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java.lang.RuntimeException: Invalid meta-data directory

yeswzcyeswzc beijingMember

I was tring CNVpipeline with command
java -Xmx4g -cp $classpath 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 $ref -ploidyMapFile $pld -genderMapFile $gdr -I $dir/input_bam_files.list -md input_metadata_directory -runDirectory $dir -jobLogDir $dir/logs -tilingWindowSize 1000 -tilingWindowOverlap 500 -maximumReferenceGapLength 1000 -boundaryPrecision 100 -minimumRefinedLength 500 -jobRunner GridEngine -gatkJobRunner Drmaa -jobNative "-V -cwd" -run
But failed with errors, in "CNVDiscoveryPipeline-48.out" file, it said:

INFO 10:21:38,207 QScriptManager - Compiling 4 QScripts
INFO 10:21:50,717 QScriptManager - Compilation complete
INFO 10:21:50,906 HelpFormatter - ----------------------------------------------------------------------
INFO 10:21:50,906 HelpFormatter - Queue v3.5.GS-r1661-0-g49c0dfe, Compiled 2016/05/17 12:41:28
INFO 10:21:50,906 HelpFormatter - Copyright (c) 2012 The Broad Institute
INFO 10:21:50,907 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 10:21:50,907 HelpFormatter - Program Args: -cp /sge/rj_group/rj/software/svtoolkit/lib/SVToolkit.jar:/sge/rj_group/rj/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/sge/rj_group/r
INFO 10:21:50,908 HelpFormatter - Executing as [email protected] on Linux 2.6.32-431.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14.
INFO 10:21:50,908 HelpFormatter - Date/Time: 2016/06/19 10:21:50
INFO 10:21:50,908 HelpFormatter - ----------------------------------------------------------------------
INFO 10:21:50,908 HelpFormatter - ----------------------------------------------------------------------
INFO 10:21:50,915 QCommandLine - Scripting CNVDiscoveryStage1
INFO 10:21:50,974 QCommandLine - Added 2 functions
INFO 10:21:50,974 QGraph - Generating graph.
INFO 10:21:50,985 QGraph - Running jobs.
INFO 10:21:51,174 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/sge/rj_group/zc/Project/GS_INFO 10:21:51,174 FunctionEdge - Output written to /sge/rj_group/zc/Project/GS_SVtest/01.T1/work/cnv_stage1/seq_chr2/logs/CNVDiscoveryStage1-1.out
INFO 10:21:51,273 DrmaaJobRunner - Submitted job id: 971325
INFO 10:21:51,274 QGraph - 1 Pend, 1 Run, 0 Fail, 0 Done
ERROR 10:22:21,194 FunctionEdge - Error: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/sge/rj_group/zc/Project/GS_SVtERROR 10:22:21,200 FunctionEdge - Contents of /sge/rj_group/zc/Project/GS_SVtest/01.T1/work/cnv_stage1/seq_chr2/logs/CNVDiscoveryStage1-1.out:
INFO 10:22:08,062 HelpFormatter - ------------------------------------------------------------
INFO 10:22:08,067 HelpFormatter - Program Name: org.broadinstitute.sv.discovery.SVDepthScanner
INFO 10:22:08,071 HelpFormatter - Program Args: -O /sge/rj_group/zc/Project/GS_SVtest/01.T1/work/cnv_stage1/seq_chr2/seq_chr2.sites.vcf.gz -R /sge/rj_group/rj/project/test/hg19.fa -genderMa
INFO 10:22:08,080 HelpFormatter - Executing as [email protected] on Linux 2.6.32-431.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14.
INFO 10:22:08,080 HelpFormatter - Date/Time: 2016/06/19 10:22:08
INFO 10:22:08,081 HelpFormatter - ------------------------------------------------------------
INFO 10:22:08,081 HelpFormatter - ------------------------------------------------------------
INFO 10:22:08,086 SVDepthScanner - Opening reference sequence ...
INFO 10:22:08,088 SVDepthScanner - Opened reference sequence.
INFO 10:22:08,090 MetaData - Opening metadata ...
Exception in thread "main" java.lang.RuntimeException: Invalid meta-data directory: input_metadata_directory
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.discovery.SVDepthScanner.main(SVDepthScanner.java:99)
Caused by: java.lang.RuntimeException: Invalid meta-data directory: input_metadata_directory
at org.broadinstitute.sv.metadata.MetaData.open(MetaData.java:72)
at org.broadinstitute.sv.discovery.SVDepthScanner.initMetaData(SVDepthScanner.java:254)
at org.broadinstitute.sv.discovery.SVDepthScanner.run(SVDepthScanner.java:119)
at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:54)
... 5 more
INFO 10:22:21,201 QGraph - Writing incremental jobs reports...
INFO 10:22:21,202 QGraph - 1 Pend, 0 Run, 1 Fail, 0 Done
INFO 10:22:21,203 QCommandLine - Writing final jobs report...
INFO 10:22:21,203 QCommandLine - Done with errors
INFO 10:22:21,205 QGraph - -------
INFO 10:22:21,206 QGraph - Failed: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/sge/rj_group/zc/Project/GS_SVtest/
INFO 10:22:21,206 QGraph - Log: /sge/rj_group/zc/Project/GS_SVtest/01.T1/work/cnv_stage1/seq_chr2/logs/CNVDiscoveryStage1-1.out
INFO 10:22:21,207 QCommandLine - Script failed: 1 Pend, 0 Run, 1 Fail, 0 Done

Anyone can help?

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