0s autopkgtest [05:39:19]: starting date and time: 2024-11-04 05:39:19+0000 0s autopkgtest [05:39:19]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [05:39:19]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.u4hmea4e/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:openjdk-24 --apt-upgrade bbmap --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=openjdk-24/24~22ea-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-big --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@lcy02-55.secgroup --name adt-plucky-amd64-bbmap-20241104-050415-juju-7f2275-prod-proposed-migration-environment-15-67baf27d-5a7f-4cc3-941f-8a4f8dfe92c2 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 44s autopkgtest [05:40:03]: testbed dpkg architecture: amd64 44s autopkgtest [05:40:03]: testbed apt version: 2.9.8 44s autopkgtest [05:40:03]: @@@@@@@@@@@@@@@@@@@@ test bed setup 44s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 44s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [2268 kB] 44s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 44s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [31.2 kB] 44s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [177 kB] 44s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [238 kB] 44s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [165 kB] 44s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 44s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [1715 kB] 44s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [833 kB] 44s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [58.6 kB] 44s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [18.1 kB] 45s Fetched 5618 kB in 1s (9052 kB/s) 45s Reading package lists... 46s Reading package lists... 46s Building dependency tree... 46s Reading state information... 47s Calculating upgrade... 47s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 47s Reading package lists... 47s Building dependency tree... 47s Reading state information... 48s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 48s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 48s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 48s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 48s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 49s Reading package lists... 49s Reading package lists... 50s Building dependency tree... 50s Reading state information... 50s Calculating upgrade... 50s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 50s Reading package lists... 51s Building dependency tree... 51s Reading state information... 51s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 52s autopkgtest [05:40:11]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 52s autopkgtest [05:40:11]: @@@@@@@@@@@@@@@@@@@@ apt-source bbmap 53s Get:1 http://ftpmaster.internal/ubuntu plucky/universe bbmap 39.08+dfsg-1 (dsc) [2286 B] 53s Get:2 http://ftpmaster.internal/ubuntu plucky/universe bbmap 39.08+dfsg-1 (tar) [5396 kB] 53s Get:3 http://ftpmaster.internal/ubuntu plucky/universe bbmap 39.08+dfsg-1 (diff) [25.4 kB] 53s gpgv: Signature made Fri Aug 9 08:31:18 2024 UTC 53s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 53s gpgv: issuer "emollier@debian.org" 53s gpgv: Can't check signature: No public key 53s dpkg-source: warning: cannot verify inline signature for ./bbmap_39.08+dfsg-1.dsc: no acceptable signature found 53s autopkgtest [05:40:12]: testing package bbmap version 39.08+dfsg-1 53s autopkgtest [05:40:12]: build not needed 54s autopkgtest [05:40:13]: test run-unit-test: preparing testbed 54s Reading package lists... 54s Building dependency tree... 54s Reading state information... 55s Starting pkgProblemResolver with broken count: 0 55s Starting 2 pkgProblemResolver with broken count: 0 55s Done 55s The following additional packages will be installed: 55s bbmap bbmap-jni ca-certificates-java java-common libapache-pom-java 55s libcommons-cli-java libcommons-codec-java libcommons-io-java 55s libcommons-parent-java libjpeg-turbo8 libjpeg8 liblcms2-2 liblog4j1.2-java 55s libmpj-java libpcsclite1 openjdk-17-jre-headless python-biopython-doc 55s Suggested packages: 55s default-jre liblcms2-utils liblog4j1.2-java-doc libmail-java pcscd 55s libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho 55s fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic 55s Recommended packages: 55s pigz libcups2t64 libfontconfig1 libharfbuzz0b libasound2t64 55s python3-biopython 55s The following NEW packages will be installed: 55s autopkgtest-satdep bbmap bbmap-jni ca-certificates-java java-common 55s libapache-pom-java libcommons-cli-java libcommons-codec-java 55s libcommons-io-java libcommons-parent-java libjpeg-turbo8 libjpeg8 liblcms2-2 55s liblog4j1.2-java libmpj-java libpcsclite1 openjdk-17-jre-headless 55s python-biopython-doc 55s 0 upgraded, 18 newly installed, 0 to remove and 0 not upgraded. 55s Need to get 77.5 MB/77.5 MB of archives. 55s After this operation, 229 MB of additional disk space will be used. 55s Get:1 /tmp/autopkgtest.vEEKU1/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [720 B] 55s Get:2 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-cli-java all 1.6.0-1 [59.9 kB] 55s Get:3 http://ftpmaster.internal/ubuntu plucky/universe amd64 libapache-pom-java all 33-2 [5874 B] 55s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-parent-java all 56-1 [10.7 kB] 55s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-codec-java all 1.16.0-1 [306 kB] 55s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-io-java all 2.16.1-1 [451 kB] 55s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblog4j1.2-java all 1.2.17-11 [439 kB] 55s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmpj-java all 0.44+dfsg-4 [443 kB] 55s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 ca-certificates-java all 20240118 [11.6 kB] 55s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 java-common all 0.76 [6852 B] 55s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.14-2build1 [161 kB] 55s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB] 55s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 55s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcsclite1 amd64 2.3.0-1 [23.9 kB] 55s Get:15 http://ftpmaster.internal/ubuntu plucky/universe amd64 openjdk-17-jre-headless amd64 17.0.13+11-2build1 [48.0 MB] 56s Get:16 http://ftpmaster.internal/ubuntu plucky/universe amd64 bbmap all 39.08+dfsg-1 [10.0 MB] 56s Get:17 http://ftpmaster.internal/ubuntu plucky/universe amd64 bbmap-jni amd64 39.08+dfsg-1 [28.7 kB] 56s Get:18 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-biopython-doc all 1.83+dfsg1-3 [17.4 MB] 57s Fetched 77.5 MB in 1s (64.4 MB/s) 57s Selecting previously unselected package libcommons-cli-java. 57s (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 ... 75323 files and directories currently installed.) 57s Preparing to unpack .../00-libcommons-cli-java_1.6.0-1_all.deb ... 57s Unpacking libcommons-cli-java (1.6.0-1) ... 57s Selecting previously unselected package libapache-pom-java. 57s Preparing to unpack .../01-libapache-pom-java_33-2_all.deb ... 57s Unpacking libapache-pom-java (33-2) ... 57s Selecting previously unselected package libcommons-parent-java. 57s Preparing to unpack .../02-libcommons-parent-java_56-1_all.deb ... 57s Unpacking libcommons-parent-java (56-1) ... 57s Selecting previously unselected package libcommons-codec-java. 57s Preparing to unpack .../03-libcommons-codec-java_1.16.0-1_all.deb ... 57s Unpacking libcommons-codec-java (1.16.0-1) ... 57s Selecting previously unselected package libcommons-io-java. 57s Preparing to unpack .../04-libcommons-io-java_2.16.1-1_all.deb ... 57s Unpacking libcommons-io-java (2.16.1-1) ... 57s Selecting previously unselected package liblog4j1.2-java. 57s Preparing to unpack .../05-liblog4j1.2-java_1.2.17-11_all.deb ... 57s Unpacking liblog4j1.2-java (1.2.17-11) ... 57s Selecting previously unselected package libmpj-java. 57s Preparing to unpack .../06-libmpj-java_0.44+dfsg-4_all.deb ... 57s Unpacking libmpj-java (0.44+dfsg-4) ... 57s Selecting previously unselected package ca-certificates-java. 57s Preparing to unpack .../07-ca-certificates-java_20240118_all.deb ... 57s Unpacking ca-certificates-java (20240118) ... 57s Selecting previously unselected package java-common. 57s Preparing to unpack .../08-java-common_0.76_all.deb ... 57s Unpacking java-common (0.76) ... 57s Selecting previously unselected package liblcms2-2:amd64. 57s Preparing to unpack .../09-liblcms2-2_2.14-2build1_amd64.deb ... 57s Unpacking liblcms2-2:amd64 (2.14-2build1) ... 57s Selecting previously unselected package libjpeg-turbo8:amd64. 57s Preparing to unpack .../10-libjpeg-turbo8_2.1.5-2ubuntu2_amd64.deb ... 57s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 57s Selecting previously unselected package libjpeg8:amd64. 57s Preparing to unpack .../11-libjpeg8_8c-2ubuntu11_amd64.deb ... 57s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 57s Selecting previously unselected package libpcsclite1:amd64. 57s Preparing to unpack .../12-libpcsclite1_2.3.0-1_amd64.deb ... 57s Unpacking libpcsclite1:amd64 (2.3.0-1) ... 57s Selecting previously unselected package openjdk-17-jre-headless:amd64. 57s Preparing to unpack .../13-openjdk-17-jre-headless_17.0.13+11-2build1_amd64.deb ... 57s Unpacking openjdk-17-jre-headless:amd64 (17.0.13+11-2build1) ... 58s Selecting previously unselected package bbmap. 58s Preparing to unpack .../14-bbmap_39.08+dfsg-1_all.deb ... 58s Unpacking bbmap (39.08+dfsg-1) ... 58s Selecting previously unselected package bbmap-jni. 58s Preparing to unpack .../15-bbmap-jni_39.08+dfsg-1_amd64.deb ... 58s Unpacking bbmap-jni (39.08+dfsg-1) ... 58s Selecting previously unselected package python-biopython-doc. 58s Preparing to unpack .../16-python-biopython-doc_1.83+dfsg1-3_all.deb ... 58s Unpacking python-biopython-doc (1.83+dfsg1-3) ... 59s Selecting previously unselected package autopkgtest-satdep. 59s Preparing to unpack .../17-1-autopkgtest-satdep.deb ... 59s Unpacking autopkgtest-satdep (0) ... 59s Setting up liblcms2-2:amd64 (2.14-2build1) ... 59s Setting up java-common (0.76) ... 59s Setting up libcommons-cli-java (1.6.0-1) ... 59s Setting up liblog4j1.2-java (1.2.17-11) ... 59s Setting up libapache-pom-java (33-2) ... 59s Setting up libpcsclite1:amd64 (2.3.0-1) ... 59s Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 59s Setting up python-biopython-doc (1.83+dfsg1-3) ... 59s Setting up bbmap-jni (39.08+dfsg-1) ... 59s Setting up ca-certificates-java (20240118) ... 59s No JRE found. Skipping Java certificates setup. 59s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 59s Setting up libcommons-parent-java (56-1) ... 59s Setting up openjdk-17-jre-headless:amd64 (17.0.13+11-2build1) ... 59s update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode 59s update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 59s update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 59s update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 59s update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 59s Setting up libcommons-codec-java (1.16.0-1) ... 59s Setting up libcommons-io-java (2.16.1-1) ... 59s Setting up libmpj-java (0.44+dfsg-4) ... 59s Processing triggers for libc-bin (2.40-1ubuntu3) ... 59s Processing triggers for man-db (2.12.1-3) ... 60s Processing triggers for ca-certificates-java (20240118) ... 60s Adding debian:ACCVRAIZ1.pem 60s Adding debian:AC_RAIZ_FNMT-RCM.pem 60s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 60s Adding debian:ANF_Secure_Server_Root_CA.pem 60s Adding debian:Actalis_Authentication_Root_CA.pem 60s Adding debian:AffirmTrust_Commercial.pem 60s Adding debian:AffirmTrust_Networking.pem 60s Adding debian:AffirmTrust_Premium.pem 60s Adding debian:AffirmTrust_Premium_ECC.pem 60s Adding debian:Amazon_Root_CA_1.pem 60s Adding debian:Amazon_Root_CA_2.pem 60s Adding debian:Amazon_Root_CA_3.pem 60s Adding debian:Amazon_Root_CA_4.pem 60s Adding debian:Atos_TrustedRoot_2011.pem 60s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 60s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 60s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 60s Adding debian:BJCA_Global_Root_CA1.pem 60s Adding debian:BJCA_Global_Root_CA2.pem 60s Adding debian:Baltimore_CyberTrust_Root.pem 60s Adding debian:Buypass_Class_2_Root_CA.pem 60s Adding debian:Buypass_Class_3_Root_CA.pem 60s Adding debian:CA_Disig_Root_R2.pem 60s Adding debian:CFCA_EV_ROOT.pem 60s Adding debian:COMODO_Certification_Authority.pem 60s Adding debian:COMODO_ECC_Certification_Authority.pem 60s Adding debian:COMODO_RSA_Certification_Authority.pem 60s Adding debian:Certainly_Root_E1.pem 60s Adding debian:Certainly_Root_R1.pem 60s Adding debian:Certigna.pem 60s Adding debian:Certigna_Root_CA.pem 60s Adding debian:Certum_EC-384_CA.pem 60s Adding debian:Certum_Trusted_Network_CA.pem 60s Adding debian:Certum_Trusted_Network_CA_2.pem 60s Adding debian:Certum_Trusted_Root_CA.pem 60s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 60s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 60s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 60s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 60s Adding debian:Comodo_AAA_Services_root.pem 60s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 60s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 60s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 60s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 60s Adding debian:DigiCert_Assured_ID_Root_CA.pem 60s Adding debian:DigiCert_Assured_ID_Root_G2.pem 60s Adding debian:DigiCert_Assured_ID_Root_G3.pem 60s Adding debian:DigiCert_Global_Root_CA.pem 60s Adding debian:DigiCert_Global_Root_G2.pem 60s Adding debian:DigiCert_Global_Root_G3.pem 60s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 60s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 60s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 60s Adding debian:DigiCert_Trusted_Root_G4.pem 60s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 60s Adding debian:Entrust_Root_Certification_Authority.pem 60s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 60s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 60s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem 60s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 60s Adding debian:GLOBALTRUST_2020.pem 60s Adding debian:GTS_Root_R1.pem 60s Adding debian:GTS_Root_R2.pem 60s Adding debian:GTS_Root_R3.pem 60s Adding debian:GTS_Root_R4.pem 60s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 60s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 60s Adding debian:GlobalSign_Root_CA.pem 60s Adding debian:GlobalSign_Root_CA_-_R3.pem 60s Adding debian:GlobalSign_Root_CA_-_R6.pem 60s Adding debian:GlobalSign_Root_E46.pem 60s Adding debian:GlobalSign_Root_R46.pem 60s Adding debian:Go_Daddy_Class_2_CA.pem 60s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 60s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 60s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 60s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 60s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 60s Adding debian:HiPKI_Root_CA_-_G1.pem 60s Adding debian:Hongkong_Post_Root_CA_3.pem 60s Adding debian:ISRG_Root_X1.pem 60s Adding debian:ISRG_Root_X2.pem 60s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 60s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 60s Adding debian:Izenpe.com.pem 60s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 60s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 60s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 60s Adding debian:NAVER_Global_Root_Certification_Authority.pem 60s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 60s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 60s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 60s Adding debian:QuoVadis_Root_CA_1_G3.pem 60s Adding debian:QuoVadis_Root_CA_2.pem 60s Adding debian:QuoVadis_Root_CA_2_G3.pem 60s Adding debian:QuoVadis_Root_CA_3.pem 60s Adding debian:QuoVadis_Root_CA_3_G3.pem 60s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 60s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 60s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 60s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 60s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 60s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 60s Adding debian:SZAFIR_ROOT_CA2.pem 60s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 60s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 60s Adding debian:SecureSign_RootCA11.pem 60s Adding debian:SecureTrust_CA.pem 60s Adding debian:Secure_Global_CA.pem 60s Adding debian:Security_Communication_ECC_RootCA1.pem 60s Adding debian:Security_Communication_RootCA2.pem 60s Adding debian:Security_Communication_RootCA3.pem 60s Adding debian:Security_Communication_Root_CA.pem 60s Adding debian:Starfield_Class_2_CA.pem 60s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 60s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 60s Adding debian:SwissSign_Gold_CA_-_G2.pem 60s Adding debian:SwissSign_Silver_CA_-_G2.pem 60s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 60s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 60s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 60s Adding debian:TWCA_Global_Root_CA.pem 60s Adding debian:TWCA_Root_Certification_Authority.pem 60s Adding debian:TeliaSonera_Root_CA_v1.pem 60s Adding debian:Telia_Root_CA_v2.pem 60s Adding debian:TrustAsia_Global_Root_CA_G3.pem 60s Adding debian:TrustAsia_Global_Root_CA_G4.pem 60s Adding debian:Trustwave_Global_Certification_Authority.pem 60s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 60s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 60s Adding debian:TunTrust_Root_CA.pem 60s Adding debian:UCA_Extended_Validation_Root.pem 60s Adding debian:UCA_Global_G2_Root.pem 60s Adding debian:USERTrust_ECC_Certification_Authority.pem 60s Adding debian:USERTrust_RSA_Certification_Authority.pem 60s Adding debian:XRamp_Global_CA_Root.pem 60s Adding debian:certSIGN_ROOT_CA.pem 60s Adding debian:certSIGN_Root_CA_G2.pem 60s Adding debian:e-Szigno_Root_CA_2017.pem 60s Adding debian:ePKI_Root_Certification_Authority.pem 60s Adding debian:emSign_ECC_Root_CA_-_C3.pem 60s Adding debian:emSign_ECC_Root_CA_-_G3.pem 60s Adding debian:emSign_Root_CA_-_C1.pem 60s Adding debian:emSign_Root_CA_-_G1.pem 60s Adding debian:vTrus_ECC_Root_CA.pem 60s Adding debian:vTrus_Root_CA.pem 60s done. 60s Setting up bbmap (39.08+dfsg-1) ... 60s Setting up autopkgtest-satdep (0) ... 62s (Reading database ... 77881 files and directories currently installed.) 63s Removing autopkgtest-satdep (0) ... 63s autopkgtest [05:40:22]: test run-unit-test: [----------------------- 63s 63s # bbmap 63s bbmap.sh --version 63s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 63s java -ea -Xmx2771m -Xms2771m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 --version 63s BBTools version 39.08 63s For help, please run the shellscript with no parameters, or look in /docs/. 63s bbmap.sh --help 63s 63s BBMap 63s Written by Brian Bushnell, from Dec. 2010 - present 63s Last modified September 15, 2022 63s 63s Description: Fast and accurate splice-aware read aligner. 63s Please read bbmap/docs/guides/BBMapGuide.txt for more information. 63s 63s To index: bbmap.sh ref= 63s To map: bbmap.sh in= out= 63s To map without writing an index: 63s bbmap.sh ref= in= out= nodisk 63s 63s in=stdin will accept reads from standard in, and out=stdout will write to 63s standard out, but file extensions are still needed to specify the format of the 63s input and output files e.g. in=stdin.fa.gz will read gzipped fasta from 63s standard in; out=stdout.sam.gz will write gzipped sam. 63s 63s Indexing Parameters (required when building the index): 63s nodisk=f Set to true to build index in memory and write nothing 63s to disk except output. 63s ref= Specify the reference sequence. Only do this ONCE, 63s when building the index (unless using 'nodisk'). 63s build=1 If multiple references are indexed in the same directory, 63s each needs a unique numeric ID (unless using 'nodisk'). 63s k=13 Kmer length, range 8-15. Longer is faster but uses 63s more memory. Shorter is more sensitive. 63s If indexing and mapping are done in two steps, K should 63s be specified each time. 63s path=<.> Specify the location to write the index, if you don't 63s want it in the current working directory. 63s usemodulo=f Throw away ~80% of kmers based on remainder modulo a 63s number (reduces RAM by 50% and sensitivity slightly). 63s Should be enabled both when building the index AND 63s when mapping. 63s rebuild=f Force a rebuild of the index (ref= should be set). 63s 63s Input Parameters: 63s build=1 Designate index to use. Corresponds to the number 63s specified when building the index. 63s in= Primary reads input; required parameter. 63s in2= For paired reads in two files. 63s interleaved=auto True forces paired/interleaved input; false forces 63s single-ended mapping. If not specified, interleaved 63s status will be autodetected from read names. 63s fastareadlen=500 Break up FASTA reads longer than this. Max is 500 for 63s BBMap and 6000 for BBMapPacBio. Only works for FASTA 63s input (use 'maxlen' for FASTQ input). The default for 63s bbmap.sh is 500, and for mapPacBio.sh is 6000. 63s unpigz=f Spawn a pigz (parallel gzip) process for faster 63s decompression than using Java. 63s Requires pigz to be installed. 63s touppercase=t (tuc) Convert lowercase letters in reads to upper case 63s (otherwise they will not match the reference). 63s 63s Sampling Parameters: 63s 63s reads=-1 Set to a positive number N to only process the first N 63s reads (or pairs), then quit. -1 means use all reads. 63s samplerate=1 Set to a number from 0 to 1 to randomly select that 63s fraction of reads for mapping. 1 uses all reads. 63s skipreads=0 Set to a number N to skip the first N reads (or pairs), 63s then map the rest. 63s 63s Mapping Parameters: 63s fast=f This flag is a macro which sets other paramters to run 63s faster, at reduced sensitivity. Bad for RNA-seq. 63s slow=f This flag is a macro which sets other paramters to run 63s slower, at greater sensitivity. 'vslow' is even slower. 63s maxindel=16000 Don't look for indels longer than this. Lower is faster. 63s Set to >=100k for RNAseq with long introns like mammals. 63s strictmaxindel=f When enabled, do not allow indels longer than 'maxindel'. 63s By default these are not sought, but may be found anyway. 63s tipsearch=100 Look this far for read-end deletions with anchors 63s shorter than K, using brute force. 63s minid=0.76 Approximate minimum alignment identity to look for. 63s Higher is faster and less sensitive. 63s minhits=1 Minimum number of seed hits required for candidate sites. 63s Higher is faster. 63s local=f Set to true to use local, rather than global, alignments. 63s This will soft-clip ugly ends of poor alignments. 63s perfectmode=f Allow only perfect mappings when set to true (very fast). 63s semiperfectmode=f Allow only perfect and semiperfect (perfect except for 63s N's in the reference) mappings. 63s threads=auto (t) Set to number of threads desired. By default, uses 63s all cores available. 63s ambiguous=best (ambig) Set behavior on ambiguously-mapped reads (with 63s multiple top-scoring mapping locations). 63s best (use the first best site) 63s toss (consider unmapped) 63s random (select one top-scoring site randomly) 63s all (retain all top-scoring sites) 63s samestrandpairs=f (ssp) Specify whether paired reads should map to the 63s same strand or opposite strands. 63s requirecorrectstrand=t (rcs) Forbid pairing of reads without correct strand 63s orientation. Set to false for long-mate-pair libraries. 63s killbadpairs=f (kbp) If a read pair is mapped with an inappropriate 63s insert size or orientation, the read with the lower 63s mapping quality is marked unmapped. 63s pairedonly=f (po) Treat unpaired reads as unmapped. Thus they will 63s be sent to 'outu' but not 'outm'. 63s rcomp=f Reverse complement both reads prior to mapping (for LMP 63s outward-facing libraries). 63s rcompmate=f Reverse complement read2 prior to mapping. 63s pairlen=32000 Set max allowed distance between paired reads. 63s (insert size)=(pairlen)+(read1 length)+(read2 length) 63s rescuedist=1200 Don't try to rescue paired reads if avg. insert size 63s greater than this. Lower is faster. 63s rescuemismatches=32 Maximum mismatches allowed in a rescued read. Lower 63s is faster. 63s averagepairdist=100 (apd) Initial average distance between paired reads. 63s Varies dynamically; does not need to be specified. 63s deterministic=f Run in deterministic mode. In this case it is good 63s to set averagepairdist. BBMap is deterministic 63s without this flag if using single-ended reads, 63s or run singlethreaded. 63s bandwidthratio=0 (bwr) If above zero, restrict alignment band to this 63s fraction of read length. Faster but less accurate. 63s bandwidth=0 (bw) Set the bandwidth directly. 63s fraction of read length. Faster but less accurate. 63s usejni=f (jni) Do alignments faster, in C code. Requires 63s compiling the C code; details are in /jni/README.txt. 63s maxsites2=800 Don't analyze (or print) more than this many alignments 63s per read. 63s ignorefrequentkmers=t (ifk) Discard low-information kmers that occur often. 63s excludefraction=0.03 (ef) Fraction of kmers to ignore. For example, 0.03 63s will ignore the most common 3% of kmers. 63s greedy=t Use a greedy algorithm to discard the least-useful 63s kmers on a per-read basis. 63s kfilter=0 If positive, potential mapping sites must have at 63s least this many consecutive exact matches. 63s 63s 63s Quality and Trimming Parameters: 63s qin=auto Set to 33 or 64 to specify input quality value ASCII 63s offset. 33 is Sanger, 64 is old Solexa. 63s qout=auto Set to 33 or 64 to specify output quality value ASCII 63s offset (only if output format is fastq). 63s qtrim=f Quality-trim ends before mapping. Options are: 63s 'f' (false), 'l' (left), 'r' (right), and 'lr' (both). 63s untrim=f Undo trimming after mapping. Untrimmed bases will be 63s soft-clipped in cigar strings. 63s trimq=6 Trim regions with average quality below this 63s (phred algorithm). 63s mintrimlength=60 (mintl) Don't trim reads to be shorter than this. 63s fakefastaquality=-1 (ffq) Set to a positive number 1-50 to generate fake 63s quality strings for fasta input reads. 63s ignorebadquality=f (ibq) Keep going, rather than crashing, if a read has 63s out-of-range quality values. 63s usequality=t Use quality scores when determining which read kmers 63s to use as seeds. 63s minaveragequality=0 (maq) Do not map reads with average quality below this. 63s maqb=0 If positive, calculate maq from this many initial bases. 63s 63s Output Parameters: 63s out= Write all reads to this file. 63s outu= Write only unmapped reads to this file. Does not 63s include unmapped paired reads with a mapped mate. 63s outm= Write only mapped reads to this file. Includes 63s unmapped paired reads with a mapped mate. 63s mappedonly=f If true, treats 'out' like 'outm'. 63s bamscript= (bs) Write a shell script to that will turn 63s the sam output into a sorted, indexed bam file. 63s ordered=f Set to true to output reads in same order as input. 63s Slower and uses more memory. 63s overwrite=f (ow) Allow process to overwrite existing files. 63s secondary=f Print secondary alignments. 63s sssr=0.95 (secondarysitescoreratio) Print only secondary alignments 63s with score of at least this fraction of primary. 63s ssao=f (secondarysiteasambiguousonly) Only print secondary 63s alignments for ambiguously-mapped reads. 63s maxsites=5 Maximum number of total alignments to print per read. 63s Only relevant when secondary=t. 63s quickmatch=f Generate cigar strings more quickly. 63s trimreaddescriptions=f (trd) Truncate read and ref names at the first whitespace, 63s assuming that the remainder is a comment or description. 63s ziplevel=2 (zl) Compression level for zip or gzip output. 63s pigz=f Spawn a pigz (parallel gzip) process for faster 63s compression than Java. Requires pigz to be installed. 63s machineout=f Set to true to output statistics in machine-friendly 63s 'key=value' format. 63s printunmappedcount=f Print the total number of unmapped reads and bases. 63s If input is paired, the number will be of pairs 63s for which both reads are unmapped. 63s showprogress=0 If positive, print a '.' every X reads. 63s showprogress2=0 If positive, print the number of seconds since the 63s last progress update (instead of a '.'). 63s renamebyinsert=f Renames reads based on their mapped insert size. 63s 63s Bloom-Filtering Parameters (bloomfilter.sh is the standalone version). 63s bloom=f Use a Bloom filter to ignore reads not sharing kmers 63s with the reference. This uses more memory, but speeds 63s mapping when most reads don't match the reference. 63s bloomhashes=2 Number of hash functions. 63s bloomminhits=3 Number of consecutive hits to be considered matched. 63s bloomk=31 Bloom filter kmer length. 63s bloomserial=t Use the serialized Bloom filter for greater loading 63s speed, if available. If not, generate and write one. 63s 63s Post-Filtering Parameters: 63s idfilter=0 Independant of minid; sets exact minimum identity 63s allowed for alignments to be printed. Range 0 to 1. 63s subfilter=-1 Ban alignments with more than this many substitutions. 63s insfilter=-1 Ban alignments with more than this many insertions. 63s delfilter=-1 Ban alignments with more than this many deletions. 63s indelfilter=-1 Ban alignments with more than this many indels. 63s editfilter=-1 Ban alignments with more than this many edits. 63s inslenfilter=-1 Ban alignments with an insertion longer than this. 63s dellenfilter=-1 Ban alignments with a deletion longer than this. 63s nfilter=-1 Ban alignments with more than this many ns. This 63s includes nocall, noref, and off scaffold ends. 63s 63s Sam flags and settings: 63s noheader=f Disable generation of header lines. 63s sam=1.4 Set to 1.4 to write Sam version 1.4 cigar strings, 63s with = and X, or 1.3 to use M. 63s saa=t (secondaryalignmentasterisks) Use asterisks instead of 63s bases for sam secondary alignments. 63s cigar=t Set to 'f' to skip generation of cigar strings (faster). 63s keepnames=f Keep original names of paired reads, rather than 63s ensuring both reads have the same name. 63s intronlen=999999999 Set to a lower number like 10 to change 'D' to 'N' in 63s cigar strings for deletions of at least that length. 63s rgid= Set readgroup ID. All other readgroup fields 63s can be set similarly, with the flag rgXX= 63s If you set a readgroup flag to the word 'filename', 63s e.g. rgid=filename, the input file name will be used. 63s mdtag=f Write MD tags. 63s nhtag=f Write NH tags. 63s xmtag=f Write XM tags (may only work correctly with ambig=all). 63s amtag=f Write AM tags. 63s nmtag=f Write NM tags. 63s xstag=f Set to 'xs=fs', 'xs=ss', or 'xs=us' to write XS tags 63s for RNAseq using firststrand, secondstrand, or 63s unstranded libraries. Needed by Cufflinks. 63s JGI mainly uses 'firststrand'. 63s stoptag=f Write a tag indicating read stop location, prefixed by YS:i: 63s lengthtag=f Write a tag indicating (query,ref) alignment lengths, 63s prefixed by YL:Z: 63s idtag=f Write a tag indicating percent identity, prefixed by YI:f: 63s inserttag=f Write a tag indicating insert size, prefixed by X8:Z: 63s scoretag=f Write a tag indicating BBMap's raw score, prefixed by YR:i: 63s timetag=f Write a tag indicating this read's mapping time, prefixed by X0:i: 63s boundstag=f Write a tag indicating whether either read in the pair 63s goes off the end of the reference, prefixed by XB:Z: 63s notags=f Turn off all optional tags. 63s 63s Histogram and statistics output parameters: 63s scafstats= Statistics on how many reads mapped to which scaffold. 63s refstats= Statistics on how many reads mapped to which reference 63s file; only for BBSplit. 63s sortscafs=t Sort scaffolds or references by read count. 63s bhist= Base composition histogram by position. 63s qhist= Quality histogram by position. 63s aqhist= Histogram of average read quality. 63s bqhist= Quality histogram designed for box plots. 63s lhist= Read length histogram. 63s ihist= Write histogram of insert sizes (for paired reads). 63s ehist= Errors-per-read histogram. 63s qahist= Quality accuracy histogram of error rates versus 63s quality score. 63s indelhist= Indel length histogram. 63s mhist= Histogram of match, sub, del, and ins rates by 63s read location. 63s gchist= Read GC content histogram. 63s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 63s gcpairs=t Use average GC of paired reads. 63s idhist= Histogram of read count versus percent identity. 63s idbins=100 Number idhist bins. Set to 'auto' to use read length. 63s statsfile=stderr Mapping statistics are printed here. 63s 63s Coverage output parameters (these may reduce speed and use more RAM): 63s covstats= Per-scaffold coverage info. 63s rpkm= Per-scaffold RPKM/FPKM counts. 63s covhist= Histogram of # occurrences of each depth level. 63s basecov= Coverage per base location. 63s bincov= Print binned coverage per location (one line per X bases). 63s covbinsize=1000 Set the binsize for binned coverage output. 63s nzo=t Only print scaffolds with nonzero coverage. 63s twocolumn=f Change to true to print only ID and Avg_fold instead of 63s all 6 columns to the 'out=' file. 63s 32bit=f Set to true if you need per-base coverage over 64k. 63s strandedcov=f Track coverage for plus and minus strand independently. 63s startcov=f Only track start positions of reads. 63s secondarycov=t Include coverage of secondary alignments. 63s physcov=f Calculate physical coverage for paired reads. 63s This includes the unsequenced bases. 63s delcoverage=t (delcov) Count bases covered by deletions as covered. 63s True is faster than false. 63s covk=0 If positive, calculate kmer coverage statistics. 63s 63s Java Parameters: 63s -Xmx This will set Java's memory usage, 63s overriding autodetection. 63s -Xmx20g will specify 20 gigs of RAM, and -Xmx800m 63s will specify 800 megs. The max is typically 85% of 63s physical memory. The human genome requires around 24g, 63s or 12g with the 'usemodulo' flag. The index uses 63s roughly 6 bytes per reference base. 63s -eoom This flag will cause the process to exit if an 63s out-of-memory exception occurs. Requires Java 8u92+. 63s -da Disable assertions. 63s 63s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter 63s any problems, or post at: http://seqanswers.com/forums/showthread.php?t=41057 63s 63s bbmap.sh ref=example.fasta 63s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 63s java -ea -Xmx2772m -Xms2772m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta 63s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta] 63s Version 39.08 63s 63s No output file. 63s Writing reference. 63s 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] 63s 63s Set genScaffoldInfo=true 63s Writing chunk 1 63s Set genome to 1 63s 63s Loaded Reference: 0.004 seconds. 63s Loading index for chunk 1-1, build 1 63s No index available; generating from reference genome: /tmp/autopkgtest.vEEKU1/autopkgtest_tmp/ref/index/1/chr1_index_k13_c16_b1.block 63s Indexing threads started for block 0-1 63s Indexing threads finished for block 0-1 64s Generated Index: 1.019 seconds. 64s No reads to process; quitting. 64s 64s Total time: 1.146 seconds. 64s test -d ref 64s bbmap.sh in=misc_dna_as_sanger.fastq out=out.sam 64s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 64s java -ea -Xmx2772m -Xms2772m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 in=misc_dna_as_sanger.fastq out=out.sam 64s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, in=misc_dna_as_sanger.fastq, out=out.sam] 64s Version 39.08 64s 65s Retaining first best site only for ambiguous mappings. 65s Set genome to 1 65s 65s Loaded Reference: 0.031 seconds. 65s Loading index for chunk 1-1, build 1 65s Generated Index: 0.531 seconds. 68s Analyzed Index: 3.212 seconds. 68s Started output stream: 0.019 seconds. 68s Cleared Memory: 0.116 seconds. 69s Processing reads in single-ended mode. 69s Started read stream. 69s Started 4 mapping threads. 69s Detecting finished threads: 0, 1, 2, 3 69s 69s ------------------ Results ------------------ 69s 69s Genome: 1 69s Key Length: 13 69s Max Indel: 16000 69s Minimum Score Ratio: 0.56 69s Mapping Mode: normal 69s Reads Used: 4 (153 bases) 69s 69s Mapping: 0.086 seconds. 69s Reads/sec: 46.29 69s kBases/sec: 1.77 69s 69s 69s Read 1 data: pct reads num reads pct bases num bases 69s 69s mapped: 0.0000% 0 0.0000% 0 69s unambiguous: 0.0000% 0 0.0000% 0 69s ambiguous: 0.0000% 0 0.0000% 0 69s low-Q discards: 25.0000% 1 19.6078% 30 69s 69s perfect best site: 0.0000% 0 0.0000% 0 69s semiperfect site: 0.0000% 0 0.0000% 0 69s 69s Match Rate: NA NA NaN% 0 69s Error Rate: NaN% 0 NaN% 0 69s Sub Rate: NaN% 0 NaN% 0 69s Del Rate: NaN% 0 NaN% 0 69s Ins Rate: NaN% 0 NaN% 0 69s N Rate: NaN% 0 NaN% 0 69s 69s Total time: 4.114 seconds. 69s test -r out.sam 69s bbmap.sh ref=example.fasta in=example.fastq out=out2.sam nodisk 69s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 69s java -ea -Xmx2772m -Xms2772m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta in=example.fastq out=out2.sam nodisk 69s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta, in=example.fastq, out=out2.sam, nodisk] 69s Version 39.08 69s 69s Retaining first best site only for ambiguous mappings. 69s 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] 69s 69s Set genScaffoldInfo=true 69s Set genome to 1 69s 69s Loaded Reference: 0.002 seconds. 69s Loading index for chunk 1-1, build 1 69s Indexing threads started for block 0-1 69s Indexing threads finished for block 0-1 69s Generated Index: 0.268 seconds. 72s Analyzed Index: 3.187 seconds. 72s Started output stream: 0.020 seconds. 72s Cleared Memory: 0.119 seconds. 73s Processing reads in single-ended mode. 73s Started read stream. 73s Started 4 mapping threads. 73s Detecting finished threads: 0, 1, 2, 3 73s 73s ------------------ Results ------------------ 73s 73s Genome: 1 73s Key Length: 13 73s Max Indel: 16000 73s Minimum Score Ratio: 0.56 73s Mapping Mode: normal 73s Reads Used: 3 (75 bases) 73s 73s Mapping: 0.107 seconds. 73s Reads/sec: 28.07 73s kBases/sec: 0.70 73s 73s 73s Read 1 data: pct reads num reads pct bases num bases 73s 73s mapped: 100.0000% 3 100.0000% 75 73s unambiguous: 100.0000% 3 100.0000% 75 73s ambiguous: 0.0000% 0 0.0000% 0 73s low-Q discards: 0.0000% 0 0.0000% 0 73s 73s perfect best site: 100.0000% 3 100.0000% 75 73s semiperfect site: 100.0000% 3 100.0000% 75 73s 73s Match Rate: NA NA 100.0000% 75 73s Error Rate: 0.0000% 0 0.0000% 0 73s Sub Rate: 0.0000% 0 0.0000% 0 73s Del Rate: 0.0000% 0 0.0000% 0 73s Ins Rate: 0.0000% 0 0.0000% 0 73s N Rate: 0.0000% 0 0.0000% 0 73s 73s Total time: 3.816 seconds. 73s test -r out2.sam 73s 73s # bbduk 73s bbduk.sh --version 73s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 73s java -ea -Xmx1386m -Xms1386m -cp /usr/share/java/bbmap.jar jgi.BBDuk --version 73s BBTools version 39.08 73s For help, please run the shellscript with no parameters, or look in /docs/. 73s bbduk.sh --help 73s 73s Written by Brian Bushnell 73s Last modified November 9, 2023 73s 73s Description: Compares reads to the kmers in a reference dataset, optionally 73s allowing an edit distance. Splits the reads into two outputs - those that 73s match the reference, and those that don't. Can also trim (remove) the matching 73s parts of the reads rather than binning the reads. 73s Please read bbmap/docs/guides/BBDukGuide.txt for more information. 73s 73s Usage: bbduk.sh in= out= ref= 73s 73s Input may be stdin or a fasta or fastq file, compressed or uncompressed. 73s If you pipe via stdin/stdout, please include the file type; e.g. for gzipped 73s fasta input, set in=stdin.fa.gz 73s 73s Input parameters: 73s in= Main input. in=stdin.fq will pipe from stdin. 73s in2= Input for 2nd read of pairs in a different file. 73s ref= Comma-delimited list of reference files. 73s In addition to filenames, you may also use the keywords: 73s adapters, artifacts, phix, lambda, pjet, mtst, kapa 73s literal= Comma-delimited list of literal reference sequences. 73s touppercase=f (tuc) Change all bases upper-case. 73s interleaved=auto (int) t/f overrides interleaved autodetection. 73s Must be set mainually when streaming fastq input. 73s qin=auto Input quality offset: 33 (Sanger), 64, or auto. 73s reads=-1 If positive, quit after processing X reads or pairs. 73s copyundefined=f (cu) Process non-AGCT IUPAC reference bases by making all 73s possible unambiguous copies. Intended for short motifs 73s or adapter barcodes, as time/memory use is exponential. 73s samplerate=1 Set lower to only process a fraction of input reads. 73s samref= Optional reference fasta for processing sam files. 73s 73s Output parameters: 73s out= (outnonmatch) Write reads here that do not contain 73s kmers matching the database. 'out=stdout.fq' will pipe 73s to standard out. 73s out2= (outnonmatch2) Use this to write 2nd read of pairs to a 73s different file. 73s outm= (outmatch) Write reads here that fail filters. In default 73s kfilter mode, this means any read with a matching kmer. 73s In any mode, it also includes reads that fail filters such 73s as minlength, mingc, maxgc, entropy, etc. In other words, 73s it includes all reads that do not go to 'out'. 73s outm2= (outmatch2) Use this to write 2nd read of pairs to a 73s different file. 73s outs= (outsingle) Use this to write singleton reads whose mate 73s was trimmed shorter than minlen. 73s stats= Write statistics about which contamininants were detected. 73s refstats= Write statistics on a per-reference-file basis. 73s rpkm= Write RPKM for each reference sequence (for RNA-seq). 73s dump= Dump kmer tables to a file, in fasta format. 73s duk= Write statistics in duk's format. *DEPRECATED* 73s nzo=t Only write statistics about ref sequences with nonzero hits. 73s overwrite=t (ow) Grant permission to overwrite files. 73s showspeed=t (ss) 'f' suppresses display of processing speed. 73s ziplevel=2 (zl) Compression level; 1 (min) through 9 (max). 73s fastawrap=70 Length of lines in fasta output. 73s qout=auto Output quality offset: 33 (Sanger), 64, or auto. 73s statscolumns=3 (cols) Number of columns for stats output, 3 or 5. 73s 5 includes base counts. 73s rename=f Rename reads to indicate which sequences they matched. 73s refnames=f Use names of reference files rather than scaffold IDs. 73s trd=f Truncate read and ref names at the first whitespace. 73s ordered=f Set to true to output reads in same order as input. 73s maxbasesout=-1 If positive, quit after writing approximately this many 73s bases to out (outu/outnonmatch). 73s maxbasesoutm=-1 If positive, quit after writing approximately this many 73s bases to outm (outmatch). 73s json=f Print to screen in json format. 73s 73s Histogram output parameters: 73s bhist= Base composition histogram by position. 73s qhist= Quality histogram by position. 73s qchist= Count of bases with each quality value. 73s aqhist= Histogram of average read quality. 73s bqhist= Quality histogram designed for box plots. 73s lhist= Read length histogram. 73s phist= Polymer length histogram. 73s gchist= Read GC content histogram. 73s enthist= Read entropy histogram. 73s ihist= Insert size histogram, for paired reads in mapped sam. 73s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 73s maxhistlen=6000 Set an upper bound for histogram lengths; higher uses 73s more memory. The default is 6000 for some histograms 73s and 80000 for others. 73s 73s Histograms for mapped sam/bam files only: 73s histbefore=t Calculate histograms from reads before processing. 73s ehist= Errors-per-read histogram. 73s qahist= Quality accuracy histogram of error rates versus quality 73s score. 73s indelhist= Indel length histogram. 73s mhist= Histogram of match, sub, del, and ins rates by position. 73s idhist= Histogram of read count versus percent identity. 73s idbins=100 Number idhist bins. Set to 'auto' to use read length. 73s varfile= Ignore substitution errors listed in this file when 73s calculating error rates. Can be generated with 73s CallVariants. 73s vcf= Ignore substitution errors listed in this VCF file 73s when calculating error rates. 73s ignorevcfindels=t Also ignore indels listed in the VCF. 73s 73s Processing parameters: 73s k=27 Kmer length used for finding contaminants. Contaminants 73s shorter than k will not be found. k must be at least 1. 73s rcomp=t Look for reverse-complements of kmers in addition to 73s forward kmers. 73s maskmiddle=t (mm) Treat the middle base of a kmer as a wildcard, to 73s increase sensitivity in the presence of errors. This may 73s also be set to a number, e.g. mm=3, to mask that many bp. 73s The default mm=t corresponds to mm=1 for odd-length kmers 73s and mm=2 for even-length kmers (as of v39.04), while 73s mm=f is always equivalent to mm=0. 73s minkmerhits=1 (mkh) Reads need at least this many matching kmers 73s to be considered as matching the reference. 73s minkmerfraction=0.0 (mkf) A reads needs at least this fraction of its total 73s kmers to hit a ref, in order to be considered a match. 73s If this and minkmerhits are set, the greater is used. 73s mincovfraction=0.0 (mcf) A reads needs at least this fraction of its total 73s bases to be covered by ref kmers to be considered a match. 73s If specified, mcf overrides mkh and mkf. 73s hammingdistance=0 (hdist) Maximum Hamming distance for ref kmers (subs only). 73s Memory use is proportional to (3*K)^hdist. 73s qhdist=0 Hamming distance for query kmers; impacts speed, not memory. 73s editdistance=0 (edist) Maximum edit distance from ref kmers (subs 73s and indels). Memory use is proportional to (8*K)^edist. 73s hammingdistance2=0 (hdist2) Sets hdist for short kmers, when using mink. 73s qhdist2=0 Sets qhdist for short kmers, when using mink. 73s editdistance2=0 (edist2) Sets edist for short kmers, when using mink. 73s forbidn=f (fn) Forbids matching of read kmers containing N. 73s By default, these will match a reference 'A' if 73s hdist>0 or edist>0, to increase sensitivity. 73s removeifeitherbad=t (rieb) Paired reads get sent to 'outmatch' if either is 73s match (or either is trimmed shorter than minlen). 73s bbduk.sh in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq \ 73s qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 73s Set to false to require both. 73s trimfailures=f Instead of discarding failed reads, trim them to 1bp. 73s This makes the statistics a bit odd. 73s findbestmatch=f (fbm) If multiple matches, associate read with sequence 73s sharing most kmers. Reduces speed. 73s skipr1=f Don't do kmer-based operations on read 1. 73s skipr2=f Don't do kmer-based operations on read 2. 73s ecco=f For overlapping paired reads only. Performs error- 73s correction with BBMerge prior to kmer operations. 73s recalibrate=f (recal) Recalibrate quality scores. Requires calibration 73s matrices generated by CalcTrueQuality. 73s sam= If recalibration is desired, and matrices have not already 73s been generated, BBDuk will create them from the sam file. 73s amino=f Run in amino acid mode. Some features have not been 73s tested, but kmer-matching works fine. Maximum k is 12. 73s 73s Speed and Memory parameters: 73s threads=auto (t) Set number of threads to use; default is number of 73s logical processors. 73s prealloc=f Preallocate memory in table. Allows faster table loading 73s and more efficient memory usage, for a large reference. 73s monitor=f Kill this process if it crashes. monitor=600,0.01 would 73s kill after 600 seconds under 1% usage. 73s minrskip=1 (mns) Force minimal skip interval when indexing reference 73s kmers. 1 means use all, 2 means use every other kmer, etc. 73s maxrskip=1 (mxs) Restrict maximal skip interval when indexing 73s reference kmers. Normally all are used for scaffolds<100kb, 73s but with longer scaffolds, up to maxrskip-1 are skipped. 73s rskip= Set both minrskip and maxrskip to the same value. 73s If not set, rskip will vary based on sequence length. 73s qskip=1 Skip query kmers to increase speed. 1 means use all. 73s speed=0 Ignore this fraction of kmer space (0-15 out of 16) in both 73s reads and reference. Increases speed and reduces memory. 73s Note: Do not use more than one of 'speed', 'qskip', and 'rskip'. 73s 73s Trimming/Filtering/Masking parameters: 73s Note - if ktrim, kmask, and ksplit are unset, the default behavior is kfilter. 73s All kmer processing modes are mutually exclusive. 73s Reads only get sent to 'outm' purely based on kmer matches in kfilter mode. 73s 73s ktrim=f Trim reads to remove bases matching reference kmers, plus 73s all bases to the left or right. 73s Values: 73s f (don't trim), 73s r (trim to the right), 73s l (trim to the left) 73s ktrimtips=0 Set this to a positive number to perform ktrim on both 73s ends, examining only the outermost X bases. 73s kmask= Replace bases matching ref kmers with another symbol. 73s Allows any non-whitespace character, and processes short 73s kmers on both ends if mink is set. 'kmask=lc' will 73s convert masked bases to lowercase. 73s maskfullycovered=f (mfc) Only mask bases that are fully covered by kmers. 73s ksplit=f For single-ended reads only. Reads will be split into 73s pairs around the kmer. If the kmer is at the end of the 73s read, it will be trimmed instead. Singletons will go to 73s out, and pairs will go to outm. Do not use ksplit with 73s other operations such as quality-trimming or filtering. 73s mink=0 Look for shorter kmers at read tips down to this length, 73s when k-trimming or masking. 0 means disabled. Enabling 73s this will disable maskmiddle. 73s qtrim=f Trim read ends to remove bases with quality below trimq. 73s Performed AFTER looking for kmers. Values: 73s rl (trim both ends), 73s f (neither end), 73s r (right end only), 73s l (left end only), 73s w (sliding window). 73s trimq=6 Regions with average quality BELOW this will be trimmed, 73s if qtrim is set to something other than f. Can be a 73s floating-point number like 7.3. 73s trimclip=f Trim soft-clipped bases from sam files. 73s minlength=10 (ml) Reads shorter than this after trimming will be 73s discarded. Pairs will be discarded if both are shorter. 73s mlf=0 (minlengthfraction) Reads shorter than this fraction of 73s original length after trimming will be discarded. 73s maxlength= Reads longer than this after trimming will be discarded. 73s minavgquality=0 (maq) Reads with average quality (after trimming) below 73s this will be discarded. 73s maqb=0 If positive, calculate maq from this many initial bases. 73s minbasequality=0 (mbq) Reads with any base below this quality (after 73s trimming) will be discarded. 73s maxns=-1 If non-negative, reads with more Ns than this 73s (after trimming) will be discarded. 73s mcb=0 (minconsecutivebases) Discard reads without at least 73s this many consecutive called bases. 73s ottm=f (outputtrimmedtomatch) Output reads trimmed to shorter 73s than minlength to outm rather than discarding. 73s tp=0 (trimpad) Trim this much extra around matching kmers. 73s tbo=f (trimbyoverlap) Trim adapters based on where paired 73s reads overlap. 73s strictoverlap=t Adjust sensitivity for trimbyoverlap mode. 73s minoverlap=14 Require this many bases of overlap for detection. 73s mininsert=40 Require insert size of at least this for overlap. 73s Should be reduced to 16 for small RNA sequencing. 73s tpe=f (trimpairsevenly) When kmer right-trimming, trim both 73s reads to the minimum length of either. 73s forcetrimleft=0 (ftl) If positive, trim bases to the left of this position 73s (exclusive, 0-based). 73s forcetrimright=0 (ftr) If positive, trim bases to the right of this position 73s (exclusive, 0-based). 73s forcetrimright2=0 (ftr2) If positive, trim this many bases on the right end. 73s forcetrimmod=0 (ftm) If positive, right-trim length to be equal to zero, 73s modulo this number. 73s restrictleft=0 If positive, only look for kmer matches in the 73s leftmost X bases. 73s restrictright=0 If positive, only look for kmer matches in the 73s rightmost X bases. 73s NOTE: restrictleft and restrictright are mutually exclusive. If trimming 73s both ends is desired, use ktrimtips. 73s mingc=0 Discard reads with GC content below this. 73s maxgc=1 Discard reads with GC content above this. 73s gcpairs=t Use average GC of paired reads. 73s Also affects gchist. 73s tossjunk=f Discard reads with invalid characters as bases. 73s swift=f Trim Swift sequences: Trailing C/T/N R1, leading G/A/N R2. 73s 73s Header-parsing parameters - these require Illumina headers: 73s chastityfilter=f (cf) Discard reads with id containing ' 1:Y:' or ' 2:Y:'. 73s barcodefilter=f Remove reads with unexpected barcodes if barcodes is set, 73s or barcodes containing 'N' otherwise. A barcode must be 73s the last part of the read header. Values: 73s t: Remove reads with bad barcodes. 73s f: Ignore barcodes. 73s crash: Crash upon encountering bad barcodes. 73s barcodes= Comma-delimited list of barcodes or files of barcodes. 73s xmin=-1 If positive, discard reads with a lesser X coordinate. 73s ymin=-1 If positive, discard reads with a lesser Y coordinate. 73s xmax=-1 If positive, discard reads with a greater X coordinate. 73s ymax=-1 If positive, discard reads with a greater Y coordinate. 73s 73s Polymer trimming: 73s trimpolya=0 If greater than 0, trim poly-A or poly-T tails of 73s at least this length on either end of reads. 73s trimpolygleft=0 If greater than 0, trim poly-G prefixes of at least this 73s length on the left end of reads. Does not trim poly-C. 73s trimpolygright=0 If greater than 0, trim poly-G tails of at least this 73s length on the right end of reads. Does not trim poly-C. 73s trimpolyg=0 This sets both left and right at once. 73s filterpolyg=0 If greater than 0, remove reads with a poly-G prefix of 73s at least this length (on the left). 73s Note: there are also equivalent poly-C flags. 73s 73s Polymer tracking: 73s pratio=base,base 'pratio=G,C' will print the ratio of G to C polymers. 73s plen=20 Length of homopolymers to count. 73s 73s Entropy/Complexity parameters: 73s entropy=-1 Set between 0 and 1 to filter reads with entropy below 73s that value. Higher is more stringent. 73s entropywindow=50 Calculate entropy using a sliding window of this length. 73s entropyk=5 Calculate entropy using kmers of this length. 73s minbasefrequency=0 Discard reads with a minimum base frequency below this. 73s entropytrim=f Values: 73s f: (false) Do not entropy-trim. 73s r: (right) Trim low entropy on the right end only. 73s l: (left) Trim low entropy on the left end only. 73s rl: (both) Trim low entropy on both ends. 73s entropymask=f Values: 73s f: (filter) Discard low-entropy sequences. 73s t: (true) Mask low-entropy parts of sequences with N. 73s lc: Change low-entropy parts of sequences to lowercase. 73s entropymark=f Mark each base with its entropy value. This is on a scale 73s of 0-41 and is reported as quality scores, so the output 73s should be fastq or fasta+qual. 73s NOTE: If set, entropytrim overrides entropymask. 73s 73s Cardinality estimation: 73s cardinality=f (loglog) Count unique kmers using the LogLog algorithm. 73s cardinalityout=f (loglogout) Count unique kmers in output reads. 73s loglogk=31 Use this kmer length for counting. 73s loglogbuckets=2048 Use this many buckets for counting. 73s khist= Kmer frequency histogram; plots number of kmers versus 73s kmer depth. This is approximate. 73s khistout= Kmer frequency histogram for output reads. 73s 73s Java Parameters: 73s 73s -Xmx This will set Java's memory usage, overriding autodetection. 73s -Xmx20g will 73s specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 73s The max is typically 85% of physical memory. 73s -eoom This flag will cause the process to exit if an 73s out-of-memory exception occurs. Requires Java 8u92+. 73s -da Disable assertions. 73s 73s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 73s 73s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 73s java -ea -Xmx1386m -Xms1386m -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 73s 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] 73s Version 39.08 73s 73s Changed from ASCII-33 to ASCII-64 on input quality X (Q55) for base A at lines 1 and 3, position 24 while prescanning. 73s Changed from ASCII-33 to ASCII-64 on input quality X (Q55) for base A at lines 1 and 3, position 24 while prescanning. 73s 0.026 seconds. 73s Initial: 73s Memory: max=1453m, total=1453m, free=1422m, used=31m 73s 73s Input is being processed as paired 73s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 73s Started output streams: 0.015 seconds. 73s Processing time: 0.004 seconds. 73s 73s Input: 8 reads 306 bases. 73s QTrimmed: 0 reads (0.00%) 0 bases (0.00%) 73s Total Removed: 8 reads (100.00%) 306 bases (100.00%) 73s Result: 0 reads (0.00%) 0 bases (0.00%) 73s 73s Time: 0.020 seconds. 73s Reads Processed: 8 0.39k reads/sec 73s Bases Processed: 306 0.01m bases/sec 73s test -r out.fastq.gz 73s 73s # bbnorm 73s bbnorm.sh --version 73s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 73s java -ea -Xmx2772m -Xms2772m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 --version 73s BBTools version 39.08 73s For help, please run the shellscript with no parameters, or look in /docs/. 73s bbnorm.sh --help 73s 73s Written by Brian Bushnell 73s Last modified October 19, 2017 73s 73s Description: Normalizes read depth based on kmer counts. 73s Can also error-correct, bin reads by kmer depth, and generate a kmer depth histogram. 73s However, Tadpole has superior error-correction to BBNorm. 73s Please read bbmap/docs/guides/BBNormGuide.txt for more information. 73s 73s Usage: bbnorm.sh in= out= outt= hist= 73s 73s Input parameters: 73s in=null Primary input. Use in2 for paired reads in a second file 73s in2=null Second input file for paired reads in two files 73s extra=null Additional files to use for input (generating hash table) but not for output 73s fastareadlen=2^31 Break up FASTA reads longer than this. Can be useful when processing scaffolded genomes 73s tablereads=-1 Use at most this many reads when building the hashtable (-1 means all) 73s kmersample=1 Process every nth kmer, and skip the rest 73s readsample=1 Process every nth read, and skip the rest 73s 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. 73s qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto. 73s 73s Output parameters: 73s out= File for normalized or corrected reads. Use out2 for paired reads in a second file 73s outt= (outtoss) File for reads that were excluded from primary output 73s reads=-1 Only process this number of reads, then quit (-1 means all) 73s sampleoutput=t Use sampling on output as well as input (not used if sample rates are 1) 73s keepall=f Set to true to keep all reads (e.g. if you just want error correction). 73s 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. 73s Default is false, to prevent confusion about how there can be 0-count kmers. 73s The reason is that based on the 'minq' and 'minprob' settings, some kmers may be excluded from the bloom filter. 73s tmpdir= This will specify a directory for temp files (only needed for multipass runs). If null, they will be written to the output directory. 73s usetempdir=t Allows enabling/disabling of temporary directory; if disabled, temp files will be written to the output directory. 73s qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input). 73s rename=f Rename reads based on their kmer depth. 73s 73s Hashing parameters: 73s k=31 Kmer length (values under 32 are most efficient, but arbitrarily high values are supported) 73s 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. 73s Large values decrease accuracy for a fixed amount of memory, so use the lowest number you can that will still capture highest-depth kmers. 73s hashes=3 Number of times each kmer is hashed and stored. Higher is slower. 73s Higher is MORE accurate if there is enough memory, and LESS accurate if there is not enough memory. 73s 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. 73s prehashes=2 Number of hashes for prefilter. 73s prefilterbits=2 (pbits) Bits per cell in prefilter. 73s prefiltersize=0.35 Fraction of memory to allocate to prefilter. 73s buildpasses=1 More passes can sometimes increase accuracy by iteratively removing low-depth kmers 73s minq=6 Ignore kmers containing bases with quality below this 73s minprob=0.5 Ignore kmers with overall probability of correctness below this 73s 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. 73s 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. 73s 73s Normalization parameters: 73s fixspikes=f (fs) Do a slower, high-precision bloom filter lookup of kmers that appear to have an abnormally high depth due to collisions. 73s target=100 (tgt) Target normalization depth. NOTE: All depth parameters control kmer depth, not read depth. 73s For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1)) 73s maxdepth=-1 (max) Reads will not be downsampled when below this depth, even if they are above the target depth. 73s mindepth=5 (min) Kmers with depth below this number will not be included when calculating the depth of a read. 73s minkmers=15 (mgkpr) Reads must have at least this many kmers over min depth to be retained. Aka 'mingoodkmersperread'. 73s 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. 73s uselowerdepth=t (uld) For pairs, use the depth of the lower read as the depth proxy. 73s deterministic=t (dr) Generate random numbers deterministically to ensure identical output between multiple runs. May decrease speed with a huge number of threads. 73s passes=2 (p) 1 pass is the basic mode. 2 passes (default) allows greater accuracy, error detection, better contol of output depth. 73s 73s Error detection parameters: 73s hdp=90.0 (highdepthpercentile) Position in sorted kmer depth array used as proxy of a read's high kmer depth. 73s ldp=25.0 (lowdepthpercentile) Position in sorted kmer depth array used as proxy of a read's low kmer depth. 73s tossbadreads=f (tbr) Throw away reads detected as containing errors. 73s requirebothbad=f (rbb) Only toss bad pairs if both reads are bad. 73s 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. 73s highthresh=12 (ht) Threshold for high kmer. A high kmer at this or above are considered non-error. 73s lowthresh=3 (lt) Threshold for low kmer. Kmers at this and below are always considered errors. 73s 73s Error correction parameters: 73s ecc=f Set to true to correct errors. NOTE: Tadpole is now preferred for ecc as it does a better job. 73s ecclimit=3 Correct up to this many errors per read. If more are detected, the read will remain unchanged. 73s errorcorrectratio=140 (ecr) Adjacent kmers with a depth ratio of at least this much between will be classified as an error. 73s echighthresh=22 (echt) Threshold for high kmer. A kmer at this or above may be considered non-error. 73s eclowthresh=2 (eclt) Threshold for low kmer. Kmers at this and below are considered errors. 73s eccmaxqual=127 Do not correct bases with quality above this value. 73s aec=f (aggressiveErrorCorrection) Sets more aggressive values of ecr=100, ecclimit=7, echt=16, eclt=3. 73s cec=f (conservativeErrorCorrection) Sets more conservative values of ecr=180, ecclimit=2, echt=30, eclt=1, sl=4, pl=4. 73s meo=f (markErrorsOnly) Marks errors by reducing quality value of suspected errors; does not correct anything. 73s mue=t (markUncorrectableErrors) Marks errors only on uncorrectable reads; requires 'ecc=t'. 73s overlap=f (ecco) Error correct by read overlap. 73s 73s Depth binning parameters: 73s lowbindepth=10 (lbd) Cutoff for low depth bin. 73s highbindepth=80 (hbd) Cutoff for high depth bin. 73s outlow= Pairs in which both reads have a median below lbd go into this file. 73s outhigh= Pairs in which both reads have a median above hbd go into this file. 73s outmid= All other pairs go into this file. 73s 73s Histogram parameters: 73s hist= Specify a file to write the input kmer depth histogram. 73s histout= Specify a file to write the output kmer depth histogram. 73s histcol=3 (histogramcolumns) Number of histogram columns, 2 or 3. 73s pzc=f (printzerocoverage) Print lines in the histogram with zero coverage. 73s histlen=1048576 Max kmer depth displayed in histogram. Also affects statistics displayed, but does not affect normalization. 73s 73s Peak calling parameters: 73s peaks= Write the peaks to this file. Default is stdout. 73s minHeight=2 (h) Ignore peaks shorter than this. 73s minVolume=5 (v) Ignore peaks with less area than this. 73s minWidth=3 (w) Ignore peaks narrower than this. 73s minPeak=2 (minp) Ignore peaks with an X-value below this. 73s maxPeak=BIG (maxp) Ignore peaks with an X-value above this. 73s maxPeakCount=8 (maxpc) Print up to this many peaks (prioritizing height). 73s 73s Java Parameters: 73s -Xmx This will set Java's memory usage, overriding autodetection. 73s -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 73s The max is typically 85% of physical memory. 73s -eoom This flag will cause the process to exit if an 73s out-of-memory exception occurs. Requires Java 8u92+. 73s -da Disable assertions. 73s 73s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 73s 73s bbnorm.sh in=sanger_full_range_original_sanger.fastq qin=33 \ 73s out=out3.fastq outt=outt.fastq hist=hist.plt 73s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 73s java -ea -Xmx2772m -Xms2772m -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 73s Executing jgi.KmerNormalize [bits=32, in=sanger_full_range_original_sanger.fastq, qin=33, out=out3.fastq, outt=outt.fastq, hist=hist.plt] 73s 73s 73s *********** Pass 1 ********** 73s 73s 73s Settings: 73s threads: 4 73s k: 31 73s deterministic: true 73s toss error reads: false 73s passes: 1 73s bits per cell: 16 73s cells: 1025.36M 73s hashes: 3 73s base min quality: 5 73s kmer min prob: 0.5 73s 73s target depth: 400 73s min depth: 3 73s max depth: 500 73s min good kmers: 15 73s depth percentile: 64.8 73s ignore dupe kmers: true 73s fix spikes: false 73s histogram length: 65536 73s print zero cov: false 73s 74s Made hash table: hashes = 3 mem = 1.91 GB cells = 1024.56M used = 0.000% 74s 74s Estimated unique kmers: 4 74s 74s Table creation time: 0.947 seconds. 74s Started output threads. 74s Started output threads. 74s Table read time: 0.007 seconds. 28.31 kb/sec 74s Total reads in: 2 0.000% Kept 74s Total bases in: 188 0.000% Kept 74s Error reads in: 2 100.000% 74s Error type 1: 2 100.000% 74s Error type 2: 0 0.000% 74s Error type 3: 0 0.000% 74s 74s Wrote histogram to hist.plt 74s Total kmers counted: 128 74s Total unique kmer count: 128 74s Includes forward kmers only. 74s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 74s The most accurate value is the greater of the two. 74s 74s Percent unique: 100.00% 74s Depth average: 1.00 (unique kmers) 74s Depth median: 1 (unique kmers) 74s Depth standard deviation: 0.00 (unique kmers) 74s Corrected depth average: 0.00 74s 74s Depth average: 1.00 (all kmers) 74s Depth median: 1 (all kmers) 74s Depth standard deviation: 0.00 (all kmers) 74s 74s Approx. read depth median: 1.47 74s 74s *********** Pass 2 ********** 74s 74s 74s Settings: 74s threads: 4 74s k: 31 74s deterministic: true 74s toss error reads: false 74s passes: 1 74s bits per cell: 16 74s cells: 1025.36M 74s hashes: 3 74s base min quality: 5 74s kmer min prob: 0.5 74s 74s target depth: 100 74s min depth: 5 74s max depth: 100 74s min good kmers: 15 74s depth percentile: 54.0 74s ignore dupe kmers: true 74s fix spikes: false 74s histogram length: 65536 74s 75s Made hash table: hashes = 3 mem = 1.91 GB cells = 1024.56M used = 0.000% 75s 75s Estimated unique kmers: 0 75s 75s Table creation time: 0.339 seconds. 75s Started output threads. 75s Started output threads. 75s Table read time: 0.001 seconds. 0.00 kb/sec 75s Total reads in: 0 NaN% Kept 75s Total bases in: 0 NaN% Kept 75s Error reads in: 0 NaN% 75s Error type 1: 0 NaN% 75s Error type 2: 0 NaN% 75s Error type 3: 0 NaN% 75s Total kmers counted: 0 75s Total unique kmer count: 0 75s Includes forward kmers only. 75s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 75s The most accurate value is the greater of the two. 75s 75s Percent unique: NaN% 75s Depth average: NaN (unique kmers) 75s Depth median: 0 (unique kmers) 75s Depth standard deviation: NaN (unique kmers) 75s Corrected depth average: NaN 75s 75s Depth average: NaN (all kmers) 75s Depth median: 0 (all kmers) 75s Depth standard deviation: 0.00 (all kmers) 75s 75s Approx. read depth median: NaN 75s 75s Removing temp files. 75s 75s Total time: 1.381 seconds. 0.14 kb/sec 75s test -r out3.fastq 75s test -r outt.fastq 75s test -r hist.plt 75s bbnorm.sh in=illumina_full_range_original_illumina.fastq qin=64 \ 75s out=out4.fastq outt=outt2.fastq hist=hist2.plt 75s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 75s java -ea -Xmx2772m -Xms2772m -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 75s Executing jgi.KmerNormalize [bits=32, in=illumina_full_range_original_illumina.fastq, qin=64, out=out4.fastq, outt=outt2.fastq, hist=hist2.plt] 75s 75s 75s *********** Pass 1 ********** 75s 75s 75s Settings: 75s threads: 4 75s k: 31 75s deterministic: true 75s toss error reads: false 75s passes: 1 75s bits per cell: 16 75s cells: 1025.36M 75s hashes: 3 75s base min quality: 5 75s kmer min prob: 0.5 75s 75s target depth: 400 75s min depth: 3 75s max depth: 500 75s min good kmers: 15 75s depth percentile: 64.8 75s ignore dupe kmers: true 75s fix spikes: false 75s histogram length: 65536 75s print zero cov: false 75s 76s Made hash table: hashes = 3 mem = 1.91 GB cells = 1024.56M used = 0.000% 76s 76s Estimated unique kmers: 4 76s 76s Table creation time: 0.905 seconds. 76s Started output threads. 76s Started output threads. 76s Table read time: 0.006 seconds. 22.14 kb/sec 76s Total reads in: 2 0.000% Kept 76s Total bases in: 126 0.000% Kept 76s Error reads in: 2 100.000% 76s Error type 1: 2 100.000% 76s Error type 2: 0 0.000% 76s Error type 3: 0 0.000% 76s 76s Wrote histogram to hist2.plt 76s Total kmers counted: 66 76s Total unique kmer count: 66 76s Includes forward kmers only. 76s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 76s The most accurate value is the greater of the two. 76s 76s Percent unique: 100.00% 76s Depth average: 1.00 (unique kmers) 76s Depth median: 1 (unique kmers) 76s Depth standard deviation: 0.00 (unique kmers) 76s Corrected depth average: 0.00 76s 76s Depth average: 1.00 (all kmers) 76s Depth median: 1 (all kmers) 76s Depth standard deviation: 0.00 (all kmers) 76s 76s Approx. read depth median: 1.91 76s 76s *********** Pass 2 ********** 76s 76s 76s Settings: 76s threads: 4 76s k: 31 76s deterministic: true 76s toss error reads: false 76s passes: 1 76s bits per cell: 16 76s cells: 1025.36M 76s hashes: 3 76s base min quality: 5 76s kmer min prob: 0.5 76s 76s target depth: 100 76s min depth: 5 76s max depth: 100 76s min good kmers: 15 76s depth percentile: 54.0 76s ignore dupe kmers: true 76s fix spikes: false 76s histogram length: 65536 76s 77s Made hash table: hashes = 3 mem = 1.91 GB cells = 1024.56M used = 0.000% 77s 77s Estimated unique kmers: 0 77s 77s Table creation time: 0.337 seconds. 77s Started output threads. 77s Started output threads. 77s Table read time: 0.001 seconds. 0.00 kb/sec 77s Total reads in: 0 NaN% Kept 77s Total bases in: 0 NaN% Kept 77s Error reads in: 0 NaN% 77s Error type 1: 0 NaN% 77s Error type 2: 0 NaN% 77s Error type 3: 0 NaN% 77s Total kmers counted: 0 77s Total unique kmer count: 0 77s Includes forward kmers only. 77s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 77s The most accurate value is the greater of the two. 77s 77s Percent unique: NaN% 77s Depth average: NaN (unique kmers) 77s Depth median: 0 (unique kmers) 77s Depth standard deviation: NaN (unique kmers) 77s Corrected depth average: NaN 77s 77s Depth average: NaN (all kmers) 77s Depth median: 0 (all kmers) 77s Depth standard deviation: 0.00 (all kmers) 77s 77s Approx. read depth median: NaN 77s 77s Removing temp files. 77s 77s Total time: 1.338 seconds. 0.09 kb/sec 77s test -r out4.fastq 77s test -r outt2.fastq 77s test -r hist2.plt 77s autopkgtest [05:40:36]: test run-unit-test: -----------------------] 77s run-unit-test PASS 77s autopkgtest [05:40:36]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 77s autopkgtest [05:40:36]: @@@@@@@@@@@@@@@@@@@@ summary 77s run-unit-test PASS 89s nova [W] Skipping flock for amd64 89s Creating nova instance adt-plucky-amd64-bbmap-20241104-050415-juju-7f2275-prod-proposed-migration-environment-15-67baf27d-5a7f-4cc3-941f-8a4f8dfe92c2 from image adt/ubuntu-plucky-amd64-server-20241103.img (UUID 35ab818c-a1b8-49b0-b1ec-61e6c5b42b5f)...