VariantRecalibrator crashes
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I have ran VariantRecalibrator on a smaller VCF file (made with UnifiedGenotyper -L chr1) and it finished with no errors. Then I ran VCF file (made with UnifiedGenotyper without -L parameter) and it crashed but also without any error. The log file of the first successful run looks like this

... INFO 13:26:21,377 VariantRecalibrator - Building FS x DP plot... INFO 13:26:21,379 VariantRecalibratorEngine - Evaluating full set of 18354 variants... INFO 13:26:23,556 VariantRecalibratorEngine - Evaluating full set of 18354 variants... INFO 13:26:25,378 VariantRecalibrator - Building QD x DP plot... INFO 13:26:25,379 VariantRecalibratorEngine - Evaluating full set of 6384 variants... INFO 13:26:26,140 VariantRecalibratorEngine - Evaluating full set of 6384 variants... INFO 13:26:26,832 VariantRecalibrator - Executing: Rscript /cluster11/podlaha/AllelicImbalance/Data/GATK_VCF_Output/13_L_VariantRecalibrator/13_all_snp.plots.R INFO 13:26:28,400 ProgressMeter - chrY:59358202 5.66e+07 14.0 m 14.0 s 98.7% 14.2 m 11.0 s INFO 13:26:58,410 ProgressMeter - chrY:59358202 5.66e+07 14.5 m 15.0 s 98.7% 14.7 m 11.0 s INFO 13:27:28,420 ProgressMeter - chrY:59358202 5.66e+07 15.0 m 15.0 s 98.7% 15.2 m 12.0 s INFO 13:27:58,429 ProgressMeter - chrY:59358202 5.66e+07 15.5 m 16.0 s 98.7% 15.7 m 12.0 s INFO 13:28:28,439 ProgressMeter - chrY:59358202 5.66e+07 16.0 m 16.0 s 98.7% 16.2 m 12.0 s INFO 13:28:58,449 ProgressMeter - chrY:59358202 5.66e+07 16.5 m 17.0 s 98.7% 16.7 m 13.0 s INFO 13:29:28,460 ProgressMeter - chrY:59358202 5.66e+07 17.0 m 18.0 s 98.7% 17.2 m 13.0 s INFO 13:29:58,469 ProgressMeter - chrY:59358202 5.66e+07 17.5 m 18.0 s 98.7% 17.7 m 14.0 s INFO 13:30:28,479 ProgressMeter - chrY:59358202 5.66e+07 18.0 m 19.0 s 98.7% 18.2 m 14.0 s INFO 13:30:58,489 ProgressMeter - chrY:59358202 5.66e+07 18.5 m 19.0 s 98.7% 18.7 m 14.0 s INFO 13:31:28,155 VariantRecalibrator - Executing: Rscript (resource)org/broadinstitute/sting/gatk/walkers/variantrecalibration/plot_Tranches.R /cluster11/podlaha/AllelicImbalance/Data/GATK_VCF_Output/13_L_VariantRecalibrator/13_all_snp.tranches 2.15 INFO 13:31:28,499 ProgressMeter - chrY:59358202 5.66e+07 19.0 m 20.0 s 98.7% 19.3 m 15.0 s INFO 13:31:28,847 ProgressMeter - done 5.66e+07 19.0 m 20.0 s 98.7% 19.3 m 15.0 s INFO 13:31:28,847 ProgressMeter - Total runtime 1140.77 secs, 19.01 min, 0.32 hours I ...

The log file of the crashed run ENDS like this ... INFO 19:09:28,987 VariantRecalibrator - Building FS x QD plot... INFO 19:09:28,988 VariantRecalibratorEngine - Evaluating full set of 7300 variants... INFO 19:09:30,191 VariantRecalibratorEngine - Evaluating full set of 7300 variants... INFO 19:09:31,214 VariantRecalibrator - Building FS x DP plot... INFO 19:09:31,217 VariantRecalibratorEngine - Evaluating full set of 21170 variants... INFO 19:09:34,703 VariantRecalibratorEngine - Evaluating full set of 21170 variants... INFO 19:09:37,357 VariantRecalibrator - Building QD x DP plot... INFO 19:09:37,358 VariantRecalibratorEngine - Evaluating full set of 7250 variants... INFO 19:09:38,552 VariantRecalibratorEngine - Evaluating full set of 7250 variants... INFO 19:09:39,550 VariantRecalibrator - Executing: Rscript /cluster11/podlaha/AllelicImbalance/Data/GATK_VCF_Output/13_VariantRecalibrator/13_all_snp.plots.R INFO 19:09:51,101 ProgressMeter - chrY:59358159 5.68e+07 16.5 m 17.0 s 98.7% 16.7 m 13.0 s INFO 19:10:21,111 ProgressMeter - chrY:59358159 5.68e+07 17.0 m 17.0 s 98.7% 17.2 m 13.0 s INFO 19:10:51,119 ProgressMeter - chrY:59358159 5.68e+07 17.5 m 18.0 s 98.7% 17.7 m 14.0 s INFO 19:11:21,129 ProgressMeter - chrY:59358159 5.68e+07 18.0 m 19.0 s 98.7% 18.2 m 14.0 s INFO 19:11:51,139 ProgressMeter - chrY:59358159 5.68e+07 18.5 m 19.0 s 98.7% 18.7 m 14.0 s INFO 19:12:21,148 ProgressMeter - chrY:59358159 5.68e+07 19.0 m 20.0 s 98.7% 19.3 m 15.0 s INFO 19:12:51,157 ProgressMeter - chrY:59358159 5.68e+07 19.5 m 20.0 s 98.7% 19.8 m 15.0 s INFO 19:13:21,167 ProgressMeter - chrY:59358159 5.68e+07 20.0 m 21.0 s 98.7% 20.3 m 16.0 s INFO 19:13:51,176 ProgressMeter - chrY:59358159 5.68e+07 20.5 m 21.0 s 98.7% 20.8 m 16.0 s

I am suspecting that the execution of the tranches Rscript crashed it? Like I said, no error showed up when it crashed. Any suggestions how to make it work?

My command line: INFO 18:53:18,124 HelpFormatter - Program Args: -T VariantRecalibrator -R /cluster8/podlaha/HumanGenome/ucsc.hg19.fasta -mode SNP -input /cluster11/podlaha/AllelicImbalance/Data/GATK_VCF_Output/12_UnifiedGenotyper/12_UG_all.vcf -resource:hapmap,known=false,training=true,truth=true,prior=15.0 /cluster11/podlaha/Software/GATK/Resources/hapmap_3.3.hg19.vcf -resource:omni,known=false,training=true,truth=false,prior=12.0 /cluster11/podlaha/Software/GATK/Resources/1000G_omni2.5.hg19.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=6.0 /cluster11/podlaha/Software/GATK/Resources/dbsnp_137.hg19.vcf -resource:1000G,known=false,training=true,truth=false,prior=10.0 /cluster11/podlaha/Software/GATK/Resources/1000G_phase1.snps.high_confidence.hg19.vcf -an MQ -an MQ0 -an QD -an HaplotypeScore -an MQRankSum -an ReadPosRankSum -an FS -an DP -an BaseQRankSum -tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 -numBad 1000 --maxGaussians 4 -recalFile /cluster11/podlaha/AllelicImbalance/Data/GATK_VCF_Output/13_VariantRecalibrator/13_all_snp.recal -tranchesFile /cluster11/podlaha/AllelicImbalance/Data/GATK_VCF_Output/13_VariantRecalibrator/13_all_snp.tranches -rscriptFile /cluster11/podlaha/AllelicImbalance/Data/GATK_VCF_Output/13_VariantRecalibrator/13_all_snp.plots.R

Running GATK 2.7.4. and R version 3.0.2 (2013-09-25) -- "Frisbee Sailing" and java version "1.7.0_40"


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