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CNV_Stage7 failed using SVToolkit version 2.00 (build 1592)

SunhyeSunhye KoreaMember
edited June 2015 in GenomeSTRiP

Hi
I used GenomeSTRiP2.0 r1592 and ran CNVDiscoveryPipeline.q.
I encountered error in CNV_stage7.
In CNV_stage7, Some chromosomes was done successfully but the others was failed .

In cnv_sentinel_files

ll .stage_7* | awk '{print $9}' 
.stage_7_seq_10.sent.done
.stage_7_seq_11.sent.done
.stage_7_seq_12.sent.done
.stage_7_seq_13.sent.fail
.stage_7_seq_14.sent.done
.stage_7_seq_15.sent.done
.stage_7_seq_16.sent.fail
.stage_7_seq_17.sent.fail
.stage_7_seq_18.sent.done
.stage_7_seq_19.sent.fail
.stage_7_seq_1.sent.done
.stage_7_seq_20.sent.fail
.stage_7_seq_21.sent.done
.stage_7_seq_22.sent.fail
.stage_7_seq_2.sent.fail
.stage_7_seq_3.sent.done
.stage_7_seq_4.sent.done
.stage_7_seq_5.sent.done
.stage_7_seq_6.sent.done
.stage_7_seq_7.sent.fail
.stage_7_seq_8.sent.done
.stage_7_seq_9.sent.done
.stage_7_seq_X.sent.done
.stage_7_seq_Y.sent.fail

So I removed .*fail files and I ran again.
But... Same problem occured.

INFO  10:05:58,332 HelpFormatter - Executing as [email protected] on Linux 3.16.0-031600-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_25-b17. 
INFO  10:05:58,333 HelpFormatter - Date/Time: 2015/06/30 10:05:58 
INFO  10:05:58,333 HelpFormatter - ------------------------------------------------------------------ 
INFO  10:05:58,333 HelpFormatter - ------------------------------------------------------------------ 
INFO  10:05:58,383 RefineCNVBoundaries - Opening reference sequence ... 
INFO  10:05:58,386 RefineCNVBoundaries - Opened reference sequence. 
INFO  10:05:58,387 RefineCNVBoundaries - Opening genome mask ... 
INFO  10:05:58,388 RefineCNVBoundaries - Opened genome mask. 
INFO  10:05:58,391 MetaData - Opening metadata ...  
INFO  10:05:58,391 MetaData - Adding metadata directory WGS_SV/metadata ... 
INFO  10:05:58,393 MetaData - Opened metadata. 
INFO  10:05:58,420 RefineCNVBoundaries - Initializing input data set ... 
INFO  10:05:58,516 RefineCNVBoundaries - Initialized data set: 1 file, 490 read groups, 40 samples. 
INFO  10:05:58,647 ReadCountDiskCache - Initializing read count disk cache [WGS_SV/metadata/rccache.bin] ... 
INFO  10:05:58,648 ReadCountDiskCache - Initialized read count disk cache with 1 file. 
Exception in thread "main" java.lang.RuntimeException
    at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:65)
    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.sv.commandline.CommandLineProgram.runAndReturnResult(CommandLineProgram.java:29)
    at org.broadinstitute.sv.commandline.CommandLineProgram.run(CommandLineProgram.java:25)
    at org.broadinstitute.sv.genotyping.RefineCNVBoundaries.main(RefineCNVBoundaries.java:128)
Caused by: java.lang.NullPointerException
    at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.computeModelFrequencyScore2(BoundaryRefinementAlgorithm.java:430)
    at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.genotypeCnp(BoundaryRefinementAlgorithm.java:281)
    at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.refineOneBoundary(BoundaryRefinementAlgorithm.java:613)
    at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.refineBoundaryStep(BoundaryRefinementAlgorithm.java:529)
    at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.refineBoundaries(BoundaryRefinementAlgorithm.java:516)
    at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.processVariant(BoundaryRefinementAlgorithm.java:223)
    at org.broadinstitute.sv.genotyping.RefineCNVBoundaries.run(RefineCNVBoundaries.java:207)
    at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:54)
    ... 5 more 
ERROR 10:06:14,883 FunctionEdge - Error:  'java'  '-Xmx2048m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/BiO/psh/Project/sv/tmpdir'  '-cp' '/BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar'  '-cp' '/BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar'  'org.broadinstitute.sv.genotyping.RefineCNVBoundaries'  '-I' '/BiO/psh/Project/sv/WGS_SV/cnv_stage6/seq_22/seq_22.merged_headers.bam'  '-O' '/BiO/psh/Project/sv/WGS_SV/cnv_stage7/seq_22/P0075/seq_22.merged.brig.vcf'  '-R' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.fasta'  '-md' 'WGS_SV/metadata'  '-configFile' '/BiO/psh/tools/svtoolkit/conf/genstrip_parameters.txt'  '-P' 'depth.readCountCacheIgnoreGenomeMask:true'  '-genomeMaskFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.svmask.fasta' '-genomeMaskFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.lcmask.fasta'  '-genderMapFile' './WGS.gender.map'  '-ploidyMapFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.ploidymap.txt'  '-vcf' 'WGS_SV/cnv_stage4/seq_22/seq_22.merged.genotypes.vcf.gz'  '-site' 'WGS_SV/cnv_stage7/seq_22/P0075.sites.list'  '-auxFilePrefix' 'WGS_SV/cnv_stage7/seq_22/P0075/seq_22.merged'  '-boundaryPrecision' '100'  '-minimumRefinedLength' '500'  '-maximumReferenceGapLength' '1000'  
ERROR 10:06:14,884 FunctionEdge - Contents of /BiO/psh/Project/sv/WGS_SV/cnv_stage7/seq_22/logs/CNVDiscoveryStage7-76.out:
INFO  10:05:54,965 HelpFormatter - ------------------------------------------------------------------ 
INFO  10:05:54,969 HelpFormatter - Program Name: org.broadinstitute.sv.genotyping.RefineCNVBoundaries 
INFO  10:05:54,975 HelpFormatter - Program Args: -I /BiO/psh/Project/sv/WGS_SV/cnv_stage6/seq_22/seq_22.merged_headers.bam -O /BiO/psh/Project/sv/WGS_SV/cnv_stage7/seq_22/P0075/seq_22.merged.brig.vcf -R /BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.fasta -md WGS_SV/metadata -configFile /BiO/psh/tools/svtoolkit/conf/genstrip_parameters.txt -P depth.readCountCacheIgnoreGenomeMask:true -genomeMaskFile /BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.svmask.fasta -genomeMaskFile /BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.lcmask.fasta -genderMapFile ./WGS.gender.map -ploidyMapFile /BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.ploidymap.txt -vcf WGS_SV/cnv_stage4/seq_22/seq_22.merged.genotypes.vcf.gz -site WGS_SV/cnv_stage7/seq_22/P0075.sites.list -auxFilePrefix WGS_SV/cnv_stage7/seq_22/P0075/seq_22.merged -boundaryPrecision 100 -minimumRefinedLength 500 -maximumReferenceGapLength 1000 
INFO  10:05:54,981 HelpFormatter - Executing as [email protected] on Linux 3.16.0-031600-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_25-b17. 
INFO  10:05:54,981 HelpFormatter - Date/Time: 2015/06/30 10:05:54 
INFO  10:05:54,981 HelpFormatter - ------------------------------------------------------------------ 
INFO  10:05:54,982 HelpFormatter - ------------------------------------------------------------------ 
INFO  10:05:54,994 RefineCNVBoundaries - Opening reference sequence ... 
INFO  10:05:54,997 RefineCNVBoundaries - Opened reference sequence. 
INFO  10:05:54,997 RefineCNVBoundaries - Opening genome mask ... 
INFO  10:05:54,999 RefineCNVBoundaries - Opened genome mask. 
INFO  10:05:55,001 MetaData - Opening metadata ...  
INFO  10:05:55,001 MetaData - Adding metadata directory WGS_SV/metadata ... 
INFO  10:05:55,027 MetaData - Opened metadata. 
INFO  10:05:55,051 RefineCNVBoundaries - Initializing input data set ... 
INFO  10:05:55,134 RefineCNVBoundaries - Initialized data set: 1 file, 490 read groups, 40 samples. 
INFO  10:05:55,318 ReadCountDiskCache - Initializing read count disk cache [WGS_SV/metadata/rccache.bin] ... 
INFO  10:05:55,319 ReadCountDiskCache - Initialized read count disk cache with 1 file. 
Exception in thread "main" java.lang.RuntimeException
    at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:65)
    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.sv.commandline.CommandLineProgram.runAndReturnResult(CommandLineProgram.java:29)
    at org.broadinstitute.sv.commandline.CommandLineProgram.run(CommandLineProgram.java:25)
    at org.broadinstitute.sv.genotyping.RefineCNVBoundaries.main(RefineCNVBoundaries.java:128)
Caused by: java.lang.NullPointerException
    at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.computeModelFrequencyScore2(BoundaryRefinementAlgorithm.java:430)
    at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.genotypeCnp(BoundaryRefinementAlgorithm.java:281)
    at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.refineOneBoundary(BoundaryRefinementAlgorithm.java:613)
    at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.refineBoundaryStep(BoundaryRefinementAlgorithm.java:532)
    at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.refineBoundaries(BoundaryRefinementAlgorithm.java:516)
    at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.processVariant(BoundaryRefinementAlgorithm.java:223)
    at org.broadinstitute.sv.genotyping.RefineCNVBoundaries.run(RefineCNVBoundaries.java:207)
    at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:54)
    ... 5 more 
INFO  10:06:14,886 QGraph - Writing incremental jobs reports... 
INFO  10:06:14,892 QGraph - 4 Pend, 0 Run, 2 Fail, 315 Done 
INFO  10:06:14,899 QCommandLine - Writing final jobs report... 
INFO  10:06:14,901 QCommandLine - Done with errors 
INFO  10:06:14,914 QGraph - ------- 
INFO  10:06:14,916 QGraph - Failed:   'java'  '-Xmx2048m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/BiO/psh/Project/sv/tmpdir'  '-cp' '/BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar'  '-cp' '/BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar'  'org.broadinstitute.sv.genotyping.RefineCNVBoundaries'  '-I' '/BiO/psh/Project/sv/WGS_SV/cnv_stage6/seq_22/seq_22.merged_headers.bam'  '-O' '/BiO/psh/Project/sv/WGS_SV/cnv_stage7/seq_22/P0058/seq_22.merged.brig.vcf'  '-R' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.fasta'  '-md' 'WGS_SV/metadata'  '-configFile' '/BiO/psh/tools/svtoolkit/conf/genstrip_parameters.txt'  '-P' 'depth.readCountCacheIgnoreGenomeMask:true'  '-genomeMaskFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.svmask.fasta' '-genomeMaskFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.lcmask.fasta'  '-genderMapFile' './WGS.gender.map'  '-ploidyMapFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.ploidymap.txt'  '-vcf' 'WGS_SV/cnv_stage4/seq_22/seq_22.merged.genotypes.vcf.gz'  '-site' 'WGS_SV/cnv_stage7/seq_22/P0058.sites.list'  '-auxFilePrefix' 'WGS_SV/cnv_stage7/seq_22/P0058/seq_22.merged'  '-boundaryPrecision' '100'  '-minimumRefinedLength' '500'  '-maximumReferenceGapLength' '1000'  
INFO  10:06:14,916 QGraph - Log:     /BiO/psh/Project/sv/WGS_SV/cnv_stage7/seq_22/logs/CNVDiscoveryStage7-59.out 
INFO  10:06:14,916 QGraph - ------- 
INFO  10:06:14,917 QGraph - Failed:   'java'  '-Xmx2048m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/BiO/psh/Project/sv/tmpdir'  '-cp' '/BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar'  '-cp' '/BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar'  'org.broadinstitute.sv.genotyping.RefineCNVBoundaries'  '-I' '/BiO/psh/Project/sv/WGS_SV/cnv_stage6/seq_22/seq_22.merged_headers.bam'  '-O' '/BiO/psh/Project/sv/WGS_SV/cnv_stage7/seq_22/P0075/seq_22.merged.brig.vcf'  '-R' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.fasta'  '-md' 'WGS_SV/metadata'  '-configFile' '/BiO/psh/tools/svtoolkit/conf/genstrip_parameters.txt'  '-P' 'depth.readCountCacheIgnoreGenomeMask:true'  '-genomeMaskFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.svmask.fasta' '-genomeMaskFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.lcmask.fasta'  '-genderMapFile' './WGS.gender.map'  '-ploidyMapFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.ploidymap.txt'  '-vcf' 'WGS_SV/cnv_stage4/seq_22/seq_22.merged.genotypes.vcf.gz'  '-site' 'WGS_SV/cnv_stage7/seq_22/P0075.sites.list'  '-auxFilePrefix' 'WGS_SV/cnv_stage7/seq_22/P0075/seq_22.merged'  '-boundaryPrecision' '100'  '-minimumRefinedLength' '500'  '-maximumReferenceGapLength' '1000'  
INFO  10:06:14,917 QGraph - Log:     /BiO/psh/Project/sv/WGS_SV/cnv_stage7/seq_22/logs/CNVDiscoveryStage7-76.out 

INFO  10:05:00,881 QGraph - Failed:   'java'  '-Xmx2048m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/BiO/psh/Project/sv/tmpdir'  '-cp' '/BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar'  '-cp' '/BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar'  'org.broadinstitute.gatk.queue.QCommandLine'  '-cp' '/BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar'  '-S' '/BiO/psh/tools/svtoolkit/qscript/discovery/cnv/CNVDiscoveryStage7.q'  '-S' '/BiO/psh/tools/svtoolkit/qscript/discovery/cnv/CNVDiscoveryStageBase.q' '-S' '/BiO/psh/tools/svtoolkit/qscript/discovery/cnv/CNVDiscoveryGenotyper.q'  '-S' '/BiO/psh/tools/svtoolkit/qscript/SVQScript.q'  '-gatk' '/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar'  '-jobLogDir' 'WGS_SV/cnv_stage7/seq_22/logs'  '-memLimit' '2.0'  '-jobRunner' 'Drmaa'  '-gatkJobRunner' 'Drmaa'  '-jobNative' '-v SV_DIR'  -run  '-sequenceName' '22'  '-runDirectory' 'WGS_SV/cnv_stage7/seq_22'  '-sentinelFile' 'WGS_SV/cnv_sentinel_files/stage_7_seq_22.sent'  --disableJobReport  '-configFile' '/BiO/psh/tools/svtoolkit/conf/genstrip_parameters.txt'  '-R' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.fasta'  '-ploidyMapFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.ploidymap.txt'  '-genomeMaskFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.svmask.fasta' '-genomeMaskFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.lcmask.fasta'  '-copyNumberMaskFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.gcmask.fasta'  '-readDepthMaskFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.rdmask.bed'  '-genderMaskBedFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.gendermask.bed'  '-vdjBedFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.vdjregions.bed'  '-genderMapFile' './WGS.gender.map'  '-md' 'WGS_SV/metadata'  -disableGATKTraversal  '-I' 'WGS_SV/cnv_stage6/seq_22/seq_22.merged_headers.bam'  '-vcf' 'WGS_SV/cnv_stage4/seq_22/seq_22.merged.genotypes.vcf.gz'  '-siteListFile' 'WGS_SV/cnv_stage6/seq_22/eval/SelectedVariants.list'  '-boundaryPrecision' '100'  '-maximumReferenceGapLength' '1000'  '-minimumRefinedLength' '500'  '-brigSiteVcfFile' 'WGS_SV/cnv_stage7/seq_22/seq_22.brig.sites.vcf.gz'  -produceAuxiliaryFiles  
INFO  10:05:00,882 QGraph - Log:     /BiO/psh/Project/sv/WGS_SV/logs/CNVDiscoveryPipeline-156.out 

My samples information is 60 individuals and about 30X coverage WGS.
My script is

java -cp ${classpath} ${mx} \
    org.broadinstitute.gatk.queue.QCommandLine \
    -jobNative "-v SV_DIR" \
    -S ${SV_DIR}/qscript/discovery/cnv/CNVDiscoveryPipeline.q \
    -S ${SV_DIR}/qscript/SVQScript.q \
    -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
    -cp ${classpath} \
    -configFile ${SV_DIR}/conf/genstrip_parameters.txt \
    -tempDir ${SV_TMPDIR} \
    -R ${bundle}/human_g1k_v37.fasta \
    -runDirectory ${runDir} \
    -md ${runDir}/metadata \
    -jobLogDir ${runDir}/logs \
    -ploidyMapFile ${bundle}/human_g1k_v37.ploidymap.txt \
    -genderMapFile ./WGS.gender.map \
    -genomeMaskFile ${bundle}/human_g1k_v37.svmask.fasta \
    -tilingWindowSize 1000 \
    -tilingWindowOverlap 500 \
    -maximumReferenceGapLength 1000 \
    -boundaryPrecision 100 \
    -minimumRefinedLength 500 \
    -produceAuxiliaryFiles \
    -I ${bamList} \
    -jobRunner Drmaa \
    -gatkJobRunner Drmaa \
    --disableJobReport \
    -run \
    || exit 1

Why do some chromosomes succeed, but others fail with same method in same enviroment ?

Post edited by Sunhye on
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