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[svtoolkit-help] (no subject)
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From: Peng C. <ant...@gm...> - 2015-02-05 23:13:42
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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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