Thread: [svtoolkit-help] genotyping.sh crashing
Status: Beta
Brought to you by:
bhandsaker
From: yw <yw...@gm...> - 2012-09-23 13:15:50
|
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 |
From: Bob H. <han...@br...> - 2012-09-25 03:22:40
|
The problem is that the previous job (bwa index test2/altalign/installtest.sites.alt.fasta) failed. And I am guessing it didn't return a non-zero exit status or it didn't create the bwt index files. There is a similar report here http://gatkforums.broadinstitute.org/discussion/1338/genome-strip-test-installation-error where they say they had an newer version of bwa installed, so this may be similar. -Bob On 9/23/12 9:12 AM, yw wrote: > 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 > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > > > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |