VQSR

Dear GATK Team,

I gave been having an issue to pass my vcf with VQSR for snps. For the indels i manage to get them out without any error. Please help. Attached is the commands and error printed.

Thank you.

[email protected]:~/10tb/Tools/GenomeAnalysisTK-3.4-0$ java -Xmx4g -jar GenomeAnalysisTK.jar -T VariantRecalibrator -R /home/dante/10tb/Reference/GATK\ Bundle/hg19/ucsc.hg19.fasta -input /home/dante/10tb/Malay\ Genome/MM/VariantCall_GATKpipeline/HaplotypeCaller/MM.marked.realigned.fixed.recaldata.bam.vcf -resource:hapmap,known=false,training=true,truth=true,prior=15.0 /home/dante/10tb/Reference/GATK\ Bundle/hg19/2.8/hapmap_3.3.hg19.vcf -resource:omni,known=false,training=true,truth=true,prior=12.0 /home/dante/10tb/Reference/GATK\ Bundle/hg19/2.8/1000G_omni2.5.hg19.vcf -resource:1000G,known=false,training=true,truth=false,prior=10.0 /home/dante/10tb/Reference/GATK\ Bundle/hg19/2.8/1000G_phase1.snps.high_confidence.hg19.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 /home/dante/10tb/Reference/GATK\ Bundle/hg19/2.8/dbsnp_138.hg19.vcf -an QD -an MQRankSum -an ReadPosRankSum -an FS -an DP -mode SNP -recalFile /home/dante/10tb/Malay\ Genome/MM/VariantCall_GATKpipeline/VQSR/MM_snp.recal -tranchesFile /home/dante/10tb/Malay\ Genome/MM/VariantCall_GATKpipeline/VQSR/MM_snp.tranches -rscriptFile /home/dante/10tb/Malay\ Genome/MM/VariantCall_GATKpipeline/VQSR/MM_snp.plots.R -rf BadCigar
INFO 11:33:54,257 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:33:54,259 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-0-g7e26428, Compiled 2015/05/15 03:25:41
INFO 11:33:54,260 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 11:33:54,260 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 11:33:54,264 HelpFormatter - Program Args: -T VariantRecalibrator -R /home/dante/10tb/Reference/GATK Bundle/hg19/ucsc.hg19.fasta -input /home/dante/10tb/Malay Genome/MM/VariantCall_GATKpipeline/HaplotypeCaller/MM.marked.realigned.fixed.recaldata.bam.vcf -resource:hapmap,known=false,training=true,truth=true,prior=15.0 /home/dante/10tb/Reference/GATK Bundle/hg19/2.8/hapmap_3.3.hg19.vcf -resource:omni,known=false,training=true,truth=true,prior=12.0 /home/dante/10tb/Reference/GATK Bundle/hg19/2.8/1000G_omni2.5.hg19.vcf -resource:1000G,known=false,training=true,truth=false,prior=10.0 /home/dante/10tb/Reference/GATK Bundle/hg19/2.8/1000G_phase1.snps.high_confidence.hg19.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 /home/dante/10tb/Reference/GATK Bundle/hg19/2.8/dbsnp_138.hg19.vcf -an QD -an MQRankSum -an ReadPosRankSum -an FS -an DP -mode SNP -recalFile /home/dante/10tb/Malay Genome/MM/VariantCall_GATKpipeline/VQSR/MM_snp.recal -tranchesFile /home/dante/10tb/Malay Genome/MM/VariantCall_GATKpipeline/VQSR/MM_snp.tranches -rscriptFile /home/dante/10tb/Malay Genome/MM/VariantCall_GATKpipeline/VQSR/MM_snp.plots.R -rf BadCigar
INFO 11:33:54,267 HelpFormatter - Executing as [email protected] on Linux 3.13.0-45-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_40-b25.
INFO 11:33:54,267 HelpFormatter - Date/Time: 2015/08/27 11:33:54
INFO 11:33:54,268 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:33:54,268 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:33:54,718 GenomeAnalysisEngine - Strictness is SILENT
INFO 11:33:54,827 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 11:33:55,283 GenomeAnalysisEngine - Preparing for traversal
INFO 11:33:55,288 GenomeAnalysisEngine - Done preparing for traversal
INFO 11:33:55,289 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 11:33:55,289 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 11:33:55,290 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 11:33:55,299 TrainingSet - Found hapmap track: Known = false Training = true Truth = true Prior = Q15.0
INFO 11:33:55,300 TrainingSet - Found omni track: Known = false Training = true Truth = true Prior = Q12.0
INFO 11:33:55,300 TrainingSet - Found 1000G track: Known = false Training = true Truth = false Prior = Q10.0
INFO 11:33:55,300 TrainingSet - Found dbsnp track: Known = true Training = false Truth = false Prior = Q2.0
INFO 11:34:25,294 ProgressMeter - chr1:109415312 2513217.0 30.0 s 11.0 s 3.5% 14.3 m 13.8 m
INFO 11:34:55,298 ProgressMeter - chr2:3300343 5361977.0 60.0 s 11.0 s 8.1% 12.4 m 11.4 m
INFO 11:35:25,300 ProgressMeter - chr2:126664368 8151082.0 90.0 s 11.0 s 12.0% 12.5 m 11.0 m
INFO 11:35:55,301 ProgressMeter - chr3:6713005 1.1031809E7 120.0 s 10.0 s 15.9% 12.6 m 10.6 m
INFO 11:36:25,303 ProgressMeter - chr3:130278427 1.3882153E7 2.5 m 10.0 s 19.9% 12.6 m 10.1 m
INFO 11:36:55,305 ProgressMeter - chr4:53897020 1.6781672E7 3.0 m 10.0 s 23.7% 12.6 m 9.6 m
INFO 11:37:25,306 ProgressMeter - chr4:176587497 1.9580094E7 3.5 m 10.0 s 27.6% 12.7 m 9.2 m
INFO 11:37:55,307 ProgressMeter - chr5:102845623 2.2296412E7 4.0 m 10.0 s 31.4% 12.7 m 8.7 m
INFO 11:38:25,309 ProgressMeter - chr6:38924168 2.5209149E7 4.5 m 10.0 s 35.1% 12.8 m 8.3 m
INFO 11:38:55,311 ProgressMeter - chr6:162095731 2.8021215E7 5.0 m 10.0 s 39.0% 12.8 m 7.8 m
INFO 11:39:25,313 ProgressMeter - chr7:109036260 3.0904998E7 5.5 m 10.0 s 42.8% 12.9 m 7.4 m
INFO 11:39:55,315 ProgressMeter - chr8:60419721 3.368605E7 6.0 m 10.0 s 46.3% 13.0 m 7.0 m
INFO 11:40:25,316 ProgressMeter - chr9:20019440 3.6239128E7 6.5 m 10.0 s 49.7% 13.1 m 6.6 m
INFO 11:40:55,317 ProgressMeter - chr10:17169179 3.9000671E7 7.0 m 10.0 s 54.1% 12.9 m 5.9 m
INFO 11:41:25,319 ProgressMeter - chr11:1849162 4.1774519E7 7.5 m 10.0 s 57.9% 12.9 m 5.4 m
INFO 11:41:55,327 ProgressMeter - chr11:114739034 4.4456797E7 8.0 m 10.0 s 61.5% 13.0 m 5.0 m
INFO 11:42:25,328 ProgressMeter - chr12:92482362 4.7092778E7 8.5 m 10.0 s 65.1% 13.0 m 4.5 m
INFO 11:42:55,330 ProgressMeter - chr13:81996057 4.9576292E7 9.0 m 10.0 s 69.1% 13.0 m 4.0 m
INFO 11:43:25,331 ProgressMeter - chr14:85213498 5.1953631E7 9.5 m 10.0 s 72.8% 13.0 m 3.5 m
INFO 11:43:55,333 ProgressMeter - chr15:100410655 5.4390963E7 10.0 m 11.0 s 76.7% 13.0 m 3.0 m
INFO 11:44:25,335 ProgressMeter - chr17:16738697 5.7097114E7 10.5 m 11.0 s 80.2% 13.1 m 2.6 m
INFO 11:44:55,358 ProgressMeter - chr18:54270830 5.978105E7 11.0 m 11.0 s 84.0% 13.1 m 2.1 m
INFO 11:45:28,194 ProgressMeter - chr20:20933017 6.2492852E7 11.5 m 11.0 s 87.3% 13.2 m 100.0 s
INFO 11:45:58,196 ProgressMeter - chr22:32726356 6.492353E7 12.0 m 11.0 s 91.2% 13.2 m 69.0 s
INFO 11:46:28,198 ProgressMeter - chrX:134488311 6.756555E7 12.5 m 11.0 s 96.1% 13.0 m 30.0 s
INFO 11:46:34,628 VariantDataManager - QD: mean = 21.40 standard deviation = 8.83
INFO 11:46:34,947 VariantDataManager - MQRankSum: mean = 0.05 standard deviation = 0.98
INFO 11:46:35,358 VariantDataManager - ReadPosRankSum: mean = 0.32 standard deviation = 1.00
INFO 11:46:35,806 VariantDataManager - FS: mean = 1.96 standard deviation = 3.48
INFO 11:46:36,083 VariantDataManager - DP: mean = 39.18 standard deviation = 8.61
INFO 11:46:38,644 VariantDataManager - Annotations are now ordered by their information content: [DP, QD, MQRankSum, FS, ReadPosRankSum]
INFO 11:46:38,770 VariantDataManager - Training with 3157019 variants after standard deviation thresholding.
WARN 11:46:38,770 VariantDataManager - WARNING: Very large training set detected. Downsampling to 2500000 training variants.
INFO 11:46:38,890 GaussianMixtureModel - Initializing model with 100 k-means iterations...
INFO 11:47:04,446 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 13.2 m 11.0 s 100.0% 13.2 m 0.0 s
INFO 11:47:34,448 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 13.7 m 12.0 s 100.0% 13.7 m 0.0 s
INFO 11:48:04,450 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 14.2 m 12.0 s 100.0% 14.2 m 0.0 s
INFO 11:48:34,454 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 14.7 m 12.0 s 100.0% 14.7 m 0.0 s
INFO 11:49:04,456 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 15.2 m 13.0 s 100.0% 15.2 m 0.0 s
INFO 11:49:34,457 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 15.7 m 13.0 s 100.0% 15.7 m 0.0 s
INFO 11:50:04,459 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 16.2 m 14.0 s 100.0% 16.2 m 0.0 s
INFO 11:50:30,596 VariantRecalibratorEngine - Finished iteration 0.
INFO 11:50:40,518 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 16.8 m 14.0 s 100.0% 16.8 m 0.0 s
INFO 11:51:10,520 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 17.3 m 15.0 s 100.0% 17.3 m 0.0 s
INFO 11:51:45,177 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 17.8 m 15.0 s 100.0% 17.8 m 0.0 s
INFO 11:52:12,532 VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.22326
INFO 11:52:15,179 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 18.3 m 16.0 s 100.0% 18.3 m 0.0 s
INFO 11:52:45,181 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 18.8 m 16.0 s 100.0% 18.8 m 0.0 s
INFO 11:53:15,182 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 19.3 m 17.0 s 100.0% 19.3 m 0.0 s
INFO 11:53:45,184 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 19.8 m 17.0 s 100.0% 19.8 m 0.0 s
INFO 11:53:50,173 VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.38245
INFO 11:54:15,185 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 20.3 m 17.0 s 100.0% 20.3 m 0.0 s
INFO 11:54:45,187 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 20.8 m 18.0 s 100.0% 20.8 m 0.0 s
INFO 11:55:15,189 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 21.3 m 18.0 s 100.0% 21.3 m 0.0 s
INFO 11:55:21,570 VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 1.25384
INFO 11:55:45,190 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 21.8 m 19.0 s 100.0% 21.8 m 0.0 s
INFO 11:56:15,192 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 22.3 m 19.0 s 100.0% 22.3 m 0.0 s
INFO 11:56:45,193 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 22.8 m 20.0 s 100.0% 22.8 m 0.0 s
INFO 11:57:00,954 VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 0.05420
INFO 11:57:15,195 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 23.3 m 20.0 s 100.0% 23.3 m 0.0 s
INFO 11:57:45,197 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 23.8 m 20.0 s 100.0% 23.8 m 0.0 s
INFO 11:58:15,200 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 24.3 m 21.0 s 100.0% 24.3 m 0.0 s
INFO 11:58:45,202 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 24.8 m 21.0 s 100.0% 24.8 m 0.0 s
INFO 11:58:48,759 VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.05460
INFO 11:59:15,400 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 25.3 m 22.0 s 100.0% 25.3 m 0.0 s
INFO 11:59:45,401 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 25.8 m 22.0 s 100.0% 25.8 m 0.0 s
INFO 12:00:15,402 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 26.3 m 23.0 s 100.0% 26.3 m 0.0 s
INFO 12:00:25,546 VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.07274
INFO 12:00:45,403 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 26.8 m 23.0 s 100.0% 26.8 m 0.0 s
INFO 12:01:15,404 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 27.3 m 24.0 s 100.0% 27.3 m 0.0 s
INFO 12:01:45,406 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 27.8 m 24.0 s 100.0% 27.8 m 0.0 s
INFO 12:02:03,373 VariantRecalibratorEngine - Finished iteration 35. Current change in mixture coefficients = 0.02559
INFO 12:02:15,407 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 28.3 m 24.0 s 100.0% 28.3 m 0.0 s
INFO 12:02:45,408 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 28.8 m 25.0 s 100.0% 28.8 m 0.0 s
INFO 12:03:16,398 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 29.4 m 25.0 s 100.0% 29.4 m 0.0 s
INFO 12:03:46,488 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 29.9 m 26.0 s 100.0% 29.9 m 0.0 s
INFO 12:03:48,133 VariantRecalibratorEngine - Finished iteration 40. Current change in mixture coefficients = 0.01108
INFO 12:04:16,490 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 30.4 m 26.0 s 100.0% 30.4 m 0.0 s
INFO 12:04:46,491 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 30.9 m 27.0 s 100.0% 30.9 m 0.0 s
INFO 12:05:16,492 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 31.4 m 27.0 s 100.0% 31.4 m 0.0 s
INFO 12:05:30,018 VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.00756
INFO 12:05:49,989 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 31.9 m 28.0 s 100.0% 31.9 m 0.0 s
INFO 12:06:20,269 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 32.4 m 28.0 s 100.0% 32.4 m 0.0 s
INFO 12:06:50,271 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 32.9 m 28.0 s 100.0% 32.9 m 0.0 s
INFO 12:07:02,783 VariantRecalibratorEngine - Finished iteration 50. Current change in mixture coefficients = 0.00584
INFO 12:07:20,391 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 33.4 m 29.0 s 100.0% 33.4 m 0.0 s
INFO 12:07:50,493 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 33.9 m 29.0 s 100.0% 33.9 m 0.0 s
INFO 12:08:20,494 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 34.4 m 30.0 s 100.0% 34.4 m 0.0 s
INFO 12:08:38,258 VariantRecalibratorEngine - Finished iteration 55. Current change in mixture coefficients = 0.00494
INFO 12:08:50,495 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 34.9 m 30.0 s 100.0% 34.9 m 0.0 s
INFO 12:09:20,496 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 35.4 m 31.0 s 100.0% 35.4 m 0.0 s
INFO 12:09:50,497 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 35.9 m 31.0 s 100.0% 35.9 m 0.0 s
INFO 12:10:15,456 VariantRecalibratorEngine - Finished iteration 60. Current change in mixture coefficients = 0.00447
INFO 12:10:20,498 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 36.4 m 32.0 s 100.0% 36.4 m 0.0 s
INFO 12:10:50,499 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 36.9 m 32.0 s 100.0% 36.9 m 0.0 s
INFO 12:11:21,291 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 37.4 m 32.0 s 100.0% 37.4 m 0.0 s
INFO 12:11:49,966 VariantRecalibratorEngine - Finished iteration 65. Current change in mixture coefficients = 0.00441
INFO 12:12:01,292 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 38.1 m 33.0 s 100.0% 38.1 m 0.0 s
INFO 12:12:31,293 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 38.6 m 33.0 s 100.0% 38.6 m 0.0 s
INFO 12:13:01,294 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 39.1 m 34.0 s 100.0% 39.1 m 0.0 s
INFO 12:13:30,140 VariantRecalibratorEngine - Finished iteration 70. Current change in mixture coefficients = 0.00489
INFO 12:13:31,295 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 39.6 m 34.0 s 100.0% 39.6 m 0.0 s
INFO 12:14:01,296 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 40.1 m 35.0 s 100.0% 40.1 m 0.0 s
INFO 12:14:31,297 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 40.6 m 35.0 s 100.0% 40.6 m 0.0 s
INFO 12:15:01,298 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 41.1 m 36.0 s 100.0% 41.1 m 0.0 s
INFO 12:15:01,806 VariantRecalibratorEngine - Finished iteration 75. Current change in mixture coefficients = 0.00648
INFO 12:15:31,299 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 41.6 m 36.0 s 100.0% 41.6 m 0.0 s
INFO 12:16:01,301 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 42.1 m 37.0 s 100.0% 42.1 m 0.0 s
INFO 12:16:31,302 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 42.6 m 37.0 s 100.0% 42.6 m 0.0 s
INFO 12:16:36,972 VariantRecalibratorEngine - Finished iteration 80. Current change in mixture coefficients = 0.01229
INFO 12:17:01,314 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 43.1 m 37.0 s 100.0% 43.1 m 0.0 s
INFO 12:17:31,315 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 43.6 m 38.0 s 100.0% 43.6 m 0.0 s
INFO 12:18:01,316 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 44.1 m 38.0 s 100.0% 44.1 m 0.0 s
INFO 12:18:17,707 VariantRecalibratorEngine - Finished iteration 85. Current change in mixture coefficients = 0.00686
INFO 12:18:31,318 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 44.6 m 39.0 s 100.0% 44.6 m 0.0 s
INFO 12:19:01,319 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 45.1 m 39.0 s 100.0% 45.1 m 0.0 s
INFO 12:19:31,920 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 45.6 m 40.0 s 100.0% 45.6 m 0.0 s
INFO 12:19:54,318 VariantRecalibratorEngine - Finished iteration 90. Current change in mixture coefficients = 0.00565
INFO 12:20:01,921 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 46.1 m 40.0 s 100.0% 46.1 m 0.0 s
INFO 12:20:31,922 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 46.6 m 40.0 s 100.0% 46.6 m 0.0 s
INFO 12:21:01,923 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 47.1 m 41.0 s 100.0% 47.1 m 0.0 s
INFO 12:21:31,924 ProgressMeter - chrUn_gl000249:14244 6.8227599E7 47.6 m 41.0 s 100.0% 47.6 m 0.0 s
INFO 12:21:38,505 VariantRecalibratorEngine - Finished iteration 95. Current change in mixture coefficients = 0.00181
INFO 12:21:38,506 VariantRecalibratorEngine - Convergence after 95 iterations!
INFO 12:21:48,726 VariantRecalibratorEngine - Evaluating full set of 4000470 variants...
INFO 12:21:48,795 VariantDataManager - Training with worst 0 scoring variants --> variants with LOD <= -5.0000.
INFO 12:21:56,083 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:88)
at org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:408)
at org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:156)
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:315)
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:106)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.4-0-g7e26428):
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 ------------------------------------------------------------------------------------------

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @roseismet
    Hi,

    Can you tell me what is in your input VCF file? How many samples are there, and are they whole genome or whole exome samples?

    Thanks,
    Sheila

  • roseismetroseismet Member

    Hi shiela, they are whole genome sample of an individual.

    Thank you.

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @roseismet
    Hi,

    Okay, I am not sure if this will work, but can you try using dbsnp_138.hg19.excluding_sites_after_129.vcf for the dbsnp file? I think the one you are using could be causing the issue because the VQSR model is based on the dbsnp version that does not include the 1000Genomes data. Please let me know if that works.

    Thanks,
    Sheila

  • tommycarstensentommycarstensen United KingdomMember ✭✭✭

    @roseismet said:
    INFO 12:21:48,726 VariantRecalibratorEngine - Evaluating full set of 4000470 variants...
    INFO 12:21:48,795 VariantDataManager - Training with worst 0 scoring variants --> variants with LOD <= -5.0000.

    @roseismet I suspect VQSR wasn't designed to be run on variants for a single sample. Despite having 4 million variants, it seems you are a bit short on data. Unfortunately I can't readily think of a solution for you :/

  • KurtKurt Member ✭✭✭

    @roseismet

    This looks/sounds like to me that it might be caused by an uninformative distribution of one the sequencing annotation features which is causing VQSR to crash. if your indel VQSR run went fine, then that makes it more likely imo. I see that you are not using MQ which is my most common culprit, but I have had an issue with MQRankSum in single whole genome SNV VQSR runs from time to time. Try taking out MQRankSum from your VariantRecalibrator command line and see if it works. If not, then you might try iteratively taking one annotation feature out and running the program.

  • Hi,

    I finally have the time to look back on this issue.Kurt's recommendation worked! MQRankSum was the culprit. It was abit weird as all my other samples analysed well even with MQRankSum.

    Thanks Shiela, Tommy & Kurt for all you help.

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