{"id":280,"date":"2013-10-31T14:19:40","date_gmt":"2013-10-31T14:19:40","guid":{"rendered":"https:\/\/blogs.ncl.ac.uk\/igmit\/?p=280"},"modified":"2013-10-31T14:23:18","modified_gmt":"2013-10-31T14:23:18","slug":"hpc-lampredi-software-update-mutect-1-1-4","status":"publish","type":"post","link":"https:\/\/blogs.ncl.ac.uk\/igmit\/?p=280","title":{"rendered":"HPC \u2013 Lampredi \u2013 software update \u2013 MuTect 1.1.4"},"content":{"rendered":"

MuTect 1.1.4 has been added to the cluster (31\/10\/2013)<\/p>\n

MuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.<\/p>\n

\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014-
\n$ module load apps\/mutect
\napps\/mutect\/1.1.4\/bin
\n|
\nOK<\/p>\n

$ ls $MUTECTDIR
\nbin doc java<\/p>\n

$ ls $MUTECTDIR\/*
\n\/opt\/gridware\/pkg\/apps\/mutect\/1.1.4\/bin\/bin:
\nmutect muTect<\/p>\n

\/opt\/gridware\/pkg\/apps\/mutect\/1.1.4\/bin\/doc:
\nLICENSE.TXT version.txt<\/p>\n

\/opt\/gridware\/pkg\/apps\/mutect\/1.1.4\/bin\/java:
\nmuTect.jar<\/p>\n

$ mutect
\n---------------------------------------------------------------------------------
\nThe Genome Analysis Toolkit (GATK) v2.2-25-g2a68eab, Compiled 2012\/11\/08 10:30:02
\nCopyright (c) 2010 The Broad Institute
\nFor support and documentation go to http:\/\/www.broadinstitute.org\/gatk
\n---------------------------------------------------------------------------------
\n---------------------------------------------------------------------------------
\nusage: java -jar muTect.jar -T [-args ] [-I ] [-rbs ] [-et
\n] [-K ] [-tag ] [-rf ] [-L ] [-XL ] [-isr
\n] [-im ] [-ip ] [-R ] [-ndrs]
\n[--disableRandomization] [-maxRuntime ] [-maxRuntimeUnits ] [-dt ]
\n[-dfrac ] [-dcov ] [-baq ] [-baqGOP ] [-PF
\n] [-OQ] [-BQSR ] [-DIQ] [-EOQ] [-preserveQ ] [-DBQ
\n] [-S ] [-rpr] [-kpr] [-U ] [-nt ] [-nct
\n] [-mte] [-bfh ] [-rgbl ] [-ped
\n] [-pedString ] [-pedValidationType ] [-l ] [-log
\n] [-h]<\/p>\n

-T,--analysis_type Type of analysis to run<\/p>\n

[snip]<\/p>\n

##### ERROR ------------------------------------------------------------------------------------------
\n##### ERROR A USER ERROR has occurred (version 2.2-25-g2a68eab):
\n##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
\n##### ERROR Please do not post this error to the GATK forum
\n##### ERROR
\n##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
\n##### ERROR Visit our website and forum for extensive documentation and answers to
\n##### ERROR commonly asked questions http:\/\/www.broadinstitute.org\/gatk
\n##### ERROR
\n##### ERROR MESSAGE: Argument with name '--analysis_type' (-T) is missing.
\n##### ERROR ------------------------------------------------------------------------------------------
\n<\/code>
\n\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014-<\/p>\n

$ module whatis apps\/mutect
\napps\/mutect :<\/p>\n

Title: MuTect
\nSummary: Reliable and accurate identification of somatic point mutations
\nLicense: NONFREE - Free for academic non-commercial research purposes only; see http:\/\/j.mp\/10q7Mmv
\nGroup: Bioinformatics
\nURL: http:\/\/www.broadinstitute.org\/cancer\/cga\/mutect<\/p>\n

Name: mutect
\nVersion: 1.1.4
\nModule: apps\/mutect\/1.1.4\/bin
\nModule path: \/opt\/gridware\/etc\/modules\/apps\/mutect\/1.1.4\/bin
\nPackage path: \/opt\/gridware\/pkg\/apps\/mutect\/1.1.4\/bin<\/p>\n

Repository: git+http:\/\/download.alces-software.com\/git\/packager-base@8cca844
\nPackage: ext\/mutect\/@3956ddde
\nLast update: 2013-04-03<\/p>\n

Builder: root@headnode1.lampredi.cluster.local
\nBuild date: 2013-10-31T12:42:07
\nBuild parameters: zipfile=\/opt\/gridware\/ext\/muTect-1.1.4-bin.zip
\nCompiler: N\/A<\/p>\n

For further information, execute:<\/p>\n

module help apps\/mutect\/1.1.4\/bin
\n<\/code>
\n\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014-<\/p>\n

$ module help apps\/mutect\/1.1.4\/bin<\/p>\n

----------- Module Specific Help for 'apps\/mutect\/1.1.4\/bin' ---------------------------<\/p>\n

======== MuTect ========
\nReliable and accurate identification of somatic point
\nmutations
\n=======================<\/p>\n

This module sets up your environment for the use of the 'mutect'
\napplication. This module sets up version '1.1.4' of the
\napplication.<\/p>\n

>> SYNOPSIS <> LICENSING <> FURTHER INFORMATION <> GET STARTED <<<\/p>\n

Please refer to the website for further details on usage of this
\npackage.<\/code><\/p>\n

\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014-<\/p>\n

$ module show apps\/mutect\/1.1.4\/bin
\n-------------------------------------------------------------------
\n\/opt\/gridware\/etc\/modules\/apps\/mutect\/1.1.4\/bin<\/p>\n

module-whatis<\/p>\n

Title: MuTect
\nSummary: Reliable and accurate identification of somatic point mutations
\nLicense: NONFREE - Free for academic non-commercial research purposes only; see http:\/\/j.mp\/10q7Mmv
\nGroup: Bioinformatics
\nURL: http:\/\/www.broadinstitute.org\/cancer\/cga\/mutect<\/p>\n

Name: mutect
\nVersion: 1.1.4
\nModule: apps\/mutect\/1.1.4\/bin
\nModule path: \/opt\/gridware\/etc\/modules\/apps\/mutect\/1.1.4\/bin
\nPackage path: \/opt\/gridware\/pkg\/apps\/mutect\/1.1.4\/bin<\/p>\n

Repository: git+http:\/\/download.alces-software.com\/git\/packager-base@8cca844
\nPackage: ext\/mutect\/@3956ddde
\nLast update: 2013-04-03<\/p>\n

Builder: root@headnode1.lampredi.cluster.local
\nBuild date: 2013-10-31T12:42:07
\nBuild parameters: zipfile=\/opt\/gridware\/ext\/muTect-1.1.4-bin.zip
\nCompiler: N\/A<\/p>\n

For further information, execute:<\/p>\n

module help apps\/mutect\/1.1.4\/bin<\/p>\n

module-conflict apps\/mutect
\nsetenv MUTECTDIR \/opt\/gridware\/pkg\/apps\/mutect\/1.1.4\/bin
\nsetenv MUTECTBIN \/opt\/gridware\/pkg\/apps\/mutect\/1.1.4\/bin\/bin
\nsetenv MUTECTDOC \/opt\/gridware\/pkg\/apps\/mutect\/1.1.4\/bin\/doc
\nsetenv MUTECTJAVA \/opt\/gridware\/pkg\/apps\/mutect\/1.1.4\/bin\/java
\nsetenv MUTECT_JAVA_MEM_MX 2g
\nsetenv MUTECT_JAVA_TMPDIR \/tmp
\nsetenv MUTECT_JAVA_OPTS -Xmx$MUTECT_JAVA_MEM_MX -Djava.io.tmpdir=$MUTECT_JAVA_TMPDIR
\nprepend-path PATH \/opt\/gridware\/pkg\/apps\/mutect\/1.1.4\/bin\/bin
\n<\/code>
\n\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014-<\/p>\n

Lampredi HPC
\nigm-lampredi-users@ncl.ac.uk<\/p>\n

IGM IT
\nigmithelp@ncl.ac.uk
\nx8625<\/p>\n","protected":false},"excerpt":{"rendered":"

MuTect 1.1.4 has been added to the cluster (31\/10\/2013) MuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes. \u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014- $ module load apps\/mutect apps\/mutect\/1.1.4\/bin | OK $ ls $MUTECTDIR bin doc java $ ls $MUTECTDIR\/* \/opt\/gridware\/pkg\/apps\/mutect\/1.1.4\/bin\/bin: mutect […]<\/a><\/p>\n","protected":false},"author":1149,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[11,10,9,21,22],"class_list":["post-280","post","type-post","status-publish","format-standard","hentry","category-uncategorized","tag-cluster","tag-hpc","tag-lampredi","tag-lampredi2","tag-linux","category-1-id","post-seq-1","post-parity-odd","meta-position-corners","fix"],"_links":{"self":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/280","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/users\/1149"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=280"}],"version-history":[{"count":8,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/280\/revisions"}],"predecessor-version":[{"id":288,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/280\/revisions\/288"}],"wp:attachment":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=280"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=280"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=280"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}