0s autopkgtest [00:53:06]: starting date and time: 2025-11-02 00:53:06+0000 0s autopkgtest [00:53:06]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [00:53:06]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.67w0ux7s/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:openjdk-26,src:jtreg8 --apt-upgrade bbmap --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=openjdk-26/26~22ea-2 jtreg8/8.1+1+ds1-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu4-ram8-disk100 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-5.secgroup --name adt-resolute-amd64-bbmap-20251102-005306-juju-7f2275-prod-proposed-migration-environment-2-c66aef97-2ef6-4139-8620-3f941c74f4b9 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-amd64-bbmap-20251102-005306-juju-7f2275-prod-proposed-migration-environment-2-c66aef97-2ef6-4139-8620-3f941c74f4b9 from image adt/ubuntu-resolute-amd64-server-20251101.img (UUID 5314c6c7-871e-4b3b-bdf9-379b5cd19a50)... 60s autopkgtest [00:54:06]: testbed dpkg architecture: amd64 60s autopkgtest [00:54:06]: testbed apt version: 3.1.11 60s autopkgtest [00:54:06]: @@@@@@@@@@@@@@@@@@@@ test bed setup 61s autopkgtest [00:54:07]: testbed release detected to be: None 61s autopkgtest [00:54:07]: updating testbed package index (apt update) 62s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB] 62s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 62s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 62s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 62s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [9848 B] 62s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [127 kB] 62s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1497 kB] 63s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [43.5 kB] 63s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [196 kB] 63s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [130 kB] 63s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [4744 B] 63s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3744 B] 63s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [64.6 kB] 63s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [336 B] 63s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [1158 kB] 63s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [453 kB] 63s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [37.2 kB] 63s Get:18 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [31.2 kB] 63s Get:19 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [8844 B] 63s Get:20 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [1752 B] 64s Fetched 3854 kB in 2s (2026 kB/s) 65s Reading package lists... 66s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 66s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 66s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 66s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 67s Reading package lists... 67s Reading package lists... 68s Building dependency tree... 68s Reading state information... 68s Calculating upgrade... 68s The following packages will be upgraded: 68s gcc-15-base gcc-15-base:i386 libatomic1 libgcc-s1 libgcc-s1:i386 libstdc++6 68s publicsuffix 68s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 68s Need to get 1249 kB of archives. 68s After this operation, 14.3 kB of additional disk space will be used. 68s Get:1 http://ftpmaster.internal/ubuntu resolute/main i386 gcc-15-base i386 15.2.0-7ubuntu1 [58.4 kB] 68s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15-base amd64 15.2.0-7ubuntu1 [58.4 kB] 68s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-s1 amd64 15.2.0-7ubuntu1 [78.0 kB] 68s Get:4 http://ftpmaster.internal/ubuntu resolute/main i386 libgcc-s1 i386 15.2.0-7ubuntu1 [94.1 kB] 68s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++6 amd64 15.2.0-7ubuntu1 [813 kB] 69s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libatomic1 amd64 15.2.0-7ubuntu1 [10.5 kB] 69s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 publicsuffix all 20251016.1743-0.1 [136 kB] 69s dpkg-preconfigure: unable to re-open stdin: No such file or directory 69s Fetched 1249 kB in 1s (1350 kB/s) 69s (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 ... 78534 files and directories currently installed.) 69s Preparing to unpack .../gcc-15-base_15.2.0-7ubuntu1_amd64.deb ... 70s De-configuring gcc-15-base:i386 (15.2.0-5ubuntu1), to allow configuration of gcc-15-base:amd64 (15.2.0-7ubuntu1) ... 70s Unpacking gcc-15-base:amd64 (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 70s Preparing to unpack .../gcc-15-base_15.2.0-7ubuntu1_i386.deb ... 70s Unpacking gcc-15-base:i386 (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 70s Preparing to unpack .../libgcc-s1_15.2.0-7ubuntu1_i386.deb ... 70s De-configuring libgcc-s1:amd64 (15.2.0-5ubuntu1), to allow configuration of libgcc-s1:i386 (15.2.0-7ubuntu1) ... 70s Unpacking libgcc-s1:i386 (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 70s Preparing to unpack .../libgcc-s1_15.2.0-7ubuntu1_amd64.deb ... 70s Unpacking libgcc-s1:amd64 (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 70s Setting up gcc-15-base:amd64 (15.2.0-7ubuntu1) ... 70s Setting up libgcc-s1:amd64 (15.2.0-7ubuntu1) ... 70s (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 ... 78534 files and directories currently installed.) 70s Preparing to unpack .../libstdc++6_15.2.0-7ubuntu1_amd64.deb ... 70s Unpacking libstdc++6:amd64 (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 70s Preparing to unpack .../libatomic1_15.2.0-7ubuntu1_amd64.deb ... 70s Unpacking libatomic1:amd64 (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 70s Preparing to unpack .../publicsuffix_20251016.1743-0.1_all.deb ... 70s Unpacking publicsuffix (20251016.1743-0.1) over (20250328.1952-0.1) ... 70s Setting up libatomic1:amd64 (15.2.0-7ubuntu1) ... 70s Setting up gcc-15-base:i386 (15.2.0-7ubuntu1) ... 70s Setting up publicsuffix (20251016.1743-0.1) ... 70s Setting up libstdc++6:amd64 (15.2.0-7ubuntu1) ... 70s Setting up libgcc-s1:i386 (15.2.0-7ubuntu1) ... 70s Processing triggers for libc-bin (2.42-0ubuntu3) ... 70s autopkgtest [00:54:16]: upgrading testbed (apt dist-upgrade and autopurge) 70s Reading package lists... 71s Building dependency tree... 71s Reading state information... 71s Calculating upgrade... 71s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 71s Reading package lists... 71s Building dependency tree... 71s Reading state information... 72s Solving dependencies... 72s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 74s autopkgtest [00:54:20]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 10:00:33 UTC 2025 74s autopkgtest [00:54:20]: @@@@@@@@@@@@@@@@@@@@ apt-source bbmap 78s Get:1 http://ftpmaster.internal/ubuntu resolute/universe bbmap 39.20+dfsg-2 (dsc) [2286 B] 78s Get:2 http://ftpmaster.internal/ubuntu resolute/universe bbmap 39.20+dfsg-2 (tar) [5748 kB] 78s Get:3 http://ftpmaster.internal/ubuntu resolute/universe bbmap 39.20+dfsg-2 (diff) [26.8 kB] 78s gpgv: Signature made Sun Apr 6 17:54:51 2025 UTC 78s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 78s gpgv: issuer "emollier@debian.org" 78s gpgv: Can't check signature: No public key 78s dpkg-source: warning: cannot verify inline signature for ./bbmap_39.20+dfsg-2.dsc: no acceptable signature found 79s autopkgtest [00:54:25]: testing package bbmap version 39.20+dfsg-2 79s autopkgtest [00:54:25]: build not needed 84s autopkgtest [00:54:30]: test run-unit-test: preparing testbed 84s Reading package lists... 84s Building dependency tree... 84s Reading state information... 84s Solving dependencies... 84s The following NEW packages will be installed: 84s bbmap bbmap-jni ca-certificates-java default-jre-headless java-common 84s libapache-pom-java libcommons-cli-java libcommons-codec-java 84s libcommons-io-java libcommons-parent-java libjpeg-turbo8 libjpeg8 84s libjs-jquery libjs-sphinxdoc libjs-underscore liblcms2-2 liblog4j1.2-java 84s libmpj-java libnspr4 libnss3 libpcsclite1 openjdk-21-jre-headless 84s python-biopython-doc 85s 0 upgraded, 23 newly installed, 0 to remove and 0 not upgraded. 85s Need to get 79.6 MB of archives. 85s After this operation, 264 MB of additional disk space will be used. 85s Get:1 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcommons-cli-java all 1.6.0-1 [59.9 kB] 85s Get:2 http://ftpmaster.internal/ubuntu resolute/universe amd64 libapache-pom-java all 33-2 [5874 B] 85s Get:3 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcommons-parent-java all 56-1 [10.7 kB] 85s Get:4 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcommons-codec-java all 1.18.0-1 [303 kB] 85s Get:5 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcommons-io-java all 2.19.0-1 [491 kB] 85s Get:6 http://ftpmaster.internal/ubuntu resolute/universe amd64 liblog4j1.2-java all 1.2.17-11 [439 kB] 85s Get:7 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmpj-java all 0.44+dfsg-4 [443 kB] 85s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 ca-certificates-java all 20240118 [11.6 kB] 85s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 java-common all 0.76 [6852 B] 85s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 86s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu2 [152 kB] 86s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 86s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libnspr4 amd64 2:4.36-1ubuntu2 [118 kB] 86s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libnss3 amd64 2:3.114-1 [1483 kB] 86s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcsclite1 amd64 2.3.3-1 [24.0 kB] 86s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 openjdk-21-jre-headless amd64 21.0.9+10-1 [46.5 MB] 89s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 default-jre-headless amd64 2:1.21-76 [3178 B] 89s Get:18 http://ftpmaster.internal/ubuntu resolute/universe amd64 bbmap all 39.20+dfsg-2 [10.6 MB] 89s Get:19 http://ftpmaster.internal/ubuntu resolute/universe amd64 bbmap-jni amd64 39.20+dfsg-2 [28.6 kB] 89s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 89s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 89s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 89s Get:23 http://ftpmaster.internal/ubuntu resolute/universe amd64 python-biopython-doc all 1.85+dfsg-4 [18.2 MB] 90s Fetched 79.6 MB in 6s (14.1 MB/s) 91s Selecting previously unselected package libcommons-cli-java. 91s (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 ... 78534 files and directories currently installed.) 91s Preparing to unpack .../00-libcommons-cli-java_1.6.0-1_all.deb ... 91s Unpacking libcommons-cli-java (1.6.0-1) ... 91s Selecting previously unselected package libapache-pom-java. 91s Preparing to unpack .../01-libapache-pom-java_33-2_all.deb ... 91s Unpacking libapache-pom-java (33-2) ... 91s Selecting previously unselected package libcommons-parent-java. 91s Preparing to unpack .../02-libcommons-parent-java_56-1_all.deb ... 91s Unpacking libcommons-parent-java (56-1) ... 91s Selecting previously unselected package libcommons-codec-java. 91s Preparing to unpack .../03-libcommons-codec-java_1.18.0-1_all.deb ... 91s Unpacking libcommons-codec-java (1.18.0-1) ... 91s Selecting previously unselected package libcommons-io-java. 91s Preparing to unpack .../04-libcommons-io-java_2.19.0-1_all.deb ... 91s Unpacking libcommons-io-java (2.19.0-1) ... 91s Selecting previously unselected package liblog4j1.2-java. 91s Preparing to unpack .../05-liblog4j1.2-java_1.2.17-11_all.deb ... 91s Unpacking liblog4j1.2-java (1.2.17-11) ... 91s Selecting previously unselected package libmpj-java. 91s Preparing to unpack .../06-libmpj-java_0.44+dfsg-4_all.deb ... 91s Unpacking libmpj-java (0.44+dfsg-4) ... 91s Selecting previously unselected package ca-certificates-java. 91s Preparing to unpack .../07-ca-certificates-java_20240118_all.deb ... 91s Unpacking ca-certificates-java (20240118) ... 91s Selecting previously unselected package java-common. 91s Preparing to unpack .../08-java-common_0.76_all.deb ... 91s Unpacking java-common (0.76) ... 91s Selecting previously unselected package liblcms2-2:amd64. 91s Preparing to unpack .../09-liblcms2-2_2.16-2_amd64.deb ... 91s Unpacking liblcms2-2:amd64 (2.16-2) ... 91s Selecting previously unselected package libjpeg-turbo8:amd64. 91s Preparing to unpack .../10-libjpeg-turbo8_2.1.5-4ubuntu2_amd64.deb ... 91s Unpacking libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 91s Selecting previously unselected package libjpeg8:amd64. 91s Preparing to unpack .../11-libjpeg8_8c-2ubuntu11_amd64.deb ... 91s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 91s Selecting previously unselected package libnspr4:amd64. 91s Preparing to unpack .../12-libnspr4_2%3a4.36-1ubuntu2_amd64.deb ... 91s Unpacking libnspr4:amd64 (2:4.36-1ubuntu2) ... 91s Selecting previously unselected package libnss3:amd64. 91s Preparing to unpack .../13-libnss3_2%3a3.114-1_amd64.deb ... 91s Unpacking libnss3:amd64 (2:3.114-1) ... 91s Selecting previously unselected package libpcsclite1:amd64. 91s Preparing to unpack .../14-libpcsclite1_2.3.3-1_amd64.deb ... 91s Unpacking libpcsclite1:amd64 (2.3.3-1) ... 91s Selecting previously unselected package openjdk-21-jre-headless:amd64. 91s Preparing to unpack .../15-openjdk-21-jre-headless_21.0.9+10-1_amd64.deb ... 91s Unpacking openjdk-21-jre-headless:amd64 (21.0.9+10-1) ... 92s Selecting previously unselected package default-jre-headless. 92s Preparing to unpack .../16-default-jre-headless_2%3a1.21-76_amd64.deb ... 92s Unpacking default-jre-headless (2:1.21-76) ... 92s Selecting previously unselected package bbmap. 92s Preparing to unpack .../17-bbmap_39.20+dfsg-2_all.deb ... 92s Unpacking bbmap (39.20+dfsg-2) ... 92s Selecting previously unselected package bbmap-jni. 92s Preparing to unpack .../18-bbmap-jni_39.20+dfsg-2_amd64.deb ... 92s Unpacking bbmap-jni (39.20+dfsg-2) ... 92s Selecting previously unselected package libjs-jquery. 92s Preparing to unpack .../19-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 92s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 92s Selecting previously unselected package libjs-underscore. 92s Preparing to unpack .../20-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 92s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 92s Selecting previously unselected package libjs-sphinxdoc. 92s Preparing to unpack .../21-libjs-sphinxdoc_8.2.3-1ubuntu2_all.deb ... 92s Unpacking libjs-sphinxdoc (8.2.3-1ubuntu2) ... 92s Selecting previously unselected package python-biopython-doc. 92s Preparing to unpack .../22-python-biopython-doc_1.85+dfsg-4_all.deb ... 92s Unpacking python-biopython-doc (1.85+dfsg-4) ... 92s Setting up liblcms2-2:amd64 (2.16-2) ... 92s Setting up java-common (0.76) ... 92s Setting up libcommons-cli-java (1.6.0-1) ... 92s Setting up liblog4j1.2-java (1.2.17-11) ... 92s Setting up libnspr4:amd64 (2:4.36-1ubuntu2) ... 92s Setting up libapache-pom-java (33-2) ... 92s Setting up libpcsclite1:amd64 (2.3.3-1) ... 92s Setting up libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 92s Setting up bbmap-jni (39.20+dfsg-2) ... 92s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 92s Setting up ca-certificates-java (20240118) ... 92s No JRE found. Skipping Java certificates setup. 92s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 92s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 92s Setting up libcommons-parent-java (56-1) ... 92s Setting up libnss3:amd64 (2:3.114-1) ... 92s Setting up libjs-sphinxdoc (8.2.3-1ubuntu2) ... 92s Setting up python-biopython-doc (1.85+dfsg-4) ... 92s Setting up libcommons-codec-java (1.18.0-1) ... 92s Setting up openjdk-21-jre-headless:amd64 (21.0.9+10-1) ... 92s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode 92s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 92s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 92s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 92s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 92s Setting up libcommons-io-java (2.19.0-1) ... 92s Setting up libmpj-java (0.44+dfsg-4) ... 92s Processing triggers for libc-bin (2.42-0ubuntu3) ... 92s Processing triggers for man-db (2.13.1-1) ... 93s Processing triggers for ca-certificates-java (20240118) ... 94s Adding debian:ACCVRAIZ1.pem 94s Adding debian:AC_RAIZ_FNMT-RCM.pem 94s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 94s Adding debian:ANF_Secure_Server_Root_CA.pem 94s Adding debian:Actalis_Authentication_Root_CA.pem 94s Adding debian:AffirmTrust_Commercial.pem 94s Adding debian:AffirmTrust_Networking.pem 94s Adding debian:AffirmTrust_Premium.pem 94s Adding debian:AffirmTrust_Premium_ECC.pem 94s Adding debian:Amazon_Root_CA_1.pem 94s Adding debian:Amazon_Root_CA_2.pem 94s Adding debian:Amazon_Root_CA_3.pem 94s Adding debian:Amazon_Root_CA_4.pem 94s Adding debian:Atos_TrustedRoot_2011.pem 94s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 94s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 94s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 94s Adding debian:BJCA_Global_Root_CA1.pem 94s Adding debian:BJCA_Global_Root_CA2.pem 94s Adding debian:Baltimore_CyberTrust_Root.pem 94s Adding debian:Buypass_Class_2_Root_CA.pem 94s Adding debian:Buypass_Class_3_Root_CA.pem 94s Adding debian:CA_Disig_Root_R2.pem 94s Adding debian:CFCA_EV_ROOT.pem 94s Adding debian:COMODO_Certification_Authority.pem 94s Adding debian:COMODO_ECC_Certification_Authority.pem 94s Adding debian:COMODO_RSA_Certification_Authority.pem 94s Adding debian:Certainly_Root_E1.pem 94s Adding debian:Certainly_Root_R1.pem 94s Adding debian:Certigna.pem 94s Adding debian:Certigna_Root_CA.pem 94s Adding debian:Certum_EC-384_CA.pem 94s Adding debian:Certum_Trusted_Network_CA.pem 94s Adding debian:Certum_Trusted_Network_CA_2.pem 94s Adding debian:Certum_Trusted_Root_CA.pem 94s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 94s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 94s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 94s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 94s Adding debian:Comodo_AAA_Services_root.pem 94s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 94s Adding debian:D-TRUST_BR_Root_CA_2_2023.pem 94s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 94s Adding debian:D-TRUST_EV_Root_CA_2_2023.pem 94s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 94s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 94s Adding debian:DigiCert_Assured_ID_Root_CA.pem 94s Adding debian:DigiCert_Assured_ID_Root_G2.pem 94s Adding debian:DigiCert_Assured_ID_Root_G3.pem 94s Adding debian:DigiCert_Global_Root_CA.pem 94s Adding debian:DigiCert_Global_Root_G2.pem 94s Adding debian:DigiCert_Global_Root_G3.pem 94s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 94s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 94s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 94s Adding debian:DigiCert_Trusted_Root_G4.pem 94s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 94s Adding debian:Entrust_Root_Certification_Authority.pem 94s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 94s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 94s Adding debian:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem 94s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 94s Adding debian:GLOBALTRUST_2020.pem 94s Adding debian:GTS_Root_R1.pem 94s Adding debian:GTS_Root_R2.pem 94s Adding debian:GTS_Root_R3.pem 94s Adding debian:GTS_Root_R4.pem 94s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 94s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 94s Adding debian:GlobalSign_Root_CA.pem 94s Adding debian:GlobalSign_Root_CA_-_R3.pem 94s Adding debian:GlobalSign_Root_CA_-_R6.pem 94s Adding debian:GlobalSign_Root_E46.pem 94s Adding debian:GlobalSign_Root_R46.pem 94s Adding debian:Go_Daddy_Class_2_CA.pem 94s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 94s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 94s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 94s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 94s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 94s Adding debian:HiPKI_Root_CA_-_G1.pem 94s Adding debian:Hongkong_Post_Root_CA_3.pem 94s Adding debian:ISRG_Root_X1.pem 94s Adding debian:ISRG_Root_X2.pem 94s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 94s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 94s Adding debian:Izenpe.com.pem 94s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 94s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 94s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 94s Adding debian:NAVER_Global_Root_Certification_Authority.pem 94s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 94s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 94s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 94s Adding debian:QuoVadis_Root_CA_1_G3.pem 94s Adding debian:QuoVadis_Root_CA_2.pem 94s Adding debian:QuoVadis_Root_CA_2_G3.pem 94s Adding debian:QuoVadis_Root_CA_3.pem 94s Adding debian:QuoVadis_Root_CA_3_G3.pem 94s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 94s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 94s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 94s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 94s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 94s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 94s Adding debian:SZAFIR_ROOT_CA2.pem 94s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 94s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 94s Adding debian:SecureSign_Root_CA12.pem 94s Adding debian:SecureSign_Root_CA14.pem 94s Adding debian:SecureSign_Root_CA15.pem 94s Adding debian:SecureTrust_CA.pem 94s Adding debian:Secure_Global_CA.pem 94s Adding debian:Security_Communication_ECC_RootCA1.pem 94s Adding debian:Security_Communication_RootCA2.pem 94s Adding debian:Starfield_Class_2_CA.pem 94s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 94s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 94s Adding debian:SwissSign_Gold_CA_-_G2.pem 94s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 94s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 94s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 94s Adding debian:TWCA_CYBER_Root_CA.pem 94s Adding debian:TWCA_Global_Root_CA.pem 94s Adding debian:TWCA_Root_Certification_Authority.pem 94s Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem 94s Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem 94s Adding debian:TeliaSonera_Root_CA_v1.pem 94s Adding debian:Telia_Root_CA_v2.pem 94s Adding debian:TrustAsia_Global_Root_CA_G3.pem 94s Adding debian:TrustAsia_Global_Root_CA_G4.pem 94s Adding debian:Trustwave_Global_Certification_Authority.pem 94s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 94s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 94s Adding debian:TunTrust_Root_CA.pem 94s Adding debian:UCA_Extended_Validation_Root.pem 94s Adding debian:UCA_Global_G2_Root.pem 94s Adding debian:USERTrust_ECC_Certification_Authority.pem 94s Adding debian:USERTrust_RSA_Certification_Authority.pem 94s Adding debian:XRamp_Global_CA_Root.pem 94s Adding debian:certSIGN_ROOT_CA.pem 94s Adding debian:certSIGN_Root_CA_G2.pem 94s Adding debian:e-Szigno_Root_CA_2017.pem 94s Adding debian:ePKI_Root_Certification_Authority.pem 94s Adding debian:emSign_ECC_Root_CA_-_C3.pem 94s Adding debian:emSign_ECC_Root_CA_-_G3.pem 94s Adding debian:emSign_Root_CA_-_C1.pem 94s Adding debian:emSign_Root_CA_-_G1.pem 94s Adding debian:vTrus_ECC_Root_CA.pem 94s Adding debian:vTrus_Root_CA.pem 94s done. 94s Setting up bbmap (39.20+dfsg-2) ... 94s Setting up default-jre-headless (2:1.21-76) ... 95s autopkgtest [00:54:41]: test run-unit-test: [----------------------- 96s 96s # bbmap 96s bbmap.sh --version 96s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 96s java -ea -Xmx2845m -Xms2845m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 --version 96s BBTools version 39.20 96s For help, please run the shellscript with no parameters, or look in /docs/. 96s bbmap.sh --help 96s 96s BBMap 96s Written by Brian Bushnell, from Dec. 2010 - present 96s Last modified September 15, 2022 96s 96s Description: Fast and accurate splice-aware read aligner. 96s Please read bbmap/docs/guides/BBMapGuide.txt for more information. 96s 96s To index: bbmap.sh ref= 96s To map: bbmap.sh in= out= 96s To map without writing an index: 96s bbmap.sh ref= in= out= nodisk 96s 96s in=stdin will accept reads from standard in, and out=stdout will write to 96s standard out, but file extensions are still needed to specify the format of the 96s input and output files e.g. in=stdin.fa.gz will read gzipped fasta from 96s standard in; out=stdout.sam.gz will write gzipped sam. 96s 96s Indexing Parameters (required when building the index): 96s nodisk=f Set to true to build index in memory and write nothing 96s to disk except output. 96s ref= Specify the reference sequence. Only do this ONCE, 96s when building the index (unless using 'nodisk'). 96s build=1 If multiple references are indexed in the same directory, 96s each needs a unique numeric ID (unless using 'nodisk'). 96s k=13 Kmer length, range 8-15. Longer is faster but uses 96s more memory. Shorter is more sensitive. 96s If indexing and mapping are done in two steps, K should 96s be specified each time. 96s path=<.> Specify the location to write the index, if you don't 96s want it in the current working directory. 96s usemodulo=f Throw away ~80% of kmers based on remainder modulo a 96s number (reduces RAM by 50% and sensitivity slightly). 96s Should be enabled both when building the index AND 96s when mapping. 96s rebuild=f Force a rebuild of the index (ref= should be set). 96s 96s Input Parameters: 96s build=1 Designate index to use. Corresponds to the number 96s specified when building the index. 96s in= Primary reads input; required parameter. 96s in2= For paired reads in two files. 96s interleaved=auto True forces paired/interleaved input; false forces 96s single-ended mapping. If not specified, interleaved 96s status will be autodetected from read names. 96s fastareadlen=500 Break up FASTA reads longer than this. Max is 500 for 96s BBMap and 6000 for BBMapPacBio. Only works for FASTA 96s input (use 'maxlen' for FASTQ input). The default for 96s bbmap.sh is 500, and for mapPacBio.sh is 6000. 96s unpigz=f Spawn a pigz (parallel gzip) process for faster 96s decompression than using Java. 96s Requires pigz to be installed. 96s touppercase=t (tuc) Convert lowercase letters in reads to upper case 96s (otherwise they will not match the reference). 96s 96s Sampling Parameters: 96s 96s reads=-1 Set to a positive number N to only process the first N 96s reads (or pairs), then quit. -1 means use all reads. 96s samplerate=1 Set to a number from 0 to 1 to randomly select that 96s fraction of reads for mapping. 1 uses all reads. 96s skipreads=0 Set to a number N to skip the first N reads (or pairs), 96s then map the rest. 96s 96s Mapping Parameters: 96s fast=f This flag is a macro which sets other paramters to run 96s faster, at reduced sensitivity. Bad for RNA-seq. 96s slow=f This flag is a macro which sets other paramters to run 96s slower, at greater sensitivity. 'vslow' is even slower. 96s maxindel=16000 Don't look for indels longer than this. Lower is faster. 96s Set to >=100k for RNAseq with long introns like mammals. 96s strictmaxindel=f When enabled, do not allow indels longer than 'maxindel'. 96s By default these are not sought, but may be found anyway. 96s tipsearch=100 Look this far for read-end deletions with anchors 96s shorter than K, using brute force. 96s minid=0.76 Approximate minimum alignment identity to look for. 96s Higher is faster and less sensitive. 96s minhits=1 Minimum number of seed hits required for candidate sites. 96s Higher is faster. 96s local=f Set to true to use local, rather than global, alignments. 96s This will soft-clip ugly ends of poor alignments. 96s perfectmode=f Allow only perfect mappings when set to true (very fast). 96s semiperfectmode=f Allow only perfect and semiperfect (perfect except for 96s N's in the reference) mappings. 96s threads=auto (t) Set to number of threads desired. By default, uses 96s all cores available. 96s ambiguous=best (ambig) Set behavior on ambiguously-mapped reads (with 96s multiple top-scoring mapping locations). 96s best (use the first best site) 96s toss (consider unmapped) 96s random (select one top-scoring site randomly) 96s all (retain all top-scoring sites) 96s samestrandpairs=f (ssp) Specify whether paired reads should map to the 96s same strand or opposite strands. 96s requirecorrectstrand=t (rcs) Forbid pairing of reads without correct strand 96s orientation. Set to false for long-mate-pair libraries. 96s killbadpairs=f (kbp) If a read pair is mapped with an inappropriate 96s insert size or orientation, the read with the lower 96s mapping quality is marked unmapped. 96s pairedonly=f (po) Treat unpaired reads as unmapped. Thus they will 96s be sent to 'outu' but not 'outm'. 96s rcomp=f Reverse complement both reads prior to mapping (for LMP 96s outward-facing libraries). 96s rcompmate=f Reverse complement read2 prior to mapping. 96s pairlen=32000 Set max allowed distance between paired reads. 96s (insert size)=(pairlen)+(read1 length)+(read2 length) 96s rescuedist=1200 Don't try to rescue paired reads if avg. insert size 96s greater than this. Lower is faster. 96s rescuemismatches=32 Maximum mismatches allowed in a rescued read. Lower 96s is faster. 96s averagepairdist=100 (apd) Initial average distance between paired reads. 96s Varies dynamically; does not need to be specified. 96s deterministic=f Run in deterministic mode. In this case it is good 96s to set averagepairdist. BBMap is deterministic 96s without this flag if using single-ended reads, 96s or run singlethreaded. 96s bandwidthratio=0 (bwr) If above zero, restrict alignment band to this 96s fraction of read length. Faster but less accurate. 96s bandwidth=0 (bw) Set the bandwidth directly. 96s fraction of read length. Faster but less accurate. 96s usejni=f (jni) Do alignments faster, in C code. Requires 96s compiling the C code; details are in /jni/README.txt. 96s maxsites2=800 Don't analyze (or print) more than this many alignments 96s per read. 96s ignorefrequentkmers=t (ifk) Discard low-information kmers that occur often. 96s excludefraction=0.03 (ef) Fraction of kmers to ignore. For example, 0.03 96s will ignore the most common 3% of kmers. 96s greedy=t Use a greedy algorithm to discard the least-useful 96s kmers on a per-read basis. 96s kfilter=0 If positive, potential mapping sites must have at 96s least this many consecutive exact matches. 96s 96s 96s Quality and Trimming Parameters: 96s qin=auto Set to 33 or 64 to specify input quality value ASCII 96s offset. 33 is Sanger, 64 is old Solexa. 96s qout=auto Set to 33 or 64 to specify output quality value ASCII 96s offset (only if output format is fastq). 96s qtrim=f Quality-trim ends before mapping. Options are: 96s 'f' (false), 'l' (left), 'r' (right), and 'lr' (both). 96s untrim=f Undo trimming after mapping. Untrimmed bases will be 96s soft-clipped in cigar strings. 96s trimq=6 Trim regions with average quality below this 96s (phred algorithm). 96s mintrimlength=60 (mintl) Don't trim reads to be shorter than this. 96s fakefastaquality=-1 (ffq) Set to a positive number 1-50 to generate fake 96s quality strings for fasta input reads. 96s ignorebadquality=f (ibq) Keep going, rather than crashing, if a read has 96s out-of-range quality values. 96s usequality=t Use quality scores when determining which read kmers 96s to use as seeds. 96s minaveragequality=0 (maq) Do not map reads with average quality below this. 96s maqb=0 If positive, calculate maq from this many initial bases. 96s 96s Output Parameters: 96s out= Write all reads to this file. 96s outu= Write only unmapped reads to this file. Does not 96s include unmapped paired reads with a mapped mate. 96s outm= Write only mapped reads to this file. Includes 96s unmapped paired reads with a mapped mate. 96s mappedonly=f If true, treats 'out' like 'outm'. 96s bamscript= (bs) Write a shell script to that will turn 96s the sam output into a sorted, indexed bam file. 96s ordered=f Set to true to output reads in same order as input. 96s Slower and uses more memory. 96s overwrite=f (ow) Allow process to overwrite existing files. 96s secondary=f Print secondary alignments. 96s sssr=0.95 (secondarysitescoreratio) Print only secondary alignments 96s with score of at least this fraction of primary. 96s ssao=f (secondarysiteasambiguousonly) Only print secondary 96s alignments for ambiguously-mapped reads. 96s maxsites=5 Maximum number of total alignments to print per read. 96s Only relevant when secondary=t. 96s quickmatch=f Generate cigar strings more quickly. 96s trimreaddescriptions=f (trd) Truncate read and ref names at the first whitespace, 96s assuming that the remainder is a comment or description. 96s ziplevel=2 (zl) Compression level for zip or gzip output. 96s pigz=f Spawn a pigz (parallel gzip) process for faster 96s compression than Java. Requires pigz to be installed. 96s machineout=f Set to true to output statistics in machine-friendly 96s 'key=value' format. 96s printunmappedcount=f Print the total number of unmapped reads and bases. 96s If input is paired, the number will be of pairs 96s for which both reads are unmapped. 96s showprogress=0 If positive, print a '.' every X reads. 96s showprogress2=0 If positive, print the number of seconds since the 96s last progress update (instead of a '.'). 96s renamebyinsert=f Renames reads based on their mapped insert size. 96s 96s Bloom-Filtering Parameters (bloomfilter.sh is the standalone version). 96s bloom=f Use a Bloom filter to ignore reads not sharing kmers 96s with the reference. This uses more memory, but speeds 96s mapping when most reads don't match the reference. 96s bloomhashes=2 Number of hash functions. 96s bloomminhits=3 Number of consecutive hits to be considered matched. 96s bloomk=31 Bloom filter kmer length. 96s bloomserial=t Use the serialized Bloom filter for greater loading 96s speed, if available. If not, generate and write one. 96s 96s Post-Filtering Parameters: 96s idfilter=0 Independant of minid; sets exact minimum identity 96s allowed for alignments to be printed. Range 0 to 1. 96s subfilter=-1 Ban alignments with more than this many substitutions. 96s insfilter=-1 Ban alignments with more than this many insertions. 96s delfilter=-1 Ban alignments with more than this many deletions. 96s indelfilter=-1 Ban alignments with more than this many indels. 96s editfilter=-1 Ban alignments with more than this many edits. 96s inslenfilter=-1 Ban alignments with an insertion longer than this. 96s dellenfilter=-1 Ban alignments with a deletion longer than this. 96s nfilter=-1 Ban alignments with more than this many ns. This 96s includes nocall, noref, and off scaffold ends. 96s 96s Sam flags and settings: 96s noheader=f Disable generation of header lines. 96s sam=1.4 Set to 1.4 to write Sam version 1.4 cigar strings, 96s with = and X, or 1.3 to use M. 96s saa=t (secondaryalignmentasterisks) Use asterisks instead of 96s bases for sam secondary alignments. 96s cigar=t Set to 'f' to skip generation of cigar strings (faster). 96s keepnames=f Keep original names of paired reads, rather than 96s ensuring both reads have the same name. 96s intronlen=999999999 Set to a lower number like 10 to change 'D' to 'N' in 96s cigar strings for deletions of at least that length. 96s rgid= Set readgroup ID. All other readgroup fields 96s can be set similarly, with the flag rgXX= 96s If you set a readgroup flag to the word 'filename', 96s e.g. rgid=filename, the input file name will be used. 96s mdtag=f Write MD tags. 96s nhtag=f Write NH tags. 96s xmtag=f Write XM tags (may only work correctly with ambig=all). 96s amtag=f Write AM tags. 96s nmtag=f Write NM tags. 96s xstag=f Set to 'xs=fs', 'xs=ss', or 'xs=us' to write XS tags 96s for RNAseq using firststrand, secondstrand, or 96s unstranded libraries. Needed by Cufflinks. 96s JGI mainly uses 'firststrand'. 96s stoptag=f Write a tag indicating read stop location, prefixed by YS:i: 96s lengthtag=f Write a tag indicating (query,ref) alignment lengths, 96s prefixed by YL:Z: 96s idtag=f Write a tag indicating percent identity, prefixed by YI:f: 96s inserttag=f Write a tag indicating insert size, prefixed by X8:Z: 96s scoretag=f Write a tag indicating BBMap's raw score, prefixed by YR:i: 96s timetag=f Write a tag indicating this read's mapping time, prefixed by X0:i: 96s boundstag=f Write a tag indicating whether either read in the pair 96s goes off the end of the reference, prefixed by XB:Z: 96s notags=f Turn off all optional tags. 96s 96s Histogram and statistics output parameters: 96s scafstats= Statistics on how many reads mapped to which scaffold. 96s refstats= Statistics on how many reads mapped to which reference 96s file; only for BBSplit. 96s sortscafs=t Sort scaffolds or references by read count. 96s bhist= Base composition histogram by position. 96s qhist= Quality histogram by position. 96s aqhist= Histogram of average read quality. 96s bqhist= Quality histogram designed for box plots. 96s lhist= Read length histogram. 96s ihist= Write histogram of insert sizes (for paired reads). 96s ehist= Errors-per-read histogram. 96s qahist= Quality accuracy histogram of error rates versus 96s quality score. 96s indelhist= Indel length histogram. 96s mhist= Histogram of match, sub, del, and ins rates by 96s read location. 96s gchist= Read GC content histogram. 96s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 96s gcpairs=t Use average GC of paired reads. 96s idhist= Histogram of read count versus percent identity. 96s idbins=100 Number idhist bins. Set to 'auto' to use read length. 96s statsfile=stderr Mapping statistics are printed here. 96s 96s Coverage output parameters (these may reduce speed and use more RAM): 96s covstats= Per-scaffold coverage info. 96s rpkm= Per-scaffold RPKM/FPKM counts. 96s covhist= Histogram of # occurrences of each depth level. 96s basecov= Coverage per base location. 96s bincov= Print binned coverage per location (one line per X bases). 96s covbinsize=1000 Set the binsize for binned coverage output. 96s nzo=t Only print scaffolds with nonzero coverage. 96s twocolumn=f Change to true to print only ID and Avg_fold instead of 96s all 6 columns to the 'out=' file. 96s 32bit=f Set to true if you need per-base coverage over 64k. 96s strandedcov=f Track coverage for plus and minus strand independently. 96s startcov=f Only track start positions of reads. 96s secondarycov=t Include coverage of secondary alignments. 96s physcov=f Calculate physical coverage for paired reads. 96s This includes the unsequenced bases. 96s delcoverage=t (delcov) Count bases covered by deletions as covered. 96s True is faster than false. 96s covk=0 If positive, calculate kmer coverage statistics. 96s 96s Java Parameters: 96s -Xmx This will set Java's memory usage, 96s overriding autodetection. 96s -Xmx20g will specify 20 gigs of RAM, and -Xmx800m 96s will specify 800 megs. The max is typically 85% of 96s physical memory. The human genome requires around 24g, 96s or 12g with the 'usemodulo' flag. The index uses 96s roughly 6 bytes per reference base. 96s -eoom This flag will cause the process to exit if an 96s out-of-memory exception occurs. Requires Java 8u92+. 96s -da Disable assertions. 96s 96s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter 96s any problems, or post at: http://seqanswers.com/forums/showthread.php?t=41057 96s 96s bbmap.sh ref=example.fasta 96s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 96s java -ea -Xmx2846m -Xms2846m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta 96s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta] 96s Version 39.20 96s 96s No output file. 96s Writing reference. 96s 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] 96s 96s Set genScaffoldInfo=true 96s Writing chunk 1 96s Set genome to 1 96s 96s Loaded Reference: 0.006 seconds. 96s Loading index for chunk 1-1, build 1 96s No index available; generating from reference genome: /tmp/autopkgtest.akYZ6L/autopkgtest_tmp/ref/index/1/chr1_index_k13_c16_b1.block 96s Indexing threads started for block 0-1 96s Indexing threads finished for block 0-1 97s Generated Index: 0.909 seconds. 97s No reads to process; quitting. 97s 97s Total time: 1.090 seconds. 97s test -d ref 97s bbmap.sh in=misc_dna_as_sanger.fastq out=out.sam 97s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 97s java -ea -Xmx2845m -Xms2845m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 in=misc_dna_as_sanger.fastq out=out.sam 97s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, in=misc_dna_as_sanger.fastq, out=out.sam] 97s Version 39.20 97s 97s Retaining first best site only for ambiguous mappings. 97s Set genome to 1 97s 97s Loaded Reference: 0.030 seconds. 97s Loading index for chunk 1-1, build 1 98s Generated Index: 0.330 seconds. 101s Analyzed Index: 2.977 seconds. 101s Started output stream: 0.023 seconds. 101s Cleared Memory: 0.121 seconds. 101s Processing reads in single-ended mode. 101s Started read stream. 101s Started 4 mapping threads. 101s Detecting finished threads: 0, 1, 2, 3 101s 101s ------------------ Results ------------------ 101s 101s Genome: 1 101s Key Length: 13 101s Max Indel: 16000 101s Minimum Score Ratio: 0.56 101s Mapping Mode: normal 101s Reads Used: 4 (153 bases) 101s 101s Mapping: 0.100 seconds. 101s Reads/sec: 39.91 101s kBases/sec: 1.53 101s 101s 101s Read 1 data: pct reads num reads pct bases num bases 101s 101s mapped: 0.0000% 0 0.0000% 0 101s unambiguous: 0.0000% 0 0.0000% 0 101s ambiguous: 0.0000% 0 0.0000% 0 101s low-Q discards: 25.0000% 1 19.6078% 30 101s 101s perfect best site: 0.0000% 0 0.0000% 0 101s semiperfect site: 0.0000% 0 0.0000% 0 101s 101s Match Rate: NA NA NaN% 0 101s Error Rate: NaN% 0 NaN% 0 101s Sub Rate: NaN% 0 NaN% 0 101s Del Rate: NaN% 0 NaN% 0 101s Ins Rate: NaN% 0 NaN% 0 101s N Rate: NaN% 0 NaN% 0 101s 101s Total time: 3.698 seconds. 101s test -r out.sam 101s bbmap.sh ref=example.fasta in=example.fastq out=out2.sam nodisk 101s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 101s java -ea -Xmx2845m -Xms2845m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta in=example.fastq out=out2.sam nodisk 101s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta, in=example.fastq, out=out2.sam, nodisk] 101s Version 39.20 101s 101s Retaining first best site only for ambiguous mappings. 101s 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] 101s 101s Set genScaffoldInfo=true 101s Set genome to 1 101s 101s Loaded Reference: 0.003 seconds. 101s Loading index for chunk 1-1, build 1 101s Indexing threads started for block 0-1 102s Indexing threads finished for block 0-1 102s Generated Index: 0.220 seconds. 105s Analyzed Index: 2.991 seconds. 105s Started output stream: 0.021 seconds. 105s Cleared Memory: 0.113 seconds. 105s Processing reads in single-ended mode. 105s Started read stream. 105s Started 4 mapping threads. 105s Detecting finished threads: 0, 1, 2, 3 105s 105s ------------------ Results ------------------ 105s 105s Genome: 1 105s Key Length: 13 105s Max Indel: 16000 105s Minimum Score Ratio: 0.56 105s Mapping Mode: normal 105s Reads Used: 3 (75 bases) 105s 105s Mapping: 0.156 seconds. 105s Reads/sec: 19.26 105s kBases/sec: 0.48 105s 105s 105s Read 1 data: pct reads num reads pct bases num bases 105s 105s mapped: 100.0000% 3 100.0000% 75 105s unambiguous: 100.0000% 3 100.0000% 75 105s ambiguous: 0.0000% 0 0.0000% 0 105s low-Q discards: 0.0000% 0 0.0000% 0 105s 105s perfect best site: 100.0000% 3 100.0000% 75 105s semiperfect site: 100.0000% 3 100.0000% 75 105s 105s Match Rate: NA NA 100.0000% 75 105s Error Rate: 0.0000% 0 0.0000% 0 105s Sub Rate: 0.0000% 0 0.0000% 0 105s Del Rate: 0.0000% 0 0.0000% 0 105s Ins Rate: 0.0000% 0 0.0000% 0 105s N Rate: 0.0000% 0 0.0000% 0 105s 105s Total time: 3.689 seconds. 105s test -r out2.sam 105s 105s # bbduk 105s bbduk.sh --version 105s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 105s java -ea -Xmx1422m -Xms1422m -cp /usr/share/java/bbmap.jar jgi.BBDuk --version 105s BBTools version 39.20 105s For help, please run the shellscript with no parameters, or look in /docs/. 105s bbduk.sh --help 105s 105s Written by Brian Bushnell 105s Last modified November 18, 2024 105s 105s Description: Compares reads to the kmers in a reference dataset, optionally 105s allowing an edit distance. Splits the reads into two outputs - those that 105s match the reference, and those that don't. Can also trim (remove) the matching 105s parts of the reads rather than binning the reads. 105s Please read bbmap/docs/guides/BBDukGuide.txt for more information. 105s 105s Usage: bbduk.sh in= out= ref= 105s 105s Input may be stdin or a fasta or fastq file, compressed or uncompressed. 105s If you pipe via stdin/stdout, please include the file type; e.g. for gzipped 105s fasta input, set in=stdin.fa.gz 105s 105s Input parameters: 105s in= Main input. in=stdin.fq will pipe from stdin. 105s in2= Input for 2nd read of pairs in a different file. 105s ref= Comma-delimited list of reference files. 105s In addition to filenames, you may also use the keywords: 105s adapters, artifacts, phix, lambda, pjet, mtst, kapa 105s literal= Comma-delimited list of literal reference sequences. 105s Polymers are also allowed with the 'poly' prefix; 105s for example, 'literal=ATGGT,polyGC' will add both ATGGT 105s and GCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGC - 32+ of them, 105s enough replicates to ensure that all kmers are present. 105s touppercase=f (tuc) Change all bases upper-case. 105s interleaved=auto (int) t/f overrides interleaved autodetection. 105s Must be set mainually when streaming fastq input. 105s qin=auto Input quality offset: 33 (Sanger), 64, or auto. 105s reads=-1 If positive, quit after processing X reads or pairs. 105s copyundefined=f (cu) Process non-AGCT IUPAC reference bases by making all 105s possible unambiguous copies. Intended for short motifs 105s or adapter barcodes, as time/memory use is exponential. 105s samplerate=1 Set lower to only process a fraction of input reads. 105s samref= Optional reference fasta for processing sam files. 105s 105s Output parameters: 105s out= (outnonmatch) Write reads here that do not contain 105s kmers matching the database. 'out=stdout.fq' will pipe 105s to standard out. 105s out2= (outnonmatch2) Use this to write 2nd read of pairs to a 105s different file. 105s outm= (outmatch) Write reads here that fail filters. In default 105s kfilter mode, this means any read with a matching kmer. 105s In any mode, it also includes reads that fail filters such 105s as minlength, mingc, maxgc, entropy, etc. In other words, 105s it includes all reads that do not go to 'out'. 105s outm2= (outmatch2) Use this to write 2nd read of pairs to a 105s different file. 105s outs= (outsingle) Use this to write singleton reads whose mate 105s was trimmed shorter than minlen. 105s stats= Write statistics about which contamininants were detected. 105s refstats= Write statistics on a per-reference-file basis. 105s rpkm= Write RPKM for each reference sequence (for RNA-seq). 105s dump= Dump kmer tables to a file, in fasta format. 105s duk= Write statistics in duk's format. *DEPRECATED* 105s nzo=t Only write statistics about ref sequences with nonzero hits. 105s overwrite=t (ow) Grant permission to overwrite files. 105s showspeed=t (ss) 'f' suppresses display of processing speed. 105s ziplevel=2 (zl) Compression level; 1 (min) through 9 (max). 105s fastawrap=70 Length of lines in fasta output. 105s qout=auto Output quality offset: 33 (Sanger), 64, or auto. 105s statscolumns=3 (cols) Number of columns for stats output, 3 or 5. 105s 5 includes base counts. 105s rename=f Rename reads to indicate which sequences they matched. 105s refnames=f Use names of reference files rather than scaffold IDs. 105s trd=f Truncate read and ref names at the first whitespace. 105s ordered=f Set to true to output reads in same order as input. 105s maxbasesout=-1 If positive, quit after writing approximately this many 105s bases to out (outu/outnonmatch). 105s maxbasesoutm=-1 If positive, quit after writing approximately this many 105s bases to outm (outmatch). 105s json=f Print to screen in json format. 105s 105s Histogram output parameters: 105s bhist= Base composition histogram by position. 105s qhist= Quality histogram by position. 105s qchist= Count of bases with each quality value. 105s aqhist= Histogram of average read quality. 105s bqhist= Quality histogram designed for box plots. 105s lhist= Read length histogram. 105s phist= Polymer length histogram. 105s gchist= Read GC content histogram. 105s enthist= Read entropy histogram. 105s ihist= Insert size histogram, for paired reads in mapped sam. 105s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 105s maxhistlen=6000 Set an upper bound for histogram lengths; higher uses 105s more memory. The default is 6000 for some histograms 105s and 80000 for others. 105s 105s Histograms for mapped sam/bam files only: 105s histbefore=t Calculate histograms from reads before processing. 105s ehist= Errors-per-read histogram. 105s qahist= Quality accuracy histogram of error rates versus quality 105s score. 105s indelhist= Indel length histogram. 105s mhist= Histogram of match, sub, del, and ins rates by position. 105s idhist= Histogram of read count versus percent identity. 105s idbins=100 Number idhist bins. Set to 'auto' to use read length. 105s varfile= Ignore substitution errors listed in this file when 105s calculating error rates. Can be generated with 105s CallVariants. 105s vcf= Ignore substitution errors listed in this VCF file 105s when calculating error rates. 105s ignorevcfindels=t Also ignore indels listed in the VCF. 105s 105s Processing parameters: 105s k=27 Kmer length used for finding contaminants. Contaminants 105s shorter than k will not be found. k must be at least 1. 105s rcomp=t Look for reverse-complements of kmers in addition to 105s forward kmers. 105s maskmiddle=t (mm) Treat the middle base of a kmer as a wildcard, to 105s increase sensitivity in the presence of errors. This may 105s also be set to a number, e.g. mm=3, to mask that many bp. 105s The default mm=t corresponds to mm=1 for odd-length kmers 105s and mm=2 for even-length kmers (as of v39.04), while 105s mm=f is always equivalent to mm=0. 105s minkmerhits=1 (mkh) Reads need at least this many matching kmers 105s to be considered as matching the reference. 105s minkmerfraction=0.0 (mkf) A reads needs at least this fraction of its total 105s kmers to hit a ref, in order to be considered a match. 105s If this and minkmerhits are set, the greater is used. 105s mincovfraction=0.0 (mcf) A reads needs at least this fraction of its total 105s bases to be covered by ref kmers to be considered a match. 105s If specified, mcf overrides mkh and mkf. 105s hammingdistance=0 (hdist) Maximum Hamming distance for ref kmers (subs only). 105s Memory use is proportional to (3*K)^hdist. 105s qhdist=0 Hamming distance for query kmers; impacts speed, not memory. 105s editdistance=0 (edist) Maximum edit distance from ref kmers (subs 105s and indels). Memory use is proportional to (8*K)^edist. 105s hammingdistance2=0 (hdist2) Sets hdist for short kmers, when using mink. 105s qhdist2=0 Sets qhdist for short kmers, when using mink. 105s editdistance2=0 (edist2) Sets edist for short kmers, when using mink. 105s forbidn=f (fn) Forbids matching of read kmers containing N. 105s By default, these will match a reference 'A' if 105s hdist>0 or edist>0, to increase sensitivity. 105s removeifeitherbad=t (rieb) Paired reads get sent to 'outmatch' if either is 105s match (or either is trimmed shorter than minlen). 105s Set to false to require both. 105s trimfailures=f Instead of discarding failed reads, trim them to 1bp. 105s This makes the statistics a bit odd. 105s findbestmatch=f (fbm) If multiple matches, associate read with sequence 105s sharing most kmers. Reduces speed. 105s skipr1=f Don't do kmer-based operations on read 1. 105s skipr2=f Don't do kmer-based operations on read 2. 105s ecco=f For overlapping paired reads only. Performs error- 105s correction with BBMerge prior to kmer operations. 105s recalibrate=f (recal) Recalibrate quality scores. Requires calibration 105s matrices generated by CalcTrueQuality. 105s sam= If recalibration is desired, and matrices have not already 105s been generated, BBDuk will create them from the sam file. 105s amino=f Run in amino acid mode. Some features have not been 105s tested, but kmer-matching works fine. Maximum k is 12. 105s 105s Speed and Memory parameters: 105s threads=auto (t) Set number of threads to use; default is number of 105s logical processors. 105s prealloc=f Preallocate memory in table. Allows faster table loading 105s and more efficient memory usage, for a large reference. 105s monitor=f Kill this process if it crashes. monitor=600,0.01 would 105s kill after 600 seconds under 1% usage. 105s minrskip=1 (mns) Force minimal skip interval when indexing reference 105s kmers. 1 means use all, 2 means use every other kmer, etc. 105s maxrskip=1 (mxs) Restrict maximal skip interval when indexing 105s reference kmers. Normally all are used for scaffolds<100kb, 105s but with longer scaffolds, up to maxrskip-1 are skipped. 105s rskip= Set both minrskip and maxrskip to the same value. 105s If not set, rskip will vary based on sequence length. 105s qskip=1 Skip query kmers to increase speed. 1 means use all. 105s speed=0 Ignore this fraction of kmer space (0-15 out of 16) in both 105s reads and reference. Increases speed and reduces memory. 105s Note: Do not use more than one of 'speed', 'qskip', and 'rskip'. 105s 105s Trimming/Filtering/Masking parameters: 105s Note - if ktrim, kmask, and ksplit are unset, the default behavior is kfilter. 105s All kmer processing modes are mutually exclusive. 105s Reads only get sent to 'outm' purely based on kmer matches in kfilter mode. 105s 105s ktrim=f Trim reads to remove bases matching reference kmers, plus 105s all bases to the left or right. 105s Values: 105s f (don't trim), 105s r (trim to the right), 105s l (trim to the left) 105s ktrimtips=0 Set this to a positive number to perform ktrim on both 105s ends, examining only the outermost X bases. 105s kmask= Replace bases matching ref kmers with another symbol. 105s Allows any non-whitespace character, and processes short 105s kmers on both ends if mink is set. 'kmask=lc' will 105s convert masked bases to lowercase. 105s maskfullycovered=f (mfc) Only mask bases that are fully covered by kmers. 105s ksplit=f For single-ended reads only. Reads will be split into 105s pairs around the kmer. If the kmer is at the end of the 105s read, it will be trimmed instead. Singletons will go to 105s out, and pairs will go to outm. Do not use ksplit with 105s other operations such as quality-trimming or filtering. 105s mink=0 Look for shorter kmers at read tips down to this length, 105s when k-trimming or masking. 0 means disabled. Enabling 105s this will disable maskmiddle. 105s qtrim=f Trim read ends to remove bases with quality below trimq. 105s Performed AFTER looking for kmers. Values: 105s rl (trim both ends), 105s f (neither end), 105s r (right end only), 105s l (left end only), 105s w (sliding window). 105s trimq=6 Regions with average quality BELOW this will be trimmed, 105s if qtrim is set to something other than f. Can be a 105s floating-point number like 7.3. 105s quantize Bin quality scores to reduce file size. quantize=2 will 105s eliminate all odd quality scores, while quantize=0,10,37 105s will only allow qualty scores of 0, 10, or 37. 105s trimclip=f Trim soft-clipped bases from sam files. 105s minlength=10 (ml) Reads shorter than this after trimming will be 105s discarded. Pairs will be discarded if both are shorter. 105s mlf=0 (minlengthfraction) Reads shorter than this fraction of 105s original length after trimming will be discarded. 105s maxlength= Reads longer than this after trimming will be discarded. 105s minavgquality=0 (maq) Reads with average quality (after trimming) below 105s this will be discarded. 105s maqb=0 If positive, calculate maq from this many initial bases. 105s minbasequality=0 (mbq) Reads with any base below this quality (after 105s trimming) will be discarded. 105s maxns=-1 If non-negative, reads with more Ns than this 105s (after trimming) will be discarded. 105s mcb=0 (minconsecutivebases) Discard reads without at least 105s this many consecutive called bases. 105s ottm=f (outputtrimmedtomatch) Output reads trimmed to shorter 105s than minlength to outm rather than discarding. 105s tp=0 (trimpad) Trim this much extra around matching kmers. 105s tbo=f (trimbyoverlap) Trim adapters based on where paired 105s reads overlap. 105s strictoverlap=t Adjust sensitivity for trimbyoverlap mode. 105s minoverlap=14 Require this many bases of overlap for detection. 105s mininsert=40 Require insert size of at least this for overlap. 105s Should be reduced to 16 for small RNA sequencing. 105s tpe=f (trimpairsevenly) When kmer right-trimming, trim both 105s reads to the minimum length of either. 105s forcetrimleft=0 (ftl) If positive, trim bases to the left of this position 105s (exclusive, 0-based). 105s forcetrimright=0 (ftr) If positive, trim bases to the right of this position 105s (exclusive, 0-based). 105s forcetrimright2=0 (ftr2) If positive, trim this many bases on the right end. 105s forcetrimmod=0 (ftm) If positive, right-trim length to be equal to zero, 105s modulo this number. 105s restrictleft=0 If positive, only look for kmer matches in the 105s leftmost X bases. 105s restrictright=0 If positive, only look for kmer matches in the 105s rightmost X bases. 105s NOTE: restrictleft and restrictright are mutually exclusive. If trimming 105s both ends is desired, use ktrimtips. 105s mingc=0 Discard reads with GC content below this. 105s maxgc=1 Discard reads with GC content above this. 105s gcpairs=t Use average GC of paired reads. 105s Also affects gchist. 105s tossjunk=f Discard reads with invalid characters as bases. 105s swift=f Trim Swift sequences: Trailing C/T/N R1, leading G/A/N R2. 105s 105s Header-parsing parameters - these require Illumina headers: 105s chastityfilter=f (cf) Discard reads with id containing ' 1:Y:' or ' 2:Y:'. 105s barcodefilter=f Remove reads with unexpected barcodes if barcodes is set, 105s or barcodes containing 'N' otherwise. A barcode must be 105s the last part of the read header. Values: 105s t: Remove reads with bad barcodes. 105s f: Ignore barcodes. 105s crash: Crash upon encountering bad barcodes. 105s barcodes= Comma-delimited list of barcodes or files of barcodes. 105s xmin=-1 If positive, discard reads with a lesser X coordinate. 105s ymin=-1 If positive, discard reads with a lesser Y coordinate. 105s xmax=-1 If positive, discard reads with a greater X coordinate. 105s ymax=-1 If positive, discard reads with a greater Y coordinate. 105s 105s Polymer trimming: 105s trimpolya=0 If greater than 0, trim poly-A or poly-T tails of 105s at least this length on either end of reads. 105s trimpolygleft=0 If greater than 0, trim poly-G prefixes of at least this 105s length on the left end of reads. Does not trim poly-C. 105s trimpolygright=0 If greater than 0, trim poly-G tails of at least this 105s length on the right end of reads. Does not trim poly-C. 105s trimpolyg=0 This sets both left and right at once. 105s filterpolyg=0 If greater than 0, remove reads with a poly-G prefix of 105s at least this length (on the left). 105s Note: there are also equivalent poly-C flags. 105s 105s Polymer tracking: 105s pratio=base,base 'pratio=G,C' will print the ratio of G to C polymers. 105s plen=20 Length of homopolymers to count. 105s 105s Entropy/Complexity parameters: 105s entropy=-1 Set between 0 and 1 to filter reads with entropy below 105s that value. Higher is more stringent. 105s entropywindow=50 Calculate entropy using a sliding window of this length. 105s entropyk=5 Calculate entropy using kmers of this length. 105s minbasefrequency=0 Discard reads with a minimum base frequency below this. 105s entropytrim=f Values: 105s f: (false) Do not entropy-trim. 105s r: (right) Trim low entropy on the right end only. 105s l: (left) Trim low entropy on the left end only. 105s rl: (both) Trim low entropy on both ends. 105s entropymask=f Values: 105s f: (filter) Discard low-entropy sequences. 105s t: (true) Mask low-entropy parts of sequences with N. 105s lc: Change low-entropy parts of sequences to lowercase. 105s entropymark=f Mark each base with its entropy value. This is on a scale 105s of 0-41 and is reported as quality scores, so the output 105s should be fastq or fasta+qual. 105s NOTE: If set, entropytrim overrides entropymask. 105s 105s Cardinality estimation: 105s cardinality=f (loglog) Count unique kmers using the LogLog algorithm. 105s cardinalityout=f (loglogout) Count unique kmers in output reads. 105s loglogk=31 Use this kmer length for counting. 105s loglogbuckets=2048 Use this many buckets for counting. 105s khist= Kmer frequency histogram; plots number of kmers versus 105s kmer depth. This is approximate. 105s khistout= Kmer frequency histogram for output reads. 105s 105s Side Channel: 105s sideout= Output for aligned reads. 105s sideref=phix Reference for side-channel alignment; must be a single 105s sequence and virtually repeat-free at selected k. 105s sidek1=17 Kmer length for seeding alignment to reference. 105s sidek2=13 Kmer length for seeding alignment of unaligned reads 105s with an aligned mate. 105s sideminid1=0.66 Minimum identity to accept individual alignments. 105s sideminid2=0.58 Minimum identity for aligning reads with aligned mates. 105s sidemm1=1 Middle mask length for sidek1. 105s sidemm2=1 Middle mask length for sidek2. 105s Note: The side channel is a special additional output that allows alignment 105s to a secondary reference while also doing trimming. Alignment does not affect 105s whether reads go to the normal outputs (out, outm). The main purpose is to 105s simplify pipelines that need trimmed, aligned phiX reads for recalibration. 105s 105s 105s Java Parameters: 105s 105s -Xmx This will set Java's memory usage, overriding autodetection. 105s -Xmx20g will 105s specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 105s The max is typically 85% of physical memory. 105s -eoom This flag will cause the process to exit if an 105s out-of-memory exception occurs. Requires Java 8u92+. 105s -da Disable assertions. 105s 105s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 105s 105s bbduk.sh in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq \ 105s qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 105s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 105s java -ea -Xmx1422m -Xms1422m -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 105s 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] 105s Version 39.20 105s 105s Changed from ASCII-33 to ASCII-64 on input quality X (Q55) for base A at lines 1 and 3, position 24 while prescanning. 105s Changed from ASCII-33 to ASCII-64 on input quality X (Q55) for base A at lines 1 and 3, position 24 while prescanning. 105s Allocating kmer table: 0.032 seconds. 105s Initial: 105s Memory: max=1491m, total=1491m, free=1459m, used=32m 105s 105s Input is being processed as paired 105s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 105s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 105s Started output streams: 0.021 seconds. 105s Processing time: 0.005 seconds. 105s 105s Input: 8 reads 306 bases. 105s QTrimmed: 0 reads (0.00%) 0 bases (0.00%) 105s Total Removed: 8 reads (100.00%) 306 bases (100.00%) 105s Result: 0 reads (0.00%) 0 bases (0.00%) 105s 105s Time: 0.028 seconds. 105s Reads Processed: 8 0.28k reads/sec 105s Bases Processed: 306 0.01m bases/sec 105s test -r out.fastq.gz 105s 105s # bbnorm 105s bbnorm.sh --version 105s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 105s java -ea -Xmx2845m -Xms2845m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 --version 106s BBTools version 39.20 106s For help, please run the shellscript with no parameters, or look in /docs/. 106s bbnorm.sh --help 106s 106s Written by Brian Bushnell 106s Last modified October 19, 2017 106s 106s Description: Normalizes read depth based on kmer counts. 106s Can also error-correct, bin reads by kmer depth, and generate a kmer depth histogram. 106s However, Tadpole has superior error-correction to BBNorm. 106s Please read bbmap/docs/guides/BBNormGuide.txt for more information. 106s 106s Usage: bbnorm.sh in= out= outt= hist= 106s 106s Input parameters: 106s in=null Primary input. Use in2 for paired reads in a second file 106s in2=null Second input file for paired reads in two files 106s extra=null Additional files to use for input (generating hash table) but not for output 106s fastareadlen=2^31 Break up FASTA reads longer than this. Can be useful when processing scaffolded genomes 106s tablereads=-1 Use at most this many reads when building the hashtable (-1 means all) 106s kmersample=1 Process every nth kmer, and skip the rest 106s readsample=1 Process every nth read, and skip the rest 106s 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. 106s qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto. 106s 106s Output parameters: 106s out= File for normalized or corrected reads. Use out2 for paired reads in a second file 106s outt= (outtoss) File for reads that were excluded from primary output 106s reads=-1 Only process this number of reads, then quit (-1 means all) 106s sampleoutput=t Use sampling on output as well as input (not used if sample rates are 1) 106s keepall=f Set to true to keep all reads (e.g. if you just want error correction). 106s 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. 106s bbnorm.sh in=sanger_full_range_original_sanger.fastq qin=33 \ 106s out=out3.fastq outt=outt.fastq hist=hist.plt 106s Default is false, to prevent confusion about how there can be 0-count kmers. 106s The reason is that based on the 'minq' and 'minprob' settings, some kmers may be excluded from the bloom filter. 106s tmpdir= This will specify a directory for temp files (only needed for multipass runs). If null, they will be written to the output directory. 106s usetempdir=t Allows enabling/disabling of temporary directory; if disabled, temp files will be written to the output directory. 106s qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input). 106s rename=f Rename reads based on their kmer depth. 106s 106s Hashing parameters: 106s k=31 Kmer length (values under 32 are most efficient, but arbitrarily high values are supported) 106s 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. 106s Large values decrease accuracy for a fixed amount of memory, so use the lowest number you can that will still capture highest-depth kmers. 106s hashes=3 Number of times each kmer is hashed and stored. Higher is slower. 106s Higher is MORE accurate if there is enough memory, and LESS accurate if there is not enough memory. 106s 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. 106s prehashes=2 Number of hashes for prefilter. 106s prefilterbits=2 (pbits) Bits per cell in prefilter. 106s prefiltersize=0.35 Fraction of memory to allocate to prefilter. 106s buildpasses=1 More passes can sometimes increase accuracy by iteratively removing low-depth kmers 106s minq=6 Ignore kmers containing bases with quality below this 106s minprob=0.5 Ignore kmers with overall probability of correctness below this 106s 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. 106s 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. 106s 106s Normalization parameters: 106s fixspikes=f (fs) Do a slower, high-precision bloom filter lookup of kmers that appear to have an abnormally high depth due to collisions. 106s target=100 (tgt) Target normalization depth. NOTE: All depth parameters control kmer depth, not read depth. 106s For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1)) 106s maxdepth=-1 (max) Reads will not be downsampled when below this depth, even if they are above the target depth. 106s mindepth=5 (min) Kmers with depth below this number will not be included when calculating the depth of a read. 106s minkmers=15 (mgkpr) Reads must have at least this many kmers over min depth to be retained. Aka 'mingoodkmersperread'. 106s 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. 106s uselowerdepth=t (uld) For pairs, use the depth of the lower read as the depth proxy. 106s deterministic=t (dr) Generate random numbers deterministically to ensure identical output between multiple runs. May decrease speed with a huge number of threads. 106s passes=2 (p) 1 pass is the basic mode. 2 passes (default) allows greater accuracy, error detection, better contol of output depth. 106s 106s Error detection parameters: 106s hdp=90.0 (highdepthpercentile) Position in sorted kmer depth array used as proxy of a read's high kmer depth. 106s ldp=25.0 (lowdepthpercentile) Position in sorted kmer depth array used as proxy of a read's low kmer depth. 106s tossbadreads=f (tbr) Throw away reads detected as containing errors. 106s requirebothbad=f (rbb) Only toss bad pairs if both reads are bad. 106s 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. 106s highthresh=12 (ht) Threshold for high kmer. A high kmer at this or above are considered non-error. 106s lowthresh=3 (lt) Threshold for low kmer. Kmers at this and below are always considered errors. 106s 106s Error correction parameters: 106s ecc=f Set to true to correct errors. NOTE: Tadpole is now preferred for ecc as it does a better job. 106s ecclimit=3 Correct up to this many errors per read. If more are detected, the read will remain unchanged. 106s errorcorrectratio=140 (ecr) Adjacent kmers with a depth ratio of at least this much between will be classified as an error. 106s echighthresh=22 (echt) Threshold for high kmer. A kmer at this or above may be considered non-error. 106s eclowthresh=2 (eclt) Threshold for low kmer. Kmers at this and below are considered errors. 106s eccmaxqual=127 Do not correct bases with quality above this value. 106s aec=f (aggressiveErrorCorrection) Sets more aggressive values of ecr=100, ecclimit=7, echt=16, eclt=3. 106s cec=f (conservativeErrorCorrection) Sets more conservative values of ecr=180, ecclimit=2, echt=30, eclt=1, sl=4, pl=4. 106s meo=f (markErrorsOnly) Marks errors by reducing quality value of suspected errors; does not correct anything. 106s mue=t (markUncorrectableErrors) Marks errors only on uncorrectable reads; requires 'ecc=t'. 106s overlap=f (ecco) Error correct by read overlap. 106s 106s Depth binning parameters: 106s lowbindepth=10 (lbd) Cutoff for low depth bin. 106s highbindepth=80 (hbd) Cutoff for high depth bin. 106s outlow= Pairs in which both reads have a median below lbd go into this file. 106s outhigh= Pairs in which both reads have a median above hbd go into this file. 106s outmid= All other pairs go into this file. 106s 106s Histogram parameters: 106s hist= Specify a file to write the input kmer depth histogram. 106s histout= Specify a file to write the output kmer depth histogram. 106s histcol=3 (histogramcolumns) Number of histogram columns, 2 or 3. 106s pzc=f (printzerocoverage) Print lines in the histogram with zero coverage. 106s histlen=1048576 Max kmer depth displayed in histogram. Also affects statistics displayed, but does not affect normalization. 106s 106s Peak calling parameters: 106s peaks= Write the peaks to this file. Default is stdout. 106s minHeight=2 (h) Ignore peaks shorter than this. 106s minVolume=5 (v) Ignore peaks with less area than this. 106s minWidth=3 (w) Ignore peaks narrower than this. 106s minPeak=2 (minp) Ignore peaks with an X-value below this. 106s maxPeak=BIG (maxp) Ignore peaks with an X-value above this. 106s maxPeakCount=8 (maxpc) Print up to this many peaks (prioritizing height). 106s 106s Java Parameters: 106s -Xmx This will set Java's memory usage, overriding autodetection. 106s -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 106s The max is typically 85% of physical memory. 106s -eoom This flag will cause the process to exit if an 106s out-of-memory exception occurs. Requires Java 8u92+. 106s -da Disable assertions. 106s 106s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 106s 106s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 106s java -ea -Xmx2845m -Xms2845m -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 106s Executing jgi.KmerNormalize [bits=32, in=sanger_full_range_original_sanger.fastq, qin=33, out=out3.fastq, outt=outt.fastq, hist=hist.plt] 106s 106s 106s *********** Pass 1 ********** 106s 106s 106s Settings: 106s threads: 4 106s k: 31 106s deterministic: true 106s toss error reads: false 106s passes: 1 106s bits per cell: 16 106s cells: 1053.69M 106s hashes: 3 106s base min quality: 5 106s kmer min prob: 0.5 106s 106s target depth: 400 106s min depth: 3 106s max depth: 500 106s min good kmers: 15 106s depth percentile: 64.8 106s ignore dupe kmers: true 106s fix spikes: false 106s histogram length: 65536 106s print zero cov: false 106s 107s Made hash table: hashes = 3 mem = 1.96 GB cells = 1053.64M used = 0.000% 107s 107s Estimated unique kmers: 4 107s 107s Table creation time: 0.858 seconds. 107s Started output threads. 107s Started output threads. 107s Table read time: 0.005 seconds. 35.06 kb/sec 107s Total reads in: 2 0.000% Kept 107s Total bases in: 188 0.000% Kept 107s Error reads in: 2 100.000% 107s Error type 1: 2 100.000% 107s Error type 2: 0 0.000% 107s Error type 3: 0 0.000% 107s 107s Wrote histogram to hist.plt 107s Total kmers counted: 128 107s Total unique kmer count: 128 107s Includes forward kmers only. 107s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 107s The most accurate value is the greater of the two. 107s 107s Percent unique: 100.00% 107s Depth average: 1.00 (unique kmers) 107s Depth median: 1 (unique kmers) 107s Depth standard deviation: 0.00 (unique kmers) 107s Corrected depth average: 0.00 107s 107s Depth average: 1.00 (all kmers) 107s Depth median: 1 (all kmers) 107s Depth standard deviation: 0.00 (all kmers) 107s 107s Approx. read depth median: 1.47 107s 107s *********** Pass 2 ********** 107s 107s 107s Settings: 107s threads: 4 107s k: 31 107s deterministic: true 107s toss error reads: false 107s passes: 1 107s bits per cell: 16 107s cells: 1053.69M 107s hashes: 3 107s base min quality: 5 107s kmer min prob: 0.5 107s 107s target depth: 100 107s min depth: 5 107s max depth: 100 107s min good kmers: 15 107s depth percentile: 54.0 107s ignore dupe kmers: true 107s fix spikes: false 107s histogram length: 65536 107s 107s Made hash table: hashes = 3 mem = 1.96 GB cells = 1053.64M used = 0.000% 107s 107s Estimated unique kmers: 0 107s 107s Table creation time: 0.281 seconds. 107s Started output threads. 107s Started output threads. 107s Table read time: 0.002 seconds. 0.00 kb/sec 107s Total reads in: 0 NaN% Kept 107s Total bases in: 0 NaN% Kept 107s Error reads in: 0 NaN% 107s Error type 1: 0 NaN% 107s Error type 2: 0 NaN% 107s Error type 3: 0 NaN% 107s Total kmers counted: 0 107s Total unique kmer count: 0 107s Includes forward kmers only. 107s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 107s The most accurate value is the greater of the two. 107s 107s Percent unique: NaN% 107s Depth average: NaN (unique kmers) 107s Depth median: 0 (unique kmers) 107s Depth standard deviation: NaN (unique kmers) 107s Corrected depth average: NaN 107s 107s Depth average: NaN (all kmers) 107s Depth median: 0 (all kmers) 107s Depth standard deviation: 0.00 (all kmers) 107s 107s Approx. read depth median: NaN 107s 107s Removing temp files. 107s 107s Total time: 1.235 seconds. 0.15 kb/sec 107s test -r out3.fastq 107s test -r outt.fastq 107s test -r hist.plt 107s bbnorm.sh in=illumina_full_range_original_illumina.fastq qin=64 \ 107s out=out4.fastq outt=outt2.fastq hist=hist2.plt 107s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 107s java -ea -Xmx2845m -Xms2845m -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 107s Executing jgi.KmerNormalize [bits=32, in=illumina_full_range_original_illumina.fastq, qin=64, out=out4.fastq, outt=outt2.fastq, hist=hist2.plt] 107s 107s 107s *********** Pass 1 ********** 107s 107s 107s Settings: 107s threads: 4 107s k: 31 107s deterministic: true 107s toss error reads: false 107s passes: 1 107s bits per cell: 16 107s cells: 1053.69M 107s hashes: 3 107s base min quality: 5 107s kmer min prob: 0.5 107s 107s target depth: 400 107s min depth: 3 107s max depth: 500 107s min good kmers: 15 107s depth percentile: 64.8 107s ignore dupe kmers: true 107s fix spikes: false 107s histogram length: 65536 107s print zero cov: false 107s 108s Made hash table: hashes = 3 mem = 1.96 GB cells = 1053.64M used = 0.000% 108s 108s Estimated unique kmers: 4 108s 108s Table creation time: 1.028 seconds. 108s Started output threads. 108s Started output threads. 108s Table read time: 0.006 seconds. 21.83 kb/sec 108s Total reads in: 2 0.000% Kept 108s Total bases in: 126 0.000% Kept 108s Error reads in: 2 100.000% 108s Error type 1: 2 100.000% 108s Error type 2: 0 0.000% 108s Error type 3: 0 0.000% 108s 108s Wrote histogram to hist2.plt 108s Total kmers counted: 66 108s Total unique kmer count: 66 108s Includes forward kmers only. 108s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 108s The most accurate value is the greater of the two. 108s 108s Percent unique: 100.00% 108s Depth average: 1.00 (unique kmers) 108s Depth median: 1 (unique kmers) 108s Depth standard deviation: 0.00 (unique kmers) 108s Corrected depth average: 0.00 108s 108s Depth average: 1.00 (all kmers) 108s Depth median: 1 (all kmers) 108s Depth standard deviation: 0.00 (all kmers) 108s 108s Approx. read depth median: 1.91 108s 108s *********** Pass 2 ********** 108s 108s 108s Settings: 108s threads: 4 108s k: 31 108s deterministic: true 108s toss error reads: false 108s passes: 1 108s bits per cell: 16 108s cells: 1053.69M 108s hashes: 3 108s base min quality: 5 108s kmer min prob: 0.5 108s 108s target depth: 100 108s min depth: 5 108s max depth: 100 108s min good kmers: 15 108s depth percentile: 54.0 108s ignore dupe kmers: true 108s fix spikes: false 108s histogram length: 65536 108s 109s Made hash table: hashes = 3 mem = 1.96 GB cells = 1053.64M used = 0.000% 109s 109s Estimated unique kmers: 0 109s 109s Table creation time: 0.573 seconds. 109s Started output threads. 109s Started output threads. 109s Table read time: 0.002 seconds. 0.00 kb/sec 109s Total reads in: 0 NaN% Kept 109s Total bases in: 0 NaN% Kept 109s Error reads in: 0 NaN% 109s Error type 1: 0 NaN% 109s Error type 2: 0 NaN% 109s Error type 3: 0 NaN% 109s Total kmers counted: 0 109s Total unique kmer count: 0 109s Includes forward kmers only. 109s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 109s The most accurate value is the greater of the two. 109s 109s Percent unique: NaN% 109s Depth average: NaN (unique kmers) 109s Depth median: 0 (unique kmers) 109s Depth standard deviation: NaN (unique kmers) 109s Corrected depth average: NaN 109s 109s Depth average: NaN (all kmers) 109s Depth median: 0 (all kmers) 109s Depth standard deviation: 0.00 (all kmers) 109s 109s Approx. read depth median: NaN 109s 109s Removing temp files. 109s 109s Total time: 1.687 seconds. 0.07 kb/sec 109s test -r out4.fastq 109s test -r outt2.fastq 109s test -r hist2.plt 109s autopkgtest [00:54:55]: test run-unit-test: -----------------------] 110s autopkgtest [00:54:56]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 110s run-unit-test PASS 110s autopkgtest [00:54:56]: @@@@@@@@@@@@@@@@@@@@ summary 110s run-unit-test PASS