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VariantRecalibrator Stack Error

Hi,

I tried to run VariantRecalibrator for one WGS sample after HaplotyopeCaller. But I got stack trace error.

The commands I run is below.
java -Xmx4g -Djava.io.tmpdir=tmp -jar /home/serein/app/GenomeAnalysisTK-3.6-0/GenomeAnalysisTK.jar -T VariantRecalibrator -R /oasis/tscc/scratch/serein/genome/hg19/bwa/karyotic/hg19.fa -input A0004/vcf/A0004.raw_variants.vcf -resource:hapmap,known=false,training=true,truth=true,prior=15.0 /oasis/tscc/scratch/serein/resources/GATK_bundle/hg19/hapmap_3.3.hg19.vcf -resource:omni,known=false,training=true,truth=true,prior=12.0 /oasis/tscc/scratch/serein/resources/GATK_bundle/hg19/1000G_omni2.5.hg19.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 /oasis/tscc/scratch/serein/resources/GATK_bundle/hg19/dbsnp_138.hg19.vcf -resource:1000G,known=false,training=true,truth=false,prior=10.0 /oasis/tscc/scratch/serein/resources/GATK_bundle/hg19/1000G_phase1.snps.high_confidence.hg19.vcf -an DP -an QD -an MQ -an SOR -an FS -an MQRankSum -an ReadPosRankSum -mode SNP -tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 -recalFile A0004/vcf/A0004.recalibrate_SNP.recal -tranchesFile A0004/vcf/A0004.recalibrate_SNP.tranches -rscriptFile A0004/vcf/A0004.recalibrate_SNP_plots.R &>A0004/log/A0004.VariantRecalibrator_SNP.log

The error message is below.

INFO 09:15:39,047 VariantRecalibratorEngine - Finished iteration 35. Current change in mixture coefficients = 0.01403
INFO 09:16:17,661 ProgressMeter - chrY:59362044 6.8249266E7 43.1 m 37.0 s 100.0% 43.1 m 0.0 s
INFO 09:16:49,156 ProgressMeter - chrY:59362044 6.8249266E7 43.6 m 38.0 s 100.0% 43.6 m 0.0 s
INFO 09:17:12,991 VariantRecalibratorEngine - Convergence after 38 iterations!
INFO 09:17:19,157 ProgressMeter - chrY:59362044 6.8249266E7 44.1 m 38.0 s 100.0% 44.1 m 0.0 s
INFO 09:17:31,148 VariantRecalibratorEngine - Evaluating full set of 4580637 variants...
INFO 09:17:31,229 VariantDataManager - Training with worst 0 scoring variants --> variants with LOD <= -5.0000.

ERROR --
ERROR stack trace

java.lang.IllegalArgumentException: No data found.

I read some similar posts but cannot figure out how I should proceed.

Thanks,
Yunjiang

Answers

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