Dear GATK Team,
I am receiving the following error while running GATK 1.6. Unfortunately, for project consistency I cannot update to a more recent version of GATK and would at least wish to understand the source of the error. I ran ValidateSamFile on the input bam files and they appear to be OK.
Any insight or advice would be greatly appreciated:
`##### ERROR ------------------------------------------------------------------------------------------
ERROR stack trace
org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Somehow the requested coordinate is not covered by the read. Too many deletions?
at org.broadinstitute.sting.utils.sam.ReadUtils.getReadCoordinateForReferenceCoordinate(ReadUtils.java:425)
at org.broadinstitute.sting.utils.sam.ReadUtils.getReadCoordinateForReferenceCoordinate(ReadUtils.java:374)
at org.broadinstitute.sting.utils.sam.ReadUtils.getReadCoordinateForReferenceCoordinate(ReadUtils.java:370)
at org.broadinstitute.sting.utils.clipping.ReadClipper.hardClipByReferenceCoordinates(ReadClipper.java:445)
at org.broadinstitute.sting.utils.clipping.ReadClipper.hardClipByReferenceCoordinatesRightTail(ReadClipper.java:176)
at org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel.computeReadHaplotypeLikelihoods(PairHMMIndelErrorModel.java:196)
at org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel.getLikelihoods(IndelGenotypeLikelihoodsCalculationModel.java:212)
at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.calculateLikelihoods(UnifiedGenotyperEngine.java:235)
at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.calculateLikelihoodsAndGenotypes(UnifiedGenotyperEngine.java:164)
at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:302)
at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:115)
at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:78)
at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:18)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:63)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:248)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:92)
ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 1.6-22-g3ec78bd):
ERROR
ERROR Please visit the wiki 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 wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
ERROR
ERROR MESSAGE: Somehow the requested coordinate is not covered by the read. Too many deletions?
ERROR ------------------------------------------------------------------------------------------`
Abbreviated commandline used:
GenomeAnalysisTK.jar -T UnifiedGenotyper -glm BOTH -et NO_ET \
-R "Saccharomyces_cerevisiae/UCSC/sacCer2/Sequence/WholeGenomeFasta/genome.fa" \
-dcov 5000 -I "someFile.bam" --output_mode EMIT_ALL_SITES -gvcf -l OFF \
-stand_call_conf 1 -L chrIV:1-1531919