133s Cleared Memory: 0.120 seconds. 133s Processing reads in single-ended mode. 133s Started read stream. 133s Started 4 mapping threads. 133s Detecting finished threads: 0, 1, 2, 3 133s 133s ------------------ Results ------------------ 133s 133s Genome: 1 133s Key Length: 13 133s Max Indel: 16000 133s Minimum Score Ratio: 0.56 133s Mapping Mode: normal 133s Reads Used: 4 (153 bases) 133s 133s Mapping: 0.088 seconds. 133s Reads/sec: 45.31 133s kBases/sec: 1.73 133s 133s 133s Read 1 data: pct reads num reads pct bases num bases 133s 133s mapped: 0.0000% 0 0.0000% 0 133s unambiguous: 0.0000% 0 0.0000% 0 133s ambiguous: 0.0000% 0 0.0000% 0 133s low-Q discards: 25.0000% 1 19.6078% 30 133s 133s perfect best site: 0.0000% 0 0.0000% 0 133s semiperfect site: 0.0000% 0 0.0000% 0 133s 133s Match Rate: NA NA NaN% 0 133s Error Rate: NaN% 0 NaN% 0 133s Sub Rate: NaN% 0 NaN% 0 133s Del Rate: NaN% 0 NaN% 0 133s Ins Rate: NaN% 0 NaN% 0 133s N Rate: NaN% 0 NaN% 0 133s 133s Total time: 4.111 seconds. 133s test -r out.sam 133s bbmap.sh ref=example.fasta in=example.fastq out=out2.sam nodisk 133s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 133s java -ea -Xmx2759m -Xms2759m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta in=example.fastq out=out2.sam nodisk 133s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta, in=example.fastq, out=out2.sam, nodisk] 133s Version 39.08 133s 133s Retaining first best site only for ambiguous mappings. 133s 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] 133s 133s Set genScaffoldInfo=true 133s Set genome to 1 133s 133s Loaded Reference: 0.002 seconds. 133s Loading index for chunk 1-1, build 1 133s Indexing threads started for block 0-1 133s Indexing threads finished for block 0-1 133s Generated Index: 0.230 seconds. 137s Analyzed Index: 3.261 seconds. 137s Started output stream: 0.045 seconds. 137s Cleared Memory: 0.122 seconds. 137s Processing reads in single-ended mode. 137s Started read stream. 137s Started 4 mapping threads. 137s Detecting finished threads: 0, 1, 2, 3 137s 137s ------------------ Results ------------------ 137s 137s Genome: 1 137s Key Length: 13 137s Max Indel: 16000 137s Minimum Score Ratio: 0.56 137s Mapping Mode: normal 137s Reads Used: 3 (75 bases) 137s 137s Mapping: 0.126 seconds. 137s Reads/sec: 23.86 137s kBases/sec: 0.60 137s 137s 137s Read 1 data: pct reads num reads pct bases num bases 137s 137s mapped: 100.0000% 3 100.0000% 75 137s unambiguous: 100.0000% 3 100.0000% 75 137s ambiguous: 0.0000% 0 0.0000% 0 137s low-Q discards: 0.0000% 0 0.0000% 0 137s 137s perfect best site: 100.0000% 3 100.0000% 75 137s semiperfect site: 100.0000% 3 100.0000% 75 137s 137s Match Rate: NA NA 100.0000% 75 137s Error Rate: 0.0000% 0 0.0000% 0 137s Sub Rate: 0.0000% 0 0.0000% 0 137s Del Rate: 0.0000% 0 0.0000% 0 137s Ins Rate: 0.0000% 0 0.0000% 0 137s N Rate: 0.0000% 0 0.0000% 0 137s 137s Total time: 4.005 seconds. 137s test -r out2.sam 137s 137s # bbduk 137s bbduk.sh --version 137s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 137s java -ea -Xmx1379m -Xms1379m -cp /usr/share/java/bbmap.jar jgi.BBDuk --version 137s BBTools version 39.08 137s For help, please run the shellscript with no parameters, or look in /docs/. 137s bbduk.sh --help 137s bbduk.sh in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq \ 137s qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 137s 137s Written by Brian Bushnell 137s Last modified November 9, 2023 137s 137s Description: Compares reads to the kmers in a reference dataset, optionally 137s allowing an edit distance. Splits the reads into two outputs - those that 137s match the reference, and those that don't. Can also trim (remove) the matching 137s parts of the reads rather than binning the reads. 137s Please read bbmap/docs/guides/BBDukGuide.txt for more information. 137s 137s Usage: bbduk.sh in= out= ref= 137s 137s Input may be stdin or a fasta or fastq file, compressed or uncompressed. 137s If you pipe via stdin/stdout, please include the file type; e.g. for gzipped 137s fasta input, set in=stdin.fa.gz 137s 137s Input parameters: 137s in= Main input. in=stdin.fq will pipe from stdin. 137s in2= Input for 2nd read of pairs in a different file. 137s ref= Comma-delimited list of reference files. 137s In addition to filenames, you may also use the keywords: 137s adapters, artifacts, phix, lambda, pjet, mtst, kapa 137s literal= Comma-delimited list of literal reference sequences. 137s touppercase=f (tuc) Change all bases upper-case. 137s interleaved=auto (int) t/f overrides interleaved autodetection. 137s Must be set mainually when streaming fastq input. 137s qin=auto Input quality offset: 33 (Sanger), 64, or auto. 137s reads=-1 If positive, quit after processing X reads or pairs. 137s copyundefined=f (cu) Process non-AGCT IUPAC reference bases by making all 137s possible unambiguous copies. Intended for short motifs 137s or adapter barcodes, as time/memory use is exponential. 137s samplerate=1 Set lower to only process a fraction of input reads. 137s samref= Optional reference fasta for processing sam files. 137s 137s Output parameters: 137s out= (outnonmatch) Write reads here that do not contain 137s kmers matching the database. 'out=stdout.fq' will pipe 137s to standard out. 137s out2= (outnonmatch2) Use this to write 2nd read of pairs to a 137s different file. 137s outm= (outmatch) Write reads here that fail filters. In default 137s kfilter mode, this means any read with a matching kmer. 137s In any mode, it also includes reads that fail filters such 137s as minlength, mingc, maxgc, entropy, etc. In other words, 137s it includes all reads that do not go to 'out'. 137s outm2= (outmatch2) Use this to write 2nd read of pairs to a 137s different file. 137s outs= (outsingle) Use this to write singleton reads whose mate 137s was trimmed shorter than minlen. 137s stats= Write statistics about which contamininants were detected. 137s refstats= Write statistics on a per-reference-file basis. 137s rpkm= Write RPKM for each reference sequence (for RNA-seq). 137s dump= Dump kmer tables to a file, in fasta format. 137s duk= Write statistics in duk's format. *DEPRECATED* 137s nzo=t Only write statistics about ref sequences with nonzero hits. 137s overwrite=t (ow) Grant permission to overwrite files. 137s showspeed=t (ss) 'f' suppresses display of processing speed. 137s ziplevel=2 (zl) Compression level; 1 (min) through 9 (max). 137s fastawrap=70 Length of lines in fasta output. 137s qout=auto Output quality offset: 33 (Sanger), 64, or auto. 137s statscolumns=3 (cols) Number of columns for stats output, 3 or 5. 137s 5 includes base counts. 137s rename=f Rename reads to indicate which sequences they matched. 137s refnames=f Use names of reference files rather than scaffold IDs. 137s trd=f Truncate read and ref names at the first whitespace. 137s ordered=f Set to true to output reads in same order as input. 137s maxbasesout=-1 If positive, quit after writing approximately this many 137s bases to out (outu/outnonmatch). 137s maxbasesoutm=-1 If positive, quit after writing approximately this many 137s bases to outm (outmatch). 137s json=f Print to screen in json format. 137s 137s Histogram output parameters: 137s bhist= Base composition histogram by position. 137s qhist= Quality histogram by position. 137s qchist= Count of bases with each quality value. 137s aqhist= Histogram of average read quality. 137s bqhist= Quality histogram designed for box plots. 137s lhist= Read length histogram. 137s phist= Polymer length histogram. 137s gchist= Read GC content histogram. 137s enthist= Read entropy histogram. 137s ihist= Insert size histogram, for paired reads in mapped sam. 137s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 137s maxhistlen=6000 Set an upper bound for histogram lengths; higher uses 137s more memory. The default is 6000 for some histograms 137s and 80000 for others. 137s 137s Histograms for mapped sam/bam files only: 137s histbefore=t Calculate histograms from reads before processing. 137s ehist= Errors-per-read histogram. 137s qahist= Quality accuracy histogram of error rates versus quality 137s score. 137s indelhist= Indel length histogram. 137s mhist= Histogram of match, sub, del, and ins rates by position. 137s idhist= Histogram of read count versus percent identity. 137s idbins=100 Number idhist bins. Set to 'auto' to use read length. 137s varfile= Ignore substitution errors listed in this file when 137s calculating error rates. Can be generated with 137s CallVariants. 137s vcf= Ignore substitution errors listed in this VCF file 137s when calculating error rates. 137s ignorevcfindels=t Also ignore indels listed in the VCF. 137s 137s Processing parameters: 137s k=27 Kmer length used for finding contaminants. Contaminants 137s shorter than k will not be found. k must be at least 1. 137s rcomp=t Look for reverse-complements of kmers in addition to 137s forward kmers. 137s maskmiddle=t (mm) Treat the middle base of a kmer as a wildcard, to 137s increase sensitivity in the presence of errors. This may 137s also be set to a number, e.g. mm=3, to mask that many bp. 137s The default mm=t corresponds to mm=1 for odd-length kmers 137s and mm=2 for even-length kmers (as of v39.04), while 137s mm=f is always equivalent to mm=0. 137s minkmerhits=1 (mkh) Reads need at least this many matching kmers 137s to be considered as matching the reference. 137s minkmerfraction=0.0 (mkf) A reads needs at least this fraction of its total 137s kmers to hit a ref, in order to be considered a match. 137s If this and minkmerhits are set, the greater is used. 137s mincovfraction=0.0 (mcf) A reads needs at least this fraction of its total 137s bases to be covered by ref kmers to be considered a match. 137s If specified, mcf overrides mkh and mkf. 137s hammingdistance=0 (hdist) Maximum Hamming distance for ref kmers (subs only). 137s Memory use is proportional to (3*K)^hdist. 137s qhdist=0 Hamming distance for query kmers; impacts speed, not memory. 137s editdistance=0 (edist) Maximum edit distance from ref kmers (subs 137s and indels). Memory use is proportional to (8*K)^edist. 137s hammingdistance2=0 (hdist2) Sets hdist for short kmers, when using mink. 137s qhdist2=0 Sets qhdist for short kmers, when using mink. 137s editdistance2=0 (edist2) Sets edist for short kmers, when using mink. 137s forbidn=f (fn) Forbids matching of read kmers containing N. 137s By default, these will match a reference 'A' if 137s hdist>0 or edist>0, to increase sensitivity. 137s removeifeitherbad=t (rieb) Paired reads get sent to 'outmatch' if either is 137s match (or either is trimmed shorter than minlen). 137s Set to false to require both. 137s trimfailures=f Instead of discarding failed reads, trim them to 1bp. 137s This makes the statistics a bit odd. 137s findbestmatch=f (fbm) If multiple matches, associate read with sequence 137s sharing most kmers. Reduces speed. 137s skipr1=f Don't do kmer-based operations on read 1. 137s skipr2=f Don't do kmer-based operations on read 2. 137s ecco=f For overlapping paired reads only. Performs error- 137s correction with BBMerge prior to kmer operations. 137s recalibrate=f (recal) Recalibrate quality scores. Requires calibration 137s matrices generated by CalcTrueQuality. 137s sam= If recalibration is desired, and matrices have not already 137s been generated, BBDuk will create them from the sam file. 137s amino=f Run in amino acid mode. Some features have not been 137s tested, but kmer-matching works fine. Maximum k is 12. 137s 137s Speed and Memory parameters: 137s threads=auto (t) Set number of threads to use; default is number of 137s logical processors. 137s prealloc=f Preallocate memory in table. Allows faster table loading 137s and more efficient memory usage, for a large reference. 137s monitor=f Kill this process if it crashes. monitor=600,0.01 would 137s kill after 600 seconds under 1% usage. 137s minrskip=1 (mns) Force minimal skip interval when indexing reference 137s kmers. 1 means use all, 2 means use every other kmer, etc. 137s maxrskip=1 (mxs) Restrict maximal skip interval when indexing 137s reference kmers. Normally all are used for scaffolds<100kb, 137s but with longer scaffolds, up to maxrskip-1 are skipped. 137s rskip= Set both minrskip and maxrskip to the same value. 137s If not set, rskip will vary based on sequence length. 137s qskip=1 Skip query kmers to increase speed. 1 means use all. 137s speed=0 Ignore this fraction of kmer space (0-15 out of 16) in both 137s reads and reference. Increases speed and reduces memory. 137s Note: Do not use more than one of 'speed', 'qskip', and 'rskip'. 137s 137s Trimming/Filtering/Masking parameters: 137s Note - if ktrim, kmask, and ksplit are unset, the default behavior is kfilter. 137s All kmer processing modes are mutually exclusive. 137s Reads only get sent to 'outm' purely based on kmer matches in kfilter mode. 137s 137s ktrim=f Trim reads to remove bases matching reference kmers, plus 137s all bases to the left or right. 137s Values: 137s f (don't trim), 137s r (trim to the right), 137s l (trim to the left) 137s ktrimtips=0 Set this to a positive number to perform ktrim on both 137s ends, examining only the outermost X bases. 137s kmask= Replace bases matching ref kmers with another symbol. 137s Allows any non-whitespace character, and processes short 137s kmers on both ends if mink is set. 'kmask=lc' will 137s convert masked bases to lowercase. 137s maskfullycovered=f (mfc) Only mask bases that are fully covered by kmers. 137s ksplit=f For single-ended reads only. Reads will be split into 137s pairs around the kmer. If the kmer is at the end of the 137s read, it will be trimmed instead. Singletons will go to 137s out, and pairs will go to outm. Do not use ksplit with 137s other operations such as quality-trimming or filtering. 137s mink=0 Look for shorter kmers at read tips down to this length, 137s when k-trimming or masking. 0 means disabled. Enabling 137s this will disable maskmiddle. 137s qtrim=f Trim read ends to remove bases with quality below trimq. 137s Performed AFTER looking for kmers. Values: 137s rl (trim both ends), 137s f (neither end), 137s r (right end only), 137s l (left end only), 137s w (sliding window). 137s trimq=6 Regions with average quality BELOW this will be trimmed, 137s if qtrim is set to something other than f. Can be a 137s floating-point number like 7.3. 137s trimclip=f Trim soft-clipped bases from sam files. 137s minlength=10 (ml) Reads shorter than this after trimming will be 137s discarded. Pairs will be discarded if both are shorter. 137s mlf=0 (minlengthfraction) Reads shorter than this fraction of 137s original length after trimming will be discarded. 137s maxlength= Reads longer than this after trimming will be discarded. 137s minavgquality=0 (maq) Reads with average quality (after trimming) below 137s this will be discarded. 137s maqb=0 If positive, calculate maq from this many initial bases. 137s minbasequality=0 (mbq) Reads with any base below this quality (after 137s trimming) will be discarded. 137s maxns=-1 If non-negative, reads with more Ns than this 137s (after trimming) will be discarded. 137s mcb=0 (minconsecutivebases) Discard reads without at least 137s this many consecutive called bases. 137s ottm=f (outputtrimmedtomatch) Output reads trimmed to shorter 137s than minlength to outm rather than discarding. 137s tp=0 (trimpad) Trim this much extra around matching kmers. 137s tbo=f (trimbyoverlap) Trim adapters based on where paired 137s reads overlap. 137s strictoverlap=t Adjust sensitivity for trimbyoverlap mode. 137s minoverlap=14 Require this many bases of overlap for detection. 137s mininsert=40 Require insert size of at least this for overlap. 137s Should be reduced to 16 for small RNA sequencing. 137s tpe=f (trimpairsevenly) When kmer right-trimming, trim both 137s reads to the minimum length of either. 137s forcetrimleft=0 (ftl) If positive, trim bases to the left of this position 137s (exclusive, 0-based). 137s forcetrimright=0 (ftr) If positive, trim bases to the right of this position 137s (exclusive, 0-based). 137s forcetrimright2=0 (ftr2) If positive, trim this many bases on the right end. 137s forcetrimmod=0 (ftm) If positive, right-trim length to be equal to zero, 137s modulo this number. 137s restrictleft=0 If positive, only look for kmer matches in the 137s leftmost X bases. 137s restrictright=0 If positive, only look for kmer matches in the 137s rightmost X bases. 137s NOTE: restrictleft and restrictright are mutually exclusive. If trimming 137s both ends is desired, use ktrimtips. 137s mingc=0 Discard reads with GC content below this. 137s maxgc=1 Discard reads with GC content above this. 137s gcpairs=t Use average GC of paired reads. 137s Also affects gchist. 137s tossjunk=f Discard reads with invalid characters as bases. 137s swift=f Trim Swift sequences: Trailing C/T/N R1, leading G/A/N R2. 137s 137s Header-parsing parameters - these require Illumina headers: 137s chastityfilter=f (cf) Discard reads with id containing ' 1:Y:' or ' 2:Y:'. 137s barcodefilter=f Remove reads with unexpected barcodes if barcodes is set, 137s or barcodes containing 'N' otherwise. A barcode must be 137s the last part of the read header. Values: 137s t: Remove reads with bad barcodes. 137s f: Ignore barcodes. 137s crash: Crash upon encountering bad barcodes. 137s barcodes= Comma-delimited list of barcodes or files of barcodes. 137s xmin=-1 If positive, discard reads with a lesser X coordinate. 137s ymin=-1 If positive, discard reads with a lesser Y coordinate. 137s xmax=-1 If positive, discard reads with a greater X coordinate. 137s ymax=-1 If positive, discard reads with a greater Y coordinate. 137s 137s Polymer trimming: 137s trimpolya=0 If greater than 0, trim poly-A or poly-T tails of 137s at least this length on either end of reads. 137s trimpolygleft=0 If greater than 0, trim poly-G prefixes of at least this 137s length on the left end of reads. Does not trim poly-C. 137s trimpolygright=0 If greater than 0, trim poly-G tails of at least this 137s length on the right end of reads. Does not trim poly-C. 137s trimpolyg=0 This sets both left and right at once. 137s filterpolyg=0 If greater than 0, remove reads with a poly-G prefix of 137s at least this length (on the left). 137s Note: there are also equivalent poly-C flags. 137s 137s Polymer tracking: 137s pratio=base,base 'pratio=G,C' will print the ratio of G to C polymers. 137s plen=20 Length of homopolymers to count. 137s 137s Entropy/Complexity parameters: 137s entropy=-1 Set between 0 and 1 to filter reads with entropy below 137s that value. Higher is more stringent. 137s entropywindow=50 Calculate entropy using a sliding window of this length. 137s entropyk=5 Calculate entropy using kmers of this length. 137s minbasefrequency=0 Discard reads with a minimum base frequency below this. 137s entropytrim=f Values: 137s f: (false) Do not entropy-trim. 137s r: (right) Trim low entropy on the right end only. 137s l: (left) Trim low entropy on the left end only. 137s rl: (both) Trim low entropy on both ends. 137s entropymask=f Values: 137s f: (filter) Discard low-entropy sequences. 137s t: (true) Mask low-entropy parts of sequences with N. 137s lc: Change low-entropy parts of sequences to lowercase. 137s entropymark=f Mark each base with its entropy value. This is on a scale 137s of 0-41 and is reported as quality scores, so the output 137s should be fastq or fasta+qual. 137s NOTE: If set, entropytrim overrides entropymask. 137s 137s Cardinality estimation: 137s cardinality=f (loglog) Count unique kmers using the LogLog algorithm. 137s cardinalityout=f (loglogout) Count unique kmers in output reads. 137s loglogk=31 Use this kmer length for counting. 137s loglogbuckets=2048 Use this many buckets for counting. 137s khist= Kmer frequency histogram; plots number of kmers versus 137s kmer depth. This is approximate. 137s khistout= Kmer frequency histogram for output reads. 137s 137s Java Parameters: 137s 137s -Xmx This will set Java's memory usage, overriding autodetection. 137s -Xmx20g will 137s specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 137s The max is typically 85% of physical memory. 137s -eoom This flag will cause the process to exit if an 137s out-of-memory exception occurs. Requires Java 8u92+. 137s -da Disable assertions. 137s 137s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 137s 137s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 137s java -ea -Xmx1379m -Xms1379m -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 138s 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] 138s Version 39.08 138s 138s Changed from ASCII-33 to ASCII-64 on input quality X (Q55) for base A at lines 1 and 3, position 24 while prescanning. 138s Changed from ASCII-33 to ASCII-64 on input quality X (Q55) for base A at lines 1 and 3, position 24 while prescanning. 138s 0.022 seconds. 138s Initial: 138s Memory: max=1447m, total=1447m, free=1416m, used=31m 138s 138s Input is being processed as paired 138s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 138s Started output streams: 0.029 seconds. 138s Processing time: 0.006 seconds. 138s 138s Input: 8 reads 306 bases. 138s QTrimmed: 0 reads (0.00%) 0 bases (0.00%) 138s Total Removed: 8 reads (100.00%) 306 bases (100.00%) 138s Result: 0 reads (0.00%) 0 bases (0.00%) 138s 138s Time: 0.037 seconds. 138s Reads Processed: 8 0.21k reads/sec 138s Bases Processed: 306 0.01m bases/sec 138s test -r out.fastq.gz 138s 138s # bbnorm 138s bbnorm.sh --version 138s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 138s java -ea -Xmx2759m -Xms2759m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 --version 138s BBTools version 39.08 138s For help, please run the shellscript with no parameters, or look in /docs/. 138s bbnorm.sh --help 138s bbnorm.sh in=sanger_full_range_original_sanger.fastq qin=33 \ 138s out=out3.fastq outt=outt.fastq hist=hist.plt 138s 138s Written by Brian Bushnell 138s Last modified October 19, 2017 138s 138s Description: Normalizes read depth based on kmer counts. 138s Can also error-correct, bin reads by kmer depth, and generate a kmer depth histogram. 138s However, Tadpole has superior error-correction to BBNorm. 138s Please read bbmap/docs/guides/BBNormGuide.txt for more information. 138s 138s Usage: bbnorm.sh in= out= outt= hist= 138s 138s Input parameters: 138s in=null Primary input. Use in2 for paired reads in a second file 138s in2=null Second input file for paired reads in two files 138s extra=null Additional files to use for input (generating hash table) but not for output 138s fastareadlen=2^31 Break up FASTA reads longer than this. Can be useful when processing scaffolded genomes 138s tablereads=-1 Use at most this many reads when building the hashtable (-1 means all) 138s kmersample=1 Process every nth kmer, and skip the rest 138s readsample=1 Process every nth read, and skip the rest 138s 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. 138s qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto. 138s 138s Output parameters: 138s out= File for normalized or corrected reads. Use out2 for paired reads in a second file 138s outt= (outtoss) File for reads that were excluded from primary output 138s reads=-1 Only process this number of reads, then quit (-1 means all) 138s sampleoutput=t Use sampling on output as well as input (not used if sample rates are 1) 138s keepall=f Set to true to keep all reads (e.g. if you just want error correction). 138s 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. 138s Default is false, to prevent confusion about how there can be 0-count kmers. 138s The reason is that based on the 'minq' and 'minprob' settings, some kmers may be excluded from the bloom filter. 138s tmpdir= This will specify a directory for temp files (only needed for multipass runs). If null, they will be written to the output directory. 138s usetempdir=t Allows enabling/disabling of temporary directory; if disabled, temp files will be written to the output directory. 138s qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input). 138s rename=f Rename reads based on their kmer depth. 138s 138s Hashing parameters: 138s k=31 Kmer length (values under 32 are most efficient, but arbitrarily high values are supported) 138s 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. 138s Large values decrease accuracy for a fixed amount of memory, so use the lowest number you can that will still capture highest-depth kmers. 138s hashes=3 Number of times each kmer is hashed and stored. Higher is slower. 138s Higher is MORE accurate if there is enough memory, and LESS accurate if there is not enough memory. 138s 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. 138s prehashes=2 Number of hashes for prefilter. 138s prefilterbits=2 (pbits) Bits per cell in prefilter. 138s prefiltersize=0.35 Fraction of memory to allocate to prefilter. 138s buildpasses=1 More passes can sometimes increase accuracy by iteratively removing low-depth kmers 138s minq=6 Ignore kmers containing bases with quality below this 138s minprob=0.5 Ignore kmers with overall probability of correctness below this 138s 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. 138s 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. 138s 138s Normalization parameters: 138s fixspikes=f (fs) Do a slower, high-precision bloom filter lookup of kmers that appear to have an abnormally high depth due to collisions. 138s target=100 (tgt) Target normalization depth. NOTE: All depth parameters control kmer depth, not read depth. 138s For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1)) 138s maxdepth=-1 (max) Reads will not be downsampled when below this depth, even if they are above the target depth. 138s mindepth=5 (min) Kmers with depth below this number will not be included when calculating the depth of a read. 138s minkmers=15 (mgkpr) Reads must have at least this many kmers over min depth to be retained. Aka 'mingoodkmersperread'. 138s 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. 138s uselowerdepth=t (uld) For pairs, use the depth of the lower read as the depth proxy. 138s deterministic=t (dr) Generate random numbers deterministically to ensure identical output between multiple runs. May decrease speed with a huge number of threads. 138s passes=2 (p) 1 pass is the basic mode. 2 passes (default) allows greater accuracy, error detection, better contol of output depth. 138s 138s Error detection parameters: 138s hdp=90.0 (highdepthpercentile) Position in sorted kmer depth array used as proxy of a read's high kmer depth. 138s ldp=25.0 (lowdepthpercentile) Position in sorted kmer depth array used as proxy of a read's low kmer depth. 138s tossbadreads=f (tbr) Throw away reads detected as containing errors. 138s requirebothbad=f (rbb) Only toss bad pairs if both reads are bad. 138s 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. 138s highthresh=12 (ht) Threshold for high kmer. A high kmer at this or above are considered non-error. 138s lowthresh=3 (lt) Threshold for low kmer. Kmers at this and below are always considered errors. 138s 138s Error correction parameters: 138s ecc=f Set to true to correct errors. NOTE: Tadpole is now preferred for ecc as it does a better job. 138s ecclimit=3 Correct up to this many errors per read. If more are detected, the read will remain unchanged. 138s errorcorrectratio=140 (ecr) Adjacent kmers with a depth ratio of at least this much between will be classified as an error. 138s echighthresh=22 (echt) Threshold for high kmer. A kmer at this or above may be considered non-error. 138s eclowthresh=2 (eclt) Threshold for low kmer. Kmers at this and below are considered errors. 138s eccmaxqual=127 Do not correct bases with quality above this value. 138s aec=f (aggressiveErrorCorrection) Sets more aggressive values of ecr=100, ecclimit=7, echt=16, eclt=3. 138s cec=f (conservativeErrorCorrection) Sets more conservative values of ecr=180, ecclimit=2, echt=30, eclt=1, sl=4, pl=4. 138s meo=f (markErrorsOnly) Marks errors by reducing quality value of suspected errors; does not correct anything. 138s mue=t (markUncorrectableErrors) Marks errors only on uncorrectable reads; requires 'ecc=t'. 138s overlap=f (ecco) Error correct by read overlap. 138s 138s Depth binning parameters: 138s lowbindepth=10 (lbd) Cutoff for low depth bin. 138s highbindepth=80 (hbd) Cutoff for high depth bin. 138s outlow= Pairs in which both reads have a median below lbd go into this file. 138s outhigh= Pairs in which both reads have a median above hbd go into this file. 138s outmid= All other pairs go into this file. 138s 138s Histogram parameters: 138s hist= Specify a file to write the input kmer depth histogram. 138s histout= Specify a file to write the output kmer depth histogram. 138s histcol=3 (histogramcolumns) Number of histogram columns, 2 or 3. 138s pzc=f (printzerocoverage) Print lines in the histogram with zero coverage. 138s histlen=1048576 Max kmer depth displayed in histogram. Also affects statistics displayed, but does not affect normalization. 138s 138s Peak calling parameters: 138s peaks= Write the peaks to this file. Default is stdout. 138s minHeight=2 (h) Ignore peaks shorter than this. 138s minVolume=5 (v) Ignore peaks with less area than this. 138s minWidth=3 (w) Ignore peaks narrower than this. 138s minPeak=2 (minp) Ignore peaks with an X-value below this. 138s maxPeak=BIG (maxp) Ignore peaks with an X-value above this. 138s maxPeakCount=8 (maxpc) Print up to this many peaks (prioritizing height). 138s 138s Java Parameters: 138s -Xmx This will set Java's memory usage, overriding autodetection. 138s -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 138s The max is typically 85% of physical memory. 138s -eoom This flag will cause the process to exit if an 138s out-of-memory exception occurs. Requires Java 8u92+. 138s -da Disable assertions. 138s 138s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 138s 138s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 138s java -ea -Xmx2759m -Xms2759m -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 138s Executing jgi.KmerNormalize [bits=32, in=sanger_full_range_original_sanger.fastq, qin=33, out=out3.fastq, outt=outt.fastq, hist=hist.plt] 138s 138s 138s *********** Pass 1 ********** 138s 138s 138s Settings: 138s threads: 4 138s k: 31 138s deterministic: true 138s toss error reads: false 138s passes: 1 138s bits per cell: 16 138s cells: 1020.77M 138s hashes: 3 138s base min quality: 5 138s kmer min prob: 0.5 138s 138s target depth: 400 138s min depth: 3 138s max depth: 500 138s min good kmers: 15 138s depth percentile: 64.8 138s ignore dupe kmers: true 138s fix spikes: false 138s histogram length: 65536 138s print zero cov: false 138s 139s Made hash table: hashes = 3 mem = 1.90 GB cells = 1020.47M used = 0.000% 139s 139s Estimated unique kmers: 4 139s 139s Table creation time: 0.862 seconds. 139s Started output threads. 139s Started output threads. 139s Table read time: 0.011 seconds. 17.78 kb/sec 139s Total reads in: 2 0.000% Kept 139s Total bases in: 188 0.000% Kept 139s Error reads in: 2 100.000% 139s Error type 1: 2 100.000% 139s Error type 2: 0 0.000% 139s Error type 3: 0 0.000% 139s 139s Wrote histogram to hist.plt 139s Total kmers counted: 128 139s Total unique kmer count: 128 139s Includes forward kmers only. 139s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 139s The most accurate value is the greater of the two. 139s 139s Percent unique: 100.00% 139s Depth average: 1.00 (unique kmers) 139s Depth median: 1 (unique kmers) 139s Depth standard deviation: 0.00 (unique kmers) 139s Corrected depth average: 0.00 139s 139s Depth average: 1.00 (all kmers) 139s Depth median: 1 (all kmers) 139s Depth standard deviation: 0.00 (all kmers) 139s 139s Approx. read depth median: 1.47 139s 139s *********** Pass 2 ********** 139s 139s 139s Settings: 139s threads: 4 139s k: 31 139s deterministic: true 139s toss error reads: false 139s passes: 1 139s bits per cell: 16 139s cells: 1020.77M 139s hashes: 3 139s base min quality: 5 139s kmer min prob: 0.5 139s 139s target depth: 100 139s min depth: 5 139s max depth: 100 139s min good kmers: 15 139s depth percentile: 54.0 139s ignore dupe kmers: true 139s fix spikes: false 139s histogram length: 65536 139s 140s Made hash table: hashes = 3 mem = 1.90 GB cells = 1020.47M used = 0.000% 140s 140s Estimated unique kmers: 0 140s 140s Table creation time: 0.396 seconds. 140s Started output threads. 140s Started output threads. 140s Table read time: 0.002 seconds. 0.00 kb/sec 140s Total reads in: 0 NaN% Kept 140s Total bases in: 0 NaN% Kept 140s Error reads in: 0 NaN% 140s Error type 1: 0 NaN% 140s Error type 2: 0 NaN% 140s Error type 3: 0 NaN% 140s Total kmers counted: 0 140s Total unique kmer count: 0 140s Includes forward kmers only. 140s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 140s The most accurate value is the greater of the two. 140s 140s Percent unique: NaN% 140s Depth average: NaN (unique kmers) 140s Depth median: 0 (unique kmers) 140s Depth standard deviation: NaN (unique kmers) 140s Corrected depth average: NaN 140s 140s Depth average: NaN (all kmers) 140s Depth median: 0 (all kmers) 140s Depth standard deviation: 0.00 (all kmers) 140s 140s Approx. read depth median: NaN 140s 140s Removing temp files. 140s 140s Total time: 1.373 seconds. 0.14 kb/sec 140s test -r out3.fastq 140s test -r outt.fastq 140s test -r hist.plt 140s bbnorm.sh in=illumina_full_range_original_illumina.fastq qin=64 \ 140s out=out4.fastq outt=outt2.fastq hist=hist2.plt 140s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 140s java -ea -Xmx2759m -Xms2759m -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 140s Executing jgi.KmerNormalize [bits=32, in=illumina_full_range_original_illumina.fastq, qin=64, out=out4.fastq, outt=outt2.fastq, hist=hist2.plt] 140s 140s 140s *********** Pass 1 ********** 140s 140s 140s Settings: 140s threads: 4 140s k: 31 140s deterministic: true 140s toss error reads: false 140s passes: 1 140s bits per cell: 16 140s cells: 1020.77M 140s hashes: 3 140s base min quality: 5 140s kmer min prob: 0.5 140s 140s target depth: 400 140s min depth: 3 140s max depth: 500 140s min good kmers: 15 140s depth percentile: 64.8 140s ignore dupe kmers: true 140s fix spikes: false 140s histogram length: 65536 140s print zero cov: false 140s 141s Made hash table: hashes = 3 mem = 1.90 GB cells = 1020.47M used = 0.000% 141s 141s Estimated unique kmers: 4 141s 141s Table creation time: 0.800 seconds. 141s Started output threads. 141s Started output threads. 141s Table read time: 0.008 seconds. 15.76 kb/sec 141s Total reads in: 2 0.000% Kept 141s Total bases in: 126 0.000% Kept 141s Error reads in: 2 100.000% 141s Error type 1: 2 100.000% 141s Error type 2: 0 0.000% 141s Error type 3: 0 0.000% 141s 141s Wrote histogram to hist2.plt 141s Total kmers counted: 66 141s Total unique kmer count: 66 141s Includes forward kmers only. 141s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 141s The most accurate value is the greater of the two. 141s 141s Percent unique: 100.00% 141s Depth average: 1.00 (unique kmers) 141s Depth median: 1 (unique kmers) 141s Depth standard deviation: 0.00 (unique kmers) 141s Corrected depth average: 0.00 141s 141s Depth average: 1.00 (all kmers) 141s Depth median: 1 (all kmers) 141s Depth standard deviation: 0.00 (all kmers) 141s 141s Approx. read depth median: 1.91 141s 141s *********** Pass 2 ********** 141s 141s 141s Settings: 141s threads: 4 141s k: 31 141s deterministic: true 141s toss error reads: false 141s passes: 1 141s bits per cell: 16 141s cells: 1020.77M 141s hashes: 3 141s base min quality: 5 141s kmer min prob: 0.5 141s 141s target depth: 100 141s min depth: 5 141s max depth: 100 141s min good kmers: 15 141s depth percentile: 54.0 141s ignore dupe kmers: true 141s fix spikes: false 141s histogram length: 65536 141s 141s Made hash table: hashes = 3 mem = 1.90 GB cells = 1020.47M used = 0.000% 141s 141s Estimated unique kmers: 0 141s 141s Table creation time: 0.294 seconds. 141s Started output threads. 141s Started output threads. 141s Table read time: 0.002 seconds. 0.00 kb/sec 141s Total reads in: 0 NaN% Kept 141s Total bases in: 0 NaN% Kept 141s Error reads in: 0 NaN% 141s Error type 1: 0 NaN% 141s Error type 2: 0 NaN% 141s Error type 3: 0 NaN% 141s Total kmers counted: 0 141s Total unique kmer count: 0 141s Includes forward kmers only. 141s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 141s The most accurate value is the greater of the two. 141s 141s Percent unique: NaN% 141s Depth average: NaN (unique kmers) 141s Depth median: 0 (unique kmers) 141s Depth standard deviation: NaN (unique kmers) 141s Corrected depth average: NaN 141s 141s Depth average: NaN (all kmers) 141s Depth median: 0 (all kmers) 141s Depth standard deviation: 0.00 (all kmers) 141s 141s Approx. read depth median: NaN 141s 141s Removing temp files. 141s 141s Total time: 1.204 seconds. 0.10 kb/sec 141s test -r out4.fastq 141s test -r outt2.fastq 141s test -r hist2.plt 142s autopkgtest [02:52:59]: test run-unit-test: -----------------------] 142s run-unit-test PASS 142s autopkgtest [02:52:59]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 143s autopkgtest [02:53:00]: @@@@@@@@@@@@@@@@@@@@ summary 143s run-unit-test PASS 157s nova [W] Skipping flock in bos03-arm64 157s Creating nova instance adt-plucky-arm64-bbmap-20241102-025037-juju-7f2275-prod-proposed-migration-environment-2-9268fbf3-0ea2-4a39-bdf1-054c51c50d05 from image adt/ubuntu-plucky-arm64-server-20241101.img (UUID 520a937f-514a-4e80-b76b-163a8c247e3e)...