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error while calling snps for ion s5 samples

KritikaKritika IndiaMember

I am running GATK for snp analysis on my Ion S5 Samples
I am currently using reference file hg19 which i downloaded from gatk resource bundle

I am getting this error
any help is highly appreciable
INFO 11:37:24,559 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
INFO 11:37:24,907 GenomeAnalysisEngine - Done preparing for traversal
INFO 11:37:24,908 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 11:37:24,909 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 11:37:24,911 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 11:37:25,012 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
WARN 11:37:25,012 InbreedingCoeff - Annotation will not be calculated. InbreedingCoeff requires at least 10 unrelated samples.
INFO 11:37:25,014 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
INFO 11:37:54,935 ProgressMeter - Starting 0.0 30.0 s 49.6 w 100.0% 30.0 s 0.0 s
INFO 11:38:24,958 ProgressMeter - Starting 0.0 60.0 s 99.3 w 100.0% 60.0 s 0.0 s
INFO 11:38:54,959 ProgressMeter - Starting 0.0 90.0 s 148.9 w 100.0% 90.0 s 0.0 s
INFO 11:39:24,959 ProgressMeter - Starting 0.0 120.0 s 198.5 w 100.0% 120.0 s 0.0 s
INFO 11:39:54,961 ProgressMeter - Starting 0.0 2.5 m 248.1 w 100.0% 2.5 m 0.0 s
INFO 11:40:24,962 ProgressMeter - Starting 0.0 3.0 m 297.7 w 100.0% 3.0 m 0.0 s
INFO 11:40:54,963 ProgressMeter - Starting 0.0 3.5 m 347.3 w 100.0% 3.5 m 0.0 s
INFO 11:41:24,964 ProgressMeter - Starting 0.0 4.0 m 396.9 w 100.0% 4.0 m 0.0 s
INFO 11:41:54,965 ProgressMeter - Starting 0.0 4.5 m 446.5 w 100.0% 4.5 m 0.0 s
INFO 11:42:24,966 ProgressMeter - Starting 0.0 5.0 m 496.1 w 100.0% 5.0 m 0.0 s
ERROR stack trace
java.lang.ArrayIndexOutOfBoundsException: 200
at org.broadinstitute.gatk.utils.contexts.ReferenceContext.getBase(ReferenceContext.java:179)
at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.getFilteredAndStratifiedContexts(UnifiedGenotypingEngine.java:482)
at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateLikelihoodsAndGenotypes(UnifiedGenotypingEngine.java:218)
at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:375)
at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:147)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:98)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:316)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.7-0-gcfedb67):
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 https://software.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: 200

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