Re: [svtoolkit-help] SVDiscovery: cannot understand error
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Re: [svtoolkit-help] SVDiscovery: cannot understand error
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From: Bob H. <han...@br...> - 2012-12-29 02:07:02
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Hi, I think the root cause is not included in the listing below. It would be somewhere around the line that says <truncated>. I suggest looking in the log file which is /local/workdir/mmc256/GenomeStrip/SVPreprocess.chr10.reheader/logs/Q-25077@cbsuwrkst3-1.out Hopefully a more informative error message will be present in the file. If you are running all of chr10 in one job, this may take a very long time, especially if you have many bam files. It would be better to run in smaller windows, say 3Mb with 10Kb overlap. -Bob On 12/28/12 8:44 AM, Margarida Cardoso Moreira wrote: > Dear Bob, > > I have tried to run SVDiscovery (builds 939 and 982) a few times unsuccessfully and from the ouput I cannot understand where the problem lies. I hope you can point me in the right direction. > > Thank you, > > Margarida > > NFO 18:09:51,476 FunctionEdge - Starting: java -Xmx4g -Djava.io.tmpdir=/local/workdir/mmc256/TMPDIR -cp svtoolkit/lib/SVToolkit.jar:svtoolkit/lib/gatk/GenomeAnalysisTK.jar:svtoolkit/lib/gatk/Queue.jar -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R /local/workdir/mmc256/human_g1k_v37.fasta -I /local/workdir/mmc256/GenomeStrip/ListBams.CBSU.chr10.list -O /local/workdir/mmc256/GenomeStrip/SVPreprocess.chr10.reheader/chr10.discovery.unfiltered.vcf -md GenomeStrip/SVPreprocess.chr10.reheader/metadata -disableGATKTraversal -configFile GenomeStrip/genstrip_parameters_Chr10.txt -runDirectory GenomeStrip/SVPreprocess.chr10.reheader -genomeMaskFile human_g1k_v37.mask.100.fasta -L 10:0-0 -filePrefix chr10 -searchLocus 10 -searchWindow 10:0-0 -searchMinimumSize 100 -searchMaximumSize 1000000 > INFO 18:09:51,476 FunctionEdge - Output written to /local/workdir/mmc256/GenomeStrip/SVPreprocess.chr10.reheader/logs/Q-25077@cbsuwrkst3-1.out > ERROR 02:39:28,674 FunctionEdge - Error: java -Xmx4g -Djava.io.tmpdir=/local/workdir/mmc256/TMPDIR -cp svtoolkit/lib/SVToolkit.jar:svtoolkit/lib/gatk/GenomeAnalysisTK.jar:svtoolkit/lib/gatk/Queue.jar -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R /local/workdir/mmc256/human_g1k_v37.fasta -I /local/workdir/mmc256/GenomeStrip/ListBams.CBSU.chr10.list -O /local/workdir/mmc256/GenomeStrip/SVPreprocess.chr10.reheader/chr10.discovery.unfiltered.vcf -md GenomeStrip/SVPreprocess.chr10.reheader/metadata -disableGATKTraversal -configFile GenomeStrip/genstrip_parameters_Chr10.txt -runDirectory GenomeStrip/SVPreprocess.chr10.reheader -genomeMaskFile human_g1k_v37.mask.100.fasta -L 10:0-0 -filePrefix chr10 -searchLocus 10 -searchWindow 10:0-0 -searchMinimumSize 100 -searchMaximumSize 1000000 > org.broadinstitute.sting.queue.util.JobExitException: Failed to run job. > Command line: > sh /local/workdir/mmc256/TMPDIR/.exec1516894392817500268 > Exit code: 1 > Standard error contained: > [GC 96128K->13273K(368448K), 0.0192090 secs] > [GC 109401K->13738K(464576K), 0.0208630 secs] > [GC 205994K->14937K(464576K), 0.0188690 secs] > [GC 207193K->16321K(656832K), 0.0193450 secs] > [GC 400833K->6968K(656832K), 0.0083910 secs] > INFO 18:09:54,786 HelpFormatter - ----------------------------------------------------------------------------------- > INFO 18:09:54,788 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.0-6121-g40e3165, Compiled 2011/09/04 20:57:29 > INFO 18:09:54,788 HelpFormatter - Copyright (c) 2010 The Broad Institute > INFO 18:09:54,788 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki > INFO 18:09:54,788 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa > INFO 18:09:54,788 HelpFormatter - Program Args: -T SVDiscovery -R /local/workdir/mmc256/human_g1k_v37.fasta -O /local/workdir/mmc256/GenomeStrip/SVPreprocess.chr10.reheader/chr10.discovery.unfiltered.vcf -md GenomeStrip/SVPreprocess.chr10.reheader/metadata -disableGATKTraversal -configFile GenomeStrip/genstrip_parameters_Chr10.txt -runDirectory GenomeStrip/SVPreprocess.chr10.reheader -genomeMaskFile human_g1k_v37.mask.100.fasta -L 10:0-0 -filePrefix chr10 -searchLocus 10 -searchWindow 10:0-0 -searchMinimumSize 100 -searchMaximumSize 1000000 > INFO 18:09:54,789 HelpFormatter - Date/Time: 2012/12/26 18:09:54 > INFO 18:09:54,789 HelpFormatter - ----------------------------------------------------------------------------------- > INFO 18:09:54,789 HelpFormatter - ----------------------------------------------------------------------------------- > INFO 18:09:54,808 GenomeAnalysisEngine - Strictness is SILENT > INFO 18:09:55,012 SVDiscovery - Initializing SVDiscovery ... > INFO 18:09:55,030 SVDiscovery - Opening reference sequence ... > INFO 18:09:55,031 SVDiscovery - Opened reference sequence. > INFO 18:09:55,031 SVDiscovery - Opening genome mask ... > INFO 18:09:55,031 SVDiscovery - Opened genome mask. > INFO 18:09:55,031 SVDiscovery - Initializing input data set ... > [GC 391480K->67565K(1014208K), 0.0361670 secs] > INFO 18:10:03,292 SVDiscovery - Initialized data set: 989 files, 1016 read groups, 989 samples. > INFO 18:10:03,292 SVDiscovery - Opening metadata from GenomeStrip/SVPreprocess.chr10.reheader/metadata ... > INFO 18:10:03,293 SVDiscovery - Opened metadata. > INFO 18:10:03,294 SVDiscovery - Initializing discovery algorithm ... > INFO 18:10:03,296 SVDiscovery - Loading insert size distributions ... > INFO 18:10:03,825 SVDiscovery - Loaded 1007 distributions. > INFO 18:10:03,827 SVDiscovery - Discovery alt home filtering is disabled. > [GC 806893K->217491K(1043904K), 0.0831660 secs] > INFO 18:10:05,154 SVDiscovery - Processing locus: 10:0-0:100-1000000 > INFO 18:10:05,155 SVDiscovery - Locus search window: 10:0-0 > INFO 18:10:05,155 SVDiscovery - Selecting read pairs ... > INFO 18:10:05,156 SVDiscovery - Reading input file chr10/A00120_D0DM2ACXX-1-ID03.10.bam ... > [GC 956819K->312712K(1466048K), 0.0679270 secs] > [Full GC 312712K->148645K(1547456K), 0.1027800 secs] > > > Then it goes through the 990 bams and then the following output: > > [GC 2155745K->1482913K(3462144K), 0.0066560 secs] > INFO 06:07:21,812 SVDiscovery - Processing clusters ... > INFO 06:07:22,189 SVDiscovery - Initializing memory-mapped read count caching > INFO 06:07:22,193 SVDiscovery - No hapmap snp genotype directory specified > INFO 06:07:22,194 SVDiscovery - No array intensity data specified > [GC 2148769K->1486917K(3455296K), 0.0150400 secs] > [GC 2145925K->1487797K(3448576K), 0.0082620 secs] > [GC 2140085K->1488453K(3443584K), 0.0124010 secs] > > ... > > [GC 2392741K->1630997K(3551424K), 0.0155810 secs] > INFO 06:21:53,398 SVDiscovery - Clustering: Generating clusters for 2 read pairs. > INFO 06:21:53,427 SVDiscovery - Clustering: Generating clusters for 2 read pairs. > INFO 06:21:53,427 SVDiscovery - Processing cluster 10:61557-61673 10:62417-62541 LR 2 > [GC 2384853K->1641320K(3543168K), 0.0100730 secs] > [GC 2386600K->1650590K(3533504K), 0.0068270 secs] > [GC 2387486K->1661004K(3530304K), 0.0066540 secs] > [GC 2389708K->1666093K(3521920K), 0.0093920 secs] > [GC 2386733K->1671487K(3515904K), 0.0189450 secs] > [GC 2384255K->1674895K(3503168K), 0.0155220 secs] > [GC 2379919K->1682929K(3501376K), 0.0104000 secs] > [GC 2380337K->1685314K(3492096K), 0.0103700 secs] > [GC 2375298K->1689139K(3488256K), 0.0108180 secs] > [GC 2371827K->1689491K(3475264K), 0.0102240 secs] > [GC 2365011K->1695845K(3474560K), 0.0104230 secs] > [GC 2364325K->1696679K(3465216K), 0.0121330 secs] > [GC 2358247K->1698277K(3460032K), 0.0158710 secs] > [GC 2353061K->1699349K(3452160K), 0.0100870 secs] > #DBG: RC Cache fill 10:51674-161673 110000 989 210.149950 sec > INFO 06:25:32,081 SVDiscovery - Clustering: Generating clusters for 4 read pairs. > INFO 06:25:32,081 SVDiscovery - Processing cluster 10:95107-95253 10:95944-96119 LR 2 > INFO 06:25:34,182 SVDiscovery - Clustering: Generating clusters for 2 read pairs. > INFO 06:25:34,182 SVDiscovery - Processing cluster 10:95824-96088 10:96537-96746 LR 4 > [GC 2347477K->1699105K(3445312K), 0.0178790 secs] > > ... > > [GC 2785507K->2065539K(3522944K), 0.0182860 secs] > INFO 10:42:07,666 SVDiscovery - Clustering: Generating clusters for 4 read pairs. > INFO 10:42:07,666 SVDiscovery - Clustering: LR split size 4 / 4 maximal clique size 1 clique count 9 > INFO 10:42:07,699 SVDiscovery - Clustering: Generating clusters for 2 read pairs. > INFO 10:42:07,699 SVDiscovery - Processing cluster 10:4740080-4740244 10:4740705-4740871 LR 2 > INFO 10:42:09,696 SVDiscovery - Clustering: Generating clusters for 2 read pairs. > INFO 10:42:09,696 SVDiscovery - Processing cluster 10:4741548-4741760 10:4742231-4742493 LR 2 > INFO 10:42:11,686 SVDiscovery - Clustering: Generating clusters for 5 read pairs. > INFO 10:42:11,686 SVDiscovery - Processing cluster 10:4742734-4742838 10:4743410-4743518 LR 2 > INFO 10:42:13,690 SVDiscovery - Clustering: Generating clusters for 3 read pairs. > INFO 10:42:13,6 > > <truncated> > at org.broadinstitute.sting.queue.util.ShellJob.run(ShellJob.scala:24) > at org.broadinstitute.sting.queue.engine.shell.ShellJobRunner.start(ShellJobRunner.scala:54) > at org.broadinstitute.sting.queue.engine.FunctionEdge.start(FunctionEdge.scala:56) > at org.broadinstitute.sting.queue.engine.QGraph.runJobs(QGraph.scala:383) > at org.broadinstitute.sting.queue.engine.QGraph.run(QGraph.scala:123) > at org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scala:111) > at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221) > at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:57) > at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala) > INFO 02:39:37,731 QGraph - 1 Pend, 1 Run, 0 Fail, 0 Done > INFO 02:39:38,253 QGraph - 1 Pend, 0 Run, 1 Fail, 0 Done > INFO 02:39:38,264 QCommandLine - Done with errors > INFO 02:39:38,406 QGraph - ------- > INFO 02:39:38,653 QGraph - Failed: java -Xmx4g -Djava.io.tmpdir=/local/workdir/mmc256/TMPDIR -cp svtoolkit/lib/SVToolkit.jar:svtoolkit/lib/gatk/GenomeAnalysisTK.jar:svtoolkit/lib/gatk/Queue.jar -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R /local/workdir/mmc256/human_g1k_v37.fasta -I /local/workdir/mmc256/GenomeStrip/ListBams.CBSU.chr10.list -O /local/workdir/mmc256/GenomeStrip/SVPreprocess.chr10.reheader/chr10.discovery.unfiltered.vcf -md GenomeStrip/SVPreprocess.chr10.reheader/metadata -disableGATKTraversal -configFile GenomeStrip/genstrip_parameters_Chr10.txt -runDirectory GenomeStrip/SVPreprocess.chr10.reheader -genomeMaskFile human_g1k_v37.mask.100.fasta -L 10:0-0 -filePrefix chr10 -searchLocus 10 -searchWindow 10:0-0 -searchMinimumSize 100 -searchMaximumSize 1000000 > INFO 02:39:38,653 QGraph - Log: /local/workdir/mmc256/GenomeStrip/SVPreprocess.chr10.reheader/logs/Q-25077@cbsuwrkst3-1.out > > > > ------------------------------------------------------------------------------ > Master HTML5, CSS3, ASP.NET, MVC, AJAX, Knockout.js, Web API and > much more. 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