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BaseRecalibrator error in a BAM validated with Picard

ocanelaocanela Posts: 5Member

Hello,

I have a BAM from RNA Seq experiment. The reads are aligned with tophat and then I filtered secondary reads, fixed mate pairs, marked duplicates with picard and realigned with gatk. However, when I try to use BaseRecalibrator function,

-T BaseRecalibrator -nct 12 -R ./SusGenome10v69/Sus_scrofa.Sscrofa10.2.69.dna.toplevel.fa -I ./7_15.corrected.ordered.sremoved.marked.fixed.realigned.fixed.corrected.ordered.sremoved.marked.fixed.realigned.fixed.bam -knownSites ./SusGenome10v69/Sus_scrofa.vcf -o ./7_15.RecalData.grp

It stops with the error:

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Trying to clip before the start or after the end of a read
at org.broadinstitute.sting.utils.clipping.ReadClipper.hardClipByReferenceCoordinates(ReadClipper.java:534)
at org.broadinstitute.sting.utils.clipping.ReadClipper.hardClipByReferenceCoordinatesLeftTail(ReadClipper.java:176)
at org.broadinstitute.sting.utils.clipping.ReadClipper.hardClipAdaptorSequence(ReadClipper.java:389)
at org.broadinstitute.sting.utils.clipping.ReadClipper.hardClipAdaptorSequence(ReadClipper.java:392)
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:244)
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:131)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:230)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:218)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler$ReadMapReduceJob.run(NanoScheduler.java:471)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:679)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.4-7-g5e89f01):
ERROR
ERROR Please visit the wiki to see if this is a known problem
ERROR If not, please post the error, with stack trace, to the GATK forum
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Trying to clip before the start or after the end of a read
ERROR ------------------------------------------------------------------------------------------

The bam file validates properly with the Picard's ValidateSamFile function. I tried with gatk versions, 2.3-9 and 2.4-7 obtaining the same results.

I used the same procedure with other samples without any problem. However, I am unable to recalibrate this sample. I tried to realign the reads with different tophat versions, applied different filters and different procedures, however i am unable to use the BaseRecalibrator function with this sample.

Could you help me?

Thanks!

Best Answer

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,781Administrator, GATK Dev admin

    Hi there,

    This sounds like a bug; we'll need to reproduce this error locally. Could you please upload a BAM snippet to our server? Detailed instructions here: http://www.broadinstitute.org/gatk/guide/article?id=1894

    Be sure to also upload your reference since you're using a custom one.

    Geraldine Van der Auwera, PhD

  • ocanelaocanela Posts: 5Member

    Hi,

    I uploaded the requested files in your ftp server (including the reference).

    The name of the compressed file is: baseracalibrator.bug.ocanela.tar.gz

    Thanks,

  • ocanelaocanela Posts: 5Member

    Ok, thank you for the software support!

  • huyvuonghuyvuong Posts: 3Member
    edited April 2013

    Hi,
    I have the exact same error with my BAM file even though I used the latest version 2.4.9-g532efad. Would you please let me know where I can download version 2.5 with the patch?
    Thanks,
    Huy

    Post edited by huyvuong on
  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,781Administrator, GATK Dev admin

    Hi @huyvuong, version 2.5 is not yet available, but you can try the latest nightly build (look on the Downloads page).

    Geraldine Van der Auwera, PhD

  • huyvuonghuyvuong Posts: 3Member

    Thank you very much. I tried the latest nightly build and it worked now.

  • ocanelaocanela Posts: 5Member

    The version 2.5-2 fixed the problem with my sample.

    Thank you for the fix!

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