Re: [svtoolkit-help] svtoolkit-help Digest, Vol 28, Issue 3

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No, the problem is with the genome mask - it doesn't contain any of the 
unplaced contigs (e.g. GL000207.1).
If you didn't run ComputeGenomeMask on the same reference, then you will 
have trouble calling variants accurately where there are paralogs or 
near paralogs on the unplaced contigs.
You need to start with the exact reference your bam files are aligned to 
(check the bam header with samtools view -H if you are not sure),
then use that exact same reference as -R and use that exact same 
reference with ComputeGenomeMask.

-Bob

On 4/19/14 6:53 AM, P?nar Kavak wrote:
>
> Thank you very much Bob,
> I think it is the ploidy map, because I built my own genome mask 
> according to my reference with ComputeGenomeMask.
> All map and fai files are attached.
> If that is the problem, how can I modify the ploidy map file?
> Thanks,
> pinar
>
> 18 Nis 2014 16:24 tarihinde 
> <svt...@li... 
> <mailto:svt...@li...>> yazdÄ±:
>
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>     Today's Topics:
>
>     Â  Â 1. Re: "Invalid sequence position" (Bob Handsaker)
>
>
>     ----------------------------------------------------------------------
>
>     Message: 1
>     Date: Fri, 18 Apr 2014 09:15:42 -0400
>     From: Bob Handsaker <han...@br...
>     <mailto:han...@br...>>
>     Subject: Re: [svtoolkit-help] "Invalid sequence position"
>     To: svt...@li...
>     <mailto:svt...@li...>
>     Message-ID: <535...@br...
>     <mailto:535...@br...>>
>     Content-Type: text/plain; charset="iso-8859-1"
>
>     It looks from the location of the NullPointerException like this is an
>     inconsistency between your reference sequence and ploidy map on
>     the one hand
>     and your genome mask on the other (i.e. it looks like the genome
>     mask is
>     based on a different reference sequence).
>     If you think this is not the case, can you post the .fai files for (a)
>     the reference sequence (b) the genome mask and also post your
>     ploidy map
>     file.
>
>     I'll put in a check for this in the code so it won't get a
>     NullPointerException and generate a better error message.
>
>     -Bob
>
>     On 4/18/14 6:17 AM, P?nar Kavak wrote:
>     > Hi,
>     >
>     > Sorry for re-posting the same error subject, but when I run the
>     > preprocessing step of SVToolkit,? I get the same error and could not
>     > find out a solution. I use the? SVToolkit version 1.04 (build 1358).
>     > I'll appreciate any help. Thanks,
>     >
>     > Pinar Kavak
>     > Researcher
>     > Turkey
>     >
>     > Here is command and the output log file is following:
>     >
>     > COMMAND
>     > -----------------------------------------------------------------
>     >
>     > SV_TMPDIR=./tmpdir
>     > SV_TMPDIR=/tmp
>     > IN_DIR=/export/storage
>     > REF_DIR=/export/working/ortak/b37_bundle_2.5
>     >
>     > runDir=/export/working/pinar/genomeStrip
>     > sites=/export/working/pinar/genomeStrip/sizofreni.discovery.vcf
>     > genotypes=/export/working/pinar/genomeStrip/sizofreni.genotypes.vcf
>     >
>     > export LD_LIBRARY_PATH=${SV_DIR}/bwa:${LD_LIBRARY_PATH}
>     >
>     > mx="-Xmx16g"
>     >
>     classpath="${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar:${SV_DIR}/lib/gatk/Queue.jar"
>     >
>     > mkdir -p ${runDir}/logs || exit 1
>     > mkdir -p ${runDir}/metadata || exit 1
>     >
>     > java -cp ${classpath} ${mx} -jar ${SV_DIR}/lib/SVToolkit.jar
>     >
>     >
>     > java -cp ${classpath} ${mx} \
>     > -Djava.io.tmpdir=${SV_TMPDIR} \
>     > -Djava.library.path=bwa \
>     > org.broadinstitute.sting.queue.QCommandLine \
>     > -cp ${classpath} \
>     > -S ${SV_DIR}/qscript/SVPreprocess.q \
>     > -S ${SV_DIR}/qscript/SVQScript.q \
>     > -md ${runDir}/metadata \
>     > -configFile installtest/conf/genstrip_installtest_parameters.txt \
>     > -tempDir ${SV_TMPDIR} \
>     > -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
>     > -R ${REF_DIR}/human_g1k_v37.fasta \
>     > -genomeMaskFile ${REF_DIR}/mask/human_g1k_v37.mask.fasta \
>     > -ploidyMapFile ${REF_DIR}/mask/humgen_g1k_v37_ploidy.map \
>     > -copyNumberMaskFile ${REF_DIR}/mask/cn2_mask_g1k_v37.fasta \
>     > -computeGCProfiles \
>     > -bamFilesAreDisjoint \
>     > -I ${IN_DIR}/Nurten_SIZOFRENI/WGS/bam/2367.realigned.bam \
>     > -I ${IN_DIR}/Nurten_SIZOFRENI/WGS/bam/855.realigned.bam \
>     > -runDirectory ${runDir} \
>     > -jobLogDir ${runDir}/logs \
>     > --disableJobReport \
>     > -run
>     >
>     >
>     > OUTPUT LOG
>     >
>     > ------------------
>     >
>     > SVToolkit version 1.04 (build 1358)
>     > Build date: 2014/02/13 15:47:19
>     > Web site:? http://www.broadinstitute.org/software/genomestrip
>     > INFO 18:46:59,457 QScriptManager - Compiling 2 QScripts
>     > INFO 18:47:13,419 QScriptManager - Compilation complete
>     > INFO 18:47:13,665 HelpFormatter -
>     >
>     ----------------------------------------------------------------------
>     > INFO 18:47:13,665 HelpFormatter - Queue v2.5-2-g5671483, Compiled
>     > 2013/08/22 15:09:27
>     > INFO 18:47:13,665 HelpFormatter - Copyright (c) 2012 The Broad
>     Institute
>     > INFO 18:47:13,666 HelpFormatter - For support and documentation
>     go to?
>     > http://www.broadinstitute.org/gatk
>     > INFO 18:47:13,666 HelpFormatter - Program Args: -cp
>     >
>     /export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar
>     > -S /export/home/ortak/TOOLS/svtoolkit/qscript/SVPreprocess.q -S
>     > /export/home/ortak/TOOLS/svtoolkit/qscript/SVQScript.q -md
>     > /export/working/pinar/genomeStrip/metadata -configFile
>     > installtest/conf/genstrip_installtest_parameters.txt -tempDir /tmp
>     > -gatk
>     /export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar
>     > -R /export/working/ortak/b37_bundle_2.5/human_g1k_v37.fasta
>     > -genomeMaskFile
>     > /export/working/ortak/b37_bundle_2.5/mask/human_g1k_v37.mask.fasta
>     > -ploidyMapFile
>     > /export/working/ortak/b37_bundle_2.5/mask/humgen_g1k_v37_ploidy.map
>     > -copyNumberMaskFile
>     > /export/working/ortak/b37_bundle_2.5/mask/cn2_mask_g1k_v37.fasta
>     > -computeGCProfiles -bamFilesAreDisjoint -I
>     > /export/storage/Nurten_SIZOFRENI/WGS/bam/2367.realigned.bam -I
>     > /export/storage/Nurten_SIZOFRENI/WGS/bam/855.realigned.bam
>     > -runDirectory /export/working/pinar/genomeStrip -jobLogDir
>     > /export/working/pinar/genomeStrip/logs --disableJobReport -run
>     > INFO 18:47:13,667 HelpFormatter - Date/Time: 2014/04/17 18:47:13
>     > INFO 18:47:13,667 HelpFormatter -
>     >
>     ----------------------------------------------------------------------
>     > INFO 18:47:13,667 HelpFormatter -
>     >
>     ----------------------------------------------------------------------
>     > INFO 18:47:13,676 QCommandLine - Scripting SVPreprocess
>     > INFO 18:47:13,887 QCommandLine - Added 12 functions
>     > INFO 18:47:13,887 QGraph - Generating graph.
>     > INFO 18:47:13,914 QGraph - Running jobs.
>     > INFO 18:47:13,969 FunctionEdge - Starting: 'java' '-Xmx4096m'
>     > '-XX:+UseParallelOldGC' '-XXarallelGCThreads=4' '-XX:GCTimeLimit=50'
>     > '-XX:GCHeapFreeLimit=10'
>     > '-Djava.io.tmpdir=/export/home/ortak/TOOLS/svtoolkit/.queue/tmp'
>     '-cp'
>     >
>     '/export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar'
>     > '-cp'
>     >
>     '/export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar'
>     > 'org.broadinstitute.sv.apps.ComputeGCProfiles' '-O'
>     >
>     '/export/working/pinar/genomeStrip/metadata/gcprofile/reference.gcprof.zip'
>     > '-R' '/export/working/ortak/b37_bundle_2.5/human_g1k_v37.fasta'
>     '-md'
>     > '/export/working/pinar/genomeStrip/metadata'
>     '-writeReferenceProfile'
>     > 'true' '-genomeMaskFile'
>     > '/export/working/ortak/b37_bundle_2.5/mask/human_g1k_v37.mask.fasta'
>     > '-copyNumberMaskFile'
>     > '/export/working/ortak/b37_bundle_2.5/mask/cn2_mask_g1k_v37.fasta'
>     > '-configFile' 'installtest/conf/genstrip_installtest_parameters.txt'
>     > INFO 18:47:13,971 FunctionEdge - Output written to
>     > /export/working/pinar/genomeStrip/logs/SVPreprocess-3.out
>     >
>     > INFO 18:58:01,912 QGraph - 6 Pend, 1 Run, 0 Fail, 5 Done
>     > ERROR 18:58:01,923 FunctionEdge - Error: 'java' '-Xmx4096m'
>     > '-XX:+UseParallelOldGC' '-XXarallelGCThreads=4' '-XX:GCTimeLimit=50'
>     > '-XX:GCHeapFreeLimit=10'
>     > '-Djava.io.tmpdir=/export/home/ortak/TOOLS/svtoolkit/.queue/tmp'
>     '-cp'
>     >
>     '/export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar'
>     > '-cp'
>     >
>     '/export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar'
>     > 'org.broadinstitute.sv.apps.ComputeGCProfiles' '-O'
>     >
>     '/export/working/pinar/genomeStrip/metadata/gcprofile/reference.gcprof.zip'
>     > '-R' '/export/working/ortak/b37_bundle_2.5/human_g1k_v37.fasta'
>     '-md'
>     > '/export/working/pinar/genomeStrip/metadata'
>     '-writeReferenceProfile'
>     > 'true' '-genomeMaskFile'
>     > '/export/working/ortak/b37_bundle_2.5/mask/human_g1k_v37.mask.fasta'
>     > '-copyNumberMaskFile'
>     > '/export/working/ortak/b37_bundle_2.5/mask/cn2_mask_g1k_v37.fasta'
>     > '-configFile' 'installtest/conf/genstrip_installtest_parameters.txt'
>     > ERROR 18:58:01,929 FunctionEdge - Contents of
>     > /export/working/pinar/genomeStrip/logs/SVPreprocess-3.out:
>     > INFO 18:47:21,668 HelpFormatter -
>     > ----------------------------------------------------------
>     > INFO 18:47:21,671 HelpFormatter - Program Name:
>     > org.broadinstitute.sv.apps.ComputeGCProfiles
>     > INFO 18:47:21,678 HelpFormatter - Program Args: -O
>     >
>     /export/working/pinar/genomeStrip/metadata/gcprofile/reference.gcprof.zip
>     > -R /export/working/ortak/b37_bundle_2.5/human_g1k_v37.fasta -md
>     > /export/working/pinar/genomeStrip/metadata
>     -writeReferenceProfile true
>     > -genomeMaskFile
>     > /export/working/ortak/b37_bundle_2.5/mask/human_g1k_v37.mask.fasta
>     > -copyNumberMaskFile
>     > /export/working/ortak/b37_bundle_2.5/mask/cn2_mask_g1k_v37.fasta
>     > -configFile installtest/conf/genstrip_installtest_parameters.txt
>     > INFO 18:47:21,678 HelpFormatter - Date/Time: 2014/04/17 18:47:21
>     > INFO 18:47:21,678 HelpFormatter -
>     > ----------------------------------------------------------
>     > INFO 18:47:21,678 HelpFormatter -
>     > ----------------------------------------------------------
>     > INFO 18:47:21,686 MetaData - Opening metadata ...
>     > INFO 18:47:21,688 MetaData - Adding metadata directory
>     > /export/working/pinar/genomeStrip/metadata ...
>     > INFO 18:47:21,690 MetaData - Opened metadata.
>     > INFO 18:47:21,690 ComputeGCProfiles - Opening reference sequence ...
>     > INFO 18:47:21,692 ComputeGCProfiles - Opened reference sequence.
>     > INFO 18:47:21,693 ComputeGCProfiles - Opening genome mask ...
>     > INFO 18:47:21,694 ComputeGCProfiles - Opened genome mask.
>     > INFO 18:47:21,694 ComputeGCProfiles - Opening copy number mask ...
>     > INFO 18:47:21,695 ComputeGCProfiles - Opened copy number mask.
>     > INFO 18:47:21,695 ComputeGCProfiles - Initializing algorithm ...
>     > #INFO: ReadCountAlgorithm: detected metadata version 1, forcing
>     legacy
>     > behavior
>     > INFO 18:47:21,701 MetaData - Loading insert size histograms ...
>     > INFO 18:47:22,451 ComputeGCProfiles - Algorithm initialized.
>     > INFO 18:47:22,452 ComputeGCProfiles - Computing reference GC
>     profile ...
>     > #DBG: Thu Apr 17 18:47:22 EEST 2014 computing reference profile for
>     > the interval 1:1-249250621
>     > #DBG: Thu Apr 17 18:48:14 EEST 2014 computing reference profile for
>     > the interval 2:1-243199373
>     > #DBG: Thu Apr 17 18:49:07 EEST 2014 computing reference profile for
>     > the interval 3:1-198022430
>     >
>     > #DBG: Thu Apr 17 18:49:49 EEST 2014 computing reference profile for
>     > the interval 4:1-191154276
>     > #DBG: Thu Apr 17 18:50:30 EEST 2014 computing reference profile for
>     > the interval 5:1-180915260
>     > #DBG: Thu Apr 17 18:51:08 EEST 2014 computing reference profile for
>     > the interval 6:1-171115067
>     > #DBG: Thu Apr 17 18:51:45 EEST 2014 computing reference profile for
>     > the interval 7:1-159138663
>     > #DBG: Thu Apr 17 18:52:18 EEST 2014 computing reference profile for
>     > the interval 8:1-146364022
>     > #DBG: Thu Apr 17 18:52:49 EEST 2014 computing reference profile for
>     > the interval 9:1-141213431
>     > #DBG: Thu Apr 17 18:53:17 EEST 2014 computing reference profile for
>     > the interval 10:1-135534747
>     > #DBG: Thu Apr 17 18:53:45 EEST 2014 computing reference profile for
>     > the interval 11:1-135006516
>     > #DBG: Thu Apr 17 18:54:14 EEST 2014 computing reference profile for
>     > the interval 12:1-133851895
>     > #DBG: Thu Apr 17 18:54:42 EEST 2014 computing reference profile for
>     > the interval 13:1-115169878
>     > #DBG: Thu Apr 17 18:55:05 EEST 2014 computing reference profile for
>     > the interval 14:1-107349540
>     > #DBG: Thu Apr 17 18:55:26 EEST 2014 computing reference profile for
>     > the interval 15:1-102531392
>     > #DBG: Thu Apr 17 18:55:46 EEST 2014 computing reference profile for
>     > the interval 16:1-90354753
>     > #DBG: Thu Apr 17 18:56:04 EEST 2014 computing reference profile for
>     > the interval 17:1-81195210
>     > #DBG: Thu Apr 17 18:56:21 EEST 2014 computing reference profile for
>     > the interval 18:1-78077248
>     > #DBG: Thu Apr 17 18:56:37 EEST 2014 computing reference profile for
>     > the interval 19:1-59128983
>     > #DBG: Thu Apr 17 18:56:49 EEST 2014 computing reference profile for
>     > the interval 20:1-63025520
>     > #DBG: Thu Apr 17 18:57:02 EEST 2014 computing reference profile for
>     > the interval 21:1-48129895
>     > #DBG: Thu Apr 17 18:57:12 EEST 2014 computing reference profile for
>     > the interval 22:1-51304566
>     > #DBG: Thu Apr 17 18:57:21 EEST 2014 computing reference profile for
>     > the interval X:1-155270560
>     > #DBG: Thu Apr 17 18:57:52 EEST 2014 computing reference profile for
>     > the interval Y:1-59373566
>     > #DBG: Thu Apr 17 18:58:01 EEST 2014 computing reference profile for
>     > the interval MT:1-16569
>     > #DBG: Thu Apr 17 18:58:01 EEST 2014 computing reference profile for
>     > the interval GL000207.1:1-4262
>     > Exception in thread "main" java.lang.RuntimeException: Invalid
>     > sequence position: GL000207.1:201
>     > at
>     >
>     org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:50)
>     > at
>     >
>     org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245)
>     > at
>     >
>     org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152)
>     > at
>     >
>     org.broadinstitute.sv.commandline.CommandLineProgram.run(CommandLineProgram.java:25)
>     > at
>     >
>     org.broadinstitute.sv.apps.ComputeGCProfiles.main(ComputeGCProfiles.java:125)
>     > Caused by: java.lang.IllegalArgumentException: Invalid sequence
>     > position: GL000207.1:201
>     > at
>     >
>     org.broadinstitute.sv.mask.GenomeMaskFastaFile.getMaskBit(GenomeMaskFastaFile.java:80)
>     > at
>     >
>     org.broadinstitute.sv.metadata.gc.GCProfileAlgorithm.computeIntervalProfile(GCProfileAlgorithm.java:332)
>     > at
>     >
>     org.broadinstitute.sv.metadata.gc.GCProfileAlgorithm.computeReferenceProfileMap(GCProfileAlgorithm.java:243)
>     > at
>     >
>     org.broadinstitute.sv.metadata.gc.GCProfileAlgorithm.computeReferenceProfile(GCProfileAlgorithm.java:191)
>     > at
>     >
>     org.broadinstitute.sv.apps.ComputeGCProfiles.run(ComputeGCProfiles.java:172)
>     > at
>     >
>     org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:39)
>     > ... 4 more
>     > INFO 18:58:01,930 QGraph - Writing incremental jobs reports...
>     > INFO 18:58:01,933 FunctionEdge - Starting: 'java' '-Xmx4096m'
>     > '-XX:+UseParallelOldGC' '-XXarallelGCThreads=4' '-XX:GCTimeLimit=50'
>     > '-XX:GCHeapFreeLimit=10'
>     > '-Djava.io.tmpdir=/export/home/ortak/TOOLS/svtoolkit/.queue/tmp'
>     '-cp'
>     >
>     '/export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar'
>     > '-cp'
>     >
>     '/export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar'
>     > 'org.broadinstitute.sv.apps.ComputeGenomeSizes' '-O'
>     > '/export/working/pinar/genomeStrip/metadata/genome_sizes.txt' '-R'
>     > '/export/working/ortak/b37_bundle_2.5/human_g1k_v37.fasta'
>     > '-ploidyMapFile'
>     >
>     '/export/working/ortak/b37_bundle_2.5/mask/humgen_g1k_v37_ploidy.map'
>     > '-genomeMaskFile'
>     > '/export/working/ortak/b37_bundle_2.5/mask/human_g1k_v37.mask.fasta'
>     > INFO 18:58:01,933 FunctionEdge - Output written to
>     > /export/working/pinar/genomeStrip/logs/SVPreprocess-2.out
>     > INFO 19:01:54,542 QGraph - 5 Pend, 1 Run, 1 Fail, 5 Done
>     > ERROR 19:01:54,549 FunctionEdge - Error: 'java' '-Xmx4096m'
>     > '-XX:+UseParallelOldGC' '-XXarallelGCThreads=4' '-XX:GCTimeLimit=50'
>     > '-XX:GCHeapFreeLimit=10'
>     > '-Djava.io.tmpdir=/export/home/ortak/TOOLS/svtoolkit/.queue/tmp'
>     '-cp'
>     >
>     '/export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar'
>     > '-cp'
>     >
>     '/export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar'
>     > 'org.broadinstitute.sv.apps.ComputeGenomeSizes' '-O'
>     > '/export/working/pinar/genomeStrip/metadata/genome_sizes.txt' '-R'
>     > '/export/working/ortak/b37_bundle_2.5/human_g1k_v37.fasta'
>     > '-ploidyMapFile'
>     >
>     '/export/working/ortak/b37_bundle_2.5/mask/humgen_g1k_v37_ploidy.map'
>     > '-genomeMaskFile'
>     > '/export/working/ortak/b37_bundle_2.5/mask/human_g1k_v37.mask.fasta'
>     > ERROR 19:01:54,551 FunctionEdge - Contents of
>     > /export/working/pinar/genomeStrip/logs/SVPreprocess-2.out:
>     > INFO 18:58:09,523 HelpFormatter -
>     > -----------------------------------------------------------
>     > INFO 18:58:09,526 HelpFormatter - Program Name:
>     > org.broadinstitute.sv.apps.ComputeGenomeSizes
>     > INFO 18:58:09,533 HelpFormatter - Program Args: -O
>     > /export/working/pinar/genomeStrip/metadata/genome_sizes.txt -R
>     > /export/working/ortak/b37_bundle_2.5/human_g1k_v37.fasta
>     > -ploidyMapFile
>     > /export/working/ortak/b37_bundle_2.5/mask/humgen_g1k_v37_ploidy.map
>     > -genomeMaskFile
>     > /export/working/ortak/b37_bundle_2.5/mask/human_g1k_v37.mask.fasta
>     > INFO 18:58:09,534 HelpFormatter - Date/Time: 2014/04/17 18:58:09
>     > INFO 18:58:09,534 HelpFormatter -
>     > -----------------------------------------------------------
>     > INFO 18:58:09,534 HelpFormatter -
>     > -----------------------------------------------------------
>     > INFO 18:58:09,549 ComputeGenomeSizes - Processing interval
>     > 1:1-249250621 ...
>     >
>     > INFO 18:58:28,244 ComputeGenomeSizes - Processing interval
>     > 2:1-243199373 ...
>     > INFO 18:58:46,064 ComputeGenomeSizes - Processing interval
>     > 3:1-198022430 ...
>     > INFO 18:59:00,273 ComputeGenomeSizes - Processing interval
>     > 4:1-191154276 ...
>     > INFO 18:59:14,199 ComputeGenomeSizes - Processing interval
>     > 5:1-180915260 ...
>     > INFO 18:59:27,249 ComputeGenomeSizes - Processing interval
>     > 6:1-171115067 ...
>     > INFO 18:59:39,596 ComputeGenomeSizes - Processing interval
>     > 7:1-159138663 ...
>     > INFO 18:59:51,039 ComputeGenomeSizes - Processing interval
>     > 8:1-146364022 ...
>     > INFO 19:00:01,565 ComputeGenomeSizes - Processing interval
>     > 9:1-141213431 ...
>     > INFO 19:00:12,362 ComputeGenomeSizes - Processing interval
>     > 10:1-135534747 ...
>     > INFO 19:00:22,179 ComputeGenomeSizes - Processing interval
>     > 11:1-135006516 ...
>     > INFO 19:00:31,886 ComputeGenomeSizes - Processing interval
>     > 12:1-133851895 ...
>     > INFO 19:00:41,484 ComputeGenomeSizes - Processing interval
>     > 13:1-115169878 ...
>     > INFO 19:00:49,752 ComputeGenomeSizes - Processing interval
>     > 14:1-107349540 ...
>     > INFO 19:00:57,475 ComputeGenomeSizes - Processing interval
>     > 15:1-102531392 ...
>     > INFO 19:01:04,955 ComputeGenomeSizes - Processing interval
>     > 16:1-90354753 ...
>     > INFO 19:01:11,456 ComputeGenomeSizes - Processing interval
>     > 17:1-81195210 ...
>     > INFO 19:01:17,264 ComputeGenomeSizes - Processing interval
>     > 18:1-78077248 ...
>     > INFO 19:01:23,082 ComputeGenomeSizes - Processing interval
>     > 19:1-59128983 ...
>     > INFO 19:01:27,400 ComputeGenomeSizes - Processing interval
>     > 20:1-63025520 ...
>     > INFO 19:01:31,924 ComputeGenomeSizes - Processing interval
>     > 21:1-48129895 ...
>     > INFO 19:01:35,388 ComputeGenomeSizes - Processing interval
>     > 22:1-51304566 ...
>     > INFO 19:01:39,081 ComputeGenomeSizes - Processing interval
>     > X:1-155270560 ...
>     > INFO 19:01:50,250 ComputeGenomeSizes - Processing interval
>     > Y:1-59373566 ...
>     > INFO 19:01:54,512 ComputeGenomeSizes - Processing interval
>     MT:1-16569 ...
>     > INFO 19:01:54,514 ComputeGenomeSizes - Processing interval
>     > GL000207.1:1-4262 ...
>     > Exception in thread "main" java.lang.RuntimeException
>     > at
>     >
>     org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:50)
>     > at
>     >
>     org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245)
>     > at
>     >
>     org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152)
>     > at
>     >
>     org.broadinstitute.sv.commandline.CommandLineProgram.run(CommandLineProgram.java:25)
>     > at
>     >
>     org.broadinstitute.sv.apps.ComputeGenomeSizes.main(ComputeGenomeSizes.java:56)
>     > Caused by: java.lang.NullPointerException
>     > at
>     >
>     org.broadinstitute.sv.apps.ComputeGenomeSizes.run(ComputeGenomeSizes.java:74)
>     > at
>     >
>     org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:39)
>     > ... 4 more
>     > INFO 19:01:54,551 QGraph - Writing incremental jobs reports...
>     > INFO 19:01:54,552 QGraph - 5 Pend, 0 Run, 2 Fail, 5 Done
>     > INFO 19:01:54,555 QCommandLine - Writing final jobs report...
>     > INFO 19:01:54,556 QCommandLine - Done with errors
>     > INFO 19:01:54,558 QGraph - -------
>     > INFO 19:01:54,560 QGraph - Failed: 'java' '-Xmx4096m'
>     > '-XX:+UseParallelOldGC' '-XXarallelGCThreads=4' '-XX:GCTimeLimit=50'
>     > '-XX:GCHeapFreeLimit=10'
>     > '-Djava.io.tmpdir=/export/home/ortak/TOOLS/svtoolkit/.queue/tmp'
>     '-cp'
>     >
>     '/export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar'
>     > '-cp'
>     >
>     '/export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar'
>     > 'org.broadinstitute.sv.apps.ComputeGCProfiles' '-O'
>     >
>     '/export/working/pinar/genomeStrip/metadata/gcprofile/reference.gcprof.zip'
>     > '-R' '/export/working/ortak/b37_bundle_2.5/human_g1k_v37.fasta'
>     '-md'
>     > '/export/working/pinar/genomeStrip/metadata'
>     '-writeReferenceProfile'
>     > 'true' '-genomeMaskFile'
>     > '/export/working/ortak/b37_bundle_2.5/mask/human_g1k_v37.mask.fasta'
>     > '-copyNumberMaskFile'
>     > '/export/working/ortak/b37_bundle_2.5/mask/cn2_mask_g1k_v37.fasta'
>     > '-configFile' 'installtest/conf/genstrip_installtest_parameters.txt'
>     > INFO 19:01:54,560 QGraph - Log:
>     > /export/working/pinar/genomeStrip/logs/SVPreprocess-3.out
>     > INFO 19:01:54,561 QGraph - -------
>     > INFO 19:01:54,562 QGraph - Failed: 'java' '-Xmx4096m'
>     > '-XX:+UseParallelOldGC' '-XXarallelGCThreads=4' '-XX:GCTimeLimit=50'
>     > '-XX:GCHeapFreeLimit=10'
>     > '-Djava.io.tmpdir=/export/home/ortak/TOOLS/svtoolkit/.queue/tmp'
>     '-cp'
>     >
>     '/export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar'
>     > '-cp'
>     >
>     '/export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar'
>     > 'org.broadinstitute.sv.apps.ComputeGenomeSizes' '-O'
>     > '/export/working/pinar/genomeStrip/metadata/genome_sizes.txt' '-R'
>     > '/export/working/ortak/b37_bundle_2.5/human_g1k_v37.fasta'
>     > '-ploidyMapFile'
>     >
>     '/export/working/ortak/b37_bundle_2.5/mask/humgen_g1k_v37_ploidy.map'
>     > '-genomeMaskFile'
>     > '/export/working/ortak/b37_bundle_2.5/mask/human_g1k_v37.mask.fasta'
>     > INFO 19:01:54,563 QGraph - Log:
>     > /export/working/pinar/genomeStrip/logs/SVPreprocess-2.out
>     > INFO 19:01:54,563 QCommandLine - Script failed with 12 total jobs
>     >
>     >
>     >
>     >
>     >
>     ------------------------------------------------------------------------------
>     > Learn Graph Databases - Download FREE O'Reilly Book
>     > "Graph Databases" is the definitive new guide to graph databases
>     and their
>     > applications. Written by three acclaimed leaders in the field,
>     > this first edition is now available. Download your free book today!
>     > http://p.sf.net/sfu/NeoTech
>     >
>     >
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>     ------------------------------
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>     ------------------------------------------------------------------------------
>     Learn Graph Databases - Download FREE O'Reilly Book
>     "Graph Databases" is the definitive new guide to graph databases
>     and their
>     applications. Written by three acclaimed leaders in the field,
>     this first edition is now available. Download your free book today!
>     http://p.sf.net/sfu/NeoTech
>
>     ------------------------------
>
>     _______________________________________________
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>
>     End of svtoolkit-help Digest, Vol 28, Issue 3
>     *********************************************
>
>
>
> ------------------------------------------------------------------------------
> Learn Graph Databases - Download FREE O'Reilly Book
> "Graph Databases" is the definitive new guide to graph databases and their
> applications. Written by three acclaimed leaders in the field,
> this first edition is now available. Download your free book today!
> http://p.sf.net/sfu/NeoTech
>
>
> _______________________________________________
> svtoolkit-help mailing list
> svt...@li...
> https://lists.sourceforge.net/lists/listinfo/svtoolkit-help