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GenomeSTRiP 2.0 don't have anything result about CNVDiscoveryPipeline.

SunhyeSunhye KoreaMember
edited June 2015 in GenomeSTRiP

Hi,

I have human whole genome sequencing data and i want to analyze copy-number variations.

So, I made subset which consists of chromosome20 ,and tested to call copy-number variation using CNVDiscoveryPipeline module in GenomeSTRiP2.0.

The CNVDiscoveryPipeline run was done successfully without error, but the results didn't exist anywhere.

My script is,

classpath="${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar:${SV_DIR}/lib/gatk/Queue.jar"

java -cp ${classpath} ${mx} \
    org.broadinstitute.gatk.queue.QCommandLine \
    -S ${SV_DIR}/qscript/discovery/cnv/CNVDiscoveryPipeline.q \
    -S ${SV_DIR}/qscript/SVQScript.q \
    -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
    -cp ${classpath} \
    -configFile ${SV_DIR}/conf/genstrip_parameters.txt \
    -tempDir ${SV_TMPDIR} \
    -R ${bundle}/human_g1k_v37.chr20.fasta \
    -runDirectory ${runDir} \
    -md ${runDir}/metadata \
    -jobLogDir ${runDir}/logs \
    -ploidyMapFile ${bundle}/human_g1k_v37.ploidymap.txt \
    -genderMapFile ${bundle}/sample_gender.map \
    -genomeMaskFile ${bundle}/human_g1k_v37.svmask.chr20.fasta \
    -L 20 \
    -tilingWindowSize 1000 \
    -tilingWindowOverlap 500 \
    -maximumReferenceGapLength 1000 \
    -boundaryPrecision 100 \
    -minimumRefinedLength 500 \
    -produceAuxiliaryFiles \
    -I ${bamList} \
    -jobRunner Drmaa \
    || exit 1

INFO 13:25:32,968 QGraph - Dry run completed successfully!
INFO 13:25:32,968 QGraph - Re-run with "-run" to execute the functions.
INFO 13:25:32,970 QCommandLine - Writing final jobs report...
INFO 13:25:32,970 QJobsReporter - Writing JobLogging GATKReport to file /BiO/psh/Project/SVtest/CNVDiscoveryPipeline.jobreport.txt
INFO 13:25:33,007 QCommandLine - Script completed successfully with 14 total jobs

ls -a cnv*/*
cnv_stage10/seq_20:
.  ..

cnv_stage11/seq_20:
.  ..

cnv_stage1/seq_20:
.  ..

cnv_stage2/seq_20:
.  ..

cnv_stage3/seq_20:
.  ..

cnv_stage4/seq_20:
.  ..

cnv_stage6/seq_20:
.  ..

cnv_stage7/seq_20:
.  ..

cnv_stage8/seq_20:
.  ..

cnv_stage9/seq_20:
.  ..
cnv_sentinel_files/:
. ..
cnv_stage12/:
. ..
cnv_stage5/:
. ..

Though this run was done successfully, Why don't the results exist anywhere?

How to run CNVDiscoveryPipeline in GenomeSTRiP2.0 ?

What is my script problem? What can i do resolve this problem ?

Best Answers

Answers

  • SunhyeSunhye KoreaMember

    Thanks bhandsaker,
    On your advice, I added '-run' to my script. But.... other error occurred.

    My revised script is classpath="${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar:${SV_DIR}/lib/gatk/Queue.jar"

                java -cp ${classpath} ${mx} \
                    org.broadinstitute.gatk.queue.QCommandLine \
                    -S ${SV_DIR}/qscript/discovery/cnv/CNVDiscoveryPipeline.q \
                    -S ${SV_DIR}/qscript/SVQScript.q \
                    -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
                    -cp ${classpath} \
                    -configFile ${SV_DIR}/conf/genstrip_parameters.txt \
                    -tempDir ${SV_TMPDIR} \
                    -R ${bundle}/human_g1k_v37.chr20.fasta \
                    -runDirectory ${runDir} \
                    -md ${runDir}/metadata \
                    -jobLogDir ${runDir}/logs \
                    -ploidyMapFile ${bundle}/human_g1k_v37.ploidymap.txt \
                    -genderMapFile ${bundle}/sample_gender.map \
                    -genomeMaskFile ${bundle}/human_g1k_v37.svmask.chr20.fasta \
                    -L 20 \
                    -tilingWindowSize 1000 \
                    -tilingWindowOverlap 500 \
                    -maximumReferenceGapLength 1000 \
                    -boundaryPrecision 100 \
                    -minimumRefinedLength 500 \
                    -produceAuxiliaryFiles \
                    -I ${bamList} \
                    -jobRunner Drmaa \
                    -run \
                    || exit 1
    

    The error is ,

        ERROR 15:43:22,884 FunctionEdge - Error:  'java'  '-Xmx2048m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/BiO/psh/Project/SVtest/tmpdir'  '-cp' '/BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar'  '-cp' '/BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar'  'org.broadinstitute.gatk.queue.QCommandLine'  '-skipAnnotator' 'CNQuality'  '-cp' '/BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar'  '-S' 'qscript/SVGenotyper2.q'  '-S' 'qscript/SVQScript.q'  '-gatk' '/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar'  '-jobLogDir' '/BiO/psh/Project/SVtest/test2_sample_chr20/cnv_stage2/seq_20/logs'  '-memLimit' '2.0'  '-jobRunner' 'Drmaa'  '-gatkJobRunner' 'Drmaa'  -run  --disableJobReport  '-configFile' '/BiO/psh/tools/svtoolkit/conf/genstrip_parameters.txt'  '-P' 'depth.readCountCacheIgnoreGenomeMask:true'  '-P' 'genotyping.modules:depth'  '-R' '/BiO/psh/tools/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/Chr20/human_g1k_v37.chr20.fasta'  '-genomeMaskFile' '/BiO/psh/tools/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/Chr20/human_g1k_v37.svmask.chr20.fasta'  '-ploidyMapFile' '/BiO/psh/tools/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/Chr20/human_g1k_v37.ploidymap.txt'  '-genderMapFile' '/BiO/psh/tools/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/Chr20/sample_gender.map'  '-md' '/BiO/psh/Project/SVtest/test2_sample_chr20/metadata'  -disableGATKTraversal  '-vcf' '/BiO/psh/Project/SVtest/test2_sample_chr20/cnv_stage1/seq_20/seq_20.sites.vcf'  '-parallelRecords' '1000'  '-I' '/BiO/psh/Project/SVtest/test2_sample_chr20/bam_headers/merged_headers.bam'  '-O' '/BiO/psh/Project/SVtest/test2_sample_chr20/cnv_stage2/seq_20/seq_20.genotypes.vcf'  '-runDirectory' '/BiO/psh/Project/SVtest/test2_sample_chr20/cnv_stage2/seq_20'  '-duplicateScoreThreshold' '0.0'  
        ERROR 15:43:22,890 FunctionEdge - Contents of /BiO/psh/Project/SVtest/test2_sample_chr20/cnv_stage2/seq_20/logs/CNVDiscoveryStage2-1.out:
        ##### ERROR ------------------------------------------------------------------------------------------
        ##### ERROR stack trace 
        org.broadinstitute.gatk.utils.exceptions.UserException$CouldNotReadInputFile: Couldn't read file /BiO/psh/Project/SVtest/qscript/SVGenotyper2.q because it does not exist.
            at org.broadinstitute.gatk.queue.QScriptManager$$anonfun$loadScripts$1.apply(QScriptManager.scala:52)
            at org.broadinstitute.gatk.queue.QScriptManager$$anonfun$loadScripts$1.apply(QScriptManager.scala:52)
            at scala.collection.immutable.List.foreach(List.scala:318)
            at org.broadinstitute.gatk.queue.QScriptManager.loadScripts(QScriptManager.scala:51)
            at org.broadinstitute.gatk.queue.QCommandLine.org$broadinstitute$gatk$queue$QCommandLine$$qScriptPluginManager$lzycompute(QCommandLine.scala:95)
            at org.broadinstitute.gatk.queue.QCommandLine.org$broadinstitute$gatk$queue$QCommandLine$$qScriptPluginManager(QCommandLine.scala:93)
            at org.broadinstitute.gatk.queue.QCommandLine.getArgumentSources(QCommandLine.scala:230)
            at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:205)
            at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
            at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:62)
            at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)
        ##### ERROR ------------------------------------------------------------------------------------------
        ##### ERROR A GATK RUNTIME ERROR has occurred (version <unknown>):
        ##### ERROR
        ##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
        ##### ERROR If not, please post the error message, with stack trace, to the GATK forum.
        ##### ERROR Visit our website and forum for extensive documentation and answers to 
        ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
        ##### ERROR
        ##### ERROR MESSAGE: Couldn't read file /BiO/psh/Project/SVtest/qscript/SVGenotyper2.q because it does not exist.
        ##### ERROR ------------------------------------------------------------------------------------------
        INFO  15:43:10,732 QCommandLine - Shutting down jobs. Please wait...  
        INFO  15:43:22,891 QGraph - Writing incremental jobs reports... 
        INFO  15:43:22,892 QGraph - 3 Pend, 0 Run, 1 Fail, 0 Done 
        INFO  15:43:22,893 QCommandLine - Writing final jobs report... 
        INFO  15:43:22,894 QCommandLine - Done with errors 
        INFO  15:43:22,896 QGraph - ------- 
    

    I ran my script in '/BiO/psh/Project/SVtest/'
    Now.... What do I need to do??

  • bhandsakerbhandsaker Member, Broadie ✭✭✭✭

    What release are you running? (you can check with java -jar ${SV_DIR}/lib/SVToolkit.jar)

  • SunhyeSunhye KoreaMember

    Hi, bhandsaker
    The svtoolkit release is version 2.00

    SVToolkit version 2.00 (build 1563)
    Build date: 2015/04/22 10:42:19
    Web site: http://www.broadinstitute.org/software/genomestrip
    
  • bhandsakerbhandsaker Member, Broadie ✭✭✭✭

    I think perhaps you don't have SV_DIR exported as an environment variable.

  • SunhyeSunhye KoreaMember
    edited June 2015

    No, I include SV_DIR exported as an environment in my script.
    My script's start is
    '#!/bin/bash
    export SV_DIR=/BiO/psh/tools/svtoolkit
    SV_TMPDIR=./tmpdir
    runDir=/BiO/psh/Project/SVtest/test2_sample_chr20 bamList=sample.chr20.bam
    sites=/BiO/psh/Project/SVtest/test2_sample_chr20.discovery.vcf
    genotypes=/BiO/psh/Project/SVtest/test2_sample_chr20.genotypes.vcf

    Once,
    To read SVGenotyper2.q, I attamp to revise CNVDiscoveryGenotype.q .

        class SVGenotyperScript(genotypesVcfFile: File) extends QueueScriptCommand {
                this.dependsOnFile +:= vcfFile
                this.commandResultFile = new File(jobLogDirectory, "SVGenotyper2")
                override def scriptName = "**SVGenotyper2.q**" →/path/to/SVGenotyper2.q
                override def commandLine =                                super.commandLine +
                    flag(" --disableJobReport ", true) +
                    optional(" -configFile ", configFile) +               required(" -P ", "depth.readCountCacheIgnoreGenomeMask:true") +                                             required(" -P ", "genotyping.modules:depth") +
                    addCommand(new DeleteAuxiliaryFiles(classifyVariants))                                                  }
            }
    

    I have failed...
    So I run my script in working directory changed to '/BiO/psh/tools/svtoolkit'.
    This time, another error occurred.

    Another error is

    INFO  16:01:10,442 HelpFormatter - ---------------------------------------------------------------------------
    INFO  16:01:10,445 HelpFormatter - The Genome Analysis Toolkit (GATK) v<unknown>, Compiled 2015/04/22 10:24:33
    INFO  16:01:10,445 HelpFormatter - Copyright (c) 2010 The Broad Institute
    INFO  16:01:10,446 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
    INFO  16:01:10,451 HelpFormatter - Program Args: -T VariantFiltration -V /BiO/psh/Project/SVtest/test2_sample_chr20/cnv_stage2/seq_20/seq_20.genotypes.annotated.vcf -o /BiO/psh/Project/SVtest/test2_sample_chr20/cnv_stage3/seq_20/seq_20.merged.input.vcf -R /BiO/psh/tools/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/Chr20/human_g1k_v37.chr20.fasta -filterName ALIGNLENGTH -filter GSELENGTH < 200 -filterName CLUSTERSEP -filter GSCLUSTERSEP == "NA" || GSCLUSTERSEP <= 2.0 -filterName GTDEPTH -filter GSM1 == "NA" || GSM1 <= 0.5 || GSM1 >= 2.0 -filterName NONVARIANT -filter GSNONVARSCORE != "NA" && GSNONVARSCORE >= 13.0 -filterName INBREEDINGCOEFF -filter GLINBREEDINGCOEFF != "NA" && GLINBREEDINGCOEFF < -0.15
    INFO  16:01:10,459 HelpFormatter - Executing as [email protected] on Linux 3.16.0-031600-generic amd64; OpenJDK 64-Bit Server VM 1.7.0_51-b31.
    INFO  16:01:10,459 HelpFormatter - Date/Time: 2015/06/02 16:01:10
    INFO  16:01:10,459 HelpFormatter - ---------------------------------------------------------------------------
    INFO  16:01:10,459 HelpFormatter - ---------------------------------------------------------------------------
    INFO  16:01:17,218 GATKRunReport - Uploaded run statistics report to AWS S3
    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR A USER ERROR has occurred (version <unknown>):
    ##### ERROR
    ##### ERROR This means that one or more arguments or inputs in your command are incorrect.
    ##### ERROR The error message below tells you what is the problem.
    ##### ERROR
    ##### ERROR If the problem is an invalid argument, please check the online documentation guide
    ##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
    ##### ERROR
    ##### ERROR Visit our website and forum for extensive documentation and answers to
    ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
    ##### ERROR
    ##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.##### ERROR
    ##### ERROR MESSAGE: Couldn't read file /BiO/psh/Project/SVtest/test2_sample_chr20/cnv_stage2/seq_20/seq_20.genotypes.annotated.vcf because file does not exist
    ##### ERROR --------------------------------------------------------
    

    I don't know what the problem...
    Why that file is not created?
    Do I need to revise the Qscript?

    Post edited by bhandsaker on
  • bhandsakerbhandsaker Member, Broadie ✭✭✭✭
    edited June 2015

    No, I still think the root of the problem is somehow with SV_DIR.
    Here from SVQScript.q, lines 585-586:
    val svHome = System.getenv().get("SV_DIR") val qscriptHome = new File(svHome, "qscript")
    and lines 604-605:
    required(" -S ", new File(qscriptHome, scriptName)) + repeat(" -S ", includeScripts map (script => new File(qscriptHome, script))) +
    You will see in your original error message that the command is being invoked with -S qscript/SVGenotyper2.q, without SV_DIR as a prefix. This is why SVGenotyper2.q is not found.

    Actually, perhaps the problem is that your batch system isn't propagating environment variables.
    Are you using LSF or SGE? I believe one of them has a special setting you have to enable so that environment variables are transmitted to the jobs when they are dispatched.

  • SunhyeSunhye KoreaMember
    edited June 2015

    Hi, bhandsaker
    I use SGE.
    My system is Ubuntu 14.04.1 LTS (GNU/Linux 3.16.0-031600-generic x86_64).
    My SGE enviroment is ,

    compute-0-1.local
    /home/sunhye
    PID=25997
    SGE_O_HOME=//home/sunhye
    SGE_O_HOST=hanyang
    SGE_O_LOGNAME=sunhye
    SGE_O_MAIL=/var/mail/sunhye           
    SGE_O_PATH=/bin:/BiO/psh/tools/samtools-1.1/bin:/BiO/psh/tools/bwa:/BiO/psh/tools/svtoolkit:/bin:/BiO/psh/tools/samtools-1.1/bin:/BiO/psh/tools/bwa:/BiO/psh/tools/svtoolkit:/bin:/BiO/psh/tools/samtools-1.1/bin:/BiO/psh/tools/bwa:/BiO/psh/tools/htslib-1.1:/BiO/psh/tools/bcftools-1.1:/BiO/psh/tools/svtoolkit:/BiO/BioTools/ROOT_5.34.09/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/BiO/BioTools/AllpathLG-50378/bin:/usr/local/bin/FastQC:/BiO/BioTools/plink-1.07-x86_64
        SGE_O_SHELL=/bin/bash
        SGE_O_WORKDIR=/home/sunhye
        ARC=lx26-amd64
        SGE_STDERR_PATH=//home/sunhye/env.e20997
        SGE_STDOUT_PATH=//home/sunhye/env.o20997
        SGE_JOB_SPOOL_DIR=/var/spool/gridengine/execd/compute-0-1/active_jobs/20997.1
        SGE_TASK_ID=undefined
        ENVIRONMENT=BATCH
        HOME=//home/sunhye
        HOSTNAME=compute-0-1.local
        JOB_ID=20997
        JOB_NAME=env
        LOGNAME=sunhye
        NHOSTS=1
        NQUEUES=1
        NSLOTS=1           
    PATH=/bin:/BiO/psh/tools/samtools-1.1/bin:/BiO/psh/tools/bwa:/BiO/psh/tools/svtoolkit:/BiO/BioTools/ROOT_5.34.09/bin:/tmp/20997.1.all.q:/usr/local/bin:/bin:/usr/bin
        QUEUE=all.q
        REQUEST=env
        RESTARTED=0
        SHELL=/bin/bash
        TMPDIR=/BiO/tmp
        TMP=/tmp/20997.1.all.q
        USER=sunhye
    

    In order to prevent errors, I set SGE_O_PATH as environment variable in ~/.profile.

    vi ~/.profile
    # if running bash
    if [ -n "$BASH_VERSION" ]; then
        # include .bashrc if it exists
        if [ -f "$HOME/.bashrc" ]; then
            . "$HOME/.bashrc"
        fi
    fi
    
    # set PATH so it includes user's private bin if it exists
    if [ -d "$HOME/bin" ] ; then
        PATH="$HOME/bin:/sbin:$PATH"
    fi
    JAVA7_HOME=/usr/lib/jvm/java-7-oracle
    JAVA6_HOME=/usr/lib/jvm/java-6-oracle
    PICARD=/BiO/psh/tools/manupulate/picard/dist/picard.jar
    GATK=/BiO/psh/tools/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar
    SAMTOOLS=/BiO/psh/tools/samtools-1.1
    REF=/BiO/Reference/g1k_v37_no_prefix/human_g1k_v37.fasta
    BWA=/BiO/psh/tools/bwa
    HTSLIB=/BiO/psh/tools/htslib-1.1
    BCFTOOLS=/BiO/psh/tools/bcftools-1.1
    SV_DIR=/BiO/psh/tools/svtoolkit
    TMPDIR=/BiO/tmp
    PATH=$JAVA_HOME/bin:$SAMTOOLS/bin:$BWA:$PATH
    SGE_O_PATH=$SV_DIR:$PATH
    

    I identify SV_DIR as environment variable in SGE_PATH , run CNVDiscoveryPipeline.q again.
    During running CNVDiscoveryPipeline.q, I confirmed that SGE_O_PATH was changed unlike before error occurred.

    Before error,
    qstat -j 20995

    ==============================================================
        job_number:                 20995
        exec_file:                  job_scripts/20995
        submission_time:            Thu Jun  4 12:42:57 2015
        owner:                      sunhye
        uid:                        1005
        group:                      sunhye
        gid:                        1005
        sge_o_home:                 //home/sunhye
        sge_o_log_name:             sunhye
        sge_o_path:                 /BiO/psh/tools/svtoolkit/bwa:/bin:/BiO/psh/tools/samtools-1.1/bin:/BiO/psh/tools/bwa:/BiO/psh/tools/svtoolkit:/bin:/BiO/psh/tools/samtools-1.1/bin:/BiO/psh/tools/bwa:/BiO/psh/tools/svtoolkit/:/bin:/BiO/psh/tools/samtools-1.1/bin:/BiO/psh/tools/bwa:/BiO/psh/tools/svtoolkit/:/bin:/BiO/psh/tools/samtools-1.1/bin:/BiO/psh/tools/bwa:/BiO/psh/tools/svtoolkit:/bin:/BiO/psh/tools/samtools-1.1/bin:/BiO/psh/tools/bwa:/bin:/BiO/psh/tools/samtools-1.1/bin:/BiO/psh/tools/bwa:/bin:/BiO/psh/tools/samtools-1.1/bin:/BiO/psh/tools/bwa:/BiO/psh/tools/htslib-1.1:/BiO/psh/tools/bcftools-1.1:/BiO/psh/tools/svtoolkit:/bin:/BiO/psh/tools/samtools-1.1/bin:/BiO/psh/tools/bwa:/BiO/psh/tools/htslib-1.1:/BiO/psh/tools/bcftools-1.1:/BiO/psh/tools/svtoolkit:/BiO/BioTools/ROOT_5.34.09/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/BiO/BioTools/AllpathLG-50378/bin:/usr/local/bin/FastQC:/BiO/BioTools/plink-1.07-x86_64
        sge_o_shell:                /bin/bash
        sge_o_workdir:              /BiO/psh/Project/SVtest
        sge_o_host:                 hanyang
        account:                    sge
        cwd:                        /BiO/psh/Project/SVtest
        merge:                      y
        mail_list:                  [email protected]
        notify:                     FALSE
        job_name:                   _function___stage_2_seq_20_sent
        stdout_path_list:           NONE:compute-0-0:/BiO/psh/Project/SVtest/test2_sample_chr20/logs/CNVDiscoveryPipeline-4.out
        jobshare:                   0
        env_list:
        job_args:                   /BiO/psh/Project/SVtest/tmpdir/.exec126135236156391764
        script_file:                sh
        verify_suitable_queues:     2
        scheduling info:            There are no messages available
    

    When error occurred ,
    qstat -j 20996

    ==============================================================
    job_number:                 20996
    exec_file:                  job_scripts/20996
    submission_time:            Thu Jun  4 12:43:43 2015
    owner:                      sunhye
    uid:                        1005
    group:                      sunhye
    gid:                        1005
    sge_o_home:                 //home/sunhye
    sge_o_log_name:             sunhye
    sge_o_path:                     /tmp/20995.1.all.q:/usr/local/bin:/bin:/usr/bin
    sge_o_shell:                /bin/bash
    sge_o_workdir:              /BiO/psh/Project/SVtest
    sge_o_host:                 compute-0-1
    account:                    sge
    cwd:                        /BiO/psh/Project/SVtest
    merge:                      y
    mail_list:                  [email protected]
    notify:                     FALSE
    job_name:                   _function___SVGenotyper2
    stdout_path_list:           NONE:compute0-1:/BiO/psh/Project/SVtest/test2_sample_chr20/cnv_stage2/seq_20/logs/CNVDiscoveryStage2-1.out
    jobshare:                   0
    env_list:
    job_args:                   /BiO/psh/Project/SVtest/tmpdir/.exec2482134828745534750
    script_file:                sh
    verify_suitable_queues:     2
    scheduling info:            There are no messages available
    

    Do you know about the part that I can adjust to the SGE in qscripts?
    I don't know why SGE_PATH's change occurrs only in CNVDiscoveryStage2.q
    I guessed that when CNVDiscoveryStage2.q sent job through SGE , this problem arise.

    Post edited by Sunhye on
  • SunhyeSunhye KoreaMember

    Thanks Bob.
    I have solved the problem about SGE.

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