0s autopkgtest [11:14:22]: starting date and time: 2026-02-10 11:14:22+0000 0s autopkgtest [11:14:22]: git checkout: 508d4a25 a-v-ssh wait_for_ssh: demote "ssh connection failed" to a debug message 0s autopkgtest [11:14:22]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ey0t5hxl/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,localhost,localdomain,internal,login.ubuntu.com,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --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' -- lxd -r lxd-armhf-10.145.243.28 lxd-armhf-10.145.243.28:autopkgtest/ubuntu/resolute/armhf 25s autopkgtest [11:14:47]: testbed dpkg architecture: armhf 27s autopkgtest [11:14:49]: testbed apt version: 3.1.15 31s autopkgtest [11:14:53]: @@@@@@@@@@@@@@@@@@@@ test bed setup 33s autopkgtest [11:14:55]: testbed release detected to be: None 40s autopkgtest [11:15:02]: updating testbed package index (apt update) 42s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 42s Get:2 http://ftpmaster.internal/ubuntu resolute InRelease [124 kB] 42s Get:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease [124 kB] 42s Get:4 http://ftpmaster.internal/ubuntu resolute-security InRelease [124 kB] 43s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1735 kB] 43s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [179 kB] 43s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [31.9 kB] 43s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf Packages [259 kB] 43s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf Packages [1495 kB] 43s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse armhf Packages [8156 B] 43s Get:11 http://ftpmaster.internal/ubuntu resolute/main Sources [1404 kB] 44s Get:12 http://ftpmaster.internal/ubuntu resolute/universe Sources [21.3 MB] 45s Get:13 http://ftpmaster.internal/ubuntu resolute/main armhf Packages [1386 kB] 45s Get:14 http://ftpmaster.internal/ubuntu resolute/universe armhf Packages [14.9 MB] 49s Fetched 43.2 MB in 7s (6414 kB/s) 50s Reading package lists... 56s autopkgtest [11:15:18]: upgrading testbed (apt dist-upgrade and autopurge) 58s Reading package lists... 58s Building dependency tree... 58s Reading state information... 58s Calculating upgrade... 59s The following packages will be upgraded: 59s libbrotli1 ubuntu-minimal ubuntu-standard 60s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 60s Need to get 345 kB of archives. 60s After this operation, 0 B of additional disk space will be used. 60s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf ubuntu-minimal armhf 1.565 [13.3 kB] 60s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf ubuntu-standard armhf 1.565 [13.3 kB] 60s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libbrotli1 armhf 1.2.0-3 [318 kB] 60s Fetched 345 kB in 0s (804 kB/s) 61s (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 ... 68691 files and directories currently installed.) 61s Preparing to unpack .../ubuntu-minimal_1.565_armhf.deb ... 61s Unpacking ubuntu-minimal (1.565) over (1.564) ... 61s Preparing to unpack .../ubuntu-standard_1.565_armhf.deb ... 61s Unpacking ubuntu-standard (1.565) over (1.564) ... 61s Preparing to unpack .../libbrotli1_1.2.0-3_armhf.deb ... 61s Unpacking libbrotli1:armhf (1.2.0-3) over (1.1.0-2build6) ... 61s Setting up ubuntu-minimal (1.565) ... 61s Setting up libbrotli1:armhf (1.2.0-3) ... 61s Setting up ubuntu-standard (1.565) ... 61s Processing triggers for libc-bin (2.42-2ubuntu4) ... 63s Reading package lists... 64s Building dependency tree... 64s Reading state information... 64s Solving dependencies... 65s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 67s autopkgtest [11:15:29]: rebooting testbed after setup commands that affected boot 107s autopkgtest [11:16:09]: testbed running kernel: Linux 6.8.0-87-generic #88~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 14 14:00:09 UTC 2 131s autopkgtest [11:16:33]: @@@@@@@@@@@@@@@@@@@@ apt-source bbmap 145s Get:1 http://ftpmaster.internal/ubuntu resolute/universe bbmap 39.20+dfsg-3 (dsc) [2286 B] 145s Get:2 http://ftpmaster.internal/ubuntu resolute/universe bbmap 39.20+dfsg-3 (tar) [5748 kB] 145s Get:3 http://ftpmaster.internal/ubuntu resolute/universe bbmap 39.20+dfsg-3 (diff) [27.0 kB] 145s gpgv: Signature made Fri Nov 7 18:57:54 2025 UTC 145s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 145s gpgv: issuer "emollier@debian.org" 145s gpgv: Can't check signature: No public key 145s dpkg-source: warning: cannot verify inline signature for ./bbmap_39.20+dfsg-3.dsc: no acceptable signature found 146s autopkgtest [11:16:48]: testing package bbmap version 39.20+dfsg-3 148s autopkgtest [11:16:50]: build not needed 151s autopkgtest [11:16:53]: test run-unit-test: preparing testbed 152s Reading package lists... 153s Building dependency tree... 153s Reading state information... 153s Solving dependencies... 154s The following NEW packages will be installed: 154s bbmap bbmap-jni ca-certificates-java default-jre-headless java-common 154s libapache-pom-java libcommons-cli-java libcommons-codec-java 154s libcommons-io-java libcommons-parent-java libjpeg-turbo8 libjpeg8 154s libjs-jquery liblcms2-2 liblog4j1.2-java libmpj-java libpcsclite1 154s openjdk-21-jre-headless python-biopython-doc 154s 0 upgraded, 19 newly installed, 0 to remove and 0 not upgraded. 154s Need to get 71.0 MB of archives. 154s After this operation, 220 MB of additional disk space will be used. 154s Get:1 http://ftpmaster.internal/ubuntu resolute/universe armhf libcommons-cli-java all 1.6.0-1 [59.9 kB] 154s Get:2 http://ftpmaster.internal/ubuntu resolute/universe armhf libapache-pom-java all 33-2build1 [5976 B] 154s Get:3 http://ftpmaster.internal/ubuntu resolute/universe armhf libcommons-parent-java all 56-1build1 [11.1 kB] 154s Get:4 http://ftpmaster.internal/ubuntu resolute/universe armhf libcommons-codec-java all 1.18.0-1 [303 kB] 154s Get:5 http://ftpmaster.internal/ubuntu resolute/universe armhf libcommons-io-java all 2.19.0-1 [491 kB] 155s Get:6 http://ftpmaster.internal/ubuntu resolute/universe armhf liblog4j1.2-java all 1.2.17-11build1 [445 kB] 155s Get:7 http://ftpmaster.internal/ubuntu resolute/universe armhf libmpj-java all 0.44+dfsg-4build1 [445 kB] 155s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf ca-certificates-java all 20240118build1 [11.7 kB] 155s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf java-common all 0.76build1 [6956 B] 155s Get:10 http://ftpmaster.internal/ubuntu resolute/main armhf liblcms2-2 armhf 2.17-1 [139 kB] 155s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg-turbo8 armhf 2.1.5-4ubuntu3 [129 kB] 155s Get:12 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg8 armhf 8c-2ubuntu12 [2142 B] 155s Get:13 http://ftpmaster.internal/ubuntu resolute/main armhf libpcsclite1 armhf 2.4.1-1 [25.3 kB] 155s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf openjdk-21-jre-headless armhf 21.0.10+7-1 [39.8 MB] 156s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf default-jre-headless armhf 2:1.21-76build1 [3268 B] 156s Get:16 http://ftpmaster.internal/ubuntu resolute/universe armhf bbmap all 39.20+dfsg-3 [10.6 MB] 156s Get:17 http://ftpmaster.internal/ubuntu resolute/universe armhf bbmap-jni armhf 39.20+dfsg-3 [20.9 kB] 156s Get:18 http://ftpmaster.internal/ubuntu resolute/main armhf libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 156s Get:19 http://ftpmaster.internal/ubuntu resolute/universe armhf python-biopython-doc all 1.86+dfsg-1 [18.1 MB] 157s Fetched 71.0 MB in 2s (28.7 MB/s) 157s Selecting previously unselected package libcommons-cli-java. 157s (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 ... 68691 files and directories currently installed.) 157s Preparing to unpack .../00-libcommons-cli-java_1.6.0-1_all.deb ... 157s Unpacking libcommons-cli-java (1.6.0-1) ... 157s Selecting previously unselected package libapache-pom-java. 157s Preparing to unpack .../01-libapache-pom-java_33-2build1_all.deb ... 157s Unpacking libapache-pom-java (33-2build1) ... 157s Selecting previously unselected package libcommons-parent-java. 157s Preparing to unpack .../02-libcommons-parent-java_56-1build1_all.deb ... 157s Unpacking libcommons-parent-java (56-1build1) ... 157s Selecting previously unselected package libcommons-codec-java. 157s Preparing to unpack .../03-libcommons-codec-java_1.18.0-1_all.deb ... 157s Unpacking libcommons-codec-java (1.18.0-1) ... 157s Selecting previously unselected package libcommons-io-java. 157s Preparing to unpack .../04-libcommons-io-java_2.19.0-1_all.deb ... 157s Unpacking libcommons-io-java (2.19.0-1) ... 157s Selecting previously unselected package liblog4j1.2-java. 157s Preparing to unpack .../05-liblog4j1.2-java_1.2.17-11build1_all.deb ... 157s Unpacking liblog4j1.2-java (1.2.17-11build1) ... 157s Selecting previously unselected package libmpj-java. 157s Preparing to unpack .../06-libmpj-java_0.44+dfsg-4build1_all.deb ... 157s Unpacking libmpj-java (0.44+dfsg-4build1) ... 157s Selecting previously unselected package ca-certificates-java. 157s Preparing to unpack .../07-ca-certificates-java_20240118build1_all.deb ... 157s Unpacking ca-certificates-java (20240118build1) ... 157s Selecting previously unselected package java-common. 157s Preparing to unpack .../08-java-common_0.76build1_all.deb ... 157s Unpacking java-common (0.76build1) ... 157s Selecting previously unselected package liblcms2-2:armhf. 157s Preparing to unpack .../09-liblcms2-2_2.17-1_armhf.deb ... 157s Unpacking liblcms2-2:armhf (2.17-1) ... 158s Selecting previously unselected package libjpeg-turbo8:armhf. 158s Preparing to unpack .../10-libjpeg-turbo8_2.1.5-4ubuntu3_armhf.deb ... 158s Unpacking libjpeg-turbo8:armhf (2.1.5-4ubuntu3) ... 158s Selecting previously unselected package libjpeg8:armhf. 158s Preparing to unpack .../11-libjpeg8_8c-2ubuntu12_armhf.deb ... 158s Unpacking libjpeg8:armhf (8c-2ubuntu12) ... 158s Selecting previously unselected package libpcsclite1:armhf. 158s Preparing to unpack .../12-libpcsclite1_2.4.1-1_armhf.deb ... 158s Unpacking libpcsclite1:armhf (2.4.1-1) ... 158s Selecting previously unselected package openjdk-21-jre-headless:armhf. 158s Preparing to unpack .../13-openjdk-21-jre-headless_21.0.10+7-1_armhf.deb ... 158s Unpacking openjdk-21-jre-headless:armhf (21.0.10+7-1) ... 159s Selecting previously unselected package default-jre-headless. 159s Preparing to unpack .../14-default-jre-headless_2%3a1.21-76build1_armhf.deb ... 159s Unpacking default-jre-headless (2:1.21-76build1) ... 159s Selecting previously unselected package bbmap. 159s Preparing to unpack .../15-bbmap_39.20+dfsg-3_all.deb ... 159s Unpacking bbmap (39.20+dfsg-3) ... 159s Selecting previously unselected package bbmap-jni. 159s Preparing to unpack .../16-bbmap-jni_39.20+dfsg-3_armhf.deb ... 159s Unpacking bbmap-jni (39.20+dfsg-3) ... 159s Selecting previously unselected package libjs-jquery. 159s Preparing to unpack .../17-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ... 159s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 159s Selecting previously unselected package python-biopython-doc. 159s Preparing to unpack .../18-python-biopython-doc_1.86+dfsg-1_all.deb ... 159s Unpacking python-biopython-doc (1.86+dfsg-1) ... 160s Setting up liblcms2-2:armhf (2.17-1) ... 160s Setting up java-common (0.76build1) ... 160s Setting up libcommons-cli-java (1.6.0-1) ... 160s Setting up liblog4j1.2-java (1.2.17-11build1) ... 160s Setting up libapache-pom-java (33-2build1) ... 160s Setting up libpcsclite1:armhf (2.4.1-1) ... 160s Setting up libjpeg-turbo8:armhf (2.1.5-4ubuntu3) ... 160s Setting up bbmap-jni (39.20+dfsg-3) ... 160s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 160s Setting up ca-certificates-java (20240118build1) ... 160s No JRE found. Skipping Java certificates setup. 160s Setting up libjpeg8:armhf (8c-2ubuntu12) ... 160s Setting up openjdk-21-jre-headless:armhf (21.0.10+7-1) ... 160s update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/java to provide /usr/bin/java (java) in auto mode 160s update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 160s update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 160s update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 160s update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 160s Setting up libcommons-parent-java (56-1build1) ... 160s Setting up python-biopython-doc (1.86+dfsg-1) ... 160s Setting up libcommons-codec-java (1.18.0-1) ... 160s Setting up libcommons-io-java (2.19.0-1) ... 160s Setting up libmpj-java (0.44+dfsg-4build1) ... 160s Processing triggers for libc-bin (2.42-2ubuntu4) ... 160s Processing triggers for man-db (2.13.1-1build1) ... 161s Processing triggers for ca-certificates-java (20240118build1) ... 162s Adding debian:ACCVRAIZ1.pem 162s Adding debian:AC_RAIZ_FNMT-RCM.pem 162s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 162s Adding debian:ANF_Secure_Server_Root_CA.pem 162s Adding debian:Actalis_Authentication_Root_CA.pem 162s Adding debian:AffirmTrust_Commercial.pem 162s Adding debian:AffirmTrust_Networking.pem 162s Adding debian:AffirmTrust_Premium.pem 162s Adding debian:AffirmTrust_Premium_ECC.pem 162s Adding debian:Amazon_Root_CA_1.pem 162s Adding debian:Amazon_Root_CA_2.pem 162s Adding debian:Amazon_Root_CA_3.pem 162s Adding debian:Amazon_Root_CA_4.pem 162s Adding debian:Atos_TrustedRoot_2011.pem 162s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 162s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 162s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 162s Adding debian:BJCA_Global_Root_CA1.pem 162s Adding debian:BJCA_Global_Root_CA2.pem 162s Adding debian:Baltimore_CyberTrust_Root.pem 162s Adding debian:Buypass_Class_2_Root_CA.pem 162s Adding debian:Buypass_Class_3_Root_CA.pem 162s Adding debian:CA_Disig_Root_R2.pem 162s Adding debian:CFCA_EV_ROOT.pem 162s Adding debian:COMODO_Certification_Authority.pem 162s Adding debian:COMODO_ECC_Certification_Authority.pem 162s Adding debian:COMODO_RSA_Certification_Authority.pem 162s Adding debian:Certainly_Root_E1.pem 162s Adding debian:Certainly_Root_R1.pem 162s Adding debian:Certigna.pem 162s Adding debian:Certigna_Root_CA.pem 162s Adding debian:Certum_EC-384_CA.pem 162s Adding debian:Certum_Trusted_Network_CA.pem 162s Adding debian:Certum_Trusted_Network_CA_2.pem 162s Adding debian:Certum_Trusted_Root_CA.pem 162s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 162s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 162s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 162s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 162s Adding debian:Comodo_AAA_Services_root.pem 162s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 162s Adding debian:D-TRUST_BR_Root_CA_2_2023.pem 162s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 162s Adding debian:D-TRUST_EV_Root_CA_2_2023.pem 162s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 163s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 163s Adding debian:DigiCert_Assured_ID_Root_CA.pem 163s Adding debian:DigiCert_Assured_ID_Root_G2.pem 163s Adding debian:DigiCert_Assured_ID_Root_G3.pem 163s Adding debian:DigiCert_Global_Root_CA.pem 163s Adding debian:DigiCert_Global_Root_G2.pem 163s Adding debian:DigiCert_Global_Root_G3.pem 163s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 163s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 163s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 163s Adding debian:DigiCert_Trusted_Root_G4.pem 163s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 163s Adding debian:Entrust_Root_Certification_Authority.pem 163s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 163s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 163s Adding debian:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem 163s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 163s Adding debian:GLOBALTRUST_2020.pem 163s Adding debian:GTS_Root_R1.pem 163s Adding debian:GTS_Root_R2.pem 163s Adding debian:GTS_Root_R3.pem 163s Adding debian:GTS_Root_R4.pem 163s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 163s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 163s Adding debian:GlobalSign_Root_CA.pem 163s Adding debian:GlobalSign_Root_CA_-_R3.pem 163s Adding debian:GlobalSign_Root_CA_-_R6.pem 163s Adding debian:GlobalSign_Root_E46.pem 163s Adding debian:GlobalSign_Root_R46.pem 163s Adding debian:Go_Daddy_Class_2_CA.pem 163s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 163s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 163s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 163s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 163s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 163s Adding debian:HiPKI_Root_CA_-_G1.pem 163s Adding debian:Hongkong_Post_Root_CA_3.pem 163s Adding debian:ISRG_Root_X1.pem 163s Adding debian:ISRG_Root_X2.pem 163s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 163s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 163s Adding debian:Izenpe.com.pem 163s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 163s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 163s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 163s Adding debian:NAVER_Global_Root_Certification_Authority.pem 163s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 163s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 163s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 163s Adding debian:QuoVadis_Root_CA_1_G3.pem 163s Adding debian:QuoVadis_Root_CA_2.pem 163s Adding debian:QuoVadis_Root_CA_2_G3.pem 163s Adding debian:QuoVadis_Root_CA_3.pem 163s Adding debian:QuoVadis_Root_CA_3_G3.pem 163s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 163s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 163s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 163s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 163s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 163s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 163s Adding debian:SZAFIR_ROOT_CA2.pem 163s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 163s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 163s Adding debian:SecureSign_Root_CA12.pem 163s Adding debian:SecureSign_Root_CA14.pem 163s Adding debian:SecureSign_Root_CA15.pem 163s Adding debian:SecureTrust_CA.pem 163s Adding debian:Secure_Global_CA.pem 163s Adding debian:Security_Communication_ECC_RootCA1.pem 163s Adding debian:Security_Communication_RootCA2.pem 163s Adding debian:Starfield_Class_2_CA.pem 163s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 163s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 163s Adding debian:SwissSign_Gold_CA_-_G2.pem 163s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 163s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 163s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 163s Adding debian:TWCA_CYBER_Root_CA.pem 163s Adding debian:TWCA_Global_Root_CA.pem 163s Adding debian:TWCA_Root_Certification_Authority.pem 163s Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem 163s Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem 163s Adding debian:TeliaSonera_Root_CA_v1.pem 163s Adding debian:Telia_Root_CA_v2.pem 163s Adding debian:TrustAsia_Global_Root_CA_G3.pem 163s Adding debian:TrustAsia_Global_Root_CA_G4.pem 163s Adding debian:Trustwave_Global_Certification_Authority.pem 163s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 163s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 163s Adding debian:TunTrust_Root_CA.pem 163s Adding debian:UCA_Extended_Validation_Root.pem 163s Adding debian:UCA_Global_G2_Root.pem 163s Adding debian:USERTrust_ECC_Certification_Authority.pem 163s Adding debian:USERTrust_RSA_Certification_Authority.pem 163s Adding debian:XRamp_Global_CA_Root.pem 163s Adding debian:certSIGN_ROOT_CA.pem 163s Adding debian:certSIGN_Root_CA_G2.pem 163s Adding debian:e-Szigno_Root_CA_2017.pem 163s Adding debian:ePKI_Root_Certification_Authority.pem 163s Adding debian:emSign_ECC_Root_CA_-_C3.pem 163s Adding debian:emSign_ECC_Root_CA_-_G3.pem 163s Adding debian:emSign_Root_CA_-_C1.pem 163s Adding debian:emSign_Root_CA_-_G1.pem 163s Adding debian:vTrus_ECC_Root_CA.pem 163s Adding debian:vTrus_Root_CA.pem 163s done. 163s Setting up bbmap (39.20+dfsg-3) ... 163s Setting up default-jre-headless (2:1.21-76build1) ... 172s autopkgtest [11:17:14]: test run-unit-test: [----------------------- 174s 174s # bbmap 174s bbmap.sh --version 174s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 174s java -ea -Xmx2000m -Xms2000m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 --version 175s BBTools version 39.20 175s For help, please run the shellscript with no parameters, or look in /docs/. 175s bbmap.sh --help 175s 175s BBMap 175s Written by Brian Bushnell, from Dec. 2010 - present 175s Last modified September 15, 2022 175s 175s Description: Fast and accurate splice-aware read aligner. 175s Please read bbmap/docs/guides/BBMapGuide.txt for more information. 175s 175s To index: bbmap.sh ref= 175s To map: bbmap.sh in= out= 175s To map without writing an index: 175s bbmap.sh ref= in= out= nodisk 175s 175s in=stdin will accept reads from standard in, and out=stdout will write to 175s standard out, but file extensions are still needed to specify the format of the 175s input and output files e.g. in=stdin.fa.gz will read gzipped fasta from 175s standard in; out=stdout.sam.gz will write gzipped sam. 175s 175s Indexing Parameters (required when building the index): 175s nodisk=f Set to true to build index in memory and write nothing 175s to disk except output. 175s ref= Specify the reference sequence. Only do this ONCE, 175s when building the index (unless using 'nodisk'). 175s build=1 If multiple references are indexed in the same directory, 175s each needs a unique numeric ID (unless using 'nodisk'). 175s k=13 Kmer length, range 8-15. Longer is faster but uses 175s more memory. Shorter is more sensitive. 175s If indexing and mapping are done in two steps, K should 175s be specified each time. 175s path=<.> Specify the location to write the index, if you don't 175s want it in the current working directory. 175s usemodulo=f Throw away ~80% of kmers based on remainder modulo a 175s number (reduces RAM by 50% and sensitivity slightly). 175s Should be enabled both when building the index AND 175s when mapping. 175s rebuild=f Force a rebuild of the index (ref= should be set). 175s 175s Input Parameters: 175s build=1 Designate index to use. Corresponds to the number 175s specified when building the index. 175s in= Primary reads input; required parameter. 175s in2= For paired reads in two files. 175s interleaved=auto True forces paired/interleaved input; false forces 175s single-ended mapping. If not specified, interleaved 175s status will be autodetected from read names. 175s fastareadlen=500 Break up FASTA reads longer than this. Max is 500 for 175s BBMap and 6000 for BBMapPacBio. Only works for FASTA 175s input (use 'maxlen' for FASTQ input). The default for 175s bbmap.sh is 500, and for mapPacBio.sh is 6000. 175s unpigz=f Spawn a pigz (parallel gzip) process for faster 175s decompression than using Java. 175s Requires pigz to be installed. 175s touppercase=t (tuc) Convert lowercase letters in reads to upper case 175s (otherwise they will not match the reference). 175s 175s Sampling Parameters: 175s 175s reads=-1 Set to a positive number N to only process the first N 175s reads (or pairs), then quit. -1 means use all reads. 175s samplerate=1 Set to a number from 0 to 1 to randomly select that 175s fraction of reads for mapping. 1 uses all reads. 175s skipreads=0 Set to a number N to skip the first N reads (or pairs), 175s then map the rest. 175s 175s Mapping Parameters: 175s fast=f This flag is a macro which sets other paramters to run 175s faster, at reduced sensitivity. Bad for RNA-seq. 175s slow=f This flag is a macro which sets other paramters to run 175s slower, at greater sensitivity. 'vslow' is even slower. 175s maxindel=16000 Don't look for indels longer than this. Lower is faster. 175s Set to >=100k for RNAseq with long introns like mammals. 175s strictmaxindel=f When enabled, do not allow indels longer than 'maxindel'. 175s By default these are not sought, but may be found anyway. 175s tipsearch=100 Look this far for read-end deletions with anchors 175s shorter than K, using brute force. 175s minid=0.76 Approximate minimum alignment identity to look for. 175s Higher is faster and less sensitive. 175s minhits=1 Minimum number of seed hits required for candidate sites. 175s Higher is faster. 175s local=f Set to true to use local, rather than global, alignments. 175s This will soft-clip ugly ends of poor alignments. 175s perfectmode=f Allow only perfect mappings when set to true (very fast). 175s semiperfectmode=f Allow only perfect and semiperfect (perfect except for 175s N's in the reference) mappings. 175s threads=auto (t) Set to number of threads desired. By default, uses 175s all cores available. 175s ambiguous=best (ambig) Set behavior on ambiguously-mapped reads (with 175s multiple top-scoring mapping locations). 175s best (use the first best site) 175s toss (consider unmapped) 175s random (select one top-scoring site randomly) 175s all (retain all top-scoring sites) 175s samestrandpairs=f (ssp) Specify whether paired reads should map to the 175s same strand or opposite strands. 175s requirecorrectstrand=t (rcs) Forbid pairing of reads without correct strand 175s orientation. Set to false for long-mate-pair libraries. 175s killbadpairs=f (kbp) If a read pair is mapped with an inappropriate 175s insert size or orientation, the read with the lower 175s mapping quality is marked unmapped. 175s pairedonly=f (po) Treat unpaired reads as unmapped. Thus they will 175s be sent to 'outu' but not 'outm'. 175s rcomp=f Reverse complement both reads prior to mapping (for LMP 175s outward-facing libraries). 175s rcompmate=f Reverse complement read2 prior to mapping. 175s pairlen=32000 Set max allowed distance between paired reads. 175s (insert size)=(pairlen)+(read1 length)+(read2 length) 175s rescuedist=1200 Don't try to rescue paired reads if avg. insert size 175s greater than this. Lower is faster. 175s rescuemismatches=32 Maximum mismatches allowed in a rescued read. Lower 175s is faster. 175s averagepairdist=100 (apd) Initial average distance between paired reads. 175s Varies dynamically; does not need to be specified. 175s deterministic=f Run in deterministic mode. In this case it is good 175s to set averagepairdist. BBMap is deterministic 175s without this flag if using single-ended reads, 175s or run singlethreaded. 175s bandwidthratio=0 (bwr) If above zero, restrict alignment band to this 175s fraction of read length. Faster but less accurate. 175s bandwidth=0 (bw) Set the bandwidth directly. 175s fraction of read length. Faster but less accurate. 175s usejni=f (jni) Do alignments faster, in C code. Requires 175s compiling the C code; details are in /jni/README.txt. 175s maxsites2=800 Don't analyze (or print) more than this many alignments 175s per read. 175s ignorefrequentkmers=t (ifk) Discard low-information kmers that occur often. 175s excludefraction=0.03 (ef) Fraction of kmers to ignore. For example, 0.03 175s will ignore the most common 3% of kmers. 175s greedy=t Use a greedy algorithm to discard the least-useful 175s kmers on a per-read basis. 175s kfilter=0 If positive, potential mapping sites must have at 175s least this many consecutive exact matches. 175s 175s 175s Quality and Trimming Parameters: 175s qin=auto Set to 33 or 64 to specify input quality value ASCII 175s offset. 33 is Sanger, 64 is old Solexa. 175s qout=auto Set to 33 or 64 to specify output quality value ASCII 175s offset (only if output format is fastq). 175s qtrim=f Quality-trim ends before mapping. Options are: 175s 'f' (false), 'l' (left), 'r' (right), and 'lr' (both). 175s untrim=f Undo trimming after mapping. Untrimmed bases will be 175s soft-clipped in cigar strings. 175s trimq=6 Trim regions with average quality below this 175s (phred algorithm). 175s mintrimlength=60 (mintl) Don't trim reads to be shorter than this. 175s fakefastaquality=-1 (ffq) Set to a positive number 1-50 to generate fake 175s quality strings for fasta input reads. 175s ignorebadquality=f (ibq) Keep going, rather than crashing, if a read has 175s out-of-range quality values. 175s usequality=t Use quality scores when determining which read kmers 175s to use as seeds. 175s minaveragequality=0 (maq) Do not map reads with average quality below this. 175s maqb=0 If positive, calculate maq from this many initial bases. 175s 175s Output Parameters: 175s out= Write all reads to this file. 175s outu= Write only unmapped reads to this file. Does not 175s include unmapped paired reads with a mapped mate. 175s outm= Write only mapped reads to this file. Includes 175s unmapped paired reads with a mapped mate. 175s mappedonly=f If true, treats 'out' like 'outm'. 175s bamscript= (bs) Write a shell script to that will turn 175s the sam output into a sorted, indexed bam file. 175s ordered=f Set to true to output reads in same order as input. 175s Slower and uses more memory. 175s overwrite=f (ow) Allow process to overwrite existing files. 175s secondary=f Print secondary alignments. 175s sssr=0.95 (secondarysitescoreratio) Print only secondary alignments 175s with score of at least this fraction of primary. 175s ssao=f (secondarysiteasambiguousonly) Only print secondary 175s alignments for ambiguously-mapped reads. 175s maxsites=5 Maximum number of total alignments to print per read. 175s Only relevant when secondary=t. 175s quickmatch=f Generate cigar strings more quickly. 175s trimreaddescriptions=f (trd) Truncate read and ref names at the first whitespace, 175s bbmap.sh ref=example.fasta 175s assuming that the remainder is a comment or description. 175s ziplevel=2 (zl) Compression level for zip or gzip output. 175s pigz=f Spawn a pigz (parallel gzip) process for faster 175s compression than Java. Requires pigz to be installed. 175s machineout=f Set to true to output statistics in machine-friendly 175s 'key=value' format. 175s printunmappedcount=f Print the total number of unmapped reads and bases. 175s If input is paired, the number will be of pairs 175s for which both reads are unmapped. 175s showprogress=0 If positive, print a '.' every X reads. 175s showprogress2=0 If positive, print the number of seconds since the 175s last progress update (instead of a '.'). 175s renamebyinsert=f Renames reads based on their mapped insert size. 175s 175s Bloom-Filtering Parameters (bloomfilter.sh is the standalone version). 175s bloom=f Use a Bloom filter to ignore reads not sharing kmers 175s with the reference. This uses more memory, but speeds 175s mapping when most reads don't match the reference. 175s bloomhashes=2 Number of hash functions. 175s bloomminhits=3 Number of consecutive hits to be considered matched. 175s bloomk=31 Bloom filter kmer length. 175s bloomserial=t Use the serialized Bloom filter for greater loading 175s speed, if available. If not, generate and write one. 175s 175s Post-Filtering Parameters: 175s idfilter=0 Independant of minid; sets exact minimum identity 175s allowed for alignments to be printed. Range 0 to 1. 175s subfilter=-1 Ban alignments with more than this many substitutions. 175s insfilter=-1 Ban alignments with more than this many insertions. 175s delfilter=-1 Ban alignments with more than this many deletions. 175s indelfilter=-1 Ban alignments with more than this many indels. 175s editfilter=-1 Ban alignments with more than this many edits. 175s inslenfilter=-1 Ban alignments with an insertion longer than this. 175s dellenfilter=-1 Ban alignments with a deletion longer than this. 175s nfilter=-1 Ban alignments with more than this many ns. This 175s includes nocall, noref, and off scaffold ends. 175s 175s Sam flags and settings: 175s noheader=f Disable generation of header lines. 175s sam=1.4 Set to 1.4 to write Sam version 1.4 cigar strings, 175s with = and X, or 1.3 to use M. 175s saa=t (secondaryalignmentasterisks) Use asterisks instead of 175s bases for sam secondary alignments. 175s cigar=t Set to 'f' to skip generation of cigar strings (faster). 175s keepnames=f Keep original names of paired reads, rather than 175s ensuring both reads have the same name. 175s intronlen=999999999 Set to a lower number like 10 to change 'D' to 'N' in 175s cigar strings for deletions of at least that length. 175s rgid= Set readgroup ID. All other readgroup fields 175s can be set similarly, with the flag rgXX= 175s If you set a readgroup flag to the word 'filename', 175s e.g. rgid=filename, the input file name will be used. 175s mdtag=f Write MD tags. 175s nhtag=f Write NH tags. 175s xmtag=f Write XM tags (may only work correctly with ambig=all). 175s amtag=f Write AM tags. 175s nmtag=f Write NM tags. 175s xstag=f Set to 'xs=fs', 'xs=ss', or 'xs=us' to write XS tags 175s for RNAseq using firststrand, secondstrand, or 175s unstranded libraries. Needed by Cufflinks. 175s JGI mainly uses 'firststrand'. 175s stoptag=f Write a tag indicating read stop location, prefixed by YS:i: 175s lengthtag=f Write a tag indicating (query,ref) alignment lengths, 175s prefixed by YL:Z: 175s idtag=f Write a tag indicating percent identity, prefixed by YI:f: 175s inserttag=f Write a tag indicating insert size, prefixed by X8:Z: 175s scoretag=f Write a tag indicating BBMap's raw score, prefixed by YR:i: 175s timetag=f Write a tag indicating this read's mapping time, prefixed by X0:i: 175s boundstag=f Write a tag indicating whether either read in the pair 175s goes off the end of the reference, prefixed by XB:Z: 175s notags=f Turn off all optional tags. 175s 175s Histogram and statistics output parameters: 175s scafstats= Statistics on how many reads mapped to which scaffold. 175s refstats= Statistics on how many reads mapped to which reference 175s file; only for BBSplit. 175s sortscafs=t Sort scaffolds or references by read count. 175s bhist= Base composition histogram by position. 175s qhist= Quality histogram by position. 175s aqhist= Histogram of average read quality. 175s bqhist= Quality histogram designed for box plots. 175s lhist= Read length histogram. 175s ihist= Write histogram of insert sizes (for paired reads). 175s ehist= Errors-per-read histogram. 175s qahist= Quality accuracy histogram of error rates versus 175s quality score. 175s indelhist= Indel length histogram. 175s mhist= Histogram of match, sub, del, and ins rates by 175s read location. 175s gchist= Read GC content histogram. 175s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 175s gcpairs=t Use average GC of paired reads. 175s idhist= Histogram of read count versus percent identity. 175s idbins=100 Number idhist bins. Set to 'auto' to use read length. 175s statsfile=stderr Mapping statistics are printed here. 175s 175s Coverage output parameters (these may reduce speed and use more RAM): 175s covstats= Per-scaffold coverage info. 175s rpkm= Per-scaffold RPKM/FPKM counts. 175s covhist= Histogram of # occurrences of each depth level. 175s basecov= Coverage per base location. 175s bincov= Print binned coverage per location (one line per X bases). 175s covbinsize=1000 Set the binsize for binned coverage output. 175s nzo=t Only print scaffolds with nonzero coverage. 175s twocolumn=f Change to true to print only ID and Avg_fold instead of 175s all 6 columns to the 'out=' file. 175s 32bit=f Set to true if you need per-base coverage over 64k. 175s strandedcov=f Track coverage for plus and minus strand independently. 175s startcov=f Only track start positions of reads. 175s secondarycov=t Include coverage of secondary alignments. 175s physcov=f Calculate physical coverage for paired reads. 175s This includes the unsequenced bases. 175s delcoverage=t (delcov) Count bases covered by deletions as covered. 175s True is faster than false. 175s covk=0 If positive, calculate kmer coverage statistics. 175s 175s Java Parameters: 175s -Xmx This will set Java's memory usage, 175s overriding autodetection. 175s -Xmx20g will specify 20 gigs of RAM, and -Xmx800m 175s will specify 800 megs. The max is typically 85% of 175s physical memory. The human genome requires around 24g, 175s or 12g with the 'usemodulo' flag. The index uses 175s roughly 6 bytes per reference base. 175s -eoom This flag will cause the process to exit if an 175s out-of-memory exception occurs. Requires Java 8u92+. 175s -da Disable assertions. 175s 175s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter 175s any problems, or post at: http://seqanswers.com/forums/showthread.php?t=41057 175s 175s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 175s java -ea -Xmx2000m -Xms2000m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta 175s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta] 175s Version 39.20 175s 175s No output file. 175s Writing reference. 175s 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] 175s 175s Set genScaffoldInfo=true 175s Writing chunk 1 175s Set genome to 1 175s 175s Loaded Reference: 0.009 seconds. 175s Loading index for chunk 1-1, build 1 175s No index available; generating from reference genome: /tmp/autopkgtest.jVrBBx/autopkgtest_tmp/ref/index/1/chr1_index_k13_c16_b1.block 175s Indexing threads started for block 0-1 175s Indexing threads finished for block 0-1 177s Generated Index: 1.702 seconds. 177s No reads to process; quitting. 177s 177s Total time: 1.945 seconds. 177s test -d ref 177s bbmap.sh in=misc_dna_as_sanger.fastq out=out.sam 177s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 177s java -ea -Xmx2000m -Xms2000m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 in=misc_dna_as_sanger.fastq out=out.sam 177s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, in=misc_dna_as_sanger.fastq, out=out.sam] 177s Version 39.20 177s 177s Retaining first best site only for ambiguous mappings. 177s Set genome to 1 177s 177s Loaded Reference: 0.043 seconds. 177s Loading index for chunk 1-1, build 1 178s Generated Index: 0.740 seconds. 183s Analyzed Index: 5.499 seconds. 183s Started output stream: 0.046 seconds. 184s Cleared Memory: 0.116 seconds. 184s Processing reads in single-ended mode. 184s Started read stream. 184s Started 8 mapping threads. 184s Detecting finished threads: 0, 1, 2, 3, 4, 5, 6, 7 184s 184s ------------------ Results ------------------ 184s 184s Genome: 1 184s Key Length: 13 184s Max Indel: 16000 184s Minimum Score Ratio: 0.56 184s Mapping Mode: normal 184s Reads Used: 4 (153 bases) 184s 184s Mapping: 0.187 seconds. 184s Reads/sec: 21.44 184s kBases/sec: 0.82 184s 184s 184s Read 1 data: pct reads num reads pct bases num bases 184s 184s mapped: 0.0000% 0 0.0000% 0 184s unambiguous: 0.0000% 0 0.0000% 0 184s ambiguous: 0.0000% 0 0.0000% 0 184s low-Q discards: 25.0000% 1 19.6078% 30 184s 184s perfect best site: 0.0000% 0 0.0000% 0 184s semiperfect site: 0.0000% 0 0.0000% 0 184s 184s Match Rate: NA NA NaN% 0 184s Error Rate: NaN% 0 NaN% 0 184s Sub Rate: NaN% 0 NaN% 0 184s Del Rate: NaN% 0 NaN% 0 184s Ins Rate: NaN% 0 NaN% 0 184s N Rate: NaN% 0 NaN% 0 184s 184s Total time: 6.805 seconds. 184s test -r out.sam 184s bbmap.sh ref=example.fasta in=example.fastq out=out2.sam nodisk 184s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 184s java -ea -Xmx2000m -Xms2000m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta in=example.fastq out=out2.sam nodisk 184s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta, in=example.fastq, out=out2.sam, nodisk] 184s Version 39.20 184s 184s Retaining first best site only for ambiguous mappings. 184s 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] 184s 184s Set genScaffoldInfo=true 184s Set genome to 1 184s 184s Loaded Reference: 0.002 seconds. 184s Loading index for chunk 1-1, build 1 184s Indexing threads started for block 0-1 185s Indexing threads finished for block 0-1 185s Generated Index: 0.289 seconds. 190s Analyzed Index: 5.518 seconds. 190s Started output stream: 0.047 seconds. 190s Cleared Memory: 0.119 seconds. 190s Processing reads in single-ended mode. 190s Started read stream. 190s Started 8 mapping threads. 190s Detecting finished threads: 0, 1, 2, 3, 4, 5, 6, 7 190s 190s ------------------ Results ------------------ 190s 190s Genome: 1 190s Key Length: 13 190s Max Indel: 16000 190s Minimum Score Ratio: 0.56 190s Mapping Mode: normal 190s Reads Used: 3 (75 bases) 190s 190s Mapping: 0.197 seconds. 190s Reads/sec: 15.23 190s kBases/sec: 0.38 190s 190s 190s Read 1 data: pct reads num reads pct bases num bases 190s 190s mapped: 100.0000% 3 100.0000% 75 190s unambiguous: 100.0000% 3 100.0000% 75 190s ambiguous: 0.0000% 0 0.0000% 0 190s low-Q discards: 0.0000% 0 0.0000% 0 190s 190s perfect best site: 100.0000% 3 100.0000% 75 190s semiperfect site: 100.0000% 3 100.0000% 75 190s 190s Match Rate: NA NA 100.0000% 75 190s Error Rate: 0.0000% 0 0.0000% 0 190s Sub Rate: 0.0000% 0 0.0000% 0 190s Del Rate: 0.0000% 0 0.0000% 0 190s Ins Rate: 0.0000% 0 0.0000% 0 190s N Rate: 0.0000% 0 0.0000% 0 191s 191s Total time: 6.413 seconds. 191s test -r out2.sam 191s 191s # bbduk 191s bbduk.sh --version 191s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 191s java -ea -Xmx2000m -Xms2000m -cp /usr/share/java/bbmap.jar jgi.BBDuk --version 191s BBTools version 39.20 191s For help, please run the shellscript with no parameters, or look in /docs/. 191s bbduk.sh --help 191s 191s Written by Brian Bushnell 191s Last modified November 18, 2024 191s 191s Description: Compares reads to the kmers in a reference dataset, optionally 191s allowing an edit distance. Splits the reads into two outputs - those that 191s match the reference, and those that don't. Can also trim (remove) the matching 191s parts of the reads rather than binning the reads. 191s Please read bbmap/docs/guides/BBDukGuide.txt for more information. 191s 191s Usage: bbduk.sh in= out= ref= 191s 191s Input may be stdin or a fasta or fastq file, compressed or uncompressed. 191s If you pipe via stdin/stdout, please include the file type; e.g. for gzipped 191s fasta input, set in=stdin.fa.gz 191s 191s Input parameters: 191s in= Main input. in=stdin.fq will pipe from stdin. 191s in2= Input for 2nd read of pairs in a different file. 191s ref= Comma-delimited list of reference files. 191s In addition to filenames, you may also use the keywords: 191s adapters, artifacts, phix, lambda, pjet, mtst, kapa 191s literal= Comma-delimited list of literal reference sequences. 191s Polymers are also allowed with the 'poly' prefix; 191s for example, 'literal=ATGGT,polyGC' will add both ATGGT 191s and GCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGC - 32+ of them, 191s enough replicates to ensure that all kmers are present. 191s touppercase=f (tuc) Change all bases upper-case. 191s interleaved=auto (int) t/f overrides interleaved autodetection. 191s Must be set mainually when streaming fastq input. 191s qin=auto Input quality offset: 33 (Sanger), 64, or auto. 191s reads=-1 If positive, quit after processing X reads or pairs. 191s copyundefined=f (cu) Process non-AGCT IUPAC reference bases by making all 191s possible unambiguous copies. Intended for short motifs 191s or adapter barcodes, as time/memory use is exponential. 191s samplerate=1 Set lower to only process a fraction of input reads. 191s samref= Optional reference fasta for processing sam files. 191s 191s Output parameters: 191s out= (outnonmatch) Write reads here that do not contain 191s kmers matching the database. 'out=stdout.fq' will pipe 191s to standard out. 191s out2= (outnonmatch2) Use this to write 2nd read of pairs to a 191s different file. 191s outm= (outmatch) Write reads here that fail filters. In default 191s kfilter mode, this means any read with a matching kmer. 191s In any mode, it also includes reads that fail filters such 191s as minlength, mingc, maxgc, entropy, etc. In other words, 191s it includes all reads that do not go to 'out'. 191s outm2= (outmatch2) Use this to write 2nd read of pairs to a 191s different file. 191s outs= (outsingle) Use this to write singleton reads whose mate 191s was trimmed shorter than minlen. 191s stats= Write statistics about which contamininants were detected. 191s refstats= Write statistics on a per-reference-file basis. 191s rpkm= Write RPKM for each reference sequence (for RNA-seq). 191s dump= Dump kmer tables to a file, in fasta format. 191s duk= Write statistics in duk's format. *DEPRECATED* 191s nzo=t Only write statistics about ref sequences with nonzero hits. 191s overwrite=t (ow) Grant permission to overwrite files. 191s showspeed=t (ss) 'f' suppresses display of processing speed. 191s ziplevel=2 (zl) Compression level; 1 (min) through 9 (max). 191s fastawrap=70 Length of lines in fasta output. 191s qout=auto Output quality offset: 33 (Sanger), 64, or auto. 191s statscolumns=3 (cols) Number of columns for stats output, 3 or 5. 191s 5 includes base counts. 191s rename=f Rename reads to indicate which sequences they matched. 191s refnames=f Use names of reference files rather than scaffold IDs. 191s trd=f bbduk.sh in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq \ 191s qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 191s Truncate read and ref names at the first whitespace. 191s ordered=f Set to true to output reads in same order as input. 191s maxbasesout=-1 If positive, quit after writing approximately this many 191s bases to out (outu/outnonmatch). 191s maxbasesoutm=-1 If positive, quit after writing approximately this many 191s bases to outm (outmatch). 191s json=f Print to screen in json format. 191s 191s Histogram output parameters: 191s bhist= Base composition histogram by position. 191s qhist= Quality histogram by position. 191s qchist= Count of bases with each quality value. 191s aqhist= Histogram of average read quality. 191s bqhist= Quality histogram designed for box plots. 191s lhist= Read length histogram. 191s phist= Polymer length histogram. 191s gchist= Read GC content histogram. 191s enthist= Read entropy histogram. 191s ihist= Insert size histogram, for paired reads in mapped sam. 191s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 191s maxhistlen=6000 Set an upper bound for histogram lengths; higher uses 191s more memory. The default is 6000 for some histograms 191s and 80000 for others. 191s 191s Histograms for mapped sam/bam files only: 191s histbefore=t Calculate histograms from reads before processing. 191s ehist= Errors-per-read histogram. 191s qahist= Quality accuracy histogram of error rates versus quality 191s score. 191s indelhist= Indel length histogram. 191s mhist= Histogram of match, sub, del, and ins rates by position. 191s idhist= Histogram of read count versus percent identity. 191s idbins=100 Number idhist bins. Set to 'auto' to use read length. 191s varfile= Ignore substitution errors listed in this file when 191s calculating error rates. Can be generated with 191s CallVariants. 191s vcf= Ignore substitution errors listed in this VCF file 191s when calculating error rates. 191s ignorevcfindels=t Also ignore indels listed in the VCF. 191s 191s Processing parameters: 191s k=27 Kmer length used for finding contaminants. Contaminants 191s shorter than k will not be found. k must be at least 1. 191s rcomp=t Look for reverse-complements of kmers in addition to 191s forward kmers. 191s maskmiddle=t (mm) Treat the middle base of a kmer as a wildcard, to 191s increase sensitivity in the presence of errors. This may 191s also be set to a number, e.g. mm=3, to mask that many bp. 191s The default mm=t corresponds to mm=1 for odd-length kmers 191s and mm=2 for even-length kmers (as of v39.04), while 191s mm=f is always equivalent to mm=0. 191s minkmerhits=1 (mkh) Reads need at least this many matching kmers 191s to be considered as matching the reference. 191s minkmerfraction=0.0 (mkf) A reads needs at least this fraction of its total 191s kmers to hit a ref, in order to be considered a match. 191s If this and minkmerhits are set, the greater is used. 191s mincovfraction=0.0 (mcf) A reads needs at least this fraction of its total 191s bases to be covered by ref kmers to be considered a match. 191s If specified, mcf overrides mkh and mkf. 191s hammingdistance=0 (hdist) Maximum Hamming distance for ref kmers (subs only). 191s Memory use is proportional to (3*K)^hdist. 191s qhdist=0 Hamming distance for query kmers; impacts speed, not memory. 191s editdistance=0 (edist) Maximum edit distance from ref kmers (subs 191s and indels). Memory use is proportional to (8*K)^edist. 191s hammingdistance2=0 (hdist2) Sets hdist for short kmers, when using mink. 191s qhdist2=0 Sets qhdist for short kmers, when using mink. 191s editdistance2=0 (edist2) Sets edist for short kmers, when using mink. 191s forbidn=f (fn) Forbids matching of read kmers containing N. 191s By default, these will match a reference 'A' if 191s hdist>0 or edist>0, to increase sensitivity. 191s removeifeitherbad=t (rieb) Paired reads get sent to 'outmatch' if either is 191s match (or either is trimmed shorter than minlen). 191s Set to false to require both. 191s trimfailures=f Instead of discarding failed reads, trim them to 1bp. 191s This makes the statistics a bit odd. 191s findbestmatch=f (fbm) If multiple matches, associate read with sequence 191s sharing most kmers. Reduces speed. 191s skipr1=f Don't do kmer-based operations on read 1. 191s skipr2=f Don't do kmer-based operations on read 2. 191s ecco=f For overlapping paired reads only. Performs error- 191s correction with BBMerge prior to kmer operations. 191s recalibrate=f (recal) Recalibrate quality scores. Requires calibration 191s matrices generated by CalcTrueQuality. 191s sam= If recalibration is desired, and matrices have not already 191s been generated, BBDuk will create them from the sam file. 191s amino=f Run in amino acid mode. Some features have not been 191s tested, but kmer-matching works fine. Maximum k is 12. 191s 191s Speed and Memory parameters: 191s threads=auto (t) Set number of threads to use; default is number of 191s logical processors. 191s prealloc=f Preallocate memory in table. Allows faster table loading 191s and more efficient memory usage, for a large reference. 191s monitor=f Kill this process if it crashes. monitor=600,0.01 would 191s kill after 600 seconds under 1% usage. 191s minrskip=1 (mns) Force minimal skip interval when indexing reference 191s kmers. 1 means use all, 2 means use every other kmer, etc. 191s maxrskip=1 (mxs) Restrict maximal skip interval when indexing 191s reference kmers. Normally all are used for scaffolds<100kb, 191s but with longer scaffolds, up to maxrskip-1 are skipped. 191s rskip= Set both minrskip and maxrskip to the same value. 191s If not set, rskip will vary based on sequence length. 191s qskip=1 Skip query kmers to increase speed. 1 means use all. 191s speed=0 Ignore this fraction of kmer space (0-15 out of 16) in both 191s reads and reference. Increases speed and reduces memory. 191s Note: Do not use more than one of 'speed', 'qskip', and 'rskip'. 191s 191s Trimming/Filtering/Masking parameters: 191s Note - if ktrim, kmask, and ksplit are unset, the default behavior is kfilter. 191s All kmer processing modes are mutually exclusive. 191s Reads only get sent to 'outm' purely based on kmer matches in kfilter mode. 191s 191s ktrim=f Trim reads to remove bases matching reference kmers, plus 191s all bases to the left or right. 191s Values: 191s f (don't trim), 191s r (trim to the right), 191s l (trim to the left) 191s ktrimtips=0 Set this to a positive number to perform ktrim on both 191s ends, examining only the outermost X bases. 191s kmask= Replace bases matching ref kmers with another symbol. 191s Allows any non-whitespace character, and processes short 191s kmers on both ends if mink is set. 'kmask=lc' will 191s convert masked bases to lowercase. 191s maskfullycovered=f (mfc) Only mask bases that are fully covered by kmers. 191s ksplit=f For single-ended reads only. Reads will be split into 191s pairs around the kmer. If the kmer is at the end of the 191s read, it will be trimmed instead. Singletons will go to 191s out, and pairs will go to outm. Do not use ksplit with 191s other operations such as quality-trimming or filtering. 191s mink=0 Look for shorter kmers at read tips down to this length, 191s when k-trimming or masking. 0 means disabled. Enabling 191s this will disable maskmiddle. 191s qtrim=f Trim read ends to remove bases with quality below trimq. 191s Performed AFTER looking for kmers. Values: 191s rl (trim both ends), 191s f (neither end), 191s r (right end only), 191s l (left end only), 191s w (sliding window). 191s trimq=6 Regions with average quality BELOW this will be trimmed, 191s if qtrim is set to something other than f. Can be a 191s floating-point number like 7.3. 191s quantize Bin quality scores to reduce file size. quantize=2 will 191s eliminate all odd quality scores, while quantize=0,10,37 191s will only allow qualty scores of 0, 10, or 37. 191s trimclip=f Trim soft-clipped bases from sam files. 191s minlength=10 (ml) Reads shorter than this after trimming will be 191s discarded. Pairs will be discarded if both are shorter. 191s mlf=0 (minlengthfraction) Reads shorter than this fraction of 191s original length after trimming will be discarded. 191s maxlength= Reads longer than this after trimming will be discarded. 191s minavgquality=0 (maq) Reads with average quality (after trimming) below 191s this will be discarded. 191s maqb=0 If positive, calculate maq from this many initial bases. 191s minbasequality=0 (mbq) Reads with any base below this quality (after 191s trimming) will be discarded. 191s maxns=-1 If non-negative, reads with more Ns than this 191s (after trimming) will be discarded. 191s mcb=0 (minconsecutivebases) Discard reads without at least 191s this many consecutive called bases. 191s ottm=f (outputtrimmedtomatch) Output reads trimmed to shorter 191s than minlength to outm rather than discarding. 191s tp=0 (trimpad) Trim this much extra around matching kmers. 191s tbo=f (trimbyoverlap) Trim adapters based on where paired 191s reads overlap. 191s strictoverlap=t Adjust sensitivity for trimbyoverlap mode. 191s minoverlap=14 Require this many bases of overlap for detection. 191s mininsert=40 Require insert size of at least this for overlap. 191s Should be reduced to 16 for small RNA sequencing. 191s tpe=f (trimpairsevenly) When kmer right-trimming, trim both 191s reads to the minimum length of either. 191s forcetrimleft=0 (ftl) If positive, trim bases to the left of this position 191s (exclusive, 0-based). 191s forcetrimright=0 (ftr) If positive, trim bases to the right of this position 191s (exclusive, 0-based). 191s forcetrimright2=0 (ftr2) If positive, trim this many bases on the right end. 191s forcetrimmod=0 (ftm) If positive, right-trim length to be equal to zero, 191s modulo this number. 191s restrictleft=0 If positive, only look for kmer matches in the 191s leftmost X bases. 191s restrictright=0 If positive, only look for kmer matches in the 191s rightmost X bases. 191s NOTE: restrictleft and restrictright are mutually exclusive. If trimming 191s both ends is desired, use ktrimtips. 191s mingc=0 Discard reads with GC content below this. 191s maxgc=1 Discard reads with GC content above this. 191s gcpairs=t Use average GC of paired reads. 191s Also affects gchist. 191s tossjunk=f Discard reads with invalid characters as bases. 191s swift=f Trim Swift sequences: Trailing C/T/N R1, leading G/A/N R2. 191s 191s Header-parsing parameters - these require Illumina headers: 191s chastityfilter=f (cf) Discard reads with id containing ' 1:Y:' or ' 2:Y:'. 191s barcodefilter=f Remove reads with unexpected barcodes if barcodes is set, 191s or barcodes containing 'N' otherwise. A barcode must be 191s the last part of the read header. Values: 191s t: Remove reads with bad barcodes. 191s f: Ignore barcodes. 191s crash: Crash upon encountering bad barcodes. 191s barcodes= Comma-delimited list of barcodes or files of barcodes. 191s xmin=-1 If positive, discard reads with a lesser X coordinate. 191s ymin=-1 If positive, discard reads with a lesser Y coordinate. 191s xmax=-1 If positive, discard reads with a greater X coordinate. 191s ymax=-1 If positive, discard reads with a greater Y coordinate. 191s 191s Polymer trimming: 191s trimpolya=0 If greater than 0, trim poly-A or poly-T tails of 191s at least this length on either end of reads. 191s trimpolygleft=0 If greater than 0, trim poly-G prefixes of at least this 191s length on the left end of reads. Does not trim poly-C. 191s trimpolygright=0 If greater than 0, trim poly-G tails of at least this 191s length on the right end of reads. Does not trim poly-C. 191s trimpolyg=0 This sets both left and right at once. 191s filterpolyg=0 If greater than 0, remove reads with a poly-G prefix of 191s at least this length (on the left). 191s Note: there are also equivalent poly-C flags. 191s 191s Polymer tracking: 191s pratio=base,base 'pratio=G,C' will print the ratio of G to C polymers. 191s plen=20 Length of homopolymers to count. 191s 191s Entropy/Complexity parameters: 191s entropy=-1 Set between 0 and 1 to filter reads with entropy below 191s that value. Higher is more stringent. 191s entropywindow=50 Calculate entropy using a sliding window of this length. 191s entropyk=5 Calculate entropy using kmers of this length. 191s minbasefrequency=0 Discard reads with a minimum base frequency below this. 191s entropytrim=f Values: 191s f: (false) Do not entropy-trim. 191s r: (right) Trim low entropy on the right end only. 191s l: (left) Trim low entropy on the left end only. 191s rl: (both) Trim low entropy on both ends. 191s entropymask=f Values: 191s f: (filter) Discard low-entropy sequences. 191s t: (true) Mask low-entropy parts of sequences with N. 191s lc: Change low-entropy parts of sequences to lowercase. 191s entropymark=f Mark each base with its entropy value. This is on a scale 191s of 0-41 and is reported as quality scores, so the output 191s should be fastq or fasta+qual. 191s NOTE: If set, entropytrim overrides entropymask. 191s 191s Cardinality estimation: 191s cardinality=f (loglog) Count unique kmers using the LogLog algorithm. 191s cardinalityout=f (loglogout) Count unique kmers in output reads. 191s loglogk=31 Use this kmer length for counting. 191s loglogbuckets=2048 Use this many buckets for counting. 191s khist= Kmer frequency histogram; plots number of kmers versus 191s kmer depth. This is approximate. 191s khistout= Kmer frequency histogram for output reads. 191s 191s Side Channel: 191s sideout= Output for aligned reads. 191s sideref=phix Reference for side-channel alignment; must be a single 191s sequence and virtually repeat-free at selected k. 191s sidek1=17 Kmer length for seeding alignment to reference. 191s sidek2=13 Kmer length for seeding alignment of unaligned reads 191s with an aligned mate. 191s sideminid1=0.66 Minimum identity to accept individual alignments. 191s sideminid2=0.58 Minimum identity for aligning reads with aligned mates. 191s sidemm1=1 Middle mask length for sidek1. 191s sidemm2=1 Middle mask length for sidek2. 191s Note: The side channel is a special additional output that allows alignment 191s to a secondary reference while also doing trimming. Alignment does not affect 191s whether reads go to the normal outputs (out, outm). The main purpose is to 191s simplify pipelines that need trimmed, aligned phiX reads for recalibration. 191s 191s 191s Java Parameters: 191s 191s -Xmx This will set Java's memory usage, overriding autodetection. 191s -Xmx20g will 191s specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 191s The max is typically 85% of physical memory. 191s -eoom This flag will cause the process to exit if an 191s out-of-memory exception occurs. Requires Java 8u92+. 191s -da Disable assertions. 191s 191s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 191s 191s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 191s java -ea -Xmx2000m -Xms2000m -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 191s 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] 191s Version 39.20 191s 191s Changed from ASCII-33 to ASCII-64 on input quality X (Q55) for base A at lines 1 and 3, position 24 while prescanning. 191s Changed from ASCII-33 to ASCII-64 on input quality X (Q55) for base A at lines 1 and 3, position 24 while prescanning. 191s Allocating kmer table: 0.033 seconds. 191s Initial: 191s Memory: max=2097m, total=2097m, free=2077m, used=20m 191s 191s Input is being processed as paired 191s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 191s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 191s Started output streams: 0.035 seconds. 191s Processing time: 0.007 seconds. 191s 191s Input: 8 reads 306 bases. 191s QTrimmed: 0 reads (0.00%) 0 bases (0.00%) 191s Total Removed: 8 reads (100.00%) 306 bases (100.00%) 191s Result: 0 reads (0.00%) 0 bases (0.00%) 191s 191s Time: 0.044 seconds. 191s Reads Processed: 8 0.18k reads/sec 191s Bases Processed: 306 0.01m bases/sec 191s test -r out.fastq.gz 191s 191s # bbnorm 191s bbnorm.sh --version 192s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 192s java -ea -Xmx2000m -Xms2000m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 --version 192s BBTools version 39.20 192s For help, please run the shellscript with no parameters, or look in /docs/. 192s bbnorm.sh --help 192s 192s Written by Brian Bushnell 192s Last modified October 19, 2017 192s 192s Description: Normalizes read depth based on kmer counts. 192s Can also error-correct, bin reads by kmer depth, and generate a kmer depth histogram. 192s However, Tadpole has superior error-correction to BBNorm. 192s Please read bbmap/docs/guides/BBNormGuide.txt for more information. 192s 192s Usage: bbnorm.sh in= out= outt= hist= 192s 192s Input parameters: 192s in=null Primary input. Use in2 for paired reads in a second file 192s in2=null Second input file for paired reads in two files 192s extra=null Additional files to use for input (generating hash table) but not for output 192s fastareadlen=2^31 Break up FASTA reads longer than this. Can be useful when processing scaffolded genomes 192s tablereads=-1 Use at most this many reads when building the hashtable (-1 means all) 192s kmersample=1 Process every nth kmer, and skip the rest 192s readsample=1 Process every nth read, and skip the rest 192s 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. 192s qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto. 192s 192s Output parameters: 192s out= File for normalized or corrected reads. Use out2 for paired reads in a second file 192s outt= (outtoss) File for reads that were excluded from primary output 192s reads=-1 Only process this number of reads, then quit (-1 means all) 192s sampleoutput=t Use sampling on output as well as input (not used if sample rates are 1) 192s keepall=f Set to true to keep all reads (e.g. if you just want error correction). 192s 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. 192s Default is false, to prevent confusion about how there can be 0-count kmers. 192s The reason is that based on the 'minq' and 'minprob' settings, some kmers may be excluded from the bloom filter. 192s tmpdir= This will specify a directory for temp files (only needed for multipass runs). If null, they will be written to the output directory. 192s usetempdir=t Allows enabling/disabling of temporary directory; if disabled, temp files will be written to the output directory. 192s qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input). 192s rename=f Rename reads based on their kmer depth. 192s 192s Hashing parameters: 192s k=31 Kmer length (values under 32 are most efficient, but arbitrarily high values are supported) 192s 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. 192s Large values decrease accuracy for a fixed amount of memory, so use the lowest number you can that will still capture highest-depth kmers. 192s hashes=3 Number of times each kmer is hashed and stored. Higher is slower. 192s Higher is MORE accurate if there is enough memory, and LESS accurate if there is not enough memory. 192s 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. 192s prehashes=2 Number of hashes for prefilter. 192s prefilterbits=2 (pbits) Bits per cell in prefilter. 192s prefiltersize=0.35 Fraction of memory to allocate to prefilter. 192s buildpasses=1 More passes can sometimes increase accuracy by iteratively removing low-depth kmers 192s minq=6 Ignore kmers containing bases with quality below this 192s minprob=0.5 Ignore kmers with overall probability of correctness below this 192s 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. 192s 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. 192s 192s Normalization parameters: 192s fixspikes=f (fs) Do a slower, high-precision bloom filter lookup of kmers that appear to have an abnormally high depth due to collisions. 192s target=100 (tgt) Target normalization depth. NOTE: All depth parameters control kmer depth, not read depth. 192s For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1)) 192s maxdepth=-1 (max) Reads will not be downsampled when below this depth, even if they are above the target depth. 192s mindepth=5 (min) Kmers with depth below this number will not be included when calculating the depth of a read. 192s minkmers=15 (mgkpr) Reads must have at least this many kmers over min depth to be retained. Aka 'mingoodkmersperread'. 192s 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. 192s uselowerdepth=t (uld) For pairs, use the depth of the lower read as the depth proxy. 192s deterministic=t (dr) Generate random numbers deterministically to ensure identical output between multiple runs. May decrease speed with a huge number of threads. 192s passes=2 (p) 1 pass is the basic mode. 2 passes (default) allows greater accuracy, error detection, better contol of output depth. 192s 192s Error detection parameters: 192s hdp=90.0 (highdepthpercentile) Position in sorted kmer depth array used as proxy of a read's high kmer depth. 192s ldp=25.0 (lowdepthpercentile) Position in sorted kmer depth array used as proxy of a read's low kmer depth. 192s tossbadreads=f (tbr) Throw away reads detected as containing errors. 192s requirebothbad=f (rbb) Only toss bad pairs if both reads are bad. 192s 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. 192s highthresh=12 (ht) Threshold for high kmer. A high kmer at this or above are considered non-error. 192s lowthresh=3 (lt) Threshold for low kmer. Kmers at this and below are always considered errors. 192s 192s Error correction parameters: 192s ecc=f Set to true to correct errors. NOTE: Tadpole is now preferred for ecc as it does a better job. 192s ecclimit=3 Correct up to this many errors per read. If more are detected, the read will remain unchanged. 192s errorcorrectratio=140 (ecr) Adjacent kmers with a depth ratio of at least this much between will be classified as an error. 192s echighthresh=22 (echt) Threshold for high kmer. A kmer at this or above may be considered non-error. 192s eclowthresh=2 (eclt) Threshold for low kmer. Kmers at this and below are considered errors. 192s eccmaxqual=127 Do not correct bases with quality above this value. 192s aec=f (aggressiveErrorCorrection) Sets more aggressive values of ecr=100, ecclimit=7, echt=16, eclt=3. 192s cec=f (conservativeErrorCorrection) Sets more conservative values of ecr=180, ecclimit=2, echt=30, eclt=1, sl=4, pl=4. 192s meo=f (markErrorsOnly) Marks errors by reducing quality value of suspected errors; does not correct anything. 192s mue=t (markUncorrectableErrors) Marks errors only on uncorrectable reads; requires 'ecc=t'. 192s overlap=f (ecco) Error correct by read overlap. 192s 192s Depth binning parameters: 192s lowbindepth=10 (lbd) Cutoff for low depth bin. 192s highbindepth=80 (hbd) Cutoff for high depth bin. 192s outlow= Pairs in which both reads have a median below lbd go into this file. 192s outhigh= Pairs in which both reads have a median above hbd go into this file. 192s outmid= All other pairs go into this file. 192s 192s Histogram parameters: 192s hist= Specify a file to write the input kmer depth histogram. 192s histout= Specify a file to write the output kmer depth histogram. 192s histcol=3 (histogramcolumns) Number of histogram columns, 2 or 3. 192s pzc=f (printzerocoverage) Print lines in the histogram with zero coverage. 192s histlen=1048576 Max kmer depth displayed in histogram. Also affects statistics displayed, but does not affect normalization. 192s 192s Peak calling parameters: 192s peaks= Write the peaks to this file. Default is stdout. 192s minHeight=2 (h) Ignore peaks shorter than this. 192s minVolume=5 (v) Ignore peaks with less area than this. 192s minWidth=3 (w) Ignore peaks narrower than this. 192s minPeak=2 (minp) Ignore peaks with an X-value below this. 192s maxPeak=BIG (maxp) Ignore peaks with an X-value above this. 192s maxPeakCount=8 (maxpc) Print up to this many peaks (prioritizing height). 192s 192s Java Parameters: 192s -Xmx This will set Java's memory usage, overriding autodetection. 192s -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 192s The max is typically 85% of physical memory. 192s -eoom This flag will cause the process to exit if an 192s out-of-memory exception occurs. Requires Java 8u92+. 192s -da Disable assertions. 192s 192s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 192s 192s bbnorm.sh in=sanger_full_range_original_sanger.fastq qin=33 \ 192s out=out3.fastq outt=outt.fastq hist=hist.plt 192s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 192s java -ea -Xmx2000m -Xms2000m -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 192s Executing jgi.KmerNormalize [bits=32, in=sanger_full_range_original_sanger.fastq, qin=33, out=out3.fastq, outt=outt.fastq, hist=hist.plt] 192s 192s 192s *********** Pass 1 ********** 192s 192s 192s Settings: 192s threads: 8 192s k: 31 192s deterministic: true 192s toss error reads: false 192s passes: 1 192s bits per cell: 16 192s cells: 729.90M 192s hashes: 3 192s base min quality: 5 192s kmer min prob: 0.5 192s 192s target depth: 400 192s min depth: 3 192s max depth: 500 192s min good kmers: 15 192s depth percentile: 64.8 192s ignore dupe kmers: true 192s fix spikes: false 192s histogram length: 65536 192s print zero cov: false 192s 193s Made hash table: hashes = 3 mem = 1.36 GB cells = 729.70M used = 0.000% 193s 193s Estimated unique kmers: 4 193s 193s Table creation time: 0.838 seconds. 193s Started output threads. 193s Started output threads. 193s Table read time: 0.013 seconds. 14.16 kb/sec 193s Total reads in: 2 0.000% Kept 193s Total bases in: 188 0.000% Kept 193s Error reads in: 2 100.000% 193s Error type 1: 2 100.000% 193s Error type 2: 0 0.000% 193s Error type 3: 0 0.000% 193s 193s Wrote histogram to hist.plt 193s Total kmers counted: 128 193s Total unique kmer count: 128 193s Includes forward kmers only. 193s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 193s The most accurate value is the greater of the two. 193s 193s Percent unique: 100.00% 193s Depth average: 1.00 (unique kmers) 193s Depth median: 1 (unique kmers) 193s Depth standard deviation: 0.00 (unique kmers) 193s Corrected depth average: 0.00 193s 193s Depth average: 1.00 (all kmers) 193s Depth median: 1 (all kmers) 193s Depth standard deviation: 0.00 (all kmers) 193s 193s Approx. read depth median: 1.47 193s 193s *********** Pass 2 ********** 193s 193s 193s Settings: 193s threads: 8 193s k: 31 193s deterministic: true 193s toss error reads: false 193s passes: 1 193s bits per cell: 16 193s cells: 729.90M 193s hashes: 3 193s base min quality: 5 193s kmer min prob: 0.5 193s 193s target depth: 100 193s min depth: 5 193s max depth: 100 193s min good kmers: 15 193s depth percentile: 54.0 193s ignore dupe kmers: true 193s fix spikes: false 193s histogram length: 65536 193s 194s Made hash table: hashes = 3 mem = 1.36 GB cells = 729.70M used = 0.000% 194s 194s Estimated unique kmers: 0 194s 194s Table creation time: 0.307 seconds. 194s Started output threads. 194s Started output threads. 194s Table read time: 0.004 seconds. 0.00 kb/sec 194s Total reads in: 0 NaN% Kept 194s Total bases in: 0 NaN% Kept 194s Error reads in: 0 NaN% 194s Error type 1: 0 NaN% 194s Error type 2: 0 NaN% 194s Error type 3: 0 NaN% 194s Total kmers counted: 0 194s Total unique kmer count: 0 194s Includes forward kmers only. 194s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 194s The most accurate value is the greater of the two. 194s 194s Percent unique: NaN% 194s Depth average: NaN (unique kmers) 194s Depth median: 0 (unique kmers) 194s Depth standard deviation: NaN (unique kmers) 194s Corrected depth average: NaN 194s 194s Depth average: NaN (all kmers) 194s Depth median: 0 (all kmers) 194s Depth standard deviation: 0.00 (all kmers) 194s 194s Approx. read depth median: NaN 194s 194s Removing temp files. 194s 194s Total time: 1.634 seconds. 0.12 kb/sec 194s test -r out3.fastq 194s test -r outt.fastq 194s test -r hist.plt 194s bbnorm.sh in=illumina_full_range_original_illumina.fastq qin=64 \ 194s out=out4.fastq outt=outt2.fastq hist=hist2.plt 194s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 194s java -ea -Xmx2000m -Xms2000m -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 194s Executing jgi.KmerNormalize [bits=32, in=illumina_full_range_original_illumina.fastq, qin=64, out=out4.fastq, outt=outt2.fastq, hist=hist2.plt] 194s 194s 194s *********** Pass 1 ********** 194s 194s 194s Settings: 194s threads: 8 194s k: 31 194s deterministic: true 194s toss error reads: false 194s passes: 1 194s bits per cell: 16 194s cells: 729.90M 194s hashes: 3 194s base min quality: 5 194s kmer min prob: 0.5 194s 194s target depth: 400 194s min depth: 3 194s max depth: 500 194s min good kmers: 15 194s depth percentile: 64.8 194s ignore dupe kmers: true 194s fix spikes: false 194s histogram length: 65536 194s print zero cov: false 194s 195s Made hash table: hashes = 3 mem = 1.36 GB cells = 729.70M used = 0.000% 195s 195s Estimated unique kmers: 4 195s 195s Table creation time: 0.787 seconds. 195s Started output threads. 195s Started output threads. 195s Table read time: 0.013 seconds. 9.75 kb/sec 195s Total reads in: 2 0.000% Kept 195s Total bases in: 126 0.000% Kept 195s Error reads in: 2 100.000% 195s Error type 1: 2 100.000% 195s Error type 2: 0 0.000% 195s Error type 3: 0 0.000% 195s 195s Wrote histogram to hist2.plt 195s Total kmers counted: 66 195s Total unique kmer count: 66 195s Includes forward kmers only. 195s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 195s The most accurate value is the greater of the two. 195s 195s Percent unique: 100.00% 195s Depth average: 1.00 (unique kmers) 195s Depth median: 1 (unique kmers) 195s Depth standard deviation: 0.00 (unique kmers) 195s Corrected depth average: 0.00 195s 195s Depth average: 1.00 (all kmers) 195s Depth median: 1 (all kmers) 195s Depth standard deviation: 0.00 (all kmers) 195s 195s Approx. read depth median: 1.91 195s 195s *********** Pass 2 ********** 195s 195s 195s Settings: 195s threads: 8 195s k: 31 195s deterministic: true 195s toss error reads: false 195s passes: 1 195s bits per cell: 16 195s cells: 729.90M 195s hashes: 3 195s base min quality: 5 195s kmer min prob: 0.5 195s 195s target depth: 100 195s min depth: 5 195s max depth: 100 195s min good kmers: 15 195s depth percentile: 54.0 195s ignore dupe kmers: true 195s fix spikes: false 195s histogram length: 65536 195s 196s Made hash table: hashes = 3 mem = 1.36 GB cells = 729.70M used = 0.000% 196s 196s Estimated unique kmers: 0 196s 196s Table creation time: 0.284 seconds. 196s Started output threads. 196s Started output threads. 196s Table read time: 0.004 seconds. 0.00 kb/sec 196s Total reads in: 0 NaN% Kept 196s Total bases in: 0 NaN% Kept 196s Error reads in: 0 NaN% 196s Error type 1: 0 NaN% 196s Error type 2: 0 NaN% 196s Error type 3: 0 NaN% 196s Total kmers counted: 0 196s Total unique kmer count: 0 196s Includes forward kmers only. 196s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 196s The most accurate value is the greater of the two. 196s 196s Percent unique: NaN% 196s Depth average: NaN (unique kmers) 196s Depth median: 0 (unique kmers) 196s Depth standard deviation: NaN (unique kmers) 196s Corrected depth average: NaN 196s 196s Depth average: NaN (all kmers) 196s Depth median: 0 (all kmers) 196s Depth standard deviation: 0.00 (all kmers) 196s 196s Approx. read depth median: NaN 196s 196s Removing temp files. 196s 196s Total time: 1.564 seconds. 0.08 kb/sec 200s test -r out4.fastq 200s test -r outt2.fastq 200s test -r hist2.plt 200s autopkgtest [11:17:42]: test run-unit-test: -----------------------] 204s autopkgtest [11:17:46]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 204s run-unit-test PASS 208s autopkgtest [11:17:50]: @@@@@@@@@@@@@@@@@@@@ summary 208s run-unit-test PASS