ERROR stack trace ; Unable to retrieve result ; A GATK RUNTIME ERROR has occurred

Answers

• Geraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

  September 2013 Accepted Answer

  Hi there,

  The problem here is that you have a very small dataset. Specifically, setting -numBad 4000 if you only have 4000 SNPs pretty much guarantees that it will fail, because it's like saying all the variants are bad. You could try reducing -numBad, but I'm afraid that ultimately your dataset is just too small for VQSR. Either run on more variants (do you have an entire genome or just chr1? VQSR does not work well on isolated chromosomes) or use the hard-filtering recommendations instead of trying to run VQSR.

  We're going to try to improve the documentation on VQSR to make it clearer what the requirements are.

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• 55816815 TNMember ✭

  July 2016

  I am performing a VQSR with GATK 3.4 on whole genome VCF file and get the same error.

  INFO 11:02:35,585 VariantRecalibratorEngine - Evaluating full set of 4837109 variants...
  INFO 11:02:35,740 VariantDataManager - Training with worst 0 scoring variants --> variants with LOD <= -5.0000.
  INFO 11:02:41,872 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(HierarchicalMicroScheduler.java:190)
  at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:315)
  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:106)
  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:408)
  at org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:156)
  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 3.4-0-g7e26428):

  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 http://www.broadinstitute.org/gatk

  ERROR

  Any clue why whole genome also have "zero" bad variants?

  thanks,

  Shuoguo

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• Sheila Broad InstituteMember, Broadie ✭✭✭✭✭

  July 2016

  @55816815
  Hi Shuoguo,

  Can you post the exact command you ran? Are you running on indels or SNPs? It is possible to just not have enough overlap between your callset and the known variant datasets, even if you have a whole genome. This is especially true for indels.

  -Sheila

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• 55816815 TNMember ✭

  July 2016

  @Sheila I have 3 samples mapped with bwa-mem, two succeeded and this is the only one failed (tried three times so not random failure).
  quite strangely, the same 3 samples were done variant call the same exact way except using bwa-aln for mapping, and VQSR all success.

  exact command i used:

  >>> Performing snp recalibration
  java -Xms20g -Xmx20g -XX:ParallelGCThreads=4 -Djava.io.tmpdir=/scratch_space \
      -jar GenomeAnalysisTK.jar \
      -T VariantRecalibrator \
      -R GCA_000001405.15_GRCh38_no_alt_analysis_set.fna \
      -nt 4 \
      -resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg38.vcf.gz \
      -resource:omni,known=false,training=true,truth=true,prior=12.0 1000G_omni2.5.hg38.vcf.gz \
      -resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.high_confidence.hg38.vcf.gz \
      -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 Homo_sapiens_assembly38.variantEvalGoldStandard.vcf.gz \
      -an QD -an DP -an FS -an  SOR -an MQ \
      -an MQRankSum -an ReadPosRankSum \
      -tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 \
      -mode SNP -input 040771_G1.mdup.vcf.gz \
      -recalFile 040771_G1.mdup.snp.recal \
      -tranchesFile 040771_G1.mdup.snp.tranches \
      -rscriptFile 040771_G1.mdup.snp.plots.R \
      -log 040771_G1.mdup.snp.recal.log 
  

  thanks!

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• Sheila Broad InstituteMember, Broadie ✭✭✭✭✭

  July 2016

  @55816815
  Hi,

  Okay. Can you try running without -nt 4. Users have reported random issues with multi-threading. Also, why are you running on each sample by itself? If you are trying to analyze the three samples together, it is best to perform joint variant calling and genotyping. https://www.broadinstitute.org/gatk/documentation/article?id=4150

  -Sheila

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• 55816815 TNMember ✭

  July 2016

  @Sheila Thanks. Will remove -nt. Yes I can try joint call as well.

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• 55816815 TNMember ✭

  July 2016

  @Sheila Removing "-nt 4" resolved the issue! Great!

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