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  • ercfrtz
    Member
    • Aug 2010
    • 23
    #1

    genome STRiP Error

    Hello all,

    I am getting the following error when trying to run the SVPreprocess of Genome STRiP. Any ideas of what is wrong would be great.
    INFO 18:36:19,129 QScriptManager - Compiling 2 QScripts
    INFO 18:36:32,249 QScriptManager - Compilation complete
    INFO 18:36:36,870 HelpFormatter - ---------------------------------------------------------
    INFO 18:36:36,871 HelpFormatter - Program Name: org.broadinstitute.sting.queue.QCommandLine
    INFO 18:36:36,871 HelpFormatter - Program Args: -S /shared/local/svtoolkit/qscript/SVPreprocess.q -S /shared/local/svtoolkit/qscript/SVQScript.q -gatk /shared/local/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -cp /shared/local/svtoolkit/lib/SVToolkit.jar:/shared/local/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -configFile /shared/local/svtoolkit/conf/conf/genstrip_parameters.txt -tempDir /storage/isu/reecy_lab/tmp_eric/STRiP_temp -md /storage/isu/reecy_lab/tmp_eric/STRiP_metadata -R /shared/local/svtoolkit/installtest/data/human_b36_chr1.fasta -genomeMaskFile /shared/local/svtoolkit/installtest/data/human_b36_chr1.mask.fasta -genderMapFile /shared/local/svtoolkit/installtest/data/installtest_gender.map -I /shared/local/svtoolkit/installtest/data/installtest.bam -run
    INFO 18:36:36,871 HelpFormatter - Date/Time: 2011/03/27 18:36:36
    INFO 18:36:36,871 HelpFormatter - ---------------------------------------------------------
    INFO 18:36:36,872 HelpFormatter - ---------------------------------------------------------
    INFO 18:36:36,874 QCommandLine - Scripting SVPreprocess
    INFO 18:36:37,034 QCommandLine - Added 7 functions
    INFO 18:36:37,034 QGraph - Generating graph.
    INFO 18:36:37,086 QGraph - Running jobs.
    INFO 18:36:37,141 ShellJobRunner - Starting: java -Xmx4g -Djava.io.tmpdir=/storage/isu/reecy_lab/tmp_eric/STRiP_temp -cp /shared/local/svtoolkit/lib/SVToolkit.jar:/shared/local/svtoolkit/lib/gatk/GenomeAnalysisTK.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeInsertSizeDistributions -R /shared/local/svtoolkit/installtest/data/human_b36_chr1.fasta -I /shared/local/svtoolkit/installtest/data/installtest.bam -O /storage/isu/reecy_lab/tmp_eric/STRiP_metadata/isd/installtest.hist.bin -md /storage/isu/reecy_lab/tmp_eric/STRiP_metadata -createEmpty
    INFO 18:36:37,142 ShellJobRunner - Output written to /home/users/ercfrtz/[email protected]
    ERROR 18:36:37,189 ShellJobRunner - Error: java -Xmx4g -Djava.io.tmpdir=/storage/isu/reecy_lab/tmp_eric/STRiP_temp -cp /shared/local/svtoolkit/lib/SVToolkit.jar:/shared/local/svtoolkit/lib/gatk/GenomeAnalysisTK.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeInsertSizeDistributions -R /shared/local/svtoolkit/installtest/data/human_b36_chr1.fasta -I /shared/local/svtoolkit/installtest/data/installtest.bam -O /storage/isu/reecy_lab/tmp_eric/STRiP_metadata/isd/installtest.hist.bin -md /storage/isu/reecy_lab/tmp_eric/STRiP_metadata -createEmpty
    ERROR 18:36:37,190 ShellJobRunner - /storage/isu/reecy_lab/tmp_eric/STRiP_temp/.exec2786000665283577153: line 2: java: command not found

    INFO 18:36:37,195 ShellJobRunner - Starting: java -Xmx4g -Djava.io.tmpdir=/storage/isu/reecy_lab/tmp_eric/STRiP_temp -cp /shared/local/svtoolkit/lib/SVToolkit.jar:/shared/local/svtoolkit/lib/gatk/GenomeAnalysisTK.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeReadDepthCoverage -R /shared/local/svtoolkit/installtest/data/human_b36_chr1.fasta -I /shared/local/svtoolkit/installtest/data/installtest.bam -O /storage/isu/reecy_lab/tmp_eric/STRiP_metadata/depth/installtest.depth.txt -md /storage/isu/reecy_lab/tmp_eric/STRiP_metadata -genomeMaskFile /shared/local/svtoolkit/installtest/data/human_b36_chr1.mask.fasta -minMapQ 10
    INFO 18:36:37,195 ShellJobRunner - Output written to /home/users/ercfrtz/[email protected]
    ERROR 18:36:37,217 ShellJobRunner - Error: java -Xmx4g -Djava.io.tmpdir=/storage/isu/reecy_lab/tmp_eric/STRiP_temp -cp /shared/local/svtoolkit/lib/SVToolkit.jar:/shared/local/svtoolkit/lib/gatk/GenomeAnalysisTK.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeReadDepthCoverage -R /shared/local/svtoolkit/installtest/data/human_b36_chr1.fasta -I /shared/local/svtoolkit/installtest/data/installtest.bam -O /storage/isu/reecy_lab/tmp_eric/STRiP_metadata/depth/installtest.depth.txt -md /storage/isu/reecy_lab/tmp_eric/STRiP_metadata -genomeMaskFile /shared/local/svtoolkit/installtest/data/human_b36_chr1.mask.fasta -minMapQ 10
    ERROR 18:36:37,218 ShellJobRunner - /storage/isu/reecy_lab/tmp_eric/STRiP_temp/.exec8096455693624243640: line 2: java: command not found

    INFO 18:36:37,220 QCommandLine - Done with errors
    INFO 18:36:37,222 QGraph - -------
    INFO 18:36:37,229 QGraph - Failed: java -Xmx4g -Djava.io.tmpdir=/storage/isu/reecy_lab/tmp_eric/STRiP_temp -cp /shared/local/svtoolkit/lib/SVToolkit.jar:/shared/local/svtoolkit/lib/gatk/GenomeAnalysisTK.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeInsertSizeDistributions -R /shared/local/svtoolkit/installtest/data/human_b36_chr1.fasta -I /shared/local/svtoolkit/installtest/data/installtest.bam -O /storage/isu/reecy_lab/tmp_eric/STRiP_metadata/isd/installtest.hist.bin -md /storage/isu/reecy_lab/tmp_eric/STRiP_metadata -createEmpty
    INFO 18:36:37,230 QGraph - Log: /home/users/ercfrtz/[email protected]
    INFO 18:36:37,230 QGraph - -------
    INFO 18:36:37,231 QGraph - Failed: java -Xmx4g -Djava.io.tmpdir=/storage/isu/reecy_lab/tmp_eric/STRiP_temp -cp /shared/local/svtoolkit/lib/SVToolkit.jar:/shared/local/svtoolkit/lib/gatk/GenomeAnalysisTK.jar org.broadinstitute.sting.gatk.CommandLineGATK -T ComputeReadDepthCoverage -R /shared/local/svtoolkit/installtest/data/human_b36_chr1.fasta -I /shared/local/svtoolkit/installtest/data/installtest.bam -O /storage/isu/reecy_lab/tmp_eric/STRiP_metadata/depth/installtest.depth.txt -md /storage/isu/reecy_lab/tmp_eric/STRiP_metadata -genomeMaskFile /shared/local/svtoolkit/installtest/data/human_b36_chr1.mask.fasta -minMapQ 10
    INFO 18:36:37,231 QGraph - Log: /home/users/ercfrtz/[email protected]
    Tags: None
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