0s autopkgtest [16:30:33]: starting date and time: 2024-11-02 16:30:33+0000 0s autopkgtest [16:30:33]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [16:30:33]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.93b6p7wb/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:openjdk-24 --apt-upgrade bbmap --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=openjdk-24/24~22ea-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-big-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-ppc64el-1.secgroup --name adt-plucky-ppc64el-bbmap-20241102-163033-juju-7f2275-prod-proposed-migration-environment-15-2579f185-b8b6-4127-afa8-570e65cd0943 --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-ppc64el -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 69s autopkgtest [16:31:42]: testbed dpkg architecture: ppc64el 70s autopkgtest [16:31:43]: testbed apt version: 2.9.8 70s autopkgtest [16:31:43]: @@@@@@@@@@@@@@@@@@@@ test bed setup 70s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 71s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 71s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [175 kB] 71s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [40.4 kB] 71s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [2484 kB] 71s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [210 kB] 71s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [1718 kB] 71s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [47.0 kB] 72s Fetched 4755 kB in 1s (3353 kB/s) 72s Reading package lists... 74s Reading package lists... 74s Building dependency tree... 74s Reading state information... 75s Calculating upgrade... 75s The following packages will be upgraded: 75s python3-zipp 75s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 75s Need to get 10.1 kB of archives. 75s After this operation, 2048 B disk space will be freed. 75s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-zipp all 3.20.2-1 [10.1 kB] 75s Fetched 10.1 kB in 0s (72.7 kB/s) 75s (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 ... 73549 files and directories currently installed.) 75s Preparing to unpack .../python3-zipp_3.20.2-1_all.deb ... 76s Unpacking python3-zipp (3.20.2-1) over (3.20.0-1) ... 76s Setting up python3-zipp (3.20.2-1) ... 76s Reading package lists... 76s Building dependency tree... 76s Reading state information... 76s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 77s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 77s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 77s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 77s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 78s Reading package lists... 78s Reading package lists... 78s Building dependency tree... 78s Reading state information... 78s Calculating upgrade... 78s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 78s Reading package lists... 79s Building dependency tree... 79s Reading state information... 79s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 81s autopkgtest [16:31:54]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 13:49:23 UTC 2024 82s autopkgtest [16:31:55]: @@@@@@@@@@@@@@@@@@@@ apt-source bbmap 84s Get:1 http://ftpmaster.internal/ubuntu plucky/universe bbmap 39.08+dfsg-1 (dsc) [2286 B] 84s Get:2 http://ftpmaster.internal/ubuntu plucky/universe bbmap 39.08+dfsg-1 (tar) [5396 kB] 84s Get:3 http://ftpmaster.internal/ubuntu plucky/universe bbmap 39.08+dfsg-1 (diff) [25.4 kB] 84s gpgv: Signature made Fri Aug 9 08:31:18 2024 UTC 84s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 84s gpgv: issuer "emollier@debian.org" 84s gpgv: Can't check signature: No public key 84s dpkg-source: warning: cannot verify inline signature for ./bbmap_39.08+dfsg-1.dsc: no acceptable signature found 85s autopkgtest [16:31:58]: testing package bbmap version 39.08+dfsg-1 85s autopkgtest [16:31:58]: build not needed 86s autopkgtest [16:31:59]: test run-unit-test: preparing testbed 89s Reading package lists... 89s Building dependency tree... 89s Reading state information... 90s Starting pkgProblemResolver with broken count: 0 90s Starting 2 pkgProblemResolver with broken count: 0 90s Done 90s The following additional packages will be installed: 90s bbmap bbmap-jni ca-certificates-java java-common libapache-pom-java 90s libcommons-cli-java libcommons-codec-java libcommons-io-java 90s libcommons-parent-java libjpeg-turbo8 libjpeg8 liblcms2-2 liblog4j1.2-java 90s libmpj-java libpcsclite1 openjdk-17-jre-headless python-biopython-doc 90s Suggested packages: 90s default-jre liblcms2-utils liblog4j1.2-java-doc libmail-java pcscd 90s libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho 90s fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic 90s Recommended packages: 90s pigz libcups2t64 libfontconfig1 libharfbuzz0b libasound2t64 90s python3-biopython 90s The following NEW packages will be installed: 90s autopkgtest-satdep bbmap bbmap-jni ca-certificates-java java-common 90s libapache-pom-java libcommons-cli-java libcommons-codec-java 90s libcommons-io-java libcommons-parent-java libjpeg-turbo8 libjpeg8 liblcms2-2 90s liblog4j1.2-java libmpj-java libpcsclite1 openjdk-17-jre-headless 90s python-biopython-doc 90s 0 upgraded, 18 newly installed, 0 to remove and 0 not upgraded. 90s Need to get 77.0 MB/77.0 MB of archives. 90s After this operation, 231 MB of additional disk space will be used. 90s Get:1 /tmp/autopkgtest.aHoqH6/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [724 B] 90s Get:2 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libcommons-cli-java all 1.6.0-1 [59.9 kB] 90s Get:3 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libapache-pom-java all 33-2 [5874 B] 90s Get:4 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libcommons-parent-java all 56-1 [10.7 kB] 90s Get:5 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libcommons-codec-java all 1.16.0-1 [306 kB] 90s Get:6 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libcommons-io-java all 2.16.1-1 [451 kB] 90s Get:7 http://ftpmaster.internal/ubuntu plucky/universe ppc64el liblog4j1.2-java all 1.2.17-11 [439 kB] 90s Get:8 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libmpj-java all 0.44+dfsg-4 [443 kB] 91s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el ca-certificates-java all 20240118 [11.6 kB] 91s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el java-common all 0.76 [6852 B] 91s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblcms2-2 ppc64el 2.14-2build1 [233 kB] 91s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu2 [219 kB] 91s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 91s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpcsclite1 ppc64el 2.3.0-1 [30.8 kB] 91s Get:15 http://ftpmaster.internal/ubuntu plucky/universe ppc64el openjdk-17-jre-headless ppc64el 17.0.13+11-2build1 [47.3 MB] 93s Get:16 http://ftpmaster.internal/ubuntu plucky/universe ppc64el bbmap all 39.08+dfsg-1 [10.0 MB] 94s Get:17 http://ftpmaster.internal/ubuntu plucky/universe ppc64el bbmap-jni ppc64el 39.08+dfsg-1 [32.9 kB] 94s Get:18 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python-biopython-doc all 1.83+dfsg1-3 [17.4 MB] 95s Fetched 77.0 MB in 5s (15.8 MB/s) 95s Selecting previously unselected package libcommons-cli-java. 95s (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 ... 73549 files and directories currently installed.) 95s Preparing to unpack .../00-libcommons-cli-java_1.6.0-1_all.deb ... 95s Unpacking libcommons-cli-java (1.6.0-1) ... 95s Selecting previously unselected package libapache-pom-java. 95s Preparing to unpack .../01-libapache-pom-java_33-2_all.deb ... 95s Unpacking libapache-pom-java (33-2) ... 95s Selecting previously unselected package libcommons-parent-java. 95s Preparing to unpack .../02-libcommons-parent-java_56-1_all.deb ... 95s Unpacking libcommons-parent-java (56-1) ... 95s Selecting previously unselected package libcommons-codec-java. 95s Preparing to unpack .../03-libcommons-codec-java_1.16.0-1_all.deb ... 95s Unpacking libcommons-codec-java (1.16.0-1) ... 95s Selecting previously unselected package libcommons-io-java. 95s Preparing to unpack .../04-libcommons-io-java_2.16.1-1_all.deb ... 95s Unpacking libcommons-io-java (2.16.1-1) ... 95s Selecting previously unselected package liblog4j1.2-java. 95s Preparing to unpack .../05-liblog4j1.2-java_1.2.17-11_all.deb ... 95s Unpacking liblog4j1.2-java (1.2.17-11) ... 95s Selecting previously unselected package libmpj-java. 95s Preparing to unpack .../06-libmpj-java_0.44+dfsg-4_all.deb ... 95s Unpacking libmpj-java (0.44+dfsg-4) ... 95s Selecting previously unselected package ca-certificates-java. 95s Preparing to unpack .../07-ca-certificates-java_20240118_all.deb ... 95s Unpacking ca-certificates-java (20240118) ... 95s Selecting previously unselected package java-common. 95s Preparing to unpack .../08-java-common_0.76_all.deb ... 95s Unpacking java-common (0.76) ... 95s Selecting previously unselected package liblcms2-2:ppc64el. 95s Preparing to unpack .../09-liblcms2-2_2.14-2build1_ppc64el.deb ... 95s Unpacking liblcms2-2:ppc64el (2.14-2build1) ... 95s Selecting previously unselected package libjpeg-turbo8:ppc64el. 95s Preparing to unpack .../10-libjpeg-turbo8_2.1.5-2ubuntu2_ppc64el.deb ... 95s Unpacking libjpeg-turbo8:ppc64el (2.1.5-2ubuntu2) ... 95s Selecting previously unselected package libjpeg8:ppc64el. 95s Preparing to unpack .../11-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 95s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 95s Selecting previously unselected package libpcsclite1:ppc64el. 95s Preparing to unpack .../12-libpcsclite1_2.3.0-1_ppc64el.deb ... 95s Unpacking libpcsclite1:ppc64el (2.3.0-1) ... 95s Selecting previously unselected package openjdk-17-jre-headless:ppc64el. 95s Preparing to unpack .../13-openjdk-17-jre-headless_17.0.13+11-2build1_ppc64el.deb ... 95s Unpacking openjdk-17-jre-headless:ppc64el (17.0.13+11-2build1) ... 96s Selecting previously unselected package bbmap. 96s Preparing to unpack .../14-bbmap_39.08+dfsg-1_all.deb ... 96s Unpacking bbmap (39.08+dfsg-1) ... 96s Selecting previously unselected package bbmap-jni. 96s Preparing to unpack .../15-bbmap-jni_39.08+dfsg-1_ppc64el.deb ... 96s Unpacking bbmap-jni (39.08+dfsg-1) ... 96s Selecting previously unselected package python-biopython-doc. 96s Preparing to unpack .../16-python-biopython-doc_1.83+dfsg1-3_all.deb ... 96s Unpacking python-biopython-doc (1.83+dfsg1-3) ... 96s Selecting previously unselected package autopkgtest-satdep. 96s Preparing to unpack .../17-1-autopkgtest-satdep.deb ... 96s Unpacking autopkgtest-satdep (0) ... 96s Setting up liblcms2-2:ppc64el (2.14-2build1) ... 96s Setting up java-common (0.76) ... 96s Setting up libcommons-cli-java (1.6.0-1) ... 96s Setting up liblog4j1.2-java (1.2.17-11) ... 96s Setting up libapache-pom-java (33-2) ... 96s Setting up libpcsclite1:ppc64el (2.3.0-1) ... 96s Setting up libjpeg-turbo8:ppc64el (2.1.5-2ubuntu2) ... 96s Setting up python-biopython-doc (1.83+dfsg1-3) ... 96s Setting up bbmap-jni (39.08+dfsg-1) ... 96s Setting up ca-certificates-java (20240118) ... 96s No JRE found. Skipping Java certificates setup. 96s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 96s Setting up libcommons-parent-java (56-1) ... 96s Setting up openjdk-17-jre-headless:ppc64el (17.0.13+11-2build1) ... 96s update-alternatives: using /usr/lib/jvm/java-17-openjdk-ppc64el/bin/java to provide /usr/bin/java (java) in auto mode 97s update-alternatives: using /usr/lib/jvm/java-17-openjdk-ppc64el/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 97s update-alternatives: using /usr/lib/jvm/java-17-openjdk-ppc64el/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 97s update-alternatives: using /usr/lib/jvm/java-17-openjdk-ppc64el/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 97s update-alternatives: using /usr/lib/jvm/java-17-openjdk-ppc64el/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 97s Setting up libcommons-codec-java (1.16.0-1) ... 97s Setting up libcommons-io-java (2.16.1-1) ... 97s Setting up libmpj-java (0.44+dfsg-4) ... 97s Processing triggers for libc-bin (2.40-1ubuntu3) ... 97s Processing triggers for man-db (2.12.1-3) ... 98s Processing triggers for ca-certificates-java (20240118) ... 98s Adding debian:ACCVRAIZ1.pem 98s Adding debian:AC_RAIZ_FNMT-RCM.pem 98s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 98s Adding debian:ANF_Secure_Server_Root_CA.pem 98s Adding debian:Actalis_Authentication_Root_CA.pem 98s Adding debian:AffirmTrust_Commercial.pem 98s Adding debian:AffirmTrust_Networking.pem 98s Adding debian:AffirmTrust_Premium.pem 98s Adding debian:AffirmTrust_Premium_ECC.pem 98s Adding debian:Amazon_Root_CA_1.pem 98s Adding debian:Amazon_Root_CA_2.pem 98s Adding debian:Amazon_Root_CA_3.pem 98s Adding debian:Amazon_Root_CA_4.pem 98s Adding debian:Atos_TrustedRoot_2011.pem 98s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 98s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 98s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 98s Adding debian:BJCA_Global_Root_CA1.pem 98s Adding debian:BJCA_Global_Root_CA2.pem 98s Adding debian:Baltimore_CyberTrust_Root.pem 98s Adding debian:Buypass_Class_2_Root_CA.pem 98s Adding debian:Buypass_Class_3_Root_CA.pem 98s Adding debian:CA_Disig_Root_R2.pem 98s Adding debian:CFCA_EV_ROOT.pem 98s Adding debian:COMODO_Certification_Authority.pem 98s Adding debian:COMODO_ECC_Certification_Authority.pem 98s Adding debian:COMODO_RSA_Certification_Authority.pem 98s Adding debian:Certainly_Root_E1.pem 98s Adding debian:Certainly_Root_R1.pem 98s Adding debian:Certigna.pem 98s Adding debian:Certigna_Root_CA.pem 98s Adding debian:Certum_EC-384_CA.pem 98s Adding debian:Certum_Trusted_Network_CA.pem 98s Adding debian:Certum_Trusted_Network_CA_2.pem 98s Adding debian:Certum_Trusted_Root_CA.pem 98s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 98s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 98s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 98s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 98s Adding debian:Comodo_AAA_Services_root.pem 98s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 98s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 98s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 98s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 98s Adding debian:DigiCert_Assured_ID_Root_CA.pem 98s Adding debian:DigiCert_Assured_ID_Root_G2.pem 98s Adding debian:DigiCert_Assured_ID_Root_G3.pem 98s Adding debian:DigiCert_Global_Root_CA.pem 98s Adding debian:DigiCert_Global_Root_G2.pem 98s Adding debian:DigiCert_Global_Root_G3.pem 98s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 98s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 98s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 98s Adding debian:DigiCert_Trusted_Root_G4.pem 98s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 98s Adding debian:Entrust_Root_Certification_Authority.pem 98s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 98s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 98s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem 98s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 98s Adding debian:GLOBALTRUST_2020.pem 98s Adding debian:GTS_Root_R1.pem 98s Adding debian:GTS_Root_R2.pem 98s Adding debian:GTS_Root_R3.pem 98s Adding debian:GTS_Root_R4.pem 98s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 98s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 98s Adding debian:GlobalSign_Root_CA.pem 98s Adding debian:GlobalSign_Root_CA_-_R3.pem 98s Adding debian:GlobalSign_Root_CA_-_R6.pem 98s Adding debian:GlobalSign_Root_E46.pem 98s Adding debian:GlobalSign_Root_R46.pem 98s Adding debian:Go_Daddy_Class_2_CA.pem 98s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 98s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 98s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 98s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 98s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 98s Adding debian:HiPKI_Root_CA_-_G1.pem 98s Adding debian:Hongkong_Post_Root_CA_3.pem 98s Adding debian:ISRG_Root_X1.pem 98s Adding debian:ISRG_Root_X2.pem 98s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 98s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 98s Adding debian:Izenpe.com.pem 98s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 98s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 98s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 98s Adding debian:NAVER_Global_Root_Certification_Authority.pem 98s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 98s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 98s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 98s Adding debian:QuoVadis_Root_CA_1_G3.pem 98s Adding debian:QuoVadis_Root_CA_2.pem 98s Adding debian:QuoVadis_Root_CA_2_G3.pem 98s Adding debian:QuoVadis_Root_CA_3.pem 98s Adding debian:QuoVadis_Root_CA_3_G3.pem 98s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 98s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 98s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 98s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 98s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 98s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 98s Adding debian:SZAFIR_ROOT_CA2.pem 98s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 98s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 98s Adding debian:SecureSign_RootCA11.pem 98s Adding debian:SecureTrust_CA.pem 98s Adding debian:Secure_Global_CA.pem 98s Adding debian:Security_Communication_ECC_RootCA1.pem 98s Adding debian:Security_Communication_RootCA2.pem 98s Adding debian:Security_Communication_RootCA3.pem 98s Adding debian:Security_Communication_Root_CA.pem 98s Adding debian:Starfield_Class_2_CA.pem 98s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 98s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 98s Adding debian:SwissSign_Gold_CA_-_G2.pem 98s Adding debian:SwissSign_Silver_CA_-_G2.pem 98s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 98s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 98s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 98s Adding debian:TWCA_Global_Root_CA.pem 98s Adding debian:TWCA_Root_Certification_Authority.pem 98s Adding debian:TeliaSonera_Root_CA_v1.pem 98s Adding debian:Telia_Root_CA_v2.pem 98s Adding debian:TrustAsia_Global_Root_CA_G3.pem 98s Adding debian:TrustAsia_Global_Root_CA_G4.pem 98s Adding debian:Trustwave_Global_Certification_Authority.pem 98s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 98s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 98s Adding debian:TunTrust_Root_CA.pem 98s Adding debian:UCA_Extended_Validation_Root.pem 98s Adding debian:UCA_Global_G2_Root.pem 98s Adding debian:USERTrust_ECC_Certification_Authority.pem 98s Adding debian:USERTrust_RSA_Certification_Authority.pem 98s Adding debian:XRamp_Global_CA_Root.pem 98s Adding debian:certSIGN_ROOT_CA.pem 98s Adding debian:certSIGN_Root_CA_G2.pem 98s Adding debian:e-Szigno_Root_CA_2017.pem 98s Adding debian:ePKI_Root_Certification_Authority.pem 98s Adding debian:emSign_ECC_Root_CA_-_C3.pem 98s Adding debian:emSign_ECC_Root_CA_-_G3.pem 98s Adding debian:emSign_Root_CA_-_C1.pem 98s Adding debian:emSign_Root_CA_-_G1.pem 98s Adding debian:vTrus_ECC_Root_CA.pem 98s Adding debian:vTrus_Root_CA.pem 98s done. 98s Setting up bbmap (39.08+dfsg-1) ... 98s Setting up autopkgtest-satdep (0) ... 101s (Reading database ... 76094 files and directories currently installed.) 101s Removing autopkgtest-satdep (0) ... 101s autopkgtest [16:32:14]: test run-unit-test: [----------------------- 101s 101s # bbmap 101s bbmap.sh --version 101s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 102s java -ea -Xmx2706m -Xms2706m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 --version 102s BBTools version 39.08 102s For help, please run the shellscript with no parameters, or look in /docs/. 102s bbmap.sh --help 102s bbmap.sh ref=example.fasta 102s 102s BBMap 102s Written by Brian Bushnell, from Dec. 2010 - present 102s Last modified September 15, 2022 102s 102s Description: Fast and accurate splice-aware read aligner. 102s Please read bbmap/docs/guides/BBMapGuide.txt for more information. 102s 102s To index: bbmap.sh ref= 102s To map: bbmap.sh in= out= 102s To map without writing an index: 102s bbmap.sh ref= in= out= nodisk 102s 102s in=stdin will accept reads from standard in, and out=stdout will write to 102s standard out, but file extensions are still needed to specify the format of the 102s input and output files e.g. in=stdin.fa.gz will read gzipped fasta from 102s standard in; out=stdout.sam.gz will write gzipped sam. 102s 102s Indexing Parameters (required when building the index): 102s nodisk=f Set to true to build index in memory and write nothing 102s to disk except output. 102s ref= Specify the reference sequence. Only do this ONCE, 102s when building the index (unless using 'nodisk'). 102s build=1 If multiple references are indexed in the same directory, 102s each needs a unique numeric ID (unless using 'nodisk'). 102s k=13 Kmer length, range 8-15. Longer is faster but uses 102s more memory. Shorter is more sensitive. 102s If indexing and mapping are done in two steps, K should 102s be specified each time. 102s path=<.> Specify the location to write the index, if you don't 102s want it in the current working directory. 102s usemodulo=f Throw away ~80% of kmers based on remainder modulo a 102s number (reduces RAM by 50% and sensitivity slightly). 102s Should be enabled both when building the index AND 102s when mapping. 102s rebuild=f Force a rebuild of the index (ref= should be set). 102s 102s Input Parameters: 102s build=1 Designate index to use. Corresponds to the number 102s specified when building the index. 102s in= Primary reads input; required parameter. 102s in2= For paired reads in two files. 102s interleaved=auto True forces paired/interleaved input; false forces 102s single-ended mapping. If not specified, interleaved 102s status will be autodetected from read names. 102s fastareadlen=500 Break up FASTA reads longer than this. Max is 500 for 102s BBMap and 6000 for BBMapPacBio. Only works for FASTA 102s input (use 'maxlen' for FASTQ input). The default for 102s bbmap.sh is 500, and for mapPacBio.sh is 6000. 102s unpigz=f Spawn a pigz (parallel gzip) process for faster 102s decompression than using Java. 102s Requires pigz to be installed. 102s touppercase=t (tuc) Convert lowercase letters in reads to upper case 102s (otherwise they will not match the reference). 102s 102s Sampling Parameters: 102s 102s reads=-1 Set to a positive number N to only process the first N 102s reads (or pairs), then quit. -1 means use all reads. 102s samplerate=1 Set to a number from 0 to 1 to randomly select that 102s fraction of reads for mapping. 1 uses all reads. 102s skipreads=0 Set to a number N to skip the first N reads (or pairs), 102s then map the rest. 102s 102s Mapping Parameters: 102s fast=f This flag is a macro which sets other paramters to run 102s faster, at reduced sensitivity. Bad for RNA-seq. 102s slow=f This flag is a macro which sets other paramters to run 102s slower, at greater sensitivity. 'vslow' is even slower. 102s maxindel=16000 Don't look for indels longer than this. Lower is faster. 102s Set to >=100k for RNAseq with long introns like mammals. 102s strictmaxindel=f When enabled, do not allow indels longer than 'maxindel'. 102s By default these are not sought, but may be found anyway. 102s tipsearch=100 Look this far for read-end deletions with anchors 102s shorter than K, using brute force. 102s minid=0.76 Approximate minimum alignment identity to look for. 102s Higher is faster and less sensitive. 102s minhits=1 Minimum number of seed hits required for candidate sites. 102s Higher is faster. 102s local=f Set to true to use local, rather than global, alignments. 102s This will soft-clip ugly ends of poor alignments. 102s perfectmode=f Allow only perfect mappings when set to true (very fast). 102s semiperfectmode=f Allow only perfect and semiperfect (perfect except for 102s N's in the reference) mappings. 102s threads=auto (t) Set to number of threads desired. By default, uses 102s all cores available. 102s ambiguous=best (ambig) Set behavior on ambiguously-mapped reads (with 102s multiple top-scoring mapping locations). 102s best (use the first best site) 102s toss (consider unmapped) 102s random (select one top-scoring site randomly) 102s all (retain all top-scoring sites) 102s samestrandpairs=f (ssp) Specify whether paired reads should map to the 102s same strand or opposite strands. 102s requirecorrectstrand=t (rcs) Forbid pairing of reads without correct strand 102s orientation. Set to false for long-mate-pair libraries. 102s killbadpairs=f (kbp) If a read pair is mapped with an inappropriate 102s insert size or orientation, the read with the lower 102s mapping quality is marked unmapped. 102s pairedonly=f (po) Treat unpaired reads as unmapped. Thus they will 102s be sent to 'outu' but not 'outm'. 102s rcomp=f Reverse complement both reads prior to mapping (for LMP 102s outward-facing libraries). 102s rcompmate=f Reverse complement read2 prior to mapping. 102s pairlen=32000 Set max allowed distance between paired reads. 102s (insert size)=(pairlen)+(read1 length)+(read2 length) 102s rescuedist=1200 Don't try to rescue paired reads if avg. insert size 102s greater than this. Lower is faster. 102s rescuemismatches=32 Maximum mismatches allowed in a rescued read. Lower 102s is faster. 102s averagepairdist=100 (apd) Initial average distance between paired reads. 102s Varies dynamically; does not need to be specified. 102s deterministic=f Run in deterministic mode. In this case it is good 102s to set averagepairdist. BBMap is deterministic 102s without this flag if using single-ended reads, 102s or run singlethreaded. 102s bandwidthratio=0 (bwr) If above zero, restrict alignment band to this 102s fraction of read length. Faster but less accurate. 102s bandwidth=0 (bw) Set the bandwidth directly. 102s fraction of read length. Faster but less accurate. 102s usejni=f (jni) Do alignments faster, in C code. Requires 102s compiling the C code; details are in /jni/README.txt. 102s maxsites2=800 Don't analyze (or print) more than this many alignments 102s per read. 102s ignorefrequentkmers=t (ifk) Discard low-information kmers that occur often. 102s excludefraction=0.03 (ef) Fraction of kmers to ignore. For example, 0.03 102s will ignore the most common 3% of kmers. 102s greedy=t Use a greedy algorithm to discard the least-useful 102s kmers on a per-read basis. 102s kfilter=0 If positive, potential mapping sites must have at 102s least this many consecutive exact matches. 102s 102s 102s Quality and Trimming Parameters: 102s qin=auto Set to 33 or 64 to specify input quality value ASCII 102s offset. 33 is Sanger, 64 is old Solexa. 102s qout=auto Set to 33 or 64 to specify output quality value ASCII 102s offset (only if output format is fastq). 102s qtrim=f Quality-trim ends before mapping. Options are: 102s 'f' (false), 'l' (left), 'r' (right), and 'lr' (both). 102s untrim=f Undo trimming after mapping. Untrimmed bases will be 102s soft-clipped in cigar strings. 102s trimq=6 Trim regions with average quality below this 102s (phred algorithm). 102s mintrimlength=60 (mintl) Don't trim reads to be shorter than this. 102s fakefastaquality=-1 (ffq) Set to a positive number 1-50 to generate fake 102s quality strings for fasta input reads. 102s ignorebadquality=f (ibq) Keep going, rather than crashing, if a read has 102s out-of-range quality values. 102s usequality=t Use quality scores when determining which read kmers 102s to use as seeds. 102s minaveragequality=0 (maq) Do not map reads with average quality below this. 102s maqb=0 If positive, calculate maq from this many initial bases. 102s 102s Output Parameters: 102s out= Write all reads to this file. 102s outu= Write only unmapped reads to this file. Does not 102s include unmapped paired reads with a mapped mate. 102s outm= Write only mapped reads to this file. Includes 102s unmapped paired reads with a mapped mate. 102s mappedonly=f If true, treats 'out' like 'outm'. 102s bamscript= (bs) Write a shell script to that will turn 102s the sam output into a sorted, indexed bam file. 102s ordered=f Set to true to output reads in same order as input. 102s Slower and uses more memory. 102s overwrite=f (ow) Allow process to overwrite existing files. 102s secondary=f Print secondary alignments. 102s sssr=0.95 (secondarysitescoreratio) Print only secondary alignments 102s with score of at least this fraction of primary. 102s ssao=f (secondarysiteasambiguousonly) Only print secondary 102s alignments for ambiguously-mapped reads. 102s maxsites=5 Maximum number of total alignments to print per read. 102s Only relevant when secondary=t. 102s quickmatch=f Generate cigar strings more quickly. 102s trimreaddescriptions=f (trd) Truncate read and ref names at the first whitespace, 102s assuming that the remainder is a comment or description. 102s ziplevel=2 (zl) Compression level for zip or gzip output. 102s pigz=f Spawn a pigz (parallel gzip) process for faster 102s compression than Java. Requires pigz to be installed. 102s machineout=f Set to true to output statistics in machine-friendly 102s 'key=value' format. 102s printunmappedcount=f Print the total number of unmapped reads and bases. 102s If input is paired, the number will be of pairs 102s for which both reads are unmapped. 102s showprogress=0 If positive, print a '.' every X reads. 102s showprogress2=0 If positive, print the number of seconds since the 102s last progress update (instead of a '.'). 102s renamebyinsert=f Renames reads based on their mapped insert size. 102s 102s Bloom-Filtering Parameters (bloomfilter.sh is the standalone version). 102s bloom=f Use a Bloom filter to ignore reads not sharing kmers 102s with the reference. This uses more memory, but speeds 102s mapping when most reads don't match the reference. 102s bloomhashes=2 Number of hash functions. 102s bloomminhits=3 Number of consecutive hits to be considered matched. 102s bloomk=31 Bloom filter kmer length. 102s bloomserial=t Use the serialized Bloom filter for greater loading 102s speed, if available. If not, generate and write one. 102s 102s Post-Filtering Parameters: 102s idfilter=0 Independant of minid; sets exact minimum identity 102s allowed for alignments to be printed. Range 0 to 1. 102s subfilter=-1 Ban alignments with more than this many substitutions. 102s insfilter=-1 Ban alignments with more than this many insertions. 102s delfilter=-1 Ban alignments with more than this many deletions. 102s indelfilter=-1 Ban alignments with more than this many indels. 102s editfilter=-1 Ban alignments with more than this many edits. 102s inslenfilter=-1 Ban alignments with an insertion longer than this. 102s dellenfilter=-1 Ban alignments with a deletion longer than this. 102s nfilter=-1 Ban alignments with more than this many ns. This 102s includes nocall, noref, and off scaffold ends. 102s 102s Sam flags and settings: 102s noheader=f Disable generation of header lines. 102s sam=1.4 Set to 1.4 to write Sam version 1.4 cigar strings, 102s with = and X, or 1.3 to use M. 102s saa=t (secondaryalignmentasterisks) Use asterisks instead of 102s bases for sam secondary alignments. 102s cigar=t Set to 'f' to skip generation of cigar strings (faster). 102s keepnames=f Keep original names of paired reads, rather than 102s ensuring both reads have the same name. 102s intronlen=999999999 Set to a lower number like 10 to change 'D' to 'N' in 102s cigar strings for deletions of at least that length. 102s rgid= Set readgroup ID. All other readgroup fields 102s can be set similarly, with the flag rgXX= 102s If you set a readgroup flag to the word 'filename', 102s e.g. rgid=filename, the input file name will be used. 102s mdtag=f Write MD tags. 102s nhtag=f Write NH tags. 102s xmtag=f Write XM tags (may only work correctly with ambig=all). 102s amtag=f Write AM tags. 102s nmtag=f Write NM tags. 102s xstag=f Set to 'xs=fs', 'xs=ss', or 'xs=us' to write XS tags 102s for RNAseq using firststrand, secondstrand, or 102s unstranded libraries. Needed by Cufflinks. 102s JGI mainly uses 'firststrand'. 102s stoptag=f Write a tag indicating read stop location, prefixed by YS:i: 102s lengthtag=f Write a tag indicating (query,ref) alignment lengths, 102s prefixed by YL:Z: 102s idtag=f Write a tag indicating percent identity, prefixed by YI:f: 102s inserttag=f Write a tag indicating insert size, prefixed by X8:Z: 102s scoretag=f Write a tag indicating BBMap's raw score, prefixed by YR:i: 102s timetag=f Write a tag indicating this read's mapping time, prefixed by X0:i: 102s boundstag=f Write a tag indicating whether either read in the pair 102s goes off the end of the reference, prefixed by XB:Z: 102s notags=f Turn off all optional tags. 102s 102s Histogram and statistics output parameters: 102s scafstats= Statistics on how many reads mapped to which scaffold. 102s refstats= Statistics on how many reads mapped to which reference 102s file; only for BBSplit. 102s sortscafs=t Sort scaffolds or references by read count. 102s bhist= Base composition histogram by position. 102s qhist= Quality histogram by position. 102s aqhist= Histogram of average read quality. 102s bqhist= Quality histogram designed for box plots. 102s lhist= Read length histogram. 102s ihist= Write histogram of insert sizes (for paired reads). 102s ehist= Errors-per-read histogram. 102s qahist= Quality accuracy histogram of error rates versus 102s quality score. 102s indelhist= Indel length histogram. 102s mhist= Histogram of match, sub, del, and ins rates by 102s read location. 102s gchist= Read GC content histogram. 102s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 102s gcpairs=t Use average GC of paired reads. 102s idhist= Histogram of read count versus percent identity. 102s idbins=100 Number idhist bins. Set to 'auto' to use read length. 102s statsfile=stderr Mapping statistics are printed here. 102s 102s Coverage output parameters (these may reduce speed and use more RAM): 102s covstats= Per-scaffold coverage info. 102s rpkm= Per-scaffold RPKM/FPKM counts. 102s covhist= Histogram of # occurrences of each depth level. 102s basecov= Coverage per base location. 102s bincov= Print binned coverage per location (one line per X bases). 102s covbinsize=1000 Set the binsize for binned coverage output. 102s nzo=t Only print scaffolds with nonzero coverage. 102s twocolumn=f Change to true to print only ID and Avg_fold instead of 102s all 6 columns to the 'out=' file. 102s 32bit=f Set to true if you need per-base coverage over 64k. 102s strandedcov=f Track coverage for plus and minus strand independently. 102s startcov=f Only track start positions of reads. 102s secondarycov=t Include coverage of secondary alignments. 102s physcov=f Calculate physical coverage for paired reads. 102s This includes the unsequenced bases. 102s delcoverage=t (delcov) Count bases covered by deletions as covered. 102s True is faster than false. 102s covk=0 If positive, calculate kmer coverage statistics. 102s 102s Java Parameters: 102s -Xmx This will set Java's memory usage, 102s overriding autodetection. 102s -Xmx20g will specify 20 gigs of RAM, and -Xmx800m 102s will specify 800 megs. The max is typically 85% of 102s physical memory. The human genome requires around 24g, 102s or 12g with the 'usemodulo' flag. The index uses 102s roughly 6 bytes per reference base. 102s -eoom This flag will cause the process to exit if an 102s out-of-memory exception occurs. Requires Java 8u92+. 102s -da Disable assertions. 102s 102s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter 102s any problems, or post at: http://seqanswers.com/forums/showthread.php?t=41057 102s 102s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 102s java -ea -Xmx2706m -Xms2706m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta 102s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta] 102s Version 39.08 102s 102s No output file. 102s Writing reference. 102s 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] 102s 102s Set genScaffoldInfo=true 102s Writing chunk 1 102s Set genome to 1 102s 102s Loaded Reference: 0.006 seconds. 102s Loading index for chunk 1-1, build 1 102s No index available; generating from reference genome: /tmp/autopkgtest.aHoqH6/autopkgtest_tmp/ref/index/1/chr1_index_k13_c16_b1.block 102s Indexing threads started for block 0-1 102s Indexing threads finished for block 0-1 103s Generated Index: 1.243 seconds. 103s No reads to process; quitting. 103s 103s Total time: 1.378 seconds. 103s test -d ref 103s bbmap.sh in=misc_dna_as_sanger.fastq out=out.sam 103s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 103s java -ea -Xmx2706m -Xms2706m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 in=misc_dna_as_sanger.fastq out=out.sam 103s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, in=misc_dna_as_sanger.fastq, out=out.sam] 103s Version 39.08 103s 103s Retaining first best site only for ambiguous mappings. 103s Set genome to 1 103s 103s Loaded Reference: 0.024 seconds. 103s Loading index for chunk 1-1, build 1 104s Generated Index: 0.469 seconds. 108s Analyzed Index: 3.778 seconds. 108s Started output stream: 0.023 seconds. 108s Cleared Memory: 0.112 seconds. 108s Processing reads in single-ended mode. 108s Started read stream. 108s Started 4 mapping threads. 108s Detecting finished threads: 0, 1, 2, 3 108s 108s ------------------ Results ------------------ 108s 108s Genome: 1 108s Key Length: 13 108s Max Indel: 16000 108s Minimum Score Ratio: 0.56 108s Mapping Mode: normal 108s Reads Used: 4 (153 bases) 108s 108s Mapping: 0.057 seconds. 108s Reads/sec: 70.57 108s kBases/sec: 2.70 108s 108s 108s Read 1 data: pct reads num reads pct bases num bases 108s 108s mapped: 0.0000% 0 0.0000% 0 108s unambiguous: 0.0000% 0 0.0000% 0 108s ambiguous: 0.0000% 0 0.0000% 0 108s low-Q discards: 25.0000% 1 19.6078% 30 108s 108s perfect best site: 0.0000% 0 0.0000% 0 108s semiperfect site: 0.0000% 0 0.0000% 0 108s 108s Match Rate: NA NA NaN% 0 108s Error Rate: NaN% 0 NaN% 0 108s Sub Rate: NaN% 0 NaN% 0 108s Del Rate: NaN% 0 NaN% 0 108s Ins Rate: NaN% 0 NaN% 0 108s N Rate: NaN% 0 NaN% 0 108s 108s Total time: 4.573 seconds. 108s test -r out.sam 108s bbmap.sh ref=example.fasta in=example.fastq out=out2.sam nodisk 108s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 108s java -ea -Xmx2706m -Xms2706m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta in=example.fastq out=out2.sam nodisk 108s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta, in=example.fastq, out=out2.sam, nodisk] 108s Version 39.08 108s 108s Retaining first best site only for ambiguous mappings. 108s 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] 108s 108s Set genScaffoldInfo=true 108s Set genome to 1 108s 108s Loaded Reference: 0.002 seconds. 108s Loading index for chunk 1-1, build 1 108s Indexing threads started for block 0-1 108s Indexing threads finished for block 0-1 108s Generated Index: 0.258 seconds. 112s Analyzed Index: 4.100 seconds. 112s Started output stream: 0.022 seconds. 113s Cleared Memory: 0.111 seconds. 113s Processing reads in single-ended mode. 113s Started read stream. 113s Started 4 mapping threads. 113s Detecting finished threads: 0, 1, 2, 3 113s 113s ------------------ Results ------------------ 113s 113s Genome: 1 113s Key Length: 13 113s Max Indel: 16000 113s Minimum Score Ratio: 0.56 113s Mapping Mode: normal 113s Reads Used: 3 (75 bases) 113s 113s Mapping: 0.086 seconds. 113s Reads/sec: 34.87 113s kBases/sec: 0.87 113s 113s 113s Read 1 data: pct reads num reads pct bases num bases 113s 113s mapped: 100.0000% 3 100.0000% 75 113s unambiguous: 100.0000% 3 100.0000% 75 113s ambiguous: 0.0000% 0 0.0000% 0 113s low-Q discards: 0.0000% 0 0.0000% 0 113s 113s perfect best site: 100.0000% 3 100.0000% 75 113s semiperfect site: 100.0000% 3 100.0000% 75 113s 113s Match Rate: NA NA 100.0000% 75 113s Error Rate: 0.0000% 0 0.0000% 0 113s Sub Rate: 0.0000% 0 0.0000% 0 113s Del Rate: 0.0000% 0 0.0000% 0 113s Ins Rate: 0.0000% 0 0.0000% 0 113s N Rate: 0.0000% 0 0.0000% 0 113s 113s Total time: 4.722 seconds. 113s test -r out2.sam 113s 113s # bbduk 113s bbduk.sh --version 113s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 113s java -ea -Xmx1353m -Xms1353m -cp /usr/share/java/bbmap.jar jgi.BBDuk --version 113s BBTools version 39.08 113s For help, please run the shellscript with no parameters, or look in /docs/. 113s bbduk.sh --help 113s 113s Written by Brian Bushnell 113s Last modified November 9, 2023 113s 113s Description: Compares reads to the kmers in a reference dataset, optionally 113s allowing an edit distance. Splits the reads into two outputs - those that 113s match the reference, and those that don't. Can also trim (remove) the matching 113s parts of the reads rather than binning the reads. 113s Please read bbmap/docs/guides/BBDukGuide.txt for more information. 113s 113s Usage: bbduk.sh in= out= ref= 113s 113s Input may be stdin or a fasta or fastq file, compressed or uncompressed. 113s If you pipe via stdin/stdout, please include the file type; e.g. for gzipped 113s fasta input, set in=stdin.fa.gz 113s 113s Input parameters: 113s in= Main input. in=stdin.fq will pipe from stdin. 113s in2= Input for 2nd read of pairs in a different file. 113s ref= Comma-delimited list of reference files. 113s In addition to filenames, you may also use the keywords: 113s adapters, artifacts, phix, lambda, pjet, mtst, kapa 113s literal= Comma-delimited list of literal reference sequences. 113s touppercase=f (tuc) Change all bases upper-case. 113s interleaved=auto (int) t/f overrides interleaved autodetection. 113s bbduk.sh in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq \ 113s qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 113s Must be set mainually when streaming fastq input. 113s qin=auto Input quality offset: 33 (Sanger), 64, or auto. 113s reads=-1 If positive, quit after processing X reads or pairs. 113s copyundefined=f (cu) Process non-AGCT IUPAC reference bases by making all 113s possible unambiguous copies. Intended for short motifs 113s or adapter barcodes, as time/memory use is exponential. 113s samplerate=1 Set lower to only process a fraction of input reads. 113s samref= Optional reference fasta for processing sam files. 113s 113s Output parameters: 113s out= (outnonmatch) Write reads here that do not contain 113s kmers matching the database. 'out=stdout.fq' will pipe 113s to standard out. 113s out2= (outnonmatch2) Use this to write 2nd read of pairs to a 113s different file. 113s outm= (outmatch) Write reads here that fail filters. In default 113s kfilter mode, this means any read with a matching kmer. 113s In any mode, it also includes reads that fail filters such 113s as minlength, mingc, maxgc, entropy, etc. In other words, 113s it includes all reads that do not go to 'out'. 113s outm2= (outmatch2) Use this to write 2nd read of pairs to a 113s different file. 113s outs= (outsingle) Use this to write singleton reads whose mate 113s was trimmed shorter than minlen. 113s stats= Write statistics about which contamininants were detected. 113s refstats= Write statistics on a per-reference-file basis. 113s rpkm= Write RPKM for each reference sequence (for RNA-seq). 113s dump= Dump kmer tables to a file, in fasta format. 113s duk= Write statistics in duk's format. *DEPRECATED* 113s nzo=t Only write statistics about ref sequences with nonzero hits. 113s overwrite=t (ow) Grant permission to overwrite files. 113s showspeed=t (ss) 'f' suppresses display of processing speed. 113s ziplevel=2 (zl) Compression level; 1 (min) through 9 (max). 113s fastawrap=70 Length of lines in fasta output. 113s qout=auto Output quality offset: 33 (Sanger), 64, or auto. 113s statscolumns=3 (cols) Number of columns for stats output, 3 or 5. 113s 5 includes base counts. 113s rename=f Rename reads to indicate which sequences they matched. 113s refnames=f Use names of reference files rather than scaffold IDs. 113s trd=f Truncate read and ref names at the first whitespace. 113s ordered=f Set to true to output reads in same order as input. 113s maxbasesout=-1 If positive, quit after writing approximately this many 113s bases to out (outu/outnonmatch). 113s maxbasesoutm=-1 If positive, quit after writing approximately this many 113s bases to outm (outmatch). 113s json=f Print to screen in json format. 113s 113s Histogram output parameters: 113s bhist= Base composition histogram by position. 113s qhist= Quality histogram by position. 113s qchist= Count of bases with each quality value. 113s aqhist= Histogram of average read quality. 113s bqhist= Quality histogram designed for box plots. 113s lhist= Read length histogram. 113s phist= Polymer length histogram. 113s gchist= Read GC content histogram. 113s enthist= Read entropy histogram. 113s ihist= Insert size histogram, for paired reads in mapped sam. 113s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 113s maxhistlen=6000 Set an upper bound for histogram lengths; higher uses 113s more memory. The default is 6000 for some histograms 113s and 80000 for others. 113s 113s Histograms for mapped sam/bam files only: 113s histbefore=t Calculate histograms from reads before processing. 113s ehist= Errors-per-read histogram. 113s qahist= Quality accuracy histogram of error rates versus quality 113s score. 113s indelhist= Indel length histogram. 113s mhist= Histogram of match, sub, del, and ins rates by position. 113s idhist= Histogram of read count versus percent identity. 113s idbins=100 Number idhist bins. Set to 'auto' to use read length. 113s varfile= Ignore substitution errors listed in this file when 113s calculating error rates. Can be generated with 113s CallVariants. 113s vcf= Ignore substitution errors listed in this VCF file 113s when calculating error rates. 113s ignorevcfindels=t Also ignore indels listed in the VCF. 113s 113s Processing parameters: 113s k=27 Kmer length used for finding contaminants. Contaminants 113s shorter than k will not be found. k must be at least 1. 113s rcomp=t Look for reverse-complements of kmers in addition to 113s forward kmers. 113s maskmiddle=t (mm) Treat the middle base of a kmer as a wildcard, to 113s increase sensitivity in the presence of errors. This may 113s also be set to a number, e.g. mm=3, to mask that many bp. 113s The default mm=t corresponds to mm=1 for odd-length kmers 113s and mm=2 for even-length kmers (as of v39.04), while 113s mm=f is always equivalent to mm=0. 113s minkmerhits=1 (mkh) Reads need at least this many matching kmers 113s to be considered as matching the reference. 113s minkmerfraction=0.0 (mkf) A reads needs at least this fraction of its total 113s kmers to hit a ref, in order to be considered a match. 113s If this and minkmerhits are set, the greater is used. 113s mincovfraction=0.0 (mcf) A reads needs at least this fraction of its total 113s bases to be covered by ref kmers to be considered a match. 113s If specified, mcf overrides mkh and mkf. 113s hammingdistance=0 (hdist) Maximum Hamming distance for ref kmers (subs only). 113s Memory use is proportional to (3*K)^hdist. 113s qhdist=0 Hamming distance for query kmers; impacts speed, not memory. 113s editdistance=0 (edist) Maximum edit distance from ref kmers (subs 113s and indels). Memory use is proportional to (8*K)^edist. 113s hammingdistance2=0 (hdist2) Sets hdist for short kmers, when using mink. 113s qhdist2=0 Sets qhdist for short kmers, when using mink. 113s editdistance2=0 (edist2) Sets edist for short kmers, when using mink. 113s forbidn=f (fn) Forbids matching of read kmers containing N. 113s By default, these will match a reference 'A' if 113s hdist>0 or edist>0, to increase sensitivity. 113s removeifeitherbad=t (rieb) Paired reads get sent to 'outmatch' if either is 113s match (or either is trimmed shorter than minlen). 113s Set to false to require both. 113s trimfailures=f Instead of discarding failed reads, trim them to 1bp. 113s This makes the statistics a bit odd. 113s findbestmatch=f (fbm) If multiple matches, associate read with sequence 113s sharing most kmers. Reduces speed. 113s skipr1=f Don't do kmer-based operations on read 1. 113s skipr2=f Don't do kmer-based operations on read 2. 113s ecco=f For overlapping paired reads only. Performs error- 113s correction with BBMerge prior to kmer operations. 113s recalibrate=f (recal) Recalibrate quality scores. Requires calibration 113s matrices generated by CalcTrueQuality. 113s sam= If recalibration is desired, and matrices have not already 113s been generated, BBDuk will create them from the sam file. 113s amino=f Run in amino acid mode. Some features have not been 113s tested, but kmer-matching works fine. Maximum k is 12. 113s 113s Speed and Memory parameters: 113s threads=auto (t) Set number of threads to use; default is number of 113s logical processors. 113s prealloc=f Preallocate memory in table. Allows faster table loading 113s and more efficient memory usage, for a large reference. 113s monitor=f Kill this process if it crashes. monitor=600,0.01 would 113s kill after 600 seconds under 1% usage. 113s minrskip=1 (mns) Force minimal skip interval when indexing reference 113s kmers. 1 means use all, 2 means use every other kmer, etc. 113s maxrskip=1 (mxs) Restrict maximal skip interval when indexing 113s reference kmers. Normally all are used for scaffolds<100kb, 113s but with longer scaffolds, up to maxrskip-1 are skipped. 113s rskip= Set both minrskip and maxrskip to the same value. 113s If not set, rskip will vary based on sequence length. 113s qskip=1 Skip query kmers to increase speed. 1 means use all. 113s speed=0 Ignore this fraction of kmer space (0-15 out of 16) in both 113s reads and reference. Increases speed and reduces memory. 113s Note: Do not use more than one of 'speed', 'qskip', and 'rskip'. 113s 113s Trimming/Filtering/Masking parameters: 113s Note - if ktrim, kmask, and ksplit are unset, the default behavior is kfilter. 113s All kmer processing modes are mutually exclusive. 113s Reads only get sent to 'outm' purely based on kmer matches in kfilter mode. 113s 113s ktrim=f Trim reads to remove bases matching reference kmers, plus 113s all bases to the left or right. 113s Values: 113s f (don't trim), 113s r (trim to the right), 113s l (trim to the left) 113s ktrimtips=0 Set this to a positive number to perform ktrim on both 113s ends, examining only the outermost X bases. 113s kmask= Replace bases matching ref kmers with another symbol. 113s Allows any non-whitespace character, and processes short 113s kmers on both ends if mink is set. 'kmask=lc' will 113s convert masked bases to lowercase. 113s maskfullycovered=f (mfc) Only mask bases that are fully covered by kmers. 113s ksplit=f For single-ended reads only. Reads will be split into 113s pairs around the kmer. If the kmer is at the end of the 113s read, it will be trimmed instead. Singletons will go to 113s out, and pairs will go to outm. Do not use ksplit with 113s other operations such as quality-trimming or filtering. 113s mink=0 Look for shorter kmers at read tips down to this length, 113s when k-trimming or masking. 0 means disabled. Enabling 113s this will disable maskmiddle. 113s qtrim=f Trim read ends to remove bases with quality below trimq. 113s Performed AFTER looking for kmers. Values: 113s rl (trim both ends), 113s f (neither end), 113s r (right end only), 113s l (left end only), 113s w (sliding window). 113s trimq=6 Regions with average quality BELOW this will be trimmed, 113s if qtrim is set to something other than f. Can be a 113s floating-point number like 7.3. 113s trimclip=f Trim soft-clipped bases from sam files. 113s minlength=10 (ml) Reads shorter than this after trimming will be 113s discarded. Pairs will be discarded if both are shorter. 113s mlf=0 (minlengthfraction) Reads shorter than this fraction of 113s original length after trimming will be discarded. 113s maxlength= Reads longer than this after trimming will be discarded. 113s minavgquality=0 (maq) Reads with average quality (after trimming) below 113s this will be discarded. 113s maqb=0 If positive, calculate maq from this many initial bases. 113s minbasequality=0 (mbq) Reads with any base below this quality (after 113s trimming) will be discarded. 113s maxns=-1 If non-negative, reads with more Ns than this 113s (after trimming) will be discarded. 113s mcb=0 (minconsecutivebases) Discard reads without at least 113s this many consecutive called bases. 113s ottm=f (outputtrimmedtomatch) Output reads trimmed to shorter 113s than minlength to outm rather than discarding. 113s tp=0 (trimpad) Trim this much extra around matching kmers. 113s tbo=f (trimbyoverlap) Trim adapters based on where paired 113s reads overlap. 113s strictoverlap=t Adjust sensitivity for trimbyoverlap mode. 113s minoverlap=14 Require this many bases of overlap for detection. 113s mininsert=40 Require insert size of at least this for overlap. 113s Should be reduced to 16 for small RNA sequencing. 113s tpe=f (trimpairsevenly) When kmer right-trimming, trim both 113s reads to the minimum length of either. 113s forcetrimleft=0 (ftl) If positive, trim bases to the left of this position 113s (exclusive, 0-based). 113s forcetrimright=0 (ftr) If positive, trim bases to the right of this position 113s (exclusive, 0-based). 113s forcetrimright2=0 (ftr2) If positive, trim this many bases on the right end. 113s forcetrimmod=0 (ftm) If positive, right-trim length to be equal to zero, 113s modulo this number. 113s restrictleft=0 If positive, only look for kmer matches in the 113s leftmost X bases. 113s restrictright=0 If positive, only look for kmer matches in the 113s rightmost X bases. 113s NOTE: restrictleft and restrictright are mutually exclusive. If trimming 113s both ends is desired, use ktrimtips. 113s mingc=0 Discard reads with GC content below this. 113s maxgc=1 Discard reads with GC content above this. 113s gcpairs=t Use average GC of paired reads. 113s Also affects gchist. 113s tossjunk=f Discard reads with invalid characters as bases. 113s swift=f Trim Swift sequences: Trailing C/T/N R1, leading G/A/N R2. 113s 113s Header-parsing parameters - these require Illumina headers: 113s chastityfilter=f (cf) Discard reads with id containing ' 1:Y:' or ' 2:Y:'. 113s barcodefilter=f Remove reads with unexpected barcodes if barcodes is set, 113s or barcodes containing 'N' otherwise. A barcode must be 113s the last part of the read header. Values: 113s t: Remove reads with bad barcodes. 113s f: Ignore barcodes. 113s crash: Crash upon encountering bad barcodes. 113s barcodes= Comma-delimited list of barcodes or files of barcodes. 113s xmin=-1 If positive, discard reads with a lesser X coordinate. 113s ymin=-1 If positive, discard reads with a lesser Y coordinate. 113s xmax=-1 If positive, discard reads with a greater X coordinate. 113s ymax=-1 If positive, discard reads with a greater Y coordinate. 113s 113s Polymer trimming: 113s trimpolya=0 If greater than 0, trim poly-A or poly-T tails of 113s at least this length on either end of reads. 113s trimpolygleft=0 If greater than 0, trim poly-G prefixes of at least this 113s length on the left end of reads. Does not trim poly-C. 113s trimpolygright=0 If greater than 0, trim poly-G tails of at least this 113s length on the right end of reads. Does not trim poly-C. 113s trimpolyg=0 This sets both left and right at once. 113s filterpolyg=0 If greater than 0, remove reads with a poly-G prefix of 113s at least this length (on the left). 113s Note: there are also equivalent poly-C flags. 113s 113s Polymer tracking: 113s pratio=base,base 'pratio=G,C' will print the ratio of G to C polymers. 113s plen=20 Length of homopolymers to count. 113s 113s Entropy/Complexity parameters: 113s entropy=-1 Set between 0 and 1 to filter reads with entropy below 113s that value. Higher is more stringent. 113s entropywindow=50 Calculate entropy using a sliding window of this length. 113s entropyk=5 Calculate entropy using kmers of this length. 113s minbasefrequency=0 Discard reads with a minimum base frequency below this. 113s entropytrim=f Values: 113s f: (false) Do not entropy-trim. 113s r: (right) Trim low entropy on the right end only. 113s l: (left) Trim low entropy on the left end only. 113s rl: (both) Trim low entropy on both ends. 113s entropymask=f Values: 113s f: (filter) Discard low-entropy sequences. 113s t: (true) Mask low-entropy parts of sequences with N. 113s lc: Change low-entropy parts of sequences to lowercase. 113s entropymark=f Mark each base with its entropy value. This is on a scale 113s of 0-41 and is reported as quality scores, so the output 113s should be fastq or fasta+qual. 113s NOTE: If set, entropytrim overrides entropymask. 113s 113s Cardinality estimation: 113s cardinality=f (loglog) Count unique kmers using the LogLog algorithm. 113s cardinalityout=f (loglogout) Count unique kmers in output reads. 113s loglogk=31 Use this kmer length for counting. 113s loglogbuckets=2048 Use this many buckets for counting. 113s khist= Kmer frequency histogram; plots number of kmers versus 113s kmer depth. This is approximate. 113s khistout= Kmer frequency histogram for output reads. 113s 113s Java Parameters: 113s 113s -Xmx This will set Java's memory usage, overriding autodetection. 113s -Xmx20g will 113s specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 113s The max is typically 85% of physical memory. 113s -eoom This flag will cause the process to exit if an 113s out-of-memory exception occurs. Requires Java 8u92+. 113s -da Disable assertions. 113s 113s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 113s 113s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 113s java -ea -Xmx1353m -Xms1353m -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 113s 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] 113s Version 39.08 113s 113s Changed from ASCII-33 to ASCII-64 on input quality X (Q55) for base A at lines 1 and 3, position 24 while prescanning. 113s Changed from ASCII-33 to ASCII-64 on input quality X (Q55) for base A at lines 1 and 3, position 24 while prescanning. 113s 0.013 seconds. 113s Initial: 113s Memory: max=1442m, total=1442m, free=1412m, used=30m 113s 113s Input is being processed as paired 113s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 113s Started output streams: 0.015 seconds. 113s Processing time: 0.004 seconds. 113s 113s Input: 8 reads 306 bases. 113s QTrimmed: 0 reads (0.00%) 0 bases (0.00%) 113s Total Removed: 8 reads (100.00%) 306 bases (100.00%) 113s Result: 0 reads (0.00%) 0 bases (0.00%) 113s 113s Time: 0.021 seconds. 113s Reads Processed: 8 0.38k reads/sec 113s Bases Processed: 306 0.01m bases/sec 113s test -r out.fastq.gz 113s 113s # bbnorm 113s bbnorm.sh --version 113s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 113s java -ea -Xmx2706m -Xms2706m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 --version 113s BBTools version 39.08 113s For help, please run the shellscript with no parameters, or look in /docs/. 113s bbnorm.sh --help 113s bbnorm.sh in=sanger_full_range_original_sanger.fastq qin=33 \ 113s out=out3.fastq outt=outt.fastq hist=hist.plt 113s 113s Written by Brian Bushnell 113s Last modified October 19, 2017 113s 113s Description: Normalizes read depth based on kmer counts. 113s Can also error-correct, bin reads by kmer depth, and generate a kmer depth histogram. 113s However, Tadpole has superior error-correction to BBNorm. 113s Please read bbmap/docs/guides/BBNormGuide.txt for more information. 113s 113s Usage: bbnorm.sh in= out= outt= hist= 113s 113s Input parameters: 113s in=null Primary input. Use in2 for paired reads in a second file 113s in2=null Second input file for paired reads in two files 113s extra=null Additional files to use for input (generating hash table) but not for output 113s fastareadlen=2^31 Break up FASTA reads longer than this. Can be useful when processing scaffolded genomes 113s tablereads=-1 Use at most this many reads when building the hashtable (-1 means all) 113s kmersample=1 Process every nth kmer, and skip the rest 113s readsample=1 Process every nth read, and skip the rest 113s 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. 113s qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto. 113s 113s Output parameters: 113s out= File for normalized or corrected reads. Use out2 for paired reads in a second file 113s outt= (outtoss) File for reads that were excluded from primary output 113s reads=-1 Only process this number of reads, then quit (-1 means all) 113s sampleoutput=t Use sampling on output as well as input (not used if sample rates are 1) 113s keepall=f Set to true to keep all reads (e.g. if you just want error correction). 113s 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. 113s Default is false, to prevent confusion about how there can be 0-count kmers. 113s The reason is that based on the 'minq' and 'minprob' settings, some kmers may be excluded from the bloom filter. 113s tmpdir= This will specify a directory for temp files (only needed for multipass runs). If null, they will be written to the output directory. 113s usetempdir=t Allows enabling/disabling of temporary directory; if disabled, temp files will be written to the output directory. 113s qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input). 113s rename=f Rename reads based on their kmer depth. 113s 113s Hashing parameters: 113s k=31 Kmer length (values under 32 are most efficient, but arbitrarily high values are supported) 113s 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. 113s Large values decrease accuracy for a fixed amount of memory, so use the lowest number you can that will still capture highest-depth kmers. 113s hashes=3 Number of times each kmer is hashed and stored. Higher is slower. 113s Higher is MORE accurate if there is enough memory, and LESS accurate if there is not enough memory. 113s 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. 113s prehashes=2 Number of hashes for prefilter. 113s prefilterbits=2 (pbits) Bits per cell in prefilter. 113s prefiltersize=0.35 Fraction of memory to allocate to prefilter. 113s buildpasses=1 More passes can sometimes increase accuracy by iteratively removing low-depth kmers 113s minq=6 Ignore kmers containing bases with quality below this 113s minprob=0.5 Ignore kmers with overall probability of correctness below this 113s 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. 113s 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. 113s 113s Normalization parameters: 113s fixspikes=f (fs) Do a slower, high-precision bloom filter lookup of kmers that appear to have an abnormally high depth due to collisions. 113s target=100 (tgt) Target normalization depth. NOTE: All depth parameters control kmer depth, not read depth. 113s For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1)) 113s maxdepth=-1 (max) Reads will not be downsampled when below this depth, even if they are above the target depth. 113s mindepth=5 (min) Kmers with depth below this number will not be included when calculating the depth of a read. 113s minkmers=15 (mgkpr) Reads must have at least this many kmers over min depth to be retained. Aka 'mingoodkmersperread'. 113s 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. 113s uselowerdepth=t (uld) For pairs, use the depth of the lower read as the depth proxy. 113s deterministic=t (dr) Generate random numbers deterministically to ensure identical output between multiple runs. May decrease speed with a huge number of threads. 113s passes=2 (p) 1 pass is the basic mode. 2 passes (default) allows greater accuracy, error detection, better contol of output depth. 113s 113s Error detection parameters: 113s hdp=90.0 (highdepthpercentile) Position in sorted kmer depth array used as proxy of a read's high kmer depth. 113s ldp=25.0 (lowdepthpercentile) Position in sorted kmer depth array used as proxy of a read's low kmer depth. 113s tossbadreads=f (tbr) Throw away reads detected as containing errors. 113s requirebothbad=f (rbb) Only toss bad pairs if both reads are bad. 113s 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. 113s highthresh=12 (ht) Threshold for high kmer. A high kmer at this or above are considered non-error. 113s lowthresh=3 (lt) Threshold for low kmer. Kmers at this and below are always considered errors. 113s 113s Error correction parameters: 113s ecc=f Set to true to correct errors. NOTE: Tadpole is now preferred for ecc as it does a better job. 113s ecclimit=3 Correct up to this many errors per read. If more are detected, the read will remain unchanged. 113s errorcorrectratio=140 (ecr) Adjacent kmers with a depth ratio of at least this much between will be classified as an error. 113s echighthresh=22 (echt) Threshold for high kmer. A kmer at this or above may be considered non-error. 113s eclowthresh=2 (eclt) Threshold for low kmer. Kmers at this and below are considered errors. 113s eccmaxqual=127 Do not correct bases with quality above this value. 113s aec=f (aggressiveErrorCorrection) Sets more aggressive values of ecr=100, ecclimit=7, echt=16, eclt=3. 113s cec=f (conservativeErrorCorrection) Sets more conservative values of ecr=180, ecclimit=2, echt=30, eclt=1, sl=4, pl=4. 113s meo=f (markErrorsOnly) Marks errors by reducing quality value of suspected errors; does not correct anything. 113s mue=t (markUncorrectableErrors) Marks errors only on uncorrectable reads; requires 'ecc=t'. 113s overlap=f (ecco) Error correct by read overlap. 113s 113s Depth binning parameters: 113s lowbindepth=10 (lbd) Cutoff for low depth bin. 113s highbindepth=80 (hbd) Cutoff for high depth bin. 113s outlow= Pairs in which both reads have a median below lbd go into this file. 113s outhigh= Pairs in which both reads have a median above hbd go into this file. 113s outmid= All other pairs go into this file. 113s 113s Histogram parameters: 113s hist= Specify a file to write the input kmer depth histogram. 113s histout= Specify a file to write the output kmer depth histogram. 113s histcol=3 (histogramcolumns) Number of histogram columns, 2 or 3. 113s pzc=f (printzerocoverage) Print lines in the histogram with zero coverage. 113s histlen=1048576 Max kmer depth displayed in histogram. Also affects statistics displayed, but does not affect normalization. 113s 113s Peak calling parameters: 113s peaks= Write the peaks to this file. Default is stdout. 113s minHeight=2 (h) Ignore peaks shorter than this. 113s minVolume=5 (v) Ignore peaks with less area than this. 113s minWidth=3 (w) Ignore peaks narrower than this. 113s minPeak=2 (minp) Ignore peaks with an X-value below this. 113s maxPeak=BIG (maxp) Ignore peaks with an X-value above this. 113s maxPeakCount=8 (maxpc) Print up to this many peaks (prioritizing height). 113s 113s Java Parameters: 113s -Xmx This will set Java's memory usage, overriding autodetection. 113s -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 113s The max is typically 85% of physical memory. 113s -eoom This flag will cause the process to exit if an 113s out-of-memory exception occurs. Requires Java 8u92+. 113s -da Disable assertions. 113s 113s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 113s 113s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 113s java -ea -Xmx2706m -Xms2706m -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 113s Executing jgi.KmerNormalize [bits=32, in=sanger_full_range_original_sanger.fastq, qin=33, out=out3.fastq, outt=outt.fastq, hist=hist.plt] 113s 113s 113s *********** Pass 1 ********** 113s 113s 113s Settings: 113s threads: 4 113s k: 31 113s deterministic: true 113s toss error reads: false 113s passes: 1 113s bits per cell: 16 113s cells: 1005.46M 113s hashes: 3 113s base min quality: 5 113s kmer min prob: 0.5 113s 113s target depth: 400 113s min depth: 3 113s max depth: 500 113s min good kmers: 15 113s depth percentile: 64.8 113s ignore dupe kmers: true 113s fix spikes: false 113s histogram length: 65536 113s print zero cov: false 113s 116s Made hash table: hashes = 3 mem = 1.87 GB cells = 1005.28M used = 0.000% 116s 116s Estimated unique kmers: 4 116s 116s Table creation time: 2.494 seconds. 116s Started output threads. 116s Started output threads. 116s Table read time: 0.006 seconds. 29.29 kb/sec 116s Total reads in: 2 0.000% Kept 116s Total bases in: 188 0.000% Kept 116s Error reads in: 2 100.000% 116s Error type 1: 2 100.000% 116s Error type 2: 0 0.000% 116s Error type 3: 0 0.000% 116s 116s Wrote histogram to hist.plt 116s Total kmers counted: 128 116s Total unique kmer count: 128 116s Includes forward kmers only. 116s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 116s The most accurate value is the greater of the two. 116s 116s Percent unique: 100.00% 116s Depth average: 1.00 (unique kmers) 116s Depth median: 1 (unique kmers) 116s Depth standard deviation: 0.00 (unique kmers) 116s Corrected depth average: 0.00 116s 116s Depth average: 1.00 (all kmers) 116s Depth median: 1 (all kmers) 116s Depth standard deviation: 0.00 (all kmers) 116s 116s Approx. read depth median: 1.47 116s 116s *********** Pass 2 ********** 116s 116s 116s Settings: 116s threads: 4 116s k: 31 116s deterministic: true 116s toss error reads: false 116s passes: 1 116s bits per cell: 16 116s cells: 1005.46M 116s hashes: 3 116s base min quality: 5 116s kmer min prob: 0.5 116s 116s target depth: 100 116s min depth: 5 116s max depth: 100 116s min good kmers: 15 116s depth percentile: 54.0 116s ignore dupe kmers: true 116s fix spikes: false 116s histogram length: 65536 116s 118s Made hash table: hashes = 3 mem = 1.87 GB cells = 1005.28M used = 0.000% 118s 118s Estimated unique kmers: 0 118s 118s Table creation time: 2.377 seconds. 118s Started output threads. 118s Started output threads. 118s Table read time: 0.002 seconds. 0.00 kb/sec 118s Total reads in: 0 NaN% Kept 118s Total bases in: 0 NaN% Kept 118s Error reads in: 0 NaN% 118s Error type 1: 0 NaN% 118s Error type 2: 0 NaN% 118s Error type 3: 0 NaN% 118s Total kmers counted: 0 118s Total unique kmer count: 0 118s Includes forward kmers only. 118s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 118s The most accurate value is the greater of the two. 118s 118s Percent unique: NaN% 118s Depth average: NaN (unique kmers) 118s Depth median: 0 (unique kmers) 118s Depth standard deviation: NaN (unique kmers) 118s Corrected depth average: NaN 118s 118s Depth average: NaN (all kmers) 118s Depth median: 0 (all kmers) 118s Depth standard deviation: 0.00 (all kmers) 118s 118s Approx. read depth median: NaN 118s 118s Removing temp files. 118s 118s Total time: 4.980 seconds. 0.04 kb/sec 118s test -r out3.fastq 118s test -r outt.fastq 118s test -r hist.plt 118s bbnorm.sh in=illumina_full_range_original_illumina.fastq qin=64 \ 118s out=out4.fastq outt=outt2.fastq hist=hist2.plt 118s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 118s java -ea -Xmx2706m -Xms2706m -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 119s Executing jgi.KmerNormalize [bits=32, in=illumina_full_range_original_illumina.fastq, qin=64, out=out4.fastq, outt=outt2.fastq, hist=hist2.plt] 119s 119s 119s *********** Pass 1 ********** 119s 119s 119s Settings: 119s threads: 4 119s k: 31 119s deterministic: true 119s toss error reads: false 119s passes: 1 119s bits per cell: 16 119s cells: 1005.46M 119s hashes: 3 119s base min quality: 5 119s kmer min prob: 0.5 119s 119s target depth: 400 119s min depth: 3 119s max depth: 500 119s min good kmers: 15 119s depth percentile: 64.8 119s ignore dupe kmers: true 119s fix spikes: false 119s histogram length: 65536 119s print zero cov: false 119s 121s Made hash table: hashes = 3 mem = 1.87 GB cells = 1005.28M used = 0.000% 121s 121s Estimated unique kmers: 4 121s 121s Table creation time: 2.482 seconds. 121s Started output threads. 121s Started output threads. 121s Table read time: 0.006 seconds. 21.48 kb/sec 121s Total reads in: 2 0.000% Kept 121s Total bases in: 126 0.000% Kept 121s Error reads in: 2 100.000% 121s Error type 1: 2 100.000% 121s Error type 2: 0 0.000% 121s Error type 3: 0 0.000% 121s 121s Wrote histogram to hist2.plt 121s Total kmers counted: 66 121s Total unique kmer count: 66 121s Includes forward kmers only. 121s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 121s The most accurate value is the greater of the two. 121s 121s Percent unique: 100.00% 121s Depth average: 1.00 (unique kmers) 121s Depth median: 1 (unique kmers) 121s Depth standard deviation: 0.00 (unique kmers) 121s Corrected depth average: 0.00 121s 121s Depth average: 1.00 (all kmers) 121s Depth median: 1 (all kmers) 121s Depth standard deviation: 0.00 (all kmers) 121s 121s Approx. read depth median: 1.91 121s 121s *********** Pass 2 ********** 121s 121s 121s Settings: 121s threads: 4 121s k: 31 121s deterministic: true 121s toss error reads: false 121s passes: 1 121s bits per cell: 16 121s cells: 1005.46M 121s hashes: 3 121s base min quality: 5 121s kmer min prob: 0.5 121s 121s target depth: 100 121s min depth: 5 121s max depth: 100 121s min good kmers: 15 121s depth percentile: 54.0 121s ignore dupe kmers: true 121s fix spikes: false 121s histogram length: 65536 121s 123s Made hash table: hashes = 3 mem = 1.87 GB cells = 1005.28M used = 0.000% 123s 123s Estimated unique kmers: 0 123s 123s Table creation time: 2.362 seconds. 123s Started output threads. 123s Started output threads. 123s Table read time: 0.002 seconds. 0.00 kb/sec 123s Total reads in: 0 NaN% Kept 123s Total bases in: 0 NaN% Kept 123s Error reads in: 0 NaN% 123s Error type 1: 0 NaN% 123s Error type 2: 0 NaN% 123s Error type 3: 0 NaN% 123s Total kmers counted: 0 123s Total unique kmer count: 0 123s Includes forward kmers only. 123s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 123s The most accurate value is the greater of the two. 123s 123s Percent unique: NaN% 123s Depth average: NaN (unique kmers) 123s Depth median: 0 (unique kmers) 123s Depth standard deviation: NaN (unique kmers) 123s Corrected depth average: NaN 123s 123s Depth average: NaN (all kmers) 123s Depth median: 0 (all kmers) 123s Depth standard deviation: 0.00 (all kmers) 123s 123s Approx. read depth median: NaN 123s 123s Removing temp files. 123s 123s Total time: 4.952 seconds. 0.03 kb/sec 123s test -r out4.fastq 123s test -r outt2.fastq 123s test -r hist2.plt 124s autopkgtest [16:32:37]: test run-unit-test: -----------------------] 124s run-unit-test PASS 124s autopkgtest [16:32:37]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 125s autopkgtest [16:32:38]: @@@@@@@@@@@@@@@@@@@@ summary 125s run-unit-test PASS 129s nova [W] Using flock in prodstack6-ppc64el 129s Creating nova instance adt-plucky-ppc64el-bbmap-20241102-163033-juju-7f2275-prod-proposed-migration-environment-15-2579f185-b8b6-4127-afa8-570e65cd0943 from image adt/ubuntu-plucky-ppc64el-server-20241102.img (UUID 6c75d7ee-3b45-4c3b-9217-03e6a1e48086)...