ReduceReads problem in GATK v2.6-2-ge03a5e9, Compiled 2013/06/20 20:07

ashishashish Oxford, UKPosts: 9Member

Hello,
While trying to run ReduceReads on my BAM outputs of PrintReads, using the latest build v2.6-2-ge03a5e9, I get the following error, kindly comment on this error trace:

Command:
java -Xmx8g -jar /path/to/my/server/ashish/tools/GenomeAnalysisTK-2.6-2-ge03a5e9/GenomeAnalysisTK.jar -T ReduceReads -R /path/to/my/server/pipeline/lib/hs37d5.fa -I /path/to/my/server/output/bamext.base.recal/41453_TTAGGC_L002_001.bam -o /path/to/my/server/output/bamext.reduced/41453_TTAGGC_L002_001.bam

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

org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Removed too many insertions, header is now negative at position 151039408
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.HeaderElement.removeInsertionToTheRight(HeaderElement.java:210)
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.actuallyUpdateHeaderForRead(SlidingWindow.java:1246)
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.updateHeaderCounts(SlidingWindow.java:1162)
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.removeFromHeader(SlidingWindow.java:1139)
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.compressVariantRegion(SlidingWindow.java:742)
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.closeVariantRegion(SlidingWindow.java:835)
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.closeVariantRegions(SlidingWindow.java:884)
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.close(SlidingWindow.java:971)
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SingleSampleCompressor.addAlignment(SingleSampleCompressor.java:113)
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.MultiSampleCompressor.addAlignment(MultiSampleCompressor.java:123)
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.ReduceReadsStash.compress(ReduceReadsStash.java:116)
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.ReduceReads.reduce(ReduceReads.java:477)
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.ReduceReads.reduce(ReduceReads.java:113)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsReduce.apply(TraverseReadsNano.java:251)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsReduce.apply(TraverseReadsNano.java:240)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:279)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:102)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:56)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:108)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:311)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.6-2-ge03a5e9):
ERROR
ERROR Please check the documentation guide 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: Removed too many insertions, header is now negative at position 151039408
ERROR ------------------------------------------------------------------------------------------

Best Answer

Answers

  • ashishashish Oxford, UKPosts: 9Member
    edited June 2013

    I've uploaded the bam snippet named "ReduceRead_problem_data.tar.gz" and reproduced the error on this snippet locally.
    Thanks for the prompt attention.

    Post edited by ashish on
  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,418Administrator, GATK Developer admin

    Thanks for the test data! We'll let you know when we have an update in this thread.

    Geraldine Van der Auwera, PhD

  • hong_010hong_010 Posts: 8Member

    Hi,I met the same problem.Would you tell me the way to resolve?

  • ashishashish Oxford, UKPosts: 9Member

    I'm also waiting for an updated solution from the GATK team.
    Hopefully, they should be able to replicate the error and then resolve this bug from my uploaded bam snippet and thereupon, release a patched up version of this version of GATK release.

    Sorry about the updated "answer tag" with this question. I'd posted for the first time and didn't realise that opting yes for "Did this answer the question" would update the final status flag of the main question rather than for that specific assistance step.

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,418Administrator, GATK Developer admin

    Hi folks,

    We have processed the test files (thanks Ashish!) and were able to replicate the error. However we haven't yet had time to solve it. We are a little short-staffed right now with several members on vacation, so it will take a bit longer than usual to get bugs fixed. But we'll do our best to minimize the wait time. Thanks for your patience!

    (I updated the answer flag to mark this as unresolved)

    Geraldine Van der Auwera, PhD

  • ashishashish Oxford, UKPosts: 9Member

    Thanks Geraldine.
    However, on the latest release notes, I see this mentioned ##Added fix for the "Removed too many insertions, header is now negative" bug.##

    But from your reply, it seems the issue has not been addressed. Could you please clarify on this?

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,418Administrator, GATK Developer admin

    That case was addressed and resolved; we think that your case is a different issue causing the same symptom.

    Geraldine Van der Auwera, PhD

  • ashishashish Oxford, UKPosts: 9Member

    I see. Now one other twist to the scenario - with the GATK verion 2.6, I've been able to generate the BAM Print Reads for all BAMs (n~1100+), but the Reduce Reads affect some BAMs, while other BAMs do generate upon the reduction step.

    However, the same error is not replicated when using the previous GATK version 2.5 on that BAM snippet for Reduce Reads. So what if I run the last step of BAM reduction using the GATK version 2.5 (assuming that it runs successfully on all BAMs) on the Print Reads from the GATK version 2.6? Would that be a reasonable hit to take, in interest of time to be able to run Unified Genotyper on this large no. of BAMs? Or you reckon there would be other ramifications on the quality of calls generated?

  • ashishashish Oxford, UKPosts: 9Member

    That's wonderful, thanks.

  • jburattijburatti Posts: 4Member

    Hi there, I have the same problem with ReduceReads.
    Is the fix already available ?
    Thanks.

  • ashishashish Oxford, UKPosts: 9Member

    Hi,

    I can confirm that the nightly build of 26/06/2013 did not give me an error on the BAM snippet that I'd provided to the GATK team.
    I am now running the reduction step on all my BAMs with this new build and shall get back if I see any further issues.

    This build details that I get from the download is:
    GenomeAnalysisTK-nightly-2013-06-26-g9fa3206

  • ashishashish Oxford, UKPosts: 9Member

    I've finished the reduction step for all 1100+ BAMs and encountered no problems in the runs.
    I also noticed faster run times than previously seen.
    Thanks GATK team :-)

  • hong_010hong_010 Posts: 8Member

    Hi.I met the same error:

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 2.6-4-g3e5ff60):
    ERROR
    ERROR Please check the documentation guide 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: Removed too many insertions, header is now negative at position 5298318
    ERROR ------------------------------------------------------------------------------------------

    Would you tell me the way to resolve?

    Thanks!

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,418Administrator, GATK Developer admin

    Hi Hong,

    This bug is fixed in our development version, and the fix is available in the latest nightly build (see the Downloads page).

    Geraldine Van der Auwera, PhD

  • zhensunzhensun Posts: 1Member

    Is there a nightly build of GATK Queue available?

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,418Administrator, GATK Developer admin

    No, development on Queue is not so fast as to need nightly builds.

    Geraldine Van der Auwera, PhD

  • michaelchaomichaelchao Posts: 15Member

    Hi I am now getting the same error message using the latest GATK:

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 2.6-4-g3e5ff60):
    ERROR
    ERROR Please check the documentation guide 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: Removed too many insertions, header is now negative at position 10485094
    ERROR ------------------------------------------------------------------------------------------
  • ashishashish Oxford, UKPosts: 9Member

    Try the version in the nightly build.

  • michaelchaomichaelchao Posts: 15Member

    problem solved with the nightly build.

    Thank you

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