INFO 11:30:54,972 HelpFormatter - --------------------------------------------------------------------------------------------- INFO 11:30:54,981 HelpFormatter - The Genome Analysis Toolkit (GATK) vnightly-2014-03-20-g65934ae, Compiled 2014/03/20 00:01:13 INFO 11:30:54,982 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 11:30:54,982 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 11:30:54,986 HelpFormatter - Program Args: -R /home/tgenref/pipeline_v0.4/bwa7/hs37d5.fa -T VariantRecalibrator -input /scratch/akurdoglu/pecanPipe/projects/GhanaTNBC_0010_KAWGL_ps201403111445//ug/GhanaTNBC_0010_1_SA_Whole_C1_KAWGL_J00022-GhanaTNBC_0010_1_BE_Whole_T2_KAWGL_J00023/GhanaTNBC_0010_1_SA_Whole_C1_KAWGL_J00022-GhanaTNBC_0010_1_BE_Whole_T2_KAWGL_J00023.UG.vcf -resource:hapmap,known=false,training=true,truth=true,prior=15.0 /home/tgenref/pipeline_v0.3/gatk_bundle_2.5/b37/hapmap_3.3.b37.vcf -resource:omni,known=false,training=true,truth=false,prior=12.0 /home/tgenref/pipeline_v0.3/gatk_bundle_2.5/b37/1000G_omni2.5.b37.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=6.0 /home/tgenref/pipeline_v0.3/gatk_bundle_2.5/b37/dbsnp_137.b37.vcf --mode BOTH -an QD -an HaplotypeScore -an MQRankSum -an ReadPosRankSum -an MQ -recalFile /scratch/akurdoglu/pecanPipe/projects/GhanaTNBC_0010_KAWGL_ps201403111445//ug/GhanaTNBC_0010_1_SA_Whole_C1_KAWGL_J00022-GhanaTNBC_0010_1_BE_Whole_T2_KAWGL_J00023/GhanaTNBC_0010_1_SA_Whole_C1_KAWGL_J00022-GhanaTNBC_0010_1_BE_Whole_T2_KAWGL_J00023.UG.vcf.recal -tranchesFile /scratch/akurdoglu/pecanPipe/projects/GhanaTNBC_0010_KAWGL_ps201403111445//ug/GhanaTNBC_0010_1_SA_Whole_C1_KAWGL_J00022-GhanaTNBC_0010_1_BE_Whole_T2_KAWGL_J00023/GhanaTNBC_0010_1_SA_Whole_C1_KAWGL_J00022-GhanaTNBC_0010_1_BE_Whole_T2_KAWGL_J00023.UG.vcf.tranches -rscriptFile /scratch/akurdoglu/pecanPipe/projects/GhanaTNBC_0010_KAWGL_ps201403111445//ug/GhanaTNBC_0010_1_SA_Whole_C1_KAWGL_J00022-GhanaTNBC_0010_1_BE_Whole_T2_KAWGL_J00023/GhanaTNBC_0010_1_SA_Whole_C1_KAWGL_J00022-GhanaTNBC_0010_1_BE_Whole_T2_KAWGL_J00023.UG.vcf.plots.R INFO 11:30:54,990 HelpFormatter - Executing as akurdoglu@pnap-pe5-s32 on Linux 2.6.32-220.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_03-b04. INFO 11:30:54,991 HelpFormatter - Date/Time: 2014/03/20 11:30:54 INFO 11:30:54,991 HelpFormatter - --------------------------------------------------------------------------------------------- INFO 11:30:54,991 HelpFormatter - --------------------------------------------------------------------------------------------- INFO 11:30:56,419 GenomeAnalysisEngine - Strictness is SILENT INFO 11:30:56,577 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 INFO 11:30:57,315 GenomeAnalysisEngine - Preparing for traversal INFO 11:30:57,341 GenomeAnalysisEngine - Done preparing for traversal INFO 11:30:57,341 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 11:30:57,342 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining WARN 11:30:57,356 Utils - ******************************************************************************** WARN 11:30:57,357 Utils - * WARNING: WARN 11:30:57,357 Utils - * WARN 11:30:57,358 Utils - * Rscript not found in environment path. WARN 11:30:57,358 Utils - * /scratch/akurdoglu/pecanPipe/projects/GhanaTNBC_0010_KAWGL_ps201403111 WARN 11:30:57,359 Utils - * 45/ug/GhanaTNBC_0010_1_SA_Whole_C1_KAWGL_J00022-GhanaTNBC_0010_1_BE_Wh WARN 11:30:57,360 Utils - * le_T2_KAWGL_J00023/GhanaTNBC_0010_1_SA_Whole_C1_KAWGL_J00022-GhanaTNBC WARN 11:30:57,360 Utils - * 0010_1_BE_Whole_T2_KAWGL_J00023.UG.vcf.plots.R will be generated but WARN 11:30:57,361 Utils - * PDF plots will not. WARN 11:30:57,361 Utils - ******************************************************************************** INFO 11:30:57,366 TrainingSet - Found hapmap track: Known = false Training = true Truth = true Prior = Q15.0 INFO 11:30:57,367 TrainingSet - Found omni track: Known = false Training = true Truth = false Prior = Q12.0 INFO 11:30:57,367 TrainingSet - Found dbsnp track: Known = true Training = false Truth = false Prior = Q6.0 INFO 11:31:27,347 ProgressMeter - 1:202106478 3.41e+06 30.0 s 8.0 s 6.4% 7.8 m 7.3 m INFO 11:31:59,125 ProgressMeter - 2:142229150 7.13e+06 61.0 s 8.0 s 12.5% 8.1 m 7.1 m INFO 11:32:33,679 ProgressMeter - 3:87365255 1.08e+07 96.0 s 8.0 s 18.5% 8.7 m 7.1 m INFO 11:33:03,680 ProgressMeter - 4:29919071 1.35e+07 2.1 m 9.0 s 23.0% 9.1 m 7.0 m INFO 11:33:34,756 ProgressMeter - 5:12823431 1.70e+07 2.6 m 9.0 s 28.5% 9.2 m 6.6 m INFO 11:34:07,988 ProgressMeter - 5:132673130 1.92e+07 3.2 m 9.0 s 32.3% 9.8 m 6.6 m INFO 11:34:40,762 ProgressMeter - 6:62485574 2.15e+07 3.7 m 10.0 s 35.9% 10.4 m 6.6 m INFO 11:35:13,433 ProgressMeter - 6:126986054 2.27e+07 4.3 m 11.0 s 37.9% 11.3 m 7.0 m INFO 11:35:48,728 ProgressMeter - 7:15305019 2.41e+07 4.9 m 12.0 s 39.8% 12.2 m 7.3 m INFO 11:36:19,143 ProgressMeter - 7:64985173 2.50e+07 5.4 m 12.0 s 41.4% 12.9 m 7.6 m INFO 11:36:51,218 ProgressMeter - 7:125247863 2.61e+07 5.9 m 13.0 s 43.3% 13.6 m 7.7 m INFO 11:37:21,488 ProgressMeter - 8:10423426 2.72e+07 6.4 m 14.0 s 44.7% 14.3 m 7.9 m INFO 11:37:59,278 ProgressMeter - 8:96997818 2.89e+07 7.0 m 14.0 s 47.5% 14.8 m 7.8 m INFO 11:38:33,152 ProgressMeter - 9:35999258 3.07e+07 7.6 m 14.0 s 50.2% 15.1 m 7.5 m INFO 11:39:06,425 ProgressMeter - 9:123393765 3.18e+07 8.2 m 15.0 s 53.0% 15.4 m 7.2 m INFO 11:39:40,067 ProgressMeter - 10:109343310 3.44e+07 8.7 m 15.0 s 57.0% 15.3 m 6.6 m INFO 11:40:11,753 ProgressMeter - 11:54802328 3.60e+07 9.2 m 15.0 s 59.6% 15.5 m 6.3 m INFO 11:40:50,813 ProgressMeter - 11:118168077 3.73e+07 9.9 m 15.0 s 61.6% 16.0 m 6.1 m INFO 11:41:23,515 ProgressMeter - 12:29991328 3.82e+07 10.4 m 16.0 s 63.1% 16.5 m 6.1 m INFO 11:42:06,264 ProgressMeter - 12:99222183 3.95e+07 11.1 m 16.0 s 65.3% 17.0 m 5.9 m INFO 11:42:37,056 ProgressMeter - 13:45248031 4.08e+07 11.7 m 17.0 s 67.9% 17.2 m 5.5 m INFO 11:43:12,661 ProgressMeter - 13:97860782 4.18e+07 12.3 m 17.0 s 69.6% 17.6 m 5.4 m INFO 11:43:47,413 ProgressMeter - 14:85480204 4.35e+07 12.8 m 17.0 s 72.8% 17.6 m 4.8 m INFO 11:44:23,898 ProgressMeter - 15:93248538 4.53e+07 13.4 m 17.0 s 76.5% 17.6 m 4.1 m INFO 11:44:54,477 ProgressMeter - 16:62205809 4.66e+07 14.0 m 17.0 s 78.8% 17.7 m 3.8 m INFO 11:45:24,478 ProgressMeter - 17:79215019 4.89e+07 14.5 m 17.0 s 82.2% 17.6 m 3.1 m INFO 11:45:56,790 ProgressMeter - 19:9287935 5.07e+07 15.0 m 17.0 s 85.1% 17.6 m 2.6 m INFO 11:46:27,003 ProgressMeter - 21:47612484 5.38e+07 15.5 m 17.0 s 90.2% 17.2 m 101.0 s INFO 11:46:46,900 VariantDataManager - QD: mean = 19.23 standard deviation = 9.64 INFO 11:46:47,333 VariantDataManager - HaplotypeScore: mean = 0.14 standard deviation = 0.39 INFO 11:46:47,743 VariantDataManager - MQRankSum: mean = -0.03 standard deviation = 0.92 INFO 11:46:48,253 VariantDataManager - ReadPosRankSum: mean = -0.02 standard deviation = 0.98 INFO 11:46:48,747 VariantDataManager - MQ: mean = 59.69 standard deviation = 1.75 INFO 11:46:57,534 ProgressMeter - GL000202.1:10465 5.68e+07 16.0 m 16.0 s 98.7% 16.2 m 12.0 s INFO 11:46:58,339 VariantDataManager - Annotations are now ordered by their information content: [MQ, QD, HaplotypeScore, MQRankSum, ReadPosRankSum] INFO 11:46:58,462 VariantDataManager - Training with 1844568 variants after standard deviation thresholding. INFO 11:46:58,467 GaussianMixtureModel - Initializing model with 100 k-means iterations... INFO 11:47:28,743 ProgressMeter - GL000202.1:10465 5.68e+07 16.5 m 17.0 s 98.7% 16.7 m 13.0 s INFO 11:47:58,775 ProgressMeter - GL000202.1:10465 5.68e+07 17.0 m 17.0 s 98.7% 17.2 m 13.0 s INFO 11:48:28,776 ProgressMeter - GL000202.1:10465 5.68e+07 17.5 m 18.0 s 98.7% 17.7 m 13.0 s INFO 11:48:58,777 ProgressMeter - GL000202.1:10465 5.68e+07 18.0 m 19.0 s 98.7% 18.3 m 14.0 s INFO 11:49:16,656 VariantRecalibratorEngine - Finished iteration 0. INFO 11:49:28,778 ProgressMeter - GL000202.1:10465 5.68e+07 18.5 m 19.0 s 98.7% 18.8 m 14.0 s INFO 11:49:58,779 ProgressMeter - GL000202.1:10465 5.68e+07 19.0 m 20.0 s 98.7% 19.3 m 15.0 s INFO 11:50:28,781 ProgressMeter - GL000202.1:10465 5.68e+07 19.5 m 20.0 s 98.7% 19.8 m 15.0 s INFO 11:50:41,739 VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 1.28435 INFO 11:50:59,098 ProgressMeter - GL000202.1:10465 5.68e+07 20.0 m 21.0 s 98.7% 20.3 m 15.0 s INFO 11:51:51,320 ProgressMeter - GL000202.1:10465 5.68e+07 20.9 m 22.0 s 98.7% 21.2 m 16.0 s INFO 11:52:56,906 ProgressMeter - GL000202.1:10465 5.68e+07 22.0 m 23.0 s 98.7% 22.3 m 17.0 s INFO 11:53:25,827 VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.47009 INFO 11:53:34,082 ProgressMeter - GL000202.1:10465 5.68e+07 22.6 m 23.0 s 98.7% 22.9 m 18.0 s INFO 11:54:04,132 ProgressMeter - GL000202.1:10465 5.68e+07 23.1 m 24.0 s 98.7% 23.4 m 18.0 s INFO 11:54:34,671 ProgressMeter - GL000202.1:10465 5.68e+07 23.6 m 24.0 s 98.7% 23.9 m 18.0 s INFO 11:54:42,799 VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 0.27567 INFO 11:55:04,672 ProgressMeter - GL000202.1:10465 5.68e+07 24.1 m 25.0 s 98.7% 24.4 m 19.0 s INFO 11:55:34,673 ProgressMeter - GL000202.1:10465 5.68e+07 24.6 m 25.0 s 98.7% 24.9 m 19.0 s INFO 11:56:02,660 VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 0.00572 INFO 11:56:04,674 ProgressMeter - GL000202.1:10465 5.68e+07 25.1 m 26.0 s 98.7% 25.5 m 20.0 s INFO 11:56:34,675 ProgressMeter - GL000202.1:10465 5.68e+07 25.6 m 27.0 s 98.7% 26.0 m 20.0 s INFO 11:57:04,676 ProgressMeter - GL000202.1:10465 5.68e+07 26.1 m 27.0 s 98.7% 26.5 m 20.0 s INFO 11:57:26,001 VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.00862 INFO 11:57:34,677 ProgressMeter - GL000202.1:10465 5.68e+07 26.6 m 28.0 s 98.7% 27.0 m 21.0 s INFO 11:58:04,679 ProgressMeter - GL000202.1:10465 5.68e+07 27.1 m 28.0 s 98.7% 27.5 m 21.0 s INFO 11:58:36,046 ProgressMeter - GL000202.1:10465 5.68e+07 27.6 m 29.0 s 98.7% 28.0 m 22.0 s INFO 11:58:46,696 VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.01272 INFO 11:59:06,047 ProgressMeter - GL000202.1:10465 5.68e+07 28.1 m 29.0 s 98.7% 28.5 m 22.0 s INFO 11:59:36,048 ProgressMeter - GL000202.1:10465 5.68e+07 28.6 m 30.0 s 98.7% 29.0 m 22.0 s INFO 12:00:14,602 ProgressMeter - GL000202.1:10465 5.68e+07 29.3 m 30.0 s 98.7% 29.7 m 23.0 s INFO 12:00:25,062 VariantRecalibratorEngine - Finished iteration 35. Current change in mixture coefficients = 0.03122 INFO 12:00:44,603 ProgressMeter - GL000202.1:10465 5.68e+07 29.8 m 31.0 s 98.7% 30.2 m 23.0 s INFO 12:01:14,604 ProgressMeter - GL000202.1:10465 5.68e+07 30.3 m 31.0 s 98.7% 30.7 m 24.0 s INFO 12:01:42,674 VariantRecalibratorEngine - Finished iteration 40. Current change in mixture coefficients = 0.03012 INFO 12:01:44,606 ProgressMeter - GL000202.1:10465 5.68e+07 30.8 m 32.0 s 98.7% 31.2 m 24.0 s INFO 12:02:23,472 ProgressMeter - GL000202.1:10465 5.68e+07 31.4 m 33.0 s 98.7% 31.9 m 25.0 s INFO 12:02:53,473 ProgressMeter - GL000202.1:10465 5.68e+07 31.9 m 33.0 s 98.7% 32.4 m 25.0 s INFO 12:03:16,652 VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.00258 INFO 12:03:23,474 ProgressMeter - GL000202.1:10465 5.68e+07 32.4 m 34.0 s 98.7% 32.9 m 25.0 s INFO 12:03:32,263 VariantRecalibratorEngine - Convergence after 46 iterations! INFO 12:03:41,008 VariantRecalibratorEngine - Evaluating full set of 4944219 variants... INFO 12:03:41,100 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.sting.gatk.walkers.variantrecalibration.VariantRecalibratorEngine.generateModel(VariantRecalibratorEngine.java:83) at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:392) at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:138) at org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:116) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:313) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:121) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:248) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:155) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:107) ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A GATK RUNTIME ERROR has occurred (version nightly-2014-03-20-g65934ae): ##### 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 ------------------------------------------------------------------------------------------ Performance counter stats for 'java -jar -Xmx4g /home/tgenref/pipeline_v0.4/bin/GenomeAnalysisTK-nightly-2014-03-20-g65934ae/GenomeAnalysisTK.jar -R /home/tgenref/pipeline_v0.4/bwa7/hs37d5.fa -T VariantRecalibrator -input /scratch/akurdoglu/pecanPipe/projects/GhanaTNBC_0010_KAWGL_ps201403111445//ug/GhanaTNBC_0010_1_SA_Whole_C1_KAWGL_J00022-GhanaTNBC_0010_1_BE_Whole_T2_KAWGL_J00023/GhanaTNBC_0010_1_SA_Whole_C1_KAWGL_J00022-GhanaTNBC_0010_1_BE_Whole_T2_KAWGL_J00023.UG.vcf -resource:hapmap,known=false,training=true,truth=true,prior=15.0 /home/tgenref/pipeline_v0.3/gatk_bundle_2.5/b37/hapmap_3.3.b37.vcf -resource:omni,known=false,training=true,truth=false,prior=12.0 /home/tgenref/pipeline_v0.3/gatk_bundle_2.5/b37/1000G_omni2.5.b37.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=6.0 /home/tgenref/pipeline_v0.3/gatk_bundle_2.5/b37/dbsnp_137.b37.vcf --mode BOTH -an QD -an HaplotypeScore -an MQRankSum -an ReadPosRankSum -an MQ -recalFile /scratch/akurdoglu/pecanPipe/projects/GhanaTNBC_0010_KAWGL_ps201403111445//ug/GhanaTNBC_0010_1_SA_Whole_C1_KAWGL_J00022-GhanaTNBC_0010_1_BE_Whole_T2_KAWGL_J00023/GhanaTNBC_0010_1_SA_Whole_C1_KAWGL_J00022-GhanaTNBC_0010_1_BE_Whole_T2_KAWGL_J00023.UG.vcf.recal -tranchesFile /scratch/akurdoglu/pecanPipe/projects/GhanaTNBC_0010_KAWGL_ps201403111445//ug/GhanaTNBC_0010_1_SA_Whole_C1_KAWGL_J00022-GhanaTNBC_0010_1_BE_Whole_T2_KAWGL_J00023/GhanaTNBC_0010_1_SA_Whole_C1_KAWGL_J00022-GhanaTNBC_0010_1_BE_Whole_T2_KAWGL_J00023.UG.vcf.tranches -rscriptFile /scratch/akurdoglu/pecanPipe/projects/GhanaTNBC_0010_KAWGL_ps201403111445//ug/GhanaTNBC_0010_1_SA_Whole_C1_KAWGL_J00022-GhanaTNBC_0010_1_BE_Whole_T2_KAWGL_J00023/GhanaTNBC_0010_1_SA_Whole_C1_KAWGL_J00022-GhanaTNBC_0010_1_BE_Whole_T2_KAWGL_J00023.UG.vcf.plots.R': 10001566.291949 task-clock # 5.064 CPUs utilized 290566 context-switches # 0.000 M/sec 4485 CPU-migrations # 0.000 M/sec 2469812 page-faults # 0.000 M/sec 22834769455586 cycles # 2.283 GHz 15741836994513 stalled-cycles-frontend # 68.94% frontend cycles idle 12499591241353 stalled-cycles-backend # 54.74% backend cycles idle 12192779724965 instructions # 0.53 insns per cycle # 1.29 stalled cycles per insn 3267512980522 branches # 326.700 M/sec 8417437016 branch-misses # 0.26% of all branches 1975.168149173 seconds time elapsed