0s autopkgtest [06:49:17]: starting date and time: 2025-11-01 06:49:17+0000 0s autopkgtest [06:49:17]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [06:49:17]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.lieuj3dg/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 autopkgtest-big-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-s390x-7.secgroup --name adt-resolute-s390x-bbmap-20251101-064917-juju-7f2275-prod-proposed-migration-environment-2-9840c53b-b5d2-4e15-8e4a-80f63f19a9b7 --image adt/ubuntu-resolute-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-s390x -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-s390x-bbmap-20251101-064917-juju-7f2275-prod-proposed-migration-environment-2-9840c53b-b5d2-4e15-8e4a-80f63f19a9b7 from image adt/ubuntu-resolute-s390x-server-20251031.img (UUID 0c045c9f-9f12-44be-973b-1d1fecbe207a)... 51s autopkgtest [06:50:08]: testbed dpkg architecture: s390x 51s autopkgtest [06:50:08]: testbed apt version: 3.1.11 52s autopkgtest [06:50:09]: @@@@@@@@@@@@@@@@@@@@ test bed setup 52s autopkgtest [06:50:09]: testbed release detected to be: None 52s autopkgtest [06:50:09]: updating testbed package index (apt update) 53s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB] 53s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 53s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 53s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 53s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [150 kB] 53s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [9848 B] 53s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [50.7 kB] 53s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [2702 kB] 54s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x Packages [212 kB] 54s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted s390x Packages [940 B] 54s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x Packages [1882 kB] 54s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse s390x Packages [29.2 kB] 54s Fetched 5124 kB in 2s (3407 kB/s) 55s Reading package lists... 55s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 55s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 56s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 56s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 56s Reading package lists... 56s Reading package lists... 56s Building dependency tree... 56s Reading state information... 56s Calculating upgrade... 57s The following packages will be upgraded: 57s gcc-15-base libatomic1 libfribidi0 libgcc-s1 libstdc++6 publicsuffix 57s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 57s Need to get 1174 kB of archives. 57s After this operation, 14.3 kB of additional disk space will be used. 57s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x libatomic1 s390x 15.2.0-7ubuntu1 [9488 B] 57s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x libstdc++6 s390x 15.2.0-7ubuntu1 [907 kB] 57s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x gcc-15-base s390x 15.2.0-7ubuntu1 [58.4 kB] 57s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x libgcc-s1 s390x 15.2.0-7ubuntu1 [35.7 kB] 57s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x libfribidi0 s390x 1.0.16-3 [27.6 kB] 57s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x publicsuffix all 20251016.1743-0.1 [136 kB] 57s dpkg-preconfigure: unable to re-open stdin: No such file or directory 57s Fetched 1174 kB in 1s (1573 kB/s) 58s (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 ... 56953 files and directories currently installed.) 58s Preparing to unpack .../libatomic1_15.2.0-7ubuntu1_s390x.deb ... 58s Unpacking libatomic1:s390x (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 58s Preparing to unpack .../libstdc++6_15.2.0-7ubuntu1_s390x.deb ... 58s Unpacking libstdc++6:s390x (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 58s Preparing to unpack .../gcc-15-base_15.2.0-7ubuntu1_s390x.deb ... 58s Unpacking gcc-15-base:s390x (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 58s Setting up gcc-15-base:s390x (15.2.0-7ubuntu1) ... 58s (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 ... 56953 files and directories currently installed.) 58s Preparing to unpack .../libgcc-s1_15.2.0-7ubuntu1_s390x.deb ... 58s Unpacking libgcc-s1:s390x (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 58s Setting up libgcc-s1:s390x (15.2.0-7ubuntu1) ... 58s (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 ... 56953 files and directories currently installed.) 58s Preparing to unpack .../libfribidi0_1.0.16-3_s390x.deb ... 58s Unpacking libfribidi0:s390x (1.0.16-3) over (1.0.16-1) ... 58s Preparing to unpack .../publicsuffix_20251016.1743-0.1_all.deb ... 58s Unpacking publicsuffix (20251016.1743-0.1) over (20250328.1952-0.1) ... 58s Setting up libfribidi0:s390x (1.0.16-3) ... 58s Setting up libatomic1:s390x (15.2.0-7ubuntu1) ... 58s Setting up publicsuffix (20251016.1743-0.1) ... 58s Setting up libstdc++6:s390x (15.2.0-7ubuntu1) ... 58s Processing triggers for libc-bin (2.42-0ubuntu3) ... 58s autopkgtest [06:50:15]: upgrading testbed (apt dist-upgrade and autopurge) 58s Reading package lists... 58s Building dependency tree... 58s Reading state information... 58s Calculating upgrade... 58s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 59s Reading package lists... 59s Building dependency tree... 59s Reading state information... 59s Solving dependencies... 59s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 61s autopkgtest [06:50:18]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP Mon Sep 22 08:56:47 UTC 2025 61s autopkgtest [06:50:18]: @@@@@@@@@@@@@@@@@@@@ apt-source bbmap 65s Get:1 http://ftpmaster.internal/ubuntu resolute/universe bbmap 39.20+dfsg-2 (dsc) [2286 B] 65s Get:2 http://ftpmaster.internal/ubuntu resolute/universe bbmap 39.20+dfsg-2 (tar) [5748 kB] 65s Get:3 http://ftpmaster.internal/ubuntu resolute/universe bbmap 39.20+dfsg-2 (diff) [26.8 kB] 65s gpgv: Signature made Sun Apr 6 17:54:51 2025 UTC 65s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 65s gpgv: issuer "emollier@debian.org" 65s gpgv: Can't check signature: No public key 65s dpkg-source: warning: cannot verify inline signature for ./bbmap_39.20+dfsg-2.dsc: no acceptable signature found 65s autopkgtest [06:50:22]: testing package bbmap version 39.20+dfsg-2 66s autopkgtest [06:50:23]: build not needed 78s autopkgtest [06:50:35]: test run-unit-test: preparing testbed 78s Reading package lists... 78s Building dependency tree... 78s Reading state information... 78s Solving dependencies... 78s The following NEW packages will be installed: 78s bbmap bbmap-jni ca-certificates-java default-jre-headless java-common 78s libapache-pom-java libcommons-cli-java libcommons-codec-java 78s libcommons-io-java libcommons-parent-java libjpeg-turbo8 libjpeg8 78s libjs-jquery libjs-sphinxdoc libjs-underscore liblcms2-2 liblog4j1.2-java 78s libmpj-java libnspr4 libnss3 libpcsclite1 openjdk-21-jre-headless 78s python-biopython-doc 78s 0 upgraded, 23 newly installed, 0 to remove and 0 not upgraded. 78s Need to get 76.9 MB of archives. 78s After this operation, 250 MB of additional disk space will be used. 78s Get:1 http://ftpmaster.internal/ubuntu resolute/universe s390x libcommons-cli-java all 1.6.0-1 [59.9 kB] 79s Get:2 http://ftpmaster.internal/ubuntu resolute/universe s390x libapache-pom-java all 33-2 [5874 B] 79s Get:3 http://ftpmaster.internal/ubuntu resolute/universe s390x libcommons-parent-java all 56-1 [10.7 kB] 79s Get:4 http://ftpmaster.internal/ubuntu resolute/universe s390x libcommons-codec-java all 1.18.0-1 [303 kB] 79s Get:5 http://ftpmaster.internal/ubuntu resolute/universe s390x libcommons-io-java all 2.19.0-1 [491 kB] 79s Get:6 http://ftpmaster.internal/ubuntu resolute/universe s390x liblog4j1.2-java all 1.2.17-11 [439 kB] 79s Get:7 http://ftpmaster.internal/ubuntu resolute/universe s390x libmpj-java all 0.44+dfsg-4 [443 kB] 79s Get:8 http://ftpmaster.internal/ubuntu resolute/main s390x ca-certificates-java all 20240118 [11.6 kB] 79s Get:9 http://ftpmaster.internal/ubuntu resolute/main s390x java-common all 0.76 [6852 B] 79s Get:10 http://ftpmaster.internal/ubuntu resolute/main s390x liblcms2-2 s390x 2.16-2 [175 kB] 79s Get:11 http://ftpmaster.internal/ubuntu resolute/main s390x libjpeg-turbo8 s390x 2.1.5-4ubuntu2 [147 kB] 79s Get:12 http://ftpmaster.internal/ubuntu resolute/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 79s Get:13 http://ftpmaster.internal/ubuntu resolute/main s390x libnspr4 s390x 2:4.36-1ubuntu2 [125 kB] 79s Get:14 http://ftpmaster.internal/ubuntu resolute/main s390x libnss3 s390x 2:3.114-1 [1506 kB] 79s Get:15 http://ftpmaster.internal/ubuntu resolute/main s390x libpcsclite1 s390x 2.3.3-1 [24.1 kB] 79s Get:16 http://ftpmaster.internal/ubuntu resolute/main s390x openjdk-21-jre-headless s390x 21.0.9+10-1 [43.8 MB] 82s Get:17 http://ftpmaster.internal/ubuntu resolute/main s390x default-jre-headless s390x 2:1.21-76 [3182 B] 82s Get:18 http://ftpmaster.internal/ubuntu resolute/universe s390x bbmap all 39.20+dfsg-2 [10.6 MB] 82s Get:19 http://ftpmaster.internal/ubuntu resolute/universe s390x bbmap-jni s390x 39.20+dfsg-2 [38.3 kB] 82s Get:20 http://ftpmaster.internal/ubuntu resolute/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 82s Get:21 http://ftpmaster.internal/ubuntu resolute/main s390x libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 82s Get:22 http://ftpmaster.internal/ubuntu resolute/main s390x libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 82s Get:23 http://ftpmaster.internal/ubuntu resolute/universe s390x python-biopython-doc all 1.85+dfsg-4 [18.2 MB] 83s Fetched 76.9 MB in 5s (15.6 MB/s) 83s Selecting previously unselected package libcommons-cli-java. 83s (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 ... 56953 files and directories currently installed.) 83s Preparing to unpack .../00-libcommons-cli-java_1.6.0-1_all.deb ... 83s Unpacking libcommons-cli-java (1.6.0-1) ... 83s Selecting previously unselected package libapache-pom-java. 83s Preparing to unpack .../01-libapache-pom-java_33-2_all.deb ... 83s Unpacking libapache-pom-java (33-2) ... 83s Selecting previously unselected package libcommons-parent-java. 83s Preparing to unpack .../02-libcommons-parent-java_56-1_all.deb ... 83s Unpacking libcommons-parent-java (56-1) ... 83s Selecting previously unselected package libcommons-codec-java. 83s Preparing to unpack .../03-libcommons-codec-java_1.18.0-1_all.deb ... 83s Unpacking libcommons-codec-java (1.18.0-1) ... 83s Selecting previously unselected package libcommons-io-java. 83s Preparing to unpack .../04-libcommons-io-java_2.19.0-1_all.deb ... 83s Unpacking libcommons-io-java (2.19.0-1) ... 83s Selecting previously unselected package liblog4j1.2-java. 83s Preparing to unpack .../05-liblog4j1.2-java_1.2.17-11_all.deb ... 83s Unpacking liblog4j1.2-java (1.2.17-11) ... 83s Selecting previously unselected package libmpj-java. 83s Preparing to unpack .../06-libmpj-java_0.44+dfsg-4_all.deb ... 83s Unpacking libmpj-java (0.44+dfsg-4) ... 83s Selecting previously unselected package ca-certificates-java. 83s Preparing to unpack .../07-ca-certificates-java_20240118_all.deb ... 83s Unpacking ca-certificates-java (20240118) ... 83s Selecting previously unselected package java-common. 83s Preparing to unpack .../08-java-common_0.76_all.deb ... 83s Unpacking java-common (0.76) ... 83s Selecting previously unselected package liblcms2-2:s390x. 83s Preparing to unpack .../09-liblcms2-2_2.16-2_s390x.deb ... 83s Unpacking liblcms2-2:s390x (2.16-2) ... 83s Selecting previously unselected package libjpeg-turbo8:s390x. 83s Preparing to unpack .../10-libjpeg-turbo8_2.1.5-4ubuntu2_s390x.deb ... 83s Unpacking libjpeg-turbo8:s390x (2.1.5-4ubuntu2) ... 84s Selecting previously unselected package libjpeg8:s390x. 84s Preparing to unpack .../11-libjpeg8_8c-2ubuntu11_s390x.deb ... 84s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 84s Selecting previously unselected package libnspr4:s390x. 84s Preparing to unpack .../12-libnspr4_2%3a4.36-1ubuntu2_s390x.deb ... 84s Unpacking libnspr4:s390x (2:4.36-1ubuntu2) ... 84s Selecting previously unselected package libnss3:s390x. 84s Preparing to unpack .../13-libnss3_2%3a3.114-1_s390x.deb ... 84s Unpacking libnss3:s390x (2:3.114-1) ... 84s Selecting previously unselected package libpcsclite1:s390x. 84s Preparing to unpack .../14-libpcsclite1_2.3.3-1_s390x.deb ... 84s Unpacking libpcsclite1:s390x (2.3.3-1) ... 84s Selecting previously unselected package openjdk-21-jre-headless:s390x. 84s Preparing to unpack .../15-openjdk-21-jre-headless_21.0.9+10-1_s390x.deb ... 84s Unpacking openjdk-21-jre-headless:s390x (21.0.9+10-1) ... 84s Selecting previously unselected package default-jre-headless. 84s Preparing to unpack .../16-default-jre-headless_2%3a1.21-76_s390x.deb ... 84s Unpacking default-jre-headless (2:1.21-76) ... 84s Selecting previously unselected package bbmap. 84s Preparing to unpack .../17-bbmap_39.20+dfsg-2_all.deb ... 84s Unpacking bbmap (39.20+dfsg-2) ... 84s Selecting previously unselected package bbmap-jni. 84s Preparing to unpack .../18-bbmap-jni_39.20+dfsg-2_s390x.deb ... 84s Unpacking bbmap-jni (39.20+dfsg-2) ... 84s Selecting previously unselected package libjs-jquery. 84s Preparing to unpack .../19-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 84s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 84s Selecting previously unselected package libjs-underscore. 84s Preparing to unpack .../20-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 84s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 84s Selecting previously unselected package libjs-sphinxdoc. 84s Preparing to unpack .../21-libjs-sphinxdoc_8.2.3-1ubuntu2_all.deb ... 84s Unpacking libjs-sphinxdoc (8.2.3-1ubuntu2) ... 84s Selecting previously unselected package python-biopython-doc. 84s Preparing to unpack .../22-python-biopython-doc_1.85+dfsg-4_all.deb ... 84s Unpacking python-biopython-doc (1.85+dfsg-4) ... 85s Setting up liblcms2-2:s390x (2.16-2) ... 85s Setting up java-common (0.76) ... 85s Setting up libcommons-cli-java (1.6.0-1) ... 85s Setting up liblog4j1.2-java (1.2.17-11) ... 85s Setting up libnspr4:s390x (2:4.36-1ubuntu2) ... 85s Setting up libapache-pom-java (33-2) ... 85s Setting up libpcsclite1:s390x (2.3.3-1) ... 85s Setting up libjpeg-turbo8:s390x (2.1.5-4ubuntu2) ... 85s Setting up bbmap-jni (39.20+dfsg-2) ... 85s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 85s Setting up ca-certificates-java (20240118) ... 85s No JRE found. Skipping Java certificates setup. 85s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 85s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 85s Setting up libcommons-parent-java (56-1) ... 85s Setting up libnss3:s390x (2:3.114-1) ... 85s Setting up libjs-sphinxdoc (8.2.3-1ubuntu2) ... 85s Setting up python-biopython-doc (1.85+dfsg-4) ... 85s Setting up libcommons-codec-java (1.18.0-1) ... 85s Setting up openjdk-21-jre-headless:s390x (21.0.9+10-1) ... 85s update-alternatives: using /usr/lib/jvm/java-21-openjdk-s390x/bin/java to provide /usr/bin/java (java) in auto mode 85s update-alternatives: using /usr/lib/jvm/java-21-openjdk-s390x/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 85s update-alternatives: using /usr/lib/jvm/java-21-openjdk-s390x/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 85s update-alternatives: using /usr/lib/jvm/java-21-openjdk-s390x/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 85s update-alternatives: using /usr/lib/jvm/java-21-openjdk-s390x/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 85s Setting up libcommons-io-java (2.19.0-1) ... 85s Setting up libmpj-java (0.44+dfsg-4) ... 85s Processing triggers for libc-bin (2.42-0ubuntu3) ... 85s Processing triggers for man-db (2.13.1-1) ... 85s Processing triggers for ca-certificates-java (20240118) ... 85s Adding debian:ACCVRAIZ1.pem 85s Adding debian:AC_RAIZ_FNMT-RCM.pem 85s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 85s Adding debian:ANF_Secure_Server_Root_CA.pem 85s Adding debian:Actalis_Authentication_Root_CA.pem 86s Adding debian:AffirmTrust_Commercial.pem 86s Adding debian:AffirmTrust_Networking.pem 86s Adding debian:AffirmTrust_Premium.pem 86s Adding debian:AffirmTrust_Premium_ECC.pem 86s Adding debian:Amazon_Root_CA_1.pem 86s Adding debian:Amazon_Root_CA_2.pem 86s Adding debian:Amazon_Root_CA_3.pem 86s Adding debian:Amazon_Root_CA_4.pem 86s Adding debian:Atos_TrustedRoot_2011.pem 86s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 86s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 86s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 86s Adding debian:BJCA_Global_Root_CA1.pem 86s Adding debian:BJCA_Global_Root_CA2.pem 86s Adding debian:Baltimore_CyberTrust_Root.pem 86s Adding debian:Buypass_Class_2_Root_CA.pem 86s Adding debian:Buypass_Class_3_Root_CA.pem 86s Adding debian:CA_Disig_Root_R2.pem 86s Adding debian:CFCA_EV_ROOT.pem 86s Adding debian:COMODO_Certification_Authority.pem 86s Adding debian:COMODO_ECC_Certification_Authority.pem 86s Adding debian:COMODO_RSA_Certification_Authority.pem 86s Adding debian:Certainly_Root_E1.pem 86s Adding debian:Certainly_Root_R1.pem 86s Adding debian:Certigna.pem 86s Adding debian:Certigna_Root_CA.pem 86s Adding debian:Certum_EC-384_CA.pem 86s Adding debian:Certum_Trusted_Network_CA.pem 86s Adding debian:Certum_Trusted_Network_CA_2.pem 86s Adding debian:Certum_Trusted_Root_CA.pem 86s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 86s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 86s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 86s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 86s Adding debian:Comodo_AAA_Services_root.pem 86s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 86s Adding debian:D-TRUST_BR_Root_CA_2_2023.pem 86s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 86s Adding debian:D-TRUST_EV_Root_CA_2_2023.pem 86s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 86s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 86s Adding debian:DigiCert_Assured_ID_Root_CA.pem 86s Adding debian:DigiCert_Assured_ID_Root_G2.pem 86s Adding debian:DigiCert_Assured_ID_Root_G3.pem 86s Adding debian:DigiCert_Global_Root_CA.pem 86s Adding debian:DigiCert_Global_Root_G2.pem 86s Adding debian:DigiCert_Global_Root_G3.pem 86s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 86s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 86s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 86s Adding debian:DigiCert_Trusted_Root_G4.pem 86s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 86s Adding debian:Entrust_Root_Certification_Authority.pem 86s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 86s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 86s Adding debian:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem 86s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 86s Adding debian:GLOBALTRUST_2020.pem 86s Adding debian:GTS_Root_R1.pem 86s Adding debian:GTS_Root_R2.pem 86s Adding debian:GTS_Root_R3.pem 86s Adding debian:GTS_Root_R4.pem 86s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 86s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 86s Adding debian:GlobalSign_Root_CA.pem 86s Adding debian:GlobalSign_Root_CA_-_R3.pem 86s Adding debian:GlobalSign_Root_CA_-_R6.pem 86s Adding debian:GlobalSign_Root_E46.pem 86s Adding debian:GlobalSign_Root_R46.pem 86s Adding debian:Go_Daddy_Class_2_CA.pem 86s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 86s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 86s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 86s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 86s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 86s Adding debian:HiPKI_Root_CA_-_G1.pem 86s Adding debian:Hongkong_Post_Root_CA_3.pem 86s Adding debian:ISRG_Root_X1.pem 86s Adding debian:ISRG_Root_X2.pem 86s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 86s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 86s Adding debian:Izenpe.com.pem 86s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 86s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 86s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 86s Adding debian:NAVER_Global_Root_Certification_Authority.pem 86s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 86s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 86s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 86s Adding debian:QuoVadis_Root_CA_1_G3.pem 86s Adding debian:QuoVadis_Root_CA_2.pem 86s Adding debian:QuoVadis_Root_CA_2_G3.pem 86s Adding debian:QuoVadis_Root_CA_3.pem 86s Adding debian:QuoVadis_Root_CA_3_G3.pem 86s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 86s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 86s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 86s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 86s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 86s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 86s Adding debian:SZAFIR_ROOT_CA2.pem 86s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 86s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 86s Adding debian:SecureSign_Root_CA12.pem 86s Adding debian:SecureSign_Root_CA14.pem 86s Adding debian:SecureSign_Root_CA15.pem 86s Adding debian:SecureTrust_CA.pem 86s Adding debian:Secure_Global_CA.pem 86s Adding debian:Security_Communication_ECC_RootCA1.pem 86s Adding debian:Security_Communication_RootCA2.pem 86s Adding debian:Starfield_Class_2_CA.pem 86s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 86s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 86s Adding debian:SwissSign_Gold_CA_-_G2.pem 86s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 86s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 86s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 86s Adding debian:TWCA_CYBER_Root_CA.pem 86s Adding debian:TWCA_Global_Root_CA.pem 86s Adding debian:TWCA_Root_Certification_Authority.pem 86s Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem 86s Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem 86s Adding debian:TeliaSonera_Root_CA_v1.pem 86s Adding debian:Telia_Root_CA_v2.pem 86s Adding debian:TrustAsia_Global_Root_CA_G3.pem 86s Adding debian:TrustAsia_Global_Root_CA_G4.pem 86s Adding debian:Trustwave_Global_Certification_Authority.pem 86s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 86s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 86s Adding debian:TunTrust_Root_CA.pem 86s Adding debian:UCA_Extended_Validation_Root.pem 86s Adding debian:UCA_Global_G2_Root.pem 86s Adding debian:USERTrust_ECC_Certification_Authority.pem 86s Adding debian:USERTrust_RSA_Certification_Authority.pem 86s Adding debian:XRamp_Global_CA_Root.pem 86s Adding debian:certSIGN_ROOT_CA.pem 86s Adding debian:certSIGN_Root_CA_G2.pem 86s Adding debian:e-Szigno_Root_CA_2017.pem 86s Adding debian:ePKI_Root_Certification_Authority.pem 86s Adding debian:emSign_ECC_Root_CA_-_C3.pem 86s Adding debian:emSign_ECC_Root_CA_-_G3.pem 86s Adding debian:emSign_Root_CA_-_C1.pem 86s Adding debian:emSign_Root_CA_-_G1.pem 86s Adding debian:vTrus_ECC_Root_CA.pem 86s Adding debian:vTrus_Root_CA.pem 86s done. 86s Setting up bbmap (39.20+dfsg-2) ... 86s Setting up default-jre-headless (2:1.21-76) ... 87s autopkgtest [06:50:44]: test run-unit-test: [----------------------- 87s 87s # bbmap 87s bbmap.sh --version 87s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 87s java -ea -Xmx2860m -Xms2860m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 --version 87s BBTools version 39.20 87s For help, please run the shellscript with no parameters, or look in /docs/. 87s bbmap.sh --help 87s 87s BBMap 87s Written by Brian Bushnell, from Dec. 2010 - present 87s Last modified September 15, 2022 87s 87s Description: Fast and accurate splice-aware read aligner. 87s Please read bbmap/docs/guides/BBMapGuide.txt for more information. 87s 87s To index: bbmap.sh ref= 87s To map: bbmap.sh in= out= 87s To map without writing an index: 87s bbmap.sh ref= in= out= nodisk 87s 87s in=stdin will accept reads from standard in, and out=stdout will write to 87s standard out, but file extensions are still needed to specify the format of the 87s input and output files e.g. in=stdin.fa.gz will read gzipped fasta from 87s standard in; out=stdout.sam.gz will write gzipped sam. 87s 87s Indexing Parameters (required when building the index): 87s nodisk=f Set to true to build index in memory and write nothing 87s to disk except output. 87s ref= Specify the reference sequence. Only do this ONCE, 87s when building the index (unless using 'nodisk'). 87s build=1 If multiple references are indexed in the same directory, 87s each needs a unique numeric ID (unless using 'nodisk'). 87s k=13 Kmer length, range 8-15. Longer is faster but uses 87s more memory. Shorter is more sensitive. 87s If indexing and mapping are done in two steps, K should 87s be specified each time. 87s path=<.> Specify the location to write the index, if you don't 87s want it in the current working directory. 87s usemodulo=f Throw away ~80% of kmers based on remainder modulo a 87s number (reduces RAM by 50% and sensitivity slightly). 87s Should be enabled both when building the index AND 87s when mapping. 87s rebuild=f Force a rebuild of the index (ref= should be set). 87s 87s Input Parameters: 87s build=1 Designate index to use. Corresponds to the number 87s specified when building the index. 87s in= Primary reads input; required parameter. 87s in2= For paired reads in two files. 87s interleaved=auto True forces paired/interleaved input; false forces 87s single-ended mapping. If not specified, interleaved 87s status will be autodetected from read names. 87s fastareadlen=500 Break up FASTA reads longer than this. Max is 500 for 87s BBMap and 6000 for BBMapPacBio. Only works for FASTA 87s input (use 'maxlen' for FASTQ input). The default for 87s bbmap.sh is 500, and for mapPacBio.sh is 6000. 87s unpigz=f Spawn a pigz (parallel gzip) process for faster 87s decompression than using Java. 87s Requires pigz to be installed. 87s touppercase=t (tuc) Convert lowercase letters in reads to upper case 87s (otherwise they will not match the reference). 87s 87s Sampling Parameters: 87s 87s reads=-1 Set to a positive number N to only process the first N 87s reads (or pairs), then quit. -1 means use all reads. 87s samplerate=1 Set to a number from 0 to 1 to randomly select that 87s fraction of reads for mapping. 1 uses all reads. 87s skipreads=0 Set to a number N to skip the first N reads (or pairs), 87s then map the rest. 87s 87s Mapping Parameters: 87s fast=f This flag is a macro which sets other paramters to run 87s faster, at reduced sensitivity. Bad for RNA-seq. 87s slow=f This flag is a macro which sets other paramters to run 87s slower, at greater sensitivity. 'vslow' is even slower. 87s maxindel=16000 Don't look for indels longer than this. Lower is faster. 87s Set to >=100k for RNAseq with long introns like mammals. 87s strictmaxindel=f When enabled, do not allow indels longer than 'maxindel'. 87s By default these are not sought, but may be found anyway. 87s tipsearch=100 Look this far for read-end deletions with anchors 87s shorter than K, using brute force. 87s minid=0.76 Approximate minimum alignment identity to look for. 87s Higher is faster and less sensitive. 87s minhits=1 Minimum number of seed hits required for candidate sites. 87s Higher is faster. 87s local=f Set to true to use local, rather than global, alignments. 87s This will soft-clip ugly ends of poor alignments. 87s perfectmode=f Allow only perfect mappings when set to true (very fast). 87s semiperfectmode=f Allow only perfect and semiperfect (perfect except for 87s N's in the reference) mappings. 87s threads=auto (t) Set to number of threads desired. By default, uses 87s all cores available. 87s ambiguous=best (ambig) Set behavior on ambiguously-mapped reads (with 87s multiple top-scoring mapping locations). 87s best (use the first best site) 87s toss (consider unmapped) 87s random (select one top-scoring site randomly) 87s all (retain all top-scoring sites) 87s samestrandpairs=f (ssp) Specify whether paired reads should map to the 87s same strand or opposite strands. 87s requirecorrectstrand=t (rcs) Forbid pairing of reads without correct strand 87s orientation. Set to false for long-mate-pair libraries. 87s killbadpairs=f (kbp) If a read pair is mapped with an inappropriate 87s insert size or orientation, the read with the lower 87s mapping quality is marked unmapped. 87s pairedonly=f (po) Treat unpaired reads as unmapped. Thus they will 87s be sent to 'outu' but not 'outm'. 87s rcomp=f Reverse complement both reads prior to mapping (for LMP 87s outward-facing libraries). 87s rcompmate=f Reverse complement read2 prior to mapping. 87s pairlen=32000 Set max allowed distance between paired reads. 87s (insert size)=(pairlen)+(read1 length)+(read2 length) 87s rescuedist=1200 Don't try to rescue paired reads if avg. insert size 87s greater than this. Lower is faster. 87s rescuemismatches=32 Maximum mismatches allowed in a rescued read. Lower 87s is faster. 87s averagepairdist=100 (apd) Initial average distance between paired reads. 87s Varies dynamically; does not need to be specified. 87s deterministic=f Run in deterministic mode. In this case it is good 87s to set averagepairdist. BBMap is deterministic 87s without this flag if using single-ended reads, 87s or run singlethreaded. 87s bandwidthratio=0 (bwr) If above zero, restrict alignment band to this 87s fraction of read length. Faster but less accurate. 87s bandwidth=0 (bw) Set the bandwidth directly. 87s fraction of read length. Faster but less accurate. 87s usejni=f (jni) Do alignments faster, in C code. Requires 87s compiling the C code; details are in /jni/README.txt. 87s maxsites2=800 Don't analyze (or print) more than this many alignments 87s per read. 87s ignorefrequentkmers=t (ifk) Discard low-information kmers that occur often. 87s excludefraction=0.03 (ef) Fraction of kmers to ignore. For example, 0.03 87s will ignore the most common 3% of kmers. 87s greedy=t Use a greedy algorithm to discard the least-useful 87s kmers on a per-read basis. 87s kfilter=0 If positive, potential mapping sites must have at 87s least this many consecutive exact matches. 87s 87s 87s Quality and Trimming Parameters: 87s qin=auto Set to 33 or 64 to specify input quality value ASCII 87s offset. 33 is Sanger, 64 is old Solexa. 87s qout=auto Set to 33 or 64 to specify output quality value ASCII 87s offset (only if output format is fastq). 87s qtrim=f Quality-trim ends before mapping. Options are: 87s 'f' (false), 'l' (left), 'r' (right), and 'lr' (both). 87s untrim=f Undo trimming after mapping. Untrimmed bases will be 87s soft-clipped in cigar strings. 87s trimq=6 Trim regions with average quality below this 87s (phred algorithm). 87s mintrimlength=60 (mintl) Don't trim reads to be shorter than this. 87s fakefastaquality=-1 (ffq) Set to a positive number 1-50 to generate fake 87s quality strings for fasta input reads. 87s ignorebadquality=f (ibq) Keep going, rather than crashing, if a read has 87s out-of-range quality values. 87s usequality=t Use quality scores when determining which read kmers 87s to use as seeds. 87s minaveragequality=0 (maq) Do not map reads with average quality below this. 87s maqb=0 If positive, calculate maq from this many initial bases. 87s 87s Output Parameters: 87s out= Write all reads to this file. 87s outu= Write only unmapped reads to this file. Does not 87s include unmapped paired reads with a mapped mate. 87s outm= Write only mapped reads to this file. Includes 87s unmapped paired reads with a mapped mate. 87s mappedonly=f If true, treats 'out' like 'outm'. 87s bamscript= (bs) Write a shell script to that will turn 87s the sam output into a sorted, indexed bam file. 87s ordered=f Set to true to output reads in same order as input. 87s Slower and uses more memory. 87s overwrite=f (ow) Allow process to overwrite existing files. 87s secondary=f Print secondary alignments. 87s sssr=0.95 (secondarysitescoreratio) Print only secondary alignments 87s with score of at least this fraction of primary. 87s ssao=f (secondarysiteasambiguousonly) Only print secondary 87s alignments for ambiguously-mapped reads. 87s maxsites=5 Maximum number of total alignments to print per read. 87s Only relevant when secondary=t. 87s quickmatch=f Generate cigar strings more quickly. 87s trimreaddescriptions=f (trd) Truncate read and ref names at the first whitespace, 87s assuming that the remainder is a comment or description. 87s ziplevel=2 (zl) Compression level for zip or gzip output. 87s pigz=f Spawn a pigz (parallel gzip) process for faster 87s compression than Java. Requires pigz to be installed. 87s machineout=f Set to true to output statistics in machine-friendly 87s 'key=value' format. 87s printunmappedcount=f Print the total number of unmapped reads and bases. 87s If input is paired, the number will be of pairs 87s for which both reads are unmapped. 87s showprogress=0 If positive, print a '.' every X reads. 87s showprogress2=0 If positive, print the number of seconds since the 87s last progress update (instead of a '.'). 87s renamebyinsert=f Renames reads based on their mapped insert size. 87s 87s Bloom-Filtering Parameters (bloomfilter.sh is the standalone version). 87s bloom=f Use a Bloom filter to ignore reads not sharing kmers 87s with the reference. This uses more memory, but speeds 87s mapping when most reads don't match the reference. 87s bloomhashes=2 Number of hash functions. 87s bloomminhits=3 Number of consecutive hits to be considered matched. 87s bloomk=31 Bloom filter kmer length. 87s bloomserial=t Use the serialized Bloom filter for greater loading 87s speed, if available. If not, generate and write one. 87s 87s Post-Filtering Parameters: 87s idfilter=0 Independant of minid; sets exact minimum identity 87s allowed for alignments to be printed. Range 0 to 1. 87s subfilter=-1 Ban alignments with more than this many substitutions. 87s insfilter=-1 Ban alignments with more than this many insertions. 87s delfilter=-1 Ban alignments with more than this many deletions. 87s indelfilter=-1 Ban alignments with more than this many indels. 87s editfilter=-1 Ban alignments with more than this many edits. 87s inslenfilter=-1 Ban alignments with an insertion longer than this. 87s dellenfilter=-1 Ban alignments with a deletion longer than this. 87s nfilter=-1 Ban alignments with more than this many ns. This 87s includes nocall, noref, and off scaffold ends. 87s 87s Sam flags and settings: 87s noheader=f Disable generation of header lines. 87s sam=1.4 Set to 1.4 to write Sam version 1.4 cigar strings, 87s with = and X, or 1.3 to use M. 87s saa=t (secondaryalignmentasterisks) Use asterisks instead of 87s bases for sam secondary alignments. 87s cigar=t Set to 'f' to skip generation of cigar strings (faster). 87s keepnames=f Keep original names of paired reads, rather than 87s ensuring both reads have the same name. 87s intronlen=999999999 Set to a lower number like 10 to change 'D' to 'N' in 87s cigar strings for deletions of at least that length. 87s rgid= Set readgroup ID. All other readgroup fields 87s can be set similarly, with the flag rgXX= 87s If you set a readgroup flag to the word 'filename', 87s e.g. rgid=filename, the input file name will be used. 87s mdtag=f Write MD tags. 87s nhtag=f Write NH tags. 87s xmtag=f Write XM tags (may only work correctly with ambig=all). 87s amtag=f Write AM tags. 87s nmtag=f Write NM tags. 87s xstag=f Set to 'xs=fs', 'xs=ss', or 'xs=us' to write XS tags 87s for RNAseq using firststrand, secondstrand, or 87s unstranded libraries. Needed by Cufflinks. 87s JGI mainly uses 'firststrand'. 87s stoptag=f Write a tag indicating read stop location, prefixed by YS:i: 87s lengthtag=f Write a tag indicating (query,ref) alignment lengths, 87s prefixed by YL:Z: 87s idtag=f Write a tag indicating percent identity, prefixed by YI:f: 87s inserttag=f Write a tag indicating insert size, prefixed by X8:Z: 87s scoretag=f Write a tag indicating BBMap's raw score, prefixed by YR:i: 87s timetag=f Write a tag indicating this read's mapping time, prefixed by X0:i: 87s boundstag=f Write a tag indicating whether either read in the pair 87s goes off the end of the reference, prefixed by XB:Z: 87s notags=f Turn off all optional tags. 87s 87s Histogram and statistics output parameters: 87s scafstats= Statistics on how many reads mapped to which scaffold. 87s refstats= Statistics on how many reads mapped to which reference 87s file; only for BBSplit. 87s sortscafs=t Sort scaffolds or references by read count. 87s bhist= Base composition histogram by position. 87s qhist= Quality histogram by position. 87s aqhist= Histogram of average read quality. 87s bqhist= Quality histogram designed for box plots. 87s lhist= Read length histogram. 87s ihist= Write histogram of insert sizes (for paired reads). 87s ehist= Errors-per-read histogram. 87s qahist= Quality accuracy histogram of error rates versus 87s quality score. 87s indelhist= Indel length histogram. 87s mhist= Histogram of match, sub, del, and ins rates by 87s read location. 87s gchist= Read GC content histogram. 87s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 87s gcpairs=t Use average GC of paired reads. 87s idhist= Histogram of read count versus percent identity. 87s idbins=100 Number idhist bins. Set to 'auto' to use read length. 87s statsfile=stderr Mapping statistics are printed here. 87s 87s Coverage output parameters (these may reduce speed and use more RAM): 87s covstats= Per-scaffold coverage info. 87s rpkm= Per-scaffold RPKM/FPKM counts. 87s covhist= Histogram of # occurrences of each depth level. 87s basecov= Coverage per base location. 87s bincov= Print binned coverage per location (one line per X bases). 87s covbinsize=1000 Set the binsize for binned coverage output. 87s nzo=t Only print scaffolds with nonzero coverage. 87s twocolumn=f Change to true to print only ID and Avg_fold instead of 87s all 6 columns to the 'out=' file. 87s 32bit=f Set to true if you need per-base coverage over 64k. 87s strandedcov=f Track coverage for plus and minus strand independently. 87s startcov=f Only track start positions of reads. 87s secondarycov=t Include coverage of secondary alignments. 87s physcov=f Calculate physical coverage for paired reads. 87s This includes the unsequenced bases. 87s delcoverage=t (delcov) Count bases covered by deletions as covered. 87s True is faster than false. 87s covk=0 If positive, calculate kmer coverage statistics. 87s 87s Java Parameters: 87s -Xmx This will set Java's memory usage, 87s overriding autodetection. 87s -Xmx20g will specify 20 gigs of RAM, and -Xmx800m 87s will specify 800 megs. The max is typically 85% of 87s physical memory. The human genome requires around 24g, 87s or 12g with the 'usemodulo' flag. The index uses 87s roughly 6 bytes per reference base. 87s -eoom This flag will cause the process to exit if an 87s out-of-memory exception occurs. Requires Java 8u92+. 87s -da Disable assertions. 87s 87s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter 87s any problems, or post at: http://seqanswers.com/forums/showthread.php?t=41057 87s 87s bbmap.sh ref=example.fasta 87s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 87s java -ea -Xmx2860m -Xms2860m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta 87s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta] 87s Version 39.20 87s 87s No output file. 87s Writing reference. 87s 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] 87s 87s Set genScaffoldInfo=true 87s Writing chunk 1 87s Set genome to 1 87s 87s Loaded Reference: 0.003 seconds. 87s Loading index for chunk 1-1, build 1 87s No index available; generating from reference genome: /tmp/autopkgtest.g6UP1m/autopkgtest_tmp/ref/index/1/chr1_index_k13_c16_b1.block 88s Indexing threads started for block 0-1 88s Indexing threads finished for block 0-1 88s Generated Index: 0.938 seconds. 88s No reads to process; quitting. 88s 88s Total time: 1.030 seconds. 88s test -d ref 88s bbmap.sh in=misc_dna_as_sanger.fastq out=out.sam 88s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 88s java -ea -Xmx2860m -Xms2860m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 in=misc_dna_as_sanger.fastq out=out.sam 88s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, in=misc_dna_as_sanger.fastq, out=out.sam] 88s Version 39.20 88s 88s Retaining first best site only for ambiguous mappings. 88s Set genome to 1 88s 88s Loaded Reference: 0.012 seconds. 88s Loading index for chunk 1-1, build 1 89s Generated Index: 0.429 seconds. 91s Analyzed Index: 1.700 seconds. 91s Started output stream: 0.014 seconds. 91s Cleared Memory: 0.120 seconds. 91s Processing reads in single-ended mode. 91s Started read stream. 91s Started 4 mapping threads. 91s Detecting finished threads: 0, 1, 2, 3 91s 91s ------------------ Results ------------------ 91s 91s Genome: 1 91s Key Length: 13 91s Max Indel: 16000 91s Minimum Score Ratio: 0.56 91s Mapping Mode: normal 91s Reads Used: 4 (153 bases) 91s 91s Mapping: 0.100 seconds. 91s Reads/sec: 39.95 91s kBases/sec: 1.53 91s 91s 91s Read 1 data: pct reads num reads pct bases num bases 91s 91s mapped: 0.0000% 0 0.0000% 0 91s unambiguous: 0.0000% 0 0.0000% 0 91s ambiguous: 0.0000% 0 0.0000% 0 91s low-Q discards: 25.0000% 1 19.6078% 30 91s 91s perfect best site: 0.0000% 0 0.0000% 0 91s semiperfect site: 0.0000% 0 0.0000% 0 91s 91s Match Rate: NA NA NaN% 0 91s Error Rate: NaN% 0 NaN% 0 91s Sub Rate: NaN% 0 NaN% 0 91s Del Rate: NaN% 0 NaN% 0 91s Ins Rate: NaN% 0 NaN% 0 91s N Rate: NaN% 0 NaN% 0 91s 91s Total time: 2.443 seconds. 91s test -r out.sam 91s bbmap.sh ref=example.fasta in=example.fastq out=out2.sam nodisk 91s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 91s java -ea -Xmx2860m -Xms2860m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta in=example.fastq out=out2.sam nodisk 91s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta, in=example.fastq, out=out2.sam, nodisk] 91s Version 39.20 91s 91s Retaining first best site only for ambiguous mappings. 91s 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] 91s 91s Set genScaffoldInfo=true 91s Set genome to 1 91s 91s Loaded Reference: 0.001 seconds. 91s Loading index for chunk 1-1, build 1 91s Indexing threads started for block 0-1 91s Indexing threads finished for block 0-1 91s Generated Index: 0.245 seconds. 93s Analyzed Index: 1.446 seconds. 93s Started output stream: 0.013 seconds. 93s Cleared Memory: 0.113 seconds. 93s Processing reads in single-ended mode. 93s Started read stream. 93s Started 4 mapping threads. 93s Detecting finished threads: 0, 1, 2, 3 93s 93s ------------------ Results ------------------ 93s 93s Genome: 1 93s Key Length: 13 93s Max Indel: 16000 93s Minimum Score Ratio: 0.56 93s Mapping Mode: normal 93s Reads Used: 3 (75 bases) 93s 93s Mapping: 0.100 seconds. 93s Reads/sec: 29.96 93s kBases/sec: 0.75 93s 93s 93s Read 1 data: pct reads num reads pct bases num bases 93s 93s mapped: 100.0000% 3 100.0000% 75 93s unambiguous: 100.0000% 3 100.0000% 75 93s ambiguous: 0.0000% 0 0.0000% 0 93s low-Q discards: 0.0000% 0 0.0000% 0 93s 93s perfect best site: 100.0000% 3 100.0000% 75 93s semiperfect site: 100.0000% 3 100.0000% 75 93s 93s Match Rate: NA NA 100.0000% 75 93s Error Rate: 0.0000% 0 0.0000% 0 93s Sub Rate: 0.0000% 0 0.0000% 0 93s Del Rate: 0.0000% 0 0.0000% 0 93s Ins Rate: 0.0000% 0 0.0000% 0 93s N Rate: 0.0000% 0 0.0000% 0 93s 93s Total time: 2.003 seconds. 93s test -r out2.sam 93s 93s # bbduk 93s bbduk.sh --version 93s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 93s java -ea -Xmx1430m -Xms1430m -cp /usr/share/java/bbmap.jar jgi.BBDuk --version 93s BBTools version 39.20 93s For help, please run the shellscript with no parameters, or look in /docs/. 93s bbduk.sh --help 93s 93s Written by Brian Bushnell 93s Last modified November 18, 2024 93s 93s Description: Compares reads to the kmers in a reference dataset, optionally 93s allowing an edit distance. Splits the reads into two outputs - those that 93s match the reference, and those that don't. Can also trim (remove) the matching 93s parts of the reads rather than binning the reads. 93s Please read bbmap/docs/guides/BBDukGuide.txt for more information. 93s 93s Usage: bbduk.sh in= out= ref= 93s 93s Input may be stdin or a fasta or fastq file, compressed or uncompressed. 93s If you pipe via stdin/stdout, please include the file type; e.g. for gzipped 93s fasta input, set in=stdin.fa.gz 93s 93s Input parameters: 93s in= Main input. in=stdin.fq will pipe from stdin. 93s in2= Input for 2nd read of pairs in a different file. 93s ref= Comma-delimited list of reference files. 93s In addition to filenames, you may also use the keywords: 93s adapters, artifacts, phix, lambda, pjet, mtst, kapa 93s literal= Comma-delimited list of literal reference sequences. 93s Polymers are also allowed with the 'poly' prefix; 93s for example, 'literal=ATGGT,polyGC' will add both ATGGT 93s and GCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGC - 32+ of them, 93s enough replicates to ensure that all kmers are present. 93s touppercase=f (tuc) Change all bases upper-case. 93s interleaved=auto (int) t/f overrides interleaved autodetection. 93s Must be set mainually when streaming fastq input. 93s qin=auto Input quality offset: 33 (Sanger), 64, or auto. 93s reads=-1 If positive, quit after processing X reads or pairs. 93s copyundefined=f (cu) Process non-AGCT IUPAC reference bases by making all 93s possible unambiguous copies. Intended for short motifs 93s or adapter barcodes, as time/memory use is exponential. 93s samplerate=1 Set lower to only process a fraction of input reads. 93s samref= Optional reference fasta for processing sam files. 93s 93s Output parameters: 93s out= (outnonmatch) Write reads here that do not contain 93s kmers matching the database. 'out=stdout.fq' will pipe 93s to standard out. 93s out2= (outnonmatch2) Use this to write 2nd read of pairs to a 93s different file. 93s outm= (outmatch) Write reads here that fail filters. In default 93s kfilter mode, this means any read with a matching kmer. 93s In any mode, it also includes reads that fail filters such 93s as minlength, mingc, maxgc, entropy, etc. In other words, 93s it includes all reads that do not go to 'out'. 93s outm2= (outmatch2) Use this to write 2nd read of pairs to a 93s different file. 93s outs= (outsingle) Use this to write singleton reads whose mate 93s was trimmed shorter than minlen. 93s stats= Write statistics about which contamininants were detected. 93s refstats= Write statistics on a per-reference-file basis. 93s rpkm= Write RPKM for each reference sequence (for RNA-seq). 93s dump= Dump kmer tables to a file, in fasta format. 93s duk= Write statistics in duk's format. *DEPRECATED* 93s nzo=t Only write statistics about ref sequences with nonzero hits. 93s overwrite=t (ow) Grant permission to overwrite files. 93s showspeed=t (ss) 'f' suppresses display of processing speed. 93s ziplevel=2 (zl) Compression level; 1 (min) through 9 (max). 93s fastawrap=70 Length of lines in fasta output. 93s qout=auto Output quality offset: 33 (Sanger), 64, or auto. 93s statscolumns=3 (cols) Number of columns for stats output, 3 or 5. 93s 5 includes base counts. 93s rename=f Rename reads to indicate which sequences they matched. 93s refnames=f Use names of reference files rather than scaffold IDs. 93s trd=f Truncate read and ref names at the first whitespace. 93s ordered=f Set to true to output reads in same order as input. 93s maxbasesout=-1 If positive, quit after writing approximately this many 93s bases to out (outu/outnonmatch). 93s maxbasesoutm=-1 If positive, quit after writing approximately this many 93s bases to outm (outmatch). 93s json=f Print to screen in json format. 93s 93s Histogram output parameters: 93s bhist= Base composition histogram by position. 93s qhist= Quality histogram by position. 93s qchist= Count of bases with each quality value. 93s aqhist= Histogram of average read quality. 93s bqhist= Quality histogram designed for box plots. 93s lhist= Read length histogram. 93s phist= Polymer length histogram. 93s gchist= Read GC content histogram. 93s enthist= Read entropy histogram. 93s ihist= Insert size histogram, for paired reads in mapped sam. 93s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 93s maxhistlen=6000 Set an upper bound for histogram lengths; higher uses 93s more memory. The default is 6000 for some histograms 93s and 80000 for others. 93s 93s Histograms for mapped sam/bam files only: 93s histbefore=t Calculate histograms from reads before processing. 93s ehist= Errors-per-read histogram. 93s qahist= Quality accuracy histogram of error rates versus quality 93s score. 93s indelhist= Indel length histogram. 93s mhist= Histogram of match, sub, del, and ins rates by position. 93s idhist= Histogram of read count versus percent identity. 93s idbins=100 Number idhist bins. Set to 'auto' to use read length. 93s varfile= Ignore substitution errors listed in this file when 93s calculating error rates. Can be generated with 93s CallVariants. 93s vcf= Ignore substitution errors listed in this VCF file 93s when calculating error rates. 93s ignorevcfindels=t Also ignore indels listed in the VCF. 93s 93s Processing parameters: 93s k=27 Kmer length used for finding contaminants. Contaminants 93s shorter than k will not be found. k must be at least 1. 93s rcomp=t Look for reverse-complements of kmers in addition to 93s forward kmers. 93s maskmiddle=t (mm) Treat the middle base of a kmer as a wildcard, to 93s increase sensitivity in the presence of errors. This may 93s also be set to a number, e.g. mm=3, to mask that many bp. 93s The default mm=t corresponds to mm=1 for odd-length kmers 93s and mm=2 for even-length kmers (as of v39.04), while 93s mm=f is always equivalent to mm=0. 93s minkmerhits=1 (mkh) Reads need at least this many matching kmers 93s to be considered as matching the reference. 93s minkmerfraction=0.0 (mkf) A reads needs at least this fraction of its total 93s kmers to hit a ref, in order to be considered a match. 93s If this and minkmerhits are set, the greater is used. 93s mincovfraction=0.0 (mcf) A reads needs at least this fraction of its total 93s bases to be covered by ref kmers to be considered a match. 93s If specified, mcf overrides mkh and mkf. 93s hammingdistance=0 (hdist) Maximum Hamming distance for ref kmers (subs only). 93s Memory use is proportional to (3*K)^hdist. 93s qhdist=0 Hamming distance for query kmers; impacts speed, not memory. 93s editdistance=0 (edist) Maximum edit distance from ref kmers (subs 93s and indels). Memory use is proportional to (8*K)^edist. 93s hammingdistance2=0 (hdist2) Sets hdist for short kmers, when using mink. 93s qhdist2=0 Sets qhdist for short kmers, when using mink. 93s editdistance2=0 (edist2) Sets edist for short kmers, when using mink. 93s forbidn=f (fn) Forbids matching of read kmers containing N. 93s By default, these will match a reference 'A' if 93s hdist>0 or edist>0, to increase sensitivity. 93s removeifeitherbad=t (rieb) Paired reads get sent to 'outmatch' if either is 93s match (or either is trimmed shorter than minlen). 93s Set to false to require both. 93s trimfailures=f Instead of discarding failed reads, trim them to 1bp. 93s This makes the statistics a bit odd. 93s findbestmatch=f (fbm) If multiple matches, associate read with sequence 93s sharing most kmers. Reduces speed. 93s skipr1=f Don't do kmer-based operations on read 1. 93s skipr2=f Don't do kmer-based operations on read 2. 93s ecco=f For overlapping paired reads only. Performs error- 93s correction with BBMerge prior to kmer operations. 93s recalibrate=f (recal) Recalibrate quality scores. Requires calibration 93s matrices generated by CalcTrueQuality. 93s sam= If recalibration is desired, and matrices have not already 93s been generated, BBDuk will create them from the sam file. 93s amino=f Run in amino acid mode. Some features have not been 93s tested, but kmer-matching works fine. Maximum k is 12. 93s 93s Speed and Memory parameters: 93s threads=auto (t) Set number of threads to use; default is number of 93s logical processors. 93s prealloc=f Preallocate memory in table. Allows faster table loading 93s and more efficient memory usage, for a large reference. 93s monitor=f Kill this process if it crashes. monitor=600,0.01 would 93s kill after 600 seconds under 1% usage. 93s minrskip=1 (mns) Force minimal skip interval when indexing reference 93s kmers. 1 means use all, 2 means use every other kmer, etc. 93s maxrskip=1 (mxs) Restrict maximal skip interval when indexing 93s reference kmers. Normally all are used for scaffolds<100kb, 93s but with longer scaffolds, up to maxrskip-1 are skipped. 93s bbduk.sh in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq \ 93s qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 93s rskip= Set both minrskip and maxrskip to the same value. 93s If not set, rskip will vary based on sequence length. 93s qskip=1 Skip query kmers to increase speed. 1 means use all. 93s speed=0 Ignore this fraction of kmer space (0-15 out of 16) in both 93s reads and reference. Increases speed and reduces memory. 93s Note: Do not use more than one of 'speed', 'qskip', and 'rskip'. 93s 93s Trimming/Filtering/Masking parameters: 93s Note - if ktrim, kmask, and ksplit are unset, the default behavior is kfilter. 93s All kmer processing modes are mutually exclusive. 93s Reads only get sent to 'outm' purely based on kmer matches in kfilter mode. 93s 93s ktrim=f Trim reads to remove bases matching reference kmers, plus 93s all bases to the left or right. 93s Values: 93s f (don't trim), 93s r (trim to the right), 93s l (trim to the left) 93s ktrimtips=0 Set this to a positive number to perform ktrim on both 93s ends, examining only the outermost X bases. 93s kmask= Replace bases matching ref kmers with another symbol. 93s Allows any non-whitespace character, and processes short 93s kmers on both ends if mink is set. 'kmask=lc' will 93s convert masked bases to lowercase. 93s maskfullycovered=f (mfc) Only mask bases that are fully covered by kmers. 93s ksplit=f For single-ended reads only. Reads will be split into 93s pairs around the kmer. If the kmer is at the end of the 93s read, it will be trimmed instead. Singletons will go to 93s out, and pairs will go to outm. Do not use ksplit with 93s other operations such as quality-trimming or filtering. 93s mink=0 Look for shorter kmers at read tips down to this length, 93s when k-trimming or masking. 0 means disabled. Enabling 93s this will disable maskmiddle. 93s qtrim=f Trim read ends to remove bases with quality below trimq. 93s Performed AFTER looking for kmers. Values: 93s rl (trim both ends), 93s f (neither end), 93s r (right end only), 93s l (left end only), 93s w (sliding window). 93s trimq=6 Regions with average quality BELOW this will be trimmed, 93s if qtrim is set to something other than f. Can be a 93s floating-point number like 7.3. 93s quantize Bin quality scores to reduce file size. quantize=2 will 93s eliminate all odd quality scores, while quantize=0,10,37 93s will only allow qualty scores of 0, 10, or 37. 93s trimclip=f Trim soft-clipped bases from sam files. 93s minlength=10 (ml) Reads shorter than this after trimming will be 93s discarded. Pairs will be discarded if both are shorter. 93s mlf=0 (minlengthfraction) Reads shorter than this fraction of 93s original length after trimming will be discarded. 93s maxlength= Reads longer than this after trimming will be discarded. 93s minavgquality=0 (maq) Reads with average quality (after trimming) below 93s this will be discarded. 93s maqb=0 If positive, calculate maq from this many initial bases. 93s minbasequality=0 (mbq) Reads with any base below this quality (after 93s trimming) will be discarded. 93s maxns=-1 If non-negative, reads with more Ns than this 93s (after trimming) will be discarded. 93s mcb=0 (minconsecutivebases) Discard reads without at least 93s this many consecutive called bases. 93s ottm=f (outputtrimmedtomatch) Output reads trimmed to shorter 93s than minlength to outm rather than discarding. 93s tp=0 (trimpad) Trim this much extra around matching kmers. 93s tbo=f (trimbyoverlap) Trim adapters based on where paired 93s reads overlap. 93s strictoverlap=t Adjust sensitivity for trimbyoverlap mode. 93s minoverlap=14 Require this many bases of overlap for detection. 93s mininsert=40 Require insert size of at least this for overlap. 93s Should be reduced to 16 for small RNA sequencing. 93s tpe=f (trimpairsevenly) When kmer right-trimming, trim both 93s reads to the minimum length of either. 93s forcetrimleft=0 (ftl) If positive, trim bases to the left of this position 93s (exclusive, 0-based). 93s forcetrimright=0 (ftr) If positive, trim bases to the right of this position 93s (exclusive, 0-based). 93s forcetrimright2=0 (ftr2) If positive, trim this many bases on the right end. 93s forcetrimmod=0 (ftm) If positive, right-trim length to be equal to zero, 93s modulo this number. 93s restrictleft=0 If positive, only look for kmer matches in the 93s leftmost X bases. 93s restrictright=0 If positive, only look for kmer matches in the 93s rightmost X bases. 93s NOTE: restrictleft and restrictright are mutually exclusive. If trimming 93s both ends is desired, use ktrimtips. 93s mingc=0 Discard reads with GC content below this. 93s maxgc=1 Discard reads with GC content above this. 93s gcpairs=t Use average GC of paired reads. 93s Also affects gchist. 93s tossjunk=f Discard reads with invalid characters as bases. 93s swift=f Trim Swift sequences: Trailing C/T/N R1, leading G/A/N R2. 93s 93s Header-parsing parameters - these require Illumina headers: 93s chastityfilter=f (cf) Discard reads with id containing ' 1:Y:' or ' 2:Y:'. 93s barcodefilter=f Remove reads with unexpected barcodes if barcodes is set, 93s or barcodes containing 'N' otherwise. A barcode must be 93s the last part of the read header. Values: 93s t: Remove reads with bad barcodes. 93s f: Ignore barcodes. 93s crash: Crash upon encountering bad barcodes. 93s barcodes= Comma-delimited list of barcodes or files of barcodes. 93s xmin=-1 If positive, discard reads with a lesser X coordinate. 93s ymin=-1 If positive, discard reads with a lesser Y coordinate. 93s xmax=-1 If positive, discard reads with a greater X coordinate. 93s ymax=-1 If positive, discard reads with a greater Y coordinate. 93s 93s Polymer trimming: 93s trimpolya=0 If greater than 0, trim poly-A or poly-T tails of 93s at least this length on either end of reads. 93s trimpolygleft=0 If greater than 0, trim poly-G prefixes of at least this 93s length on the left end of reads. Does not trim poly-C. 93s trimpolygright=0 If greater than 0, trim poly-G tails of at least this 93s length on the right end of reads. Does not trim poly-C. 93s trimpolyg=0 This sets both left and right at once. 93s filterpolyg=0 If greater than 0, remove reads with a poly-G prefix of 93s at least this length (on the left). 93s Note: there are also equivalent poly-C flags. 93s 93s Polymer tracking: 93s pratio=base,base 'pratio=G,C' will print the ratio of G to C polymers. 93s plen=20 Length of homopolymers to count. 93s 93s Entropy/Complexity parameters: 93s entropy=-1 Set between 0 and 1 to filter reads with entropy below 93s that value. Higher is more stringent. 93s entropywindow=50 Calculate entropy using a sliding window of this length. 93s entropyk=5 Calculate entropy using kmers of this length. 93s minbasefrequency=0 Discard reads with a minimum base frequency below this. 93s entropytrim=f Values: 93s f: (false) Do not entropy-trim. 93s r: (right) Trim low entropy on the right end only. 93s l: (left) Trim low entropy on the left end only. 93s rl: (both) Trim low entropy on both ends. 93s entropymask=f Values: 93s f: (filter) Discard low-entropy sequences. 93s t: (true) Mask low-entropy parts of sequences with N. 93s lc: Change low-entropy parts of sequences to lowercase. 93s entropymark=f Mark each base with its entropy value. This is on a scale 93s of 0-41 and is reported as quality scores, so the output 93s should be fastq or fasta+qual. 93s NOTE: If set, entropytrim overrides entropymask. 93s 93s Cardinality estimation: 93s cardinality=f (loglog) Count unique kmers using the LogLog algorithm. 93s cardinalityout=f (loglogout) Count unique kmers in output reads. 93s loglogk=31 Use this kmer length for counting. 93s loglogbuckets=2048 Use this many buckets for counting. 93s khist= Kmer frequency histogram; plots number of kmers versus 93s kmer depth. This is approximate. 93s khistout= Kmer frequency histogram for output reads. 93s 93s Side Channel: 93s sideout= Output for aligned reads. 93s sideref=phix Reference for side-channel alignment; must be a single 93s sequence and virtually repeat-free at selected k. 93s sidek1=17 Kmer length for seeding alignment to reference. 93s sidek2=13 Kmer length for seeding alignment of unaligned reads 93s with an aligned mate. 93s sideminid1=0.66 Minimum identity to accept individual alignments. 93s sideminid2=0.58 Minimum identity for aligning reads with aligned mates. 93s sidemm1=1 Middle mask length for sidek1. 93s sidemm2=1 Middle mask length for sidek2. 93s Note: The side channel is a special additional output that allows alignment 93s to a secondary reference while also doing trimming. Alignment does not affect 93s whether reads go to the normal outputs (out, outm). The main purpose is to 93s simplify pipelines that need trimmed, aligned phiX reads for recalibration. 93s 93s 93s Java Parameters: 93s 93s -Xmx This will set Java's memory usage, overriding autodetection. 93s -Xmx20g will 93s specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 93s The max is typically 85% of physical memory. 93s -eoom This flag will cause the process to exit if an 93s out-of-memory exception occurs. Requires Java 8u92+. 93s -da Disable assertions. 93s 93s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 93s 93s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 93s java -ea -Xmx1430m -Xms1430m -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 93s 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] 93s Version 39.20 93s 93s Changed from ASCII-33 to ASCII-64 on input quality X (Q55) for base A at lines 1 and 3, position 24 while prescanning. 93s Changed from ASCII-33 to ASCII-64 on input quality X (Q55) for base A at lines 1 and 3, position 24 while prescanning. 93s Allocating kmer table: 0.015 seconds. 93s Initial: 93s Memory: max=1499m, total=1499m, free=1467m, used=32m 93s 93s Input is being processed as paired 93s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 93s Started output streams: 0.010 seconds. 93s Processing time: 0.002 seconds. 93s 93s Input: 8 reads 306 bases. 93s QTrimmed: 0 reads (0.00%) 0 bases (0.00%) 93s Total Removed: 8 reads (100.00%) 306 bases (100.00%) 93s Result: 0 reads (0.00%) 0 bases (0.00%) 93s 93s Time: 0.013 seconds. 93s Reads Processed: 8 0.63k reads/sec 93s Bases Processed: 306 0.02m bases/sec 93s test -r out.fastq.gz 93s 93s # bbnorm 93s bbnorm.sh --version 93s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 93s java -ea -Xmx2860m -Xms2860m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 --version 93s BBTools version 39.20 93s For help, please run the shellscript with no parameters, or look in /docs/. 93s bbnorm.sh --help 93s 93s Written by Brian Bushnell 93s Last modified October 19, 2017 93s 93s Description: Normalizes read depth based on kmer counts. 93s Can also error-correct, bin reads by kmer depth, and generate a kmer depth histogram. 93s However, Tadpole has superior error-correction to BBNorm. 93s Please read bbmap/docs/guides/BBNormGuide.txt for more information. 93s 93s Usage: bbnorm.sh in= out= outt= hist= 93s 93s Input parameters: 93s in=null Primary input. Use in2 for paired reads in a second file 93s in2=null Second input file for paired reads in two files 93s extra=null Additional files to use for input (generating hash table) but not for output 93s fastareadlen=2^31 Break up FASTA reads longer than this. Can be useful when processing scaffolded genomes 93s tablereads=-1 Use at most this many reads when building the hashtable (-1 means all) 93s kmersample=1 Process every nth kmer, and skip the rest 93s readsample=1 Process every nth read, and skip the rest 93s 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. 93s qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto. 93s 93s Output parameters: 93s out= File for normalized or corrected reads. Use out2 for paired reads in a second file 93s outt= (outtoss) File for reads that were excluded from primary output 93s reads=-1 Only process this number of reads, then quit (-1 means all) 93s sampleoutput=t Use sampling on output as well as input (not used if sample rates are 1) 93s keepall=f Set to true to keep all reads (e.g. if you just want error correction). 93s 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. 93s Default is false, to prevent confusion about how there can be 0-count kmers. 93s The reason is that based on the 'minq' and 'minprob' settings, some kmers may be excluded from the bloom filter. 93s tmpdir= This will specify a directory for temp files (only needed for multipass runs). If null, they will be written to the output directory. 93s usetempdir=t Allows enabling/disabling of temporary directory; if disabled, temp files will be written to the output directory. 93s qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input). 93s rename=f Rename reads based on their kmer depth. 93s 93s Hashing parameters: 93s k=31 Kmer length (values under 32 are most efficient, but arbitrarily high values are supported) 93s 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. 93s Large values decrease accuracy for a fixed amount of memory, so use the lowest number you can that will still capture highest-depth kmers. 93s hashes=3 Number of times each kmer is hashed and stored. Higher is slower. 93s Higher is MORE accurate if there is enough memory, and LESS accurate if there is not enough memory. 93s 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. 93s prehashes=2 Number of hashes for prefilter. 93s prefilterbits=2 (pbits) Bits per cell in prefilter. 93s prefiltersize=0.35 Fraction of memory to allocate to prefilter. 93s buildpasses=1 More passes can sometimes increase accuracy by iteratively removing low-depth kmers 93s minq=6 Ignore kmers containing bases with quality below this 93s minprob=0.5 Ignore kmers with overall probability of correctness below this 93s 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. 93s 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. 93s 93s Normalization parameters: 93s fixspikes=f (fs) Do a slower, high-precision bloom filter lookup of kmers that appear to have an abnormally high depth due to collisions. 93s target=100 (tgt) Target normalization depth. NOTE: All depth parameters control kmer depth, not read depth. 93s For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1)) 93s maxdepth=-1 (max) Reads will not be downsampled when below this depth, even if they are above the target depth. 93s mindepth=5 (min) Kmers with depth below this number will not be included when calculating the depth of a read. 93s minkmers=15 (mgkpr) Reads must have at least this many kmers over min depth to be retained. Aka 'mingoodkmersperread'. 93s 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. 93s uselowerdepth=t (uld) For pairs, use the depth of the lower read as the depth proxy. 93s deterministic=t (dr) Generate random numbers deterministically to ensure identical output between multiple runs. May decrease speed with a huge number of threads. 93s passes=2 (p) 1 pass is the basic mode. 2 passes (default) allows greater accuracy, error detection, better contol of output depth. 93s 93s Error detection parameters: 93s hdp=90.0 (highdepthpercentile) Position in sorted kmer depth array used as proxy of a read's high kmer depth. 93s ldp=25.0 (lowdepthpercentile) Position in sorted kmer depth array used as proxy of a read's low kmer depth. 93s tossbadreads=f (tbr) Throw away reads detected as containing errors. 93s requirebothbad=f (rbb) Only toss bad pairs if both reads are bad. 93s 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. 93s highthresh=12 (ht) Threshold for high kmer. A high kmer at this or above are considered non-error. 93s lowthresh=3 (lt) Threshold for low kmer. Kmers at this and below are always considered errors. 93s 93s Error correction parameters: 93s ecc=f Set to true to correct errors. NOTE: Tadpole is now preferred for ecc as it does a better job. 93s ecclimit=3 Correct up to this many errors per read. If more are detected, the read will remain unchanged. 93s errorcorrectratio=140 (ecr) Adjacent kmers with a depth ratio of at least this much between will be classified as an error. 93s echighthresh=22 (echt) Threshold for high kmer. A kmer at this or above may be considered non-error. 93s eclowthresh=2 (eclt) Threshold for low kmer. Kmers at this and below are considered errors. 93s eccmaxqual=127 Do not correct bases with quality above this value. 93s aec=f (aggressiveErrorCorrection) Sets more aggressive values of ecr=100, ecclimit=7, echt=16, eclt=3. 93s cec=f (conservativeErrorCorrection) Sets more conservative values of ecr=180, ecclimit=2, echt=30, eclt=1, sl=4, pl=4. 93s meo=f (markErrorsOnly) Marks errors by reducing quality value of suspected errors; does not correct anything. 93s mue=t (markUncorrectableErrors) Marks errors only on uncorrectable reads; requires 'ecc=t'. 93s overlap=f (ecco) Error correct by read overlap. 93s 93s Depth binning parameters: 93s lowbindepth=10 (lbd) Cutoff for low depth bin. 93s highbindepth=80 (hbd) Cutoff for high depth bin. 93s outlow= Pairs in which both reads have a median below lbd go into this file. 93s outhigh= Pairs in which both reads have a median above hbd go into this file. 93s outmid= All other pairs go into this file. 93s 93s Histogram parameters: 93s hist= Specify a file to write the input kmer depth histogram. 93s histout= Specify a file to write the output kmer depth histogram. 93s histcol=3 (histogramcolumns) Number of histogram columns, 2 or 3. 93s pzc=f (printzerocoverage) Print lines in the histogram with zero coverage. 93s histlen=1048576 Max kmer depth displayed in histogram. Also affects statistics displayed, but does not affect normalization. 93s 93s Peak calling parameters: 93s peaks= Write the peaks to this file. Default is stdout. 93s minHeight=2 (h) Ignore peaks shorter than this. 93s minVolume=5 (v) Ignore peaks with less area than this. 93s minWidth=3 (w) Ignore peaks narrower than this. 93s minPeak=2 (minp) Ignore peaks with an X-value below this. 93s maxPeak=BIG (maxp) Ignore peaks with an X-value above this. 93s maxPeakCount=8 (maxpc) Print up to this many peaks (prioritizing height). 93s 93s Java Parameters: 93s -Xmx This will set Java's memory usage, overriding autodetection. 93s -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 93s The max is typically 85% of physical memory. 93s -eoom This flag will cause the process to exit if an 93s out-of-memory exception occurs. Requires Java 8u92+. 93s -da Disable assertions. 93s 93s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 93s 93s bbnorm.sh in=sanger_full_range_original_sanger.fastq qin=33 \ 93s out=out3.fastq outt=outt.fastq hist=hist.plt 93s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 93s java -ea -Xmx2860m -Xms2860m -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 94s Executing jgi.KmerNormalize [bits=32, in=sanger_full_range_original_sanger.fastq, qin=33, out=out3.fastq, outt=outt.fastq, hist=hist.plt] 94s 94s 94s *********** Pass 1 ********** 94s 94s 94s Settings: 94s threads: 4 94s k: 31 94s deterministic: true 94s toss error reads: false 94s passes: 1 94s bits per cell: 16 94s cells: 1059.04M 94s hashes: 3 94s base min quality: 5 94s kmer min prob: 0.5 94s 94s target depth: 400 94s min depth: 3 94s max depth: 500 94s min good kmers: 15 94s depth percentile: 64.8 94s ignore dupe kmers: true 94s fix spikes: false 94s histogram length: 65536 94s print zero cov: false 94s 95s Made hash table: hashes = 3 mem = 1.97 GB cells = 1058.92M used = 0.000% 95s 95s Estimated unique kmers: 4 95s 95s Table creation time: 1.157 seconds. 95s Started output threads. 95s Started output threads. 95s Table read time: 0.004 seconds. 47.36 kb/sec 95s Total reads in: 2 0.000% Kept 95s Total bases in: 188 0.000% Kept 95s Error reads in: 2 100.000% 95s Error type 1: 2 100.000% 95s Error type 2: 0 0.000% 95s Error type 3: 0 0.000% 95s 95s Wrote histogram to hist.plt 95s Total kmers counted: 128 95s Total unique kmer count: 128 95s Includes forward kmers only. 95s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 95s The most accurate value is the greater of the two. 95s 95s Percent unique: 100.00% 95s Depth average: 1.00 (unique kmers) 95s Depth median: 1 (unique kmers) 95s Depth standard deviation: 0.00 (unique kmers) 95s Corrected depth average: 0.00 95s 95s Depth average: 1.00 (all kmers) 95s Depth median: 1 (all kmers) 95s Depth standard deviation: 0.00 (all kmers) 95s 95s Approx. read depth median: 1.47 95s 95s *********** Pass 2 ********** 95s 95s 95s Settings: 95s threads: 4 95s k: 31 95s deterministic: true 95s toss error reads: false 95s passes: 1 95s bits per cell: 16 95s cells: 1059.04M 95s hashes: 3 95s base min quality: 5 95s kmer min prob: 0.5 95s 95s target depth: 100 95s min depth: 5 95s max depth: 100 95s min good kmers: 15 95s depth percentile: 54.0 95s ignore dupe kmers: true 95s fix spikes: false 95s histogram length: 65536 95s 95s Made hash table: hashes = 3 mem = 1.97 GB cells = 1058.92M used = 0.000% 95s 95s Estimated unique kmers: 0 95s 95s Table creation time: 0.569 seconds. 95s Started output threads. 95s Started output threads. 95s Table read time: 0.001 seconds. 0.00 kb/sec 95s Total reads in: 0 NaN% Kept 95s Total bases in: 0 NaN% Kept 95s Error reads in: 0 NaN% 95s Error type 1: 0 NaN% 95s Error type 2: 0 NaN% 95s Error type 3: 0 NaN% 95s Total kmers counted: 0 95s Total unique kmer count: 0 95s Includes forward kmers only. 95s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 95s The most accurate value is the greater of the two. 95s 95s Percent unique: NaN% 95s Depth average: NaN (unique kmers) 95s Depth median: 0 (unique kmers) 95s Depth standard deviation: NaN (unique kmers) 95s Corrected depth average: NaN 95s 95s Depth average: NaN (all kmers) 95s Depth median: 0 (all kmers) 95s Depth standard deviation: 0.00 (all kmers) 95s 95s Approx. read depth median: NaN 95s 95s Removing temp files. 95s 95s Total time: 1.778 seconds. 0.11 kb/sec 95s test -r out3.fastq 95s test -r outt.fastq 95s test -r hist.plt 95s bbnorm.sh in=illumina_full_range_original_illumina.fastq qin=64 \ 95s out=out4.fastq outt=outt2.fastq hist=hist2.plt 96s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 96s java -ea -Xmx2860m -Xms2860m -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 96s Executing jgi.KmerNormalize [bits=32, in=illumina_full_range_original_illumina.fastq, qin=64, out=out4.fastq, outt=outt2.fastq, hist=hist2.plt] 96s 96s 96s *********** Pass 1 ********** 96s 96s 96s Settings: 96s threads: 4 96s k: 31 96s deterministic: true 96s toss error reads: false 96s passes: 1 96s bits per cell: 16 96s cells: 1059.04M 96s hashes: 3 96s base min quality: 5 96s kmer min prob: 0.5 96s 96s target depth: 400 96s min depth: 3 96s max depth: 500 96s min good kmers: 15 96s depth percentile: 64.8 96s ignore dupe kmers: true 96s fix spikes: false 96s histogram length: 65536 96s print zero cov: false 96s 96s Made hash table: hashes = 3 mem = 1.97 GB cells = 1058.92M used = 0.000% 96s 96s Estimated unique kmers: 4 96s 96s Table creation time: 0.652 seconds. 96s Started output threads. 96s Started output threads. 96s Table read time: 0.004 seconds. 29.52 kb/sec 96s Total reads in: 2 0.000% Kept 96s Total bases in: 126 0.000% Kept 96s Error reads in: 2 100.000% 96s Error type 1: 2 100.000% 96s Error type 2: 0 0.000% 96s Error type 3: 0 0.000% 96s 96s Wrote histogram to hist2.plt 96s Total kmers counted: 66 96s Total unique kmer count: 66 96s Includes forward kmers only. 96s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 96s The most accurate value is the greater of the two. 96s 96s Percent unique: 100.00% 96s Depth average: 1.00 (unique kmers) 96s Depth median: 1 (unique kmers) 96s Depth standard deviation: 0.00 (unique kmers) 96s Corrected depth average: 0.00 96s 96s Depth average: 1.00 (all kmers) 96s Depth median: 1 (all kmers) 96s Depth standard deviation: 0.00 (all kmers) 96s 96s Approx. read depth median: 1.91 96s 96s *********** Pass 2 ********** 96s 96s 96s Settings: 96s threads: 4 96s k: 31 96s deterministic: true 96s toss error reads: false 96s passes: 1 96s bits per cell: 16 96s cells: 1059.04M 96s hashes: 3 96s base min quality: 5 96s kmer min prob: 0.5 96s 96s target depth: 100 96s min depth: 5 96s max depth: 100 96s min good kmers: 15 96s depth percentile: 54.0 96s ignore dupe kmers: true 96s fix spikes: false 96s histogram length: 65536 96s 97s Made hash table: hashes = 3 mem = 1.97 GB cells = 1058.92M used = 0.000% 97s 97s Estimated unique kmers: 0 97s 97s Table creation time: 0.379 seconds. 97s Started output threads. 97s Started output threads. 97s Table read time: 0.001 seconds. 0.00 kb/sec 97s Total reads in: 0 NaN% Kept 97s Total bases in: 0 NaN% Kept 97s Error reads in: 0 NaN% 97s Error type 1: 0 NaN% 97s Error type 2: 0 NaN% 97s Error type 3: 0 NaN% 97s Total kmers counted: 0 97s Total unique kmer count: 0 97s Includes forward kmers only. 97s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 97s The most accurate value is the greater of the two. 97s 97s Percent unique: NaN% 97s Depth average: NaN (unique kmers) 97s Depth median: 0 (unique kmers) 97s Depth standard deviation: NaN (unique kmers) 97s Corrected depth average: NaN 97s 97s Depth average: NaN (all kmers) 97s Depth median: 0 (all kmers) 97s Depth standard deviation: 0.00 (all kmers) 97s 97s Approx. read depth median: NaN 97s 97s Removing temp files. 97s 97s Total time: 1.079 seconds. 0.12 kb/sec 97s test -r out4.fastq 97s test -r outt2.fastq 97s test -r hist2.plt 97s autopkgtest [06:50:54]: test run-unit-test: -----------------------] 98s autopkgtest [06:50:55]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 98s run-unit-test PASS 98s autopkgtest [06:50:55]: @@@@@@@@@@@@@@@@@@@@ summary 98s run-unit-test PASS