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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)