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java.lang.NumberFormatException: For input string: "R"

y4dary4dar TexasMember

I am attempting to run Churchill, a pipeline that is designed to speed up variant calling on whole genomes and run into the error I post below. I've read several threads on this site that discuss the same problem and most suggest there is a problem with my .vcf header. I've tried for several days but can't find where that problem might be. If anyone can help I would appreciate it.

I hesitate to post the vcf header because it's huge but will if there are no objections. Below are the error details.

Running GATK3.2.2 (as per the Churchill documentation) on an SGE cluster.

Thank you.

.....

  • /opt/apps/nfs/intel/samtools/1.2/bin/samtools index /lustre/scratch/daray/churchill/testquanah/iter1_mBra_quanah_72/mBra/merge_dedup_chri/mBra.merged.sorted.region_0015.dedup.bam
    INFO 2017-10-24 13:15:43 MergeSamFiles Finished reading inputs.
ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.NumberFormatException: For input string: "R"
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Integer.parseInt(Integer.java:580)
at java.lang.Integer.valueOf(Integer.java:766)
at htsjdk.variant.vcf.VCFCompoundHeaderLine.(VCFCompoundHeaderLine.java:171)
at htsjdk.variant.vcf.VCFFormatHeaderLine.(VCFFormatHeaderLine.java:49)
at htsjdk.variant.vcf.AbstractVCFCodec.parseHeaderFromLines(AbstractVCFCodec.java:211)
at htsjdk.variant.vcf.VCFCodec.readActualHeader(VCFCodec.java:111)
at htsjdk.tribble.AsciiFeatureCodec.readHeader(AsciiFeatureCodec.java:88)
at htsjdk.tribble.AsciiFeatureCodec.readHeader(AsciiFeatureCodec.java:41)
at htsjdk.tribble.index.IndexFactory$FeatureIterator.readHeader(IndexFactory.java:413)
at htsjdk.tribble.index.IndexFactory$FeatureIterator.(IndexFactory.java:401)
at htsjdk.tribble.index.IndexFactory.createDynamicIndex(IndexFactory.java:312)
at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.createIndexInMemory(RMDTrackBuilder.java:402)
at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.attemptToLockAndLoadIndexFromDisk(RMDTrackBuilder.java:317)
at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.loadIndex(RMDTrackBuilder.java:279)
at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.getFeatureSource(RMDTrackBuilder.java:225)
at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.createInstanceOfTrack(RMDTrackBuilder.java:148)
at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.(ReferenceOrderedDataSource.java:208)
at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource.(ReferenceOrderedDataSource.java:88)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.getReferenceOrderedDataSources(GenomeAnalysisEngine.java:990)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.initializeDataSources(GenomeAnalysisEngine.java:772)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:285)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:107)

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