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GATK runtime error in VariantRecalibrator

apolyakapolyak State College, PA, USAMember

I'm sorry I keep posting these questions, but this error has me baffled!

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:319)
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:88)
at org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:399)
at org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:143)
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 3.3-0-g37228af):
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 MESSAGE: Unable to retrieve result
ERROR ------------------------------------------------------------------------------------------

Here is the input I use to get it:

java -d64 -Xmx8g -jar $GATKDIR/GenomeAnalysisTK.jar \
-T VariantRecalibrator \
-input k_family_out.vcf \
-R $REF \
-resource:hapmap,VCF,known=false,training=true,truth=true,prior=15.0 $HAPMAP \
-resource:omni,VCF,known=false,training=true,truth=false,prior=12.0 $OMNI \
-resource:dbsnp,VCF,known=true,training=false,truth=false,prior=8.0 $DBSNP \
-resource:mills,VCF,known=true,training=true,truth=true,prior=12.0 $MILLS \
-an QD -an MQ -an MQRankSum -an ReadPosRankSum \
-mode BOTH \
-U ALL \
-recalFile k_family.recal \
-tranchesFile k_family.tranches \
-rscriptFile k_family.R \
-nt 6 --TStranche 100.0 --TStranche 99.9 --TStranche 99.5 --TStranche 99.0 \
--TStranche 98.0 --TStranche 97.0 --TStranche 96.0 --TStranche 95.0 --TStranche 94.0 \
--TStranche 93.0 --TStranche 92.0 --TStranche 91.0 --TStranche 90.0

I thought this was similar to a multithreading error, so I reduced my pipeline to execute with only a single node, and the problem persists.

Any help will be appreciated.

Best Answer


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