Question on VariantRecalibrator INDEL model

I run the VariantRecalibrator according to the GATK document but somehow encounter with the following error. And there is limited information to debug. May I ask for some help. Thanks very much.

java -jar GATK/GenomeAnalysisTK.jar -T VariantRecalibrator -R /home/hufeng/Research/WESEBV/b37/human_g1k_v37_decoy.fasta -input /home/hufeng/Research/WESEBV/Data/VCF/CAEBV1raw.vcf -resource:mills,known=false,training=true,truth=true,prior=12.0 /home/hufeng/Research/WESEBV/b37/Mills_and_1000G_gold_standard.indels.b37.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 /home/hufeng/Research/WESEBV/b37/dbsnp_138.b37.vcf -an DP -an QD -an FS -an MQRankSum -an ReadPosRankSum -mode INDEL -recalFile /home/hufeng/Research/WESEBV/Data/VCF/CAEBV1rawindelvcf.recal -tranchesFile /home/hufeng/Research/WESEBV/Data/VCF/CAEBV1rawindelvcf.tranches -rscriptFile /home/hufeng/Research/WESEBV/Data/Plots/CAEBV1rawindelrecal.plots.r

INFO 17:34:43,127 HelpFormatter - --------------------------------------------------------------------------------
INFO 17:34:43,129 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03
INFO 17:34:43,129 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 17:34:43,129 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 17:34:43,134 HelpFormatter - Program Args: -T VariantRecalibrator -R /home/hufeng/Research/WESEBV/b37/human_g1k_v37_decoy.fasta -input /home/hufeng/Research/WESEBV/Data/VCF/CAEBV1raw.vcf -resource:mills,known=false,training=true,truth=true,prior=12.0 /home/hufeng/Research/WESEBV/b37/Mills_and_1000G_gold_standard.indels.b37.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 /home/hufeng/Research/WESEBV/b37/dbsnp_138.b37.vcf -an DP -an QD -an FS -an MQRankSum -an ReadPosRankSum -mode INDEL -recalFile /home/hufeng/Research/WESEBV/Data/VCF/CAEBV1rawindelvcf.recal -tranchesFile /home/hufeng/Research/WESEBV/Data/VCF/CAEBV1rawindelvcf.tranches -rscriptFile /home/hufeng/Research/WESEBV/Data/Plots/CAEBV1rawindelrecal.plots.r
INFO 17:34:43,137 HelpFormatter - Executing as [email protected] on Linux 3.13.0-43-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_72-b14.
INFO 17:34:43,137 HelpFormatter - Date/Time: 2015/01/07 17:34:43
INFO 17:34:43,137 HelpFormatter - --------------------------------------------------------------------------------
INFO 17:34:43,138 HelpFormatter - --------------------------------------------------------------------------------
INFO 17:34:43,672 GenomeAnalysisEngine - Strictness is SILENT
INFO 17:34:43,784 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 17:34:44,090 GenomeAnalysisEngine - Preparing for traversal
INFO 17:34:44,110 GenomeAnalysisEngine - Done preparing for traversal
INFO 17:34:44,110 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 17:34:44,111 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 17:34:44,111 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 17:34:44,116 TrainingSet - Found mills track: Known = false Training = true Truth = true Prior = Q12.0
INFO 17:34:44,117 TrainingSet - Found dbsnp track: Known = true Training = false Truth = false Prior = Q2.0
INFO 17:35:14,115 ProgressMeter - 1:221431916 4600141.0 30.0 s 6.0 s 7.1% 7.1 m 6.6 m
INFO 17:35:44,116 ProgressMeter - 2:188027873 9620887.0 60.0 s 6.0 s 13.9% 7.2 m 6.2 m
INFO 17:36:14,117 ProgressMeter - 3:156995703 1.455409E7 90.0 s 6.0 s 20.7% 7.2 m 5.7 m
INFO 17:36:44,119 ProgressMeter - 4:176340129 1.9695731E7 120.0 s 6.0 s 27.6% 7.2 m 5.2 m
INFO 17:37:14,120 ProgressMeter - 6:21396661 2.4873576E7 2.5 m 6.0 s 34.5% 7.2 m 4.7 m
INFO 17:37:44,121 ProgressMeter - 7:41915101 2.9533675E7 3.0 m 6.0 s 40.7% 7.4 m 4.4 m
INFO 17:38:14,122 ProgressMeter - 8:85887473 3.4434441E7 3.5 m 6.0 s 47.1% 7.4 m 3.9 m
INFO 17:38:44,123 ProgressMeter - 10:22468459 3.9343993E7 4.0 m 6.0 s 54.3% 7.4 m 3.4 m
INFO 17:39:14,125 ProgressMeter - 11:91563736 4.4168871E7 4.5 m 6.0 s 60.8% 7.4 m 2.9 m
INFO 17:39:44,126 ProgressMeter - 13:54194818 4.9246617E7 5.0 m 6.0 s 68.2% 7.3 m 2.3 m
INFO 17:40:14,127 ProgressMeter - 15:87498966 5.4364863E7 5.5 m 6.0 s 76.3% 7.2 m 102.0 s
INFO 17:40:44,128 ProgressMeter - 18:28948071 5.9537768E7 6.0 m 6.0 s 83.2% 7.2 m 72.0 s
INFO 17:41:24,129 ProgressMeter - X:44799155 6.6515745E7 6.7 m 6.0 s 93.3% 7.1 m 28.0 s
INFO 17:41:35,424 VariantDataManager - DP: mean = 37.89 standard deviation = 43.69
INFO 17:41:35,432 VariantDataManager - QD: mean = 18.91 standard deviation = 9.95
INFO 17:41:35,436 VariantDataManager - FS: mean = 0.61 standard deviation = 2.36
INFO 17:41:35,440 VariantDataManager - MQRankSum: mean = -0.30 standard deviation = 1.55
INFO 17:41:35,450 VariantDataManager - ReadPosRankSum: mean = -0.09 standard deviation = 1.08
INFO 17:41:35,505 VariantDataManager - Annotations are now ordered by their information content: [DP, QD, FS, MQRankSum, ReadPosRankSum]
INFO 17:41:35,508 VariantDataManager - Training with 8352 variants after standard deviation thresholding.
INFO 17:41:35,513 GaussianMixtureModel - Initializing model with 100 k-means iterations...
INFO 17:41:35,979 VariantRecalibratorEngine - Finished iteration 0.
INFO 17:41:36,201 VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.52554
INFO 17:41:36,361 VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 7.55004
INFO 17:41:36,527 VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 0.21921
INFO 17:41:36,707 VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 0.90779
INFO 17:41:36,887 VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.01133
INFO 17:41:37,064 VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.00924
INFO 17:41:37,242 VariantRecalibratorEngine - Finished iteration 35. Current change in mixture coefficients = 0.00805
INFO 17:41:37,410 VariantRecalibratorEngine - Finished iteration 40. Current change in mixture coefficients = 0.00708
INFO 17:41:37,594 VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.00625
INFO 17:41:37,773 VariantRecalibratorEngine - Finished iteration 50. Current change in mixture coefficients = 0.00552
INFO 17:41:37,941 VariantRecalibratorEngine - Finished iteration 55. Current change in mixture coefficients = 0.00488
INFO 17:41:38,107 VariantRecalibratorEngine - Finished iteration 60. Current change in mixture coefficients = 0.00429
INFO 17:41:38,284 VariantRecalibratorEngine - Finished iteration 65. Current change in mixture coefficients = 0.00373
INFO 17:41:38,464 VariantRecalibratorEngine - Finished iteration 70. Current change in mixture coefficients = 0.00320
INFO 17:41:38,642 VariantRecalibratorEngine - Finished iteration 75. Current change in mixture coefficients = 0.00270
INFO 17:41:38,819 VariantRecalibratorEngine - Finished iteration 80. Current change in mixture coefficients = 0.00232
INFO 17:41:38,996 VariantRecalibratorEngine - Finished iteration 85. Current change in mixture coefficients = 0.00206
INFO 17:41:39,068 VariantRecalibratorEngine - Convergence after 87 iterations!
INFO 17:41:39,124 VariantRecalibratorEngine - Evaluating full set of 15499 variants...
INFO 17:41:39,128 VariantDataManager - Training with worst 0 scoring variants --> variants with LOD <= -5.0000.
INFO 17:41:40,401 GATKRunReport - Uploaded run statistics report to AWS S3

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

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.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:116)
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)

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: No data found.
ERROR ------------------------------------------------------------------------------------------

[email protected]:~/Programs$

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