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Having problems with BQRS (java.lang.ArrayIndexOutOfBoundsException: -37)

Looking in the forum, I can´t see how to correct this.
I am using java 1.7, sorted HG19 from UCSC and sorted HG19 dbnsp from the bundle

java -Xmx4g -jar GenomeAnalysisTK.jar -T BaseRecalibrator -I PAN001N.rmdup.bam -R HG19.fasta -knownSites dbsnp_137.hg19.sorted.vcf -o recalibration_report.grp

The Genome Analysis Toolkit (GATK) v2.7-4-g6f46d11, Compiled 2013/10/10 17:27:51

ERROR stack trace

java.lang.ArrayIndexOutOfBoundsException: -37
at org.broadinstitute.sting.utils.BaseUtils.convertIUPACtoN(
at org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(
at org.broadinstitute.sting.gatk.datasources.providers.ReferenceView.getReferenceBases(
at org.broadinstitute.sting.gatk.datasources.providers.ReadReferenceView$Provider.getBases(
at org.broadinstitute.sting.gatk.contexts.ReferenceContext.fetchBasesFromProvider(
at org.broadinstitute.sting.gatk.contexts.ReferenceContext.getBases(
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.calculateIsSNP(
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(
at org.broadinstitute.sting.commandline.CommandLineProgram.start(
at org.broadinstitute.sting.commandline.CommandLineProgram.start(
at org.broadinstitute.sting.gatk.CommandLineGATK.main(

As a note, I validated the BAM with picard/validateSamFile, with no errors found

Do you have some ideas?


Best Answer


  • JorgeJorge Member

    You are totally right. I modified the ref file to suit my reads and something went horribly wrong :). Now it is running. Thanks!

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