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ArrayIndexOutOfBoundsException with BaseRecalibrator

VergiliusVergilius ItalyMember

Dear GATK maintainers,

I am using GATK for variant calling and doing IndelRealign and BaseRecalibration before using HaplotypeCaller but getting an error with BaseRecalibrator.

I am using BaseRecalibrator in such a way it is doing it per-chromosome

jre/1.7.0_72/none/bin/java -Xmx4g -jar gatk/3.4.46/jre--1.7.0_72/GenomeAnalysisTK.jar -T BaseRecalibrator -I VN_TRIOS06F_trim_mergepe_align_mrdup_sortidx_realtar_indreal_1.bam -R reference//ucsc.hg19.fa -nct 8 -knownSites db/snp//Mills_and_1000G_gold_standard.indels.hg19.vcf.gz -knownSites db/snp//dbsnp_144_hg19.vcf.gz -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov ContextCovariate -L chrom_reg/chr_1.bed -o VN_TRIOS06F_trim_mergepe_align_mrdup_sortidx_realtar_indreal_baserecal_1.grp

and getting this error:

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

java.lang.ArrayIndexOutOfBoundsException: -30
at org.broadinstitute.gatk.utils.baq.BAQ.calcEpsilon(BAQ.java:185)
at org.broadinstitute.gatk.utils.baq.BAQ.hmm_glocal(BAQ.java:251)
at org.broadinstitute.gatk.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:553)
at org.broadinstitute.gatk.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:610)
at org.broadinstitute.gatk.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:536)
at org.broadinstitute.gatk.utils.baq.BAQ.baqRead(BAQ.java:680)
at org.broadinstitute.gatk.tools.walkers.bqsr.BaseRecalibrator.calculateBAQArray(BaseRecalibrator.java:493)
at org.broadinstitute.gatk.tools.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:263)
at org.broadinstitute.gatk.tools.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:136)
at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:228)
at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:216)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler$ReadMapReduceJob.run(NanoScheduler.java:471)
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.4-46-gbc02625):
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 ------------------------------------------------------------------------------------------

Can you tell me if there could be something in my input file or is something related with Java or GATK versions?

I tried both with java 1.7 an 1.8, getting the same.




  • SheilaSheila Broad InstituteMember, Broadie admin

    Hi Francesco,

    I suspect the error is from the use of -nct. Can you try running without -nct 8?
    Also, BaseRecalibrator needs a lot of data to build a proper model. You should really try to run on your entire dataset instead of per-chromosome. Have a look at this thread for more information.


    P.S. You can check out WDL for ways to speed up your pipeline without using -nt/-nct.

  • VergiliusVergilius ItalyMember

    I am now running it not per-chromosome and I solved.


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