Hi, we are getting the following runtime error while processing a SNPs only Whole Exome VCF file with four samples and approx 90,000 variants. Searching the forum we found other people had reported the same issue with earlier versions of GATK (3.2.2 or higher) and in most of those cases it was due to too low number of variants in VCF or MQ values are out of range (60 or higher). We checked and our MQ values are within range. If you need, we can upload the VCF file used as input to reproduce this error.
Command Line -
Program Args: -R human_g1k_v37_decoy.fasta -T VariantRecalibrator -nt 4 -mG 4 -mNG 1 --minNumBadVariants 0 -input 734869496_SNPs.vcf -resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.high_confidence.b37.vcf -resource:omni,known=false,training=true,truth=true,prior=12.0 1000G_omni2.5.b37.vcf -resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.b37.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_149.hg19.vcf -an QD -an FS -an DP -an MQRankSum -tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 -mode SNP -recalFile 734869496_snps_vqsr.recal -tranchesFile 734869496_snps_tranches.csv -rscriptFile 734869496_snps_recal.R --read_filter OverclippedRead
ERROR -
ERROR stack trace
org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: Unable to retrieve result
at org.broadinstitute.gatk.engine.executive.HierarchicalMicroScheduler.execute(HierarchicalMicroScheduler.java:190)
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)
Caused by: 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:489)
at org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:185)
at org.broadinstitute.gatk.engine.executive.HierarchicalMicroScheduler.notifyTraversalDone(HierarchicalMicroScheduler.java:226)
at org.broadinstitute.gatk.engine.executive.HierarchicalMicroScheduler.execute(HierarchicalMicroScheduler.java:183)
... 5 more
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.
Thanks and Best
Sowmi