My command lines are as following:
java -Xmx8g -jar $CLASSPATH/GenomeAnalysisTK.jar \
-T VariantRecalibrator \
-R $GenomeReference \
-input $InputVCF \
-nt 6 \
-resource:mills,known=true,training=true,truth=true,prior=12.0 $resource1 \
-resource:dbsnp,known=true,training=false,truth=false,prior=2.0 $resource2 \
-an DP -an QD -an MQRankSum -an ReadPosRankSum -an FS -an MQ \
--maxGaussians 8 \
-mode INDEL \
-tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 \
-log $IndelsOutput/Indels.log \
-recalFile $IndelsOutput/exome.indels.vcf.recal \
-tranchesFile $IndelsOutput/exome.indels.tranches \
-rscriptFile $IndelsOutput/exome.indels.recal.plots.R
But I got the following error when running this:
##### 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:314)
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:107)
Caused by: java.lang.IllegalArgumentException: No data found.
at org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibratorEngine.generateModel(VariantRecalibratorEngine.java:83)
at org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:392)
at org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:138)
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 3.2-2-gec30cee):
So I am suspecting this is a bug with GATK 3.2.2 ?