Bug Bulletin: The GenomeLocPArser error in SplitNCigarReads has been fixed; if you encounter it, use the latest nightly build.

VariantRecalibrator - no data found

tgenahmettgenahmet Posts: 4Member

I just updated to the latest nightly and got the same error:

INFO 12:03:16,652 VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.00258 INFO 12:03:23,474 ProgressMeter - GL000202.1:10465 5.68e+07 32.4 m 34.0 s 98.7% 32.9 m 25.0 s INFO 12:03:32,263 VariantRecalibratorEngine - Convergence after 46 iterations! INFO 12:03:41,008 VariantRecalibratorEngine - Evaluating full set of 4944219 variants... INFO 12:03:41,100 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.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.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:116) 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)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version nightly-2014-03-20-g65934ae):
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: No data found.
ERROR ------------------------------------------------------------------------------------------

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