[svtoolkit-help] genotyping.sh crashing
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[svtoolkit-help] genotyping.sh crashing
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From: yw <yw...@gm...> - 2012-09-23 13:15:50
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Hi, I am trying to configure GenomeSTRiP. Till now, I have run discovery.sh without error. When I came to genotyping.sh. It went wrong. All the output information is shown below: 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 15:58:10,295 QScriptManager - Compiling 2 QScripts INFO 15:58:20,855 QScriptManager - Compilation complete INFO 15:58:20,987 HelpFormatter - --------------------------------------------------------- INFO 15:58:20,987 HelpFormatter - Program Name: org.broadinstitute.sting.queue.QCommandLine INFO 15:58:20,988 HelpFormatter - Program Args: -S /home/wbxie/software/svtoolkit/qscript/SVPreprocess.q -S /home/wbxie/software/svtoolkit/qscript/SVQScript.q -gatk /home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/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 -copyNumberMaskFile data/cn2_mask_g1k_b36_chr1.fasta -runDirectory test2 -md test2/metadata -computeGCProfiles -jobLogDir test2/logs -I data/installtest.bam -run INFO 15:58:20,988 HelpFormatter - Date/Time: 2012/09/23 15:58:20 INFO 15:58:20,989 HelpFormatter - --------------------------------------------------------- INFO 15:58:20,989 HelpFormatter - --------------------------------------------------------- INFO 15:58:20,995 QCommandLine - Scripting SVPreprocess INFO 15:58:21,326 QCommandLine - Added 10 functions INFO 15:58:21,326 QGraph - Generating graph. INFO 15:58:21,371 QGraph - Generating scatter gather jobs. INFO 15:58:21,373 QGraph - Removing original jobs. INFO 15:58:21,375 QGraph - Adding scatter gather jobs. INFO 15:58:21,376 QGraph - Regenerating graph. INFO 15:58:21,388 QGraph - Running jobs. INFO 15:58:21,479 FunctionEdge - Starting: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeInsertSizeHistograms -R /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd/installtest.hist.bin -md test2/metadata -createEmpty INFO 15:58:21,480 FunctionEdge - Output written to /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-1.out INFO 15:59:14,762 QGraph - 9 Pend, 1 Run, 0 Fail, 0 Done INFO 15:59:14,773 FunctionEdge - Done: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeInsertSizeHistograms -R /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd/installtest.hist.bin -md test2/metadata -createEmpty INFO 15:59:14,778 FunctionEdge - Starting: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" org.broadinstitute.sv.apps.MergeInsertSizeHistograms -I /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd/installtest.hist.bin -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd.hist.bin INFO 15:59:14,778 FunctionEdge - Output written to /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-2.out INFO 15:59:15,234 FunctionEdge - Starting: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeReadDepthCoverage -R /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/depth/installtest.depth.txt -md test2/metadata -genomeMaskFile data/human_b36_chr1.mask.fasta -minMapQ 10 INFO 15:59:15,235 FunctionEdge - Output written to /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-4.out INFO 16:00:08,246 QGraph - 7 Pend, 2 Run, 0 Fail, 1 Done INFO 16:00:08,249 FunctionEdge - Done: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" org.broadinstitute.sv.apps.MergeInsertSizeHistograms -I /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd/installtest.hist.bin -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd.hist.bin INFO 16:00:08,252 FunctionEdge - Done: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeReadDepthCoverage -R /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/depth/installtest.depth.txt -md test2/metadata -genomeMaskFile data/human_b36_chr1.mask.fasta -minMapQ 10 INFO 16:00:08,255 FunctionEdge - Starting: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" org.broadinstitute.sv.apps.ComputeInsertStatistics -I /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd.hist.bin -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd.stats.dat INFO 16:00:08,255 FunctionEdge - Output written to /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-3.out INFO 16:00:09,077 FunctionEdge - Starting: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeReadSpanCoverage -R /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/spans/installtest.spans.txt -md test2/metadata -maxInsertSizeStandardDeviations 3 INFO 16:00:09,077 FunctionEdge - Output written to /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-6.out INFO 16:01:02,106 QGraph - 5 Pend, 2 Run, 0 Fail, 3 Done INFO 16:01:02,110 FunctionEdge - Done: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" org.broadinstitute.sv.apps.ComputeInsertStatistics -I /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd.hist.bin -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd.stats.dat INFO 16:01:02,113 FunctionEdge - Done: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeReadSpanCoverage -R /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/spans/installtest.spans.txt -md test2/metadata -maxInsertSizeStandardDeviations 3 INFO 16:01:02,116 FunctionEdge - Starting: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" org.broadinstitute.sv.apps.MergeReadSpanCoverage -I /home/wbxie/software/svtoolkit/installtest/test2/metadata/spans/installtest.spans.txt -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/spans.dat INFO 16:01:02,116 FunctionEdge - Output written to /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-7.out INFO 16:01:02,840 FunctionEdge - Starting: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" org.broadinstitute.sv.apps.MergeReadDepthCoverage -I /home/wbxie/software/svtoolkit/installtest/test2/metadata/depth/installtest.depth.txt -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/depth.dat INFO 16:01:02,840 FunctionEdge - Output written to /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-5.out INFO 16:01:03,514 FunctionEdge - Starting: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" org.broadinstitute.sv.apps.ComputeGCProfiles -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/gcprofile/reference.gcprof.zip -R data/human_b36_chr1.fasta -md test2/metadata -writeReferenceProfile true -genomeMaskFile data/human_b36_chr1.mask.fasta -copyNumberMaskFile data/cn2_mask_g1k_b36_chr1.fasta INFO 16:01:03,515 FunctionEdge - Output written to /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-8.out INFO 16:01:52,913 QGraph - 2 Pend, 3 Run, 0 Fail, 5 Done INFO 16:01:52,921 FunctionEdge - Done: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" org.broadinstitute.sv.apps.MergeReadSpanCoverage -I /home/wbxie/software/svtoolkit/installtest/test2/metadata/spans/installtest.spans.txt -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/spans.dat INFO 16:01:52,923 FunctionEdge - Done: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" org.broadinstitute.sv.apps.MergeReadDepthCoverage -I /home/wbxie/software/svtoolkit/installtest/test2/metadata/depth/installtest.depth.txt -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/depth.dat INFO 16:01:52,925 FunctionEdge - Done: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" org.broadinstitute.sv.apps.ComputeGCProfiles -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/gcprofile/reference.gcprof.zip -R data/human_b36_chr1.fasta -md test2/metadata -writeReferenceProfile true -genomeMaskFile data/human_b36_chr1.mask.fasta -copyNumberMaskFile data/cn2_mask_g1k_b36_chr1.fasta INFO 16:01:52,927 FunctionEdge - Starting: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" org.broadinstitute.sv.apps.ComputeGCProfiles -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/gcprofile/installtest.bam.gcprof.zip -R data/human_b36_chr1.fasta -md test2/metadata -referenceProfile test2/metadata/gcprofile/reference.gcprof.zip -genomeMaskFile data/human_b36_chr1.mask.fasta -copyNumberMaskFile data/cn2_mask_g1k_b36_chr1.fasta INFO 16:01:52,928 FunctionEdge - Output written to /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-9.out INFO 16:02:00,425 QGraph - 1 Pend, 1 Run, 0 Fail, 8 Done INFO 16:02:22,924 FunctionEdge - Done: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" org.broadinstitute.sv.apps.ComputeGCProfiles -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/gcprofile/installtest.bam.gcprof.zip -R data/human_b36_chr1.fasta -md test2/metadata -referenceProfile test2/metadata/gcprofile/reference.gcprof.zip -genomeMaskFile data/human_b36_chr1.mask.fasta -copyNumberMaskFile data/cn2_mask_g1k_b36_chr1.fasta INFO 16:02:22,926 FunctionEdge - Starting: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" org.broadinstitute.sv.apps.MergeGCProfiles -I /home/wbxie/software/svtoolkit/installtest/test2/metadata/gcprofile/installtest.bam.gcprof.zip -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/gcprofiles.zip INFO 16:02:22,927 FunctionEdge - Output written to /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-10.out INFO 16:02:23,629 QGraph - 0 Pend, 1 Run, 0 Fail, 9 Done INFO 16:02:52,932 FunctionEdge - Done: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" org.broadinstitute.sv.apps.MergeGCProfiles -I /home/wbxie/software/svtoolkit/installtest/test2/metadata/gcprofile/installtest.bam.gcprof.zip -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/gcprofiles.zip INFO 16:02:52,933 QGraph - 0 Pend, 0 Run, 0 Fail, 10 Done INFO 16:02:52,935 QCommandLine - Done INFO 16:03:01,726 QScriptManager - Compiling 2 QScripts INFO 16:03:12,978 QScriptManager - Compilation complete INFO 16:03:13,101 HelpFormatter - --------------------------------------------------------- INFO 16:03:13,102 HelpFormatter - Program Name: org.broadinstitute.sting.queue.QCommandLine INFO 16:03:13,103 HelpFormatter - Program Args: -S /home/wbxie/software/svtoolkit/qscript/SVAltAlign.q -S /home/wbxie/software/svtoolkit/qscript/SVQScript.q -gatk /home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/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 -runDirectory test2 -md test2/metadata -jobLogDir test2/logs -vcf data/installtest.sites.vcf -I data/installtest.bam -O test2/installtest.alt.bam -run INFO 16:03:13,103 HelpFormatter - Date/Time: 2012/09/23 16:03:13 INFO 16:03:13,104 HelpFormatter - --------------------------------------------------------- INFO 16:03:13,104 HelpFormatter - --------------------------------------------------------- INFO 16:03:13,110 QCommandLine - Scripting SVAltAlign INFO 16:03:13,365 QCommandLine - Added 7 functions INFO 16:03:13,366 QGraph - Generating graph. INFO 16:03:13,407 QGraph - Generating scatter gather jobs. INFO 16:03:13,409 QGraph - Removing original jobs. INFO 16:03:13,411 QGraph - Adding scatter gather jobs. INFO 16:03:13,412 QGraph - Regenerating graph. INFO 16:03:13,419 QGraph - Running jobs. INFO 16:03:13,484 FunctionEdge - Starting: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" org.broadinstitute.sv.apps.GenerateAltAlleleFasta -I /home/wbxie/software/svtoolkit/installtest/data/installtest.sites.vcf -O /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.sites.alt.fasta -R data/human_b36_chr1.fasta INFO 16:03:13,484 FunctionEdge - Output written to /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16882@r910-1.out INFO 16:03:14,183 QGraph - 6 Pend, 1 Run, 0 Fail, 0 Done INFO 16:03:43,481 FunctionEdge - Done: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" org.broadinstitute.sv.apps.GenerateAltAlleleFasta -I /home/wbxie/software/svtoolkit/installtest/data/installtest.sites.vcf -O /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.sites.alt.fasta -R data/human_b36_chr1.fasta INFO 16:03:43,484 FunctionEdge - Starting: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" net.sf.picard.sam.CreateSequenceDictionary O=/home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.sites.alt.dict R=test2/altalign/installtest.sites.alt.fasta TRUNCATE_NAMES_AT_WHITESPACE=TRUE INFO 16:03:43,485 FunctionEdge - Output written to /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16882@r910-2.out INFO 16:03:43,986 FunctionEdge - Starting: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" org.broadinstitute.sv.apps.IndexFastaFile -I /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.sites.alt.fasta -O /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.sites.alt.fasta.fai INFO 16:03:43,987 FunctionEdge - Output written to /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16882@r910-3.out INFO 16:03:44,572 FunctionEdge - Starting: bwa index test2/altalign/installtest.sites.alt.fasta INFO 16:03:44,572 FunctionEdge - Output written to /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16882@r910-4.out INFO 16:03:44,680 QGraph - 3 Pend, 3 Run, 0 Fail, 1 Done INFO 16:04:13,485 FunctionEdge - Done: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" net.sf.picard.sam.CreateSequenceDictionary O=/home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.sites.alt.dict R=test2/altalign/installtest.sites.alt.fasta TRUNCATE_NAMES_AT_WHITESPACE=TRUE INFO 16:04:13,487 FunctionEdge - Done: java -Xmx4g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar -cp "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" org.broadinstitute.sv.apps.IndexFastaFile -I /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.sites.alt.fasta -O /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.sites.alt.fasta.fai INFO 16:04:13,489 FunctionEdge - Done: bwa index test2/altalign/installtest.sites.alt.fasta INFO 16:04:13,514 FunctionEdge - Starting: java -Xmx1g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar org.broadinstitute.sting.gatk.CommandLineGATK -T SVAltAligner -R /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.alt.bam -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true INFO 16:04:13,514 FunctionEdge - Output written to /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16882@r910-5.out ERROR 16:05:01,564 FunctionEdge - Error: java -Xmx1g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar org.broadinstitute.sting.gatk.CommandLineGATK -T SVAltAligner -R /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.alt.bam -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true org.broadinstitute.sting.queue.util.JobExitException: Failed to run job. Command line: sh /home/wbxie/software/svtoolkit/installtest/tmpdir/.exec5518112783651967939 Exit code: 1 Standard error contained: INFO 16:04:19,251 HelpFormatter - ----------------------------------------------------------------------------------- INFO 16:04:19,256 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.0-6121-g40e3165, Compiled 2011/09/04 20:57:29 INFO 16:04:19,256 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 16:04:19,257 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki INFO 16:04:19,257 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa INFO 16:04:19,258 HelpFormatter - Program Args: -T SVAltAligner -R /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.alt.bam -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true INFO 16:04:19,258 HelpFormatter - Date/Time: 2012/09/23 16:04:19 INFO 16:04:19,259 HelpFormatter - ----------------------------------------------------------------------------------- INFO 16:04:19,259 HelpFormatter - ----------------------------------------------------------------------------------- INFO 16:04:19,271 GenomeAnalysisEngine - Strictness is SILENT ##### 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.<init>(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:234) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:87) ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0-6121-g40e3165): ##### ERROR ##### ERROR Please visit the 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 ------------------------------------------------------------------------------------------ at org.broadinstitute.sting.queue.util.ShellJob.run(ShellJob.scala:24) at org.broadinstitute.sting.queue.engine.shell.ShellJobRunner.start(ShellJobRunner.scala:54) at org.broadinstitute.sting.queue.engine.FunctionEdge.start(FunctionEdge.scala:56) at org.broadinstitute.sting.queue.engine.QGraph.runJobs(QGraph.scala:383) at org.broadinstitute.sting.queue.engine.QGraph.run(QGraph.scala:123) at org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scala:111) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221) at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:57) at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala) INFO 16:05:01,566 QGraph - 2 Pend, 1 Run, 0 Fail, 4 Done INFO 16:05:01,567 QGraph - 2 Pend, 0 Run, 1 Fail, 4 Done INFO 16:05:01,567 QCommandLine - Done with errors INFO 16:05:01,569 QGraph - ------- INFO 16:05:01,575 QGraph - Failed: java -Xmx1g -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar org.broadinstitute.sting.gatk.CommandLineGATK -T SVAltAligner -R /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.alt.bam -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true INFO 16:05:01,576 QGraph - Log: /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16882@r910-5.out Any advices? Thank you in advance. Andrew |
