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Runtime Error in VariantRecalibrator for Germline Indels

daveliudaveliu Cambridge, MAMember, Broadie


Apologies if this is an inappropriate place to ask the question. I am doing germline haplotype calling on human normal (non-tumor) WES in preparation for allelic capseg, and ran into a runtime error in Variant Recalibrator for Germline Indels. I'm not sure whether it's a configuration issue, data issue, or something else -- any pointers appreciated! Note: I've tried rerunning the prior steps in the pipeline and rerunning this task multiple times (if there was a temporary communication error that would resolve with time).

Relevant (I believe) portions from stderr.txt (also attached in full):

INFO 15:46:55,009 VariantDataManager - Training with 2539 variants after standard deviation thresholding.
INFO 15:46:55,016 GaussianMixtureModel - Initializing model with 100 k-means iterations...
INFO 15:46:55,338 VariantRecalibratorEngine - Finished iteration 0.
INFO 15:46:55,479 VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.19718
INFO 15:46:55,533 VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.02991
INFO 15:46:55,568 VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 0.00455
INFO 15:46:55,592 VariantRecalibratorEngine - Convergence after 19 iterations!
INFO 15:46:55,642 VariantDataManager - Training with worst 0 scoring variants --> variants with LOD <= -5.0000.
INFO 15:47:00,062 GATKRunReport - Uploaded run statistics report to AWS S3

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:313)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:107)
Caused by: java.lang.IllegalArgumentException: No data found.
at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorEngine.generateModel(VariantRecalibratorEngine.java:83)
at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:392)
at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:138)
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 3.1-1-g07a4bf8):
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 ------------------------------------------------------------------------------------------


Best Answer


  • daveliudaveliu Cambridge, MAMember, Broadie

    Edit: After looking through the forum, I found that the problem is possibly that I have insufficient indels. Though these are WES human samples, I do have 54 of them, so I would be surprised that this is the problem...

  • daveliudaveliu Cambridge, MAMember, Broadie

    Thanks! That actually fixed the problem.

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