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)