Re: [svtoolkit-help] (no subject)
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Re: [svtoolkit-help] (no subject)
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From: Bob H. <han...@br...> - 2015-02-06 16:19:57
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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
>
>
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