BaseRecalibrator showing error MESSAGE: START (90) > (89) STOP

We have used bwa 0.7.4 aln and sampe to align illumina reads. Then used the following command java -Xmx6g -jar ~/GenomeAnalysisTK-2.8-1/GenomeAnalysisTK.jar -T BaseRecalibrator -I ~/temp/BIR-08_130330_I288_FCD1P68ACXX_L7_SZAIPI025187-74.sortedindelrealigned.bam -R ~/hg19/ucsc.hg19.fasta -knownSites ~/dbSNP/dbsnp_137.hg19.vcf -o ~/BIR-08_130330_I288_FCD1P68ACXX_L7_SZAIPI025187-74.sortedBQSR.grp Which gave the following error message

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

org.broadinstitute.sting.utils.exceptions.ReviewedStingException: START (90) > (89) STOP -- this should never happen, please check read: FCD1P68ACXX:7:1315:19572:52424#CGCGGTGA 1/2 90b aligned read. (CIGAR: 85M4I1M2D) at org.broadinstitute.sting.utils.clipping.ReadClipper.hardClipByReferenceCoordinates(ReadClipper.java:537) at org.broadinstitute.sting.utils.clipping.ReadClipper.hardClipByReferenceCoordinatesRightTail(ReadClipper.java:193) at org.broadinstitute.sting.utils.clipping.ReadClipper.hardClipAdaptorSequence(ReadClipper.java:389) at org.broadinstitute.sting.utils.clipping.ReadClipper.hardClipAdaptorSequence(ReadClipper.java:392) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:245) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:132) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:228) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:216) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:102) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:56) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:108) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:313) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.8-1-g932cd3a):
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 http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: START (90) > (89) STOP -- this should never happen, please check read: FCD1P68ACXX:7:1315:19572:52424#CGCGGTGA 1/2 90b aligned read. (CIGAR: 85M4I1M2D)

can you help me in this error message? Why its coming and how to rectify it? Thanks in advance Mayukh

Best Answer

Sign In or Register to comment.