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The error of the genomestrip's Svpreprocess

ahfydhahfydh ChinaMember

Hi,I'm just use the genomestrip to call the sv from pigs. I have 30 bams and then follow the introduction to prepare the reference file ,genomeMaskFile ,copyNumberMaskFile and ploidyMapFile files.But when I run the SVpreprocess I got the following three errors

INFO 01:50:01,554 QGraph - Writing incremental jobs reports...
INFO 01:50:01,565 QGraph - 578 Pend, 0 Run, 3 Fail, 152 Done
INFO 01:50:01,572 QCommandLine - Writing final jobs report...
INFO 01:50:01,572 QCommandLine - Done with errors
INFO 01:50:01,587 QGraph - -------
INFO 01:50:01,588 QGraph - Failed: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/WORK/cau_jfliu_1/SVmap/genomestrip/test/tmpdir' '-cp' '/WORK/cau_jfliu_1/SVmap/software/svtoolkit/lib/SVToolkit.jar:/WORK/cau_jfliu_1/SVmap/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/WORK/cau_jfliu_1/SVmap/software/svtoolkit/lib/gatk/Queue.jar' '-cp' '/WORK/cau_jfliu_1/SVmap/software/svtoolkit/lib/SVToolkit.jar:/WORK/cau_jfliu_1/SVmap/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/WORK/cau_jfliu_1/SVmap/software/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/WORK/cau_jfliu_1/SVmap/genomestrip/test/test1/metadata/rccache/20161017.recal.rc.bin' '-O' '/WORK/cau_jfliu_1/SVmap/genomestrip/test/test1/metadata/rccache/20161017.recal.rc.bin.idx'
INFO 01:50:01,588 QGraph - Log: /WORK/cau_jfliu_1/SVmap/genomestrip/test/test1/logs/SVPreprocess-166.out
INFO 01:50:01,588 QGraph - -------
INFO 01:50:01,589 QGraph - Failed: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/WORK/cau_jfliu_1/SVmap/genomestrip/test/tmpdir' '-cp' '/WORK/cau_jfliu_1/SVmap/software/svtoolkit/lib/SVToolkit.jar:/WORK/cau_jfliu_1/SVmap/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/WORK/cau_jfliu_1/SVmap/software/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/WORK/cau_jfliu_1/SVmap/reference_metadata_bundle/test/pig.fa' '-I' '/WORK/cau_jfliu_1/SVmap/RC/20160995/20160995.recal.bam' '-O' '/WORK/cau_jfliu_1/SVmap/genomestrip/test/test1/metadata/rccache/20160995.recal.rc.bin' '-disableGATKTraversal' 'true' '-md' 'test1/metadata' '-configFile' '/WORK/cau_jfliu_1/SVmap/software/svtoolkit/conf/genstrip_parameters.txt' '-P' 'chimerism.use.correction:false' '-insertSizeRadius' '10.0'
INFO 01:50:01,589 QGraph - Log: /WORK/cau_jfliu_1/SVmap/genomestrip/test/test1/logs/SVPreprocess-171.out
INFO 01:50:01,589 QGraph - -------
INFO 01:50:01,589 QGraph - Failed: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/WORK/cau_jfliu_1/SVmap/genomestrip/test/tmpdir' '-cp' '/WORK/cau_jfliu_1/SVmap/software/svtoolkit/lib/SVToolkit.jar:/WORK/cau_jfliu_1/SVmap/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/WORK/cau_jfliu_1/SVmap/software/svtoolkit/lib/gatk/Queue.jar' '-cp' '/WORK/cau_jfliu_1/SVmap/software/svtoolkit/lib/SVToolkit.jar:/WORK/cau_jfliu_1/SVmap/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/WORK/cau_jfliu_1/SVmap/software/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeGCProfiles' '-O' '/WORK/cau_jfliu_1/SVmap/genomestrip/test/test1/metadata/gcprofile/reference.gcprof.zip' '-R' '/WORK/cau_jfliu_1/SVmap/reference_metadata_bundle/test/pig.fa' '-md' 'test1/metadata' '-writeReferenceProfile' 'true' '-genomeMaskFile' '/WORK/cau_jfliu_1/SVmap/reference_metadata_bundle/test/pig.svmask.75.fa' '-copyNumberMaskFile' '/WORK/cau_jfliu_1/SVmap/reference_metadata_bundle/test/pig.gcmask.fasta' '-configFile' '/WORK/cau_jfliu_1/SVmap/software/svtoolkit/conf/genstrip_parameters.txt' '-P' 'chimerism.use.correction:false'
INFO 01:50:01,589 QGraph - Log: /WORK/cau_jfliu_1/SVmap/genomestrip/test/test1/logs/SVPreprocess-6.out
INFO 01:50:01,590 QCommandLine - Script failed: 578 Pend, 0 Run, 3 Fail, 152 Done

But When I check the log files SVPreprocess-166.out ,SVPreprocess-171.out and SVPreprocess-6.out ,there are no errors reported from these log files.

The scripts list as follows:

    #!/bin/bash
    export SV_DIR=/WORK/cau_jfliu_1/SVmap/software/svtoolkit
    SV_TMPDIR=./tmpdir
    runDir=test1
    export PATH=${SV_DIR}/bwa:${PATH}
    export LD_LIBRARY_PATH=${SV_DIR}/bwa:${LD_LIBRARY_PATH}
    mx="-Xmx4g"
    classpath="${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar:${SV_DIR}/lib/gatk/Queue.jar"
    mkdir -p ${runDir}/logs || exit 1
    mkdir -p ${runDir}/metadata || exit 1
    # Display version information.
    java -cp ${classpath} ${mx} -jar ${SV_DIR}/lib/SVToolkit.jar

    # Run preprocessing.
    # For large scale use, you should use -reduceInsertSizeDistributions, but this is too slow for the installation test.
    # The method employed by -computeGCProfiles requires a GC mask and is currently only supported for human genomes.
    java -cp ${classpath} ${mx} \
        org.broadinstitute.gatk.queue.QCommandLine \
        -S ${SV_DIR}/qscript/SVPreprocess.q \
        -S ${SV_DIR}/qscript/SVQScript.q \
        -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
        --disableJobReport \
        -cp ${classpath} \
        -configFile ${SV_DIR}/conf/genstrip_parameters.txt \
        -tempDir ${SV_TMPDIR} \
        -R /WORK/cau_jfliu_1/SVmap/reference_metadata_bundle/test/pig.fa \
        -genomeMaskFile /WORK/cau_jfliu_1/SVmap/reference_metadata_bundle/test/pig.svmask.75.fa \
        -copyNumberMaskFile /WORK/cau_jfliu_1/SVmap/reference_metadata_bundle/test/pig.gcmask.fasta \
        -ploidyMapFile /WORK/cau_jfliu_1/SVmap/reference_metadata_bundle/test/pig.ploidymap.txt \
        -runDirectory ${runDir} \
        -md ${runDir}/metadata \
        -disableGATKTraversal \
        -useMultiStep \
        -reduceInsertSizeDistributions false \
        -computeReadCounts true \
        -jobLogDir ${runDir}/logs \
        -I /WORK/cau_jfliu_1/SVmap/genomestrip/test/file.list \
        -P chimerism.use.correction:false \
        -run \
        || exit 1

And it seems I can't post the detail log files , is there any ohter methods to post the log informations?
Thank you!

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