VariantRecalibrator error

nansnans Member
edited December 2016 in Ask the GATK team

Hello,
I am running the Variant Recalibrator command and running run into this error. is this because of multi threading or a different issue ?

Many thanks,

INFO 15:36:38,675 HelpFormatter - -------------------------------------------------------------------------------------------
INFO 15:36:38,678 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.6-0-g89b7209, Compiled 2016/06/01 22:27:29
INFO 15:36:38,678 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 15:36:38,678 HelpFormatter - For support and documentation go to https://www.broadinstitute.org/gatk
INFO 15:36:38,678 HelpFormatter - [Tue Dec 13 15:36:38 GMT 2016] Executing on Linux 2.6.32-642.11.1.el6.Bull.106.x86_64 amd64
INFO 15:36:38,678 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_45-b14 JdkDeflater
INFO 15:36:38,682 HelpFormatter - Program Args: -T VariantRecalibrator -R /reference_data/g1k.fasta -input input.vcf --maxGaussians 4 -resource:mills,known=false,training=true,truth=true,prior=12.0 /reference_data/Mills_and_1000G_gold_standard.indels.b37.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 /reference_data/dbsnp_137.b37.vcf -an QD -an DP -an FS -an SOR -an ReadPosRankSum -an MQRankSum -an InbreedingCoeff -mode INDEL -nt 6 -tranche 100.0 -tranche 99.95 -tranche 99.9 -tranche 99.5 -tranche 99.0 -tranche 97.0 -tranche 96.0 -tranche 95.0 -tranche 94.0 -tranche 93.5 -tranche 93.0 -tranche 92.0 -tranche 91.0 -tranche 90.0 -recalFile /recalFiles/recalibrate_INDELS.recal -tranchesFile /recalFiles/recalibrate_INDELS.tranches
INFO 15:36:38,686 HelpFormatter - Executing as user1@hpc1 on Linux 2.6.32-642.11.1.el6.Bull.106.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_45-b14.
INFO 15:36:38,687 HelpFormatter - Date/Time: 2016/12/13 15:36:38
INFO 15:36:38,687 HelpFormatter - -------------------------------------------------------------------------------------------
INFO 15:36:38,687 HelpFormatter - -------------------------------------------------------------------------------------------
INFO 15:36:38,757 GenomeAnalysisEngine - Strictness is SILENT
INFO 15:36:38,861 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 15:36:39,405 MicroScheduler - Running the GATK in parallel mode with 6 total threads, 1 CPU thread(s) for each of 6 data thread(s), of 16 processors available on this machine
INFO 15:36:39,470 GenomeAnalysisEngine - Preparing for traversal
INFO 15:36:39,476 GenomeAnalysisEngine - Done preparing for traversal
INFO 15:36:39,476 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 15:36:39,477 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 15:36:39,477 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 15:36:39,481 TrainingSet - Found mills track: Known = false Training = true Truth = true Prior = Q12.0
INFO 15:36:39,481 TrainingSet - Found dbsnp track: Known = true Training = false Truth = false Prior = Q2.0
INFO 15:37:09,480 ProgressMeter - 6:72046160 2.1724971E7 30.0 s 1.0 s 36.6% 82.0 s 52.0 s
INFO 15:37:39,481 ProgressMeter - 15:100996386 4.5712917E7 60.0 s 1.0 s 77.6% 77.0 s 17.0 s
INFO 15:37:53,861 VariantDataManager - QD: mean = 18.93 standard deviation = 8.02
INFO 15:37:53,868 VariantDataManager - DP: mean = 2706.47 standard deviation = 1807.03
INFO 15:37:53,873 VariantDataManager - FS: mean = 3.67 standard deviation = 12.11
INFO 15:37:53,879 VariantDataManager - SOR: mean = 1.02 standard deviation = 0.90
INFO 15:37:53,884 VariantDataManager - ReadPosRankSum: mean = -0.03 standard deviation = 0.71
INFO 15:37:53,887 VariantDataManager - MQRankSum: mean = 0.21 standard deviation = 0.89
INFO 15:37:53,890 VariantDataManager - InbreedingCoeff: mean = -0.04 standard deviation = 0.27
INFO 15:37:53,916 VariantDataManager - Annotations are now ordered by their information content: [DP, QD, FS, MQRankSum, SOR, InbreedingCoeff, ReadPosRankSum]
INFO 15:37:53,918 VariantDataManager - Training with 3407 variants after standard deviation thresholding.
INFO 15:37:53,922 GaussianMixtureModel - Initializing model with 100 k-means iterations...
INFO 15:37:54,078 VariantRecalibratorEngine - Finished iteration 0.
INFO 15:37:54,164 VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.39916
INFO 15:37:54,213 VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.19187
INFO 15:37:54,260 VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 0.03694
INFO 15:37:54,304 VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 0.03467
INFO 15:37:54,348 VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.08800
INFO 15:37:54,392 VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.02064
INFO 15:37:54,436 VariantRecalibratorEngine - Finished iteration 35. Current change in mixture coefficients = 0.00774
INFO 15:37:54,479 VariantRecalibratorEngine - Finished iteration 40. Current change in mixture coefficients = 0.00360
INFO 15:37:54,523 VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.00219
INFO 15:37:54,540 VariantRecalibratorEngine - Convergence after 47 iterations!
INFO 15:37:54,558 VariantRecalibratorEngine - Evaluating full set of 14247 variants...
INFO 15:37:54,736 VariantDataManager - Training with worst 0 scoring variants --> variants with LOD <= -5.0000.

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:311)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:255)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:157)
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:489)
at org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:185)
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 3.6-0-g89b7209):
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://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Unable to retrieve result
ERROR ------------------------------------------------------------------------------------------

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