Re: [svtoolkit-help] genomestrip CNV pipeline
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Re: [svtoolkit-help] genomestrip CNV pipeline
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From: Peng C. <ant...@gm...> - 2015-02-17 22:37:26
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Hi Bob, I tested the new version r1533. It works perfect. Thank you for your help. Peng On Sat, Feb 7, 2015 at 5:00 AM, < svt...@li...> wrote: > Send svtoolkit-help mailing list submissions to > svt...@li... > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help > or, via email, send a message with subject or body 'help' to > svt...@li... > > You can reach the person managing the list at > svt...@li... > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of svtoolkit-help digest..." > > > Today's Topics: > > 1. Re: (no subject) (Bob Handsaker) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 06 Feb 2015 11:19:47 -0500 > From: Bob Handsaker <han...@br...> > Subject: Re: [svtoolkit-help] (no subject) > To: svt...@li... > Cc: Seva Kashin <sk...@br...> > Message-ID: <54D...@br...> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, Peng, > > This was reported by a couple of other people too. > The code was expecting a bed file specifying the locations of V(D)J > recombination regions as part of the metadata bundle (and was failing if > this file was not found). > So this affects people who are not using one of the pre-built reference > metadata bundles. > > We just pushed out a new release (r1533) that fixes this problem (now if > there is no reference.vdjregions.bed file, then VDJ flagging/filtering > will just not be done). > If you need to use the previous release for some reason, there are two > workarounds: Either create a small dummy vdjregions.bed file or edit > the Queue scripts to remove this. > > If you encounter more problems, let us know. > > -Bob > > On 2/5/15, 6:13 PM, Peng Chen wrote: > > I am trying to run the CNV pipeline of genomestrip 2.0. However, I got > > an error message that I can not figure out what is wrong. I would > > appreciate if you could help me out of here. The command I ran and > > part of the log file is in the following. > > > > java -cp ${classpath} ${mx} \ > > org.broadinstitute.gatk.queue.QCommandLine \ > > -S ${SV_DIR}/qscript/discovery/cnv/CNVDiscoveryPipeline.q \ > > -S ${SV_DIR}/qscript/SVQScript.q \ > > -cp ${classpath} \ > > -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \ > > -configFile ${SV_DIR}/conf/genstrip_parameters.txt \ > > -R /home/chenp4/cp/sv/fastqc/cp-qced/fq/gs/gmask/hg38_chr21.fasta \ > > -genomeMaskFile > > /home/chenp4/cp/sv/fastqc/cp-qced/fq/gs/gmask/hg38_mask_100_chr21.fasta \ > > -I ${bam} \ > > -genderMapFile ${SV_DIR}/gender_map \ > > -md > > /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/batch2_run/metadata \ > > -runDirectory ${runDir} \ > > -jobLogDir ${runDir}/logs \ > > -ploidyMapFile > > /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/chr21_ploidymayfile.txt \ > > -tilingWindowSize 1000 \ > > -tilingWindowOverlap 500 \ > > -maximumReferenceGapLength 1000 \ > > -boundaryPrecision 100 \ > > -minimumRefinedLength 500 \ > > -run > > > > > > > ------------------------------------------------------------------------------------------------------------ > > The error message: > > > > INFO 14:18:05,148 HelpFormatter - Program Args: -cp > > > /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/lib/SVToolkit.jar:/home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/lib/gatk/Queue.jar > > -S > > /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/qscript/SVGenotyper2.q > > -S /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/qscript/SVQScript.q > > -gatk > > > /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/lib/gatk/GenomeAnalysisTK.jar > > -jobLogDir > > > /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/batch1_run/cnv_stage2/seq_chr21/logs > > -memLimit 2.0 -jobRunner Shell -gatkJobRunner Shell -run > > --disableJobReport -configFile > > > /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/conf/genstrip_parameters.txt > > -P depth.readCountCacheIgnoreGenomeMask:true -P > > genotyping.modules:depth -R > > /home/chenp4/cp/sv/fastqc/cp-qced/fq/gs/gmask/hg38_chr21.fasta > > -genomeMaskFile > > /home/chenp4/cp/sv/fastqc/cp-qced/fq/gs/gmask/hg38_mask_100_chr21.fasta > -ploidyMapFile > > /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/chr21_ploidymayfile.txt > > -genderMapFile > > /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/gender_map -md > > /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/batch2_run/metadata > > -disableGATKTraversal -vcf > > > /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/batch1_run/cnv_stage1/seq_chr21/seq_chr21.sites.vcf > > -parallelRecords 1000 -I > > > /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/batch1_run/bam_headers/merged_headers.bam > > -O > > > /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/batch1_run/cnv_stage2/seq_chr21/seq_chr21.genotypes.vcf > > -runDirectory > > > /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/batch1_run/cnv_stage2/seq_chr21 > > -duplicateScoreThreshold 0.0 > > INFO 14:18:05,150 HelpFormatter - Executing as p692 on Linux > > 2.6.18-128.el5 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_05-b06. > > INFO 14:18:05,150 HelpFormatter - Date/Time: 2015/02/05 14:18:05 > > INFO 14:18:05,150 HelpFormatter - > > ---------------------------------------------------------------------- > > INFO 14:18:05,150 HelpFormatter - > > ---------------------------------------------------------------------- > > INFO 14:18:05,160 QCommandLine - Scripting SVGenotyper > > INFO 14:18:05,800 QCommandLine - Done with errors > > ##### ERROR > > > ------------------------------------------------------------------------------------------ > > ##### ERROR stack trace > > > org.broadinstitute.gatk.utils.exceptions.UserException$CannotExecuteQScript: > > Unable to execute QScript: SVGenotyper.script() threw the following > > exception: java.lang.NullPointerException > > at > > > org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:159) > > at > > > org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:147) > > at scala.collection.Iterator$class.foreach(Iterator.scala:727) > > at scala.collection.AbstractIterator.foreach(Iterator.scala:1157) > > at > > scala.collection.IterableLike$class.foreach(IterableLike.scala:72) > > at scala.collection.AbstractIterable.foreach(Iterable.scala:54) > > at > > > org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:147) > > at > > > org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248) > > at > > > org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155) > > at > > org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:62) > > at > > org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala) > > Caused by: java.lang.NullPointerException > > at > > > org.broadinstitute.sv.qscript.SVQScript$GenotyperDefaultFilterAnnotations.<init>(SVQScript.q:1133) > > at SVGenotyper.script(SVGenotyper2.q:37) > > at > > > org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:156) > > ... 10 more > > ##### ERROR > > > ------------------------------------------------------------------------------------------ > > ##### ERROR A GATK RUNTIME ERROR has occurred (version <unknown>): > > ##### ERROR > > ##### ERROR This might be a bug. Please check the documentation guide > > to see if this is a known problem. > > ##### ERROR If not, please post the error message, with stack trace, > > to the GATK forum. > > ##### ERROR Visit our website and forum for extensive documentation > > and answers to > > ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk > > ##### ERROR > > ##### ERROR MESSAGE: Unable to execute QScript: SVGenotyper.script() > > threw the following exception: java.lang.NullPointerException > > ##### ERROR > > > ------------------------------------------------------------------------------------------ > > INFO 14:18:05,807 QCommandLine - Shutting down jobs. Please wait... > > INFO 14:18:17,930 QGraph - Writing incremental jobs reports... > > INFO 14:18:17,930 QGraph - 2 Pend, 0 Run, 1 Fail, 0 Done > > INFO 14:18:17,933 QCommandLine - Writing final jobs report... > > INFO 14:18:17,934 QCommandLine - Done with errors > > INFO 14:18:17,936 QGraph - ------- > > > > > > Thank you. > > Peng > > > > > > > ------------------------------------------------------------------------------ > > Dive into the World of Parallel Programming. The Go Parallel Website, > > sponsored by Intel and developed in partnership with Slashdot Media, is > your > > hub for all things parallel software development, from weekly thought > > leadership blogs to news, videos, case studies, tutorials and more. Take > a > > look and join the conversation now. http://goparallel.sourceforge.net/ > > > > > > _______________________________________________ > > svtoolkit-help mailing list > > svt...@li... > > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help > > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > > ------------------------------------------------------------------------------ > Dive into the World of Parallel Programming. The Go Parallel Website, > sponsored by Intel and developed in partnership with Slashdot Media, is > your > hub for all things parallel software development, from weekly thought > leadership blogs to news, videos, case studies, tutorials and more. Take a > look and join the conversation now. http://goparallel.sourceforge.net/ > > ------------------------------ > > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help > > > End of svtoolkit-help Digest, Vol 31, Issue 2 > ********************************************* > |
