0s autopkgtest [20:28:17]: starting date and time: 2025-11-01 20:28:17+0000 0s autopkgtest [20:28:17]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [20:28:17]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.i13y7jjz/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:openjdk-26,src:jtreg8 --apt-upgrade bbmap --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=openjdk-26/26~22ea-2 jtreg8/8.1+1+ds1-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-big-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-ppc64el-5.secgroup --name adt-resolute-ppc64el-bbmap-20251101-202817-juju-7f2275-prod-proposed-migration-environment-15-59303e02-fca8-4a1c-a3c6-12f4d55e9e6e --image adt/ubuntu-resolute-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-ppc64el -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-ppc64el-bbmap-20251101-202817-juju-7f2275-prod-proposed-migration-environment-15-59303e02-fca8-4a1c-a3c6-12f4d55e9e6e from image adt/ubuntu-resolute-ppc64el-server-20251101.img (UUID d697cb25-9ab9-4704-adbb-3eefcc081274)... 49s autopkgtest [20:29:06]: testbed dpkg architecture: ppc64el 49s autopkgtest [20:29:06]: testbed apt version: 3.1.11 50s autopkgtest [20:29:07]: @@@@@@@@@@@@@@@@@@@@ test bed setup 50s autopkgtest [20:29:07]: testbed release detected to be: None 51s autopkgtest [20:29:08]: updating testbed package index (apt update) 51s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB] 51s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 51s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 51s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 51s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [9848 B] 51s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [48.6 kB] 51s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1791 kB] 52s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [138 kB] 52s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el Packages [197 kB] 52s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted ppc64el Packages [940 B] 52s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el Packages [1323 kB] 52s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse ppc64el Packages [32.4 kB] 52s Fetched 3629 kB in 2s (2355 kB/s) 53s Reading package lists... 54s Failed to check for VM: Permission denied 54s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 54s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 54s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 54s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 55s Reading package lists... 55s Reading package lists... 55s Building dependency tree... 55s Reading state information... 55s Calculating upgrade... 56s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 56s autopkgtest [20:29:13]: upgrading testbed (apt dist-upgrade and autopurge) 56s Reading package lists... 56s Building dependency tree... 56s Reading state information... 56s Calculating upgrade... 56s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 56s Reading package lists... 57s Building dependency tree... 57s Reading state information... 57s Solving dependencies... 57s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 60s autopkgtest [20:29:17]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 10:02:41 UTC 2025 60s autopkgtest [20:29:17]: @@@@@@@@@@@@@@@@@@@@ apt-source bbmap 63s Get:1 http://ftpmaster.internal/ubuntu resolute/universe bbmap 39.20+dfsg-2 (dsc) [2286 B] 63s Get:2 http://ftpmaster.internal/ubuntu resolute/universe bbmap 39.20+dfsg-2 (tar) [5748 kB] 63s Get:3 http://ftpmaster.internal/ubuntu resolute/universe bbmap 39.20+dfsg-2 (diff) [26.8 kB] 63s gpgv: Signature made Sun Apr 6 17:54:51 2025 UTC 63s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 63s gpgv: issuer "emollier@debian.org" 63s gpgv: Can't check signature: No public key 63s dpkg-source: warning: cannot verify inline signature for ./bbmap_39.20+dfsg-2.dsc: no acceptable signature found 64s autopkgtest [20:29:21]: testing package bbmap version 39.20+dfsg-2 64s autopkgtest [20:29:21]: build not needed 65s autopkgtest [20:29:22]: test run-unit-test: preparing testbed 65s Reading package lists... 65s Building dependency tree... 65s Reading state information... 66s Solving dependencies... 66s The following NEW packages will be installed: 66s bbmap bbmap-jni ca-certificates-java default-jre-headless java-common 66s libapache-pom-java libcommons-cli-java libcommons-codec-java 66s libcommons-io-java libcommons-parent-java libjpeg-turbo8 libjpeg8 66s libjs-jquery libjs-sphinxdoc libjs-underscore liblcms2-2 liblog4j1.2-java 66s libmpj-java libnspr4 libnss3 libpcsclite1 openjdk-21-jre-headless 66s python-biopython-doc 66s 0 upgraded, 23 newly installed, 0 to remove and 0 not upgraded. 66s Need to get 79.5 MB of archives. 66s After this operation, 267 MB of additional disk space will be used. 66s Get:1 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libcommons-cli-java all 1.6.0-1 [59.9 kB] 66s Get:2 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libapache-pom-java all 33-2 [5874 B] 66s Get:3 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libcommons-parent-java all 56-1 [10.7 kB] 66s Get:4 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libcommons-codec-java all 1.18.0-1 [303 kB] 66s Get:5 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libcommons-io-java all 2.19.0-1 [491 kB] 66s Get:6 http://ftpmaster.internal/ubuntu resolute/universe ppc64el liblog4j1.2-java all 1.2.17-11 [439 kB] 66s Get:7 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libmpj-java all 0.44+dfsg-4 [443 kB] 67s Get:8 http://ftpmaster.internal/ubuntu resolute/main ppc64el ca-certificates-java all 20240118 [11.6 kB] 67s Get:9 http://ftpmaster.internal/ubuntu resolute/main ppc64el java-common all 0.76 [6852 B] 67s Get:10 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblcms2-2 ppc64el 2.16-2 [243 kB] 67s Get:11 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-4ubuntu2 [215 kB] 67s Get:12 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 67s Get:13 http://ftpmaster.internal/ubuntu resolute/main ppc64el libnspr4 ppc64el 2:4.36-1ubuntu2 [135 kB] 67s Get:14 http://ftpmaster.internal/ubuntu resolute/main ppc64el libnss3 ppc64el 2:3.114-1 [1876 kB] 67s Get:15 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpcsclite1 ppc64el 2.3.3-1 [30.6 kB] 67s Get:16 http://ftpmaster.internal/ubuntu resolute/main ppc64el openjdk-21-jre-headless ppc64el 21.0.9+10-1 [45.9 MB] 68s Get:17 http://ftpmaster.internal/ubuntu resolute/main ppc64el default-jre-headless ppc64el 2:1.21-76 [3184 B] 68s Get:18 http://ftpmaster.internal/ubuntu resolute/universe ppc64el bbmap all 39.20+dfsg-2 [10.6 MB] 68s Get:19 http://ftpmaster.internal/ubuntu resolute/universe ppc64el bbmap-jni ppc64el 39.20+dfsg-2 [32.9 kB] 68s Get:20 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 68s Get:21 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 68s Get:22 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 68s Get:23 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python-biopython-doc all 1.85+dfsg-4 [18.2 MB] 69s Fetched 79.5 MB in 3s (24.6 MB/s) 69s Selecting previously unselected package libcommons-cli-java. 69s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 76562 files and directories currently installed.) 69s Preparing to unpack .../00-libcommons-cli-java_1.6.0-1_all.deb ... 69s Unpacking libcommons-cli-java (1.6.0-1) ... 69s Selecting previously unselected package libapache-pom-java. 69s Preparing to unpack .../01-libapache-pom-java_33-2_all.deb ... 69s Unpacking libapache-pom-java (33-2) ... 69s Selecting previously unselected package libcommons-parent-java. 69s Preparing to unpack .../02-libcommons-parent-java_56-1_all.deb ... 69s Unpacking libcommons-parent-java (56-1) ... 69s Selecting previously unselected package libcommons-codec-java. 69s Preparing to unpack .../03-libcommons-codec-java_1.18.0-1_all.deb ... 69s Unpacking libcommons-codec-java (1.18.0-1) ... 70s Selecting previously unselected package libcommons-io-java. 70s Preparing to unpack .../04-libcommons-io-java_2.19.0-1_all.deb ... 70s Unpacking libcommons-io-java (2.19.0-1) ... 70s Selecting previously unselected package liblog4j1.2-java. 70s Preparing to unpack .../05-liblog4j1.2-java_1.2.17-11_all.deb ... 70s Unpacking liblog4j1.2-java (1.2.17-11) ... 70s Selecting previously unselected package libmpj-java. 70s Preparing to unpack .../06-libmpj-java_0.44+dfsg-4_all.deb ... 70s Unpacking libmpj-java (0.44+dfsg-4) ... 70s Selecting previously unselected package ca-certificates-java. 70s Preparing to unpack .../07-ca-certificates-java_20240118_all.deb ... 70s Unpacking ca-certificates-java (20240118) ... 70s Selecting previously unselected package java-common. 70s Preparing to unpack .../08-java-common_0.76_all.deb ... 70s Unpacking java-common (0.76) ... 70s Selecting previously unselected package liblcms2-2:ppc64el. 70s Preparing to unpack .../09-liblcms2-2_2.16-2_ppc64el.deb ... 70s Unpacking liblcms2-2:ppc64el (2.16-2) ... 70s Selecting previously unselected package libjpeg-turbo8:ppc64el. 70s Preparing to unpack .../10-libjpeg-turbo8_2.1.5-4ubuntu2_ppc64el.deb ... 70s Unpacking libjpeg-turbo8:ppc64el (2.1.5-4ubuntu2) ... 70s Selecting previously unselected package libjpeg8:ppc64el. 70s Preparing to unpack .../11-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 70s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 70s Selecting previously unselected package libnspr4:ppc64el. 70s Preparing to unpack .../12-libnspr4_2%3a4.36-1ubuntu2_ppc64el.deb ... 70s Unpacking libnspr4:ppc64el (2:4.36-1ubuntu2) ... 70s Selecting previously unselected package libnss3:ppc64el. 70s Preparing to unpack .../13-libnss3_2%3a3.114-1_ppc64el.deb ... 70s Unpacking libnss3:ppc64el (2:3.114-1) ... 70s Selecting previously unselected package libpcsclite1:ppc64el. 70s Preparing to unpack .../14-libpcsclite1_2.3.3-1_ppc64el.deb ... 70s Unpacking libpcsclite1:ppc64el (2.3.3-1) ... 70s Selecting previously unselected package openjdk-21-jre-headless:ppc64el. 70s Preparing to unpack .../15-openjdk-21-jre-headless_21.0.9+10-1_ppc64el.deb ... 70s Unpacking openjdk-21-jre-headless:ppc64el (21.0.9+10-1) ... 71s Selecting previously unselected package default-jre-headless. 71s Preparing to unpack .../16-default-jre-headless_2%3a1.21-76_ppc64el.deb ... 71s Unpacking default-jre-headless (2:1.21-76) ... 71s Selecting previously unselected package bbmap. 71s Preparing to unpack .../17-bbmap_39.20+dfsg-2_all.deb ... 71s Unpacking bbmap (39.20+dfsg-2) ... 71s Selecting previously unselected package bbmap-jni. 71s Preparing to unpack .../18-bbmap-jni_39.20+dfsg-2_ppc64el.deb ... 71s Unpacking bbmap-jni (39.20+dfsg-2) ... 71s Selecting previously unselected package libjs-jquery. 71s Preparing to unpack .../19-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 71s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 71s Selecting previously unselected package libjs-underscore. 71s Preparing to unpack .../20-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 71s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 71s Selecting previously unselected package libjs-sphinxdoc. 71s Preparing to unpack .../21-libjs-sphinxdoc_8.2.3-1ubuntu2_all.deb ... 71s Unpacking libjs-sphinxdoc (8.2.3-1ubuntu2) ... 71s Selecting previously unselected package python-biopython-doc. 71s Preparing to unpack .../22-python-biopython-doc_1.85+dfsg-4_all.deb ... 71s Unpacking python-biopython-doc (1.85+dfsg-4) ... 71s Setting up liblcms2-2:ppc64el (2.16-2) ... 71s Setting up java-common (0.76) ... 71s Setting up libcommons-cli-java (1.6.0-1) ... 71s Setting up liblog4j1.2-java (1.2.17-11) ... 71s Setting up libnspr4:ppc64el (2:4.36-1ubuntu2) ... 71s Setting up libapache-pom-java (33-2) ... 71s Setting up libpcsclite1:ppc64el (2.3.3-1) ... 71s Setting up libjpeg-turbo8:ppc64el (2.1.5-4ubuntu2) ... 71s Setting up bbmap-jni (39.20+dfsg-2) ... 71s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 71s Setting up ca-certificates-java (20240118) ... 71s No JRE found. Skipping Java certificates setup. 71s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 71s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 71s Setting up libcommons-parent-java (56-1) ... 71s Setting up libnss3:ppc64el (2:3.114-1) ... 71s Setting up libjs-sphinxdoc (8.2.3-1ubuntu2) ... 71s Setting up python-biopython-doc (1.85+dfsg-4) ... 71s Setting up libcommons-codec-java (1.18.0-1) ... 71s Setting up openjdk-21-jre-headless:ppc64el (21.0.9+10-1) ... 71s update-alternatives: using /usr/lib/jvm/java-21-openjdk-ppc64el/bin/java to provide /usr/bin/java (java) in auto mode 71s update-alternatives: using /usr/lib/jvm/java-21-openjdk-ppc64el/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 71s update-alternatives: using /usr/lib/jvm/java-21-openjdk-ppc64el/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 71s update-alternatives: using /usr/lib/jvm/java-21-openjdk-ppc64el/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 71s update-alternatives: using /usr/lib/jvm/java-21-openjdk-ppc64el/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 71s Setting up libcommons-io-java (2.19.0-1) ... 71s Setting up libmpj-java (0.44+dfsg-4) ... 71s Processing triggers for libc-bin (2.42-0ubuntu3) ... 71s Processing triggers for man-db (2.13.1-1) ... 72s Processing triggers for ca-certificates-java (20240118) ... 73s Adding debian:ACCVRAIZ1.pem 73s Adding debian:AC_RAIZ_FNMT-RCM.pem 73s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 73s Adding debian:ANF_Secure_Server_Root_CA.pem 73s Adding debian:Actalis_Authentication_Root_CA.pem 73s Adding debian:AffirmTrust_Commercial.pem 73s Adding debian:AffirmTrust_Networking.pem 73s Adding debian:AffirmTrust_Premium.pem 73s Adding debian:AffirmTrust_Premium_ECC.pem 73s Adding debian:Amazon_Root_CA_1.pem 73s Adding debian:Amazon_Root_CA_2.pem 73s Adding debian:Amazon_Root_CA_3.pem 73s Adding debian:Amazon_Root_CA_4.pem 73s Adding debian:Atos_TrustedRoot_2011.pem 73s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 73s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 73s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 73s Adding debian:BJCA_Global_Root_CA1.pem 73s Adding debian:BJCA_Global_Root_CA2.pem 73s Adding debian:Baltimore_CyberTrust_Root.pem 73s Adding debian:Buypass_Class_2_Root_CA.pem 73s Adding debian:Buypass_Class_3_Root_CA.pem 73s Adding debian:CA_Disig_Root_R2.pem 73s Adding debian:CFCA_EV_ROOT.pem 73s Adding debian:COMODO_Certification_Authority.pem 73s Adding debian:COMODO_ECC_Certification_Authority.pem 73s Adding debian:COMODO_RSA_Certification_Authority.pem 73s Adding debian:Certainly_Root_E1.pem 73s Adding debian:Certainly_Root_R1.pem 73s Adding debian:Certigna.pem 73s Adding debian:Certigna_Root_CA.pem 73s Adding debian:Certum_EC-384_CA.pem 73s Adding debian:Certum_Trusted_Network_CA.pem 73s Adding debian:Certum_Trusted_Network_CA_2.pem 73s Adding debian:Certum_Trusted_Root_CA.pem 73s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 73s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 73s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 73s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 73s Adding debian:Comodo_AAA_Services_root.pem 73s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 73s Adding debian:D-TRUST_BR_Root_CA_2_2023.pem 73s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 73s Adding debian:D-TRUST_EV_Root_CA_2_2023.pem 73s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 73s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 73s Adding debian:DigiCert_Assured_ID_Root_CA.pem 73s Adding debian:DigiCert_Assured_ID_Root_G2.pem 73s Adding debian:DigiCert_Assured_ID_Root_G3.pem 73s Adding debian:DigiCert_Global_Root_CA.pem 73s Adding debian:DigiCert_Global_Root_G2.pem 73s Adding debian:DigiCert_Global_Root_G3.pem 73s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 73s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 73s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 73s Adding debian:DigiCert_Trusted_Root_G4.pem 73s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 73s Adding debian:Entrust_Root_Certification_Authority.pem 73s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 73s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 73s Adding debian:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem 73s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 73s Adding debian:GLOBALTRUST_2020.pem 73s Adding debian:GTS_Root_R1.pem 73s Adding debian:GTS_Root_R2.pem 73s Adding debian:GTS_Root_R3.pem 73s Adding debian:GTS_Root_R4.pem 73s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 73s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 73s Adding debian:GlobalSign_Root_CA.pem 73s Adding debian:GlobalSign_Root_CA_-_R3.pem 73s Adding debian:GlobalSign_Root_CA_-_R6.pem 73s Adding debian:GlobalSign_Root_E46.pem 73s Adding debian:GlobalSign_Root_R46.pem 73s Adding debian:Go_Daddy_Class_2_CA.pem 73s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 73s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 73s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 73s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 73s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 73s Adding debian:HiPKI_Root_CA_-_G1.pem 73s Adding debian:Hongkong_Post_Root_CA_3.pem 73s Adding debian:ISRG_Root_X1.pem 73s Adding debian:ISRG_Root_X2.pem 73s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 73s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 73s Adding debian:Izenpe.com.pem 73s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 73s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 73s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 73s Adding debian:NAVER_Global_Root_Certification_Authority.pem 73s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 73s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 73s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 73s Adding debian:QuoVadis_Root_CA_1_G3.pem 73s Adding debian:QuoVadis_Root_CA_2.pem 73s Adding debian:QuoVadis_Root_CA_2_G3.pem 73s Adding debian:QuoVadis_Root_CA_3.pem 73s Adding debian:QuoVadis_Root_CA_3_G3.pem 73s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 73s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 73s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 73s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 73s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 73s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 73s Adding debian:SZAFIR_ROOT_CA2.pem 73s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 73s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 73s Adding debian:SecureSign_Root_CA12.pem 73s Adding debian:SecureSign_Root_CA14.pem 73s Adding debian:SecureSign_Root_CA15.pem 73s Adding debian:SecureTrust_CA.pem 73s Adding debian:Secure_Global_CA.pem 73s Adding debian:Security_Communication_ECC_RootCA1.pem 73s Adding debian:Security_Communication_RootCA2.pem 73s Adding debian:Starfield_Class_2_CA.pem 73s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 73s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 73s Adding debian:SwissSign_Gold_CA_-_G2.pem 73s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 73s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 73s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 73s Adding debian:TWCA_CYBER_Root_CA.pem 73s Adding debian:TWCA_Global_Root_CA.pem 73s Adding debian:TWCA_Root_Certification_Authority.pem 73s Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem 73s Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem 73s Adding debian:TeliaSonera_Root_CA_v1.pem 73s Adding debian:Telia_Root_CA_v2.pem 73s Adding debian:TrustAsia_Global_Root_CA_G3.pem 73s Adding debian:TrustAsia_Global_Root_CA_G4.pem 73s Adding debian:Trustwave_Global_Certification_Authority.pem 73s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 73s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 73s Adding debian:TunTrust_Root_CA.pem 73s Adding debian:UCA_Extended_Validation_Root.pem 73s Adding debian:UCA_Global_G2_Root.pem 73s Adding debian:USERTrust_ECC_Certification_Authority.pem 73s Adding debian:USERTrust_RSA_Certification_Authority.pem 73s Adding debian:XRamp_Global_CA_Root.pem 73s Adding debian:certSIGN_ROOT_CA.pem 73s Adding debian:certSIGN_Root_CA_G2.pem 73s Adding debian:e-Szigno_Root_CA_2017.pem 73s Adding debian:ePKI_Root_Certification_Authority.pem 73s Adding debian:emSign_ECC_Root_CA_-_C3.pem 73s Adding debian:emSign_ECC_Root_CA_-_G3.pem 73s Adding debian:emSign_Root_CA_-_C1.pem 73s Adding debian:emSign_Root_CA_-_G1.pem 73s Adding debian:vTrus_ECC_Root_CA.pem 73s Adding debian:vTrus_Root_CA.pem 74s done. 74s Setting up bbmap (39.20+dfsg-2) ... 74s Setting up default-jre-headless (2:1.21-76) ... 75s autopkgtest [20:29:32]: test run-unit-test: [----------------------- 75s 75s # bbmap 75s bbmap.sh --version 75s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 75s java -ea -Xmx2786m -Xms2786m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 --version 75s BBTools version 39.20 75s For help, please run the shellscript with no parameters, or look in /docs/. 75s bbmap.sh --help 75s 75s BBMap 75s Written by Brian Bushnell, from Dec. 2010 - present 75s Last modified September 15, 2022 75s 75s Description: Fast and accurate splice-aware read aligner. 75s Please read bbmap/docs/guides/BBMapGuide.txt for more information. 75s 75s To index: bbmap.sh ref= 75s To map: bbmap.sh in= out= 75s To map without writing an index: 75s bbmap.sh ref= in= out= nodisk 75s 75s in=stdin will accept reads from standard in, and out=stdout will write to 75s standard out, but file extensions are still needed to specify the format of the 75s input and output files e.g. in=stdin.fa.gz will read gzipped fasta from 75s standard in; out=stdout.sam.gz will write gzipped sam. 75s 75s Indexing Parameters (required when building the index): 75s nodisk=f Set to true to build index in memory and write nothing 75s to disk except output. 75s ref= Specify the reference sequence. Only do this ONCE, 75s when building the index (unless using 'nodisk'). 75s build=1 If multiple references are indexed in the same directory, 75s each needs a unique numeric ID (unless using 'nodisk'). 75s k=13 Kmer length, range 8-15. Longer is faster but uses 75s more memory. Shorter is more sensitive. 75s If indexing and mapping are done in two steps, K should 75s be specified each time. 75s path=<.> Specify the location to write the index, if you don't 75s want it in the current working directory. 75s usemodulo=f Throw away ~80% of kmers based on remainder modulo a 75s number (reduces RAM by 50% and sensitivity slightly). 75s Should be enabled both when building the index AND 75s when mapping. 75s rebuild=f Force a rebuild of the index (ref= should be set). 75s 75s Input Parameters: 75s build=1 Designate index to use. Corresponds to the number 75s specified when building the index. 75s in= Primary reads input; required parameter. 75s in2= For paired reads in two files. 75s interleaved=auto True forces paired/interleaved input; false forces 75s single-ended mapping. If not specified, interleaved 75s status will be autodetected from read names. 75s fastareadlen=500 Break up FASTA reads longer than this. Max is 500 for 75s BBMap and 6000 for BBMapPacBio. Only works for FASTA 75s input (use 'maxlen' for FASTQ input). The default for 75s bbmap.sh is 500, and for mapPacBio.sh is 6000. 75s unpigz=f Spawn a pigz (parallel gzip) process for faster 75s decompression than using Java. 75s Requires pigz to be installed. 75s touppercase=t (tuc) Convert lowercase letters in reads to upper case 75s (otherwise they will not match the reference). 75s 75s Sampling Parameters: 75s 75s reads=-1 Set to a positive number N to only process the first N 75s reads (or pairs), then quit. -1 means use all reads. 75s samplerate=1 Set to a number from 0 to 1 to randomly select that 75s fraction of reads for mapping. 1 uses all reads. 75s skipreads=0 Set to a number N to skip the first N reads (or pairs), 75s then map the rest. 75s 75s Mapping Parameters: 75s fast=f This flag is a macro which sets other paramters to run 75s faster, at reduced sensitivity. Bad for RNA-seq. 75s slow=f This flag is a macro which sets other paramters to run 75s slower, at greater sensitivity. 'vslow' is even slower. 75s maxindel=16000 Don't look for indels longer than this. Lower is faster. 75s Set to >=100k for RNAseq with long introns like mammals. 75s strictmaxindel=f When enabled, do not allow indels longer than 'maxindel'. 75s By default these are not sought, but may be found anyway. 75s tipsearch=100 Look this far for read-end deletions with anchors 75s shorter than K, using brute force. 75s minid=0.76 Approximate minimum alignment identity to look for. 75s Higher is faster and less sensitive. 75s minhits=1 Minimum number of seed hits required for candidate sites. 75s Higher is faster. 75s local=f Set to true to use local, rather than global, alignments. 75s This will soft-clip ugly ends of poor alignments. 75s perfectmode=f Allow only perfect mappings when set to true (very fast). 75s semiperfectmode=f Allow only perfect and semiperfect (perfect except for 75s N's in the reference) mappings. 75s threads=auto (t) Set to number of threads desired. By default, uses 75s all cores available. 75s ambiguous=best (ambig) Set behavior on ambiguously-mapped reads (with 75s multiple top-scoring mapping locations). 75s best (use the first best site) 75s toss (consider unmapped) 75s random (select one top-scoring site randomly) 75s all (retain all top-scoring sites) 75s samestrandpairs=f (ssp) Specify whether paired reads should map to the 75s same strand or opposite strands. 75s requirecorrectstrand=t (rcs) Forbid pairing of reads without correct strand 75s orientation. Set to false for long-mate-pair libraries. 75s killbadpairs=f (kbp) If a read pair is mapped with an inappropriate 75s insert size or orientation, the read with the lower 75s mapping quality is marked unmapped. 75s pairedonly=f (po) Treat unpaired reads as unmapped. Thus they will 75s be sent to 'outu' but not 'outm'. 75s rcomp=f Reverse complement both reads prior to mapping (for LMP 75s outward-facing libraries). 75s rcompmate=f Reverse complement read2 prior to mapping. 75s pairlen=32000 Set max allowed distance between paired reads. 75s (insert size)=(pairlen)+(read1 length)+(read2 length) 75s rescuedist=1200 Don't try to rescue paired reads if avg. insert size 75s greater than this. Lower is faster. 75s rescuemismatches=32 Maximum mismatches allowed in a rescued read. Lower 75s is faster. 75s averagepairdist=100 (apd) Initial average distance between paired reads. 75s Varies dynamically; does not need to be specified. 75s deterministic=f Run in deterministic mode. In this case it is good 75s to set averagepairdist. BBMap is deterministic 75s without this flag if using single-ended reads, 75s or run singlethreaded. 75s bandwidthratio=0 (bwr) If above zero, restrict alignment band to this 75s fraction of read length. Faster but less accurate. 75s bandwidth=0 (bw) Set the bandwidth directly. 75s fraction of read length. Faster but less accurate. 75s usejni=f (jni) Do alignments faster, in C code. Requires 75s compiling the C code; details are in /jni/README.txt. 75s maxsites2=800 Don't analyze (or print) more than this many alignments 75s per read. 75s ignorefrequentkmers=t (ifk) Discard low-information kmers that occur often. 75s excludefraction=0.03 (ef) Fraction of kmers to ignore. For example, 0.03 75s will ignore the most common 3% of kmers. 75s greedy=t Use a greedy algorithm to discard the least-useful 75s kmers on a per-read basis. 75s kfilter=0 If positive, potential mapping sites must have at 75s least this many consecutive exact matches. 75s 75s 75s Quality and Trimming Parameters: 75s qin=auto Set to 33 or 64 to specify input quality value ASCII 75s offset. 33 is Sanger, 64 is old Solexa. 75s qout=auto Set to 33 or 64 to specify output quality value ASCII 75s offset (only if output format is fastq). 75s qtrim=f Quality-trim ends before mapping. Options are: 75s 'f' (false), 'l' (left), 'r' (right), and 'lr' (both). 75s untrim=f Undo trimming after mapping. Untrimmed bases will be 75s soft-clipped in cigar strings. 75s trimq=6 Trim regions with average quality below this 75s (phred algorithm). 75s mintrimlength=60 (mintl) Don't trim reads to be shorter than this. 75s fakefastaquality=-1 (ffq) Set to a positive number 1-50 to generate fake 75s quality strings for fasta input reads. 75s ignorebadquality=f (ibq) Keep going, rather than crashing, if a read has 75s out-of-range quality values. 75s usequality=t Use quality scores when determining which read kmers 75s to use as seeds. 75s minaveragequality=0 (maq) Do not map reads with average quality below this. 75s maqb=0 If positive, calculate maq from this many initial bases. 75s 75s Output Parameters: 75s out= Write all reads to this file. 75s outu= Write only unmapped reads to this file. Does not 75s include unmapped paired reads with a mapped mate. 75s outm= Write only mapped reads to this file. Includes 75s unmapped paired reads with a mapped mate. 75s mappedonly=f If true, treats 'out' like 'outm'. 75s bamscript= (bs) Write a shell script to that will turn 75s the sam output into a sorted, indexed bam file. 75s ordered=f Set to true to output reads in same order as input. 75s Slower and uses more memory. 75s overwrite=f (ow) Allow process to overwrite existing files. 75s secondary=f Print secondary alignments. 75s sssr=0.95 (secondarysitescoreratio) Print only secondary alignments 75s with score of at least this fraction of primary. 75s ssao=f (secondarysiteasambiguousonly) Only print secondary 75s alignments for ambiguously-mapped reads. 75s maxsites=5 Maximum number of total alignments to print per read. 75s Only relevant when secondary=t. 75s quickmatch=f Generate cigar strings more quickly. 75s trimreaddescriptions=f (trd) Truncate read and ref names at the first whitespace, 75s assuming that the remainder is a comment or description. 75s ziplevel=2 (zl) Compression level for zip or gzip output. 75s pigz=f Spawn a pigz (parallel gzip) process for faster 75s compression than Java. Requires pigz to be installed. 75s machineout=f Set to true to output statistics in machine-friendly 75s 'key=value' format. 75s printunmappedcount=f Print the total number of unmapped reads and bases. 75s If input is paired, the number will be of pairs 75s for which both reads are unmapped. 75s showprogress=0 If positive, print a '.' every X reads. 75s showprogress2=0 If positive, print the number of seconds since the 75s last progress update (instead of a '.'). 75s renamebyinsert=f Renames reads based on their mapped insert size. 75s 75s Bloom-Filtering Parameters (bloomfilter.sh is the standalone version). 75s bloom=f Use a Bloom filter to ignore reads not sharing kmers 75s with the reference. This uses more memory, but speeds 75s mapping when most reads don't match the reference. 75s bloomhashes=2 Number of hash functions. 75s bloomminhits=3 Number of consecutive hits to be considered matched. 75s bloomk=31 Bloom filter kmer length. 75s bloomserial=t Use the serialized Bloom filter for greater loading 75s speed, if available. If not, generate and write one. 75s 75s Post-Filtering Parameters: 75s idfilter=0 Independant of minid; sets exact minimum identity 75s allowed for alignments to be printed. Range 0 to 1. 75s subfilter=-1 Ban alignments with more than this many substitutions. 75s insfilter=-1 Ban alignments with more than this many insertions. 75s delfilter=-1 Ban alignments with more than this many deletions. 75s indelfilter=-1 Ban alignments with more than this many indels. 75s editfilter=-1 Ban alignments with more than this many edits. 75s inslenfilter=-1 Ban alignments with an insertion longer than this. 75s dellenfilter=-1 Ban alignments with a deletion longer than this. 75s nfilter=-1 Ban alignments with more than this many ns. This 75s includes nocall, noref, and off scaffold ends. 75s 75s Sam flags and settings: 75s noheader=f Disable generation of header lines. 75s sam=1.4 Set to 1.4 to write Sam version 1.4 cigar strings, 75s with = and X, or 1.3 to use M. 75s saa=t (secondaryalignmentasterisks) Use asterisks instead of 75s bases for sam secondary alignments. 75s cigar=t Set to 'f' to skip generation of cigar strings (faster). 75s keepnames=f Keep original names of paired reads, rather than 75s ensuring both reads have the same name. 75s intronlen=999999999 Set to a lower number like 10 to change 'D' to 'N' in 75s cigar strings for deletions of at least that length. 75s rgid= Set readgroup ID. All other readgroup fields 75s can be set similarly, with the flag rgXX= 75s If you set a readgroup flag to the word 'filename', 75s e.g. rgid=filename, the input file name will be used. 75s mdtag=f Write MD tags. 75s nhtag=f Write NH tags. 75s xmtag=f Write XM tags (may only work correctly with ambig=all). 75s amtag=f Write AM tags. 75s nmtag=f Write NM tags. 75s xstag=f Set to 'xs=fs', 'xs=ss', or 'xs=us' to write XS tags 75s for RNAseq using firststrand, secondstrand, or 75s unstranded libraries. Needed by Cufflinks. 75s JGI mainly uses 'firststrand'. 75s stoptag=f Write a tag indicating read stop location, prefixed by YS:i: 75s lengthtag=f Write a tag indicating (query,ref) alignment lengths, 75s prefixed by YL:Z: 75s idtag=f Write a tag indicating percent identity, prefixed by YI:f: 75s inserttag=f Write a tag indicating insert size, prefixed by X8:Z: 75s scoretag=f Write a tag indicating BBMap's raw score, prefixed by YR:i: 75s timetag=f Write a tag indicating this read's mapping time, prefixed by X0:i: 75s boundstag=f Write a tag indicating whether either read in the pair 75s goes off the end of the reference, prefixed by XB:Z: 75s notags=f Turn off all optional tags. 75s 75s Histogram and statistics output parameters: 75s scafstats= Statistics on how many reads mapped to which scaffold. 75s refstats= Statistics on how many reads mapped to which reference 75s file; only for BBSplit. 75s sortscafs=t Sort scaffolds or references by read count. 75s bhist= Base composition histogram by position. 75s qhist= Quality histogram by position. 75s aqhist= Histogram of average read quality. 75s bqhist= Quality histogram designed for box plots. 75s lhist= Read length histogram. 75s ihist= Write histogram of insert sizes (for paired reads). 75s ehist= Errors-per-read histogram. 75s qahist= Quality accuracy histogram of error rates versus 75s quality score. 75s indelhist= Indel length histogram. 75s mhist= Histogram of match, sub, del, and ins rates by 75s read location. 75s gchist= Read GC content histogram. 75s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 75s gcpairs=t Use average GC of paired reads. 75s idhist= Histogram of read count versus percent identity. 75s idbins=100 Number idhist bins. Set to 'auto' to use read length. 75s statsfile=stderr Mapping statistics are printed here. 75s 75s Coverage output parameters (these may reduce speed and use more RAM): 75s covstats= Per-scaffold coverage info. 75s rpkm= Per-scaffold RPKM/FPKM counts. 75s covhist= Histogram of # occurrences of each depth level. 75s basecov= Coverage per base location. 75s bincov= Print binned coverage per location (one line per X bases). 75s covbinsize=1000 Set the binsize for binned coverage output. 75s nzo=t Only print scaffolds with nonzero coverage. 75s twocolumn=f Change to true to print only ID and Avg_fold instead of 75s all 6 columns to the 'out=' file. 75s 32bit=f Set to true if you need per-base coverage over 64k. 75s strandedcov=f Track coverage for plus and minus strand independently. 75s startcov=f Only track start positions of reads. 75s secondarycov=t Include coverage of secondary alignments. 75s physcov=f Calculate physical coverage for paired reads. 75s This includes the unsequenced bases. 75s delcoverage=t (delcov) Count bases covered by deletions as covered. 75s True is faster than false. 75s covk=0 If positive, calculate kmer coverage statistics. 75s 75s Java Parameters: 75s -Xmx This will set Java's memory usage, 75s overriding autodetection. 75s -Xmx20g will specify 20 gigs of RAM, and -Xmx800m 75s will specify 800 megs. The max is typically 85% of 75s physical memory. The human genome requires around 24g, 75s or 12g with the 'usemodulo' flag. The index uses 75s roughly 6 bytes per reference base. 75s -eoom This flag will cause the process to exit if an 75s out-of-memory exception occurs. Requires Java 8u92+. 75s -da Disable assertions. 75s 75s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter 75s any problems, or post at: http://seqanswers.com/forums/showthread.php?t=41057 75s 75s bbmap.sh ref=example.fasta 75s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 75s java -ea -Xmx2786m -Xms2786m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta 75s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta] 75s Version 39.20 75s 75s No output file. 75s Writing reference. 75s 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] 75s 75s Set genScaffoldInfo=true 75s Writing chunk 1 75s Set genome to 1 75s 75s Loaded Reference: 0.004 seconds. 75s Loading index for chunk 1-1, build 1 75s No index available; generating from reference genome: /tmp/autopkgtest.LvtQAa/autopkgtest_tmp/ref/index/1/chr1_index_k13_c16_b1.block 75s Indexing threads started for block 0-1 75s Indexing threads finished for block 0-1 77s Generated Index: 1.163 seconds. 77s No reads to process; quitting. 77s 77s Total time: 1.321 seconds. 77s test -d ref 77s bbmap.sh in=misc_dna_as_sanger.fastq out=out.sam 77s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 77s java -ea -Xmx2786m -Xms2786m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 in=misc_dna_as_sanger.fastq out=out.sam 77s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, in=misc_dna_as_sanger.fastq, out=out.sam] 77s Version 39.20 77s 77s Retaining first best site only for ambiguous mappings. 77s Set genome to 1 77s 77s Loaded Reference: 0.024 seconds. 77s Loading index for chunk 1-1, build 1 77s Generated Index: 0.409 seconds. 81s Analyzed Index: 3.666 seconds. 81s Started output stream: 0.023 seconds. 81s Cleared Memory: 0.120 seconds. 81s Processing reads in single-ended mode. 81s Started read stream. 81s Started 4 mapping threads. 81s Detecting finished threads: 0, 1, 2, 3 81s 81s ------------------ Results ------------------ 81s 81s Genome: 1 81s Key Length: 13 81s Max Indel: 16000 81s Minimum Score Ratio: 0.56 81s Mapping Mode: normal 81s Reads Used: 4 (153 bases) 81s 81s Mapping: 0.121 seconds. 81s Reads/sec: 33.02 81s kBases/sec: 1.26 81s 81s 81s Read 1 data: pct reads num reads pct bases num bases 81s 81s mapped: 0.0000% 0 0.0000% 0 81s unambiguous: 0.0000% 0 0.0000% 0 81s ambiguous: 0.0000% 0 0.0000% 0 81s low-Q discards: 25.0000% 1 19.6078% 30 81s 81s perfect best site: 0.0000% 0 0.0000% 0 81s semiperfect site: 0.0000% 0 0.0000% 0 81s 81s Match Rate: NA NA NaN% 0 81s Error Rate: NaN% 0 NaN% 0 81s Sub Rate: NaN% 0 NaN% 0 81s Del Rate: NaN% 0 NaN% 0 81s Ins Rate: NaN% 0 NaN% 0 81s N Rate: NaN% 0 NaN% 0 81s 81s Total time: 4.476 seconds. 81s test -r out.sam 81s bbmap.sh ref=example.fasta in=example.fastq out=out2.sam nodisk 81s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 81s java -ea -Xmx2786m -Xms2786m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta in=example.fastq out=out2.sam nodisk 81s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta, in=example.fastq, out=out2.sam, nodisk] 81s Version 39.20 81s 81s Retaining first best site only for ambiguous mappings. 81s 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] 81s 81s Set genScaffoldInfo=true 81s Set genome to 1 81s 81s Loaded Reference: 0.002 seconds. 81s Loading index for chunk 1-1, build 1 81s Indexing threads started for block 0-1 82s Indexing threads finished for block 0-1 82s Generated Index: 0.212 seconds. 85s Analyzed Index: 3.745 seconds. 85s Started output stream: 0.022 seconds. 86s Cleared Memory: 0.117 seconds. 86s Processing reads in single-ended mode. 86s Started read stream. 86s Started 4 mapping threads. 86s Detecting finished threads: 0, 1, 2, 3 86s 86s ------------------ Results ------------------ 86s 86s Genome: 1 86s Key Length: 13 86s Max Indel: 16000 86s Minimum Score Ratio: 0.56 86s Mapping Mode: normal 86s Reads Used: 3 (75 bases) 86s 86s Mapping: 0.115 seconds. 86s Reads/sec: 26.11 86s kBases/sec: 0.65 86s 86s 86s Read 1 data: pct reads num reads pct bases num bases 86s 86s mapped: 100.0000% 3 100.0000% 75 86s unambiguous: 100.0000% 3 100.0000% 75 86s ambiguous: 0.0000% 0 0.0000% 0 86s low-Q discards: 0.0000% 0 0.0000% 0 86s 86s perfect best site: 100.0000% 3 100.0000% 75 86s semiperfect site: 100.0000% 3 100.0000% 75 86s 86s Match Rate: NA NA 100.0000% 75 86s Error Rate: 0.0000% 0 0.0000% 0 86s Sub Rate: 0.0000% 0 0.0000% 0 86s Del Rate: 0.0000% 0 0.0000% 0 86s Ins Rate: 0.0000% 0 0.0000% 0 86s N Rate: 0.0000% 0 0.0000% 0 86s 86s Total time: 4.365 seconds. 86s test -r out2.sam 86s 86s # bbduk 86s bbduk.sh --version 86s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 86s java -ea -Xmx1393m -Xms1393m -cp /usr/share/java/bbmap.jar jgi.BBDuk --version 86s BBTools version 39.20 86s For help, please run the shellscript with no parameters, or look in /docs/. 86s bbduk.sh --help 86s 86s Written by Brian Bushnell 86s Last modified November 18, 2024 86s 86s Description: Compares reads to the kmers in a reference dataset, optionally 86s allowing an edit distance. Splits the reads into two outputs - those that 86s match the reference, and those that don't. Can also trim (remove) the matching 86s parts of the reads rather than binning the reads. 86s Please read bbmap/docs/guides/BBDukGuide.txt for more information. 86s 86s Usage: bbduk.sh in= out= ref= 86s 86s Input may be stdin or a fasta or fastq file, compressed or uncompressed. 86s If you pipe via stdin/stdout, please include the file type; e.g. for gzipped 86s fasta input, set in=stdin.fa.gz 86s 86s Input parameters: 86s in= Main input. in=stdin.fq will pipe from stdin. 86s in2= Input for 2nd read of pairs in a different file. 86s ref= Comma-delimited list of reference files. 86s In addition to filenames, you may also use the keywords: 86s adapters, artifacts, phix, lambda, pjet, mtst, kapa 86s literal= Comma-delimited list of literal reference sequences. 86s Polymers are also allowed with the 'poly' prefix; 86s for example, 'literal=ATGGT,polyGC' will add both ATGGT 86s and GCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGC - 32+ of them, 86s enough replicates to ensure that all kmers are present. 86s touppercase=f (tuc) Change all bases upper-case. 86s interleaved=auto (int) t/f overrides interleaved autodetection. 86s Must be set mainually when streaming fastq input. 86s qin=auto Input quality offset: 33 (Sanger), 64, or auto. 86s reads=-1 If positive, quit after processing X reads or pairs. 86s copyundefined=f (cu) Process non-AGCT IUPAC reference bases by making all 86s possible unambiguous copies. Intended for short motifs 86s or adapter barcodes, as time/memory use is exponential. 86s samplerate=1 Set lower to only process a fraction of input reads. 86s samref= Optional reference fasta for processing sam files. 86s 86s Output parameters: 86s out= (outnonmatch) Write reads here that do not contain 86s kmers matching the database. 'out=stdout.fq' will pipe 86s to standard out. 86s out2= (outnonmatch2) Use this to write 2nd read of pairs to a 86s different file. 86s outm= (outmatch) Write reads here that fail filters. In default 86s kfilter mode, this means any read with a matching kmer. 86s In any mode, it also includes reads that fail filters such 86s as minlength, mingc, maxgc, entropy, etc. In other words, 86s it includes all reads that do not go to 'out'. 86s outm2= (outmatch2) Use this to write 2nd read of pairs to a 86s different file. 86s outs= (outsingle) Use this to write singleton reads whose mate 86s was trimmed shorter than minlen. 86s stats= Write statistics about which contamininants were detected. 86s refstats= Write statistics on a per-reference-file basis. 86s rpkm= Write RPKM for each reference sequence (for RNA-seq). 86s dump= Dump kmer tables to a file, in fasta format. 86s duk= Write statistics in duk's format. *DEPRECATED* 86s nzo=t Only write statistics about ref sequences with nonzero hits. 86s overwrite=t (ow) Grant permission to overwrite files. 86s showspeed=t (ss) 'f' suppresses display of processing speed. 86s ziplevel=2 (zl) Compression level; 1 (min) through 9 (max). 86s fastawrap=70 Length of lines in fasta output. 86s qout=auto Output quality offset: 33 (Sanger), 64, or auto. 86s statscolumns=3 (cols) Number of columns for stats output, 3 or 5. 86s 5 includes base counts. 86s rename=f Rename reads to indicate which sequences they matched. 86s refnames=f Use names of reference files rather than scaffold IDs. 86s trd=f Truncate read and ref names at the first whitespace. 86s ordered=f Set to true to output reads in same order as input. 86s maxbasesout=-1 If positive, quit after writing approximately this many 86s bases to out (outu/outnonmatch). 86s maxbasesoutm=-1 If positive, quit after writing approximately this many 86s bases to outm (outmatch). 86s json=f Print to screen in json format. 86s 86s Histogram output parameters: 86s bhist= Base composition histogram by position. 86s qhist= Quality histogram by position. 86s qchist= Count of bases with each quality value. 86s aqhist= Histogram of average read quality. 86s bqhist= Quality histogram designed for box plots. 86s lhist= Read length histogram. 86s phist= Polymer length histogram. 86s gchist= Read GC content histogram. 86s enthist= Read entropy histogram. 86s ihist= Insert size histogram, for paired reads in mapped sam. 86s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 86s maxhistlen=6000 Set an upper bound for histogram lengths; higher uses 86s more memory. The default is 6000 for some histograms 86s and 80000 for others. 86s 86s Histograms for mapped sam/bam files only: 86s histbefore=t Calculate histograms from reads before processing. 86s ehist= Errors-per-read histogram. 86s qahist= Quality accuracy histogram of error rates versus quality 86s score. 86s indelhist= Indel length histogram. 86s mhist= Histogram of match, sub, del, and ins rates by position. 86s idhist= Histogram of read count versus percent identity. 86s idbins=100 Number idhist bins. Set to 'auto' to use read length. 86s varfile= Ignore substitution errors listed in this file when 86s calculating error rates. Can be generated with 86s CallVariants. 86s vcf= Ignore substitution errors listed in this VCF file 86s when calculating error rates. 86s ignorevcfindels=t Also ignore indels listed in the VCF. 86s 86s Processing parameters: 86s k=27 Kmer length used for finding contaminants. Contaminants 86s shorter than k will not be found. k must be at least 1. 86s rcomp=t Look for reverse-complements of kmers in addition to 86s forward kmers. 86s maskmiddle=t (mm) Treat the middle base of a kmer as a wildcard, to 86s increase sensitivity in the presence of errors. This may 86s also be set to a number, e.g. mm=3, to mask that many bp. 86s The default mm=t corresponds to mm=1 for odd-length kmers 86s and mm=2 for even-length kmers (as of v39.04), while 86s mm=f is always equivalent to mm=0. 86s minkmerhits=1 (mkh) Reads need at least this many matching kmers 86s to be considered as matching the reference. 86s minkmerfraction=0.0 (mkf) A reads needs at least this fraction of its total 86s kmers to hit a ref, in order to be considered a match. 86s If this and minkmerhits are set, the greater is used. 86s mincovfraction=0.0 (mcf) A reads needs at least this fraction of its total 86s bases to be covered by ref kmers to be considered a match. 86s If specified, mcf overrides mkh and mkf. 86s hammingdistance=0 (hdist) Maximum Hamming distance for ref kmers (subs only). 86s Memory use is proportional to (3*K)^hdist. 86s qhdist=0 Hamming distance for query kmers; impacts speed, not memory. 86s editdistance=0 (edist) Maximum edit distance from ref kmers (subs 86s and indels). Memory use is proportional to (8*K)^edist. 86s hammingdistance2=0 (hdist2) Sets hdist for short kmers, when using mink. 86s qhdist2=0 Sets qhdist for short kmers, when using mink. 86s editdistance2=0 (edist2) Sets edist for short kmers, when using mink. 86s forbidn=f (fn) Forbids matching of read kmers containing N. 86s By default, these will match a reference 'A' if 86s hdist>0 or edist>0, to increase sensitivity. 86s removeifeitherbad=t (rieb) Paired reads get sent to 'outmatch' if either is 86s match (or either is trimmed shorter than minlen). 86s Set to false to require both. 86s trimfailures=f Instead of discarding failed reads, trim them to 1bp. 86s This makes the statistics a bit odd. 86s findbestmatch=f (fbm) If multiple matches, associate read with sequence 86s sharing most kmers. Reduces speed. 86s skipr1=f Don't do kmer-based operations on read 1. 86s skipr2=f Don't do kmer-based operations on read 2. 86s ecco=f For overlapping paired reads only. Performs error- 86s correction with BBMerge prior to kmer operations. 86s recalibrate=f (recal) Recalibrate quality scores. Requires calibration 86s matrices generated by CalcTrueQuality. 86s sam= If recalibration is desired, and matrices have not already 86s been generated, BBDuk will create them from the sam file. 86s amino=f Run in amino acid mode. Some features have not been 86s tested, but kmer-matching works fine. Maximum k is 12. 86s 86s Speed and Memory parameters: 86s threads=auto (t) Set number of threads to use; default is number of 86s logical processors. 86s prealloc=f Preallocate memory in table. Allows faster table loading 86s and more efficient memory usage, for a large reference. 86s monitor=f Kill this process if it crashes. monitor=600,0.01 would 86s kill after 600 seconds under 1% usage. 86s minrskip=1 (mns) Force minimal skip interval when indexing reference 86s kmers. 1 means use all, 2 means use every other kmer, etc. 86s maxrskip=1 (mxs) Restrict maximal skip interval when indexing 86s reference kmers. Normally all are used for scaffolds<100kb, 86s but with longer scaffolds, up to maxrskip-1 are skipped. 86s rskip= Set both minrskip and maxrskip to the same value. 86s If not set, rskip will vary based on sequence length. 86s qskip=1 Skip query kmers to increase speed. 1 means use all. 86s speed=0 Ignore this fraction of kmer space (0-15 out of 16) in both 86s reads and reference. Increases speed and reduces memory. 86s Note: Do not use more than one of 'speed', 'qskip', and 'rskip'. 86s 86s Trimming/Filtering/Masking parameters: 86s Note - if ktrim, kmask, and ksplit are unset, the default behavior is kfilter. 86s All kmer processing modes are mutually exclusive. 86s Reads only get sent to 'outm' purely based on kmer matches in kfilter mode. 86s 86s ktrim=f Trim reads to remove bases matching reference kmers, plus 86s all bases to the left or right. 86s Values: 86s f (don't trim), 86s r (trim to the right), 86s l (trim to the left) 86s ktrimtips=0 Set this to a positive number to perform ktrim on both 86s ends, examining only the outermost X bases. 86s kmask= Replace bases matching ref kmers with another symbol. 86s Allows any non-whitespace character, and processes short 86s kmers on both ends if mink is set. 'kmask=lc' will 86s convert masked bases to lowercase. 86s maskfullycovered=f (mfc) Only mask bases that are fully covered by kmers. 86s ksplit=f For single-ended reads only. Reads will be split into 86s pairs around the kmer. If the kmer is at the end of the 86s read, it will be trimmed instead. Singletons will go to 86s out, and pairs will go to outm. Do not use ksplit with 86s other operations such as quality-trimming or filtering. 86s mink=0 Look for shorter kmers at read tips down to this length, 86s when k-trimming or masking. 0 means disabled. Enabling 86s this will disable maskmiddle. 86s qtrim=f Trim read ends to remove bases with quality below trimq. 86s Performed AFTER looking for kmers. Values: 86s bbduk.sh in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq \ 86s qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 86s rl (trim both ends), 86s f (neither end), 86s r (right end only), 86s l (left end only), 86s w (sliding window). 86s trimq=6 Regions with average quality BELOW this will be trimmed, 86s if qtrim is set to something other than f. Can be a 86s floating-point number like 7.3. 86s quantize Bin quality scores to reduce file size. quantize=2 will 86s eliminate all odd quality scores, while quantize=0,10,37 86s will only allow qualty scores of 0, 10, or 37. 86s trimclip=f Trim soft-clipped bases from sam files. 86s minlength=10 (ml) Reads shorter than this after trimming will be 86s discarded. Pairs will be discarded if both are shorter. 86s mlf=0 (minlengthfraction) Reads shorter than this fraction of 86s original length after trimming will be discarded. 86s maxlength= Reads longer than this after trimming will be discarded. 86s minavgquality=0 (maq) Reads with average quality (after trimming) below 86s this will be discarded. 86s maqb=0 If positive, calculate maq from this many initial bases. 86s minbasequality=0 (mbq) Reads with any base below this quality (after 86s trimming) will be discarded. 86s maxns=-1 If non-negative, reads with more Ns than this 86s (after trimming) will be discarded. 86s mcb=0 (minconsecutivebases) Discard reads without at least 86s this many consecutive called bases. 86s ottm=f (outputtrimmedtomatch) Output reads trimmed to shorter 86s than minlength to outm rather than discarding. 86s tp=0 (trimpad) Trim this much extra around matching kmers. 86s tbo=f (trimbyoverlap) Trim adapters based on where paired 86s reads overlap. 86s strictoverlap=t Adjust sensitivity for trimbyoverlap mode. 86s minoverlap=14 Require this many bases of overlap for detection. 86s mininsert=40 Require insert size of at least this for overlap. 86s Should be reduced to 16 for small RNA sequencing. 86s tpe=f (trimpairsevenly) When kmer right-trimming, trim both 86s reads to the minimum length of either. 86s forcetrimleft=0 (ftl) If positive, trim bases to the left of this position 86s (exclusive, 0-based). 86s forcetrimright=0 (ftr) If positive, trim bases to the right of this position 86s (exclusive, 0-based). 86s forcetrimright2=0 (ftr2) If positive, trim this many bases on the right end. 86s forcetrimmod=0 (ftm) If positive, right-trim length to be equal to zero, 86s modulo this number. 86s restrictleft=0 If positive, only look for kmer matches in the 86s leftmost X bases. 86s restrictright=0 If positive, only look for kmer matches in the 86s rightmost X bases. 86s NOTE: restrictleft and restrictright are mutually exclusive. If trimming 86s both ends is desired, use ktrimtips. 86s mingc=0 Discard reads with GC content below this. 86s maxgc=1 Discard reads with GC content above this. 86s gcpairs=t Use average GC of paired reads. 86s Also affects gchist. 86s tossjunk=f Discard reads with invalid characters as bases. 86s swift=f Trim Swift sequences: Trailing C/T/N R1, leading G/A/N R2. 86s 86s Header-parsing parameters - these require Illumina headers: 86s chastityfilter=f (cf) Discard reads with id containing ' 1:Y:' or ' 2:Y:'. 86s barcodefilter=f Remove reads with unexpected barcodes if barcodes is set, 86s or barcodes containing 'N' otherwise. A barcode must be 86s the last part of the read header. Values: 86s t: Remove reads with bad barcodes. 86s f: Ignore barcodes. 86s crash: Crash upon encountering bad barcodes. 86s barcodes= Comma-delimited list of barcodes or files of barcodes. 86s xmin=-1 If positive, discard reads with a lesser X coordinate. 86s ymin=-1 If positive, discard reads with a lesser Y coordinate. 86s xmax=-1 If positive, discard reads with a greater X coordinate. 86s ymax=-1 If positive, discard reads with a greater Y coordinate. 86s 86s Polymer trimming: 86s trimpolya=0 If greater than 0, trim poly-A or poly-T tails of 86s at least this length on either end of reads. 86s trimpolygleft=0 If greater than 0, trim poly-G prefixes of at least this 86s length on the left end of reads. Does not trim poly-C. 86s trimpolygright=0 If greater than 0, trim poly-G tails of at least this 86s length on the right end of reads. Does not trim poly-C. 86s trimpolyg=0 This sets both left and right at once. 86s filterpolyg=0 If greater than 0, remove reads with a poly-G prefix of 86s at least this length (on the left). 86s Note: there are also equivalent poly-C flags. 86s 86s Polymer tracking: 86s pratio=base,base 'pratio=G,C' will print the ratio of G to C polymers. 86s plen=20 Length of homopolymers to count. 86s 86s Entropy/Complexity parameters: 86s entropy=-1 Set between 0 and 1 to filter reads with entropy below 86s that value. Higher is more stringent. 86s entropywindow=50 Calculate entropy using a sliding window of this length. 86s entropyk=5 Calculate entropy using kmers of this length. 86s minbasefrequency=0 Discard reads with a minimum base frequency below this. 86s entropytrim=f Values: 86s f: (false) Do not entropy-trim. 86s r: (right) Trim low entropy on the right end only. 86s l: (left) Trim low entropy on the left end only. 86s rl: (both) Trim low entropy on both ends. 86s entropymask=f Values: 86s f: (filter) Discard low-entropy sequences. 86s t: (true) Mask low-entropy parts of sequences with N. 86s lc: Change low-entropy parts of sequences to lowercase. 86s entropymark=f Mark each base with its entropy value. This is on a scale 86s of 0-41 and is reported as quality scores, so the output 86s should be fastq or fasta+qual. 86s NOTE: If set, entropytrim overrides entropymask. 86s 86s Cardinality estimation: 86s cardinality=f (loglog) Count unique kmers using the LogLog algorithm. 86s cardinalityout=f (loglogout) Count unique kmers in output reads. 86s loglogk=31 Use this kmer length for counting. 86s loglogbuckets=2048 Use this many buckets for counting. 86s khist= Kmer frequency histogram; plots number of kmers versus 86s kmer depth. This is approximate. 86s khistout= Kmer frequency histogram for output reads. 86s 86s Side Channel: 86s sideout= Output for aligned reads. 86s sideref=phix Reference for side-channel alignment; must be a single 86s sequence and virtually repeat-free at selected k. 86s sidek1=17 Kmer length for seeding alignment to reference. 86s sidek2=13 Kmer length for seeding alignment of unaligned reads 86s with an aligned mate. 86s sideminid1=0.66 Minimum identity to accept individual alignments. 86s sideminid2=0.58 Minimum identity for aligning reads with aligned mates. 86s sidemm1=1 Middle mask length for sidek1. 86s sidemm2=1 Middle mask length for sidek2. 86s Note: The side channel is a special additional output that allows alignment 86s to a secondary reference while also doing trimming. Alignment does not affect 86s whether reads go to the normal outputs (out, outm). The main purpose is to 86s simplify pipelines that need trimmed, aligned phiX reads for recalibration. 86s 86s 86s Java Parameters: 86s 86s -Xmx This will set Java's memory usage, overriding autodetection. 86s -Xmx20g will 86s specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 86s The max is typically 85% of physical memory. 86s -eoom This flag will cause the process to exit if an 86s out-of-memory exception occurs. Requires Java 8u92+. 86s -da Disable assertions. 86s 86s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 86s 86s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 86s java -ea -Xmx1393m -Xms1393m -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 86s 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] 86s Version 39.20 86s 86s Changed from ASCII-33 to ASCII-64 on input quality X (Q55) for base A at lines 1 and 3, position 24 while prescanning. 86s Changed from ASCII-33 to ASCII-64 on input quality X (Q55) for base A at lines 1 and 3, position 24 while prescanning. 86s Allocating kmer table: 0.016 seconds. 86s Initial: 86s Memory: max=1476m, total=1476m, free=1444m, used=32m 86s 86s Input is being processed as paired 86s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 86s Started output streams: 0.019 seconds. 86s Processing time: 0.004 seconds. 86s 86s Input: 8 reads 306 bases. 86s QTrimmed: 0 reads (0.00%) 0 bases (0.00%) 86s Total Removed: 8 reads (100.00%) 306 bases (100.00%) 86s Result: 0 reads (0.00%) 0 bases (0.00%) 86s 86s Time: 0.025 seconds. 86s Reads Processed: 8 0.32k reads/sec 86s Bases Processed: 306 0.01m bases/sec 86s test -r out.fastq.gz 86s 86s # bbnorm 86s bbnorm.sh --version 86s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 86s java -ea -Xmx2786m -Xms2786m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 --version 86s BBTools version 39.20 86s For help, please run the shellscript with no parameters, or look in /docs/. 86s bbnorm.sh --help 86s 86s Written by Brian Bushnell 86s Last modified October 19, 2017 86s 86s Description: Normalizes read depth based on kmer counts. 86s Can also error-correct, bin reads by kmer depth, and generate a kmer depth histogram. 86s However, Tadpole has superior error-correction to BBNorm. 86s Please read bbmap/docs/guides/BBNormGuide.txt for more information. 86s 86s Usage: bbnorm.sh in= out= outt= hist= 86s 86s Input parameters: 86s in=null Primary input. Use in2 for paired reads in a second file 86s in2=null Second input file for paired reads in two files 86s extra=null Additional files to use for input (generating hash table) but not for output 86s fastareadlen=2^31 Break up FASTA reads longer than this. Can be useful when processing scaffolded genomes 86s tablereads=-1 Use at most this many reads when building the hashtable (-1 means all) 86s kmersample=1 Process every nth kmer, and skip the rest 86s readsample=1 Process every nth read, and skip the rest 86s 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. 86s qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto. 86s 86s Output parameters: 86s out= File for normalized or corrected reads. Use out2 for paired reads in a second file 86s outt= (outtoss) File for reads that were excluded from primary output 86s reads=-1 Only process this number of reads, then quit (-1 means all) 86s sampleoutput=t Use sampling on output as well as input (not used if sample rates are 1) 86s keepall=f Set to true to keep all reads (e.g. if you just want error correction). 86s 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. 86s Default is false, to prevent confusion about how there can be 0-count kmers. 86s The reason is that based on the 'minq' and 'minprob' settings, some kmers may be excluded from the bloom filter. 86s tmpdir= This will specify a directory for temp files (only needed for multipass runs). If null, they will be written to the output directory. 86s usetempdir=t Allows enabling/disabling of temporary directory; if disabled, temp files will be written to the output directory. 86s qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input). 86s rename=f Rename reads based on their kmer depth. 86s 86s Hashing parameters: 86s k=31 Kmer length (values under 32 are most efficient, but arbitrarily high values are supported) 86s 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. 86s Large values decrease accuracy for a fixed amount of memory, so use the lowest number you can that will still capture highest-depth kmers. 86s hashes=3 Number of times each kmer is hashed and stored. Higher is slower. 86s Higher is MORE accurate if there is enough memory, and LESS accurate if there is not enough memory. 86s 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. 86s prehashes=2 Number of hashes for prefilter. 86s prefilterbits=2 (pbits) Bits per cell in prefilter. 86s prefiltersize=0.35 Fraction of memory to allocate to prefilter. 86s buildpasses=1 More passes can sometimes increase accuracy by iteratively removing low-depth kmers 86s minq=6 Ignore kmers containing bases with quality below this 86s minprob=0.5 Ignore kmers with overall probability of correctness below this 86s 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. 86s 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. 86s 86s Normalization parameters: 86s fixspikes=f (fs) Do a slower, high-precision bloom filter lookup of kmers that appear to have an abnormally high depth due to collisions. 86s target=100 (tgt) Target normalization depth. NOTE: All depth parameters control kmer depth, not read depth. 86s For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1)) 86s maxdepth=-1 (max) Reads will not be downsampled when below this depth, even if they are above the target depth. 86s mindepth=5 (min) Kmers with depth below this number will not be included when calculating the depth of a read. 86s minkmers=15 (mgkpr) Reads must have at least this many kmers over min depth to be retained. Aka 'mingoodkmersperread'. 86s 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. 86s uselowerdepth=t (uld) For pairs, use the depth of the lower read as the depth proxy. 86s deterministic=t (dr) Generate random numbers deterministically to ensure identical output between multiple runs. May decrease speed with a huge number of threads. 86s passes=2 (p) 1 pass is the basic mode. 2 passes (default) allows greater accuracy, error detection, better contol of output depth. 86s 86s Error detection parameters: 86s hdp=90.0 (highdepthpercentile) Position in sorted kmer depth array used as proxy of a read's high kmer depth. 86s ldp=25.0 (lowdepthpercentile) Position in sorted kmer depth array used as proxy of a read's low kmer depth. 86s tossbadreads=f (tbr) Throw away reads detected as containing errors. 86s requirebothbad=f (rbb) Only toss bad pairs if both reads are bad. 86s 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. 86s highthresh=12 (ht) Threshold for high kmer. A high kmer at this or above are considered non-error. 86s lowthresh=3 (lt) Threshold for low kmer. Kmers at this and below are always considered errors. 86s 86s Error correction parameters: 86s ecc=f Set to true to correct errors. NOTE: Tadpole is now preferred for ecc as it does a better job. 86s ecclimit=3 Correct up to this many errors per read. If more are detected, the read will remain unchanged. 86s errorcorrectratio=140 (ecr) Adjacent kmers with a depth ratio of at least this much between will be classified as an error. 86s echighthresh=22 (echt) Threshold for high kmer. A kmer at this or above may be considered non-error. 86s eclowthresh=2 (eclt) Threshold for low kmer. Kmers at this and below are considered errors. 86s eccmaxqual=127 Do not correct bases with quality above this value. 86s aec=f (aggressiveErrorCorrection) Sets more aggressive values of ecr=100, ecclimit=7, echt=16, eclt=3. 86s cec=f (conservativeErrorCorrection) Sets more conservative values of ecr=180, ecclimit=2, echt=30, eclt=1, sl=4, pl=4. 86s meo=f (markErrorsOnly) Marks errors by reducing quality value of suspected errors; does not correct anything. 86s mue=t (markUncorrectableErrors) Marks errors only on uncorrectable reads; requires 'ecc=t'. 86s overlap=f (ecco) Error correct by read overlap. 86s 86s Depth binning parameters: 86s lowbindepth=10 (lbd) Cutoff for low depth bin. 86s highbindepth=80 (hbd) Cutoff for high depth bin. 86s outlow= Pairs in which both reads have a median below lbd go into this file. 86s outhigh= Pairs in which both reads have a median above hbd go into this file. 86s outmid= All other pairs go into this file. 86s 86s Histogram parameters: 86s hist= Specify a file to write the input kmer depth histogram. 86s histout= Specify a file to write the output kmer depth histogram. 86s histcol=3 (histogramcolumns) Number of histogram columns, 2 or 3. 86s pzc=f (printzerocoverage) Print lines in the histogram with zero coverage. 86s histlen=1048576 Max kmer depth displayed in histogram. Also affects statistics displayed, but does not affect normalization. 86s 86s Peak calling parameters: 86s peaks= Write the peaks to this file. Default is stdout. 86s minHeight=2 (h) Ignore peaks shorter than this. 86s minVolume=5 (v) Ignore peaks with less area than this. 86s minWidth=3 (w) Ignore peaks narrower than this. 86s minPeak=2 (minp) Ignore peaks with an X-value below this. 86s maxPeak=BIG (maxp) Ignore peaks with an X-value above this. 86s maxPeakCount=8 (maxpc) Print up to this many peaks (prioritizing height). 86s 86s Java Parameters: 86s -Xmx This will set Java's memory usage, overriding autodetection. 86s -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 86s The max is typically 85% of physical memory. 86s -eoom This flag will cause the process to exit if an 86s out-of-memory exception occurs. Requires Java 8u92+. 86s -da Disable assertions. 86s 86s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 86s 86s bbnorm.sh in=sanger_full_range_original_sanger.fastq qin=33 \ 86s out=out3.fastq outt=outt.fastq hist=hist.plt 86s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 86s java -ea -Xmx2786m -Xms2786m -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 87s Executing jgi.KmerNormalize [bits=32, in=sanger_full_range_original_sanger.fastq, qin=33, out=out3.fastq, outt=outt.fastq, hist=hist.plt] 87s 87s 87s *********** Pass 1 ********** 87s 87s 87s Settings: 87s threads: 4 87s k: 31 87s deterministic: true 87s toss error reads: false 87s passes: 1 87s bits per cell: 16 87s cells: 1042.20M 87s hashes: 3 87s base min quality: 5 87s kmer min prob: 0.5 87s 87s target depth: 400 87s min depth: 3 87s max depth: 500 87s min good kmers: 15 87s depth percentile: 64.8 87s ignore dupe kmers: true 87s fix spikes: false 87s histogram length: 65536 87s print zero cov: false 87s 89s Made hash table: hashes = 3 mem = 1.94 GB cells = 1042.12M used = 0.000% 89s 89s Estimated unique kmers: 4 89s 89s Table creation time: 2.588 seconds. 89s Started output threads. 89s Started output threads. 89s Table read time: 0.009 seconds. 21.35 kb/sec 89s Total reads in: 2 0.000% Kept 89s Total bases in: 188 0.000% Kept 89s Error reads in: 2 100.000% 89s Error type 1: 2 100.000% 89s Error type 2: 0 0.000% 89s Error type 3: 0 0.000% 89s 89s Wrote histogram to hist.plt 89s Total kmers counted: 128 89s Total unique kmer count: 128 89s Includes forward kmers only. 89s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 89s The most accurate value is the greater of the two. 89s 89s Percent unique: 100.00% 89s Depth average: 1.00 (unique kmers) 89s Depth median: 1 (unique kmers) 89s Depth standard deviation: 0.00 (unique kmers) 89s Corrected depth average: 0.00 89s 89s Depth average: 1.00 (all kmers) 89s Depth median: 1 (all kmers) 89s Depth standard deviation: 0.00 (all kmers) 89s 89s Approx. read depth median: 1.47 89s 89s *********** Pass 2 ********** 89s 89s 89s Settings: 89s threads: 4 89s k: 31 89s deterministic: true 89s toss error reads: false 89s passes: 1 89s bits per cell: 16 89s cells: 1042.20M 89s hashes: 3 89s base min quality: 5 89s kmer min prob: 0.5 89s 89s target depth: 100 89s min depth: 5 89s max depth: 100 89s min good kmers: 15 89s depth percentile: 54.0 89s ignore dupe kmers: true 89s fix spikes: false 89s histogram length: 65536 89s 92s Made hash table: hashes = 3 mem = 1.94 GB cells = 1042.12M used = 0.000% 92s 92s Estimated unique kmers: 0 92s 92s Table creation time: 2.491 seconds. 92s Started output threads. 92s Started output threads. 92s Table read time: 0.002 seconds. 0.00 kb/sec 92s Total reads in: 0 NaN% Kept 92s Total bases in: 0 NaN% Kept 92s Error reads in: 0 NaN% 92s Error type 1: 0 NaN% 92s Error type 2: 0 NaN% 92s Error type 3: 0 NaN% 92s Total kmers counted: 0 92s Total unique kmer count: 0 92s Includes forward kmers only. 92s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 92s The most accurate value is the greater of the two. 92s 92s Percent unique: NaN% 92s Depth average: NaN (unique kmers) 92s Depth median: 0 (unique kmers) 92s Depth standard deviation: NaN (unique kmers) 92s Corrected depth average: NaN 92s 92s Depth average: NaN (all kmers) 92s Depth median: 0 (all kmers) 92s Depth standard deviation: 0.00 (all kmers) 92s 92s Approx. read depth median: NaN 92s 92s Removing temp files. 92s 92s Total time: 5.203 seconds. 0.04 kb/sec 92s test -r out3.fastq 92s test -r outt.fastq 92s test -r hist.plt 92s bbnorm.sh in=illumina_full_range_original_illumina.fastq qin=64 \ 92s out=out4.fastq outt=outt2.fastq hist=hist2.plt 92s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 92s java -ea -Xmx2786m -Xms2786m -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 92s Executing jgi.KmerNormalize [bits=32, in=illumina_full_range_original_illumina.fastq, qin=64, out=out4.fastq, outt=outt2.fastq, hist=hist2.plt] 92s 92s 92s *********** Pass 1 ********** 92s 92s 92s Settings: 92s threads: 4 92s k: 31 92s deterministic: true 92s toss error reads: false 92s passes: 1 92s bits per cell: 16 92s cells: 1042.20M 92s hashes: 3 92s base min quality: 5 92s kmer min prob: 0.5 92s 92s target depth: 400 92s min depth: 3 92s max depth: 500 92s min good kmers: 15 92s depth percentile: 64.8 92s ignore dupe kmers: true 92s fix spikes: false 92s histogram length: 65536 92s print zero cov: false 92s 95s Made hash table: hashes = 3 mem = 1.94 GB cells = 1042.12M used = 0.000% 95s 95s Estimated unique kmers: 4 95s 95s Table creation time: 2.581 seconds. 95s Started output threads. 95s Started output threads. 95s Table read time: 0.007 seconds. 19.07 kb/sec 95s Total reads in: 2 0.000% Kept 95s Total bases in: 126 0.000% Kept 95s Error reads in: 2 100.000% 95s Error type 1: 2 100.000% 95s Error type 2: 0 0.000% 95s Error type 3: 0 0.000% 95s 95s Wrote histogram to hist2.plt 95s Total kmers counted: 66 95s Total unique kmer count: 66 95s Includes forward kmers only. 95s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 95s The most accurate value is the greater of the two. 95s 95s Percent unique: 100.00% 95s Depth average: 1.00 (unique kmers) 95s Depth median: 1 (unique kmers) 95s Depth standard deviation: 0.00 (unique kmers) 95s Corrected depth average: 0.00 95s 95s Depth average: 1.00 (all kmers) 95s Depth median: 1 (all kmers) 95s Depth standard deviation: 0.00 (all kmers) 95s 95s Approx. read depth median: 1.91 95s 95s *********** Pass 2 ********** 95s 95s 95s Settings: 95s threads: 4 95s k: 31 95s deterministic: true 95s toss error reads: false 95s passes: 1 95s bits per cell: 16 95s cells: 1042.20M 95s hashes: 3 95s base min quality: 5 95s kmer min prob: 0.5 95s 95s target depth: 100 95s min depth: 5 95s max depth: 100 95s min good kmers: 15 95s depth percentile: 54.0 95s ignore dupe kmers: true 95s fix spikes: false 95s histogram length: 65536 95s 97s Made hash table: hashes = 3 mem = 1.94 GB cells = 1042.12M used = 0.000% 97s 97s Estimated unique kmers: 0 97s 97s Table creation time: 2.536 seconds. 97s Started output threads. 97s Started output threads. 97s Table read time: 0.009 seconds. 0.00 kb/sec 97s Total reads in: 0 NaN% Kept 97s Total bases in: 0 NaN% Kept 97s Error reads in: 0 NaN% 97s Error type 1: 0 NaN% 97s Error type 2: 0 NaN% 97s Error type 3: 0 NaN% 97s Total kmers counted: 0 97s Total unique kmer count: 0 97s Includes forward kmers only. 97s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 97s The most accurate value is the greater of the two. 97s 97s Percent unique: NaN% 97s Depth average: NaN (unique kmers) 97s Depth median: 0 (unique kmers) 97s Depth standard deviation: NaN (unique kmers) 97s Corrected depth average: NaN 97s 97s Depth average: NaN (all kmers) 97s Depth median: 0 (all kmers) 97s Depth standard deviation: 0.00 (all kmers) 97s 97s Approx. read depth median: NaN 97s 97s Removing temp files. 97s 97s Total time: 5.244 seconds. 0.02 kb/sec 97s test -r out4.fastq 97s test -r outt2.fastq 97s test -r hist2.plt 98s autopkgtest [20:29:55]: test run-unit-test: -----------------------] 98s autopkgtest [20:29:55]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 98s run-unit-test PASS 99s autopkgtest [20:29:56]: @@@@@@@@@@@@@@@@@@@@ summary 99s run-unit-test PASS