I just installed Genome STRIP and ran the 2 test scripts provided. The 2nd script, genotyping.sh, failed after 1.5 mins with the error appended below. It looks like I should run 'bwa aln' again, but with what parameters? All suggestions appreciated.....

INFO 13:34:56,460 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.0.5039M, Compiled 2011/01/20 22:58:34 INFO 13:34:56,461 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 13:34:56,461 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki INFO 13:34:56,461 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa INFO 13:34:56,461 HelpFormatter - Program Args: -T SVAltAligner -R /usr/local/gatk/svtoolkit/installtest/data/human_b36_chr1.fasta -I /usr/local/gatk/svtoolkit/installtest/data/installtest.bam -O /usr/local/gatk/svtoolkit/installtest/test2/altalign/installtest.alt.bam -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true INFO 13:34:56,461 HelpFormatter - Date/Time: 2012/08/14 13:34:56 INFO 13:34:56,462 HelpFormatter - --------------------------------------------------------------------------- INFO 13:34:56,462 HelpFormatter - --------------------------------------------------------------------------- INFO 13:34:56,466 GenomeAnalysisEngine - Strictness is SILENT INFO 13:34:57,226 GATKRunReport - Aggregating data for run report

ERROR ------------------------------------------------------------------------------------------

ERROR stack trace

org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Reverse BWT file is missing; please rerun 'bwa aln' to regenerate it. at org.broadinstitute.sting.alignment.bwa.c.BWACAligner.(BWACAligner.java:39) at org.broadinstitute.sv.breakpoint.BreakpointAligner.initialize(BreakpointAligner.java:46) at org.broadinstitute.sv.breakpoint.SVAltAlignerWalker.initialize(SVAltAlignerWalker.java:86) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:49) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:217) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:111) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:239) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:87)

ERROR ------------------------------------------------------------------------------------------

ERROR A GATK RUNTIME ERROR has occurred (version 1.0.5039M):

ERROR

ERROR Please visit to wiki to see if this is a known problem

ERROR If not, please post the error, with stack trace, to the GATK forum

ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki

ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa

ERROR

ERROR MESSAGE: Reverse BWT file is missing; please rerun 'bwa aln' to regenerate it.

ERROR ------------------------------------------------------------------------------------------

ERROR A GATK RUNTIME ERROR has occurred (version 1.0.5039M): ERROR MESSAGE: Error running script path/svtoolkit/R/discovery/compute_ranksum_pvalue.R: Failed with error: 'coin' is not a valid installed package ERROR Error in compute.ranksum.pvalue.coin(dataFile) : ERROR could not find function "wilcox_test" ERROR Calls: main -> compute.ranksum.pvalue.coin ERROR Execution halted

When running the GenomeSTRiP test scripts, I get the following error:

hovelson@fantasia:/net/amd/hovelson/bin/svtoolkit/installtest$ ./discovery.sh
SVToolkit version 1.03 (build 619)
Build date: 2011/02/12 17:23:22
Web site: http://www.broadinstitute.org/gsa/wiki/index.php/Genome_STRiP
INFO  11:28:59,836 QScriptManager - Compiling 2 QScripts
INFO  11:29:05,070 QScriptManager - Compilation complete
INFO  11:29:07,186 HelpFormatter - ---------------------------------------------------------
INFO  11:29:07,186 HelpFormatter - Program Name: org.broadinstitute.sting.queue.QCommandLine
INFO  11:29:07,187 HelpFormatter - Program Args: -S /net/amd/hovelson/bin/svtoolkit/qscript/SVPreprocess.q -S /net/amd/hovelson/bin/svtoolkit/qscript/SVQScript.q -gatk /net/amd/hovelson/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -cp /net/amd/hovelson/bin/svtoolkit/lib/SVToolkit.jar:/net/amd/hovelson/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/net/amd/hovelson/bin/svtoolkit/lib/gatk/Queue.jar -configFile conf/genstrip_installtest_parameters.txt -tempDir ./tmpdir -R data/human_b36_chr1.fasta -genomeMaskFile data/human_b36_chr1.mask.fasta -genderMapFile data/installtest_gender.map -runDirectory test1 -md test1/metadata -jobLogDir test1/logs -I data/installtest.bam -run
INFO  11:29:07,187 HelpFormatter - Date/Time: 2013/01/02 11:29:07
INFO  11:29:07,187 HelpFormatter - ---------------------------------------------------------
INFO  11:29:07,187 HelpFormatter - ---------------------------------------------------------
INFO  11:29:07,189 QCommandLine - Scripting SVPreprocess
INFO  11:29:07,274 QCommandLine - Added 7 functions
INFO  11:29:07,275 QGraph - Generating graph.
INFO  11:29:07,295 QGraph - Running jobs.
INFO  11:29:07,301 QGraph - Deleting intermediate files.
INFO  11:29:07,302 QCommandLine - Done
INFO  11:29:09,298 QScriptManager - Compiling 2 QScripts
INFO  11:29:14,170 QScriptManager - Compilation complete
INFO  11:29:16,335 HelpFormatter - ---------------------------------------------------------
INFO  11:29:16,335 HelpFormatter - Program Name: org.broadinstitute.sting.queue.QCommandLine
INFO  11:29:16,335 HelpFormatter - Program Args: -S /net/amd/hovelson/bin/svtoolkit/qscript/SVDiscovery.q -S /net/amd/hovelson/bin/svtoolkit/qscript/SVQScript.q -gatk /net/amd/hovelson/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -cp /net/amd/hovelson/bin/svtoolkit/lib/SVToolkit.jar:/net/amd/hovelson/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/net/amd/hovelson/bin/svtoolkit/lib/gatk/Queue.jar -configFile conf/genstrip_installtest_parameters.txt -tempDir ./tmpdir -R data/human_b36_chr1.fasta -genomeMaskFile data/human_b36_chr1.mask.fasta -genderMapFile data/installtest_gender.map -runDirectory test1 -md test1/metadata -jobLogDir test1/logs -L 1 -minimumSize 100 -maximumSize 1000000 -I data/installtest.bam -O test1.discovery.vcf -run
INFO  11:29:16,335 HelpFormatter - Date/Time: 2013/01/02 11:29:16
INFO  11:29:16,335 HelpFormatter - ---------------------------------------------------------
INFO  11:29:16,336 HelpFormatter - ---------------------------------------------------------
INFO  11:29:16,337 QCommandLine - Scripting SVDiscovery
INFO  11:29:16,406 QCommandLine - Added 2 functions
INFO  11:29:16,406 QGraph - Generating graph.
INFO  11:29:16,417 QGraph - Running jobs.
INFO  11:29:16,422 QGraph - Deleting intermediate files.
INFO  11:29:16,423 QCommandLine - Done
Files - and benchmark/test1.discovery.vcf differ
Error: test results do not match benchmark data

When I run diff on the test1.discovery.vcf file and benchmark/test1.discovery.vcf files, I see the only difference (aside from header lines in the new test1.discovery.vcf) is that for the variant at chr1:61892810 in the new test1.discovery.vcf file, the GSDEPTHRANKSUMPVALUE=0.008935781, while in the benchmark test1.discovery.vcf, GSDEPTHRANKSUMPVALUE=0.00893578.

hovelson@fantasia:/net/amd/hovelson/bin/svtoolkit/installtest$ diff test1.discovery.vcf benchmark/test1.discovery.vcf
64,65d63
< ##fileDate=20130102
< ##source=GenomeSTRiP_v1.03
71c69
< 1     61892810        DEL_5   C       <DEL>   .       PASS    CIEND=-48,49;CIPOS=-48,49;END=61893084;GSCOHERENCE=-1.9466175377489223;GSCOHFN=-0.9733087688744612;GSCOHPVALUE=0.424;GSCOORDS=61892760,61892812,61893082,61893133;GSDEPTHCALLTHRESHOLD=0.044234556389327793;GSDEPTHNOBSSAMPLES=2;GSDEPTHNTOTALSAMPLES=2;GSDEPTHOBSSAMPLES=NA11919,NA12155;GSDEPTHPVALUE=1.15E-4;GSDEPTHRANKSUMPVALUE=0.008935781;GSDEPTHRATIO=0.056153717139996895;GSDMAX=369;GSDMIN=1;GSDOPT=166;GSDSPAN=269;GSMEMBNPAIRS=2;GSMEMBNSAMPLES=2;GSMEMBOBSSAMPLES=NA12155,NA11919;GSMEMBPVALUE=0.1092;GSMEMBSTATISTIC=62.062109599506876;GSNDEPTHCALLS=2;GSNPAIRS=2;GSNSAMPLES=2;GSOBSINREADS=1;GSOBSOUTREADS=12458;GSOUTLEFT=0;GSOUTLIERS=0;GSOUTRIGHT=0;GSREADGROUPS=SRR003123,SRR006158;GSREADNAMES=SRR003123.2623325,SRR006158.13888082;GSSAMPLES=NA12155,NA11919;GSUNOBSINREADS=492;GSUNOBSOUTREADS=344185;IMPRECISE;SVLEN=-166;SVTYPE=DEL
---
> 1     61892810        DEL_5   C       <DEL>   .       PASS    CIEND=-48,49;CIPOS=-48,49;END=61893084;GSCOHERENCE=-1.9466175377489223;GSCOHFN=-0.9733087688744612;GSCOHPVALUE=0.424;GSCOORDS=61892760,61892812,61893082,61893133;GSDEPTHCALLTHRESHOLD=0.044234556389327793;GSDEPTHNOBSSAMPLES=2;GSDEPTHNTOTALSAMPLES=2;GSDEPTHOBSSAMPLES=NA11919,NA12155;GSDEPTHPVALUE=1.15E-4;GSDEPTHRANKSUMPVALUE=0.00893578;GSDEPTHRATIO=0.056153717139996895;GSDMAX=369;GSDMIN=1;GSDOPT=166;GSDSPAN=269;GSMEMBNPAIRS=2;GSMEMBNSAMPLES=2;GSMEMBOBSSAMPLES=NA12155,NA11919;GSMEMBPVALUE=0.1092;GSMEMBSTATISTIC=62.062109599506876;GSNDEPTHCALLS=2;GSNPAIRS=2;GSNSAMPLES=2;GSOBSINREADS=1;GSOBSOUTREADS=12458;GSOUTLEFT=0;GSOUTLIERS=0;GSOUTRIGHT=0;GSREADGROUPS=SRR003123,SRR006158;GSREADNAMES=SRR003123.2623325,SRR006158.13888082;GSSAMPLES=NA12155,NA11919;GSUNOBSINREADS=492;GSUNOBSOUTREADS=344185;IMPRECISE;SVLEN=-166;SVTYPE=DEL

Any thoughts on why I'm seeing this difference?

can GenomeSTRiP be run with LSF?

Hi,

Based on the discovery.sh from install_test folder, I found there were CN mask files for human, which might give better results. Where can we download them?

Thanks.

Hello, could I use GenomeStrip for non human genome? I have a de novo genome, so there is no annotation or such things.

Thanks!

Roberto

Hi,

I'm trying to generate a genome mask file for my reference genome and am following the instructions given on the GenomeStrip ComputeGenomeMask page.

When I try running my script for chromosome 1, I get the following error:

Exception in thread "main" java.lang.NoClassDefFoundError: org/broadinstitute/sv/apps/ComputeGenomeMask Caused by: java.lang.ClassNotFoundException: org.broadinstitute.sv.apps.ComputeGenomeMask at java.net.URLClassLoader$1.run(URLClassLoader.java:217) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:205) at java.lang.ClassLoader.loadClass(ClassLoader.java:321) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) at java.lang.ClassLoader.loadClass(ClassLoader.java:266)

Could not find the main class: org.broadinstitute.sv.apps.ComputeGenomeMask. Program will exit.

This is the command I use in my shell script:

!/bin/bash

classpath="${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar:${SV_DIR}/lib/gatk/Queue.jar"

java ${mx} -cp lib/SVToolkit.jar:lib/gatk/GenomeAnalysisTK.jar \ org.broadinstitute.sv.apps.ComputeGenomeMask \ -gatk GenomeAnalysisTK.jar \ -R /net/bipolar/bridges/sequencedata/CNV_shweta/mask_file/hs37d5.fa \ -O /net/bipolar/bridges/sequencedata/CNV_shweta/mask_file/chr1mask.hs37d5.fa \ -readLength 100 \

-sequence chr1

I'm unable to determine the source of this error--if someone could help me with this, I'd appreciate it very much.

Thanks, Shweta

I just installed Genome STRIP the svtoolkit_1.04.982.tar.gz version. I am new with Genome STRIP, but I need to run it on a SGE GridEngine with the parameter -qsub (-jobRunner GridEngine) I modify the discovery.sh script in the installationtest directory with the correct path for the software requirements and I added the options -jobRunner GridEngine -jobQueue bld.q at the pre-processing command line.

This is the ouput:

`SVToolkit version 1.04 (build 982) Build date: 2012/08/10 18:30:21 Web site: http://www.broadinstitute.org/gsa/wiki/index.php/Genome_STRiP INFO 22:50:57,055 QScriptManager - Compiling 2 QScripts INFO 22:51:05,792 QScriptManager - Compilation complete INFO 22:51:05,866 HelpFormatter - --------------------------------------------------------- INFO 22:51:05,866 HelpFormatter - Program Name: org.broadinstitute.sting.queue.QCommandLine INFO 22:51:05,867 HelpFormatter - Program Args: -S /mpba0/mpba-sw/svtoolkit/qscript/SVPreprocess.q -S /mpba0/mpba-sw/svtoolkit/qscript/SVQScript.q -gatk /mpba0/mpba-sw/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -cp /mpba0/mpba-sw/svtoolkit/lib/SVToolkit.jar:/mpba0/mpba-sw/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/mpba0/mpba-sw/svtoolkit/lib/gatk/Queue.jar -configFile conf/genstrip_installtest_parameters.txt -tempDir ./tmpdir -R data/human_b36_chr1.fasta -genomeMaskFile data/human_b36_chr1.mask.fasta -copyNumberMaskFile data/cn2_mask_g1k_b36_chr1.fasta -genderMapFile data/installtest_gender.map -runDirectory test1 -md test1/metadata -computeGCProfiles -jobLogDir test1/logs -I data/installtest.bam -run -jobRunner GridEngine
INFO 22:51:05,867 HelpFormatter - Date/Time: 2013/01/11 22:51:05 INFO 22:51:05,867 HelpFormatter - --------------------------------------------------------- INFO 22:51:05,867 HelpFormatter - --------------------------------------------------------- INFO 22:51:05,870 QCommandLine - Scripting SVPreprocess INFO 22:51:06,007 QCommandLine - Added 10 functions INFO 22:51:06,007 QGraph - Generating graph. INFO 22:51:06,027 QGraph - Generating scatter gather jobs. INFO 22:51:06,028 QGraph - Removing original jobs. INFO 22:51:06,029 QGraph - Adding scatter gather jobs. INFO 22:51:06,030 QGraph - Regenerating graph. INFO 22:51:06,036 QGraph - Running jobs. ERROR 22:51:06,037 QGraph - Uncaught error running jobs. org.broadinstitute.sting.utils.exceptions.UserException: Could not find JobManager with name: GridEngine at org.broadinstitute.sting.utils.classloader.PluginManager.createByName(PluginManager.java:239) at org.broadinstitute.sting.queue.engine.QGraph.runJobs(QGraph.scala:360) 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)

ERROR ------------------------------------------------------------------------------------------

ERROR stack trace`

Maybe I am missing some other parameters.

Any help will be appreciated!

I keep getting an error (output below) telling me an R script 'plot_ISD.R' is missing. I'm guessing from the name this is an internal script, but though I've a fresh install of GATK and SV running I don't appear to have it.

Is this a known issue, or is there something I've overlooked?

thanks

-s

bash-3.2$ java -Xmx2g -cp $classpath     org.broadinstitute.sv.apps.PlotInsertSizeDistributions  -I insert_sizes.gatkreport.txt -O plot.pdf  
INFO  14:16:05,833 HelpFormatter - -------------------------------------------------------------------- 
INFO  14:16:05,835 HelpFormatter - Program Name: org.broadinstitute.sv.apps.PlotInsertSizeDistributions 
INFO  14:16:05,835 HelpFormatter - Program Args: -I insert_sizes.gatkreport.txt -O plot.pdf 
INFO  14:16:05,835 HelpFormatter - Date/Time: 2012/12/20 14:16:05 
INFO  14:16:05,836 HelpFormatter - -------------------------------------------------------------------- 
INFO  14:16:05,836 HelpFormatter - -------------------------------------------------------------------- 
Exception in thread "main" java.lang.RuntimeException: Cannot locate R script: metadata/plot_isd.R (SV_DIR = /Users/seth/Work/software/svtoolkit)
    at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:36)
    at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:239)
    at org.broadinstitute.sv.commandline.CommandLineProgram.run(CommandLineProgram.java:23)
    at org.broadinstitute.sv.apps.PlotInsertSizeDistributions.main(PlotInsertSizeDistributions.java:53)
Caused by: java.lang.RuntimeException: Cannot locate R script: metadata/plot_isd.R (SV_DIR = /Users/seth/Work/software/svtoolkit)
    at org.broadinstitute.sv.util.RUtilities.findRScript(RUtilities.java:45)
    at org.broadinstitute.sv.metadata.isize.InsertSizeHistogramPlotter.<init>(InsertSizeHistogramPlotter.java:37)
    at org.broadinstitute.sv.apps.PlotInsertSizeDistributions.run(PlotInsertSizeDistributions.java:59)
    at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:33)
    missing R script in PlotInsertSizeDistributions?... 3 more

Hi,

I'm trying to generate a mask file using ComputeGenomeMask, but I get the following error:

Exception in thread "main" java.lang.RuntimeException: ANN file is missing; please rerun 'bwa aln' to regenerate it. at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:40) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221) at org.broadinstitute.sv.commandline.CommandLineProgram.run(CommandLineProgram.java:23) at org.broadinstitute.sv.apps.ComputeGenomeMask.main(ComputeGenomeMask.java:64) Caused by: org.broadinstitute.sting.utils.exceptions.ReviewedStingException: ANN file is missing; please rerun 'bwa aln' to regenerate it. at org.broadinstitute.sting.alignment.bwa.c.BWACAligner.(BWACAligner.java:34) at org.broadinstitute.sv.util.bwa.BWACAligner.(BWACAligner.java:26) at org.broadinstitute.sv.mask.GenomeMaskAlgorithm.getAligner(GenomeMaskAlgorithm.java:331) at org.broadinstitute.sv.mask.GenomeMaskAlgorithm.getAlignmentCode(GenomeMaskAlgorithm.java:174) at org.broadinstitute.sv.mask.GenomeMaskAlgorithm.generateMaskForSequence(GenomeMaskAlgorithm.java:143) at org.broadinstitute.sv.apps.ComputeGenomeMask.run(ComputeGenomeMask.java:90) at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:37) ... 3 more

The code I'm running is:

java -cp /net/sv/pipeline/svtoolkit/lib/SVToolkit.jar:/net/sv/pipeline/svtoolkit/lib/gatk/GenomeAnalysisTK.jar org.broadinstitute.sv.apps.ComputeGenomeMask -R /net/sequencedata/CNV_shweta/mask_file/hs37d5.fa \ -O /net/sequencedata/CNV_shweta/mask_file/chr1mask.hs37d5.fa \ -readLength 100 \

Is there a step I'm missing prior to this step?

Thanks, Shweta

I just installed Genome STRIP the svtoolkit_1.04.982.tar.gz version. I am new with Genome STRIP, but I need to run it on a SGE GridEngine with the parameter -qsub (-jobRunner GridEngine) I modify the discovery.sh script in the installationtest directory with the correct path for the software requirements and I added the options -jobRunner GridEngine -jobQueue bld.q at the pre-processing command line.

This is the ouput:

`SVToolkit version 1.04 (build 982) Build date: 2012/08/10 18:30:21 Web site: http://www.broadinstitute.org/gsa/wiki/index.php/Genome_STRiP INFO 22:50:57,055 QScriptManager - Compiling 2 QScripts INFO 22:51:05,792 QScriptManager - Compilation complete INFO 22:51:05,866 HelpFormatter - --------------------------------------------------------- INFO 22:51:05,866 HelpFormatter - Program Name: org.broadinstitute.sting.queue.QCommandLine INFO 22:51:05,867 HelpFormatter - Program Args: -S /mpba0/mpba-sw/svtoolkit/qscript/SVPreprocess.q -S /mpba0/mpba-sw/svtoolkit/qscript/SVQScript.q -gatk /mpba0/mpba-sw/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -cp /mpba0/mpba-sw/svtoolkit/lib/SVToolkit.jar:/mpba0/mpba-sw/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/mpba0/mpba-sw/svtoolkit/lib/gatk/Queue.jar -configFile conf/genstrip_installtest_parameters.txt -tempDir ./tmpdir -R data/human_b36_chr1.fasta -genomeMaskFile data/human_b36_chr1.mask.fasta -copyNumberMaskFile data/cn2_mask_g1k_b36_chr1.fasta -genderMapFile data/installtest_gender.map -runDirectory test1 -md test1/metadata -computeGCProfiles -jobLogDir test1/logs -I data/installtest.bam -run -jobRunner GridEngine
INFO 22:51:05,867 HelpFormatter - Date/Time: 2013/01/11 22:51:05 INFO 22:51:05,867 HelpFormatter - --------------------------------------------------------- INFO 22:51:05,867 HelpFormatter - --------------------------------------------------------- INFO 22:51:05,870 QCommandLine - Scripting SVPreprocess INFO 22:51:06,007 QCommandLine - Added 10 functions INFO 22:51:06,007 QGraph - Generating graph. INFO 22:51:06,027 QGraph - Generating scatter gather jobs. INFO 22:51:06,028 QGraph - Removing original jobs. INFO 22:51:06,029 QGraph - Adding scatter gather jobs. INFO 22:51:06,030 QGraph - Regenerating graph. INFO 22:51:06,036 QGraph - Running jobs. ERROR 22:51:06,037 QGraph - Uncaught error running jobs. org.broadinstitute.sting.utils.exceptions.UserException: Could not find JobManager with name: GridEngine at org.broadinstitute.sting.utils.classloader.PluginManager.createByName(PluginManager.java:239) at org.broadinstitute.sting.queue.engine.QGraph.runJobs(QGraph.scala:360) 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)

ERROR ------------------------------------------------------------------------------------------

ERROR stack trace`

Maybe I am missing some other parameters.

Any help will be appreciated!

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!

I'm trying to run the sv_discovery.pl script, and I repeatedly get this error:

INFO 21:08:31,551 SVDiscovery - Clustering: Generating clusters for 4 read pairs.
INFO 21:08:31,551 SVDiscovery - Processing cluster 6:666202-666319 6:667844-668096 LR 4
DBG: RC Cache fill 6:656320-766319 110000 2 0.196780 sec
Error: Exception processing cluster: Error running script /net/svtoolkit/R/discovery/compute_ranksum_pvalue.R: Error in wilcox.test.default(a, b, alternative = "l") : not enough 'y' observations Calls: main -> compute.ranksum.pvalue Execution halted

Cluster: 6:666202-666319 6:667844-668096 LR 4 [GC 415417K->12575K(2009792K), 0.0389180 secs] [Full GC 12575K->12068K(2009792K), 0.0949060 secs]

ERROR ------------------------------------------------------------------------------------------

ERROR stack trace

java.lang.RuntimeException: Error running script /net/svtoolkit/R/discovery/compute_ranksum_pvalue.R: Error in wilcox.test.default(a, b, alternative = "l") : not enough 'y' observations Calls: main -> compute.ranksum.pvalue Execution halted

    at org.broadinstitute.sv.discovery.ClusterDepthModule.computeRankSumPValue(ClusterDepthModule.java:287)
    at org.broadinstitute.sv.discovery.ClusterDepthModule.computeDepth(ClusterDepthModule.java:197)
    at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processCluster(DeletionDiscoveryAlgorithm.java:434)
    at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processClusters(DeletionDiscoveryAlgorithm.java:342)
    at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.runDiscovery(DeletionDiscoveryAlgorithm.java:191)
    at org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:168)
    at org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:45)
    at org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129)
    at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:76)
    at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:234)
    at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
    at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:105)
    at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221)
    at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:67)
    at org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21)

The command I ran was:

java -Xmx4g -cp /net/svtoolkit/lib/SVToolkit.jar:/net/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/net/svtoolkit/lib/gatk/Queue.jar \ org.broadinstitute.sting.queue.QCommandLine \ -S /net/svtoolkit/qscript/SVDiscovery.q \ -S /net/svtoolkit/qscript/SVQScript.q \ -gatk /net/svtoolkit/lib/gatk/GenomeAnalysisTK.jar \ -configFile /net/CNV_shweta/mask_file/genstrip_parameters.txt \ -tempDir /net/CNV_shweta/runningByChromosome/chr6_2bams_withcnmask_svdiscovery \ -R /net/CNV_shweta/mask_file/hs37d5.fa \ -genomeMaskFile /net/CNV_shweta/mask_file/compiledgenomemask.hs37d5.fa \ -copyNumberMaskFile /net/CNV_shweta//mask_file/cn2_mask_t2dgo_v37_new.fasta \ -runDirectory /net/CNV_shweta/runningByChromosome/chr6_2bams_svdiscovery/chr6 \ -md /net/CNV_shweta/runningByChromosome/chr6plate12_withcnmask_tempbams/metadata \ -L 6 \ -jobLogDir /net/CNV_shweta/runningByChromosome/chr6_2bams_svdiscovery/chr6/logs \ -vcfCachingDistance 50000 \ -minimumSize 100 -maximumSize 1000000 \ -windowSize 2000000 -windowPadding 10000 \ -I /net/CNV_shweta/plate12/1497-RMM-1031.chr6.bam -I /net/bipolar/bridges/sequencedata/CNV_shweta/plate12/1497-RMM-1023.chr6.bam \ -O /net/CNV_shweta/runningByChromosome/chr6_2bams_svdiscovery/chr6.discovery.vcf -run

Is there something wrong with this step? If someone could help me out with this, I'd appreciate it very much.

Thanks, Shweta

How can I run ComputeReadDepthCoverage separately to get only depth.dat output file

I'm attempting to run GenomeSTRiP's SVPreprocess.q script on a large number of samples (N=~1400; note that this is exome-sequencing data). During the MergeInsertSizeHistograms portion of the SVPreprocess.q script, the command returns prematurely and the log file reports a Java heap space error that looks like this:

INFO  12:47:02,554 HelpFormatter - Date/Time: 2013/02/07 12:47:02
INFO  12:47:02,555 HelpFormatter - ------------------------------------------------------------------
INFO  12:47:02,555 HelpFormatter - ------------------------------------------------------------------
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
        at java.util.TreeMap.put(TreeMap.java:571)
        at org.broadinstitute.sv.metadata.isize.InsertSizeHistogram.readObject(InsertSizeHistogram.java:416)
        at sun.reflect.GeneratedMethodAccessor8.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:616)
        at java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:988)
        at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1865)
        at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1770)
        at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1346)
        at java.io.ObjectInputStream.readObject(ObjectInputStream.java:368)
        at org.broadinstitute.sv.metadata.isize.InsertSizeHistogramFile$FileIterator.readHistogram(InsertSizeHistogramFile.java:140)
        at org.broadinstitute.sv.metadata.isize.InsertSizeHistogramFile$FileIterator.advance(InsertSizeHistogramFile.java:129)
        at org.broadinstitute.sv.metadata.isize.InsertSizeHistogramFile$FileIterator.next(InsertSizeHistogramFile.java:107)
        at org.broadinstitute.sv.metadata.isize.InsertSizeHistogramFile$FileIterator.next(InsertSizeHistogramFile.java:86)
        at org.broadinstitute.sv.metadata.isize.InsertSizeHistogramMerger.mergeNonDisjoint(InsertSizeHistogramMerger.java:72)
        at org.broadinstitute.sv.metadata.isize.InsertSizeHistogramMerger.mergeHistograms(InsertSizeHistogramMerger.java:51)
        at org.broadinstitute.sv.apps.MergeInsertSizeHistograms.run(MergeInsertSizeHistograms.java:45)
        at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:38)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:237)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:147)
        at org.broadinstitute.sv.commandline.CommandLineProgram.run(CommandLineProgram.java:24)
        at org.broadinstitute.sv.apps.MergeInsertSizeHistograms.main(MergeInsertSizeHistograms.java:39)

I've experimented with -Xmx up to 16g, with the same errors every time. Given the large number of samples, is there any way to avoid running into this error? I assume similar problems might also occur with the MergeInsertSizeDistributions portion of SVPreprocess.q.

Any feedback/recommendations would be greatly appreciated - thanks very much!

Hello, Bob,

Genome STRiP pipeline Queue scripts work on LSF scheduler or on SGE scheduler. But our Linux cluster uses Torque/PBS job scheduler. Is there a guideline to use GATK/SVToolkit commandline directly or without using the Scala/Queue pipelining?

Best, Guangfa

The authors of GenomeSTRiP will respond to questions posed in this section. You can also comment on the articles in the "GenomeSTRiP Documentation" subcategory.

Please don't post your question as a new comment on this announcement; you can create a new question by using the big "Ask a Question" button on the left.

Hello, I re-compute genome masks and want to do statistics for mask, but when I run following comands, there are some errors:

**********command******* java -cp ${classpath} ${mx} \ org.broadinstitute.sv.apps.ComputeGenomeMaskStats \ -R ${reference} \ -I ${runDIR}/${refV}.mask.fasta \ -O ${runDIR}/${refV}.mask.fasta.stats \

*********error************** Exception in thread "main" java.lang.NoClassDefFoundError: org/broadinstitute/sv/apps/ComputeGenomeMaskStats Caused by: java.lang.ClassNotFoundException: org.broadinstitute.sv.apps.ComputeGenomeMaskStats at java.net.URLClassLoader$1.run(URLClassLoader.java:200) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:188) at java.lang.ClassLoader.loadClass(ClassLoader.java:307) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301) at java.lang.ClassLoader.loadClass(ClassLoader.java:252) at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:320) Could not find the main class: org.broadinstitute.sv.apps.ComputeGenomeMaskStats. Program will exit.

Why "BadMateFilter" is applied in RealignerTargetCreator, if we want to give the output for SV detection?

Hi, I am not getting any result from computeGCProfiles for my bam file (the first bam file in the input list). There is no error, rather GenomeStrip appears to be running without any new log information or output files generated in the past 36 hours or so.

The output of the log file where its getting hung up is:

INFO 09:58:03,256 HelpFormatter - ---------------------------------------------------------- INFO 09:58:03,258 HelpFormatter - Program Name: org.broadinstitute.sv.apps.ComputeGCProfiles INFO 09:58:03,265 HelpFormatter - Program Args: -I /scratch/temp/ehalper/LIBRARY_2A_L4_bwa_SRT3.bam -O /local_data/scratch/temp/ehalper/svtoolkit/test1KG/test1/metadata/gcp rofile/LIBRARY_2A_L4_bwa_SRT3.bam.gcprof.zip -R data/hs37d5.fasta -md test1/metadata -referenceProfile test1/metadata/gcprofile/reference.gcprof.zip -genomeMaskFile data/hs3 7d5.mask.100.fasta -copyNumberMaskFile data/hs37d5.cn2_mask.100.fasta -configFile conf/genstrip_installtest_parameters.txt INFO 09:58:03,265 HelpFormatter - Date/Time: 2013/04/02 09:58:03 INFO 09:58:03,265 HelpFormatter - ---------------------------------------------------------- INFO 09:58:03,266 HelpFormatter - ---------------------------------------------------------- INFO 09:58:03,307 ComputeGCProfiles - Opening reference sequence ... INFO 09:58:03,308 ComputeGCProfiles - Opened reference sequence. INFO 09:58:03,309 ComputeGCProfiles - Opening genome mask ... INFO 09:58:03,309 ComputeGCProfiles - Opened genome mask. INFO 09:58:03,310 ComputeGCProfiles - Opening copy number mask ... INFO 09:58:03,310 ComputeGCProfiles - Opened copy number mask. INFO 09:58:03,310 ComputeGCProfiles - Initializing algorithm ...

INFO: ReadCountAlgorithm: detected metadata version 1, forcing legacy behavior

INFO 09:58:56,372 ComputeGCProfiles - Algorithm initialized. INFO 09:58:56,372 ComputeGCProfiles - Opening reference GC profile ... INFO 09:58:56,402 ComputeGCProfiles - Opened reference GC profile. INFO 09:58:56,404 ComputeGCProfiles - Processing input file org.broadinstitute.sv.dataset.SAMFileLocation@e4836322 ...

Any help would be appreciated, thanks!

-Eitan