To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at https://software.broadinstitute.org/firecloud/documentation/freecredits

muTect2: ": Somehow the requested coordinate is not covered by the read. Too many deletions?"

Hello! I am using muTect2 (in particular I am following this pipeline: http://gatkforums.broadinstitute.org/gatk/discussion/5963/tumor-normal-paired-exome-sequencing-pipeline) but today I am getting this error on chromosome 3:

ERROR --
ERROR stack trace

org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: Somehow the requested coordinate is not covered by the read. Too many deletions?

at org.broadinstitute.gatk.utils.sam.ReadUtils.getReadCoordinateForReferenceCoordinate(ReadUtils.java:490)

at org.broadinstitute.gatk.utils.sam.ReadUtils.getReadCoordinateForReferenceCoordinate(ReadUtils.java:436)

at org.broadinstitute.gatk.utils.sam.ReadUtils.getReadCoordinateForReferenceCoordinate(ReadUtils.java:427)

at org.broadinstitute.gatk.utils.clipping.ReadClipper.hardClipByReferenceCoordinates(ReadClipper.java:543)

at org.broadinstitute.gatk.utils.clipping.ReadClipper.hardClipByReferenceCoordinatesLeftTail(ReadClipper.java:177)

at org.broadinstitute.gatk.utils.clipping.ReadClipper.hardClipAdaptorSequence(ReadClipper.java:408)

at org.broadinstitute.gatk.utils.clipping.ReadClipper.hardClipAdaptorSequence(ReadClipper.java:411)

at org.broadinstitute.gatk.tools.walkers.cancer.m2.MuTect2.finalizeActiveRegion(MuTect2.java:1201)

at org.broadinstitute.gatk.tools.walkers.cancer.m2.MuTect2.assembleReads(MuTect2.java:1145)

at org.broadinstitute.gatk.tools.walkers.cancer.m2.MuTect2.map(MuTect2.java:536)

at org.broadinstitute.gatk.tools.walkers.cancer.m2.MuTect2.map(MuTect2.java:176)

at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:709)

at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:705)

at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler$ReadMapReduceJob.run(NanoScheduler.java:471)

at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)

at java.util.concurrent.FutureTask.run(FutureTask.java:266)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)

at java.lang.Thread.run(Thread.java:745)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.6-0-g89b7209):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions https://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Somehow the requested coordinate is not covered by the read. Too many deletions?
ERROR ------------------------------------------------------------------------------------------

Thank you in advance!
Best

Best Answer

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator
    Accepted Answer

    @edAL
    Hi,

    I suspect you are running with -nt or -nct. Can you try running without those? This error usually arises from multi-threading issues.

    -Sheila

  • YingLiuYingLiu ChinaMember

    @edAL said:
    Hello! I am using muTect2 (in particular I am following this pipeline: http://gatkforums.broadinstitute.org/gatk/discussion/5963/tumor-normal-paired-exome-sequencing-pipeline) but today I am getting this error on chromosome 3:

    ERROR --
    ERROR stack trace

    org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: Somehow the requested coordinate is not covered by the read. Too many deletions?

    at org.broadinstitute.gatk.utils.sam.ReadUtils.getReadCoordinateForReferenceCoordinate(ReadUtils.java:490)

    at org.broadinstitute.gatk.utils.sam.ReadUtils.getReadCoordinateForReferenceCoordinate(ReadUtils.java:436)

    at org.broadinstitute.gatk.utils.sam.ReadUtils.getReadCoordinateForReferenceCoordinate(ReadUtils.java:427)

    at org.broadinstitute.gatk.utils.clipping.ReadClipper.hardClipByReferenceCoordinates(ReadClipper.java:543)

    at org.broadinstitute.gatk.utils.clipping.ReadClipper.hardClipByReferenceCoordinatesLeftTail(ReadClipper.java:177)

    at org.broadinstitute.gatk.utils.clipping.ReadClipper.hardClipAdaptorSequence(ReadClipper.java:408)

    at org.broadinstitute.gatk.utils.clipping.ReadClipper.hardClipAdaptorSequence(ReadClipper.java:411)

    at org.broadinstitute.gatk.tools.walkers.cancer.m2.MuTect2.finalizeActiveRegion(MuTect2.java:1201)

    at org.broadinstitute.gatk.tools.walkers.cancer.m2.MuTect2.assembleReads(MuTect2.java:1145)

    at org.broadinstitute.gatk.tools.walkers.cancer.m2.MuTect2.map(MuTect2.java:536)

    at org.broadinstitute.gatk.tools.walkers.cancer.m2.MuTect2.map(MuTect2.java:176)

    at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:709)

    at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:705)

    at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler$ReadMapReduceJob.run(NanoScheduler.java:471)

    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)

    at java.util.concurrent.FutureTask.run(FutureTask.java:266)

    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)

    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)

    at java.lang.Thread.run(Thread.java:745)

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 3.6-0-g89b7209):
    ERROR
    ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
    ERROR If not, please post the error message, with stack trace, to the GATK forum.
    ERROR Visit our website and forum for extensive documentation and answers to
    ERROR commonly asked questions https://www.broadinstitute.org/gatk
    ERROR
    ERROR MESSAGE: Somehow the requested coordinate is not covered by the read. Too many deletions?
    ERROR ------------------------------------------------------------------------------------------

    Thank you in advance!
    Best

    @edAL I have met same errors with you . do you have solved that without -nct or -nt ??

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @YingLiu
    Hi,

    Have you tried without -nct / -nt?

    -Sheila

Sign In or Register to comment.