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Error stack trace Error Message: For input string: "R"

Hi, I've run Samtools1.0 & bcftools1.0 which output vcf4.2 which caused issuse. So I've updated to the latest version of GATK & am now getting this Error which I cannot resolve.

Program Args: --variant SPARK.common.vcf -R Documents/RefSeqIndexAllPrograms/GATK/hg19_1stM_unmask_ran_all.fa -T SelectVariants -o 24999.SPARK.common.vcf -sn 24999 -env -nt 4

ERROR stack trace

java.lang.NumberFormatException: For input string: "R"
ERROR A GATK RUNTIME ERROR has occurred (version 3.2-2-gec30cee):
ERROR MESSAGE: For input string: "R"

Any help would be gratefully received.
Thanks alig


  • airtimeairtime Member


    it looks like your pathway of R is wrong or your reference file is not in correct order?
    Did you check this?

    Best Air

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    @alig Can you please post the complete stack trace (meaning the full error message)? This will help us narrow down the source of the error.

  • aligalig Member

    Hi, Here is the complete stack trace, thanks alig

    INFO 17:31:34,943 HelpFormatter - --------------------------------------------------------------------------------
    INFO 17:31:34,946 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03
    INFO 17:31:34,946 HelpFormatter - Copyright (c) 2010 The Broad Institute
    INFO 17:31:34,946 HelpFormatter - For support and documentation go to
    INFO 17:31:34,950 HelpFormatter - Program Args: --variant SPARKS.common.vcf -R /home/neuro/Documents/RefSeqIndexAllPrograms/GATK/hg19_1stM_unmask_ran_all.fa -T SelectVariants -o 24919.SPARKS.common.vcf -sn 24919 -env -nt 4
    INFO 17:31:34,957 HelpFormatter - Executing as [email protected] on Linux 3.2.0-67-generic amd64; OpenJDK 64-Bit Server VM 1.7.0_65-b32.
    INFO 17:31:34,957 HelpFormatter - Date/Time: 2014/09/01 17:31:34
    INFO 17:31:34,957 HelpFormatter - --------------------------------------------------------------------------------
    INFO 17:31:34,958 HelpFormatter - --------------------------------------------------------------------------------
    INFO 17:31:35,041 GenomeAnalysisEngine - Strictness is SILENT
    INFO 17:31:35,201 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
    INFO 17:31:37,130 GATKRunReport - Uploaded run statistics report to AWS S3

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

    java.lang.NumberFormatException: For input string: "R"
    at java.lang.NumberFormatException.forInputString(
    at java.lang.Integer.parseInt(
    at java.lang.Integer.valueOf(
    at htsjdk.variant.vcf.VCFCompoundHeaderLine.(
    at htsjdk.variant.vcf.VCFInfoHeaderLine.(
    at htsjdk.variant.vcf.AbstractVCFCodec.parseHeaderFromLines(
    at htsjdk.variant.vcf.VCFCodec.readActualHeader(
    at htsjdk.tribble.AsciiFeatureCodec.readHeader(
    at htsjdk.tribble.AsciiFeatureCodec.readHeader(
    at htsjdk.tribble.index.IndexFactory$FeatureIterator.readHeader(
    at htsjdk.tribble.index.IndexFactory$FeatureIterator.(
    at htsjdk.tribble.index.IndexFactory.createDynamicIndex(
    at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.createIndexInMemory(
    at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.loadIndex(
    at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.getFeatureSource(
    at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.createInstanceOfTrack(
    at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.(
    at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource.(
    at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.getReferenceOrderedDataSources(
    at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.initializeDataSources(
    at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(
    at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(
    at org.broadinstitute.gatk.engine.CommandLineGATK.main(

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 3.2-2-gec30cee):
    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
    ERROR MESSAGE: For input string: "R"
    ERROR --------------------------------
  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    OK, so this tells us the error occurs while parsing a VCF header. Since you're only passing in the one VCF file, SPARK.common.vcf, the error must be in that one. It looks like one of the annotation field definitions may be responsible; there is a "R" character where the program expects to see a number. If you can't find it yourself, post the file header here and we'll try to help you identify it.

  • aligalig Member

    Thank you, I have found the R character in one of the annotation fields & replaced with a number, alig

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