Stack trace error while running VQSR

I'm trying to run VQSR on a vcf I just called with HaplotypeCaller. Here is my command:

java -Xmx32g -jar /Commands/GATK/GenomeAnalysisTK.jar \
-T VariantRecalibrator \
-R /Reference/ucsc.hg19.fasta \
-input H3H5.HTC.raw.vcf \
-resource:hapmap,known=false,training=true,truth=true,prior=15.0 /Reference/hapmap3.3.hg19.vcf \
-resource:omni,known=false,training=true,truth=false,prior=12.0 /Reference/1000G.omni2.5.hg19.vcf \
-resource:1000G,known=false,training=true,truth=false,prior=10.0 /Reference/1000G.ph1.SNP.HC.hg19.vcf \
-resource:dbsnp,known=true,training=true,truth=false,prior=6.0 /Reference/dbsnp138.hg19.vcf \
-an QD -an MQRankSum -an ReadPosRankSum -an FS \
-mode SNP \
-tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 \
-recalFile VQSR/H3H5.SNP.VQSR \
-tranchesFile VQSR/H3H5.SNP.Tranches \
-rscriptFile VQSR/H3H5.SNP.VQSR.R \
-nt 16

Each time I try to run VQSR it gives me this error:

INFO 12:23:34,122 VariantRecalibratorEngine - Finished iteration 95. Current change in mixture coefficients = 0.00198
INFO 12:23:34,122 VariantRecalibratorEngine - Convergence after 95 iterations!
INFO 12:23:34,461 VariantRecalibratorEngine - Evaluating full set of 251205 variants...
INFO 12:23:34,476 VariantDataManager - Training with worst 0 scoring variants --> variants with LOD <= -5.0000.
INFO 12:23:39,194 GATKRunReport - Uploaded run statistics report to AWS S3

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

org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: Unable to retrieve result
at org.broadinstitute.gatk.engine.executive.HierarchicalMicroScheduler.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(
Caused by: java.lang.IllegalArgumentException: No data found.
at org.broadinstitute.gatk.engine.executive.HierarchicalMicroScheduler.notifyTraversalDone(
at org.broadinstitute.gatk.engine.executive.HierarchicalMicroScheduler.execute(
... 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
ERROR MESSAGE: Unable to retrieve result
ERROR ------------------------------------------------------------------------------------------

In the discussion of similar errors, I've seen that too little data and MQ annotation can cause similar problems, but I didn't use either of them.

I'm going to guess that it is something simple, but any help would be appreciated.



Best Answer


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