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VariantRecalibrator Error

My task:

task VariantRecalibratorSNPs {

  File Raw_VCF
  String CohortName
  String Chromosome
  File? Parallelization
  String? InbreedingCoeff

  Map[String, String] Paths
  Array[String] RuntimeParams

  command {
    ${Paths["java"]} -Xmx4G -jar ${Paths["gatk"]} \
      -T VariantRecalibrator \
      -R ${Paths["refFasta"]} \
      -input ${Raw_VCF} \
      -recalFile ${CohortName}_${Chromosome}_SNPs.recal \
      -tranchesFile ${CohortName}_${Chromosome}_SNPs.tranches \
      -nt 4 \
      -L ${default=Chromosome Parallelization} \
      -resource:hapmap,known=false,training=true,truth=true,prior=15.0 ${Paths["hapmap"]} \
      -resource:omni,known=false,training=true,truth=true,prior=12.0 ${Paths["omni"]} \
      -resource:1000G,known=false,training=true,truth=false,prior=10.0 ${Paths["1000G"]} \
      -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 ${Paths["dbsnp"]} \
      -an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -an DP ${default="" InbreedingCoeff}\
      -mode SNP \
  }

  runtime {
    runtime_minutes: RuntimeParams[3]
    cpus: RuntimeParams[12]
    requested_memory_mb_per_core: RuntimeParams[21]
    queue: RuntimeParams[30]
  }

  output {
    File recal_SNPs_VCF = "${CohortName}_${Chromosome}_SNPs.recal"
    File tranches_SNPs_VCF = "${CohortName}_${Chromosome}_SNPs.tranches"
  }
}

GATK Error (full stderr attached):

##### 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:323)
        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:536)
        at org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:191)
        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 3.8-0-ge9d806836):
##### 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.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions https://software.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Unable to retrieve result
##### ERROR ------------------------------------------------------------------------------------------

Interesting to note, my VariantRecalibrator for Indels works just fine:

task VariantRecalibratorIndels {

  File Raw_VCF
  String CohortName
  String Chromosome
  File? Parallelization
  String? InbreedingCoeff

  Map[String, String] Paths
  Array[String] RuntimeParams

  command {
    ${Paths["java"]} -Xmx4G -jar ${Paths["gatk"]} \
      -T VariantRecalibrator \
      -R ${Paths["refFasta"]} \
      -input ${Raw_VCF} \
      -recalFile ${CohortName}_${Chromosome}_Indels.recal \
      -tranchesFile ${CohortName}_${Chromosome}_Indels.tranches \
      -nt 4 \
      -L ${default=Chromosome Parallelization} \
      --maxGaussians 4 \
      -resource:mills,known=false,training=true,truth=true,prior=12.0 ${Paths["mills"]} \
      -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 ${Paths["dbsnp"]} \
      -an QD -an DP -an FS -an SOR -an ReadPosRankSum -an MQRankSum ${default="" InbreedingCoeff} \
      -mode INDEL \
  }

  runtime {
    runtime_minutes: RuntimeParams[4]
    cpus: RuntimeParams[13]
    requested_memory_mb_per_core: RuntimeParams[22]
    queue: RuntimeParams[31]
  }

  output {
    File recal_Indels_VCF = "${CohortName}_${Chromosome}_Indels.recal"
    File tranches_Indels_VCF = "${CohortName}_${Chromosome}_Indels.tranches"
  }
}

I am running all the most recent versions. Attaching my entire script for reference.

Thanks a lot,

Alon

Best Answer

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