0s autopkgtest [07:38:17]: starting date and time: 2025-05-02 07:38:17+0000 0s autopkgtest [07:38:17]: git checkout: 9986aa8c Merge branch 'skia/fix_network_interface' into 'ubuntu/production' 0s autopkgtest [07:38:17]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.79401tou/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:openjdk-25 --apt-upgrade bbmap --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=openjdk-25/25~20ea-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu4-ram16-disk100-arm64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-arm64-3.secgroup --name adt-questing-arm64-bbmap-20250502-073817-juju-7f2275-prod-proposed-migration-environment-2-3489025a-b423-4a6a-9176-9c5151c1767e --image adt/ubuntu-questing-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-arm64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 58s autopkgtest [07:39:15]: testbed dpkg architecture: arm64 58s autopkgtest [07:39:15]: testbed apt version: 3.0.0 59s autopkgtest [07:39:16]: @@@@@@@@@@@@@@@@@@@@ test bed setup 59s autopkgtest [07:39:16]: testbed release detected to be: None 59s autopkgtest [07:39:16]: updating testbed package index (apt update) 60s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB] 60s Hit:2 http://ftpmaster.internal/ubuntu questing InRelease 60s Hit:3 http://ftpmaster.internal/ubuntu questing-updates InRelease 60s Hit:4 http://ftpmaster.internal/ubuntu questing-security InRelease 60s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [2202 kB] 60s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [57.4 kB] 60s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [184 kB] 60s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 Packages [227 kB] 60s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 Packages [1472 kB] 60s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/multiverse arm64 Packages [16.5 kB] 60s Fetched 4269 kB in 1s (7274 kB/s) 61s Reading package lists... 61s autopkgtest [07:39:18]: upgrading testbed (apt dist-upgrade and autopurge) 62s Reading package lists... 62s Building dependency tree... 62s Reading state information... 62s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 62s Starting 2 pkgProblemResolver with broken count: 0 62s Done 63s Entering ResolveByKeep 63s 64s Calculating upgrade... 64s The following packages will be upgraded: 64s libperl5.40 perl perl-base perl-modules-5.40 64s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 64s Need to get 10.0 MB of archives. 64s After this operation, 0 B of additional disk space will be used. 64s Get:1 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 libperl5.40 arm64 5.40.1-3 [4780 kB] 64s Get:2 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 perl arm64 5.40.1-3 [262 kB] 64s Get:3 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 perl-base arm64 5.40.1-3 [1786 kB] 64s Get:4 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 perl-modules-5.40 all 5.40.1-3 [3217 kB] 65s Fetched 10.0 MB in 0s (28.8 MB/s) 65s (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 ... 85224 files and directories currently installed.) 65s Preparing to unpack .../libperl5.40_5.40.1-3_arm64.deb ... 65s Unpacking libperl5.40:arm64 (5.40.1-3) over (5.40.1-2ubuntu0.1) ... 65s Preparing to unpack .../perl_5.40.1-3_arm64.deb ... 65s Unpacking perl (5.40.1-3) over (5.40.1-2ubuntu0.1) ... 65s Preparing to unpack .../perl-base_5.40.1-3_arm64.deb ... 65s Unpacking perl-base (5.40.1-3) over (5.40.1-2ubuntu0.1) ... 65s Setting up perl-base (5.40.1-3) ... 65s (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 ... 85224 files and directories currently installed.) 65s Preparing to unpack .../perl-modules-5.40_5.40.1-3_all.deb ... 65s Unpacking perl-modules-5.40 (5.40.1-3) over (5.40.1-2ubuntu0.1) ... 66s Setting up perl-modules-5.40 (5.40.1-3) ... 66s Setting up libperl5.40:arm64 (5.40.1-3) ... 66s Setting up perl (5.40.1-3) ... 66s Processing triggers for man-db (2.13.0-1) ... 66s Processing triggers for libc-bin (2.41-6ubuntu1) ... 66s Reading package lists... 67s Building dependency tree... 67s Reading state information... 67s Starting pkgProblemResolver with broken count: 0 67s Starting 2 pkgProblemResolver with broken count: 0 67s Done 67s Solving dependencies... 68s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 70s autopkgtest [07:39:27]: testbed running kernel: Linux 6.14.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Sun Apr 6 14:37:51 UTC 2025 70s autopkgtest [07:39:27]: @@@@@@@@@@@@@@@@@@@@ apt-source bbmap 72s Get:1 http://ftpmaster.internal/ubuntu questing/universe bbmap 39.20+dfsg-1 (dsc) [2286 B] 72s Get:2 http://ftpmaster.internal/ubuntu questing/universe bbmap 39.20+dfsg-1 (tar) [5748 kB] 72s Get:3 http://ftpmaster.internal/ubuntu questing/universe bbmap 39.20+dfsg-1 (diff) [26.7 kB] 72s gpgv: Signature made Sat Apr 5 12:21:02 2025 UTC 72s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 72s gpgv: issuer "emollier@debian.org" 72s gpgv: Can't check signature: No public key 72s dpkg-source: warning: cannot verify inline signature for ./bbmap_39.20+dfsg-1.dsc: no acceptable signature found 72s autopkgtest [07:39:29]: testing package bbmap version 39.20+dfsg-1 73s autopkgtest [07:39:30]: build not needed 74s autopkgtest [07:39:31]: test run-unit-test: preparing testbed 74s Reading package lists... 74s Building dependency tree... 74s Reading state information... 75s Starting pkgProblemResolver with broken count: 0 75s Starting 2 pkgProblemResolver with broken count: 0 75s Done 75s The following NEW packages will be installed: 75s bbmap bbmap-jni ca-certificates-java default-jre-headless java-common 75s libapache-pom-java libcommons-cli-java libcommons-codec-java 75s libcommons-io-java libcommons-parent-java libjpeg-turbo8 libjpeg8 75s libjs-jquery libjs-sphinxdoc libjs-underscore liblcms2-2 liblog4j1.2-java 75s libmpj-java libpcsclite1 openjdk-21-jre-headless python-biopython-doc 75s 0 upgraded, 21 newly installed, 0 to remove and 0 not upgraded. 75s Need to get 77.2 MB of archives. 75s After this operation, 259 MB of additional disk space will be used. 75s Get:1 http://ftpmaster.internal/ubuntu questing/universe arm64 libcommons-cli-java all 1.6.0-1 [59.9 kB] 75s Get:2 http://ftpmaster.internal/ubuntu questing/universe arm64 libapache-pom-java all 33-2 [5874 B] 75s Get:3 http://ftpmaster.internal/ubuntu questing/universe arm64 libcommons-parent-java all 56-1 [10.7 kB] 75s Get:4 http://ftpmaster.internal/ubuntu questing/universe arm64 libcommons-codec-java all 1.17.1-1 [302 kB] 75s Get:5 http://ftpmaster.internal/ubuntu questing/universe arm64 libcommons-io-java all 2.18.0-1 [477 kB] 75s Get:6 http://ftpmaster.internal/ubuntu questing/universe arm64 liblog4j1.2-java all 1.2.17-11 [439 kB] 75s Get:7 http://ftpmaster.internal/ubuntu questing/universe arm64 libmpj-java all 0.44+dfsg-4 [443 kB] 75s Get:8 http://ftpmaster.internal/ubuntu questing/main arm64 ca-certificates-java all 20240118 [11.6 kB] 75s Get:9 http://ftpmaster.internal/ubuntu questing/main arm64 java-common all 0.76 [6852 B] 75s Get:10 http://ftpmaster.internal/ubuntu questing/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 75s Get:11 http://ftpmaster.internal/ubuntu questing/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 75s Get:12 http://ftpmaster.internal/ubuntu questing/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 75s Get:13 http://ftpmaster.internal/ubuntu questing/main arm64 libpcsclite1 arm64 2.3.1-1 [25.0 kB] 75s Get:14 http://ftpmaster.internal/ubuntu questing/main arm64 openjdk-21-jre-headless arm64 21.0.7~8ea-1 [45.7 MB] 76s Get:15 http://ftpmaster.internal/ubuntu questing/main arm64 default-jre-headless arm64 2:1.21-76 [3176 B] 77s Get:16 http://ftpmaster.internal/ubuntu questing/universe arm64 bbmap all 39.20+dfsg-1 [10.6 MB] 77s Get:17 http://ftpmaster.internal/ubuntu questing/universe arm64 bbmap-jni arm64 39.20+dfsg-1 [28.6 kB] 77s Get:18 http://ftpmaster.internal/ubuntu questing/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 77s Get:19 http://ftpmaster.internal/ubuntu questing/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 77s Get:20 http://ftpmaster.internal/ubuntu questing/main arm64 libjs-sphinxdoc all 8.1.3-5 [31.0 kB] 77s Get:21 http://ftpmaster.internal/ubuntu questing/universe arm64 python-biopython-doc all 1.85+dfsg-2build1 [18.2 MB] 78s Fetched 77.2 MB in 3s (28.3 MB/s) 78s Selecting previously unselected package libcommons-cli-java. 79s (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 ... 85224 files and directories currently installed.) 79s Preparing to unpack .../00-libcommons-cli-java_1.6.0-1_all.deb ... 79s Unpacking libcommons-cli-java (1.6.0-1) ... 79s Selecting previously unselected package libapache-pom-java. 79s Preparing to unpack .../01-libapache-pom-java_33-2_all.deb ... 79s Unpacking libapache-pom-java (33-2) ... 79s Selecting previously unselected package libcommons-parent-java. 79s Preparing to unpack .../02-libcommons-parent-java_56-1_all.deb ... 79s Unpacking libcommons-parent-java (56-1) ... 79s Selecting previously unselected package libcommons-codec-java. 79s Preparing to unpack .../03-libcommons-codec-java_1.17.1-1_all.deb ... 79s Unpacking libcommons-codec-java (1.17.1-1) ... 79s Selecting previously unselected package libcommons-io-java. 79s Preparing to unpack .../04-libcommons-io-java_2.18.0-1_all.deb ... 79s Unpacking libcommons-io-java (2.18.0-1) ... 79s Selecting previously unselected package liblog4j1.2-java. 79s Preparing to unpack .../05-liblog4j1.2-java_1.2.17-11_all.deb ... 79s Unpacking liblog4j1.2-java (1.2.17-11) ... 79s Selecting previously unselected package libmpj-java. 79s Preparing to unpack .../06-libmpj-java_0.44+dfsg-4_all.deb ... 79s Unpacking libmpj-java (0.44+dfsg-4) ... 79s Selecting previously unselected package ca-certificates-java. 79s Preparing to unpack .../07-ca-certificates-java_20240118_all.deb ... 79s Unpacking ca-certificates-java (20240118) ... 79s Selecting previously unselected package java-common. 79s Preparing to unpack .../08-java-common_0.76_all.deb ... 79s Unpacking java-common (0.76) ... 79s Selecting previously unselected package liblcms2-2:arm64. 79s Preparing to unpack .../09-liblcms2-2_2.16-2_arm64.deb ... 79s Unpacking liblcms2-2:arm64 (2.16-2) ... 79s Selecting previously unselected package libjpeg-turbo8:arm64. 79s Preparing to unpack .../10-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ... 79s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 79s Selecting previously unselected package libjpeg8:arm64. 79s Preparing to unpack .../11-libjpeg8_8c-2ubuntu11_arm64.deb ... 79s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 79s Selecting previously unselected package libpcsclite1:arm64. 79s Preparing to unpack .../12-libpcsclite1_2.3.1-1_arm64.deb ... 79s Unpacking libpcsclite1:arm64 (2.3.1-1) ... 79s Selecting previously unselected package openjdk-21-jre-headless:arm64. 79s Preparing to unpack .../13-openjdk-21-jre-headless_21.0.7~8ea-1_arm64.deb ... 79s Unpacking openjdk-21-jre-headless:arm64 (21.0.7~8ea-1) ... 80s Selecting previously unselected package default-jre-headless. 80s Preparing to unpack .../14-default-jre-headless_2%3a1.21-76_arm64.deb ... 80s Unpacking default-jre-headless (2:1.21-76) ... 80s Selecting previously unselected package bbmap. 80s Preparing to unpack .../15-bbmap_39.20+dfsg-1_all.deb ... 80s Unpacking bbmap (39.20+dfsg-1) ... 80s Selecting previously unselected package bbmap-jni. 80s Preparing to unpack .../16-bbmap-jni_39.20+dfsg-1_arm64.deb ... 80s Unpacking bbmap-jni (39.20+dfsg-1) ... 80s Selecting previously unselected package libjs-jquery. 80s Preparing to unpack .../17-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 80s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 80s Selecting previously unselected package libjs-underscore. 80s Preparing to unpack .../18-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 80s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 80s Selecting previously unselected package libjs-sphinxdoc. 80s Preparing to unpack .../19-libjs-sphinxdoc_8.1.3-5_all.deb ... 80s Unpacking libjs-sphinxdoc (8.1.3-5) ... 80s Selecting previously unselected package python-biopython-doc. 80s Preparing to unpack .../20-python-biopython-doc_1.85+dfsg-2build1_all.deb ... 80s Unpacking python-biopython-doc (1.85+dfsg-2build1) ... 81s Setting up liblcms2-2:arm64 (2.16-2) ... 81s Setting up java-common (0.76) ... 81s Setting up libcommons-cli-java (1.6.0-1) ... 81s Setting up liblog4j1.2-java (1.2.17-11) ... 81s Setting up libapache-pom-java (33-2) ... 81s Setting up libpcsclite1:arm64 (2.3.1-1) ... 81s Setting up libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 81s Setting up bbmap-jni (39.20+dfsg-1) ... 81s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 81s Setting up ca-certificates-java (20240118) ... 81s No JRE found. Skipping Java certificates setup. 81s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 81s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 81s Setting up openjdk-21-jre-headless:arm64 (21.0.7~8ea-1) ... 81s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode 81s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 81s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 81s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 81s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 81s Setting up libcommons-parent-java (56-1) ... 81s Setting up libjs-sphinxdoc (8.1.3-5) ... 81s Setting up python-biopython-doc (1.85+dfsg-2build1) ... 81s Setting up libcommons-codec-java (1.17.1-1) ... 81s Setting up libcommons-io-java (2.18.0-1) ... 81s Setting up libmpj-java (0.44+dfsg-4) ... 81s Processing triggers for libc-bin (2.41-6ubuntu1) ... 81s Processing triggers for man-db (2.13.0-1) ... 81s Processing triggers for ca-certificates-java (20240118) ... 82s Adding debian:ACCVRAIZ1.pem 82s Adding debian:AC_RAIZ_FNMT-RCM.pem 82s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 82s Adding debian:ANF_Secure_Server_Root_CA.pem 82s Adding debian:Actalis_Authentication_Root_CA.pem 82s Adding debian:AffirmTrust_Commercial.pem 82s Adding debian:AffirmTrust_Networking.pem 82s Adding debian:AffirmTrust_Premium.pem 82s Adding debian:AffirmTrust_Premium_ECC.pem 82s Adding debian:Amazon_Root_CA_1.pem 82s Adding debian:Amazon_Root_CA_2.pem 82s Adding debian:Amazon_Root_CA_3.pem 82s Adding debian:Amazon_Root_CA_4.pem 82s Adding debian:Atos_TrustedRoot_2011.pem 82s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 82s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 82s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 82s Adding debian:BJCA_Global_Root_CA1.pem 82s Adding debian:BJCA_Global_Root_CA2.pem 82s Adding debian:Baltimore_CyberTrust_Root.pem 82s Adding debian:Buypass_Class_2_Root_CA.pem 82s Adding debian:Buypass_Class_3_Root_CA.pem 82s Adding debian:CA_Disig_Root_R2.pem 82s Adding debian:CFCA_EV_ROOT.pem 82s Adding debian:COMODO_Certification_Authority.pem 82s Adding debian:COMODO_ECC_Certification_Authority.pem 82s Adding debian:COMODO_RSA_Certification_Authority.pem 82s Adding debian:Certainly_Root_E1.pem 82s Adding debian:Certainly_Root_R1.pem 82s Adding debian:Certigna.pem 82s Adding debian:Certigna_Root_CA.pem 82s Adding debian:Certum_EC-384_CA.pem 82s Adding debian:Certum_Trusted_Network_CA.pem 82s Adding debian:Certum_Trusted_Network_CA_2.pem 82s Adding debian:Certum_Trusted_Root_CA.pem 82s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 82s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 82s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 82s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 82s Adding debian:Comodo_AAA_Services_root.pem 82s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 82s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 82s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 82s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 82s Adding debian:DigiCert_Assured_ID_Root_CA.pem 82s Adding debian:DigiCert_Assured_ID_Root_G2.pem 82s Adding debian:DigiCert_Assured_ID_Root_G3.pem 82s Adding debian:DigiCert_Global_Root_CA.pem 82s Adding debian:DigiCert_Global_Root_G2.pem 82s Adding debian:DigiCert_Global_Root_G3.pem 82s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 82s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 82s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 82s Adding debian:DigiCert_Trusted_Root_G4.pem 82s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 82s Adding debian:Entrust_Root_Certification_Authority.pem 82s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 82s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 82s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem 82s Adding debian:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem 82s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 82s Adding debian:GLOBALTRUST_2020.pem 82s Adding debian:GTS_Root_R1.pem 82s Adding debian:GTS_Root_R2.pem 82s Adding debian:GTS_Root_R3.pem 82s Adding debian:GTS_Root_R4.pem 82s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 82s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 82s Adding debian:GlobalSign_Root_CA.pem 82s Adding debian:GlobalSign_Root_CA_-_R3.pem 82s Adding debian:GlobalSign_Root_CA_-_R6.pem 82s Adding debian:GlobalSign_Root_E46.pem 82s Adding debian:GlobalSign_Root_R46.pem 82s Adding debian:Go_Daddy_Class_2_CA.pem 82s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 82s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 82s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 82s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 82s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 82s Adding debian:HiPKI_Root_CA_-_G1.pem 82s Adding debian:Hongkong_Post_Root_CA_3.pem 82s Adding debian:ISRG_Root_X1.pem 82s Adding debian:ISRG_Root_X2.pem 82s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 82s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 82s Adding debian:Izenpe.com.pem 82s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 82s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 82s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 82s Adding debian:NAVER_Global_Root_Certification_Authority.pem 82s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 82s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 82s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 82s Adding debian:QuoVadis_Root_CA_1_G3.pem 82s Adding debian:QuoVadis_Root_CA_2.pem 82s Adding debian:QuoVadis_Root_CA_2_G3.pem 82s Adding debian:QuoVadis_Root_CA_3.pem 82s Adding debian:QuoVadis_Root_CA_3_G3.pem 82s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 82s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 82s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 82s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 82s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 82s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 82s Adding debian:SZAFIR_ROOT_CA2.pem 82s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 82s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 82s Adding debian:SecureSign_RootCA11.pem 82s Adding debian:SecureSign_Root_CA12.pem 82s Adding debian:SecureSign_Root_CA14.pem 82s Adding debian:SecureSign_Root_CA15.pem 82s Adding debian:SecureTrust_CA.pem 82s Adding debian:Secure_Global_CA.pem 82s Adding debian:Security_Communication_ECC_RootCA1.pem 82s Adding debian:Security_Communication_RootCA2.pem 82s Adding debian:Security_Communication_RootCA3.pem 82s Adding debian:Starfield_Class_2_CA.pem 82s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 82s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 82s Adding debian:SwissSign_Gold_CA_-_G2.pem 82s Adding debian:SwissSign_Silver_CA_-_G2.pem 82s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 82s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 82s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 82s Adding debian:TWCA_CYBER_Root_CA.pem 82s Adding debian:TWCA_Global_Root_CA.pem 82s Adding debian:TWCA_Root_Certification_Authority.pem 82s Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem 82s Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem 82s Adding debian:TeliaSonera_Root_CA_v1.pem 82s Adding debian:Telia_Root_CA_v2.pem 82s Adding debian:TrustAsia_Global_Root_CA_G3.pem 82s Adding debian:TrustAsia_Global_Root_CA_G4.pem 82s Adding debian:Trustwave_Global_Certification_Authority.pem 82s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 82s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 82s Adding debian:TunTrust_Root_CA.pem 82s Adding debian:UCA_Extended_Validation_Root.pem 82s Adding debian:UCA_Global_G2_Root.pem 82s Adding debian:USERTrust_ECC_Certification_Authority.pem 82s Adding debian:USERTrust_RSA_Certification_Authority.pem 82s Adding debian:XRamp_Global_CA_Root.pem 82s Adding debian:certSIGN_ROOT_CA.pem 82s Adding debian:certSIGN_Root_CA_G2.pem 82s Adding debian:e-Szigno_Root_CA_2017.pem 82s Adding debian:ePKI_Root_Certification_Authority.pem 82s Adding debian:emSign_ECC_Root_CA_-_C3.pem 82s Adding debian:emSign_ECC_Root_CA_-_G3.pem 82s Adding debian:emSign_Root_CA_-_C1.pem 82s Adding debian:emSign_Root_CA_-_G1.pem 82s Adding debian:vTrus_ECC_Root_CA.pem 82s Adding debian:vTrus_Root_CA.pem 82s done. 82s Setting up bbmap (39.20+dfsg-1) ... 82s Setting up default-jre-headless (2:1.21-76) ... 83s autopkgtest [07:39:40]: test run-unit-test: [----------------------- 83s 83s # bbmap 83s bbmap.sh --version 83s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 83s java -ea -Xmx6150m -Xms6150m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 --version 83s BBTools version 39.20 83s For help, please run the shellscript with no parameters, or look in /docs/. 83s bbmap.sh --help 83s 83s BBMap 83s Written by Brian Bushnell, from Dec. 2010 - present 83s Last modified September 15, 2022 83s 83s Description: Fast and accurate splice-aware read aligner. 83s Please read bbmap/docs/guides/BBMapGuide.txt for more information. 83s 83s To index: bbmap.sh ref= 83s To map: bbmap.sh in= out= 83s To map without writing an index: 83s bbmap.sh ref= in= out= nodisk 83s 83s in=stdin will accept reads from standard in, and out=stdout will write to 83s standard out, but file extensions are still needed to specify the format of the 83s input and output files e.g. in=stdin.fa.gz will read gzipped fasta from 83s standard in; out=stdout.sam.gz will write gzipped sam. 83s 83s Indexing Parameters (required when building the index): 83s nodisk=f Set to true to build index in memory and write nothing 83s to disk except output. 83s ref= Specify the reference sequence. Only do this ONCE, 83s when building the index (unless using 'nodisk'). 83s build=1 If multiple references are indexed in the same directory, 83s each needs a unique numeric ID (unless using 'nodisk'). 83s k=13 Kmer length, range 8-15. Longer is faster but uses 83s more memory. Shorter is more sensitive. 83s If indexing and mapping are done in two steps, K should 83s be specified each time. 83s path=<.> Specify the location to write the index, if you don't 83s want it in the current working directory. 83s usemodulo=f Throw away ~80% of kmers based on remainder modulo a 83s number (reduces RAM by 50% and sensitivity slightly). 83s Should be enabled both when building the index AND 83s when mapping. 83s rebuild=f Force a rebuild of the index (ref= should be set). 83s 83s Input Parameters: 83s build=1 Designate index to use. Corresponds to the number 83s specified when building the index. 83s in= Primary reads input; required parameter. 83s in2= For paired reads in two files. 83s interleaved=auto True forces paired/interleaved input; false forces 83s single-ended mapping. If not specified, interleaved 83s status will be autodetected from read names. 83s fastareadlen=500 Break up FASTA reads longer than this. Max is 500 for 83s BBMap and 6000 for BBMapPacBio. Only works for FASTA 83s input (use 'maxlen' for FASTQ input). The default for 83s bbmap.sh is 500, and for mapPacBio.sh is 6000. 83s unpigz=f Spawn a pigz (parallel gzip) process for faster 83s decompression than using Java. 83s Requires pigz to be installed. 83s touppercase=t (tuc) Convert lowercase letters in reads to upper case 83s (otherwise they will not match the reference). 83s 83s Sampling Parameters: 83s 83s reads=-1 Set to a positive number N to only process the first N 83s reads (or pairs), then quit. -1 means use all reads. 83s samplerate=1 Set to a number from 0 to 1 to randomly select that 83s fraction of reads for mapping. 1 uses all reads. 83s skipreads=0 Set to a number N to skip the first N reads (or pairs), 83s then map the rest. 83s 83s Mapping Parameters: 83s fast=f This flag is a macro which sets other paramters to run 83s faster, at reduced sensitivity. Bad for RNA-seq. 83s slow=f This flag is a macro which sets other paramters to run 83s slower, at greater sensitivity. 'vslow' is even slower. 83s maxindel=16000 Don't look for indels longer than this. Lower is faster. 83s Set to >=100k for RNAseq with long introns like mammals. 83s strictmaxindel=f When enabled, do not allow indels longer than 'maxindel'. 83s By default these are not sought, but may be found anyway. 83s tipsearch=100 Look this far for read-end deletions with anchors 83s shorter than K, using brute force. 83s minid=0.76 Approximate minimum alignment identity to look for. 83s Higher is faster and less sensitive. 83s minhits=1 Minimum number of seed hits required for candidate sites. 83s Higher is faster. 83s local=f Set to true to use local, rather than global, alignments. 83s This will soft-clip ugly ends of poor alignments. 83s perfectmode=f Allow only perfect mappings when set to true (very fast). 83s semiperfectmode=f Allow only perfect and semiperfect (perfect except for 83s N's in the reference) mappings. 83s threads=auto (t) Set to number of threads desired. By default, uses 83s all cores available. 83s ambiguous=best (ambig) Set behavior on ambiguously-mapped reads (with 83s multiple top-scoring mapping locations). 83s best (use the first best site) 83s toss (consider unmapped) 83s random (select one top-scoring site randomly) 83s all (retain all top-scoring sites) 83s samestrandpairs=f (ssp) Specify whether paired reads should map to the 83s same strand or opposite strands. 83s requirecorrectstrand=t (rcs) Forbid pairing of reads without correct strand 83s orientation. Set to false for long-mate-pair libraries. 83s killbadpairs=f (kbp) If a read pair is mapped with an inappropriate 83s insert size or orientation, the read with the lower 83s mapping quality is marked unmapped. 83s pairedonly=f (po) Treat unpaired reads as unmapped. Thus they will 83s be sent to 'outu' but not 'outm'. 83s rcomp=f Reverse complement both reads prior to mapping (for LMP 83s outward-facing libraries). 83s rcompmate=f Reverse complement read2 prior to mapping. 83s pairlen=32000 Set max allowed distance between paired reads. 83s (insert size)=(pairlen)+(read1 length)+(read2 length) 83s rescuedist=1200 Don't try to rescue paired reads if avg. insert size 83s greater than this. Lower is faster. 83s rescuemismatches=32 Maximum mismatches allowed in a rescued read. Lower 83s is faster. 83s averagepairdist=100 (apd) Initial average distance between paired reads. 83s Varies dynamically; does not need to be specified. 83s deterministic=f Run in deterministic mode. In this case it is good 83s to set averagepairdist. BBMap is deterministic 83s without this flag if using single-ended reads, 83s or run singlethreaded. 83s bandwidthratio=0 (bwr) If above zero, restrict alignment band to this 83s fraction of read length. Faster but less accurate. 83s bandwidth=0 (bw) Set the bandwidth directly. 83s fraction of read length. Faster but less accurate. 83s usejni=f (jni) Do alignments faster, in C code. Requires 83s compiling the C code; details are in /jni/README.txt. 83s maxsites2=800 Don't analyze (or print) more than this many alignments 83s per read. 83s ignorefrequentkmers=t (ifk) Discard low-information kmers that occur often. 83s excludefraction=0.03 (ef) Fraction of kmers to ignore. For example, 0.03 83s will ignore the most common 3% of kmers. 83s greedy=t Use a greedy algorithm to discard the least-useful 83s kmers on a per-read basis. 83s kfilter=0 If positive, potential mapping sites must have at 83s least this many consecutive exact matches. 83s 83s 83s Quality and Trimming Parameters: 83s qin=auto Set to 33 or 64 to specify input quality value ASCII 83s offset. 33 is Sanger, 64 is old Solexa. 83s qout=auto Set to 33 or 64 to specify output quality value ASCII 83s offset (only if output format is fastq). 83s qtrim=f Quality-trim ends before mapping. Options are: 83s 'f' (false), 'l' (left), 'r' (right), and 'lr' (both). 83s untrim=f Undo trimming after mapping. Untrimmed bases will be 83s soft-clipped in cigar strings. 83s trimq=6 Trim regions with average quality below this 83s (phred algorithm). 83s mintrimlength=60 (mintl) Don't trim reads to be shorter than this. 83s fakefastaquality=-1 (ffq) Set to a positive number 1-50 to generate fake 83s quality strings for fasta input reads. 83s ignorebadquality=f (ibq) Keep going, rather than crashing, if a read has 83s out-of-range quality values. 83s usequality=t Use quality scores when determining which read kmers 83s to use as seeds. 83s minaveragequality=0 (maq) Do not map reads with average quality below this. 83s maqb=0 If positive, calculate maq from this many initial bases. 83s 83s Output Parameters: 83s out= Write all reads to this file. 83s outu= Write only unmapped reads to this file. Does not 83s include unmapped paired reads with a mapped mate. 83s outm= Write only mapped reads to this file. Includes 83s unmapped paired reads with a mapped mate. 83s mappedonly=f If true, treats 'out' like 'outm'. 83s bamscript= (bs) Write a shell script to that will turn 83s the sam output into a sorted, indexed bam file. 83s ordered=f Set to true to output reads in same order as input. 83s Slower and uses more memory. 83s overwrite=f (ow) Allow process to overwrite existing files. 83s secondary=f Print secondary alignments. 83s sssr=0.95 (secondarysitescoreratio) Print only secondary alignments 83s with score of at least this fraction of primary. 83s ssao=f (secondarysiteasambiguousonly) Only print secondary 83s alignments for ambiguously-mapped reads. 83s maxsites=5 Maximum number of total alignments to print per read. 83s Only relevant when secondary=t. 83s quickmatch=f Generate cigar strings more quickly. 83s trimreaddescriptions=f (trd) Truncate read and ref names at the first whitespace, 83s assuming that the remainder is a comment or description. 83s ziplevel=2 (zl) Compression level for zip or gzip output. 83s pigz=f Spawn a pigz (parallel gzip) process for faster 83s compression than Java. Requires pigz to be installed. 83s machineout=f Set to true to output statistics in machine-friendly 83s 'key=value' format. 83s printunmappedcount=f Print the total number of unmapped reads and bases. 83s If input is paired, the number will be of pairs 83s for which both reads are unmapped. 83s showprogress=0 If positive, print a '.' every X reads. 83s showprogress2=0 If positive, print the number of seconds since the 83s last progress update (instead of a '.'). 83s renamebyinsert=f Renames reads based on their mapped insert size. 83s 83s Bloom-Filtering Parameters (bloomfilter.sh is the standalone version). 83s bloom=f Use a Bloom filter to ignore reads not sharing kmers 83s with the reference. This uses more memory, but speeds 83s mapping when most reads don't match the reference. 83s bloomhashes=2 Number of hash functions. 83s bloomminhits=3 Number of consecutive hits to be considered matched. 83s bloomk=31 Bloom filter kmer length. 83s bloomserial=t Use the serialized Bloom filter for greater loading 83s speed, if available. If not, generate and write one. 83s 83s Post-Filtering Parameters: 83s idfilter=0 Independant of minid; sets exact minimum identity 83s allowed for alignments to be printed. Range 0 to 1. 83s subfilter=-1 Ban alignments with more than this many substitutions. 83s insfilter=-1 Ban alignments with more than this many insertions. 83s delfilter=-1 Ban alignments with more than this many deletions. 83s indelfilter=-1 Ban alignments with more than this many indels. 83s editfilter=-1 Ban alignments with more than this many edits. 83s inslenfilter=-1 Ban alignments with an insertion longer than this. 83s dellenfilter=-1 Ban alignments with a deletion longer than this. 83s nfilter=-1 Ban alignments with more than this many ns. This 83s includes nocall, noref, and off scaffold ends. 83s 83s Sam flags and settings: 83s noheader=f Disable generation of header lines. 83s sam=1.4 Set to 1.4 to write Sam version 1.4 cigar strings, 83s with = and X, or 1.3 to use M. 83s saa=t (secondaryalignmentasterisks) Use asterisks instead of 83s bases for sam secondary alignments. 83s cigar=t Set to 'f' to skip generation of cigar strings (faster). 83s keepnames=f Keep original names of paired reads, rather than 83s ensuring both reads have the same name. 83s intronlen=999999999 Set to a lower number like 10 to change 'D' to 'N' in 83s cigar strings for deletions of at least that length. 83s rgid= Set readgroup ID. All other readgroup fields 83s can be set similarly, with the flag rgXX= 83s If you set a readgroup flag to the word 'filename', 83s e.g. rgid=filename, the input file name will be used. 83s mdtag=f Write MD tags. 83s nhtag=f Write NH tags. 83s xmtag=f Write XM tags (may only work correctly with ambig=all). 83s amtag=f Write AM tags. 83s nmtag=f Write NM tags. 83s xstag=f Set to 'xs=fs', 'xs=ss', or 'xs=us' to write XS tags 83s for RNAseq using firststrand, secondstrand, or 83s unstranded libraries. Needed by Cufflinks. 83s JGI mainly uses 'firststrand'. 83s stoptag=f Write a tag indicating read stop location, prefixed by YS:i: 83s lengthtag=f Write a tag indicating (query,ref) alignment lengths, 83s prefixed by YL:Z: 83s idtag=f Write a tag indicating percent identity, prefixed by YI:f: 83s inserttag=f Write a tag indicating insert size, prefixed by X8:Z: 83s scoretag=f Write a tag indicating BBMap's raw score, prefixed by YR:i: 83s timetag=f Write a tag indicating this read's mapping time, prefixed by X0:i: 83s boundstag=f Write a tag indicating whether either read in the pair 83s goes off the end of the reference, prefixed by XB:Z: 83s notags=f Turn off all optional tags. 83s 83s Histogram and statistics output parameters: 83s scafstats= Statistics on how many reads mapped to which scaffold. 83s refstats= Statistics on how many reads mapped to which reference 83s file; only for BBSplit. 83s sortscafs=t Sort scaffolds or references by read count. 83s bhist= Base composition histogram by position. 83s qhist= Quality histogram by position. 83s aqhist= Histogram of average read quality. 83s bqhist= Quality histogram designed for box plots. 83s lhist= Read length histogram. 83s ihist= Write histogram of insert sizes (for paired reads). 83s ehist= Errors-per-read histogram. 83s qahist= Quality accuracy histogram of error rates versus 83s quality score. 83s indelhist= Indel length histogram. 83s mhist= Histogram of match, sub, del, and ins rates by 83s read location. 83s gchist= Read GC content histogram. 83s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 83s gcpairs=t Use average GC of paired reads. 83s idhist= Histogram of read count versus percent identity. 83s idbins=100 Number idhist bins. Set to 'auto' to use read length. 83s statsfile=stderr Mapping statistics are printed here. 83s 83s Coverage output parameters (these may reduce speed and use more RAM): 83s covstats= Per-scaffold coverage info. 83s rpkm= Per-scaffold RPKM/FPKM counts. 83s covhist= Histogram of # occurrences of each depth level. 83s basecov= Coverage per base location. 83s bincov= Print binned coverage per location (one line per X bases). 83s covbinsize=1000 Set the binsize for binned coverage output. 83s nzo=t Only print scaffolds with nonzero coverage. 83s twocolumn=f Change to true to print only ID and Avg_fold instead of 83s all 6 columns to the 'out=' file. 83s 32bit=f Set to true if you need per-base coverage over 64k. 83s strandedcov=f Track coverage for plus and minus strand independently. 83s startcov=f Only track start positions of reads. 83s secondarycov=t Include coverage of secondary alignments. 83s physcov=f Calculate physical coverage for paired reads. 83s This includes the unsequenced bases. 83s delcoverage=t (delcov) Count bases covered by deletions as covered. 83s True is faster than false. 83s covk=0 If positive, calculate kmer coverage statistics. 83s 83s Java Parameters: 83s -Xmx This will set Java's memory usage, 83s overriding autodetection. 83s -Xmx20g will specify 20 gigs of RAM, and -Xmx800m 83s will specify 800 megs. The max is typically 85% of 83s physical memory. The human genome requires around 24g, 83s or 12g with the 'usemodulo' flag. The index uses 83s roughly 6 bytes per reference base. 83s -eoom This flag will cause the process to exit if an 83s out-of-memory exception occurs. Requires Java 8u92+. 83s -da Disable assertions. 83s 83s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter 83s any problems, or post at: http://seqanswers.com/forums/showthread.php?t=41057 83s 83s bbmap.sh ref=example.fasta 83s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 83s java -ea -Xmx6150m -Xms6150m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta 84s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta] 84s Version 39.20 84s 84s No output file. 84s Writing reference. 84s 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] 84s 84s Set genScaffoldInfo=true 84s Writing chunk 1 84s Set genome to 1 84s 84s Loaded Reference: 0.005 seconds. 84s Loading index for chunk 1-1, build 1 84s No index available; generating from reference genome: /tmp/autopkgtest.tlw5hT/autopkgtest_tmp/ref/index/1/chr1_index_k13_c16_b1.block 84s Indexing threads started for block 0-1 84s Indexing threads finished for block 0-1 85s Generated Index: 0.836 seconds. 85s No reads to process; quitting. 85s 85s Total time: 0.987 seconds. 85s test -d ref 85s bbmap.sh in=misc_dna_as_sanger.fastq out=out.sam 85s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 85s java -ea -Xmx6150m -Xms6150m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 in=misc_dna_as_sanger.fastq out=out.sam 85s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, in=misc_dna_as_sanger.fastq, out=out.sam] 85s Version 39.20 85s 85s Retaining first best site only for ambiguous mappings. 85s Set genome to 1 85s 85s Loaded Reference: 0.025 seconds. 85s Loading index for chunk 1-1, build 1 85s Generated Index: 0.308 seconds. 88s Analyzed Index: 3.010 seconds. 88s Started output stream: 0.024 seconds. 88s Cleared Memory: 0.118 seconds. 88s Processing reads in single-ended mode. 88s Started read stream. 88s Started 4 mapping threads. 88s Detecting finished threads: 0, 1, 2, 3 88s 88s ------------------ Results ------------------ 88s 88s Genome: 1 88s Key Length: 13 88s Max Indel: 16000 88s Minimum Score Ratio: 0.56 88s Mapping Mode: normal 88s Reads Used: 4 (153 bases) 88s 88s Mapping: 0.076 seconds. 88s Reads/sec: 52.82 88s kBases/sec: 2.02 88s 88s 88s Read 1 data: pct reads num reads pct bases num bases 88s 88s mapped: 0.0000% 0 0.0000% 0 88s unambiguous: 0.0000% 0 0.0000% 0 88s ambiguous: 0.0000% 0 0.0000% 0 88s low-Q discards: 25.0000% 1 19.6078% 30 88s 88s perfect best site: 0.0000% 0 0.0000% 0 88s semiperfect site: 0.0000% 0 0.0000% 0 88s 88s Match Rate: NA NA NaN% 0 88s Error Rate: NaN% 0 NaN% 0 88s Sub Rate: NaN% 0 NaN% 0 88s Del Rate: NaN% 0 NaN% 0 88s Ins Rate: NaN% 0 NaN% 0 88s N Rate: NaN% 0 NaN% 0 88s 88s Total time: 3.666 seconds. 88s test -r out.sam 88s bbmap.sh ref=example.fasta in=example.fastq out=out2.sam nodisk 88s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 88s java -ea -Xmx6150m -Xms6150m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta in=example.fastq out=out2.sam nodisk 89s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta, in=example.fastq, out=out2.sam, nodisk] 89s Version 39.20 89s 89s Retaining first best site only for ambiguous mappings. 89s 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] 89s 89s Set genScaffoldInfo=true 89s Set genome to 1 89s 89s Loaded Reference: 0.002 seconds. 89s Loading index for chunk 1-1, build 1 89s Indexing threads started for block 0-1 89s Indexing threads finished for block 0-1 89s Generated Index: 0.204 seconds. 92s Analyzed Index: 3.185 seconds. 92s Started output stream: 0.026 seconds. 92s Cleared Memory: 0.123 seconds. 92s Processing reads in single-ended mode. 92s Started read stream. 92s Started 4 mapping threads. 92s Detecting finished threads: 0, 1, 2, 3 92s 92s ------------------ Results ------------------ 92s 92s Genome: 1 92s Key Length: 13 92s Max Indel: 16000 92s Minimum Score Ratio: 0.56 92s Mapping Mode: normal 92s Reads Used: 3 (75 bases) 92s 92s Mapping: 0.096 seconds. 92s Reads/sec: 31.31 92s kBases/sec: 0.78 92s 92s 92s Read 1 data: pct reads num reads pct bases num bases 92s 92s mapped: 100.0000% 3 100.0000% 75 92s unambiguous: 100.0000% 3 100.0000% 75 92s ambiguous: 0.0000% 0 0.0000% 0 92s low-Q discards: 0.0000% 0 0.0000% 0 92s 92s perfect best site: 100.0000% 3 100.0000% 75 92s semiperfect site: 100.0000% 3 100.0000% 75 92s 92s Match Rate: NA NA 100.0000% 75 92s Error Rate: 0.0000% 0 0.0000% 0 92s Sub Rate: 0.0000% 0 0.0000% 0 92s Del Rate: 0.0000% 0 0.0000% 0 92s Ins Rate: 0.0000% 0 0.0000% 0 92s N Rate: 0.0000% 0 0.0000% 0 92s 92s Total time: 3.785 seconds. 92s test -r out2.sam 92s 92s # bbduk 92s bbduk.sh --version 92s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 92s java -ea -Xmx3075m -Xms3075m -cp /usr/share/java/bbmap.jar jgi.BBDuk --version 92s BBTools version 39.20 92s For help, please run the shellscript with no parameters, or look in /docs/. 93s bbduk.sh --help 93s 93s Written by Brian Bushnell 93s Last modified November 18, 2024 93s 93s Description: Compares reads to the kmers in a reference dataset, optionally 93s allowing an edit distance. Splits the reads into two outputs - those that 93s match the reference, and those that don't. Can also trim (remove) the matching 93s parts of the reads rather than binning the reads. 93s Please read bbmap/docs/guides/BBDukGuide.txt for more information. 93s 93s Usage: bbduk.sh in= out= ref= 93s 93s Input may be stdin or a fasta or fastq file, compressed or uncompressed. 93s If you pipe via stdin/stdout, please include the file type; e.g. for gzipped 93s fasta input, set in=stdin.fa.gz 93s 93s Input parameters: 93s in= Main input. in=stdin.fq will pipe from stdin. 93s in2= Input for 2nd read of pairs in a different file. 93s ref= Comma-delimited list of reference files. 93s In addition to filenames, you may also use the keywords: 93s adapters, artifacts, phix, lambda, pjet, mtst, kapa 93s literal= Comma-delimited list of literal reference sequences. 93s Polymers are also allowed with the 'poly' prefix; 93s for example, 'literal=ATGGT,polyGC' will add both ATGGT 93s and GCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGC - 32+ of them, 93s enough replicates to ensure that all kmers are present. 93s touppercase=f (tuc) Change all bases upper-case. 93s interleaved=auto (int) t/f overrides interleaved autodetection. 93s Must be set mainually when streaming fastq input. 93s qin=auto Input quality offset: 33 (Sanger), 64, or auto. 93s reads=-1 If positive, quit after processing X reads or pairs. 93s copyundefined=f (cu) Process non-AGCT IUPAC reference bases by making all 93s possible unambiguous copies. Intended for short motifs 93s or adapter barcodes, as time/memory use is exponential. 93s samplerate=1 Set lower to only process a fraction of input reads. 93s samref= Optional reference fasta for processing sam files. 93s 93s Output parameters: 93s out= (outnonmatch) Write reads here that do not contain 93s kmers matching the database. 'out=stdout.fq' will pipe 93s to standard out. 93s out2= (outnonmatch2) Use this to write 2nd read of pairs to a 93s different file. 93s outm= (outmatch) Write reads here that fail filters. In default 93s kfilter mode, this means any read with a matching kmer. 93s In any mode, it also includes reads that fail filters such 93s as minlength, mingc, maxgc, entropy, etc. In other words, 93s it includes all reads that do not go to 'out'. 93s outm2= (outmatch2) Use this to write 2nd read of pairs to a 93s different file. 93s outs= (outsingle) Use this to write singleton reads whose mate 93s was trimmed shorter than minlen. 93s stats= Write statistics about which contamininants were detected. 93s refstats= Write statistics on a per-reference-file basis. 93s rpkm= Write RPKM for each reference sequence (for RNA-seq). 93s dump= Dump kmer tables to a file, in fasta format. 93s duk= Write statistics in duk's format. *DEPRECATED* 93s nzo=t Only write statistics about ref sequences with nonzero hits. 93s overwrite=t (ow) Grant permission to overwrite files. 93s showspeed=t (ss) 'f' suppresses display of processing speed. 93s ziplevel=2 (zl) Compression level; 1 (min) through 9 (max). 93s fastawrap=70 Length of lines in fasta output. 93s qout=auto Output quality offset: 33 (Sanger), 64, or auto. 93s statscolumns=3 (cols) Number of columns for stats output, 3 or 5. 93s 5 includes base counts. 93s rename=f Rename reads to indicate which sequences they matched. 93s refnames=f Use names of reference files rather than scaffold IDs. 93s trd=f Truncate read and ref names at the first whitespace. 93s ordered=f Set to true to output reads in same order as input. 93s maxbasesout=-1 If positive, quit after writing approximately this many 93s bases to out (outu/outnonmatch). 93s maxbasesoutm=-1 If positive, quit after writing approximately this many 93s bases to outm (outmatch). 93s json=f Print to screen in json format. 93s 93s Histogram output parameters: 93s bhist= Base composition histogram by position. 93s qhist= Quality histogram by position. 93s qchist= Count of bases with each quality value. 93s aqhist= Histogram of average read quality. 93s bqhist= Quality histogram designed for box plots. 93s lhist= Read length histogram. 93s phist= Polymer length histogram. 93s gchist= Read GC content histogram. 93s enthist= Read entropy histogram. 93s ihist= Insert size histogram, for paired reads in mapped sam. 93s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 93s maxhistlen=6000 Set an upper bound for histogram lengths; higher uses 93s more memory. The default is 6000 for some histograms 93s and 80000 for others. 93s 93s Histograms for mapped sam/bam files only: 93s histbefore=t Calculate histograms from reads before processing. 93s ehist= Errors-per-read histogram. 93s qahist= Quality accuracy histogram of error rates versus quality 93s score. 93s indelhist= Indel length histogram. 93s mhist= Histogram of match, sub, del, and ins rates by position. 93s idhist= Histogram of read count versus percent identity. 93s idbins=100 Number idhist bins. Set to 'auto' to use read length. 93s varfile= Ignore substitution errors listed in this file when 93s calculating error rates. Can be generated with 93s CallVariants. 93s vcf= Ignore substitution errors listed in this VCF file 93s when calculating error rates. 93s ignorevcfindels=t Also ignore indels listed in the VCF. 93s 93s Processing parameters: 93s k=27 Kmer length used for finding contaminants. Contaminants 93s shorter than k will not be found. k must be at least 1. 93s rcomp=t Look for reverse-complements of kmers in addition to 93s forward kmers. 93s maskmiddle=t (mm) Treat the middle base of a kmer as a wildcard, to 93s increase sensitivity in the presence of errors. This may 93s also be set to a number, e.g. mm=3, to mask that many bp. 93s The default mm=t corresponds to mm=1 for odd-length kmers 93s and mm=2 for even-length kmers (as of v39.04), while 93s mm=f is always equivalent to mm=0. 93s minkmerhits=1 (mkh) Reads need at least this many matching kmers 93s to be considered as matching the reference. 93s minkmerfraction=0.0 (mkf) A reads needs at least this fraction of its total 93s kmers to hit a ref, in order to be considered a match. 93s If this and minkmerhits are set, the greater is used. 93s mincovfraction=0.0 (mcf) A reads needs at least this fraction of its total 93s bases to be covered by ref kmers to be considered a match. 93s If specified, mcf overrides mkh and mkf. 93s hammingdistance=0 (hdist) Maximum Hamming distance for ref kmers (subs only). 93s Memory use is proportional to (3*K)^hdist. 93s qhdist=0 Hamming distance for query kmers; impacts speed, not memory. 93s editdistance=0 (edist) Maximum edit distance from ref kmers (subs 93s and indels). Memory use is proportional to (8*K)^edist. 93s hammingdistance2=0 (hdist2) Sets hdist for short kmers, when using mink. 93s qhdist2=0 Sets qhdist for short kmers, when using mink. 93s editdistance2=0 (edist2) Sets edist for short kmers, when using mink. 93s forbidn=f (fn) Forbids matching of read kmers containing N. 93s By default, these will match a reference 'A' if 93s hdist>0 or edist>0, to increase sensitivity. 93s removeifeitherbad=t (rieb) Paired reads get sent to 'outmatch' if either is 93s match (or either is trimmed shorter than minlen). 93s Set to false to require both. 93s trimfailures=f Instead of discarding failed reads, trim them to 1bp. 93s This makes the statistics a bit odd. 93s findbestmatch=f (fbm) If multiple matches, associate read with sequence 93s sharing most kmers. Reduces speed. 93s skipr1=f Don't do kmer-based operations on read 1. 93s skipr2=f Don't do kmer-based operations on read 2. 93s ecco=f For overlapping paired reads only. Performs error- 93s correction with BBMerge prior to kmer operations. 93s recalibrate=f (recal) Recalibrate quality scores. Requires calibration 93s matrices generated by CalcTrueQuality. 93s sam= If recalibration is desired, and matrices have not already 93s been generated, BBDuk will create them from the sam file. 93s amino=f Run in amino acid mode. Some features have not been 93s tested, but kmer-matching works fine. Maximum k is 12. 93s 93s Speed and Memory parameters: 93s threads=auto (t) Set number of threads to use; default is number of 93s logical processors. 93s prealloc=f Preallocate memory in table. Allows faster table loading 93s and more efficient memory usage, for a large reference. 93s monitor=f Kill this process if it crashes. monitor=600,0.01 would 93s kill after 600 seconds under 1% usage. 93s minrskip=1 (mns) Force minimal skip interval when indexing reference 93s kmers. 1 means use all, 2 means use every other kmer, etc. 93s maxrskip=1 (mxs) Restrict maximal skip interval when indexing 93s reference kmers. Normally all are used for scaffolds<100kb, 93s but with longer scaffolds, up to maxrskip-1 are skipped. 93s rskip= Set both minrskip and maxrskip to the same value. 93s If not set, rskip will vary based on sequence length. 93s qskip=1 Skip query kmers to increase speed. 1 means use all. 93s speed=0 Ignore this fraction of kmer space (0-15 out of 16) in both 93s reads and reference. Increases speed and reduces memory. 93s Note: Do not use more than one of 'speed', 'qskip', and 'rskip'. 93s 93s Trimming/Filtering/Masking parameters: 93s Note - if ktrim, kmask, and ksplit are unset, the default behavior is kfilter. 93s All kmer processing modes are mutually exclusive. 93s Reads only get sent to 'outm' purely based on kmer matches in kfilter mode. 93s 93s ktrim=f Trim reads to remove bases matching reference kmers, plus 93s all bases to the left or right. 93s Values: 93s f (don't trim), 93s r (trim to the right), 93s l (trim to the left) 93s ktrimtips=0 Set this to a positive number to perform ktrim on both 93s ends, examining only the outermost X bases. 93s kmask= Replace bases matching ref kmers with another symbol. 93s Allows any non-whitespace character, and processes short 93s kmers on both ends if mink is set. 'kmask=lc' will 93s convert masked bases to lowercase. 93s maskfullycovered=f (mfc) Only mask bases that are fully covered by kmers. 93s ksplit=f For single-ended reads only. Reads will be split into 93s pairs around the kmer. If the kmer is at the end of the 93s read, it will be trimmed instead. Singletons will go to 93s out, and pairs will go to outm. Do not use ksplit with 93s other operations such as quality-trimming or filtering. 93s mink=0 Look for shorter kmers at read tips down to this length, 93s when k-trimming or masking. 0 means disabled. Enabling 93s this will disable maskmiddle. 93s qtrim=f Trim read ends to remove bases with quality below trimq. 93s Performed AFTER looking for kmers. Values: 93s rl (trim both ends), 93s f (neither end), 93s r (right end only), 93s l (left end only), 93s w (sliding window). 93s trimq=6 Regions with average quality BELOW this will be trimmed, 93s if qtrim is set to something other than f. Can be a 93s floating-point number like 7.3. 93s quantize Bin quality scores to reduce file size. quantize=2 will 93s eliminate all odd quality scores, while quantize=0,10,37 93s will only allow qualty scores of 0, 10, or 37. 93s trimclip=f Trim soft-clipped bases from sam files. 93s minlength=10 (ml) Reads shorter than this after trimming will be 93s discarded. Pairs will be discarded if both are shorter. 93s mlf=0 (minlengthfraction) Reads shorter than this fraction of 93s original length after trimming will be discarded. 93s maxlength= Reads longer than this after trimming will be discarded. 93s minavgquality=0 (maq) Reads with average quality (after trimming) below 93s this will be discarded. 93s maqb=0 If positive, calculate maq from this many initial bases. 93s minbasequality=0 (mbq) Reads with any base below this quality (after 93s trimming) will be discarded. 93s maxns=-1 If non-negative, reads with more Ns than this 93s (after trimming) will be discarded. 93s mcb=0 (minconsecutivebases) Discard reads without at least 93s this many consecutive called bases. 93s ottm=f (outputtrimmedtomatch) Output reads trimmed to shorter 93s than minlength to outm rather than discarding. 93s tp=0 (trimpad) Trim this much extra around matching kmers. 93s tbo=f (trimbyoverlap) Trim adapters based on where paired 93s reads overlap. 93s strictoverlap=t Adjust sensitivity for trimbyoverlap mode. 93s minoverlap=14 Require this many bases of overlap for detection. 93s mininsert=40 Require insert size of at least this for overlap. 93s Should be reduced to 16 for small RNA sequencing. 93s tpe=f (trimpairsevenly) When kmer right-trimming, trim both 93s reads to the minimum length of either. 93s forcetrimleft=0 (ftl) If positive, trim bases to the left of this position 93s (exclusive, 0-based). 93s forcetrimright=0 (ftr) If positive, trim bases to the right of this position 93s (exclusive, 0-based). 93s forcetrimright2=0 (ftr2) If positive, trim this many bases on the right end. 93s forcetrimmod=0 (ftm) If positive, right-trim length to be equal to zero, 93s modulo this number. 93s restrictleft=0 If positive, only look for kmer matches in the 93s leftmost X bases. 93s restrictright=0 If positive, only look for kmer matches in the 93s rightmost X bases. 93s NOTE: restrictleft and restrictright are mutually exclusive. If trimming 93s both ends is desired, use ktrimtips. 93s mingc=0 Discard reads with GC content below this. 93s maxgc=1 Discard reads with GC content above this. 93s gcpairs=t Use average GC of paired reads. 93s Also affects gchist. 93s tossjunk=f Discard reads with invalid characters as bases. 93s swift=f Trim Swift sequences: Trailing C/T/N R1, leading G/A/N R2. 93s 93s Header-parsing parameters - these require Illumina headers: 93s chastityfilter=f (cf) Discard reads with id containing ' 1:Y:' or ' 2:Y:'. 93s barcodefilter=f Remove reads with unexpected barcodes if barcodes is set, 93s or barcodes containing 'N' otherwise. A barcode must be 93s the last part of the read header. Values: 93s t: Remove reads with bad barcodes. 93s f: Ignore barcodes. 93s crash: Crash upon encountering bad barcodes. 93s barcodes= Comma-delimited list of barcodes or files of barcodes. 93s xmin=-1 If positive, discard reads with a lesser X coordinate. 93s ymin=-1 If positive, discard reads with a lesser Y coordinate. 93s xmax=-1 If positive, discard reads with a greater X coordinate. 93s ymax=-1 If positive, discard reads with a greater Y coordinate. 93s 93s Polymer trimming: 93s trimpolya=0 If greater than 0, trim poly-A or poly-T tails of 93s at least this length on either end of reads. 93s trimpolygleft=0 If greater than 0, trim poly-G prefixes of at least this 93s length on the left end of reads. Does not trim poly-C. 93s trimpolygright=0 If greater than 0, trim poly-G tails of at least this 93s length on the right end of reads. Does not trim poly-C. 93s trimpolyg=0 This sets both left and right at once. 93s filterpolyg=0 If greater than 0, remove reads with a poly-G prefix of 93s at least this length (on the left). 93s Note: there are also equivalent poly-C flags. 93s 93s Polymer tracking: 93s pratio=base,base 'pratio=G,C' will print the ratio of G to C polymers. 93s plen=20 Length of homopolymers to count. 93s 93s Entropy/Complexity parameters: 93s entropy=-1 Set between 0 and 1 to filter reads with entropy below 93s that value. Higher is more stringent. 93s entropywindow=50 Calculate entropy using a sliding window of this length. 93s entropyk=5 Calculate entropy using kmers of this length. 93s minbasefrequency=0 Discard reads with a minimum base frequency below this. 93s entropytrim=f Values: 93s f: (false) Do not entropy-trim. 93s r: (right) Trim low entropy on the right end only. 93s l: (left) Trim low entropy on the left end only. 93s rl: (both) Trim low entropy on both ends. 93s entropymask=f Values: 93s f: (filter) Discard low-entropy sequences. 93s t: (true) Mask low-entropy parts of sequences with N. 93s lc: Change low-entropy parts of sequences to lowercase. 93s entropymark=f Mark each base with its entropy value. This is on a scale 93s of 0-41 and is reported as quality scores, so the output 93s should be fastq or fasta+qual. 93s NOTE: If set, entropytrim overrides entropymask. 93s 93s Cardinality estimation: 93s cardinality=f (loglog) Count unique kmers using the LogLog algorithm. 93s cardinalityout=f (loglogout) Count unique kmers in output reads. 93s loglogk=31 Use this kmer length for counting. 93s loglogbuckets=2048 Use this many buckets for counting. 93s khist= Kmer frequency histogram; plots number of kmers versus 93s kmer depth. This is approximate. 93s khistout= Kmer frequency histogram for output reads. 93s 93s Side Channel: 93s sideout= Output for aligned reads. 93s sideref=phix Reference for side-channel alignment; must be a single 93s sequence and virtually repeat-free at selected k. 93s sidek1=17 Kmer length for seeding alignment to reference. 93s sidek2=13 Kmer length for seeding alignment of unaligned reads 93s with an aligned mate. 93s sideminid1=0.66 Minimum identity to accept individual alignments. 93s sideminid2=0.58 Minimum identity for aligning reads with aligned mates. 93s sidemm1=1 Middle mask length for sidek1. 93s sidemm2=1 Middle mask length for sidek2. 93s Note: The side channel is a special additional output that allows alignment 93s to a secondary reference while also doing trimming. Alignment does not affect 93s whether reads go to the normal outputs (out, outm). The main purpose is to 93s simplify pipelines that need trimmed, aligned phiX reads for recalibration. 93s 93s 93s Java Parameters: 93s 93s -Xmx This will set Java's memory usage, overriding autodetection. 93s -Xmx20g will 93s specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 93s The max is typically 85% of physical memory. 93s -eoom This flag will cause the process to exit if an 93s out-of-memory exception occurs. Requires Java 8u92+. 93s -da Disable assertions. 93s 93s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 93s 93s bbduk.sh in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq \ 93s qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 93s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 93s java -ea -Xmx3075m -Xms3075m -cp /usr/share/java/bbmap.jar jgi.BBDuk in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 93s Executing jgi.BBDuk [in1=misc_dna_as_illumina.fastq, in2=misc_rna_as_illumina.fastq, qtrim=rl, trimq=15, minlen=75, out=out.fastq.gz] 93s Version 39.20 93s 93s Changed from ASCII-33 to ASCII-64 on input quality X (Q55) for base A at lines 1 and 3, position 24 while prescanning. 93s Changed from ASCII-33 to ASCII-64 on input quality X (Q55) for base A at lines 1 and 3, position 24 while prescanning. 93s Allocating kmer table: 0.014 seconds. 93s Initial: 93s Memory: max=3225m, total=3225m, free=3194m, used=31m 93s 93s Input is being processed as paired 93s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 93s Started output streams: 0.020 seconds. 93s Processing time: 0.004 seconds. 93s 93s Input: 8 reads 306 bases. 93s QTrimmed: 0 reads (0.00%) 0 bases (0.00%) 93s Total Removed: 8 reads (100.00%) 306 bases (100.00%) 93s Result: 0 reads (0.00%) 0 bases (0.00%) 93s 93s Time: 0.025 seconds. 93s Reads Processed: 8 0.31k reads/sec 93s Bases Processed: 306 0.01m bases/sec 93s test -r out.fastq.gz 93s 93s # bbnorm 93s bbnorm.sh --version 93s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 93s java -ea -Xmx6150m -Xms6150m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 --version 93s BBTools version 39.20 93s For help, please run the shellscript with no parameters, or look in /docs/. 93s bbnorm.sh --help 93s 93s Written by Brian Bushnell 93s Last modified October 19, 2017 93s 93s Description: Normalizes read depth based on kmer counts. 93s Can also error-correct, bin reads by kmer depth, and generate a kmer depth histogram. 93s However, Tadpole has superior error-correction to BBNorm. 93s Please read bbmap/docs/guides/BBNormGuide.txt for more information. 93s 93s Usage: bbnorm.sh in= out= outt= hist= 93s 93s Input parameters: 93s in=null Primary input. Use in2 for paired reads in a second file 93s in2=null Second input file for paired reads in two files 93s extra=null Additional files to use for input (generating hash table) but not for output 93s fastareadlen=2^31 Break up FASTA reads longer than this. Can be useful when processing scaffolded genomes 93s tablereads=-1 Use at most this many reads when building the hashtable (-1 means all) 93s kmersample=1 Process every nth kmer, and skip the rest 93s readsample=1 Process every nth read, and skip the rest 93s interleaved=auto May be set to true or false to force the input read file to ovverride autodetection of the input file as paired interleaved. 93s qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto. 93s 93s Output parameters: 93s out= File for normalized or corrected reads. Use out2 for paired reads in a second file 93s outt= (outtoss) File for reads that were excluded from primary output 93s reads=-1 Only process this number of reads, then quit (-1 means all) 93s sampleoutput=t Use sampling on output as well as input (not used if sample rates are 1) 93s keepall=f Set to true to keep all reads (e.g. if you just want error correction). 93s zerobin=f Set to true if you want kmers with a count of 0 to go in the 0 bin instead of the 1 bin in histograms. 93s Default is false, to prevent confusion about how there can be 0-count kmers. 93s The reason is that based on the 'minq' and 'minprob' settings, some kmers may be excluded from the bloom filter. 93s tmpdir= This will specify a directory for temp files (only needed for multipass runs). If null, they will be written to the output directory. 93s usetempdir=t Allows enabling/disabling of temporary directory; if disabled, temp files will be written to the output directory. 93s qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input). 93s rename=f Rename reads based on their kmer depth. 93s 93s Hashing parameters: 93s k=31 Kmer length (values under 32 are most efficient, but arbitrarily high values are supported) 93s bits=32 Bits per cell in bloom filter; must be 2, 4, 8, 16, or 32. Maximum kmer depth recorded is 2^cbits. Automatically reduced to 16 in 2-pass. 93s Large values decrease accuracy for a fixed amount of memory, so use the lowest number you can that will still capture highest-depth kmers. 93s hashes=3 Number of times each kmer is hashed and stored. Higher is slower. 93s Higher is MORE accurate if there is enough memory, and LESS accurate if there is not enough memory. 93s prefilter=f True is slower, but generally more accurate; filters out low-depth kmers from the main hashtable. The prefilter is more memory-efficient because it uses 2-bit cells. 93s prehashes=2 Number of hashes for prefilter. 93s prefilterbits=2 (pbits) Bits per cell in prefilter. 93s prefiltersize=0.35 Fraction of memory to allocate to prefilter. 93s buildpasses=1 More passes can sometimes increase accuracy by iteratively removing low-depth kmers 93s minq=6 Ignore kmers containing bases with quality below this 93s minprob=0.5 Ignore kmers with overall probability of correctness below this 93s threads=auto (t) Spawn exactly X hashing threads (default is number of logical processors). Total active threads may exceed X due to I/O threads. 93s rdk=t (removeduplicatekmers) When true, a kmer's count will only be incremented once per read pair, even if that kmer occurs more than once. 93s 93s Normalization parameters: 93s fixspikes=f (fs) Do a slower, high-precision bloom filter lookup of kmers that appear to have an abnormally high depth due to collisions. 93s target=100 (tgt) Target normalization depth. NOTE: All depth parameters control kmer depth, not read depth. 93s For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1)) 93s maxdepth=-1 (max) Reads will not be downsampled when below this depth, even if they are above the target depth. 93s mindepth=5 (min) Kmers with depth below this number will not be included when calculating the depth of a read. 93s minkmers=15 (mgkpr) Reads must have at least this many kmers over min depth to be retained. Aka 'mingoodkmersperread'. 93s percentile=54.0 (dp) Read depth is by default inferred from the 54th percentile of kmer depth, but this may be changed to any number 1-100. 93s uselowerdepth=t (uld) For pairs, use the depth of the lower read as the depth proxy. 93s deterministic=t (dr) Generate random numbers deterministically to ensure identical output between multiple runs. May decrease speed with a huge number of threads. 93s passes=2 (p) 1 pass is the basic mode. 2 passes (default) allows greater accuracy, error detection, better contol of output depth. 93s 93s Error detection parameters: 93s hdp=90.0 (highdepthpercentile) Position in sorted kmer depth array used as proxy of a read's high kmer depth. 93s ldp=25.0 (lowdepthpercentile) Position in sorted kmer depth array used as proxy of a read's low kmer depth. 93s tossbadreads=f (tbr) Throw away reads detected as containing errors. 93s requirebothbad=f (rbb) Only toss bad pairs if both reads are bad. 93s errordetectratio=125 (edr) Reads with a ratio of at least this much between their high and low depth kmers will be classified as error reads. 93s highthresh=12 (ht) Threshold for high kmer. A high kmer at this or above are considered non-error. 93s lowthresh=3 (lt) Threshold for low kmer. Kmers at this and below are always considered errors. 93s 93s Error correction parameters: 93s ecc=f Set to true to correct errors. NOTE: Tadpole is now preferred for ecc as it does a better job. 93s ecclimit=3 Correct up to this many errors per read. If more are detected, the read will remain unchanged. 93s errorcorrectratio=140 (ecr) Adjacent kmers with a depth ratio of at least this much between will be classified as an error. 93s echighthresh=22 (echt) Threshold for high kmer. A kmer at this or above may be considered non-error. 93s eclowthresh=2 (eclt) Threshold for low kmer. Kmers at this and below are considered errors. 93s eccmaxqual=127 Do not correct bases with quality above this value. 93s aec=f (aggressiveErrorCorrection) Sets more aggressive values of ecr=100, ecclimit=7, echt=16, eclt=3. 93s cec=f (conservativeErrorCorrection) Sets more conservative values of ecr=180, ecclimit=2, echt=30, eclt=1, sl=4, pl=4. 93s meo=f (markErrorsOnly) Marks errors by reducing quality value of suspected errors; does not correct anything. 93s mue=t (markUncorrectableErrors) Marks errors only on uncorrectable reads; requires 'ecc=t'. 93s overlap=f (ecco) Error correct by read overlap. 93s 93s Depth binning parameters: 93s lowbindepth=10 (lbd) Cutoff for low depth bin. 93s highbindepth=80 (hbd) Cutoff for high depth bin. 93s outlow= Pairs in which both reads have a median below lbd go into this file. 93s outhigh= Pairs in which both reads have a median above hbd go into this file. 93s outmid= All other pairs go into this file. 93s 93s Histogram parameters: 93s hist= Specify a file to write the input kmer depth histogram. 93s histout= Specify a file to write the output kmer depth histogram. 93s histcol=3 (histogramcolumns) Number of histogram columns, 2 or 3. 93s pzc=f (printzerocoverage) Print lines in the histogram with zero coverage. 93s histlen=1048576 Max kmer depth displayed in histogram. Also affects statistics displayed, but does not affect normalization. 93s 93s Peak calling parameters: 93s peaks= Write the peaks to this file. Default is stdout. 93s minHeight=2 (h) Ignore peaks shorter than this. 93s minVolume=5 (v) Ignore peaks with less area than this. 93s minWidth=3 (w) Ignore peaks narrower than this. 93s minPeak=2 (minp) Ignore peaks with an X-value below this. 93s maxPeak=BIG (maxp) Ignore peaks with an X-value above this. 93s maxPeakCount=8 (maxpc) Print up to this many peaks (prioritizing height). 93s 93s Java Parameters: 93s -Xmx This will set Java's memory usage, overriding autodetection. 93s -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 93s The max is typically 85% of physical memory. 93s -eoom This flag will cause the process to exit if an 93s out-of-memory exception occurs. Requires Java 8u92+. 93s -da Disable assertions. 93s 93s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 93s 93s bbnorm.sh in=sanger_full_range_original_sanger.fastq qin=33 \ 93s out=out3.fastq outt=outt.fastq hist=hist.plt 93s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 93s java -ea -Xmx6150m -Xms6150m -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 93s Executing jgi.KmerNormalize [bits=32, in=sanger_full_range_original_sanger.fastq, qin=33, out=out3.fastq, outt=outt.fastq, hist=hist.plt] 93s 93s 93s *********** Pass 1 ********** 93s 93s 93s Settings: 93s threads: 4 93s k: 31 93s deterministic: true 93s toss error reads: false 93s passes: 1 93s bits per cell: 16 93s cells: 2318.99M 93s hashes: 3 93s base min quality: 5 93s kmer min prob: 0.5 93s 93s target depth: 400 93s min depth: 3 93s max depth: 500 93s min good kmers: 15 93s depth percentile: 64.8 93s ignore dupe kmers: true 93s fix spikes: false 93s histogram length: 65536 93s print zero cov: false 93s 95s Made hash table: hashes = 3 mem = 4.32 GB cells = 2318.43M used = 0.000% 95s 95s Estimated unique kmers: 4 95s 95s Table creation time: 1.367 seconds. 95s Started output threads. 95s Started output threads. 95s Table read time: 0.006 seconds. 33.75 kb/sec 95s Total reads in: 2 0.000% Kept 95s Total bases in: 188 0.000% Kept 95s Error reads in: 2 100.000% 95s Error type 1: 2 100.000% 95s Error type 2: 0 0.000% 95s Error type 3: 0 0.000% 95s 95s Wrote histogram to hist.plt 95s Total kmers counted: 128 95s Total unique kmer count: 128 95s Includes forward kmers only. 95s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 95s The most accurate value is the greater of the two. 95s 95s Percent unique: 100.00% 95s Depth average: 1.00 (unique kmers) 95s Depth median: 1 (unique kmers) 95s Depth standard deviation: 0.00 (unique kmers) 95s Corrected depth average: 0.00 95s 95s Depth average: 1.00 (all kmers) 95s Depth median: 1 (all kmers) 95s Depth standard deviation: 0.00 (all kmers) 95s 95s Approx. read depth median: 1.47 95s 95s *********** Pass 2 ********** 95s 95s 95s Settings: 95s threads: 4 95s k: 31 95s deterministic: true 95s toss error reads: false 95s passes: 1 95s bits per cell: 16 95s cells: 2318.99M 95s hashes: 3 95s base min quality: 5 95s kmer min prob: 0.5 95s 95s target depth: 100 95s min depth: 5 95s max depth: 100 95s min good kmers: 15 95s depth percentile: 54.0 95s ignore dupe kmers: true 95s fix spikes: false 95s histogram length: 65536 95s 95s Made hash table: hashes = 3 mem = 4.32 GB cells = 2318.43M used = 0.000% 95s 95s Estimated unique kmers: 0 95s 95s Table creation time: 0.574 seconds. 95s Started output threads. 95s Started output threads. 95s Table read time: 0.001 seconds. 0.00 kb/sec 95s Total reads in: 0 NaN% Kept 95s Total bases in: 0 NaN% Kept 95s Error reads in: 0 NaN% 95s Error type 1: 0 NaN% 95s Error type 2: 0 NaN% 95s Error type 3: 0 NaN% 95s Total kmers counted: 0 95s Total unique kmer count: 0 95s Includes forward kmers only. 95s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 95s The most accurate value is the greater of the two. 95s 95s Percent unique: NaN% 95s Depth average: NaN (unique kmers) 95s Depth median: 0 (unique kmers) 95s Depth standard deviation: NaN (unique kmers) 95s Corrected depth average: NaN 95s 95s Depth average: NaN (all kmers) 95s Depth median: 0 (all kmers) 95s Depth standard deviation: 0.00 (all kmers) 95s 95s Approx. read depth median: NaN 95s 95s Removing temp files. 95s 95s Total time: 2.018 seconds. 0.09 kb/sec 95s test -r out3.fastq 95s test -r outt.fastq 95s test -r hist.plt 95s bbnorm.sh in=illumina_full_range_original_illumina.fastq qin=64 \ 95s out=out4.fastq outt=outt2.fastq hist=hist2.plt 96s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 96s java -ea -Xmx6150m -Xms6150m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 in=illumina_full_range_original_illumina.fastq qin=64 out=out4.fastq outt=outt2.fastq hist=hist2.plt 96s Executing jgi.KmerNormalize [bits=32, in=illumina_full_range_original_illumina.fastq, qin=64, out=out4.fastq, outt=outt2.fastq, hist=hist2.plt] 96s 96s 96s *********** Pass 1 ********** 96s 96s 96s Settings: 96s threads: 4 96s k: 31 96s deterministic: true 96s toss error reads: false 96s passes: 1 96s bits per cell: 16 96s cells: 2318.99M 96s hashes: 3 96s base min quality: 5 96s kmer min prob: 0.5 96s 96s target depth: 400 96s min depth: 3 96s max depth: 500 96s min good kmers: 15 96s depth percentile: 64.8 96s ignore dupe kmers: true 96s fix spikes: false 96s histogram length: 65536 96s print zero cov: false 96s 97s Made hash table: hashes = 3 mem = 4.32 GB cells = 2318.43M used = 0.000% 97s 97s Estimated unique kmers: 4 97s 97s Table creation time: 1.593 seconds. 97s Started output threads. 97s Started output threads. 97s Table read time: 0.005 seconds. 27.66 kb/sec 97s Total reads in: 2 0.000% Kept 97s Total bases in: 126 0.000% Kept 97s Error reads in: 2 100.000% 97s Error type 1: 2 100.000% 97s Error type 2: 0 0.000% 97s Error type 3: 0 0.000% 97s 97s Wrote histogram to hist2.plt 97s Total kmers counted: 66 97s Total unique kmer count: 66 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: 100.00% 97s Depth average: 1.00 (unique kmers) 97s Depth median: 1 (unique kmers) 97s Depth standard deviation: 0.00 (unique kmers) 97s Corrected depth average: 0.00 97s 97s Depth average: 1.00 (all kmers) 97s Depth median: 1 (all kmers) 97s Depth standard deviation: 0.00 (all kmers) 97s 97s Approx. read depth median: 1.91 97s 97s *********** Pass 2 ********** 97s 97s 97s Settings: 97s threads: 4 97s k: 31 97s deterministic: true 97s toss error reads: false 97s passes: 1 97s bits per cell: 16 97s cells: 2318.99M 97s hashes: 3 97s base min quality: 5 97s kmer min prob: 0.5 97s 97s target depth: 100 97s min depth: 5 97s max depth: 100 97s min good kmers: 15 97s depth percentile: 54.0 97s ignore dupe kmers: true 97s fix spikes: false 97s histogram length: 65536 97s 98s Made hash table: hashes = 3 mem = 4.32 GB cells = 2318.43M used = 0.000% 98s 98s Estimated unique kmers: 0 98s 98s Table creation time: 0.878 seconds. 98s Started output threads. 98s Started output threads. 98s Table read time: 0.001 seconds. 0.00 kb/sec 98s Total reads in: 0 NaN% Kept 98s Total bases in: 0 NaN% Kept 98s Error reads in: 0 NaN% 98s Error type 1: 0 NaN% 98s Error type 2: 0 NaN% 98s Error type 3: 0 NaN% 98s Total kmers counted: 0 98s Total unique kmer count: 0 98s Includes forward kmers only. 98s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 98s The most accurate value is the greater of the two. 98s 98s Percent unique: NaN% 98s Depth average: NaN (unique kmers) 98s Depth median: 0 (unique kmers) 98s Depth standard deviation: NaN (unique kmers) 98s Corrected depth average: NaN 98s 98s Depth average: NaN (all kmers) 98s Depth median: 0 (all kmers) 98s Depth standard deviation: 0.00 (all kmers) 98s 98s Approx. read depth median: NaN 98s 98s Removing temp files. 98s 98s Total time: 2.548 seconds. 0.05 kb/sec 99s test -r out4.fastq 99s test -r outt2.fastq 99s test -r hist2.plt 99s autopkgtest [07:39:56]: test run-unit-test: -----------------------] 99s autopkgtest [07:39:56]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 99s run-unit-test PASS 100s autopkgtest [07:39:57]: @@@@@@@@@@@@@@@@@@@@ summary 100s run-unit-test PASS 103s nova [W] Using flock in prodstack7-arm64 103s Creating nova instance adt-questing-arm64-bbmap-20250502-073817-juju-7f2275-prod-proposed-migration-environment-2-3489025a-b423-4a6a-9176-9c5151c1767e from image adt/ubuntu-questing-arm64-server-20250501.img (UUID 137c3127-57d2-4bf2-a106-d904ad6e43f4)... 103s nova [W] Timed out waiting for ce361fc3-e6dd-4cd2-8e9d-5409c40cf9de to get deleted.