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no error in SVpreprocess but output files eg. depth.dat is empty‏

I ran this with no ERROR message:
java -Xmx2g -cp Queue.jar:SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sting.queue.QCommandLine -S /hpctmp/svtoolkit/qscript/SVPreprocess.q -S /hpctmp/svtoolkit/qscript/SVQScript.q -gatk GenomeAnalysisTK.jar -cp SVToolkit.jar:GenomeAnalysisTK.jar -configFile /hpctmp/svtoolkit/conf/conf/genstrip_parameters.txt -tempDir /hpctmp/shumei/tempdir -md /hpctmp/shumei/svprocess_out -R /hpctmp/shumei/refhg19/ucsc.hg19.fasta -genomeMaskFile /hpctmp/shumei/masked/human_g1k_v37.mask.100.fasta -genderMapFile /home/svu/ephtsm/sample.map -I /hpctmp/bam_sm/SS6002734.realign.dedup.recal.bam -I /hpctmp/bam_sm/SS6002735.realign.dedup.recal.bam -run -bsub -jobQueue atlas7_parallel -jobProject lsf_project -jobLogDir /hpctmp/shumei/logs INFO 16:32:28,661 QScriptManager - Compiling 2 QScripts INFO 16:32:34,003 QScriptManager - Compilation complete INFO 16:32:36,690 HelpFormatter - --------------------------------------------------------- INFO 16:32:36,691 HelpFormatter - Program Name: org.broadinstitute.sting.queue.QCommandLine INFO 16:32:36,691 HelpFormatter - Program Args: -S /hpctmp/svtoolkit/qscript/SVPreprocess.q -S /hpctmp/svtoolkit/qscript/SVQScript.q -gatk GenomeAnalysisTK.jar -cp SVToolkit.jar:GenomeAnalysisTK.jar -configFile /hpctmp/svtoolkit/conf/conf/genstrip_parameters.txt -tempDir /hpctmp/shumei/tempdir -md /hpctmp/shumei/svprocess_out -R /hpctmp/shumei/refhg19/ucsc.hg19.fasta -genomeMaskFile /hpctmp/shumei/masked/human_g1k_v37.mask.100.fasta -genderMapFile /home/svu/ephtsm/sample.map -I /hpctmp/bam_sm/SS6002734.realign.dedup.recal.bam -I /hpctmp/bam_sm/SS6002735.realign.dedup.recal.bam -run -bsub -jobQueue atlas7_parallel -jobProject lsf_project -jobLogDir /hpctmp/shumei/logs INFO 16:32:36,692 HelpFormatter - Date/Time: 2012/12/20 16:32:36 INFO 16:32:36,692 HelpFormatter - --------------------------------------------------------- INFO 16:32:36,693 HelpFormatter - --------------------------------------------------------- INFO 16:32:36,695 QCommandLine - Scripting SVPreprocess INFO 16:32:36,824 QCommandLine - Added 10 functions INFO 16:32:36,825 QGraph - Generating graph. INFO 16:32:36,861 QGraph - Generating scatter gather jobs. INFO 16:32:36,863 QGraph - Removing original jobs. INFO 16:32:36,865 QGraph - Adding scatter gather jobs. INFO 16:32:36,865 QGraph - Regenerating graph. INFO 16:32:36,887 QGraph - Running jobs. INFO 16:32:37,077 Lsf706JobRunner - Starting: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeInsertSizeDistributions -R /hpctmp/shumei/refhg19/ucsc.hg19.fasta -I /hpctmp/bam_sm/SS6002734.realign.dedup.recal.bam -O /hpctmp/shumei/svprocess_out/isd/SS6002734.realign.dedup.recal.hist.bin -md /hpctmp/shumei/svprocess_out -createEmpty
INFO 16:32:37,263 Lsf706JobRunner - Submitted LSF job id: 9048 INFO 16:32:37,306 Lsf706JobRunner - Starting: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeInsertSizeDistributions -R /hpctmp/shumei/refhg19/ucsc.hg19.fasta -I /hpctmp/bam_sm/SS6002735.realign.dedup.recal.bam -O /hpctmp/shumei/svprocess_out/isd/SS6002735.realign.dedup.recal.hist.bin -md /hpctmp/shumei/svprocess_out -createEmpty
INFO 16:32:37,467 Lsf706JobRunner - Submitted LSF job id: 9049 INFO 16:32:37,495 Lsf706JobRunner - Starting: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeReadDepthCoverage -R /hpctmp/shumei/refhg19/ucsc.hg19.fasta -I /hpctmp/bam_sm/SS6002734.realign.dedup.recal.bam -O /hpctmp/shumei/svprocess_out/depth/SS6002734.realign.dedup.recal.depth.txt -md /hpctmp/shumei/svprocess_out -genomeMaskFile /hpctmp/shumei/masked/human_g1k_v37.mask.100.fasta -minMapQ 10 INFO 16:32:37,611 Lsf706JobRunner - Submitted LSF job id: 9050 INFO 16:32:37,640 Lsf706JobRunner - Starting: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeReadDepthCoverage -R /hpctmp/shumei/refhg19/ucsc.hg19.fasta -I /hpctmp/bam_sm/SS6002735.realign.dedup.recal.bam -O /hpctmp/shumei/svprocess_out/depth/SS6002735.realign.dedup.recal.depth.txt -md /hpctmp/shumei/svprocess_out -genomeMaskFile /hpctmp/shumei/masked/human_g1k_v37.mask.100.fasta -minMapQ 10 INFO 16:32:37,801 Lsf706JobRunner - Submitted LSF job id: 9051 INFO 16:39:11,177 Lsf706JobRunner - Done: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeReadDepthCoverage -R /hpctmp/shumei/refhg19/ucsc.hg19.fasta -I /hpctmp/bam_sm/SS6002735.realign.dedup.recal.bam -O /hpctmp/shumei/svprocess_out/depth/SS6002735.realign.dedup.recal.depth.txt -md /hpctmp/shumei/svprocess_out -genomeMaskFile /hpctmp/shumei/masked/human_g1k_v37.mask.100.fasta -minMapQ 10 INFO 16:39:41,314 Lsf706JobRunner - Done: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeInsertSizeDistributions -R /hpctmp/shumei/refhg19/ucsc.hg19.fasta -I /hpctmp/bam_sm/SS6002734.realign.dedup.recal.bam -O /hpctmp/shumei/svprocess_out/isd/SS6002734.realign.dedup.recal.hist.bin -md /hpctmp/shumei/svprocess_out -createEmpty
INFO 16:39:41,386 Lsf706JobRunner - Done: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeInsertSizeDistributions -R /hpctmp/shumei/refhg19/ucsc.hg19.fasta -I /hpctmp/bam_sm/SS6002735.realign.dedup.recal.bam -O /hpctmp/shumei/svprocess_out/isd/SS6002735.realign.dedup.recal.hist.bin -md /hpctmp/shumei/svprocess_out -createEmpty
INFO 16:39:41,448 Lsf706JobRunner - Done: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeReadDepthCoverage -R /hpctmp/shumei/refhg19/ucsc.hg19.fasta -I /hpctmp/bam_sm/SS6002734.realign.dedup.recal.bam -O /hpctmp/shumei/svprocess_out/depth/SS6002734.realign.dedup.recal.depth.txt -md /hpctmp/shumei/svprocess_out -genomeMaskFile /hpctmp/shumei/masked/human_g1k_v37.mask.100.fasta -minMapQ 10 INFO 16:39:41,453 Lsf706JobRunner - Starting: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sv.apps.MergeInsertSizeHistograms -I /hpctmp/shumei/svprocess_out/isd/SS6002734.realign.dedup.recal.hist.bin -I /hpctmp/shumei/svprocess_out/isd/SS6002735.realign.dedup.recal.hist.bin -O /hpctmp/shumei/svprocess_out/isd.hist.bin INFO 16:39:41,676 Lsf706JobRunner - Submitted LSF job id: 9064 INFO 16:39:41,706 Lsf706JobRunner - Starting: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sv.apps.MergeReadDepthCoverage -I /hpctmp/shumei/svprocess_out/depth/SS6002734.realign.dedup.recal.depth.txt -I /hpctmp/shumei/svprocess_out/depth/SS6002735.realign.dedup.recal.depth.txt -O /hpctmp/shumei/svprocess_out/depth.dat INFO 16:39:41,927 Lsf706JobRunner - Submitted LSF job id: 9065 INFO 16:40:12,185 Lsf706JobRunner - Done: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sv.apps.MergeInsertSizeHistograms -I /hpctmp/shumei/svprocess_out/isd/SS6002734.realign.dedup.recal.hist.bin -I /hpctmp/shumei/svprocess_out/isd/SS6002735.realign.dedup.recal.hist.bin -O /hpctmp/shumei/svprocess_out/isd.hist.bin INFO 16:40:12,215 Lsf706JobRunner - Done: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sv.apps.MergeReadDepthCoverage -I /hpctmp/shumei/svprocess_out/depth/SS6002734.realign.dedup.recal.depth.txt -I /hpctmp/shumei/svprocess_out/depth/SS6002735.realign.dedup.recal.depth.txt -O /hpctmp/shumei/svprocess_out/depth.dat INFO 16:40:12,219 Lsf706JobRunner - Starting: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sv.apps.ComputeInsertStatistics -I /hpctmp/shumei/svprocess_out/isd.hist.bin -O /hpctmp/shumei/svprocess_out/isd.stats.dat INFO 16:40:13,471 Lsf706JobRunner - Submitted LSF job id: 9066 INFO 16:40:13,552 Lsf706JobRunner - Starting: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeReadSpanCoverage -R /hpctmp/shumei/refhg19/ucsc.hg19.fasta -I /hpctmp/bam_sm/SS6002734.realign.dedup.recal.bam -O /hpctmp/shumei/svprocess_out/spans/SS6002734.realign.dedup.recal.spans.txt -md /hpctmp/shumei/svprocess_out -maxInsertSizeStandardDeviations 3 INFO 16:40:13,702 Lsf706JobRunner - Submitted LSF job id: 9067 INFO 16:40:13,732 Lsf706JobRunner - Starting: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeReadSpanCoverage -R /hpctmp/shumei/refhg19/ucsc.hg19.fasta -I /hpctmp/bam_sm/SS6002735.realign.dedup.recal.bam -O /hpctmp/shumei/svprocess_out/spans/SS6002735.realign.dedup.recal.spans.txt -md /hpctmp/shumei/svprocess_out -maxInsertSizeStandardDeviations 3 INFO 16:40:13,856 Lsf706JobRunner - Submitted LSF job id: 9068 INFO 16:41:14,669 Lsf706JobRunner - Done: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sv.apps.ComputeInsertStatistics -I /hpctmp/shumei/svprocess_out/isd.hist.bin -O /hpctmp/shumei/svprocess_out/isd.stats.dat INFO 16:45:46,258 Lsf706JobRunner - Done: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeReadSpanCoverage -R /hpctmp/shumei/refhg19/ucsc.hg19.fasta -I /hpctmp/bam_sm/SS6002735.realign.dedup.recal.bam -O /hpctmp/shumei/svprocess_out/spans/SS6002735.realign.dedup.recal.spans.txt -md /hpctmp/shumei/svprocess_out -maxInsertSizeStandardDeviations 3 INFO 16:46:16,342 Lsf706JobRunner - Done: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeReadSpanCoverage -R /hpctmp/shumei/refhg19/ucsc.hg19.fasta -I /hpctmp/bam_sm/SS6002734.realign.dedup.recal.bam -O /hpctmp/shumei/svprocess_out/spans/SS6002734.realign.dedup.recal.spans.txt -md /hpctmp/shumei/svprocess_out -maxInsertSizeStandardDeviations 3 INFO 16:46:16,346 Lsf706JobRunner - Starting: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sv.apps.MergeReadSpanCoverage -I /hpctmp/shumei/svprocess_out/spans/SS6002734.realign.dedup.recal.spans.txt -I /hpctmp/shumei/svprocess_out/spans/SS6002735.realign.dedup.recal.spans.txt -O /hpctmp/shumei/svprocess_out/spans.dat INFO 16:46:17,273 Lsf706JobRunner - Submitted LSF job id: 9074 INFO 16:46:47,967 Lsf706JobRunner - Done: bsub java -Xmx4g -Djava.io.tmpdir=/hpctmp/shumei/tempdir -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sv.apps.MergeReadSpanCoverage -I /hpctmp/shumei/svprocess_out/spans/SS6002734.realign.dedup.recal.spans.txt -I /hpctmp/shumei/svprocess_out/spans/SS6002735.realign.dedup.recal.spans.txt -O /hpctmp/shumei/svprocess_out/spans.dat INFO 16:46:47,971 QGraph - Deleting intermediate files. INFO 16:46:47,977 QCommandLine - Done

But yet depth.dat has no output
more depth.dat
SAMPLE LIBRARY READGROUP COUNT

What could be the reason? The bam files have been indexed and recalibrated following GATK best practices. Because there is no error message, I am not sure how to start troubleshooting what could have gone wrong.
Hope to receive some help here!

Answers

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