Variant Recalibration Error

analyst123analyst123 Boston, MAMember

Hi
I am using getting error at variant recalibration step, I have a single sample WGS variant called with UnifiedGenotyper.
The step goes fine with SNP but in indels it is giving the error. Any suggestions are welcome.
Thanks

INFO 09:46:25,830 HelpFormatter - Program Args: -T VariantRecalibrator -R hs37d5.fa -input rawINDELs.vcf -nt 8 -resource:mills,known=true,training=true,truth=true,prior=12.0 Mills_and_1000G_gold_standard.indels.b37.vcf -an DP -an FS -an ReadPosRankSum -mode INDEL -tranchesFile rawINDELs.tranches -recalFile rawINDELs.recal -rscriptFile TSNanoExt_rawINDELs.R
INFO 09:46:25,835 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.7.0_75-b13.
INFO 09:46:25,836 HelpFormatter - Date/Time: 2016/03/16 09:46:25
INFO 09:46:25,836 HelpFormatter - --------------------------------------------------------------------------------
INFO 09:46:25,836 HelpFormatter - --------------------------------------------------------------------------------
INFO 09:46:26,850 GenomeAnalysisEngine - Strictness is SILENT
INFO 09:46:27,580 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 09:46:27,820 MicroScheduler - Running the GATK in parallel mode with 8 total threads, 1 CPU thread(s) for each of 8 data thread(s), of 16 processors available on this machine
INFO 09:46:28,012 GenomeAnalysisEngine - Preparing for traversal
INFO 09:46:28,027 GenomeAnalysisEngine - Done preparing for traversal
INFO 09:46:28,027 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 09:46:28,027 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 09:46:28,028 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 09:46:28,071 TrainingSet - Found mills track: Known = true Training = true Truth = true Prior = Q12.0
INFO 09:46:51,202 VariantDataManager - DP: mean = 28.91 standard deviation = 8.35
INFO 09:46:51,243 VariantDataManager - FS: mean = 1.73 standard deviation = 3.18
INFO 09:46:51,267 VariantDataManager - ReadPosRankSum: mean = 0.14 standard deviation = 1.04
INFO 09:46:51,419 VariantDataManager - Annotations are now ordered by their information content: [DP, FS, ReadPosRankSum]
INFO 09:46:51,443 VariantDataManager - Training with 176902 variants after standard deviation thresholding.
INFO 09:46:51,447 GaussianMixtureModel - Initializing model with 100 k-means iterations...
INFO 09:46:58,031 ProgressMeter - Y:59002805 3894973.0 30.0 s 7.0 s 98.7% 30.0 s 0.0 s
INFO 09:47:04,295 VariantRecalibratorEngine - Finished iteration 0.
INFO 09:47:08,579 VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.26750
INFO 09:47:12,627 VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.40692
INFO 09:47:16,716 VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 0.08926
INFO 09:47:20,816 VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 0.09034
INFO 09:47:24,884 VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.17357
INFO 09:47:28,032 ProgressMeter - Y:59002805 3894973.0 60.0 s 15.0 s 98.7% 60.0 s 0.0 s
INFO 09:47:28,932 VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.74162
INFO 09:47:33,113 VariantRecalibratorEngine - Finished iteration 35. Current change in mixture coefficients = 0.01455
INFO 09:47:37,544 VariantRecalibratorEngine - Finished iteration 40. Current change in mixture coefficients = 0.01201
INFO 09:47:43,763 VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.00935
INFO 09:47:50,260 VariantRecalibratorEngine - Finished iteration 50. Current change in mixture coefficients = 0.00703
INFO 09:47:55,527 VariantRecalibratorEngine - Finished iteration 55. Current change in mixture coefficients = 0.00521
INFO 09:47:58,034 ProgressMeter - Y:59002805 3894973.0 90.0 s 23.0 s 98.7% 91.0 s 1.0 s
INFO 09:47:59,143 VariantRecalibratorEngine - Finished iteration 60. Current change in mixture coefficients = 0.00384
INFO 09:48:02,753 VariantRecalibratorEngine - Finished iteration 65. Current change in mixture coefficients = 0.00282
INFO 09:48:06,359 VariantRecalibratorEngine - Finished iteration 70. Current change in mixture coefficients = 0.00207
INFO 09:48:07,081 VariantRecalibratorEngine - Convergence after 71 iterations!
INFO 09:48:07,499 VariantRecalibratorEngine - Evaluating full set of 319181 variants...
INFO 09:48:07,515 VariantDataManager - Training with worst 0 scoring variants --> variants with LOD <= -5.0000.
INFO 09:48:09,354 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:314)
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:107)
Caused by: java.lang.IllegalArgumentException: No data found.
at org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibratorEngine.generateModel(VariantRecalibratorEngine.java:83)
at org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:392)
at org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:138)
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 3.2-2-gec30cee):
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
ERROR MESSAGE: Unable to retrieve result
ERROR ------------------------------------------------------------------------------------------

Best Answer

Answers

  • analyst123analyst123 Boston, MAMember

    UPDATE:

    following a discussion on GATK thread, I tried leaving "-an DP" argument out and it worked.
    I am not sure what would be the consequences and if it impacts any further analysis. ANy clarification you can provide will be great.

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