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

Dear support team,

I used GATK VariantRecalibrator and had the following error.

Command I used:

java -jar GenomeAnalysisTK.jar -T VariantRecalibrator -R hs37d5.fa -input raw.vcf -resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.b37.vcf -resource:omni,known=false,training=true,truth=true,prior=12.0 1000G_omni2.5.b37.vcf -resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.high_confidence.b37.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.b37.vcf -an DP -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 23:01:41,585 VariantRecalibratorEngine - Convergence after 73 iterations!
INFO 23:01:52,388 VariantRecalibratorEngine - Evaluating full set of 4681872 variants...
INFO 23:01:52,442 VariantDataManager - Training with worst 0 scoring variants --> variants with LOD <= -5.0000.
INFO 23:01:55,685 GATKRunReport - Uploaded run statistics report to AWS S3

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

java.lang.IllegalArgumentException: No data found.
at org.broadinstitute.gatk.engine.executive.Accumulator$StandardAccumulator.finishTraversal(
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(
at org.broadinstitute.gatk.engine.CommandLineGATK.main(

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
ERROR MESSAGE: No data found.
ERROR ------------------------------------------------------------------------------------------

Best Answer


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