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java.lang.ArrayIndexOutOfBoundsException: arraycopy: source index -26 out of bounds for byte[355]
at java.base/java.lang.System.arraycopy(Native Method)
at java.base/java.util.Arrays.copyOfRange(Arrays.java:3823)
at org.broadinstitute.hellbender.tools.walkers.annotator.TandemRepeat.getNumTandemRepeatUnits(TandemRepeat.java:54)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyRegionTrimmer.trim(AssemblyRegionTrimmer.java:189)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.callRegion(HaplotypeCallerEngine.java:656)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller.apply(HaplotypeCaller.java:271)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:200)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:173)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1098)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:149)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:198)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:217)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)
They also report that when they increase the --assembly-region-padding from the default 100, to 150, the problem resolves.
The text was updated successfully, but these errors were encountered:
A user reports in https://gatk.broadinstitute.org/hc/en-us/community/posts/21559395629723-haplotycaller-alleles-arrayIndexOutofBoundsException that they are running into an edge-case
ArrayIndexOutOfBoundsException
inTandemRepeat.getNumTandemRepeatUnits()
while runningHaplotypeCaller
in--alleles
mode to re-genotype a 175bp deletion:They also report that when they increase the
--assembly-region-padding
from the default 100, to 150, the problem resolves.The text was updated successfully, but these errors were encountered: