INFO 17:34:10,872 HelpFormatter - -------------------------------------------------------------------------------- INFO 17:34:10,876 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22 INFO 17:34:10,876 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 17:34:10,877 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 17:34:10,883 HelpFormatter - Program Args: -T VariantRecalibrator -R /home/lvwen/reference/hg19/ucsc.hg19.fasta -input combined_229_pbs.vcf -resource:hapmap,known=false,training=true,truth=true,prior=15.0 /home/lvwen/reference/hg19/snp/hapmap_3.3.hg19.sites.vcf -resource:omni,known=false,training=true,truth=false,prior=12.0 /home/lvwen/reference/hg19/snp/1000G_omni2.5.hg19.sites.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=6.0 /home/lvwen/reference/hg19/snp/dbsnp_138.hg19.vcf -an QD -an MQRankSum -an ReadPosRankSum -an FS -an MQ -mode SNP -recalFile combined_229_pbs.vcf.recal -tranchesFile combined_229_pbs.vcf.tranches -rscriptFile combined_229_pbs.vcf.plots.R INFO 17:34:10,893 HelpFormatter - Executing as lvwen@SGB01 on Linux 3.2.0-69-generic amd64; OpenJDK 64-Bit Server VM 1.7.0_65-b32. INFO 17:34:10,894 HelpFormatter - Date/Time: 2014/11/14 17:34:10 INFO 17:34:10,894 HelpFormatter - -------------------------------------------------------------------------------- INFO 17:34:10,894 HelpFormatter - -------------------------------------------------------------------------------- INFO 17:34:11,227 GenomeAnalysisEngine - Strictness is SILENT INFO 17:34:11,370 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 INFO 17:34:12,183 GenomeAnalysisEngine - Preparing for traversal INFO 17:34:12,216 GenomeAnalysisEngine - Done preparing for traversal INFO 17:34:12,217 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 17:34:12,218 ProgressMeter - | processed | time | per 1M | | total | remaining INFO 17:34:12,218 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime INFO 17:34:12,236 TrainingSet - Found hapmap track: Known = false Training = true Truth = true Prior = Q15.0 INFO 17:34:12,236 TrainingSet - Found omni track: Known = false Training = true Truth = false Prior = Q12.0 INFO 17:34:12,237 TrainingSet - Found dbsnp track: Known = true Training = false Truth = false Prior = Q6.0 INFO 17:34:42,222 ProgressMeter - chr2:4031777 5365669.0 30.0 s 5.0 s 8.1% 6.2 m 5.7 m INFO 17:35:12,223 ProgressMeter - chr3:13934110 1.1161927E7 60.0 s 5.0 s 16.1% 6.2 m 5.2 m INFO 17:35:42,225 ProgressMeter - chr4:79156214 1.7337975E7 90.0 s 5.0 s 24.5% 6.1 m 4.6 m INFO 17:36:12,226 ProgressMeter - chr5:165625922 2.3654996E7 120.0 s 5.0 s 33.4% 6.0 m 4.0 m INFO 17:36:42,227 ProgressMeter - chr7:77709183 3.0038671E7 2.5 m 4.0 s 41.8% 6.0 m 3.5 m INFO 17:37:12,228 ProgressMeter - chr9:4871944 3.5612902E7 3.0 m 5.0 s 49.2% 6.1 m 3.1 m INFO 17:37:42,230 ProgressMeter - chr10:87660985 4.0392741E7 3.5 m 5.0 s 56.4% 6.2 m 2.7 m INFO 17:38:12,231 ProgressMeter - chr12:71351690 4.6426722E7 4.0 m 5.0 s 64.5% 6.2 m 2.2 m INFO 17:38:42,233 ProgressMeter - chr14:95437122 5.196092E7 4.5 m 5.0 s 73.2% 6.2 m 99.0 s INFO 17:39:12,234 ProgressMeter - chr18:3730211 5.839834E7 5.0 m 5.0 s 82.4% 6.1 m 64.0 s INFO 17:39:42,235 ProgressMeter - chr22:38918203 6.4780401E7 5.5 m 5.0 s 91.4% 6.0 m 30.0 s INFO 17:39:56,326 VariantDataManager - QD: mean = 17.02 standard deviation = 6.20 INFO 17:39:56,339 VariantDataManager - MQRankSum: mean = 0.02 standard deviation = 0.44 INFO 17:39:56,347 VariantDataManager - ReadPosRankSum: mean = 0.53 standard deviation = 0.48 INFO 17:39:56,353 VariantDataManager - FS: mean = 0.88 standard deviation = 3.66 INFO 17:39:56,359 VariantDataManager - MQ: mean = 59.89 standard deviation = 1.43 INFO 17:39:56,426 VariantDataManager - Annotations are now ordered by their information content: [MQ, QD, ReadPosRankSum, FS, MQRankSum] INFO 17:39:56,436 VariantDataManager - Training with 14851 variants after standard deviation thresholding. INFO 17:39:56,439 GaussianMixtureModel - Initializing model with 100 k-means iterations... INFO 17:39:57,081 VariantRecalibratorEngine - Finished iteration 0. INFO 17:39:57,376 VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.87467 INFO 17:39:57,591 VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.24959 INFO 17:39:57,807 VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 0.22953 INFO 17:39:58,026 VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 0.11138 INFO 17:39:58,243 VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.07574 INFO 17:39:58,460 VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.04234 INFO 17:39:58,677 VariantRecalibratorEngine - Finished iteration 35. Current change in mixture coefficients = 0.02871 INFO 17:39:58,895 VariantRecalibratorEngine - Finished iteration 40. Current change in mixture coefficients = 0.02649 INFO 17:39:59,111 VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.03948 INFO 17:39:59,328 VariantRecalibratorEngine - Finished iteration 50. Current change in mixture coefficients = 0.03138 INFO 17:39:59,545 VariantRecalibratorEngine - Finished iteration 55. Current change in mixture coefficients = 0.02719 INFO 17:39:59,763 VariantRecalibratorEngine - Finished iteration 60. Current change in mixture coefficients = 0.02890 INFO 17:39:59,981 VariantRecalibratorEngine - Finished iteration 65. Current change in mixture coefficients = 0.07158 INFO 17:40:00,204 VariantRecalibratorEngine - Finished iteration 70. Current change in mixture coefficients = 0.05405 INFO 17:40:00,442 VariantRecalibratorEngine - Finished iteration 75. Current change in mixture coefficients = 0.34936 INFO 17:40:00,666 VariantRecalibratorEngine - Finished iteration 80. Current change in mixture coefficients = 0.03136 INFO 17:40:00,890 VariantRecalibratorEngine - Finished iteration 85. Current change in mixture coefficients = 0.03782 INFO 17:40:01,116 VariantRecalibratorEngine - Finished iteration 90. Current change in mixture coefficients = 7.50717 INFO 17:40:01,346 VariantRecalibratorEngine - Finished iteration 95. Current change in mixture coefficients = 0.03751 INFO 17:40:01,577 VariantRecalibratorEngine - Finished iteration 100. Current change in mixture coefficients = 0.05767 INFO 17:40:01,811 VariantRecalibratorEngine - Finished iteration 105. Current change in mixture coefficients = 0.07804 INFO 17:40:02,055 VariantRecalibratorEngine - Finished iteration 110. Current change in mixture coefficients = 0.00566 INFO 17:40:02,153 VariantRecalibratorEngine - Convergence after 112 iterations! INFO 17:40:02,242 VariantRecalibratorEngine - Evaluating full set of 75855 variants... INFO 17:40:02,252 VariantDataManager - Training with worst 0 scoring variants --> variants with LOD <= -5.0000. INFO 17:40:05,701 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:399) at org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:143) 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:319) 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:107) ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A GATK RUNTIME ERROR has occurred (version 3.3-0-g37228af): ##### 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 ------------------------------------------------------------------------------------------ INFO 17:40:07,894 HelpFormatter - -------------------------------------------------------------------------------- INFO 17:40:07,897 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22 INFO 17:40:07,897 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 17:40:07,897 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 17:40:07,900 HelpFormatter - Program Args: -T ApplyRecalibration -R /home/lvwen/reference/hg19/ucsc.hg19.fasta -input combined_229_pbs.vcf --ts_filter_level 99.0 -tranchesFile combined_229_pbs.vcf.tranches -recalFile combined_229_pbs.vcf.recal -mode SNP -o combined_229_pbs.vcf.recalibrated.filtered.vcf INFO 17:40:07,905 HelpFormatter - Executing as lvwen@SGB01 on Linux 3.2.0-69-generic amd64; OpenJDK 64-Bit Server VM 1.7.0_65-b32. INFO 17:40:07,905 HelpFormatter - Date/Time: 2014/11/14 17:40:07 INFO 17:40:07,905 HelpFormatter - -------------------------------------------------------------------------------- INFO 17:40:07,905 HelpFormatter - -------------------------------------------------------------------------------- INFO 17:40:10,009 GATKRunReport - Uploaded run statistics report to AWS S3 ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A USER ERROR has occurred (version 3.3-0-g37228af): ##### ERROR ##### ERROR This means that one or more arguments or inputs in your command are incorrect. ##### ERROR The error message below tells you what is the problem. ##### ERROR ##### ERROR If the problem is an invalid argument, please check the online documentation guide ##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool. ##### ERROR ##### ERROR Visit our website and forum for extensive documentation and answers to ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk ##### ERROR ##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself. ##### ERROR ##### ERROR MESSAGE: Invalid command line: No tribble type was provided on the command line and the type of the file could not be determined dynamically. Please add an explicit type tag :NAME listing the correct type from among the supported types: ##### ERROR Name FeatureType Documentation ##### ERROR BCF2 VariantContext (this is an external codec and is not documented within GATK) ##### ERROR VCF VariantContext (this is an external codec and is not documented within GATK) ##### ERROR VCF3 VariantContext (this is an external codec and is not documented within GATK) ##### ERROR ------------------------------------------------------------------------------------------ INFO 17:40:12,047 HelpFormatter - -------------------------------------------------------------------------------- INFO 17:40:12,049 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22 INFO 17:40:12,049 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 17:40:12,050 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 17:40:12,053 HelpFormatter - Program Args: -T VariantEval -R /home/lvwen/reference/hg19/ucsc.hg19.fasta --eval:combined_229_pbs.vcf combined_229_pbs.vcf.recalibrated.filtered.vcf -o combined_229_pbs.vcf.report -D /home/lvwen/reference/hg19/snp/dbsnp_138.hg19.vcf -ST Sample -ST Filter -noEV -EV TiTvVariantEvaluator -EV CountVariants -EV IndelSummary -EV MultiallelicSummary INFO 17:40:12,058 HelpFormatter - Executing as lvwen@SGB01 on Linux 3.2.0-69-generic amd64; OpenJDK 64-Bit Server VM 1.7.0_65-b32. INFO 17:40:12,058 HelpFormatter - Date/Time: 2014/11/14 17:40:12 INFO 17:40:12,058 HelpFormatter - -------------------------------------------------------------------------------- INFO 17:40:12,058 HelpFormatter - -------------------------------------------------------------------------------- INFO 17:40:14,563 GATKRunReport - Uploaded run statistics report to AWS S3 ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A USER ERROR has occurred (version 3.3-0-g37228af): ##### ERROR ##### ERROR This means that one or more arguments or inputs in your command are incorrect. ##### ERROR The error message below tells you what is the problem. ##### ERROR ##### ERROR If the problem is an invalid argument, please check the online documentation guide ##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool. ##### ERROR ##### ERROR Visit our website and forum for extensive documentation and answers to ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk ##### ERROR ##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself. ##### ERROR ##### ERROR MESSAGE: Couldn't read file /nfs/home/lvwen/analysis/mapping4/gvcf/combined_229_pbs.vcf.recalibrated.filtered.vcf because file does not exist ##### ERROR ------------------------------------------------------------------------------------------