0s autopkgtest [11:15:58]: starting date and time: 2026-02-10 11:15:58+0000 0s autopkgtest [11:15:58]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [11:15:58]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.7lsccwhp/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:openjdk-26 --apt-upgrade bbmap --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=openjdk-26/26~34ea-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu4-ram16-disk100-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-s390x-18.secgroup --name adt-resolute-s390x-bbmap-20260210-111558-juju-7f2275-prod-proposed-migration-environment-2-dfc1cc0b-862b-4e4f-aba1-62712042834f --image adt/ubuntu-resolute-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-s390x -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-s390x-bbmap-20260210-111558-juju-7f2275-prod-proposed-migration-environment-2-dfc1cc0b-862b-4e4f-aba1-62712042834f from image adt/ubuntu-resolute-s390x-server-20260210.img (UUID 6b7378ab-57e8-4ce9-99f5-fc485e5dec1f)... 63s autopkgtest [11:17:01]: testbed dpkg architecture: s390x 63s autopkgtest [11:17:01]: testbed apt version: 3.1.15 64s autopkgtest [11:17:02]: @@@@@@@@@@@@@@@@@@@@ test bed setup 64s autopkgtest [11:17:02]: testbed release detected to be: None 65s autopkgtest [11:17:03]: updating testbed package index (apt update) 65s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 65s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 65s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 65s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 65s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [31.9 kB] 65s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [179 kB] 65s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1735 kB] 66s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x Packages [252 kB] 66s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x Packages [1566 kB] 66s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse s390x Packages [8828 B] 66s Fetched 3898 kB in 1s (3489 kB/s) 68s Reading package lists... 69s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 69s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 69s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 69s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 71s Reading package lists... 71s Reading package lists... 71s Building dependency tree... 71s Reading state information... 71s Calculating upgrade... 71s The following packages will be upgraded: 71s libbrotli1 ubuntu-kernel-accessories ubuntu-standard 71s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 71s Need to get 403 kB of archives. 71s After this operation, 4096 B disk space will be freed. 71s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x ubuntu-standard s390x 1.565 [13.3 kB] 71s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x libbrotli1 s390x 1.2.0-3 [377 kB] 71s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x ubuntu-kernel-accessories s390x 1.565 [13.1 kB] 72s dpkg-preconfigure: unable to re-open stdin: No such file or directory 72s Fetched 403 kB in 0s (23.0 MB/s) 72s (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 ... 88760 files and directories currently installed.) 72s Preparing to unpack .../ubuntu-standard_1.565_s390x.deb ... 72s Unpacking ubuntu-standard (1.565) over (1.564) ... 73s Preparing to unpack .../libbrotli1_1.2.0-3_s390x.deb ... 73s Unpacking libbrotli1:s390x (1.2.0-3) over (1.1.0-2build6) ... 73s Preparing to unpack .../ubuntu-kernel-accessories_1.565_s390x.deb ... 73s Unpacking ubuntu-kernel-accessories (1.565) over (1.564) ... 73s Setting up ubuntu-kernel-accessories (1.565) ... 73s Setting up libbrotli1:s390x (1.2.0-3) ... 73s Setting up ubuntu-standard (1.565) ... 73s Processing triggers for libc-bin (2.42-2ubuntu4) ... 73s autopkgtest [11:17:11]: upgrading testbed (apt dist-upgrade and autopurge) 73s Reading package lists... 74s Building dependency tree... 74s Reading state information... 74s Calculating upgrade... 74s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 74s Reading package lists... 75s Building dependency tree... 75s Reading state information... 75s Solving dependencies... 75s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 78s autopkgtest [11:17:16]: testbed running kernel: Linux 6.19.0-3-generic #3-Ubuntu SMP Fri Jan 23 19:02:49 UTC 2026 79s autopkgtest [11:17:17]: @@@@@@@@@@@@@@@@@@@@ apt-source bbmap 81s Get:1 http://ftpmaster.internal/ubuntu resolute/universe bbmap 39.20+dfsg-3 (dsc) [2286 B] 81s Get:2 http://ftpmaster.internal/ubuntu resolute/universe bbmap 39.20+dfsg-3 (tar) [5748 kB] 81s Get:3 http://ftpmaster.internal/ubuntu resolute/universe bbmap 39.20+dfsg-3 (diff) [27.0 kB] 81s gpgv: Signature made Fri Nov 7 18:57:54 2025 UTC 81s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 81s gpgv: issuer "emollier@debian.org" 81s gpgv: Can't check signature: No public key 81s dpkg-source: warning: cannot verify inline signature for ./bbmap_39.20+dfsg-3.dsc: no acceptable signature found 83s autopkgtest [11:17:21]: testing package bbmap version 39.20+dfsg-3 83s autopkgtest [11:17:21]: build not needed 84s autopkgtest [11:17:22]: test run-unit-test: preparing testbed 84s Reading package lists... 84s Building dependency tree... 84s Reading state information... 84s Solving dependencies... 85s The following NEW packages will be installed: 85s bbmap bbmap-jni ca-certificates-java default-jre-headless java-common 85s libapache-pom-java libcommons-cli-java libcommons-codec-java 85s libcommons-io-java libcommons-parent-java libjpeg-turbo8 libjpeg8 85s libjs-jquery liblcms2-2 liblog4j1.2-java libmpj-java libpcsclite1 85s openjdk-21-jre-headless python-biopython-doc 85s 0 upgraded, 19 newly installed, 0 to remove and 0 not upgraded. 85s Need to get 75.0 MB of archives. 85s After this operation, 242 MB of additional disk space will be used. 85s Get:1 http://ftpmaster.internal/ubuntu resolute/universe s390x libcommons-cli-java all 1.6.0-1 [59.9 kB] 85s Get:2 http://ftpmaster.internal/ubuntu resolute/universe s390x libapache-pom-java all 33-2build1 [5976 B] 85s Get:3 http://ftpmaster.internal/ubuntu resolute/universe s390x libcommons-parent-java all 56-1build1 [11.1 kB] 85s Get:4 http://ftpmaster.internal/ubuntu resolute/universe s390x libcommons-codec-java all 1.18.0-1 [303 kB] 85s Get:5 http://ftpmaster.internal/ubuntu resolute/universe s390x libcommons-io-java all 2.19.0-1 [491 kB] 85s Get:6 http://ftpmaster.internal/ubuntu resolute/universe s390x liblog4j1.2-java all 1.2.17-11build1 [445 kB] 85s Get:7 http://ftpmaster.internal/ubuntu resolute/universe s390x libmpj-java all 0.44+dfsg-4build1 [445 kB] 85s Get:8 http://ftpmaster.internal/ubuntu resolute/main s390x ca-certificates-java all 20240118build1 [11.7 kB] 85s Get:9 http://ftpmaster.internal/ubuntu resolute/main s390x java-common all 0.76build1 [6956 B] 85s Get:10 http://ftpmaster.internal/ubuntu resolute/main s390x liblcms2-2 s390x 2.17-1 [176 kB] 85s Get:11 http://ftpmaster.internal/ubuntu resolute/main s390x libjpeg-turbo8 s390x 2.1.5-4ubuntu3 [156 kB] 85s Get:12 http://ftpmaster.internal/ubuntu resolute/main s390x libjpeg8 s390x 8c-2ubuntu12 [2144 B] 85s Get:13 http://ftpmaster.internal/ubuntu resolute/main s390x libpcsclite1 s390x 2.4.1-1 [24.5 kB] 85s Get:14 http://ftpmaster.internal/ubuntu resolute/main s390x openjdk-21-jre-headless s390x 21.0.10+7-1 [43.8 MB] 87s Get:15 http://ftpmaster.internal/ubuntu resolute/main s390x default-jre-headless s390x 2:1.21-76build1 [3268 B] 87s Get:16 http://ftpmaster.internal/ubuntu resolute/universe s390x bbmap all 39.20+dfsg-3 [10.6 MB] 87s Get:17 http://ftpmaster.internal/ubuntu resolute/universe s390x bbmap-jni s390x 39.20+dfsg-3 [39.0 kB] 87s Get:18 http://ftpmaster.internal/ubuntu resolute/main s390x libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 87s Get:19 http://ftpmaster.internal/ubuntu resolute/universe s390x python-biopython-doc all 1.86+dfsg-1 [18.1 MB] 88s Fetched 75.0 MB in 4s (20.7 MB/s) 89s Selecting previously unselected package libcommons-cli-java. 89s (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 ... 88760 files and directories currently installed.) 89s Preparing to unpack .../00-libcommons-cli-java_1.6.0-1_all.deb ... 89s Unpacking libcommons-cli-java (1.6.0-1) ... 89s Selecting previously unselected package libapache-pom-java. 89s Preparing to unpack .../01-libapache-pom-java_33-2build1_all.deb ... 89s Unpacking libapache-pom-java (33-2build1) ... 89s Selecting previously unselected package libcommons-parent-java. 89s Preparing to unpack .../02-libcommons-parent-java_56-1build1_all.deb ... 89s Unpacking libcommons-parent-java (56-1build1) ... 89s Selecting previously unselected package libcommons-codec-java. 89s Preparing to unpack .../03-libcommons-codec-java_1.18.0-1_all.deb ... 89s Unpacking libcommons-codec-java (1.18.0-1) ... 89s Selecting previously unselected package libcommons-io-java. 89s Preparing to unpack .../04-libcommons-io-java_2.19.0-1_all.deb ... 89s Unpacking libcommons-io-java (2.19.0-1) ... 89s Selecting previously unselected package liblog4j1.2-java. 89s Preparing to unpack .../05-liblog4j1.2-java_1.2.17-11build1_all.deb ... 89s Unpacking liblog4j1.2-java (1.2.17-11build1) ... 89s Selecting previously unselected package libmpj-java. 89s Preparing to unpack .../06-libmpj-java_0.44+dfsg-4build1_all.deb ... 89s Unpacking libmpj-java (0.44+dfsg-4build1) ... 89s Selecting previously unselected package ca-certificates-java. 89s Preparing to unpack .../07-ca-certificates-java_20240118build1_all.deb ... 89s Unpacking ca-certificates-java (20240118build1) ... 89s Selecting previously unselected package java-common. 89s Preparing to unpack .../08-java-common_0.76build1_all.deb ... 89s Unpacking java-common (0.76build1) ... 89s Selecting previously unselected package liblcms2-2:s390x. 89s Preparing to unpack .../09-liblcms2-2_2.17-1_s390x.deb ... 89s Unpacking liblcms2-2:s390x (2.17-1) ... 89s Selecting previously unselected package libjpeg-turbo8:s390x. 89s Preparing to unpack .../10-libjpeg-turbo8_2.1.5-4ubuntu3_s390x.deb ... 89s Unpacking libjpeg-turbo8:s390x (2.1.5-4ubuntu3) ... 89s Selecting previously unselected package libjpeg8:s390x. 89s Preparing to unpack .../11-libjpeg8_8c-2ubuntu12_s390x.deb ... 89s Unpacking libjpeg8:s390x (8c-2ubuntu12) ... 89s Selecting previously unselected package libpcsclite1:s390x. 89s Preparing to unpack .../12-libpcsclite1_2.4.1-1_s390x.deb ... 89s Unpacking libpcsclite1:s390x (2.4.1-1) ... 89s Selecting previously unselected package openjdk-21-jre-headless:s390x. 89s Preparing to unpack .../13-openjdk-21-jre-headless_21.0.10+7-1_s390x.deb ... 89s Unpacking openjdk-21-jre-headless:s390x (21.0.10+7-1) ... 92s Selecting previously unselected package default-jre-headless. 92s Preparing to unpack .../14-default-jre-headless_2%3a1.21-76build1_s390x.deb ... 92s Unpacking default-jre-headless (2:1.21-76build1) ... 92s Selecting previously unselected package bbmap. 92s Preparing to unpack .../15-bbmap_39.20+dfsg-3_all.deb ... 92s Unpacking bbmap (39.20+dfsg-3) ... 92s Selecting previously unselected package bbmap-jni. 92s Preparing to unpack .../16-bbmap-jni_39.20+dfsg-3_s390x.deb ... 92s Unpacking bbmap-jni (39.20+dfsg-3) ... 92s Selecting previously unselected package libjs-jquery. 92s Preparing to unpack .../17-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ... 92s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 92s Selecting previously unselected package python-biopython-doc. 92s Preparing to unpack .../18-python-biopython-doc_1.86+dfsg-1_all.deb ... 92s Unpacking python-biopython-doc (1.86+dfsg-1) ... 93s Setting up liblcms2-2:s390x (2.17-1) ... 93s Setting up java-common (0.76build1) ... 93s Setting up libcommons-cli-java (1.6.0-1) ... 93s Setting up liblog4j1.2-java (1.2.17-11build1) ... 93s Setting up libapache-pom-java (33-2build1) ... 93s Setting up libpcsclite1:s390x (2.4.1-1) ... 93s Setting up libjpeg-turbo8:s390x (2.1.5-4ubuntu3) ... 93s Setting up bbmap-jni (39.20+dfsg-3) ... 93s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 93s Setting up ca-certificates-java (20240118build1) ... 93s No JRE found. Skipping Java certificates setup. 93s Setting up libjpeg8:s390x (8c-2ubuntu12) ... 93s Setting up openjdk-21-jre-headless:s390x (21.0.10+7-1) ... 93s update-alternatives: using /usr/lib/jvm/java-21-openjdk-s390x/bin/java to provide /usr/bin/java (java) in auto mode 93s update-alternatives: using /usr/lib/jvm/java-21-openjdk-s390x/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 93s update-alternatives: using /usr/lib/jvm/java-21-openjdk-s390x/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 93s update-alternatives: using /usr/lib/jvm/java-21-openjdk-s390x/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 93s update-alternatives: using /usr/lib/jvm/java-21-openjdk-s390x/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 93s Setting up libcommons-parent-java (56-1build1) ... 93s Setting up python-biopython-doc (1.86+dfsg-1) ... 93s Setting up libcommons-codec-java (1.18.0-1) ... 93s Setting up libcommons-io-java (2.19.0-1) ... 93s Setting up libmpj-java (0.44+dfsg-4build1) ... 93s Processing triggers for libc-bin (2.42-2ubuntu4) ... 93s Processing triggers for man-db (2.13.1-1build1) ... 94s Processing triggers for ca-certificates-java (20240118build1) ... 95s Adding debian:ACCVRAIZ1.pem 95s Adding debian:AC_RAIZ_FNMT-RCM.pem 95s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 95s Adding debian:ANF_Secure_Server_Root_CA.pem 95s Adding debian:Actalis_Authentication_Root_CA.pem 95s Adding debian:AffirmTrust_Commercial.pem 95s Adding debian:AffirmTrust_Networking.pem 95s Adding debian:AffirmTrust_Premium.pem 95s Adding debian:AffirmTrust_Premium_ECC.pem 95s Adding debian:Amazon_Root_CA_1.pem 95s Adding debian:Amazon_Root_CA_2.pem 95s Adding debian:Amazon_Root_CA_3.pem 95s Adding debian:Amazon_Root_CA_4.pem 95s Adding debian:Atos_TrustedRoot_2011.pem 95s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 95s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 95s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 95s Adding debian:BJCA_Global_Root_CA1.pem 95s Adding debian:BJCA_Global_Root_CA2.pem 95s Adding debian:Baltimore_CyberTrust_Root.pem 95s Adding debian:Buypass_Class_2_Root_CA.pem 95s Adding debian:Buypass_Class_3_Root_CA.pem 95s Adding debian:CA_Disig_Root_R2.pem 95s Adding debian:CFCA_EV_ROOT.pem 95s Adding debian:COMODO_Certification_Authority.pem 95s Adding debian:COMODO_ECC_Certification_Authority.pem 95s Adding debian:COMODO_RSA_Certification_Authority.pem 95s Adding debian:Certainly_Root_E1.pem 95s Adding debian:Certainly_Root_R1.pem 95s Adding debian:Certigna.pem 95s Adding debian:Certigna_Root_CA.pem 95s Adding debian:Certum_EC-384_CA.pem 95s Adding debian:Certum_Trusted_Network_CA.pem 95s Adding debian:Certum_Trusted_Network_CA_2.pem 95s Adding debian:Certum_Trusted_Root_CA.pem 95s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 95s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 95s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 95s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 95s Adding debian:Comodo_AAA_Services_root.pem 95s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 95s Adding debian:D-TRUST_BR_Root_CA_2_2023.pem 95s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 95s Adding debian:D-TRUST_EV_Root_CA_2_2023.pem 95s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 95s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 95s Adding debian:DigiCert_Assured_ID_Root_CA.pem 95s Adding debian:DigiCert_Assured_ID_Root_G2.pem 95s Adding debian:DigiCert_Assured_ID_Root_G3.pem 95s Adding debian:DigiCert_Global_Root_CA.pem 95s Adding debian:DigiCert_Global_Root_G2.pem 95s Adding debian:DigiCert_Global_Root_G3.pem 95s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 95s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 95s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 95s Adding debian:DigiCert_Trusted_Root_G4.pem 95s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 95s Adding debian:Entrust_Root_Certification_Authority.pem 95s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 95s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 95s Adding debian:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem 95s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 95s Adding debian:GLOBALTRUST_2020.pem 95s Adding debian:GTS_Root_R1.pem 95s Adding debian:GTS_Root_R2.pem 95s Adding debian:GTS_Root_R3.pem 96s Adding debian:GTS_Root_R4.pem 96s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 96s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 96s Adding debian:GlobalSign_Root_CA.pem 96s Adding debian:GlobalSign_Root_CA_-_R3.pem 96s Adding debian:GlobalSign_Root_CA_-_R6.pem 96s Adding debian:GlobalSign_Root_E46.pem 96s Adding debian:GlobalSign_Root_R46.pem 96s Adding debian:Go_Daddy_Class_2_CA.pem 96s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 96s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 96s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 96s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 96s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 96s Adding debian:HiPKI_Root_CA_-_G1.pem 96s Adding debian:Hongkong_Post_Root_CA_3.pem 96s Adding debian:ISRG_Root_X1.pem 96s Adding debian:ISRG_Root_X2.pem 96s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 96s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 96s Adding debian:Izenpe.com.pem 96s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 96s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 96s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 96s Adding debian:NAVER_Global_Root_Certification_Authority.pem 96s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 96s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 96s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 96s Adding debian:QuoVadis_Root_CA_1_G3.pem 96s Adding debian:QuoVadis_Root_CA_2.pem 96s Adding debian:QuoVadis_Root_CA_2_G3.pem 96s Adding debian:QuoVadis_Root_CA_3.pem 96s Adding debian:QuoVadis_Root_CA_3_G3.pem 96s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 96s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 96s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 96s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 96s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 96s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 96s Adding debian:SZAFIR_ROOT_CA2.pem 96s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 96s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 96s Adding debian:SecureSign_Root_CA12.pem 96s Adding debian:SecureSign_Root_CA14.pem 96s Adding debian:SecureSign_Root_CA15.pem 96s Adding debian:SecureTrust_CA.pem 96s Adding debian:Secure_Global_CA.pem 96s Adding debian:Security_Communication_ECC_RootCA1.pem 96s Adding debian:Security_Communication_RootCA2.pem 96s Adding debian:Starfield_Class_2_CA.pem 96s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 96s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 96s Adding debian:SwissSign_Gold_CA_-_G2.pem 96s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 96s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 96s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 96s Adding debian:TWCA_CYBER_Root_CA.pem 96s Adding debian:TWCA_Global_Root_CA.pem 96s Adding debian:TWCA_Root_Certification_Authority.pem 96s Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem 96s Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem 96s Adding debian:TeliaSonera_Root_CA_v1.pem 96s Adding debian:Telia_Root_CA_v2.pem 96s Adding debian:TrustAsia_Global_Root_CA_G3.pem 96s Adding debian:TrustAsia_Global_Root_CA_G4.pem 96s Adding debian:Trustwave_Global_Certification_Authority.pem 96s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 96s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 96s Adding debian:TunTrust_Root_CA.pem 96s Adding debian:UCA_Extended_Validation_Root.pem 96s Adding debian:UCA_Global_G2_Root.pem 96s Adding debian:USERTrust_ECC_Certification_Authority.pem 96s Adding debian:USERTrust_RSA_Certification_Authority.pem 96s Adding debian:XRamp_Global_CA_Root.pem 96s Adding debian:certSIGN_ROOT_CA.pem 96s Adding debian:certSIGN_Root_CA_G2.pem 96s Adding debian:e-Szigno_Root_CA_2017.pem 96s Adding debian:ePKI_Root_Certification_Authority.pem 96s Adding debian:emSign_ECC_Root_CA_-_C3.pem 96s Adding debian:emSign_ECC_Root_CA_-_G3.pem 96s Adding debian:emSign_Root_CA_-_C1.pem 96s Adding debian:emSign_Root_CA_-_G1.pem 96s Adding debian:vTrus_ECC_Root_CA.pem 96s Adding debian:vTrus_Root_CA.pem 96s done. 96s Setting up bbmap (39.20+dfsg-3) ... 96s Setting up default-jre-headless (2:1.21-76build1) ... 98s autopkgtest [11:17:36]: test run-unit-test: [----------------------- 99s 99s # bbmap 99s bbmap.sh --version 99s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 99s java -ea -Xmx4000m -Xms4000m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 --version 99s BBTools version 39.20 99s For help, please run the shellscript with no parameters, or look in /docs/. 100s bbmap.sh --help 100s bbmap.sh ref=example.fasta 100s 100s BBMap 100s Written by Brian Bushnell, from Dec. 2010 - present 100s Last modified September 15, 2022 100s 100s Description: Fast and accurate splice-aware read aligner. 100s Please read bbmap/docs/guides/BBMapGuide.txt for more information. 100s 100s To index: bbmap.sh ref= 100s To map: bbmap.sh in= out= 100s To map without writing an index: 100s bbmap.sh ref= in= out= nodisk 100s 100s in=stdin will accept reads from standard in, and out=stdout will write to 100s standard out, but file extensions are still needed to specify the format of the 100s input and output files e.g. in=stdin.fa.gz will read gzipped fasta from 100s standard in; out=stdout.sam.gz will write gzipped sam. 100s 100s Indexing Parameters (required when building the index): 100s nodisk=f Set to true to build index in memory and write nothing 100s to disk except output. 100s ref= Specify the reference sequence. Only do this ONCE, 100s when building the index (unless using 'nodisk'). 100s build=1 If multiple references are indexed in the same directory, 100s each needs a unique numeric ID (unless using 'nodisk'). 100s k=13 Kmer length, range 8-15. Longer is faster but uses 100s more memory. Shorter is more sensitive. 100s If indexing and mapping are done in two steps, K should 100s be specified each time. 100s path=<.> Specify the location to write the index, if you don't 100s want it in the current working directory. 100s usemodulo=f Throw away ~80% of kmers based on remainder modulo a 100s number (reduces RAM by 50% and sensitivity slightly). 100s Should be enabled both when building the index AND 100s when mapping. 100s rebuild=f Force a rebuild of the index (ref= should be set). 100s 100s Input Parameters: 100s build=1 Designate index to use. Corresponds to the number 100s specified when building the index. 100s in= Primary reads input; required parameter. 100s in2= For paired reads in two files. 100s interleaved=auto True forces paired/interleaved input; false forces 100s single-ended mapping. If not specified, interleaved 100s status will be autodetected from read names. 100s fastareadlen=500 Break up FASTA reads longer than this. Max is 500 for 100s BBMap and 6000 for BBMapPacBio. Only works for FASTA 100s input (use 'maxlen' for FASTQ input). The default for 100s bbmap.sh is 500, and for mapPacBio.sh is 6000. 100s unpigz=f Spawn a pigz (parallel gzip) process for faster 100s decompression than using Java. 100s Requires pigz to be installed. 100s touppercase=t (tuc) Convert lowercase letters in reads to upper case 100s (otherwise they will not match the reference). 100s 100s Sampling Parameters: 100s 100s reads=-1 Set to a positive number N to only process the first N 100s reads (or pairs), then quit. -1 means use all reads. 100s samplerate=1 Set to a number from 0 to 1 to randomly select that 100s fraction of reads for mapping. 1 uses all reads. 100s skipreads=0 Set to a number N to skip the first N reads (or pairs), 100s then map the rest. 100s 100s Mapping Parameters: 100s fast=f This flag is a macro which sets other paramters to run 100s faster, at reduced sensitivity. Bad for RNA-seq. 100s slow=f This flag is a macro which sets other paramters to run 100s slower, at greater sensitivity. 'vslow' is even slower. 100s maxindel=16000 Don't look for indels longer than this. Lower is faster. 100s Set to >=100k for RNAseq with long introns like mammals. 100s strictmaxindel=f When enabled, do not allow indels longer than 'maxindel'. 100s By default these are not sought, but may be found anyway. 100s tipsearch=100 Look this far for read-end deletions with anchors 100s shorter than K, using brute force. 100s minid=0.76 Approximate minimum alignment identity to look for. 100s Higher is faster and less sensitive. 100s minhits=1 Minimum number of seed hits required for candidate sites. 100s Higher is faster. 100s local=f Set to true to use local, rather than global, alignments. 100s This will soft-clip ugly ends of poor alignments. 100s perfectmode=f Allow only perfect mappings when set to true (very fast). 100s semiperfectmode=f Allow only perfect and semiperfect (perfect except for 100s N's in the reference) mappings. 100s threads=auto (t) Set to number of threads desired. By default, uses 100s all cores available. 100s ambiguous=best (ambig) Set behavior on ambiguously-mapped reads (with 100s multiple top-scoring mapping locations). 100s best (use the first best site) 100s toss (consider unmapped) 100s random (select one top-scoring site randomly) 100s all (retain all top-scoring sites) 100s samestrandpairs=f (ssp) Specify whether paired reads should map to the 100s same strand or opposite strands. 100s requirecorrectstrand=t (rcs) Forbid pairing of reads without correct strand 100s orientation. Set to false for long-mate-pair libraries. 100s killbadpairs=f (kbp) If a read pair is mapped with an inappropriate 100s insert size or orientation, the read with the lower 100s mapping quality is marked unmapped. 100s pairedonly=f (po) Treat unpaired reads as unmapped. Thus they will 100s be sent to 'outu' but not 'outm'. 100s rcomp=f Reverse complement both reads prior to mapping (for LMP 100s outward-facing libraries). 100s rcompmate=f Reverse complement read2 prior to mapping. 100s pairlen=32000 Set max allowed distance between paired reads. 100s (insert size)=(pairlen)+(read1 length)+(read2 length) 100s rescuedist=1200 Don't try to rescue paired reads if avg. insert size 100s greater than this. Lower is faster. 100s rescuemismatches=32 Maximum mismatches allowed in a rescued read. Lower 100s is faster. 100s averagepairdist=100 (apd) Initial average distance between paired reads. 100s Varies dynamically; does not need to be specified. 100s deterministic=f Run in deterministic mode. In this case it is good 100s to set averagepairdist. BBMap is deterministic 100s without this flag if using single-ended reads, 100s or run singlethreaded. 100s bandwidthratio=0 (bwr) If above zero, restrict alignment band to this 100s fraction of read length. Faster but less accurate. 100s bandwidth=0 (bw) Set the bandwidth directly. 100s fraction of read length. Faster but less accurate. 100s usejni=f (jni) Do alignments faster, in C code. Requires 100s compiling the C code; details are in /jni/README.txt. 100s maxsites2=800 Don't analyze (or print) more than this many alignments 100s per read. 100s ignorefrequentkmers=t (ifk) Discard low-information kmers that occur often. 100s excludefraction=0.03 (ef) Fraction of kmers to ignore. For example, 0.03 100s will ignore the most common 3% of kmers. 100s greedy=t Use a greedy algorithm to discard the least-useful 100s kmers on a per-read basis. 100s kfilter=0 If positive, potential mapping sites must have at 100s least this many consecutive exact matches. 100s 100s 100s Quality and Trimming Parameters: 100s qin=auto Set to 33 or 64 to specify input quality value ASCII 100s offset. 33 is Sanger, 64 is old Solexa. 100s qout=auto Set to 33 or 64 to specify output quality value ASCII 100s offset (only if output format is fastq). 100s qtrim=f Quality-trim ends before mapping. Options are: 100s 'f' (false), 'l' (left), 'r' (right), and 'lr' (both). 100s untrim=f Undo trimming after mapping. Untrimmed bases will be 100s soft-clipped in cigar strings. 100s trimq=6 Trim regions with average quality below this 100s (phred algorithm). 100s mintrimlength=60 (mintl) Don't trim reads to be shorter than this. 100s fakefastaquality=-1 (ffq) Set to a positive number 1-50 to generate fake 100s quality strings for fasta input reads. 100s ignorebadquality=f (ibq) Keep going, rather than crashing, if a read has 100s out-of-range quality values. 100s usequality=t Use quality scores when determining which read kmers 100s to use as seeds. 100s minaveragequality=0 (maq) Do not map reads with average quality below this. 100s maqb=0 If positive, calculate maq from this many initial bases. 100s 100s Output Parameters: 100s out= Write all reads to this file. 100s outu= Write only unmapped reads to this file. Does not 100s include unmapped paired reads with a mapped mate. 100s outm= Write only mapped reads to this file. Includes 100s unmapped paired reads with a mapped mate. 100s mappedonly=f If true, treats 'out' like 'outm'. 100s bamscript= (bs) Write a shell script to that will turn 100s the sam output into a sorted, indexed bam file. 100s ordered=f Set to true to output reads in same order as input. 100s Slower and uses more memory. 100s overwrite=f (ow) Allow process to overwrite existing files. 100s secondary=f Print secondary alignments. 100s sssr=0.95 (secondarysitescoreratio) Print only secondary alignments 100s with score of at least this fraction of primary. 100s ssao=f (secondarysiteasambiguousonly) Only print secondary 100s alignments for ambiguously-mapped reads. 100s maxsites=5 Maximum number of total alignments to print per read. 100s Only relevant when secondary=t. 100s quickmatch=f Generate cigar strings more quickly. 100s trimreaddescriptions=f (trd) Truncate read and ref names at the first whitespace, 100s assuming that the remainder is a comment or description. 100s ziplevel=2 (zl) Compression level for zip or gzip output. 100s pigz=f Spawn a pigz (parallel gzip) process for faster 100s compression than Java. Requires pigz to be installed. 100s machineout=f Set to true to output statistics in machine-friendly 100s 'key=value' format. 100s printunmappedcount=f Print the total number of unmapped reads and bases. 100s If input is paired, the number will be of pairs 100s for which both reads are unmapped. 100s showprogress=0 If positive, print a '.' every X reads. 100s showprogress2=0 If positive, print the number of seconds since the 100s last progress update (instead of a '.'). 100s renamebyinsert=f Renames reads based on their mapped insert size. 100s 100s Bloom-Filtering Parameters (bloomfilter.sh is the standalone version). 100s bloom=f Use a Bloom filter to ignore reads not sharing kmers 100s with the reference. This uses more memory, but speeds 100s mapping when most reads don't match the reference. 100s bloomhashes=2 Number of hash functions. 100s bloomminhits=3 Number of consecutive hits to be considered matched. 100s bloomk=31 Bloom filter kmer length. 100s bloomserial=t Use the serialized Bloom filter for greater loading 100s speed, if available. If not, generate and write one. 100s 100s Post-Filtering Parameters: 100s idfilter=0 Independant of minid; sets exact minimum identity 100s allowed for alignments to be printed. Range 0 to 1. 100s subfilter=-1 Ban alignments with more than this many substitutions. 100s insfilter=-1 Ban alignments with more than this many insertions. 100s delfilter=-1 Ban alignments with more than this many deletions. 100s indelfilter=-1 Ban alignments with more than this many indels. 100s editfilter=-1 Ban alignments with more than this many edits. 100s inslenfilter=-1 Ban alignments with an insertion longer than this. 100s dellenfilter=-1 Ban alignments with a deletion longer than this. 100s nfilter=-1 Ban alignments with more than this many ns. This 100s includes nocall, noref, and off scaffold ends. 100s 100s Sam flags and settings: 100s noheader=f Disable generation of header lines. 100s sam=1.4 Set to 1.4 to write Sam version 1.4 cigar strings, 100s with = and X, or 1.3 to use M. 100s saa=t (secondaryalignmentasterisks) Use asterisks instead of 100s bases for sam secondary alignments. 100s cigar=t Set to 'f' to skip generation of cigar strings (faster). 100s keepnames=f Keep original names of paired reads, rather than 100s ensuring both reads have the same name. 100s intronlen=999999999 Set to a lower number like 10 to change 'D' to 'N' in 100s cigar strings for deletions of at least that length. 100s rgid= Set readgroup ID. All other readgroup fields 100s can be set similarly, with the flag rgXX= 100s If you set a readgroup flag to the word 'filename', 100s e.g. rgid=filename, the input file name will be used. 100s mdtag=f Write MD tags. 100s nhtag=f Write NH tags. 100s xmtag=f Write XM tags (may only work correctly with ambig=all). 100s amtag=f Write AM tags. 100s nmtag=f Write NM tags. 100s xstag=f Set to 'xs=fs', 'xs=ss', or 'xs=us' to write XS tags 100s for RNAseq using firststrand, secondstrand, or 100s unstranded libraries. Needed by Cufflinks. 100s JGI mainly uses 'firststrand'. 100s stoptag=f Write a tag indicating read stop location, prefixed by YS:i: 100s lengthtag=f Write a tag indicating (query,ref) alignment lengths, 100s prefixed by YL:Z: 100s idtag=f Write a tag indicating percent identity, prefixed by YI:f: 100s inserttag=f Write a tag indicating insert size, prefixed by X8:Z: 100s scoretag=f Write a tag indicating BBMap's raw score, prefixed by YR:i: 100s timetag=f Write a tag indicating this read's mapping time, prefixed by X0:i: 100s boundstag=f Write a tag indicating whether either read in the pair 100s goes off the end of the reference, prefixed by XB:Z: 100s notags=f Turn off all optional tags. 100s 100s Histogram and statistics output parameters: 100s scafstats= Statistics on how many reads mapped to which scaffold. 100s refstats= Statistics on how many reads mapped to which reference 100s file; only for BBSplit. 100s sortscafs=t Sort scaffolds or references by read count. 100s bhist= Base composition histogram by position. 100s qhist= Quality histogram by position. 100s aqhist= Histogram of average read quality. 100s bqhist= Quality histogram designed for box plots. 100s lhist= Read length histogram. 100s ihist= Write histogram of insert sizes (for paired reads). 100s ehist= Errors-per-read histogram. 100s qahist= Quality accuracy histogram of error rates versus 100s quality score. 100s indelhist= Indel length histogram. 100s mhist= Histogram of match, sub, del, and ins rates by 100s read location. 100s gchist= Read GC content histogram. 100s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 100s gcpairs=t Use average GC of paired reads. 100s idhist= Histogram of read count versus percent identity. 100s idbins=100 Number idhist bins. Set to 'auto' to use read length. 100s statsfile=stderr Mapping statistics are printed here. 100s 100s Coverage output parameters (these may reduce speed and use more RAM): 100s covstats= Per-scaffold coverage info. 100s rpkm= Per-scaffold RPKM/FPKM counts. 100s covhist= Histogram of # occurrences of each depth level. 100s basecov= Coverage per base location. 100s bincov= Print binned coverage per location (one line per X bases). 100s covbinsize=1000 Set the binsize for binned coverage output. 100s nzo=t Only print scaffolds with nonzero coverage. 100s twocolumn=f Change to true to print only ID and Avg_fold instead of 100s all 6 columns to the 'out=' file. 100s 32bit=f Set to true if you need per-base coverage over 64k. 100s strandedcov=f Track coverage for plus and minus strand independently. 100s startcov=f Only track start positions of reads. 100s secondarycov=t Include coverage of secondary alignments. 100s physcov=f Calculate physical coverage for paired reads. 100s This includes the unsequenced bases. 100s delcoverage=t (delcov) Count bases covered by deletions as covered. 100s True is faster than false. 100s covk=0 If positive, calculate kmer coverage statistics. 100s 100s Java Parameters: 100s -Xmx This will set Java's memory usage, 100s overriding autodetection. 100s -Xmx20g will specify 20 gigs of RAM, and -Xmx800m 100s will specify 800 megs. The max is typically 85% of 100s physical memory. The human genome requires around 24g, 100s or 12g with the 'usemodulo' flag. The index uses 100s roughly 6 bytes per reference base. 100s -eoom This flag will cause the process to exit if an 100s out-of-memory exception occurs. Requires Java 8u92+. 100s -da Disable assertions. 100s 100s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter 100s any problems, or post at: http://seqanswers.com/forums/showthread.php?t=41057 100s 100s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 100s java -ea -Xmx4000m -Xms4000m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta 100s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta] 100s Version 39.20 100s 100s No output file. 100s Writing reference. 100s 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] 100s 100s Set genScaffoldInfo=true 100s Writing chunk 1 100s Set genome to 1 100s 100s Loaded Reference: 0.069 seconds. 100s Loading index for chunk 1-1, build 1 100s No index available; generating from reference genome: /tmp/autopkgtest.QiqTJv/autopkgtest_tmp/ref/index/1/chr1_index_k13_c16_b1.block 101s Indexing threads started for block 0-1 101s Indexing threads finished for block 0-1 104s Generated Index: 3.696 seconds. 104s No reads to process; quitting. 104s 104s Total time: 4.191 seconds. 104s test -d ref 104s bbmap.sh in=misc_dna_as_sanger.fastq out=out.sam 104s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 104s java -ea -Xmx4000m -Xms4000m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 in=misc_dna_as_sanger.fastq out=out.sam 104s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, in=misc_dna_as_sanger.fastq, out=out.sam] 104s Version 39.20 104s 104s Retaining first best site only for ambiguous mappings. 104s Set genome to 1 104s 104s Loaded Reference: 0.015 seconds. 104s Loading index for chunk 1-1, build 1 106s Generated Index: 1.526 seconds. 119s Analyzed Index: 13.460 seconds. 119s Started output stream: 0.170 seconds. 119s Cleared Memory: 0.179 seconds. 120s Processing reads in single-ended mode. 120s Started read stream. 120s Started 4 mapping threads. 120s Detecting finished threads: 0, 1, 2, 3 120s 120s ------------------ Results ------------------ 120s 120s Genome: 1 120s Key Length: 13 120s Max Indel: 16000 120s Minimum Score Ratio: 0.56 120s Mapping Mode: normal 120s Reads Used: 4 (153 bases) 120s 120s Mapping: 0.263 seconds. 120s Reads/sec: 15.20 120s kBases/sec: 0.58 120s 120s 120s Read 1 data: pct reads num reads pct bases num bases 120s 120s mapped: 0.0000% 0 0.0000% 0 120s unambiguous: 0.0000% 0 0.0000% 0 120s ambiguous: 0.0000% 0 0.0000% 0 120s low-Q discards: 25.0000% 1 19.6078% 30 120s 120s perfect best site: 0.0000% 0 0.0000% 0 120s semiperfect site: 0.0000% 0 0.0000% 0 120s 120s Match Rate: NA NA NaN% 0 120s Error Rate: NaN% 0 NaN% 0 120s Sub Rate: NaN% 0 NaN% 0 120s Del Rate: NaN% 0 NaN% 0 120s Ins Rate: NaN% 0 NaN% 0 120s N Rate: NaN% 0 NaN% 0 120s 120s Total time: 15.687 seconds. 120s test -r out.sam 120s bbmap.sh ref=example.fasta in=example.fastq out=out2.sam nodisk 120s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 120s java -ea -Xmx4000m -Xms4000m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta in=example.fastq out=out2.sam nodisk 120s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta, in=example.fastq, out=out2.sam, nodisk] 120s Version 39.20 120s 120s Retaining first best site only for ambiguous mappings. 120s 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] 120s 120s Set genScaffoldInfo=true 120s Set genome to 1 120s 120s Loaded Reference: 0.001 seconds. 120s Loading index for chunk 1-1, build 1 120s Indexing threads started for block 0-1 120s Indexing threads finished for block 0-1 121s Generated Index: 0.276 seconds. 135s Analyzed Index: 14.573 seconds. 135s Started output stream: 0.181 seconds. 135s Cleared Memory: 0.118 seconds. 136s Processing reads in single-ended mode. 136s Started read stream. 136s Started 4 mapping threads. 136s Detecting finished threads: 0, 1, 2, 3 136s 136s ------------------ Results ------------------ 136s 136s Genome: 1 136s Key Length: 13 136s Max Indel: 16000 136s Minimum Score Ratio: 0.56 136s Mapping Mode: normal 136s Reads Used: 3 (75 bases) 136s 136s Mapping: 0.072 seconds. 136s Reads/sec: 41.65 136s kBases/sec: 1.04 136s 136s 136s Read 1 data: pct reads num reads pct bases num bases 136s 136s mapped: 100.0000% 3 100.0000% 75 136s unambiguous: 100.0000% 3 100.0000% 75 136s ambiguous: 0.0000% 0 0.0000% 0 136s low-Q discards: 0.0000% 0 0.0000% 0 136s 136s perfect best site: 100.0000% 3 100.0000% 75 136s semiperfect site: 100.0000% 3 100.0000% 75 136s 136s Match Rate: NA NA 100.0000% 75 136s Error Rate: 0.0000% 0 0.0000% 0 136s Sub Rate: 0.0000% 0 0.0000% 0 136s Del Rate: 0.0000% 0 0.0000% 0 136s Ins Rate: 0.0000% 0 0.0000% 0 136s N Rate: 0.0000% 0 0.0000% 0 136s 136s Total time: 15.443 seconds. 136s test -r out2.sam 136s 136s # bbduk 136s bbduk.sh --version 136s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 136s java -ea -Xmx3093m -Xms3093m -cp /usr/share/java/bbmap.jar jgi.BBDuk --version 136s BBTools version 39.20 136s For help, please run the shellscript with no parameters, or look in /docs/. 136s bbduk.sh --help 136s bbduk.sh in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq \ 136s qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 136s 136s Written by Brian Bushnell 136s Last modified November 18, 2024 136s 136s Description: Compares reads to the kmers in a reference dataset, optionally 136s allowing an edit distance. Splits the reads into two outputs - those that 136s match the reference, and those that don't. Can also trim (remove) the matching 136s parts of the reads rather than binning the reads. 136s Please read bbmap/docs/guides/BBDukGuide.txt for more information. 136s 136s Usage: bbduk.sh in= out= ref= 136s 136s Input may be stdin or a fasta or fastq file, compressed or uncompressed. 136s If you pipe via stdin/stdout, please include the file type; e.g. for gzipped 136s fasta input, set in=stdin.fa.gz 136s 136s Input parameters: 136s in= Main input. in=stdin.fq will pipe from stdin. 136s in2= Input for 2nd read of pairs in a different file. 136s ref= Comma-delimited list of reference files. 136s In addition to filenames, you may also use the keywords: 136s adapters, artifacts, phix, lambda, pjet, mtst, kapa 136s literal= Comma-delimited list of literal reference sequences. 136s Polymers are also allowed with the 'poly' prefix; 136s for example, 'literal=ATGGT,polyGC' will add both ATGGT 136s and GCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGC - 32+ of them, 136s enough replicates to ensure that all kmers are present. 136s touppercase=f (tuc) Change all bases upper-case. 136s interleaved=auto (int) t/f overrides interleaved autodetection. 136s Must be set mainually when streaming fastq input. 136s qin=auto Input quality offset: 33 (Sanger), 64, or auto. 136s reads=-1 If positive, quit after processing X reads or pairs. 136s copyundefined=f (cu) Process non-AGCT IUPAC reference bases by making all 136s possible unambiguous copies. Intended for short motifs 136s or adapter barcodes, as time/memory use is exponential. 136s samplerate=1 Set lower to only process a fraction of input reads. 136s samref= Optional reference fasta for processing sam files. 136s 136s Output parameters: 136s out= (outnonmatch) Write reads here that do not contain 136s kmers matching the database. 'out=stdout.fq' will pipe 136s to standard out. 136s out2= (outnonmatch2) Use this to write 2nd read of pairs to a 136s different file. 136s outm= (outmatch) Write reads here that fail filters. In default 136s kfilter mode, this means any read with a matching kmer. 136s In any mode, it also includes reads that fail filters such 136s as minlength, mingc, maxgc, entropy, etc. In other words, 136s it includes all reads that do not go to 'out'. 136s outm2= (outmatch2) Use this to write 2nd read of pairs to a 136s different file. 136s outs= (outsingle) Use this to write singleton reads whose mate 136s was trimmed shorter than minlen. 136s stats= Write statistics about which contamininants were detected. 136s refstats= Write statistics on a per-reference-file basis. 136s rpkm= Write RPKM for each reference sequence (for RNA-seq). 136s dump= Dump kmer tables to a file, in fasta format. 136s duk= Write statistics in duk's format. *DEPRECATED* 136s nzo=t Only write statistics about ref sequences with nonzero hits. 136s overwrite=t (ow) Grant permission to overwrite files. 136s showspeed=t (ss) 'f' suppresses display of processing speed. 136s ziplevel=2 (zl) Compression level; 1 (min) through 9 (max). 136s fastawrap=70 Length of lines in fasta output. 136s qout=auto Output quality offset: 33 (Sanger), 64, or auto. 136s statscolumns=3 (cols) Number of columns for stats output, 3 or 5. 136s 5 includes base counts. 136s rename=f Rename reads to indicate which sequences they matched. 136s refnames=f Use names of reference files rather than scaffold IDs. 136s trd=f Truncate read and ref names at the first whitespace. 136s ordered=f Set to true to output reads in same order as input. 136s maxbasesout=-1 If positive, quit after writing approximately this many 136s bases to out (outu/outnonmatch). 136s maxbasesoutm=-1 If positive, quit after writing approximately this many 136s bases to outm (outmatch). 136s json=f Print to screen in json format. 136s 136s Histogram output parameters: 136s bhist= Base composition histogram by position. 136s qhist= Quality histogram by position. 136s qchist= Count of bases with each quality value. 136s aqhist= Histogram of average read quality. 136s bqhist= Quality histogram designed for box plots. 136s lhist= Read length histogram. 136s phist= Polymer length histogram. 136s gchist= Read GC content histogram. 136s enthist= Read entropy histogram. 136s ihist= Insert size histogram, for paired reads in mapped sam. 136s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 136s maxhistlen=6000 Set an upper bound for histogram lengths; higher uses 136s more memory. The default is 6000 for some histograms 136s and 80000 for others. 136s 136s Histograms for mapped sam/bam files only: 136s histbefore=t Calculate histograms from reads before processing. 136s ehist= Errors-per-read histogram. 136s qahist= Quality accuracy histogram of error rates versus quality 136s score. 136s indelhist= Indel length histogram. 136s mhist= Histogram of match, sub, del, and ins rates by position. 136s idhist= Histogram of read count versus percent identity. 136s idbins=100 Number idhist bins. Set to 'auto' to use read length. 136s varfile= Ignore substitution errors listed in this file when 136s calculating error rates. Can be generated with 136s CallVariants. 136s vcf= Ignore substitution errors listed in this VCF file 136s when calculating error rates. 136s ignorevcfindels=t Also ignore indels listed in the VCF. 136s 136s Processing parameters: 136s k=27 Kmer length used for finding contaminants. Contaminants 136s shorter than k will not be found. k must be at least 1. 136s rcomp=t Look for reverse-complements of kmers in addition to 136s forward kmers. 136s maskmiddle=t (mm) Treat the middle base of a kmer as a wildcard, to 136s increase sensitivity in the presence of errors. This may 136s also be set to a number, e.g. mm=3, to mask that many bp. 136s The default mm=t corresponds to mm=1 for odd-length kmers 136s and mm=2 for even-length kmers (as of v39.04), while 136s mm=f is always equivalent to mm=0. 136s minkmerhits=1 (mkh) Reads need at least this many matching kmers 136s to be considered as matching the reference. 136s minkmerfraction=0.0 (mkf) A reads needs at least this fraction of its total 136s kmers to hit a ref, in order to be considered a match. 136s If this and minkmerhits are set, the greater is used. 136s mincovfraction=0.0 (mcf) A reads needs at least this fraction of its total 136s bases to be covered by ref kmers to be considered a match. 136s If specified, mcf overrides mkh and mkf. 136s hammingdistance=0 (hdist) Maximum Hamming distance for ref kmers (subs only). 136s Memory use is proportional to (3*K)^hdist. 136s qhdist=0 Hamming distance for query kmers; impacts speed, not memory. 136s editdistance=0 (edist) Maximum edit distance from ref kmers (subs 136s and indels). Memory use is proportional to (8*K)^edist. 136s hammingdistance2=0 (hdist2) Sets hdist for short kmers, when using mink. 136s qhdist2=0 Sets qhdist for short kmers, when using mink. 136s editdistance2=0 (edist2) Sets edist for short kmers, when using mink. 136s forbidn=f (fn) Forbids matching of read kmers containing N. 136s By default, these will match a reference 'A' if 136s hdist>0 or edist>0, to increase sensitivity. 136s removeifeitherbad=t (rieb) Paired reads get sent to 'outmatch' if either is 136s match (or either is trimmed shorter than minlen). 136s Set to false to require both. 136s trimfailures=f Instead of discarding failed reads, trim them to 1bp. 136s This makes the statistics a bit odd. 136s findbestmatch=f (fbm) If multiple matches, associate read with sequence 136s sharing most kmers. Reduces speed. 136s skipr1=f Don't do kmer-based operations on read 1. 136s skipr2=f Don't do kmer-based operations on read 2. 136s ecco=f For overlapping paired reads only. Performs error- 136s correction with BBMerge prior to kmer operations. 136s recalibrate=f (recal) Recalibrate quality scores. Requires calibration 136s matrices generated by CalcTrueQuality. 136s sam= If recalibration is desired, and matrices have not already 136s been generated, BBDuk will create them from the sam file. 136s amino=f Run in amino acid mode. Some features have not been 136s tested, but kmer-matching works fine. Maximum k is 12. 136s 136s Speed and Memory parameters: 136s threads=auto (t) Set number of threads to use; default is number of 136s logical processors. 136s prealloc=f Preallocate memory in table. Allows faster table loading 136s and more efficient memory usage, for a large reference. 136s monitor=f Kill this process if it crashes. monitor=600,0.01 would 136s kill after 600 seconds under 1% usage. 136s minrskip=1 (mns) Force minimal skip interval when indexing reference 136s kmers. 1 means use all, 2 means use every other kmer, etc. 136s maxrskip=1 (mxs) Restrict maximal skip interval when indexing 136s reference kmers. Normally all are used for scaffolds<100kb, 136s but with longer scaffolds, up to maxrskip-1 are skipped. 136s rskip= Set both minrskip and maxrskip to the same value. 136s If not set, rskip will vary based on sequence length. 136s qskip=1 Skip query kmers to increase speed. 1 means use all. 136s speed=0 Ignore this fraction of kmer space (0-15 out of 16) in both 136s reads and reference. Increases speed and reduces memory. 136s Note: Do not use more than one of 'speed', 'qskip', and 'rskip'. 136s 136s Trimming/Filtering/Masking parameters: 136s Note - if ktrim, kmask, and ksplit are unset, the default behavior is kfilter. 136s All kmer processing modes are mutually exclusive. 136s Reads only get sent to 'outm' purely based on kmer matches in kfilter mode. 136s 136s ktrim=f Trim reads to remove bases matching reference kmers, plus 136s all bases to the left or right. 136s Values: 136s f (don't trim), 136s r (trim to the right), 136s l (trim to the left) 136s ktrimtips=0 Set this to a positive number to perform ktrim on both 136s ends, examining only the outermost X bases. 136s kmask= Replace bases matching ref kmers with another symbol. 136s Allows any non-whitespace character, and processes short 136s kmers on both ends if mink is set. 'kmask=lc' will 136s convert masked bases to lowercase. 136s maskfullycovered=f (mfc) Only mask bases that are fully covered by kmers. 136s ksplit=f For single-ended reads only. Reads will be split into 136s pairs around the kmer. If the kmer is at the end of the 136s read, it will be trimmed instead. Singletons will go to 136s out, and pairs will go to outm. Do not use ksplit with 136s other operations such as quality-trimming or filtering. 136s mink=0 Look for shorter kmers at read tips down to this length, 136s when k-trimming or masking. 0 means disabled. Enabling 136s this will disable maskmiddle. 136s qtrim=f Trim read ends to remove bases with quality below trimq. 136s Performed AFTER looking for kmers. Values: 136s rl (trim both ends), 136s f (neither end), 136s r (right end only), 136s l (left end only), 136s w (sliding window). 136s trimq=6 Regions with average quality BELOW this will be trimmed, 136s if qtrim is set to something other than f. Can be a 136s floating-point number like 7.3. 136s quantize Bin quality scores to reduce file size. quantize=2 will 136s eliminate all odd quality scores, while quantize=0,10,37 136s will only allow qualty scores of 0, 10, or 37. 136s trimclip=f Trim soft-clipped bases from sam files. 136s minlength=10 (ml) Reads shorter than this after trimming will be 136s discarded. Pairs will be discarded if both are shorter. 136s mlf=0 (minlengthfraction) Reads shorter than this fraction of 136s original length after trimming will be discarded. 136s maxlength= Reads longer than this after trimming will be discarded. 136s minavgquality=0 (maq) Reads with average quality (after trimming) below 136s this will be discarded. 136s maqb=0 If positive, calculate maq from this many initial bases. 136s minbasequality=0 (mbq) Reads with any base below this quality (after 136s trimming) will be discarded. 136s maxns=-1 If non-negative, reads with more Ns than this 136s (after trimming) will be discarded. 136s mcb=0 (minconsecutivebases) Discard reads without at least 136s this many consecutive called bases. 136s ottm=f (outputtrimmedtomatch) Output reads trimmed to shorter 136s than minlength to outm rather than discarding. 136s tp=0 (trimpad) Trim this much extra around matching kmers. 136s tbo=f (trimbyoverlap) Trim adapters based on where paired 136s reads overlap. 136s strictoverlap=t Adjust sensitivity for trimbyoverlap mode. 136s minoverlap=14 Require this many bases of overlap for detection. 136s mininsert=40 Require insert size of at least this for overlap. 136s Should be reduced to 16 for small RNA sequencing. 136s tpe=f (trimpairsevenly) When kmer right-trimming, trim both 136s reads to the minimum length of either. 136s forcetrimleft=0 (ftl) If positive, trim bases to the left of this position 136s (exclusive, 0-based). 136s forcetrimright=0 (ftr) If positive, trim bases to the right of this position 136s (exclusive, 0-based). 136s forcetrimright2=0 (ftr2) If positive, trim this many bases on the right end. 136s forcetrimmod=0 (ftm) If positive, right-trim length to be equal to zero, 136s modulo this number. 136s restrictleft=0 If positive, only look for kmer matches in the 136s leftmost X bases. 136s restrictright=0 If positive, only look for kmer matches in the 136s rightmost X bases. 136s NOTE: restrictleft and restrictright are mutually exclusive. If trimming 136s both ends is desired, use ktrimtips. 136s mingc=0 Discard reads with GC content below this. 136s maxgc=1 Discard reads with GC content above this. 136s gcpairs=t Use average GC of paired reads. 136s Also affects gchist. 136s tossjunk=f Discard reads with invalid characters as bases. 136s swift=f Trim Swift sequences: Trailing C/T/N R1, leading G/A/N R2. 136s 136s Header-parsing parameters - these require Illumina headers: 136s chastityfilter=f (cf) Discard reads with id containing ' 1:Y:' or ' 2:Y:'. 136s barcodefilter=f Remove reads with unexpected barcodes if barcodes is set, 136s or barcodes containing 'N' otherwise. A barcode must be 136s the last part of the read header. Values: 136s t: Remove reads with bad barcodes. 136s f: Ignore barcodes. 136s crash: Crash upon encountering bad barcodes. 136s barcodes= Comma-delimited list of barcodes or files of barcodes. 136s xmin=-1 If positive, discard reads with a lesser X coordinate. 136s ymin=-1 If positive, discard reads with a lesser Y coordinate. 136s xmax=-1 If positive, discard reads with a greater X coordinate. 136s ymax=-1 If positive, discard reads with a greater Y coordinate. 136s 136s Polymer trimming: 136s trimpolya=0 If greater than 0, trim poly-A or poly-T tails of 136s at least this length on either end of reads. 136s trimpolygleft=0 If greater than 0, trim poly-G prefixes of at least this 136s length on the left end of reads. Does not trim poly-C. 136s trimpolygright=0 If greater than 0, trim poly-G tails of at least this 136s length on the right end of reads. Does not trim poly-C. 136s trimpolyg=0 This sets both left and right at once. 136s filterpolyg=0 If greater than 0, remove reads with a poly-G prefix of 136s at least this length (on the left). 136s Note: there are also equivalent poly-C flags. 136s 136s Polymer tracking: 136s pratio=base,base 'pratio=G,C' will print the ratio of G to C polymers. 136s plen=20 Length of homopolymers to count. 136s 136s Entropy/Complexity parameters: 136s entropy=-1 Set between 0 and 1 to filter reads with entropy below 136s that value. Higher is more stringent. 136s entropywindow=50 Calculate entropy using a sliding window of this length. 136s entropyk=5 Calculate entropy using kmers of this length. 136s minbasefrequency=0 Discard reads with a minimum base frequency below this. 136s entropytrim=f Values: 136s f: (false) Do not entropy-trim. 136s r: (right) Trim low entropy on the right end only. 136s l: (left) Trim low entropy on the left end only. 136s rl: (both) Trim low entropy on both ends. 136s entropymask=f Values: 136s f: (filter) Discard low-entropy sequences. 136s t: (true) Mask low-entropy parts of sequences with N. 136s lc: Change low-entropy parts of sequences to lowercase. 136s entropymark=f Mark each base with its entropy value. This is on a scale 136s of 0-41 and is reported as quality scores, so the output 136s should be fastq or fasta+qual. 136s NOTE: If set, entropytrim overrides entropymask. 136s 136s Cardinality estimation: 136s cardinality=f (loglog) Count unique kmers using the LogLog algorithm. 136s cardinalityout=f (loglogout) Count unique kmers in output reads. 136s loglogk=31 Use this kmer length for counting. 136s loglogbuckets=2048 Use this many buckets for counting. 136s khist= Kmer frequency histogram; plots number of kmers versus 136s kmer depth. This is approximate. 136s khistout= Kmer frequency histogram for output reads. 136s 136s Side Channel: 136s sideout= Output for aligned reads. 136s sideref=phix Reference for side-channel alignment; must be a single 136s sequence and virtually repeat-free at selected k. 136s sidek1=17 Kmer length for seeding alignment to reference. 136s sidek2=13 Kmer length for seeding alignment of unaligned reads 136s with an aligned mate. 136s sideminid1=0.66 Minimum identity to accept individual alignments. 136s sideminid2=0.58 Minimum identity for aligning reads with aligned mates. 136s sidemm1=1 Middle mask length for sidek1. 136s sidemm2=1 Middle mask length for sidek2. 136s Note: The side channel is a special additional output that allows alignment 136s to a secondary reference while also doing trimming. Alignment does not affect 136s whether reads go to the normal outputs (out, outm). The main purpose is to 136s simplify pipelines that need trimmed, aligned phiX reads for recalibration. 136s 136s 136s Java Parameters: 136s 136s -Xmx This will set Java's memory usage, overriding autodetection. 136s -Xmx20g will 136s specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 136s The max is typically 85% of physical memory. 136s -eoom This flag will cause the process to exit if an 136s out-of-memory exception occurs. Requires Java 8u92+. 136s -da Disable assertions. 136s 136s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 136s 136s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 136s java -ea -Xmx3093m -Xms3093m -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 137s 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] 137s Version 39.20 137s 137s Changed from ASCII-33 to ASCII-64 on input quality X (Q55) for base A at lines 1 and 3, position 24 while prescanning. 137s Changed from ASCII-33 to ASCII-64 on input quality X (Q55) for base A at lines 1 and 3, position 24 while prescanning. 137s Allocating kmer table: 0.017 seconds. 137s Initial: 137s Memory: max=3244m, total=3244m, free=3213m, used=31m 137s 137s Input is being processed as paired 137s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 137s Started output streams: 0.015 seconds. 137s Processing time: 0.009 seconds. 137s 137s Input: 8 reads 306 bases. 137s QTrimmed: 0 reads (0.00%) 0 bases (0.00%) 137s Total Removed: 8 reads (100.00%) 306 bases (100.00%) 137s Result: 0 reads (0.00%) 0 bases (0.00%) 137s 137s Time: 0.026 seconds. 137s Reads Processed: 8 0.31k reads/sec 137s Bases Processed: 306 0.01m bases/sec 137s test -r out.fastq.gz 137s 137s # bbnorm 137s bbnorm.sh --version 137s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 137s java -ea -Xmx4000m -Xms4000m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 --version 137s BBTools version 39.20 137s For help, please run the shellscript with no parameters, or look in /docs/. 137s bbnorm.sh --help 137s 137s Written by Brian Bushnell 137s Last modified October 19, 2017 137s 137s Description: Normalizes read depth based on kmer counts. 137s Can also error-correct, bin reads by kmer depth, and generate a kmer depth histogram. 137s However, Tadpole has superior error-correction to BBNorm. 137s Please read bbmap/docs/guides/BBNormGuide.txt for more information. 137s 137s Usage: bbnorm.sh in= out= outt= hist= 137s 137s Input parameters: 137s in=null Primary input. Use in2 for paired reads in a second file 137s in2=null Second input file for paired reads in two files 137s extra=null Additional files to use for input (generating hash table) but not for output 137s fastareadlen=2^31 Break up FASTA reads longer than this. Can be useful when processing scaffolded genomes 137s tablereads=-1 Use at most this many reads when building the hashtable (-1 means all) 137s kmersample=1 Process every nth kmer, and skip the rest 137s readsample=1 Process every nth read, and skip the rest 137s 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. 137s qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto. 137s 137s Output parameters: 137s out= File for normalized or corrected reads. Use out2 for paired reads in a second file 137s outt= (outtoss) File for reads that were excluded from primary output 137s reads=-1 Only process this number of reads, then quit (-1 means all) 137s sampleoutput=t Use sampling on output as well as input (not used if sample rates are 1) 137s keepall=f Set to true to keep all reads (e.g. if you just want error correction). 137s 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. 137s Default is false, to prevent confusion about how there can be 0-count kmers. 137s The reason is that based on the 'minq' and 'minprob' settings, some kmers may be excluded from the bloom filter. 137s tmpdir= This will specify a directory for temp files (only needed for multipass runs). If null, they will be written to the output directory. 137s usetempdir=t Allows enabling/disabling of temporary directory; if disabled, temp files will be written to the output directory. 137s qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input). 137s rename=f Rename reads based on their kmer depth. 137s 137s Hashing parameters: 137s k=31 Kmer length (values under 32 are most efficient, but arbitrarily high values are supported) 137s 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. 137s Large values decrease accuracy for a fixed amount of memory, so use the lowest number you can that will still capture highest-depth kmers. 137s hashes=3 Number of times each kmer is hashed and stored. Higher is slower. 137s Higher is MORE accurate if there is enough memory, and LESS accurate if there is not enough memory. 137s 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. 137s prehashes=2 Number of hashes for prefilter. 137s prefilterbits=2 (pbits) Bits per cell in prefilter. 137s prefiltersize=0.35 Fraction of memory to allocate to prefilter. 137s buildpasses=1 More passes can sometimes increase accuracy by iteratively removing low-depth kmers 137s minq=6 Ignore kmers containing bases with quality below this 137s minprob=0.5 Ignore kmers with overall probability of correctness below this 137s 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. 137s 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. 137s 137s Normalization parameters: 137s fixspikes=f (fs) Do a slower, high-precision bloom filter lookup of kmers that appear to have an abnormally high depth due to collisions. 137s target=100 (tgt) Target normalization depth. NOTE: All depth parameters control kmer depth, not read depth. 137s For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1)) 137s maxdepth=-1 (max) Reads will not be downsampled when below this depth, even if they are above the target depth. 137s mindepth=5 (min) Kmers with depth below this number will not be included when calculating the depth of a read. 137s minkmers=15 (mgkpr) Reads must have at least this many kmers over min depth to be retained. Aka 'mingoodkmersperread'. 137s 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. 137s uselowerdepth=t (uld) For pairs, use the depth of the lower read as the depth proxy. 137s deterministic=t (dr) Generate random numbers deterministically to ensure identical output between multiple runs. May decrease speed with a huge number of threads. 137s passes=2 (p) 1 pass is the basic mode. 2 passes (default) allows greater accuracy, error detection, better contol of output depth. 137s 137s Error detection parameters: 137s hdp=90.0 (highdepthpercentile) Position in sorted kmer depth array used as proxy of a read's high kmer depth. 137s ldp=25.0 (lowdepthpercentile) Position in sorted kmer depth array used as proxy of a read's low kmer depth. 137s tossbadreads=f (tbr) Throw away reads detected as containing errors. 137s requirebothbad=f (rbb) Only toss bad pairs if both reads are bad. 137s 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. 137s highthresh=12 (ht) Threshold for high kmer. A high kmer at this or above are considered non-error. 137s lowthresh=3 (lt) Threshold for low kmer. Kmers at this and below are always considered errors. 137s 137s Error correction parameters: 137s ecc=f Set to true to correct errors. NOTE: Tadpole is now preferred for ecc as it does a better job. 137s ecclimit=3 Correct up to this many errors per read. If more are detected, the read will remain unchanged. 137s errorcorrectratio=140 (ecr) Adjacent kmers with a depth ratio of at least this much between will be classified as an error. 137s echighthresh=22 (echt) Threshold for high kmer. A kmer at this or above may be considered non-error. 137s eclowthresh=2 (eclt) Threshold for low kmer. Kmers at this and below are considered errors. 137s eccmaxqual=127 Do not correct bases with quality above this value. 137s aec=f (aggressiveErrorCorrection) Sets more aggressive values of ecr=100, ecclimit=7, echt=16, eclt=3. 137s cec=f (conservativeErrorCorrection) Sets more conservative values of ecr=180, ecclimit=2, echt=30, eclt=1, sl=4, pl=4. 137s meo=f (markErrorsOnly) Marks errors by reducing quality value of suspected errors; does not correct anything. 137s mue=t (markUncorrectableErrors) Marks errors only on uncorrectable reads; requires 'ecc=t'. 137s overlap=f (ecco) Error correct by read overlap. 137s 137s Depth binning parameters: 137s lowbindepth=10 (lbd) Cutoff for low depth bin. 137s highbindepth=80 (hbd) Cutoff for high depth bin. 137s outlow= Pairs in which both reads have a median below lbd go into this file. 137s outhigh= Pairs in which both reads have a median above hbd go into this file. 137s outmid= All other pairs go into this file. 137s 137s Histogram parameters: 137s hist= Specify a file to write the input kmer depth histogram. 137s histout= Specify a file to write the output kmer depth histogram. 137s histcol=3 (histogramcolumns) Number of histogram columns, 2 or 3. 137s pzc=f (printzerocoverage) Print lines in the histogram with zero coverage. 137s histlen=1048576 Max kmer depth displayed in histogram. Also affects statistics displayed, but does not affect normalization. 137s 137s Peak calling parameters: 137s peaks= Write the peaks to this file. Default is stdout. 137s minHeight=2 (h) Ignore peaks shorter than this. 137s minVolume=5 (v) Ignore peaks with less area than this. 137s minWidth=3 (w) Ignore peaks narrower than this. 137s minPeak=2 (minp) Ignore peaks with an X-value below this. 137s maxPeak=BIG (maxp) Ignore peaks with an X-value above this. 137s maxPeakCount=8 (maxpc) Print up to this many peaks (prioritizing height). 137s 137s Java Parameters: 137s -Xmx This will set Java's memory usage, overriding autodetection. 137s -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 137s The max is typically 85% of physical memory. 137s -eoom This flag will cause the process to exit if an 137s out-of-memory exception occurs. Requires Java 8u92+. 137s -da Disable assertions. 137s 137s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 137s 137s bbnorm.sh in=sanger_full_range_original_sanger.fastq qin=33 \ 137s out=out3.fastq outt=outt.fastq hist=hist.plt 137s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 137s java -ea -Xmx4000m -Xms4000m -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 137s Executing jgi.KmerNormalize [bits=32, in=sanger_full_range_original_sanger.fastq, qin=33, out=out3.fastq, outt=outt.fastq, hist=hist.plt] 137s 137s 137s *********** Pass 1 ********** 137s 137s 137s Settings: 137s threads: 4 137s k: 31 137s deterministic: true 137s toss error reads: false 137s passes: 1 137s bits per cell: 16 137s cells: 1495.36M 137s hashes: 3 137s base min quality: 5 137s kmer min prob: 0.5 137s 137s target depth: 400 137s min depth: 3 137s max depth: 500 137s min good kmers: 15 137s depth percentile: 64.8 137s ignore dupe kmers: true 137s fix spikes: false 137s histogram length: 65536 137s print zero cov: false 137s 144s Made hash table: hashes = 3 mem = 2.78 GB cells = 1494.95M used = 0.000% 144s 144s Estimated unique kmers: 4 144s 144s Table creation time: 7.088 seconds. 144s Started output threads. 144s Started output threads. 144s Table read time: 0.005 seconds. 37.79 kb/sec 144s Total reads in: 2 0.000% Kept 144s Total bases in: 188 0.000% Kept 144s Error reads in: 2 100.000% 144s Error type 1: 2 100.000% 144s Error type 2: 0 0.000% 144s Error type 3: 0 0.000% 144s 144s Wrote histogram to hist.plt 144s Total kmers counted: 128 144s Total unique kmer count: 128 144s Includes forward kmers only. 144s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 144s The most accurate value is the greater of the two. 144s 144s Percent unique: 100.00% 144s Depth average: 1.00 (unique kmers) 144s Depth median: 1 (unique kmers) 144s Depth standard deviation: 0.00 (unique kmers) 144s Corrected depth average: 0.00 144s 144s Depth average: 1.00 (all kmers) 144s Depth median: 1 (all kmers) 144s Depth standard deviation: 0.00 (all kmers) 144s 144s Approx. read depth median: 1.47 144s 144s *********** Pass 2 ********** 144s 144s 144s Settings: 144s threads: 4 144s k: 31 144s deterministic: true 144s toss error reads: false 144s passes: 1 144s bits per cell: 16 144s cells: 1495.36M 144s hashes: 3 144s base min quality: 5 144s kmer min prob: 0.5 144s 144s target depth: 100 144s min depth: 5 144s max depth: 100 144s min good kmers: 15 144s depth percentile: 54.0 144s ignore dupe kmers: true 144s fix spikes: false 144s histogram length: 65536 144s 147s Made hash table: hashes = 3 mem = 2.78 GB cells = 1494.95M used = 0.000% 147s 147s Estimated unique kmers: 0 147s 147s Table creation time: 2.636 seconds. 147s Started output threads. 147s Started output threads. 147s Table read time: 0.006 seconds. 0.00 kb/sec 147s Total reads in: 0 NaN% Kept 147s Total bases in: 0 NaN% Kept 147s Error reads in: 0 NaN% 147s Error type 1: 0 NaN% 147s Error type 2: 0 NaN% 147s Error type 3: 0 NaN% 147s Total kmers counted: 0 147s Total unique kmer count: 0 147s Includes forward kmers only. 147s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 147s The most accurate value is the greater of the two. 147s 147s Percent unique: NaN% 147s Depth average: NaN (unique kmers) 147s Depth median: 0 (unique kmers) 147s Depth standard deviation: NaN (unique kmers) 147s Corrected depth average: NaN 147s 147s Depth average: NaN (all kmers) 147s Depth median: 0 (all kmers) 147s Depth standard deviation: 0.00 (all kmers) 147s 147s Approx. read depth median: NaN 147s 147s Removing temp files. 147s 147s Total time: 9.849 seconds. 0.02 kb/sec 148s test -r out3.fastq 148s test -r outt.fastq 148s test -r hist.plt 148s bbnorm.sh in=illumina_full_range_original_illumina.fastq qin=64 \ 148s out=out4.fastq outt=outt2.fastq hist=hist2.plt 148s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 148s java -ea -Xmx4000m -Xms4000m -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 148s Executing jgi.KmerNormalize [bits=32, in=illumina_full_range_original_illumina.fastq, qin=64, out=out4.fastq, outt=outt2.fastq, hist=hist2.plt] 148s 148s 148s *********** Pass 1 ********** 148s 148s 148s Settings: 148s threads: 4 148s k: 31 148s deterministic: true 148s toss error reads: false 148s passes: 1 148s bits per cell: 16 148s cells: 1495.36M 148s hashes: 3 148s base min quality: 5 148s kmer min prob: 0.5 148s 148s target depth: 400 148s min depth: 3 148s max depth: 500 148s min good kmers: 15 148s depth percentile: 64.8 148s ignore dupe kmers: true 148s fix spikes: false 148s histogram length: 65536 148s print zero cov: false 148s 150s Made hash table: hashes = 3 mem = 2.78 GB cells = 1494.95M used = 0.000% 150s 150s Estimated unique kmers: 4 150s 150s Table creation time: 2.536 seconds. 150s Started output threads. 150s Started output threads. 150s Table read time: 0.004 seconds. 29.21 kb/sec 150s Total reads in: 2 0.000% Kept 150s Total bases in: 126 0.000% Kept 150s Error reads in: 2 100.000% 150s Error type 1: 2 100.000% 150s Error type 2: 0 0.000% 150s Error type 3: 0 0.000% 150s 150s Wrote histogram to hist2.plt 150s Total kmers counted: 66 150s Total unique kmer count: 66 150s Includes forward kmers only. 150s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 150s The most accurate value is the greater of the two. 150s 150s Percent unique: 100.00% 150s Depth average: 1.00 (unique kmers) 150s Depth median: 1 (unique kmers) 150s Depth standard deviation: 0.00 (unique kmers) 150s Corrected depth average: 0.00 150s 150s Depth average: 1.00 (all kmers) 150s Depth median: 1 (all kmers) 150s Depth standard deviation: 0.00 (all kmers) 150s 150s Approx. read depth median: 1.91 150s 150s *********** Pass 2 ********** 150s 150s 150s Settings: 150s threads: 4 150s k: 31 150s deterministic: true 150s toss error reads: false 150s passes: 1 150s bits per cell: 16 150s cells: 1495.36M 150s hashes: 3 150s base min quality: 5 150s kmer min prob: 0.5 150s 150s target depth: 100 150s min depth: 5 150s max depth: 100 150s min good kmers: 15 150s depth percentile: 54.0 150s ignore dupe kmers: true 150s fix spikes: false 150s histogram length: 65536 150s 152s Made hash table: hashes = 3 mem = 2.78 GB cells = 1494.95M used = 0.000% 152s 152s Estimated unique kmers: 0 152s 152s Table creation time: 1.392 seconds. 152s Started output threads. 152s Started output threads. 152s Table read time: 0.001 seconds. 0.00 kb/sec 152s Total reads in: 0 NaN% Kept 152s Total bases in: 0 NaN% Kept 152s Error reads in: 0 NaN% 152s Error type 1: 0 NaN% 152s Error type 2: 0 NaN% 152s Error type 3: 0 NaN% 152s Total kmers counted: 0 152s Total unique kmer count: 0 152s Includes forward kmers only. 152s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 152s The most accurate value is the greater of the two. 152s 152s Percent unique: NaN% 152s Depth average: NaN (unique kmers) 152s Depth median: 0 (unique kmers) 152s Depth standard deviation: NaN (unique kmers) 152s Corrected depth average: NaN 152s 152s Depth average: NaN (all kmers) 152s Depth median: 0 (all kmers) 152s Depth standard deviation: 0.00 (all kmers) 152s 152s Approx. read depth median: NaN 152s 152s Removing temp files. 152s 152s Total time: 3.992 seconds. 0.03 kb/sec 152s test -r out4.fastq 152s test -r outt2.fastq 152s test -r hist2.plt 153s autopkgtest [11:18:31]: test run-unit-test: -----------------------] 153s autopkgtest [11:18:31]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 153s run-unit-test PASS 153s autopkgtest [11:18:31]: @@@@@@@@@@@@@@@@@@@@ summary 153s run-unit-test PASS