BaseRecalibrator Error message

nfarzanehnfarzaneh vancouverMember

Hello,

I keep getting an uninformative error message when I run BaseRecalibrator. I did add these parameters to make it get this far: --fix_misencoded_quality_scores -fixMisencodedQuals --filter_mismatching_base_and_quals. But it seems that I have reached a dead end.

Here is the command I run:
java -Xmx2g -jar /usr/local/bin/gatk-2.3/GenomeAnalysisTKLite.jar -T BaseRecalibrator -R /home/ubuntu/db/hg19/ucsc.hg19.fasta -I S14694.bwa.clean.sort.dup.grp.reorder.realign.bam -o S14694.bwa.clean.sort.dup.grp.reorder.realign.recalibration_report.grp -knownSites /home/ubuntu/db/hg19/dbsnp.hg19.b141.vcf -DIQ -nct 3 --logging_level INFO --validation_strictness LENIENT --fix_misencoded_quality_scores -fixMisencodedQuals --filter_mismatching_base_and_quals

Here is the error message:

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

java.lang.ArrayIndexOutOfBoundsException: -28
at org.broadinstitute.sting.utils.baq.BAQ.calcEpsilon(BAQ.java:158)
at org.broadinstitute.sting.utils.baq.BAQ.hmm_glocal(BAQ.java:225)
at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:542)
at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:595)
at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:530)
at org.broadinstitute.sting.utils.baq.BAQ.baqRead(BAQ.java:663)
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.calculateBAQArray(BaseRecalibrator.java:428)
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:243)
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:112)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:203)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:191)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler$MapReduceJob.run(NanoScheduler.java:468)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.3-0-g28e02c2):
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 website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: -28
ERROR ------------------------------------------------------------------------------------------

====================================================================================================

Please let me know if you require any further information.

Kind regards,
Nima Farzaneh

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