[svtoolkit-help] running error for CNV calling
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[svtoolkit-help] running error for CNV calling
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From: JINGJING J. <jjj...@gm...> - 2015-11-26 08:24:25
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Dear all, I try to use svtoolkit to find the CNV across different samples like this: java -Xmx150g -cp /gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar org.broadinstitute.gatk.queue.QCommandLine -S /gpfs01/home/jingjing/software/svtoolkit/qscript/discovery/cnv/CNVDiscoveryPipeline.q -S /gpfs01/home/jingjing/software/svtoolkit/qscript/SVQScript.q -cp /gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar -gatk /gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -configFile /gpfs01/home/jingjing/software/svtoolkit/conf/genstrip_parameters.txt -R /gpfs01/home/jingjing/project/tobacco/index/split/Ntab_scaffold_32687.fa -I input_bam_files.list -tilingWindowSize 1000 -tilingWindowOverlap 500 -maximumReferenceGapLength 1000 -boundaryPrecision 100 -minimumRefinedLength 500 -run The following is the error message: INFO 16:00:55,482 QScriptManager - Compiling 2 QScripts INFO 16:01:03,449 QScriptManager - Compilation complete INFO 16:01:03,516 HelpFormatter - ---------------------------------------------------------------------- INFO 16:01:03,516 HelpFormatter - Queue v3.3.GS2-0-g7ad6c61, Compiled 2015/10/04 09:18:40 INFO 16:01:03,516 HelpFormatter - Copyright (c) 2012 The Broad Institute INFO 16:01:03,517 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 16:01:03,518 HelpFormatter - Program Args: -S /gpfs01/home/jingjing/software/svtoolkit/qscript/discovery/cnv/CNVDiscoveryPipeline.q -S /gpfs01/home/jingjing/software/svtoolkit/qscript/SVQScript.q -cp /gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar -gatk /gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -configFile /gpfs01/home/jingjing/software/svtoolkit/conf/genstrip_parameters.txt -R /gpfs01/home/jingjing/project/tobacco/index/split/Ntab_scaffold_32687.fa -I input_bam_files.list -tilingWindowSize 1000 -tilingWindowOverlap 500 -maximumReferenceGapLength 1000 -boundaryPrecision 100 -minimumRefinedLength 500 -run INFO 16:01:03,519 HelpFormatter - Executing as jingjing@node-1-7 on Linux 2.6.32-431.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_60-b27. INFO 16:01:03,519 HelpFormatter - Date/Time: 2015/11/26 16:01:03 INFO 16:01:03,520 HelpFormatter - ---------------------------------------------------------------------- INFO 16:01:03,520 HelpFormatter - ---------------------------------------------------------------------- INFO 16:01:03,528 QCommandLine - Scripting CNVDiscoveryPipeline INFO 16:01:03,791 QCommandLine - Added 15 functions INFO 16:01:03,791 QGraph - Generating graph. INFO 16:01:03,811 QGraph - Running jobs. INFO 16:01:03,842 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/.queue/tmp' '-cp' '/gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar' '-cp' '/gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ExtractBAMSubset' '-I' '/gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/input_bam_files.list' '-O' '/gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/bam_headers/merged_headers.bam' '-L' 'NONE' INFO 16:01:03,842 FunctionEdge - Output written to /gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/CNVDiscoveryPipeline-1.out INFO 16:01:39,124 QGraph - 14 Pend, 1 Run, 0 Fail, 0 Done INFO 16:01:39,130 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/.queue/tmp' '-cp' '/gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar' '-cp' '/gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ExtractBAMSubset' '-I' '/gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/input_bam_files.list' '-O' '/gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/bam_headers/merged_headers.bam' '-L' 'NONE' INFO 16:01:39,132 QGraph - Writing incremental jobs reports... INFO 16:01:39,133 QJobsReporter - Writing JobLogging GATKReport to file /gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/CNVDiscoveryPipeline.jobreport.txt INFO 16:01:39,183 FunctionEdge - Starting: samtools index bam_headers/merged_headers.bam INFO 16:01:39,184 FunctionEdge - Output written to /gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/CNVDiscoveryPipeline-2.out INFO 16:01:39,260 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/.queue/tmp' '-cp' '/gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar' '-cp' '/gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.CreateGenderGenotypeFilterFile' '-O' '/gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/gender_gt_filters/gender_gt_filter.txt' '-R' '/gpfs01/home/jingjing/project/tobacco/index/split/Ntab_scaffold_32687.fa' '-filterDescriptionFile' 'gender_gt_filters/gender_gt_filter_descr.txt' INFO 16:01:39,260 FunctionEdge - Output written to /gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/CNVDiscoveryPipeline-3.out INFO 16:01:43,885 QGraph - 12 Pend, 2 Run, 0 Fail, 1 Done INFO 16:02:09,130 FunctionEdge - Done: samtools index bam_headers/merged_headers.bam ERROR 16:02:09,136 FunctionEdge - Error: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/.queue/tmp' '-cp' '/gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar' '-cp' '/gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.CreateGenderGenotypeFilterFile' '-O' '/gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/gender_gt_filters/gender_gt_filter.txt' '-R' '/gpfs01/home/jingjing/project/tobacco/index/split/Ntab_scaffold_32687.fa' '-filterDescriptionFile' 'gender_gt_filters/gender_gt_filter_descr.txt' ERROR 16:02:09,139 FunctionEdge - Contents of /gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/CNVDiscoveryPipeline-3.out: Exception in thread "main" org.broadinstitute.gatk.utils.commandline.MissingArgumentException: Argument with name '--ploidyMapFile' (-ploidyMapFile) is missing. Argument with name '--genderMapFile' (-genderMapFile) is missing. at org.broadinstitute.gatk.utils.commandline.ParsingEngine.validate(ParsingEngine.java:299) at org.broadinstitute.gatk.utils.commandline.ParsingEngine.validate(ParsingEngine.java:279) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:224) 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.apps.CreateGenderGenotypeFilterFile.main(CreateGenderGenotypeFilterFile.java:59) INFO 16:02:09,140 QGraph - Writing incremental jobs reports... INFO 16:02:09,140 QJobsReporter - Writing JobLogging GATKReport to file /gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/CNVDiscoveryPipeline.jobreport.txt INFO 16:02:09,264 QGraph - 12 Pend, 0 Run, 1 Fail, 2 Done INFO 16:02:09,265 QCommandLine - Writing final jobs report... INFO 16:02:09,266 QJobsReporter - Writing JobLogging GATKReport to file /gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/CNVDiscoveryPipeline.jobreport.txt INFO 16:02:09,271 QJobsReporter - Plotting JobLogging GATKReport to file /gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/CNVDiscoveryPipeline.jobreport.pdf WARN 16:02:09,810 RScriptExecutor - RScript exited with 1. Run with -l DEBUG for more info. INFO 16:02:09,812 QCommandLine - Done with errors INFO 16:02:09,814 QGraph - ------- INFO 16:02:09,815 QGraph - Failed: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/.queue/tmp' '-cp' '/gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar' '-cp' '/gpfs01/home/jingjing/software/svtoolkit/lib/SVToolkit.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs01/home/jingjing/software/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.CreateGenderGenotypeFilterFile' '-O' '/gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/gender_gt_filters/gender_gt_filter.txt' '-R' '/gpfs01/home/jingjing/project/tobacco/index/split/Ntab_scaffold_32687.fa' '-filterDescriptionFile' 'gender_gt_filters/gender_gt_filter_descr.txt' INFO 16:02:09,815 QGraph - Log: /gpfs01/home/jingjing/software/svtoolkit/installtest/split/Ntab_scaffold_32687/CNVDiscoveryPipeline-3.out INFO 16:02:09,816 QCommandLine - Script failed: 12 Pend, 0 Run, 1 Fail, 2 Done Can anyone give me some suggestions about how to deal with it? Thanks! Jingjing |
