Re: [svtoolkit-help] no error in SVpreprocess but output files eg. depth.dat is empty

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I don't know if this is the only problem, but it looks like you are 
using hg19 as the reference but using a genome mask built for the 
g1k_v37 reference.
References must match exactly but this isn't always checked in the code.
You need to make sure that
(a) your bams are aligned against the reference you specify
(b) the genome mask you are using is built for the same reference
(c) you update your config file with the appropriate genome sizes based 
on your reference and mask
(for more details, see notes in this presentation: 
http://www.broadinstitute.org/files/shared/mpg/nextgen2011/nextgen2011_handsaker.pdf)
-Bob

On 12/21/12 3:22 AM, Shu Mei Teo wrote:
> 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 Lsf706Jo bRunner - 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.de 
> dup.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_ou t -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 16:39:41,7 06 
> 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/svp rocess_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.tmp 
> dir=/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.broadinst 
> itute.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!
>
>
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