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Picard 2.9.0 is now available. Download and read release notes here.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

Problem with BaseRecalibrator in v2.2-8-gec077cd

Hello dear GATK People,

I'm failing with BaseRecalibrator from the new GATK version - my pipeline worked with the 2.1-11, below is my error message.
Any quick fix or should I stick to the old version?

Ania

ERROR stack trace

java.lang.IllegalArgumentException: fromIndex(402) > toIndex(101)
at java.util.Arrays.rangeCheck(Unknown Source)
at java.util.Arrays.fill(Unknown Source)
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.calculateKnownSites(BaseRecalibrator.java:280)
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.calculateSkipArray(BaseRecalibrator.java:259)
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:239)
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:112)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:203)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:191)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:287)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:252)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:91)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:55)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:281)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:93)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.2-8-gec077cd):

.....

ERROR MESSAGE: fromIndex(402) > toIndex(101)
ERROR ------------------------------------------------------------------------------------------

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAPosts: 11,743 admin

    Hi there, this could be a bug -- could you please check that your BAM file passes validation (with validateSAMFile) and if it does, try to narrow this down as much as possible to a small set of reads + known sites that triggers the error, and then send us the snippets for testing?

    Geraldine Van der Auwera, PhD

  • loranialorania Posts: 9

    Hi Geraldine,

    so the input file validates with picard, it also works with the walker from GATK 2.1-11. I can see that the offensive reads are in several places, as after removing the first problematic region it continues through the rest of the chromosome, but fails on the next one.
    The alignement is mRNAseq against mm10, done with Tophat. Might it be that introns are the issue here? For the attached file I'm getting

     ##### ERROR stack trace 
    java.lang.IllegalArgumentException: fromIndex(8872) > toIndex(101)
        at java.util.Arrays.rangeCheck(Unknown Source)
        at java.util.Arrays.fill(Unknown Source)
        at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.calculateKnownSites(BaseRecalibrator.java:280)
        at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.calculateSkipArray(BaseRecalibrator.java:259) 
  • ebanksebanks Broad InstitutePosts: 693 ✭✭✭

    Hi there,

    I think I've fixed this issue for you. The fix should be available in a few hours when version 2.2-9 is released.

    Eric Banks, PhD -- Director, Data Sciences and Data Engineering, Broad Institute of Harvard and MIT

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