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Error for Variant recalibrator on Targeted Sequecing data " Unable to retrieve result"

RduqueRduque Member Posts: 7

Hi,

I was running GATK version 2.1-13 and got always the following error when running the variant recalibrator.

java -jar GenomeAnalysisTK.jar -T VariantRecalibrator -R human_g1k_v37.fasta -an QD -an HaplotypeScore -an MQRankSum -an ReadPosRankSum -an FS -an MQ -nt 30 --maxGaussians 6 -mode SNP -log ISDB10654.snps.VarRecal.log -recalFile ISDB10654.snps.VarRecal.recal -tranchesFile ISDB10654.snps.VarRecal.tranches -rscriptFile ISDB10654.snps.VarRecal.plot.R -resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.b37.vcf -resource:omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.b37.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=8.0 dbsnp_135.b37.vcf -input ISDB10654.snps.raw.vcf

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 2.1-13-g1706365):
ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
ERROR Please do not post this error to the GATK forum
ERROR
ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: NaN LOD value assigned. Clustering with this few variants and these annotations is unsafe. Please consider raising the number of variants used to train the negative model (via --percentBadVariants 0.05, for example) or lowering the maximum number of Gaussians to use in the model (via --maxGaussians 4, for example)
ERROR ------------------------------------------------------------------------------------------

I executed it with the proposed suggestions but is still gave the same error.

Because i am not running the latest version of GATK i first installed and tried the it with the latest version of GATK and now i am getting this error:

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

org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Unable to retrieve result
at org.broadinstitute.sting.gatk.executive.HierarchicalMicroScheduler.execute(HierarchicalMicroScheduler.java:190)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:311)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)
Caused by: java.lang.IllegalArgumentException: log10p: Values must be non-infinite and non-NAN
at org.broadinstitute.sting.utils.MathUtils.log10sumLog10(MathUtils.java:236)
at org.broadinstitute.sting.utils.MathUtils.log10sumLog10(MathUtils.java:224)
at org.broadinstitute.sting.utils.MathUtils.log10sumLog10(MathUtils.java:249)
at org.broadinstitute.sting.gatk.walkers.variantrecalibration.GaussianMixtureModel.evaluateDatumMarginalized(GaussianMixtureModel.java:272)
at org.broadinstitute.sting.gatk.walkers.variantrecalibration.GaussianMixtureModel.evaluateDatum(GaussianMixtureModel.java:230)
at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorEngine.evaluateDatum(VariantRecalibratorEngine.java:167)
at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorEngine.evaluateData(VariantRecalibratorEngine.java:100)
at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:330)
at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:132)
at org.broadinstitute.sting.gatk.executive.HierarchicalMicroScheduler.notifyTraversalDone(HierarchicalMicroScheduler.java:226)
at org.broadinstitute.sting.gatk.executive.HierarchicalMicroScheduler.execute(HierarchicalMicroScheduler.java:183)
... 5 more

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.6-5-gba531bd):
ERROR
ERROR Please check the documentation guide to see if this is a known problem
ERROR If not, please post the error, 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
ERROR MESSAGE: Unable to retrieve result
ERROR ------------------------------------------------------------------------------------------

I do not really have an idea of what causes this error, do someone have some suggestions to help me?

Thanks,

Robin

Best Answer

Answers

  • RduqueRduque Member Posts: 7

    Thank you Geraldine.

  • RduqueRduque Member Posts: 7

    Lowering the threads gave me the same error as for the old version of GATK. So i lowered the --maxGaussians. From 4 to 2, at two it worked. I also put this argument --percentBadVariants 0.05 and didn't raise it.

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