Exception in SplitNCigarReads

[sooheelee]

@jamesemery, researcher has uploaded data to </humgen/gsa-scr1/pub/incoming/Exception_in_SplitNCigarReads.tgz> and has clarified a few other details within the forum thread, e.g. running ValidateSamFile IGNORE=MISSING_TAG_NM IGNORE=MATE_NOT_FOUND allows for validation.

Thanks for looking into this.

---

Hello,

I am getting the following exception when running SplitNCigarReads on RNA-Seq data using GATK 4.0.8.1:

java.lang.ArrayIndexOutOfBoundsException: 100
	at org.broadinstitute.hellbender.tools.walkers.rnaseq.OverhangFixingManager.overhangingBasesMismatch(OverhangFixingManager.java:313)
	at org.broadinstitute.hellbender.tools.walkers.rnaseq.OverhangFixingManager.fixSplit(OverhangFixingManager.java:252)
	at org.broadinstitute.hellbender.tools.walkers.rnaseq.OverhangFixingManager.addReadGroup(OverhangFixingManager.java:209)
	at org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReads.splitNCigarRead(SplitNCigarReads.java:270)
	at org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReads.firstPassApply(SplitNCigarReads.java:180)
	at org.broadinstitute.hellbender.engine.TwoPassReadWalker.lambda$traverseReads$0(TwoPassReadWalker.java:62)
	at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
	at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
	at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
	at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
	at java.util.Iterator.forEachRemaining(Iterator.java:116)
	at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
	at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
	at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
	at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
	at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
	at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
	at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
	at org.broadinstitute.hellbender.engine.TwoPassReadWalker.traverseReads(TwoPassReadWalker.java:60)
	at org.broadinstitute.hellbender.engine.TwoPassReadWalker.traverse(TwoPassReadWalker.java:42)
	at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201)
	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)

Command:

./gatk/gatk \
   SplitNCigarReads \
   --reference $REF \
   --input test3.bam \
   --output output.bam \
   --verbosity DEBUG \
    > split.log 2>&1

Running ValidateSamFile does not reveal anything suspicious and visual inspection of the reads also appears to be fine.

This Issue was generated from your [forums]
[forums]: https://gatkforums.broadinstitute.org/gatk/discussion/12801/exception-in-splitncigarreads/p1

[mozack]

Thanks for looking into this and please let me know if I can provide assistance.

[jamesemery]

Hi @mozack, I see on the forum you have a minimal bam file that reproduces the issue? Looking at the stack trace it looks like a bug related to some property of the splice site misaligning with the read in a damaging way. I would love to take a look and see if I can fix the issue on your file.

[sooheelee]

@jamesemery, the bug report, i.e. test data from the researcher, is at /humgen/gsa-scr1/pub/incoming/Exception_in_SplitNCigarReads.tgz, as stated above.