Enumerated data type arguments

ynnusynnus everywhereMember Posts: 4

I am working on a Queue script that uses the selectVariants walker. Two of the arguments that I am trying to use both use an enumerated type: restrictAllelesTo and selectTypeToInclude. I have tried passing these as strings however I get java type mismatch errors. What is the simplest way to pass these parameters to the selectVariant walker in the qscript?

Best Answer

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 10,296 admin

    Hi there,

    Have a look at the presentations from our recent Queue workshop, I think we give some examples of how to pass the different types in there:

    http://www.broadinstitute.org/gatk/guide/events?id=3391

    Geraldine Van der Auwera, PhD

  • ynnusynnus everywhereMember Posts: 4

    Maybe it's my lack of understanding scala but I still can't pass an enumerated data type. The workshop shows this as an example:

    @Argument(doc=”gender identity") // some object defined elsewhere 
     var gender: Gender = Gender.UNKNOWN

    my code uses this
    @Argument(doc="Select only variants of a particular allelicity.", shortName="restrictAllelesTo", required=false)
      var rAT: restrictAllelesTo = restrictAllelesTo.BIALLELIC

    This still errors with "not found: type restrictAllelesTo".

    I've even tried defining the object itself:

    object restrictAllelesTo extends Enumeration {
        type restrictAllelesTo = Value
        val BIALLELIC, ALLELIC, BOTH = Value
      }
      import restrictAllelesTo._

    However, this then errors with "Can't process command-line arguments of type: scala.Enumeration$Value"
  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 10,296 admin

    I believe the correct way to define your object should look like this (from a real object defined in the Queue codebase):

    object RunnerStatus extends Enumeration {
         val PENDING = Value("pending")
         val RUNNING = Value("running")
         val FAILED = Value("failed")
         val DONE = Value("done")
         val SKIPPED = Value("skipped")
    }
    

    Geraldine Van der Auwera, PhD

  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 10,296 admin

    @pdexheimer's suggestion should do the trick. Also, I haven't tested it at the moment, but java enums may be parseable by Sting (including Queue) as @Argument variable types, eliminating the need for string-to-enum mapping. FYI- walkers exclusively use Java enums, including the NumberAlleleRestriction shown here.

    Geraldine Van der Auwera, PhD

  • pdexheimerpdexheimer Member, Dev Posts: 534 ✭✭✭✭

    Ah, I had it backwards - I remembered that one of the enumerated types didn't work properly, and thought it was Java. But I was thinking of the 11th question in the Scala FAQ, which says that Scala enums can't be used as arguments

  • ynnusynnus everywhereMember Posts: 4

    Thanks a bunch guys, I think I'll be able to get it working from here.

  • DavidRiesDavidRies Member Posts: 11

    Hi,

    I have a similar Problem, but I want to select for SNPs.
    Although org.broadinstitute.variant.variantcontext.VariantContext.Type is accessible, there doesn't seem to be a type SNP.

    Running the following SelectVariants walker:

    val selectVars = new SelectVariants with UnifiedGenotyperArguments    
        selectVars.variant = "Variations.vcf"
        selectVars.select = Seq("QD < 2.0 || FS > 60.0 || MQ < 40.0 || HaplotypeScore > 13.0 || MappingQualityRankSum < -12.5 || ReadPosRankSum < -8.0")
        selectVars.selectTypeToInclude = List[org.broadinstitute.variant.variantcontext.VariantContext.Type.SNP]
        selectVars.restrictAllelesTo = org.broadinstitute.sting.gatk.walkers.variantutils.SelectVariants.NumberAlleleRestriction.BIALLELIC
        selectVars.excludeNonVariants = true
        selectVars.out = "biallelic_true_SNPS.qual.filtered.vcf"
        add(selectVars)

    gives me the error message:

    INFO 17:58:31,089 QScriptManager - Compiling 1 QScript
    ERROR 17:58:34,029 QScriptManager - SelectVariants.scala:66: type SNP is not a member of object org.broadinstitute.variant.variantcontext.VariantContext.Type
    ERROR 17:58:34,037 QScriptManager - selectVars.selectTypeToInclude = List[org.broadinstitute.variant.variantcontext.VariantContext.Type.SNP]
    ERROR 17:58:34,038 QScriptManager - ^
    ERROR 17:58:34,137 QScriptManager - one error found

    ERROR ------------------------------------------------------------------------------------------
    ERROR stack trace

    org.broadinstitute.sting.queue.QException: Compile of ./SelectVariants.scala failed with 1 error
    at org.broadinstitute.sting.queue.QScriptManager.loadScripts(QScriptManager.scala:71)
    at org.broadinstitute.sting.queue.QCommandLine.org$broadinstitute$sting$queue$QCommandLine$$qScriptPluginManager(QCommandLine.scala:95)
    at org.broadinstitute.sting.queue.QCommandLine.getArgumentSources(QCommandLine.scala:227)
    at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:202)
    at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152)
    at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:62)
    at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala)

    Other than NumberAlleleRestriction, I don't see a way to set the List<VariantContext.Type> directly.

    Help much appreciated,

    David

  • ynnusynnus everywhereMember Posts: 4

    Here is a snippet from my code that I used to get it working, I wanted to be able to change the type selection on the fly so I had to define a function to convert the list of inputed strings into a list of "Type".

    import org.broadinstitute.variant.variantcontext.VariantContext.Type
    
    //define a function that takes a list of strings as input and 
    //returns a list of enumerated data values of type "Type"
    def getTypeSelect : List[Type] = {
    
        //create enumerated list of type "Type"
        var LtypeSelect: List[Type] = Nil
    
        //if list sTTI contains a value, append that value to the enumerated list
        if(sTTI.contains("INDEL")){
            LtypeSelect :+ Type.INDEL
        }   
        if(sTTI.contains("SNP")){
        LtypeSelect :+ Type.SNP
        }
        if(sTTI.contains("MIXED")){
        LtypeSelect :+ Type.MIXED
        }
        if(sTTI.contains("MNP")){
        LtypeSelect :+ Type.MNP
        }   
        if(sTTI.contains("SYMBOLIC")){
        LtypeSelect :+ Type.SYMBOLIC
        }
        if(sTTI.contains("NO_VARIATION")){
        LtypeSelect :+ Type.NO_VARIATION
        }   
        return LtypeSelect
    }
    //Apply the previously defined function to select variants parameter
    selectVars.selectTypeToInclude = getTypeSelect
    

    Hopefully this helps.

  • pdexheimerpdexheimer Member, Dev Posts: 534 ✭✭✭✭

    @DavidRies -

    SNP is definitely one of the members of VariantContext.Type, so I think the error you're getting from the Scala compiler is misleading. Is it possible that you're not even seeing the org.broadinstitute.variant packages? They've moved out of the main GATK repository and into a separate "variant" jar, which I believe is hosted and built by the Picard team. It's possible - especially if you built Queue yourself - that you somehow lost that dependency.

  • DavidRiesDavidRies Member Posts: 11

    @ynnus -

    That did the trick. I suppose my mistake was, that I tried to directly assign the type to selectVars.selectTypeToInclude,
    rather than first creating the empty list, adding the types and then assigning it. I now do it directly like this:

    `
    var LtypeSelect2: List[Type] = Nil
    LtypeSelect2 :+ Type.INDEL

    val selectIndels = new SelectVariants with VariantFiltrationArguments
    selectIndels.variant = variantFile
    selectIndels.select = Seq("QD < 2.0 || FS > 60.0 || MQ < 40.0 || HaplotypeScore > 13.0 || MappingQualityRankSum < -12.5 || ReadPosRankSum < -8.0")
    selectIndels.selectTypeToInclude = LtypeSelect2
    selectVars.restrictAllelesTo = org.broadinstitute.sting.gatk.walkers.variantutils.SelectVariants.NumberAlleleRestriction.BIALLELIC
    selectIndels.out = "biallelic_true_INDELS.qual.filtered.vcf"
    add(selectIndels)`
    

    Thanks for your help!

    David

  • DavidRiesDavidRies Member Posts: 11

    I don't know how to edit my previous post, so:

    It has to be
    LtypeSelect2 :+= Type.INDEL

  • amitgsiramitgsir Busan, South KoreaMember Posts: 3

    Hi,
    I am trying to use Queue for Variant Calling and then Hard-Filtering.

    So, I am trying to select the variants by INDEL and SNPs in two steps.
    Below is my scala script:

    import org.broadinstitute.gatk.queue.QScript
    import org.broadinstitute.gatk.queue.extensions.gatk._

    class GATKBAMtoHCvcf extends QScript
    {
    qscript =>

    // Required arguments. All initialized to empty values. 
    
    @Input(doc="One or more bam files.", shortName="I", required=true)
    var bamFile: File = _
    
    
    
    @Input(doc="The reference file for the bam files.", shortName="R", required=false)
    var referenceFile: File = "/data01_EDICO/BIO/data/ucsc.hg19.fasta"
    
    @Input(doc = "the -L interval string to be used by GATK - output bams at interval only", fullName = "gatk_interval_string", shortName = "L", required = false)
    var intervalFile: File = _
    var hg19intervalFile: File = "/data01_EDICO/BIO/data/hg19.bed"
    
    @Input(doc = "dbsnp ROD to use (must be in VCF format)", fullName = "dbsnp", shortName = "dbsnp", required = false)
    var dbSNP: File = "/data01_EDICO/BIO/data/dbsnp147_All_20160408.vcf"
    
    
    
    // filteroptions
    //@Argument(doc="Filter mode: BOTH, SNP or INDEL", shortName="mode1", required=false)
    //var filterMode1: List[Type] = Nil
    var filterMode1 :+= Type.INDEL
    
    //@Argument(doc="Filter mode: BOTH, SNP or INDEL", shortName="mode2", required=false)
    //var filterMode2: List[Type] = Nil
    var filterMode1 :+= Type.SNP
    
    @Argument(doc="A optional list of SNPfilter names.", shortName="snpFilterName", required=false)
    var snpFilterNames: List[String] = _
    
    @Argument(doc="An optional list of filter expressions.", shortName="snpFilterExpression", required=false)
    var snpFilterExp: List[String] = _
    
    @Argument(doc="An optional list of INDEL filter names.", shortName="indelFilterName", required=false)
    var indelFilterNames: List[String] = _
    
    @Argument(doc="An optional list of INDEL filter expressions.", shortName="indelFilterExpression", required=false)
    var indelFilterExp: List[String] = _
    
    
    
    
    /* Optional arguments...  */
    
    @Argument(doc="A optional list of filter names.", shortName="filter", required=false)
    var filterNames: List[String] = Nil
    
    @Argument(doc="An optional list of filter expressions.", shortName="filterExpression", required=false)
    var filterExpressions: List[String] = Nil 
    
    @Output
    var out: File = _
    
    
    def script()
    {
    
    
    //HaplotypeCaller Variant Caller Initiated
    val haplotyper = new HaplotypeCaller
    haplotyper.reference_sequence = qscript.referenceFile
    haplotyper.input_file :+= qscript.bamFile
    haplotyper.intervals :+= qscript.hg19intervalFile
    haplotyper.dbsnp = qscript.dbSNP
    haplotyper.out = swapExt(qscript.bamFile, "bam", "unfiltered.vcf")
    haplotyper.memoryLimit = 8
    haplotyper.scatterCount = 48
    add(haplotyper)
    
    
    
    
    //SelectVariants Unfildetered INDEL Initiated
    val selectUnfilteredINDEL = new SelectVariants
    selectUnfilteredINDEL.reference_sequence = qscript.referenceFile
    selectUnfilteredINDEL.variant = haplotyper.out
    selectUnfilteredINDEL.out = swapExt(haplotyper.out, "vcf", "INDEL.vcf")
    selectUnfilteredINDEL.selectType = qscript.filterMode1
    //selectUnfilteredINDEL.selectType :+= org.broadinstitute.gatk.variant.variantcontext.VariantContext.Type.INDEL 
    selectUnfilteredINDEL.memoryLimit = 8
    selectUnfilteredINDEL.scatterCount = 48
    add(selectUnfilteredINDEL)
    
    
    //VariantFiltration Filtering the INDEL Initiated
    val variantFilterINDEL = new VariantFiltration
    variantFilterINDEL.reference_sequence = qscript.referenceFile
    variantFilterINDEL.variant = selectUnfilteredINDEL.out
    variantFilterINDEL.out = swapExt(qscript.bamFile, "bam", "filteredINDEL.vcf")
    //variantFilterINDEL.filterName = "My_indel_filter"
    //variantFilterINDEL.filterExpression = "QD < 2.0"
    //variantFilterINDEL.filterExpression = "FS > 200.0"
    //variantFilterINDEL.filterExpression = "ReadPosRankSum < -20.0"
    variantFilterINDEL.filterName = qscript.indelFilterNames
    variantFilterINDEL.filterExpression = qscript.indelFilterExp
    variantFilterINDEL.memoryLimit = 8
    variantFilterINDEL.scatterCount = 48
    add(variantFilterINDEL)
    
    
    
    
    
    //SelectVariants Unfildetered INDEL Initiated
    //Check true/false Value for "selectFilteredINDEL.excludeFiltered"
    val selectFilteredINDEL = new SelectVariants
    selectFilteredINDEL.reference_sequence = qscript.referenceFile
    selectFilteredINDEL.variant = variantFilterINDEL.out
    selectFilteredINDEL.out = swapExt(variantFilterINDEL.out, "vcf", "Passed.vcf")
    selectFilteredINDEL.excludeFiltered = true
    selectFilteredINDEL.memoryLimit = 8
    selectFilteredINDEL.scatterCount = 48
    add(selectFilteredINDEL)
    
    
    
    
    
    //SelectVariants Unfildetered SNP Initiated
    val selectUnfilteredSNP = new SelectVariants
    selectUnfilteredSNP.reference_sequence = qscript.referenceFile
    selectUnfilteredSNP.variant = haplotyper.out
    selectUnfilteredSNP.out = swapExt(haplotyper.out, "vcf", "SNP.vcf")
    selectUnfilteredSNP.selectType = qscript.filterMode2
    //selectUnfilteredSNP.selectType :+= org.broadinstitute.variant.variantcontext.VariantContext.Type.SNP
    selectUnfilteredSNP.memoryLimit = 8
    selectUnfilteredSNP.scatterCount = 48
    add(selectUnfilteredSNP)
    
    
    //VariantFiltration Filtering the SNP Initiated
    val variantFilterSNP = new VariantFiltration
    variantFilterSNP.reference_sequence = qscript.referenceFile
    variantFilterSNP.variant = selectUnfilteredSNP.out
    variantFilterSNP.out = swapExt(qscript.bamFile, "bam", "filteredSNP.vcf")
    //variantFilterSNP.filterName = "My_SNP_filter"
    //variantFilterSNP.filterExpression = "QD < 2.0"
    //variantFilterSNP.filterExpression = "FS > 60.0"
    //variantFilterSNP.filterExpression = "MQ < 40.0"
    //variantFilterSNP.filterExpression = "HaplotypeScore > 13.0"
    //variantFilterSNP.filterExpression = "MappingQualityRankSum < -12.5"
    //variantFilterSNP.filterExpression = "ReadPosRankSum < -8.0"
    variantFilterSNP.filterName = qscript.snpFilterNames
    variantFilterSNP.filterExpression = qscript.snpFilterExp    
    variantFilterSNP.memoryLimit = 8
    variantFilterSNP.scatterCount = 48
    add(variantFilterSNP)
    
    
    //SelectVariants Unfildetered SNP Initiated
    //Check true/false Value for "selectFilteredSNP.excludeFiltered"
    val selectFilteredSNP = new SelectVariants
    selectFilteredSNP.reference_sequence = qscript.referenceFile
    selectFilteredSNP.variant = variantFilterSNP.out
    selectFilteredSNP.out = swapExt(variantFilterSNP.out, "vcf", "Passed.vcf")
    selectFilteredSNP.excludeFiltered = true
    selectFilteredSNP.memoryLimit = 8
    selectFilteredSNP.scatterCount = 48
    add(selectFilteredSNP)
    
    }
    

    }

    But, I am getting error
    [agoyal@edico GATKBAM_HC]$ java -jar /opt/Queue-3.5/Queue.jar -S GATKBAM_HC.scala -jobRunner ParallelShell -I ../NA12878D_GATK.bam --indelFilterNames "My_Indel_Filter" --indelFilterExp "QD < 2.0 ||FS > 200.0 || ReadPosRankSum < -20.0" --snpFilterNames "My_SNP_Filter" --snpFilterExp "QD < 2.0 || FS > 60.0 || MQ < 40.0 || HaplotypeScore > 13.0 || MappingQualityRankSum < -12.5 || ReadPosRankSum < -8.0"
    INFO 17:41:27,016 QScriptManager - Compiling 1 QScript
    ERROR 17:41:27,276 QScriptManager - GATKBAM_HC.scala:37: '=' expected but ';' found.
    ERROR 17:41:27,286 QScriptManager - var filterMode1 :+= Type.SNP
    ERROR 17:41:27,287 QScriptManager - ^
    ERROR 17:41:27,288 QScriptManager - GATKBAM_HC.scala:39: '=' expected but ';' found.
    ERROR 17:41:27,296 QScriptManager - @Argument(doc="A optional list of SNPfilter names.", shortName="snpFilterName", required=false)
    ERROR 17:41:27,296 QScriptManager - ^
    ERROR 17:41:27,303 QScriptManager - four errors found

    ERROR ------------------------------------------------------------------------------------------
    ERROR stack trace

    org.broadinstitute.gatk.queue.QException: Compile of GATKBAM_HC.scala failed with 4 errors
    at org.broadinstitute.gatk.queue.QScriptManager.loadScripts(QScriptManager.scala:79)
    at org.broadinstitute.gatk.queue.QCommandLine.org$broadinstitute$gatk$queue$QCommandLine$$qScriptPluginManager$lzycompute(QCommandLine.scala:94)
    at org.broadinstitute.gatk.queue.QCommandLine.org$broadinstitute$gatk$queue$QCommandLine$$qScriptPluginManager(QCommandLine.scala:92)
    at org.broadinstitute.gatk.queue.QCommandLine.getArgumentSources(QCommandLine.scala:229)
    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:61)
    at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 3.5-0-g36282e4):
    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: Compile of GATKBAM_HC.scala failed with 4 errors
    ERROR ------------------------------------------------------------------------------------------

    INFO 17:41:27,417 QCommandLine - Shutting down jobs. Please wait...

    Is there any specific format to feed INDEL/SNP value to SelectVariants?
    I tried various suggestions by searching on google and other GATK related blogs, but couldn't get it working.

  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 10,296 admin
    Those arguments are ENUM types, which takes a bit of special handling. We have discussed this previously on the forum, so try searching the forum for "Queue ENUM". If you don't find anything let me know, but I think you should.

    Geraldine Van der Auwera, PhD

  • amitgsiramitgsir Busan, South KoreaMember Posts: 3
    edited June 23

    I think, I am having trouble with "import the correct type object".

    Is there any documentation regarding how or what to import for each tools/GATK Walker.
    I couldn't find any working information.

    For most of the solution provided, the import statements similar to:
    import org.broadinstitute.variant.variantcontext.VariantContext.Type
    import org.broadinstitute..gatk.tools.variant.variantcontext.VariantContext.Type.SNP

    is suggested, but looks like its not working for current Queue version.

    Post edited by amitgsir on
  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 10,296 admin
    Yes that's the idea. Be sure to use an IDE that understands Java and Scala (like IntelliJ) as it will help you determine what import to use.

    If you still run into problems (you say it's not working?) please post the error message you get.

    Geraldine Van der Auwera, PhD

  • amitgsiramitgsir Busan, South KoreaMember Posts: 3

    Hi, I am still getting error.

    This is how my script looks like:

    import org.broadinstitute.gatk.queue.QScript
    import org.broadinstitute.gatk.queue.extensions.gatk._
    import org.broadinstitute.variant.variantcontext.VariantContext.Type
    import org.broadinstitute.gatk.tools.variant.variantcontext.VariantContext.Type.SNP

    //SelectVariants Unfildetered INDEL Initiated
    val selectUnfilteredINDEL = new SelectVariants
    selectUnfilteredINDEL.reference_sequence = qscript.referenceFile
    selectUnfilteredINDEL.variant = haplotyper.out
    selectUnfilteredINDEL.out = swapExt(haplotyper.out, "vcf", "INDEL.vcf")
    selectUnfilteredINDEL.selectType = INDEL
    selectUnfilteredINDEL.memoryLimit = 8
    selectUnfilteredINDEL.scatterCount = 48
    add(selectUnfilteredINDEL)
    
    
    //SelectVariants Unfildetered SNP Initiated
    val selectUnfilteredSNP = new SelectVariants
    selectUnfilteredSNP.reference_sequence = qscript.referenceFile
    selectUnfilteredSNP.variant = haplotyper.out
    selectUnfilteredSNP.out = swapExt(haplotyper.out, "vcf", "SNP.vcf")
    selectUnfilteredSNP.selectType = SNP
    selectUnfilteredSNP.memoryLimit = 8
    selectUnfilteredSNP.scatterCount = 48
    add(selectUnfilteredSNP)
    

    I am getting the error:
    [agoyal@edico Test_5GATKBAM_HC]$ java -jar /opt/Queue-3.5/Queue.jar -S GATKBAM_HC.scala -jobRunner ParallelShell -I ../NA12878D_GATK.bam --indelFilterNames "My_Indel_Filter" --indelFilterExp "QD < 2.0 ||FS > 200.0 || ReadPosRankSum < -20.0" --snpFilterNames "My_SNP_Filter" --snpFilterExp "QD < 2.0 || FS > 60.0 || MQ < 40.0 || HaplotypeScore > 13.0 || MappingQualityRankSum < -12.5 || ReadPosRankSum < -8.0"
    INFO 09:59:34,971 QScriptManager - Compiling 1 QScript
    ERROR 09:59:35,193 QScriptManager - GATKBAM_HC.scala:3: object variant is not a member of package org.broadinstitute
    ERROR 09:59:35,203 QScriptManager - import org.broadinstitute.variant.variantcontext.VariantContext.Type
    ERROR 09:59:35,204 QScriptManager - ^
    ERROR 09:59:35,207 QScriptManager - GATKBAM_HC.scala:4: object variant is not a member of package org.broadinstitute.gatk.tools
    ERROR 09:59:35,213 QScriptManager - import org.broadinstitute.gatk.tools.variant.variantcontext.VariantContext.Type.SNP
    ERROR 09:59:35,214 QScriptManager - ^
    ERROR 09:59:56,339 QScriptManager - GATKBAM_HC.scala:92: not found: value INDEL
    ERROR 09:59:56,340 QScriptManager - selectUnfilteredINDEL.selectType = INDEL
    ERROR 09:59:56,341 QScriptManager - ^
    ERROR 09:59:56,622 QScriptManager - GATKBAM_HC.scala:138: not found: value SNP
    ERROR 09:59:56,623 QScriptManager - selectUnfilteredSNP.selectType = SNP
    ERROR 09:59:56,623 QScriptManager - ^
    ERROR 09:59:56,674 QScriptManager - 8 errors found

    ERROR ------------------------------------------------------------------------------------------
    ERROR stack trace

    org.broadinstitute.gatk.queue.QException: Compile of GATKBAM_HC.scala failed with 8 errors
    at org.broadinstitute.gatk.queue.QScriptManager.loadScripts(QScriptManager.scala:79)
    at org.broadinstitute.gatk.queue.QCommandLine.org$broadinstitute$gatk$queue$QCommandLine$$qScriptPluginManager$lzycompute(QCommandLine.scala:94)
    at org.broadinstitute.gatk.queue.QCommandLine.org$broadinstitute$gatk$queue$QCommandLine$$qScriptPluginManager(QCommandLine.scala:92)
    at org.broadinstitute.gatk.queue.QCommandLine.getArgumentSources(QCommandLine.scala:229)
    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:61)
    at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 3.5-0-g36282e4):
    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: Compile of GATKBAM_HC.scala failed with 8 errors
    ERROR ------------------------------------------------------------------------------------------

    INFO 09:59:56,745 QCommandLine - Shutting down jobs. Please wait...

    Here, I am not sure what to import (So, if there is some specific information/guide that will be great.

    Thanks,
    Amit

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