Having problems with BQRS (java.lang.ArrayIndexOutOfBoundsException: -37)
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Hi, Looking in the forum, I canĀ“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(BaseUtils.java:172) at org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:288) at org.broadinstitute.sting.gatk.datasources.providers.ReferenceView.getReferenceBases(ReferenceView.java:116) at org.broadinstitute.sting.gatk.datasources.providers.ReadReferenceView$Provider.getBases(ReadReferenceView.java:87) at org.broadinstitute.sting.gatk.contexts.ReferenceContext.fetchBasesFromProvider(ReferenceContext.java:145) at org.broadinstitute.sting.gatk.contexts.ReferenceContext.getBases(ReferenceContext.java:189) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.calculateIsSNP(BaseRecalibrator.java:335) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:253) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:132) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:228) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:216) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:102) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:56) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:108) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:313) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

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

Do you have some ideas? Thanks!!


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