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ArrayIndexOutOfBoundsException: -2 with BaseRecalibrator

hmviithmviit Member
edited February 2013 in Ask the GATK team

Hi,

I did search on the site and seems several have had a similar problem but I couldn't fix mine based on those. I've managed to get to this point succesfully with creating a realigned bam file with IndelRealigner. I'm using a non-model organism with self created masking list from a VCF run done before the realignment (list in bed format). I've had to use the -fixMisencodedQuals so far through out my runs. I checked the masking file so that the ranges do not go over the ranges that are specified in my list of regions to cover (-L option).

Is there anything else I would need to check still?

Command line view:

sulyba@hippu4:/fs/lustre/wrk/sulyba/stickleback_capture> java -jar ./GenomeAnalysisTK-2.3-9-ge5ebf34/GenomeAnalysisTK.jar -T BaseRecalibrator -R gasAcu_combinedbac_inv7.fa -I realigned_FF1_inv7c.bam -knownSites Sites_to_Mask.bed -L Capture_Target_Regions.intervals -o recalc_FF1_inv7c.grp -plots recal_FF1_plots.grp.pdf -fixMisencodedQuals

INFO  12:34:10,502 HelpFormatter - --------------------------------------------------------------------------------
INFO  12:34:10,510 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-9-ge5ebf34, Compiled 2013/01/11 22:43:14
INFO  12:34:10,510 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  12:34:10,510 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  12:34:10,516 HelpFormatter - Program Args: -T BaseRecalibrator -R gasAcu_combinedbac_inv7.fa -I realigned_FF1_inv7c.bam -knownSites Sites_to_Mask.bed -L Capture_Target_Regions.intervals -o recalc_FF1_inv7c.grp -plots recal_FF1_plots.grp.pdf -fixMisencodedQuals
INFO  12:34:10,516 HelpFormatter - Date/Time: 2013/02/01 12:34:10
INFO  12:34:10,517 HelpFormatter - --------------------------------------------------------------------------------
INFO  12:34:10,517 HelpFormatter - --------------------------------------------------------------------------------
INFO  12:34:10,551 ArgumentTypeDescriptor - Dynamically determined type of Sites_to_Mask.bed to be BED
INFO  12:34:10,563 GenomeAnalysisEngine - Strictness is SILENT
INFO  12:34:11,309 GenomeAnalysisEngine - Downsampling Settings: No downsampling
INFO  12:34:11,319 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO  12:34:11,392 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
INFO  12:34:11,416 RMDTrackBuilder - Loading Tribble index from disk for file Sites_to_Mask.bed
INFO  12:34:11,660 GenomeAnalysisEngine - Processing 20350670 bp from intervals
INFO  12:34:11,672 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO  12:34:11,674 ProgressMeter -        Location processed.reads  runtime per.1M.reads completed total.runtime remaining
INFO  12:34:11,946 BaseRecalibrator - The covariates being used here:
INFO  12:34:11,947 BaseRecalibrator -   ReadGroupCovariate
INFO  12:34:11,947 BaseRecalibrator -   QualityScoreCovariate
INFO  12:34:11,947 BaseRecalibrator -   ContextCovariate
INFO  12:34:11,947 ContextCovariate -           Context sizes: base substitution model 2, indel substitution model 3
INFO  12:34:11,947 BaseRecalibrator -   CycleCovariate
INFO  12:34:11,952 NestedIntegerArray - Creating NestedIntegerArray with dimensions [1, 3]
INFO  12:34:11,952 NestedIntegerArray - Pre-allocating first 2 dimensions
INFO  12:34:11,952 NestedIntegerArray - Done pre-allocating first 2 dimensions
INFO  12:34:11,953 NestedIntegerArray - Creating NestedIntegerArray with dimensions [1, 94, 3]
INFO  12:34:11,953 NestedIntegerArray - Pre-allocating first 2 dimensions
INFO  12:34:11,953 NestedIntegerArray - Done pre-allocating first 2 dimensions
INFO  12:34:11,953 NestedIntegerArray - Creating NestedIntegerArray with dimensions [1, 94, 1012, 3]
INFO  12:34:11,953 NestedIntegerArray - Pre-allocating first 2 dimensions
INFO  12:34:11,953 NestedIntegerArray - Done pre-allocating first 2 dimensions
INFO  12:34:11,953 NestedIntegerArray - Creating NestedIntegerArray with dimensions [1, 94, 1002, 3]
INFO  12:34:11,954 NestedIntegerArray - Pre-allocating first 2 dimensions
INFO  12:34:11,954 NestedIntegerArray - Done pre-allocating first 2 dimensions
INFO  12:34:12,109 ReadShardBalancer$1 - Loading BAM index data for next contig
INFO  12:34:12,120 ReadShardBalancer$1 - Done loading BAM index data for next contig
INFO  12:34:12,644 ReadShardBalancer$1 - Loading BAM index data for next contig
INFO  12:34:12,645 ReadShardBalancer$1 - Done loading BAM index data for next contig
INFO  12:34:14,901 GATKRunReport - Uploaded run statistics report to AWS S3
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
java.lang.ArrayIndexOutOfBoundsException: -2
        at org.broadinstitute.sting.utils.baq.BAQ.calcEpsilon(BAQ.java:158)
        at org.broadinstitute.sting.utils.baq.BAQ.hmm_glocal(BAQ.java:246)
        at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:542)
        at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:595)
        at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:530)
        at org.broadinstitute.sting.utils.baq.BAQ.baqRead(BAQ.java:663)
        at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.calculateBAQArray(BaseRecalibrator.java:428)
        at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:243)
        at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:112)
        at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:203)
        at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:191)
        at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:248)
        at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:219)
        at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:91)
        at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:55)
        at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83)
        at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:281)
        at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:237)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:147)
        at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 2.3-9-ge5ebf34):
##### 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: -2
##### ERROR ------------------------------------------------------------------------------------------
Post edited by Geraldine_VdAuwera on

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