Mutect2 error: Code exception (see stack trace for error itself)

Hi,

I'm trying to run Mutect2 (GATK v3.7-0-gcfedb67 - installed via conda) on a tumour normal pair with a panel of normals.

As a first step (following this)
I'm calling each normal sample individually, and then I want to create a PON to run against my tumour sample.

However, when I run:

gatk -T MuTect2 -R <genome.fa> -I:tumor <normal1.bam> \
    --artifact_detection_mode \
    -o <normal1_normal.vcf

I get the error:

[...]

Using AVX accelerated implementation of PairHMM
INFO  10:13:55,175 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
INFO  10:13:55,176 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
##### ERROR --
##### ERROR stack trace
java.lang.ArrayIndexOutOfBoundsException
    at java.lang.System.arraycopy(Native Method)
    at org.broadinstitute.gatk.utils.clipping.ClippingOp.hardClip(ClippingOp.java:380)
    at org.broadinstitute.gatk.utils.clipping.ClippingOp.apply(ClippingOp.java:117)
    at org.broadinstitute.gatk.utils.clipping.ReadClipper.clipRead(ReadClipper.java:157)
    at org.broadinstitute.gatk.utils.clipping.ReadClipper.hardClipSoftClippedBases(ReadClipper.java:334)
    at org.broadinstitute.gatk.utils.clipping.ReadClipper.hardClipSoftClippedBases(ReadClipper.java:337)
    at org.broadinstitute.gatk.tools.walkers.cancer.m2.MuTect2.finalizeActiveRegion(MuTect2.java:994)
    at org.broadinstitute.gatk.tools.walkers.cancer.m2.MuTect2.assembleReads(MuTect2.java:951)
    at org.broadinstitute.gatk.tools.walkers.cancer.m2.MuTect2.map(MuTect2.java:581)
    at org.broadinstitute.gatk.tools.walkers.cancer.m2.MuTect2.map(MuTect2.java:171)
    at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:709)
    at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:705)
    at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
    at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
    at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:274)
    at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:78)
    at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:98)
    at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:316)
    at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
    at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.7-0-gcfedb67):
##### 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 https://software.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Code exception (see stack trace for error itself)
##### ERROR ------------------------------------------------------------------------------------------

Thanks,

Nick

Tagged:

Answers

Sign In or Register to comment.