Hi,
gatk VariantRecalibrator (v3.7) used to work on my WGS data (about 600 samples) . I've added 100 more samples (via .gvcf) to my data set and now I've got a No data found.
I'm just surprised that I get this message after adding more samples. How can I get this error when I'm 'just' adding more data to train.
(...)
INFO 09:35:00,234 VariantDataManager - QD: mean = 19.63 standard deviation = 4.90
INFO 09:35:00,336 VariantDataManager - FS: mean = 1.61 standard deviation = 3.23
INFO 09:35:00,421 VariantDataManager - SOR: mean = 0.73 standard deviation = 0.27
INFO 09:35:00,485 VariantDataManager - MQ: mean = 38.37 standard deviation = 19.78
INFO 09:35:00,549 VariantDataManager - MQRankSum: mean = 0.02 standard deviation = 0.40
INFO 09:35:00,612 VariantDataManager - ReadPosRankSum: mean = 0.32 standard deviation = 0.53
INFO 09:35:00,675 VariantDataManager - InbreedingCoeff: mean = 0.01 standard deviation = 0.07
INFO 09:35:01,391 VariantDataManager - Annotations are now ordered by their information content: [MQ, QD, FS, ReadPosRankSum, SOR, MQRankSum, InbreedingCoeff]
INFO 09:35:01,425 VariantDataManager - Training with 386960 variants after standard deviation thresholding.
INFO 09:35:01,429 GaussianMixtureModel - Initializing model with 100 k-means iterations...
INFO 09:35:15,123 ProgressMeter - chr18:78016669 2800393.0 8.5 m 3.0 m 99.9% 8.5 m 0.0 s
(...)
INFO 09:39:15,324 ProgressMeter - chr18:78016669 2800393.0 12.5 m 4.5 m 99.9% 12.5 m 0.0 s
INFO 09:39:17,150 VariantRecalibratorEngine - Finished iteration 125. Current change in mixture coefficients = 0.00239
INFO 09:39:22,734 VariantRecalibratorEngine - Convergence after 128 iterations!
INFO 09:39:23,872 VariantDataManager - Training with worst 0 scoring variants --> variants with LOD <= -5.0000.
##### ERROR --
##### ERROR stack trace
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.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:115)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:316)
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)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.7-0-gcfedb67):
##### 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: No data found.
##### ERROR ------------------------------------------------------------------------------------------
#executed by process 1 in 764.869s with status 0 : JETER/targets.bash 5
