Re: [svtoolkit-help] "Invalid sequence position"
Status: Beta
Brought to you by:
bhandsaker
Menu
▾
▴
Re: [svtoolkit-help] "Invalid sequence position"
|
From: Pinar Kavak(BİLGEM-U. <pin...@tu...> - 2014-04-17 16:28:52
|
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' '-XX:ParallelGCThreads=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' '-XX:ParallelGCThreads=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' '-XX:ParallelGCThreads=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' '-XX:ParallelGCThreads=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' '-XX:ParallelGCThreads=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' '-XX:ParallelGCThreads=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
|
