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SplitNCigarReads: Cannot split this read despite using -fixNDN

Hi All.

I am trying to run SplitNCigarReads on my RNA Seq data generated by tophatp.. It keeps failing with the following error despite i used -fixNDN true flag. Could you look into it ? I also tried using --refactor-cigar-string true

My version is gatk4 commit 12104fc

java version "1.8.0_66"
Java(TM) SE Runtime Environment (build 1.8.0_66-b17)
Java HotSpot(TM) 64-Bit Server VM (build 25.66-b17, mixed mode)
Thanks,

    java.lang.IllegalArgumentException: Cannot split this read (might be an empty section between Ns, for example 1N1D1N): 15M15600N69M58N1D7569N16M
            at org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReads.splitReadBasedOnCigar(SplitNCigarReads.java:301)
            at org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReads.splitNCigarRead(SplitNCigarReads.java:246)
            at org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReads.splitNCigarRead(SplitNCigarReads.java:219)
            at org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReads.firstPassApply(SplitNCigarReads.java:180)
            at org.broadinstitute.hellbender.engine.TwoPassReadWalker.lambda$traverseReads$123(TwoPassReadWalker.java:62)
            at java.util.stream.ForEachOps$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)

Answers

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