org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: Somehow the requested coordinate is not covered by the read. Alignment 60055114 | 38S113M

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via GitHub by malinlarsson
, 1 year ago
Somehow the requested coordinate is not covered by the read. Alignment 60055114 | 38S113M
via broadinstitute.org by Unknown author, 1 year ago
Somehow the requested coordinate is not covered by the read. Alignment 10357 | 86M15H
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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