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Exception thrown while running VariantRecalibrator
The command I am running is
gatk VariantRecalibrator -R /home/nick/Exome/reference/ucsc.hg19.fasta -input GRC14335721.vcf -recalFile GRC14335721.recal -tranchesFile GRC14335721_recalibrate_SNP.tranches -resource:hapmap,known=false,training=true,truth=true,prior=15.0 /misc/exome/datasets/bundle/2.8/hg19/hapmap_3.3.hg19.sites.vcf -resource:omni,known=false,training=true,truth=true,prior=12.0 /misc/exome/datasets/bundle/2.8/hg19/1000G_omni2.5.hg19.sites.vcf -resource:1000G,known=false,training=true,truth=false,prior=10.0 /misc/exome/datasets/bundle/2.8/hg19/1000G_phase1.snps.high_confidence.hg19.sites.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 /misc/exome/datasets/bundle/2.8/hg19/dbsnp_138.hg19.vcf -an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -an DP -mode SNP -l debug &> ../log/variant-recalibrator.log
and the debug output is in the attached log (scroll to the end to see error message). I thought maybe the execution was OK, but the generated recal and tranches files are empty.