VariantRecalibrator Error; No Data Found

Hi, I'm trying to run VariantRecalibrator on my vcf files. I have followed most of the pipeline - using HaplotypeCaller before this step. I am working with file of specific extracted genes from a whole genome sequence of a tumor sample - and am trying to run VariantRecalibrator on SNP mode.

Here is the error message:
INFO 15:14:35,232 HelpFormatter - --------------------------------------------------------------------------------
INFO 15:14:35,235 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.7-0-gcfedb67, Compiled 2016/12/12 11:21:18
INFO 15:14:35,235 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 15:14:35,235 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
INFO 15:14:35,236 HelpFormatter - [Tue Jul 24 15:14:35 BST 2018] Executing on Linux 3.10.0-693.el7.x86_64 amd64
INFO 15:14:35,236 HelpFormatter - OpenJDK 64-Bit Server VM 1.8.0_131-b12
INFO 15:14:35,238 HelpFormatter - Program Args: -T VariantRecalibrator -R resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta -input extracted.genotyped.vcf -resource:hapmap,known=false,training=true,truth=true,prior=15.0 resources_broad_hg38_v0_hapmap_3.3.hg38.vcf -resource:omni,known=false,training=true,truth=true,prior=12.0 resources_broad_hg38_v0_1000G_omni2.5.hg38.vcf -resource:1000G,known=false,training=true,truth=false,prior=10.0 resources_broad_hg38_v0_1000G_phase1.snps.high_confidence.hg38.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=.20 resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf -an FS -an SOR -an MQ -an MQRankSum -an ReadPosRankSum -an QD -mode SNP -recalFile extracted.output.recal -tranchesFile extracted.output.tranches -rscriptFile output.genotyped.plots.R
INFO 15:14:35,286 HelpFormatter - Executing as [email protected] on Linux 3.10.0-693.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_131-b12.
INFO 15:14:35,286 HelpFormatter - Date/Time: 2018/07/24 15:14:35
INFO 15:14:35,286 HelpFormatter - --------------------------------------------------------------------------------
INFO 15:14:35,286 HelpFormatter - --------------------------------------------------------------------------------
INFO 15:14:35,314 GenomeAnalysisEngine - Strictness is SILENT
INFO 15:14:36,339 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 15:14:38,780 GenomeAnalysisEngine - Preparing for traversal
INFO 15:14:38,787 GenomeAnalysisEngine - Done preparing for traversal
INFO 15:14:38,787 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 15:14:38,787 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 15:14:38,787 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 15:14:38,794 TrainingSet - Found hapmap track: Known = false Training = true Truth = true Prior = Q15.0
INFO 15:14:38,794 TrainingSet - Found omni track: Known = false Training = true Truth = true Prior = Q12.0
INFO 15:14:38,794 TrainingSet - Found 1000G track: Known = false Training = true Truth = false Prior = Q10.0
INFO 15:14:38,795 TrainingSet - Found dbsnp track: Known = true Training = false Truth = false Prior = Q0.2
INFO 15:15:08,790 ProgressMeter - chr1:158866731 3040060.0 30.0 s 9.0 s 4.9% 10.1 m 9.6 m
INFO 15:15:38,790 ProgressMeter - chr2:32996905 5958581.0 60.0 s 10.0 s 8.8% 11.4 m 10.4 m
INFO 15:16:08,791 ProgressMeter - chr2:164765745 8934105.0 90.0 s 10.0 s 12.9% 11.7 m 10.2 m
INFO 15:16:38,792 ProgressMeter - chr3:45607274 1.1837802E7 120.0 s 10.0 s 16.7% 12.0 m 10.0 m
INFO 15:17:08,793 ProgressMeter - chr3:173995509 1.4702158E7 2.5 m 10.0 s 20.7% 12.1 m 9.6 m
INFO 15:17:48,794 ProgressMeter - chr4:146994206 1.8753018E7 3.2 m 10.0 s 26.0% 12.2 m 9.0 m
INFO 15:18:18,795 ProgressMeter - chr5:84721074 2.1717071E7 3.7 m 10.0 s 30.0% 12.2 m 8.6 m
INFO 15:18:48,795 ProgressMeter - chr6:29998321 2.4723551E7 4.2 m 10.0 s 33.9% 12.3 m 8.1 m
INFO 15:19:18,796 ProgressMeter - chr6:158998294 2.770885E7 4.7 m 10.0 s 37.9% 12.3 m 7.6 m
INFO 15:19:48,797 ProgressMeter - chr7:117998677 3.0823038E7 5.2 m 10.0 s 42.0% 12.3 m 7.1 m
INFO 15:20:28,798 ProgressMeter - chr8:121277023 3.4763574E7 5.8 m 10.0 s 47.0% 12.4 m 6.6 m
INFO 15:20:58,799 ProgressMeter - chr9:116352967 3.7647625E7 6.3 m 10.0 s 51.4% 12.3 m 6.0 m
INFO 15:21:28,799 ProgressMeter - chr10:95120082 4.04697E7 6.8 m 10.0 s 55.0% 12.4 m 5.6 m
INFO 15:21:58,800 ProgressMeter - chr11:80387285 4.3313383E7 7.3 m 10.0 s 58.7% 12.5 m 5.2 m
INFO 15:22:28,806 ProgressMeter - chr12:61686300 4.6067319E7 7.8 m 10.0 s 62.3% 12.6 m 4.7 m
INFO 15:22:58,807 ProgressMeter - chr13:71168017 4.8988535E7 8.3 m 10.0 s 66.8% 12.5 m 4.1 m
INFO 15:23:38,808 ProgressMeter - chr15:60998995 5.3047905E7 9.0 m 10.0 s 73.3% 12.3 m 3.3 m
INFO 15:24:08,810 ProgressMeter - chr16:88819894 5.6127061E7 9.5 m 10.0 s 77.4% 12.3 m 2.8 m
INFO 15:24:48,811 ProgressMeter - chr19:14848081 6.0360246E7 10.2 m 10.0 s 83.0% 12.3 m 2.1 m
INFO 15:25:18,812 ProgressMeter - chr21:30210373 6.3574404E7 10.7 m 10.0 s 87.3% 12.2 m 93.0 s
INFO 15:25:48,812 ProgressMeter - chrX:113562949 6.6694362E7 11.2 m 10.0 s 92.9% 12.0 m 51.0 s
INFO 15:25:56,610 VariantDataManager - FS: mean = 0.00 standard deviation = 0.13
INFO 15:25:56,666 VariantDataManager - SOR: mean = 1.47 standard deviation = 0.73
INFO 15:25:56,710 VariantDataManager - MQ: mean = 59.74 standard deviation = 1.69
INFO 15:25:56,759 VariantDataManager - MQRankSum: mean = -0.00 standard deviation = 0.51
INFO 15:25:56,857 VariantDataManager - ReadPosRankSum: mean = 0.21 standard deviation = 0.88
INFO 15:25:56,936 VariantDataManager - QD: mean = 30.70 standard deviation = 3.26
INFO 15:25:57,191 VariantDataManager - Annotations are now ordered by their information content: [MQ, QD, FS, SOR, MQRankSum, ReadPosRankSum]
INFO 15:25:57,216 VariantDataManager - Training with 543153 variants after standard deviation thresholding.
INFO 15:25:57,219 GaussianMixtureModel - Initializing model with 100 k-means iterations...
INFO 15:26:14,865 VariantRecalibratorEngine - Finished iteration 0.
INFO 15:26:18,813 ProgressMeter - chrUn_JTFH01001976v1_decoy:1087 6.7557875E7 11.7 m 10.0 s 99.9% 11.7 m 0.0 s
INFO 15:26:24,537 VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 1.81969
INFO 15:26:33,560 VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.50173
INFO 15:26:42,845 VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 2.36851
INFO 15:26:48,815 ProgressMeter - chrUn_JTFH01001976v1_decoy:1087 6.7557875E7 12.2 m 10.0 s 99.9% 12.2 m 0.0 s
INFO 15:26:53,744 VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 0.07550
INFO 15:27:04,513 VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.06077
INFO 15:27:15,536 VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.02782
INFO 15:27:18,816 ProgressMeter - chrUn_JTFH01001976v1_decoy:1087 6.7557875E7 12.7 m 11.0 s 99.9% 12.7 m 0.0 s
INFO 15:27:26,437 VariantRecalibratorEngine - Finished iteration 35. Current change in mixture coefficients = 0.02561
INFO 15:27:37,924 VariantRecalibratorEngine - Finished iteration 40. Current change in mixture coefficients = 0.02931
INFO 15:27:48,817 ProgressMeter - chrUn_JTFH01001976v1_decoy:1087 6.7557875E7 13.2 m 11.0 s 99.9% 13.2 m 0.0 s
INFO 15:27:49,460 VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.03923
INFO 15:28:00,461 VariantRecalibratorEngine - Finished iteration 50. Current change in mixture coefficients = 0.04987
INFO 15:28:11,614 VariantRecalibratorEngine - Finished iteration 55. Current change in mixture coefficients = 0.08558
INFO 15:28:18,818 ProgressMeter - chrUn_JTFH01001976v1_decoy:1087 6.7557875E7 13.7 m 12.0 s 99.9% 13.7 m 0.0 s
INFO 15:28:22,738 VariantRecalibratorEngine - Finished iteration 60. Current change in mixture coefficients = 0.11308
INFO 15:28:33,851 VariantRecalibratorEngine - Finished iteration 65. Current change in mixture coefficients = 0.03488
INFO 15:28:44,767 VariantRecalibratorEngine - Finished iteration 70. Current change in mixture coefficients = 0.00368
INFO 15:28:48,819 ProgressMeter - chrUn_JTFH01001976v1_decoy:1087 6.7557875E7 14.2 m 12.0 s 99.9% 14.2 m 0.0 s
INFO 15:28:49,297 VariantRecalibratorEngine - Convergence after 72 iterations!
INFO 15:28:50,143 VariantRecalibratorEngine - Evaluating full set of 618296 variants...
INFO 15:28:50,163 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.

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