Error when using VariantRecalibrator indel mode

I ran this command:

java -Xmx20G -Djava.io.tmpdir=/scratch/ -jar \$GATK_JAR \ -R /software6/bioinfo/apps/mugqic_space/genomes/species/Homo_sapiens.GRCh37_1000Genomes_decoy/genome/bwa_index/Homo_sapiens.GRCh37_decoy.fa \ -T VariantRecalibrator \ -nt 4 \ --minNumBadVariants 5000 \ -resource:mills,known=false,training=true,truth=true,prior=12.0 Mills_and_1000G_gold_standard.indels.b37.vcf \ -resource:1000G,known=false,training=true,truth=true,prior=10.0 1000G_phase1.indels.b37.vcf \ -an MQRankSum \ -an ReadPosRankSum \ -an FS \ -input ${file} \ -recalFile ${id}_indel_recal \ -tranchesFile ${id}_indel_tranches \ -rscriptFile ${id}_indel_plots.R \ -mode INDEL

And this is the output:

INFO 09:23:12,391 HelpFormatter - --------------------------------------------------------------------------------
INFO 09:23:12,394 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
INFO 09:23:12,394 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 09:23:12,395 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 09:23:12,398 HelpFormatter - Program Args: -R Homo_sapiens.GRCh37_decoy.fa -T VariantRecalibrator -nt 4 --minNumBadVariants 5000 -resource:mills,known=false,training=true,truth=true,prior=12.0 Mills_and_1000G_gold_standard.indels.b37.vcf -resource:1000G,known=false,training=true,truth=true,prior=10.0 1000G_phase1.indels.b37.vcf -an MQRankSum -an ReadPosRankSum -an FS -input DE.chr15.vcf -recalFile DE.chr15_indel_recal -tranchesFile DE.chr15_indel_tranches -rscriptFile DE.chr15_indel_plots.R -mode INDEL
INFO 09:23:12,404 HelpFormatter - Executing as [email protected] on Linux 2.6.32-573.8.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_60-ea-b07.
INFO 09:23:12,404 HelpFormatter - Date/Time: 2015/12/09 09:23:12
INFO 09:23:12,404 HelpFormatter - --------------------------------------------------------------------------------
INFO 09:23:12,405 HelpFormatter - --------------------------------------------------------------------------------
INFO 09:23:13,308 GenomeAnalysisEngine - Strictness is SILENT
INFO 09:23:13,468 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 09:23:13,988 MicroScheduler - Running the GATK in parallel mode with 4 total threads, 1 CPU thread(s) for each of 4 data thread(s), of 8 processors available on this machine
INFO 09:23:14,067 GenomeAnalysisEngine - Preparing for traversal
INFO 09:23:14,078 GenomeAnalysisEngine - Done preparing for traversal
INFO 09:23:14,079 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 09:23:14,079 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 09:23:14,079 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
WARN 09:23:14,090 Utils - ********************************************************************************
WARN 09:23:14,091 Utils - * WARNING:
WARN 09:23:14,091 Utils - *
WARN 09:23:14,091 Utils - * Rscript not found in environment path. DE.chr15_indel_plots.R will be
WARN 09:23:14,092 Utils - * generated but PDF plots will not.
WARN 09:23:14,092 Utils - ********************************************************************************
INFO 09:23:14,104 TrainingSet - Found mills track: Known = false Training = true Truth = true Prior = Q12.0
INFO 09:23:14,104 TrainingSet - Found 1000G track: Known = false Training = true Truth = true Prior = Q10.0
INFO 09:23:46,005 ProgressMeter - 15:30100414 3926585.0 31.0 s 8.0 s 74.5% 41.0 s 10.0 s
INFO 09:24:16,006 ProgressMeter - 15:68237128 4269674.0 61.0 s 14.0 s 75.7% 80.0 s 19.0 s
INFO 09:24:35,237 VariantDataManager - MQRankSum: mean = 0.43 standard deviation = 0.60
INFO 09:24:35,264 VariantDataManager - ReadPosRankSum: mean = 0.47 standard deviation = 0.55
INFO 09:24:35,276 VariantDataManager - FS: mean = 1.07 standard deviation = 2.90
INFO 09:24:35,361 VariantDataManager - Annotations are now ordered by their information content: [FS, ReadPosRankSum, MQRankSum]
INFO 09:24:35,372 VariantDataManager - Training with 23911 variants after standard deviation thresholding.
INFO 09:24:35,377 GaussianMixtureModel - Initializing model with 100 k-means iterations...
INFO 09:24:36,790 VariantRecalibratorEngine - Finished iteration 0.
INFO 09:24:37,323 VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.68995
INFO 09:24:37,894 VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.14727
INFO 09:24:38,484 VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 0.01537
INFO 09:24:39,086 VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 0.00449
INFO 09:24:39,691 VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.00404
INFO 09:24:40,297 VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.00445
INFO 09:24:40,900 VariantRecalibratorEngine - Finished iteration 35. Current change in mixture coefficients = 0.00206
INFO 09:24:41,022 VariantRecalibratorEngine - Convergence after 36 iterations!
INFO 09:24:41,114 VariantRecalibratorEngine - Evaluating full set of 71455 variants...
INFO 09:24:41,125 VariantDataManager - Training with worst 0 scoring variants --> variants with LOD <= -5.0000.
INFO 09:24:42,801 HttpMethodDirector - I/O exception (java.net.ConnectException) caught when processing request: Network is unreachable
INFO 09:24:42,801 HttpMethodDirector - Retrying request
INFO 09:24:42,803 HttpMethodDirector - I/O exception (java.net.ConnectException) caught when processing request: Network is unreachable
INFO 09:24:42,803 HttpMethodDirector - Retrying request
INFO 09:24:42,804 HttpMethodDirector - I/O exception (java.net.ConnectException) caught when processing request: Network is unreachable
INFO 09:24:42,805 HttpMethodDirector - Retrying request
INFO 09:24:42,806 HttpMethodDirector - I/O exception (java.net.ConnectException) caught when processing request: Network is unreachable
INFO 09:24:42,806 HttpMethodDirector - Retrying request
INFO 09:24:42,807 HttpMethodDirector - I/O exception (java.net.ConnectException) caught when processing request: Network is unreachable
INFO 09:24:42,807 HttpMethodDirector - Retrying request

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: Unable to retrieve result
at org.broadinstitute.gatk.engine.executive.HierarchicalMicroScheduler.execute(HierarchicalMicroScheduler.java:190)
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)
Caused by: 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.HierarchicalMicroScheduler.notifyTraversalDone(HierarchicalMicroScheduler.java:226)
at org.broadinstitute.gatk.engine.executive.HierarchicalMicroScheduler.execute(HierarchicalMicroScheduler.java:183)
... 5 more

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: Unable to retrieve result
ERROR ------------------------------------------------------------------------------------------

I have redone the calling on this VCF to be sure, recalibration of SNPs goes well, indel cannot pass.

Best Answer

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @emixaM
    Hi,

    I think this thread will help solve your problem.

    -Sheila

  • emixaMemixaM CanadaMember

    I tried the nt 1 solution but no luck...

    I tried to recalibrate all chromosomes together, but it stopped at the SNP step this time:

    INFO 15:55:39,642 HelpFormatter - --------------------------------------------------------------------------------
    INFO 15:55:39,647 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
    INFO 15:55:39,647 HelpFormatter - Copyright (c) 2010 The Broad Institute
    INFO 15:55:39,647 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
    INFO 15:55:39,651 HelpFormatter - Program Args: -R Homo_sapiens.GRCh37_decoy.fa -T VariantRecalibrator -nt 4 --minNumBadVariants 5000 -resource:hapmap,known=false,training=true,tr
    uth=true,prior=15.0 hapmap_3.3.b37.vcf -resource:omni,known=false,training=true,truth=true,prior=12.0 1000G_omni2.5.b37.vcf -resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_
    phase1.snps.high_confidence.b37.vcf -an QD -an MQRankSum -an ReadPosRankSum -an FS -an InbreedingCoeff -input DE.cat.vcf -recalFile DE.cat_snp_r
    ecal -tranchesFile DE.cat_snp_tranches -rscriptFile DE.cat_snp_plots.R -mode SNP
    INFO 15:55:39,661 HelpFormatter - Executing as [email protected] on Linux 2.6.32-573.8.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.
    0_60-ea-b07.
    INFO 15:55:39,661 HelpFormatter - Date/Time: 2015/12/09 15:55:39
    INFO 15:55:39,661 HelpFormatter - --------------------------------------------------------------------------------
    INFO 15:55:39,662 HelpFormatter - --------------------------------------------------------------------------------
    INFO 15:55:40,536 GenomeAnalysisEngine - Strictness is SILENT
    INFO 15:55:40,837 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
    INFO 15:55:41,333 MicroScheduler - Running the GATK in parallel mode with 4 total threads, 1 CPU thread(s) for each of 4 data thread(s), of 8 p
    rocessors available on this machine
    INFO 15:55:41,437 GenomeAnalysisEngine - Preparing for traversal
    INFO 15:55:41,448 GenomeAnalysisEngine - Done preparing for traversal
    INFO 15:55:41,449 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
    INFO 15:55:41,449 ProgressMeter - | processed | time | per 1M | | total | remaining
    INFO 15:55:41,450 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
    WARN 15:55:41,459 Utils - ********************************************************************************
    WARN 15:55:41,460 Utils - * WARNING:
    WARN 15:55:41,460 Utils - *
    WARN 15:55:41,460 Utils - * Rscript not found in environment path. DE.cat_snp_plots.R will be
    WARN 15:55:41,461 Utils - * generated but PDF plots will not.
    WARN 15:55:41,461 Utils - ********************************************************************************
    INFO 15:55:41,464 TrainingSet - Found hapmap track: Known = false Training = true Truth = true Prior = Q15.0
    INFO 15:55:41,465 TrainingSet - Found omni track: Known = false Training = true Truth = true Prior = Q12.0
    INFO 15:55:41,465 TrainingSet - Found 1000G track: Known = false Training = true Truth = false Prior = Q10.0
    INFO 15:56:11,453 ProgressMeter - 1:106032755 1643672.0 30.0 s 18.0 s 3.4% 14.8 m 14.3 m
    INFO 15:56:46,604 ProgressMeter - 1:163292362 2144816.0 65.0 s 30.0 s 5.2% 20.8 m 19.7 m
    INFO 15:57:16,662 ProgressMeter - 1:182086358 2436159.0 95.0 s 39.0 s 5.8% 27.3 m 25.7 m
    INFO 15:57:52,156 ProgressMeter - 1:204110433 2766313.0 2.2 m 47.0 s 6.5% 33.3 m 31.1 m
    INFO 15:58:25,724 ProgressMeter - 2:63302464 4586714.0 2.7 m 35.0 s 10.0% 27.4 m 24.7 m
    INFO 15:58:55,731 ProgressMeter - 2:193025280 6431680.0 3.2 m 30.0 s 14.1% 22.9 m 19.7 m
    INFO 15:59:27,855 ProgressMeter - 3:41458634 7924940.0 3.8 m 28.0 s 17.0% 22.1 m 18.4 m
    INFO 15:59:57,862 ProgressMeter - 3:176443932 9928015.0 4.3 m 25.0 s 21.3% 20.0 m 15.7 m
    INFO 16:00:27,870 ProgressMeter - 4:102817161 1.190612E7 4.8 m 24.0 s 25.3% 18.9 m 14.1 m
    INFO 16:01:01,064 ProgressMeter - 5:38414014 1.3946267E7 5.3 m 22.0 s 29.3% 18.1 m 12.8 m
    INFO 16:01:31,074 ProgressMeter - 5:174056906 1.5904541E7 5.8 m 21.0 s 33.6% 17.3 m 11.5 m
    INFO 16:02:01,126 ProgressMeter - 6:105090026 1.7738687E7 6.3 m 21.0 s 37.2% 17.0 m 10.7 m
    INFO 16:02:31,135 ProgressMeter - 7:48010218 1.9642674E7 6.8 m 20.0 s 40.9% 16.7 m 9.9 m
    INFO 16:03:01,142 ProgressMeter - 8:6232119 2.144776E7 7.3 m 20.0 s 44.6% 16.4 m 9.1 m
    INFO 16:03:31,150 ProgressMeter - 8:136038887 2.3518239E7 7.8 m 19.0 s 48.7% 16.0 m 8.2 m
    INFO 16:04:02,321 ProgressMeter - 9:107263646 2.5025759E7 8.3 m 20.0 s 52.5% 15.9 m 7.5 m
    INFO 16:04:32,328 ProgressMeter - 10:69067487 2.6735581E7 8.8 m 19.0 s 55.8% 15.8 m 7.0 m
    INFO 16:05:02,362 ProgressMeter - 11:44023509 2.8581587E7 9.3 m 19.0 s 59.3% 15.7 m 6.4 m
    INFO 16:05:37,253 ProgressMeter - 12:5267846 3.0079346E7 9.9 m 19.0 s 62.3% 15.9 m 6.0 m
    INFO 16:06:07,345 ProgressMeter - 12:120324631 3.1829666E7 10.4 m 19.0 s 66.0% 15.8 m 5.4 m
    INFO 16:06:37,375 ProgressMeter - 14:19026624 3.3644437E7 10.9 m 19.0 s 70.7% 15.4 m 4.5 m
    INFO 16:07:07,383 ProgressMeter - 15:35044160 3.5295881E7 11.4 m 19.0 s 74.7% 15.3 m 3.9 m
    INFO 16:07:40,174 ProgressMeter - 16:26712326 3.6939068E7 12.0 m 19.0 s 77.7% 15.4 m 3.4 m
    INFO 16:08:10,181 ProgressMeter - 17:44296148 3.8601676E7 12.5 m 19.0 s 81.1% 15.4 m 2.9 m
    INFO 16:08:40,191 ProgressMeter - 19:327814 4.0429124E7 13.0 m 19.0 s 84.8% 15.3 m 2.3 m
    INFO 16:09:10,796 ProgressMeter - 20:20072153 4.1899869E7 13.5 m 19.0 s 87.3% 15.4 m 117.0 s
    INFO 16:09:40,815 ProgressMeter - 22:25129679 4.341173E7 14.0 m 19.0 s 91.0% 15.4 m 83.0 s
    INFO 16:10:10,830 ProgressMeter - X:129040271 4.5315317E7 14.5 m 19.0 s 95.9% 15.1 m 36.0 s
    INFO 16:10:19,218 VariantDataManager - QD: mean = 21.14 standard deviation = 6.53
    INFO 16:10:20,349 VariantDataManager - MQRankSum: mean = 0.40 standard deviation = 0.60
    INFO 16:10:22,035 VariantDataManager - ReadPosRankSum: mean = 0.50 standard deviation = 0.56
    INFO 16:10:23,669 VariantDataManager - FS: mean = 1.07 standard deviation = 2.42
    INFO 16:10:24,735 VariantDataManager - InbreedingCoeff: mean = 0.23 standard deviation = 0.29
    INFO 16:10:41,113 VariantDataManager - Annotations are now ordered by their information content: [QD, InbreedingCoeff, FS, MQRankSum, ReadPosRa
    nkSum]
    INFO 16:10:41,491 VariantDataManager - Training with 7577234 variants after standard deviation thresholding.
    WARN 16:10:41,491 VariantDataManager - WARNING: Very large training set detected. Downsampling to 2500000 training variants.
    INFO 16:10:42,033 GaussianMixtureModel - Initializing model with 100 k-means iterations...
    INFO 16:10:49,770 ProgressMeter - GL000202.1:10465 4.5626609E7 15.1 m 19.0 s 98.7% 15.3 m 12.0 s
    INFO 16:11:19,773 ProgressMeter - GL000202.1:10465 4.5626609E7 15.6 m 20.0 s 98.7% 15.8 m 12.0 s
    INFO 16:11:49,783 ProgressMeter - GL000202.1:10465 4.5626609E7 16.1 m 21.0 s 98.7% 16.3 m 12.0 s
    INFO 16:12:19,791 ProgressMeter - GL000202.1:10465 4.5626609E7 16.6 m 21.0 s 98.7% 16.9 m 13.0 s
    INFO 16:12:49,801 ProgressMeter - GL000202.1:10465 4.5626609E7 17.1 m 22.0 s 98.7% 17.4 m 13.0 s
    INFO 16:13:19,811 ProgressMeter - GL000202.1:10465 4.5626609E7 17.6 m 23.0 s 98.7% 17.9 m 14.0 s
    INFO 16:13:49,819 ProgressMeter - GL000202.1:10465 4.5626609E7 18.1 m 23.0 s 98.7% 18.4 m 14.0 s
    INFO 16:14:19,829 ProgressMeter - GL000202.1:10465 4.5626609E7 18.6 m 24.0 s 98.7% 18.9 m 14.0 s
    INFO 16:14:49,838 ProgressMeter - GL000202.1:10465 4.5626609E7 19.1 m 25.0 s 98.7% 19.4 m 15.0 s
    INFO 16:15:19,848 ProgressMeter - GL000202.1:10465 4.5626609E7 19.6 m 25.0 s 98.7% 19.9 m 15.0 s
    INFO 16:15:49,857 ProgressMeter - GL000202.1:10465 4.5626609E7 20.1 m 26.0 s 98.7% 20.4 m 16.0 s
    INFO 16:16:19,866 ProgressMeter - GL000202.1:10465 4.5626609E7 20.6 m 27.0 s 98.7% 20.9 m 16.0 s
    INFO 16:16:23,580 VariantRecalibratorEngine - Finished iteration 0.
    INFO 16:16:49,875 ProgressMeter - GL000202.1:10465 4.5626609E7 21.1 m 27.0 s 98.7% 21.4 m 16.0 s
    INFO 16:17:19,883 ProgressMeter - GL000202.1:10465 4.5626609E7 21.6 m 28.0 s 98.7% 21.9 m 17.0 s
    INFO 16:17:49,893 ProgressMeter - GL000202.1:10465 4.5626609E7 22.1 m 29.0 s 98.7% 22.4 m 17.0 s
    INFO 16:18:10,016 VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.95404
    INFO 16:18:19,902 ProgressMeter - GL000202.1:10465 4.5626609E7 22.6 m 29.0 s 98.7% 22.9 m 18.0 s
    INFO 16:18:49,905 ProgressMeter - GL000202.1:10465 4.5626609E7 23.1 m 30.0 s 98.7% 23.4 m 18.0 s
    INFO 16:19:19,915 ProgressMeter - GL000202.1:10465 4.5626609E7 23.6 m 31.0 s 98.7% 23.9 m 18.0 s
    INFO 16:19:49,924 ProgressMeter - GL000202.1:10465 4.5626609E7 24.1 m 31.0 s 98.7% 24.5 m 19.0 s
    INFO 16:20:03,466 VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.27053
    INFO 16:20:19,932 ProgressMeter - GL000202.1:10465 4.5626609E7 24.6 m 32.0 s 98.7% 25.0 m 19.0 s
    INFO 16:20:49,941 ProgressMeter - GL000202.1:10465 4.5626609E7 25.1 m 33.0 s 98.7% 25.5 m 20.0 s
    INFO 16:21:19,951 ProgressMeter - GL000202.1:10465 4.5626609E7 25.6 m 33.0 s 98.7% 26.0 m 20.0 s
    INFO 16:21:49,959 ProgressMeter - GL000202.1:10465 4.5626609E7 26.1 m 34.0 s 98.7% 26.5 m 20.0 s
    INFO 16:21:56,526 VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 0.17216
    INFO 16:22:19,968 ProgressMeter - GL000202.1:10465 4.5626609E7 26.6 m 35.0 s 98.7% 27.0 m 21.0 s
    INFO 16:22:49,976 ProgressMeter - GL000202.1:10465 4.5626609E7 27.1 m 35.0 s 98.7% 27.5 m 21.0 s
    INFO 16:23:19,986 ProgressMeter - GL000202.1:10465 4.5626609E7 27.6 m 36.0 s 98.7% 28.0 m 22.0 s
    INFO 16:23:49,996 ProgressMeter - GL000202.1:10465 4.5626609E7 28.1 m 37.0 s 98.7% 28.5 m 22.0 s
    INFO 16:23:52,074 VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 0.07452
    INFO 16:24:20,007 ProgressMeter - GL000202.1:10465 4.5626609E7 28.6 m 37.0 s 98.7% 29.0 m 22.0 s
    INFO 16:24:50,018 ProgressMeter - GL000202.1:10465 4.5626609E7 29.1 m 38.0 s 98.7% 29.5 m 23.0 s
    INFO 16:25:20,027 ProgressMeter - GL000202.1:10465 4.5626609E7 29.6 m 38.0 s 98.7% 30.0 m 23.0 s
    INFO 16:25:48,051 VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.02007
    INFO 16:25:50,036 ProgressMeter - GL000202.1:10465 4.5626609E7 30.1 m 39.0 s 98.7% 30.5 m 24.0 s
    INFO 16:26:20,038 ProgressMeter - GL000202.1:10465 4.5626609E7 30.6 m 40.0 s 98.7% 31.0 m 24.0 s
    INFO 16:26:50,047 ProgressMeter - GL000202.1:10465 4.5626609E7 31.1 m 40.0 s 98.7% 31.5 m 24.0 s
    INFO 16:27:20,056 ProgressMeter - GL000202.1:10465 4.5626609E7 31.6 m 41.0 s 98.7% 32.1 m 25.0 s
    INFO 16:27:43,579 VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.00872
    INFO 16:27:50,066 ProgressMeter - GL000202.1:10465 4.5626609E7 32.1 m 42.0 s 98.7% 32.6 m 25.0 s
    INFO 16:28:20,069 ProgressMeter - GL000202.1:10465 4.5626609E7 32.6 m 42.0 s 98.7% 33.1 m 26.0 s
    INFO 16:28:50,078 ProgressMeter - GL000202.1:10465 4.5626609E7 33.1 m 43.0 s 98.7% 33.6 m 26.0 s
    INFO 16:29:20,088 ProgressMeter - GL000202.1:10465 4.5626609E7 33.6 m 44.0 s 98.7% 34.1 m 26.0 s
    INFO 16:29:39,291 VariantRecalibratorEngine - Finished iteration 35. Current change in mixture coefficients = 0.00766
    INFO 16:29:50,097 ProgressMeter - GL000202.1:10465 4.5626609E7 34.1 m 44.0 s 98.7% 34.6 m 27.0 s
    INFO 16:30:20,103 ProgressMeter - GL000202.1:10465 4.5626609E7 34.6 m 45.0 s 98.7% 35.1 m 27.0 s
    INFO 16:30:50,113 ProgressMeter - GL000202.1:10465 4.5626609E7 35.1 m 46.0 s 98.7% 35.6 m 28.0 s
    INFO 16:31:20,122 ProgressMeter - GL000202.1:10465 4.5626609E7 35.6 m 46.0 s 98.7% 36.1 m 28.0 s
    INFO 16:31:35,066 VariantRecalibratorEngine - Finished iteration 40. Current change in mixture coefficients = 0.01707
    INFO 16:31:50,131 ProgressMeter - GL000202.1:10465 4.5626609E7 36.1 m 47.0 s 98.7% 36.6 m 28.0 s
    INFO 16:32:20,142 ProgressMeter - GL000202.1:10465 4.5626609E7 36.6 m 48.0 s 98.7% 37.1 m 29.0 s
    INFO 16:32:50,152 ProgressMeter - GL000202.1:10465 4.5626609E7 37.1 m 48.0 s 98.7% 37.6 m 29.0 s
    INFO 16:33:20,161 ProgressMeter - GL000202.1:10465 4.5626609E7 37.6 m 49.0 s 98.7% 38.1 m 30.0 s
    INFO 16:33:30,763 VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.04035
    INFO 16:33:50,170 ProgressMeter - GL000202.1:10465 4.5626609E7 38.1 m 50.0 s 98.7% 38.6 m 30.0 s
    INFO 16:34:20,179 ProgressMeter - GL000202.1:10465 4.5626609E7 38.6 m 50.0 s 98.7% 39.1 m 30.0 s
    INFO 16:34:50,188 ProgressMeter - GL000202.1:10465 4.5626609E7 39.1 m 51.0 s 98.7% 39.7 m 31.0 s
    INFO 16:35:20,198 ProgressMeter - GL000202.1:10465 4.5626609E7 39.6 m 52.0 s 98.7% 40.2 m 31.0 s
    INFO 16:35:26,725 VariantRecalibratorEngine - Finished iteration 50. Current change in mixture coefficients = 0.03729
    INFO 16:35:50,208 ProgressMeter - GL000202.1:10465 4.5626609E7 40.1 m 52.0 s 98.7% 40.7 m 32.0 s
    INFO 16:36:20,218 ProgressMeter - GL000202.1:10465 4.5626609E7 40.6 m 53.0 s 98.7% 41.2 m 32.0 s
    INFO 16:36:50,227 ProgressMeter - GL000202.1:10465 4.5626609E7 41.1 m 54.0 s 98.7% 41.7 m 32.0 s
    INFO 16:37:20,236 ProgressMeter - GL000202.1:10465 4.5626609E7 41.6 m 54.0 s 98.7% 42.2 m 33.0 s
    INFO 16:37:22,812 VariantRecalibratorEngine - Finished iteration 55. Current change in mixture coefficients = 0.00461
    INFO 16:37:50,244 ProgressMeter - GL000202.1:10465 4.5626609E7 42.1 m 55.0 s 98.7% 42.7 m 33.0 s
    INFO 16:38:20,253 ProgressMeter - GL000202.1:10465 4.5626609E7 42.6 m 56.0 s 98.7% 43.2 m 34.0 s
    INFO 16:38:50,261 ProgressMeter - GL000202.1:10465 4.5626609E7 43.1 m 56.0 s 98.7% 43.7 m 34.0 s
    INFO 16:38:55,785 VariantRecalibratorEngine - Convergence after 59 iterations!
    INFO 16:39:11,694 VariantRecalibratorEngine - Evaluating full set of 15903218 variants...
    INFO 16:39:11,973 VariantDataManager - Training with worst 0 scoring variants --> variants with LOD <= -5.0000.
    INFO 16:39:20,271 ProgressMeter - GL000202.1:10465 4.5626609E7 43.6 m 57.0 s 98.7% 44.2 m 34.0 s
    INFO 16:39:22,244 HttpMethodDirector - I/O exception (java.net.ConnectException) caught when processing request: Network is unreachable
    INFO 16:39:22,245 HttpMethodDirector - Retrying request
    INFO 16:39:22,247 HttpMethodDirector - I/O exception (java.net.ConnectException) caught when processing request: Network is unreachable
    INFO 16:39:22,247 HttpMethodDirector - Retrying request
    INFO 16:39:22,248 HttpMethodDirector - I/O exception (java.net.ConnectException) caught when processing request: Network is unreachable
    INFO 16:39:22,249 HttpMethodDirector - Retrying request
    INFO 16:39:22,250 HttpMethodDirector - I/O exception (java.net.ConnectException) caught when processing request: Network is unreachable
    INFO 16:39:22,250 HttpMethodDirector - Retrying request
    INFO 16:39:22,251 HttpMethodDirector - I/O exception (java.net.ConnectException) caught when processing request: Network is unreachable
    INFO 16:39:22,251 HttpMethodDirector - Retrying request

    ERROR ------------------------------------------------------------------------------------------
    ERROR stack trace

    org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: Unable to retrieve result
    at org.broadinstitute.gatk.engine.executive.HierarchicalMicroScheduler.execute(HierarchicalMicroScheduler.java:190)
    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)
    Caused by: 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.HierarchicalMicroScheduler.notifyTraversalDone(HierarchicalMicroScheduler.java:226)
    at org.broadinstitute.gatk.engine.executive.HierarchicalMicroScheduler.execute(HierarchicalMicroScheduler.java:183)
    ... 5 more

    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: Unable to retrieve result
    ERROR ------------------------------------------------------------------------------------------
  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @emixaM
    Hi,

    Sorry for the late response. What exactly does your input VCF contain? Is it human data? How many samples, and are they whole exome or whole genome? It looks like you may not have enough variant data points to train the model.

    Thanks,
    Sheila

  • emixaMemixaM CanadaMember

    It is human exome, chromosome 15 only, with a 396 samples cohort. Smaller chromosomes went fine.

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