org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException

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  • remove threading from MuTect2.
    via GitHub by malinlarsson
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  • GATK | GATK | Tagged #bug
    via by Unknown author,
    • org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: Somehow the requested coordinate is not covered by the read. Alignment 60055114 | 38S113M at org.broadinstitute.gatk.utils.sam.ReadUtils.getReadCoordinateForReferenceCoordinate(ReadUtils.java:580) 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:548) at org.broadinstitute.gatk.utils.clipping.ReadClipper.hardClipByReferenceCoordinatesRightTail(ReadClipper.java:197) at org.broadinstitute.gatk.utils.clipping.ReadClipper.hardClipToRegion(ReadClipper.java:377) at org.broadinstitute.gatk.utils.clipping.ReadClipper.hardClipToRegion(ReadClipper.java:352) at org.broadinstitute.gatk.utils.activeregion.ActiveRegion.trim(ActiveRegion.java:482) at org.broadinstitute.gatk.utils.activeregion.ActiveRegion.trim(ActiveRegion.java:437) at org.broadinstitute.gatk.tools.walkers.haplotypecaller.ActiveRegionTrimmer$Result.getCallableRegion(ActiveRegionTrimmer.java:383) at org.broadinstitute.gatk.tools.walkers.cancer.m2.MuTect2.map(MuTect2.java:551) at org.broadinstitute.gatk.tools.walkers.cancer.m2.MuTect2.map(MuTect2.java:176) at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$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)
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