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GATK Runtime Error occured while running VQSR

Hello everyone!

While trying to build SNP recalibration model using GATK, I have encountered following runtime error, Please help in resolving this issue,

$ java -jar GenomeAnalysisTK.jar -T VariantRecalibrator -R Reference/breast_chr13_17.fa -input raw_variants.vcf -resource:hapmap,known=false,training=true,truth=true,prior=15.0 Reference/hapmap_3.3.hg19.vcf -resource:omni,known=false,training=true,truth=true,prior=12.0 Reference/1000G_omni2.5.hg19.vcf -resource:1000G,known=false,training=true,truth=false,prior=10.0 Reference/1000G_phase1.snps.high_confidence.hg19.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 Reference/dbsnp_138.hg19.vcf -an QD -an FS -an SOR -an MQ -an MQRankSum -an ReadPosRankSum -mode SNP -tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 -recalFile recalibrate_SNP.recal -tranchesFile recalibrate_SNP.tranches -rscriptFile recalibrate_SNP_plots.R

INFO 21:31:26,112 ProgressMeter - chr17:81189249 4210099.0 8.5 m 2.0 m 99.0% 8.6 m 5.0 s
INFO 21:31:29,622 GATKRunReport - Uploaded run statistics report to AWS S3

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

java.lang.IllegalArgumentException: No data found.
at org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibratorEngine.generateModel(VariantRecalibratorEngine.java:88)
at org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:409)
at org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:157)
at org.broadinstitute.gatk.engine.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:116)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:315)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:106)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.5-0-g36282e4):
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: No data found.
ERROR ------------------------------------------------------------------------------------------******

Answers

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