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Illegal argument exception when running HaplotypeCaller

maryawoodmaryawood Member
edited October 2017 in Ask the GATK team

Hello,

One of my jobs is consistently failing to run HaplotypeCaller with the following error message:

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

java.lang.IllegalArgumentException
at java.nio.Buffer.limit(Buffer.java:275)
at org.broadinstitute.gatk.engine.datasources.reads.GATKBAMIndex.getBuffer(GATKBAMIndex.java:428)
at org.broadinstitute.gatk.engine.datasources.reads.GATKBAMIndex.readLongs(GATKBAMIndex.java:360)
at org.broadinstitute.gatk.engine.datasources.reads.GATKBAMIndex.readReferenceSequence(GATKBAMIndex.java:138)
at org.broadinstitute.gatk.engine.datasources.reads.BAMSchedule.(BAMSchedule.java:105)
at org.broadinstitute.gatk.engine.datasources.reads.BAMScheduler.getNextOverlappingBAMScheduleEntry(BAMScheduler.java:296)
at org.broadinstitute.gatk.engine.datasources.reads.BAMScheduler.advance(BAMScheduler.java:185)
at org.broadinstitute.gatk.engine.datasources.reads.BAMScheduler.next(BAMScheduler.java:156)
at org.broadinstitute.gatk.engine.datasources.reads.BAMScheduler.next(BAMScheduler.java:46)
at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:68)
at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:54)
at org.broadinstitute.gatk.engine.datasources.reads.IntervalSharder.next(IntervalSharder.java:79)
at org.broadinstitute.gatk.engine.datasources.reads.IntervalSharder.next(IntervalSharder.java:39)
at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:68)
at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:54)
at org.broadinstitute.gatk.engine.datasources.reads.ActiveRegionShardBalancer.getCombinedFilePointersOnSingleContig(ActiveRegionShardBalancer.java:80)
at org.broadinstitute.gatk.engine.datasources.reads.ActiveRegionShardBalancer.access$000(ActiveRegionShardBalancer.java:40)
at org.broadinstitute.gatk.engine.datasources.reads.ActiveRegionShardBalancer$1.next(ActiveRegionShardBalancer.java:52)
at org.broadinstitute.gatk.engine.datasources.reads.ActiveRegionShardBalancer$1.next(ActiveRegionShardBalancer.java:46)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:90)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:315)
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:106)

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: Code exception (see stack trace for error itself)
ERROR ------------------------------------------------------------------------------------------

I'm just running the program with the default arguments, a reference genome that has worked fine with other files, and a input bam that appears to be in good shape (i.e. can be viewed using samtools with no problem). Any insight into what may be causing this would be greatly appreciated! Thanks!

Answers

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