Bug Bulletin: The GenomeLocPArser error in SplitNCigarReads has been fixed; if you encounter it, use the latest nightly build.

ERROR MESSAGE: Unable to retrieve result

raphael123raphael123 MontrealPosts: 3Member

Here is my error .. I lauch the same command on 3 svg generated by the same UnifiedGenotyper commen ..

thx!

`java -Djava.io.tmpdir=/scratch/ymb-542-aa/temp -Xmx22g -jar /rap/ymb-542-aa/utils/tools/dna_tools/post_alignment_tools/GenomeAnalysisTK-2.8-1/GenomeAnalysisTK.jar -nt 8 -et NO_ET -K /rap/ymb-542-aa/utils/tools/dna_tools/post_alignment_tools/GenomeAnalysisTK-2.8-1/raphael.poujol_umontreal.ca.key -T VariantRecalibrator -R /scratch/ymb-542-aa/pancreas/Genomes/hg19.fa -input /scratch/ymb-542-aa/pancreas/Calling/sub1_focus.haplo.vcf -mode SNP -resource:hapmap,known=false,training=true,truth=true,prior=15.0 /scratch/ymb-542-aa/pancreas/Genomes/hapmap_3.3.hg19.vcf -resource:omni,known=false,training=true,truth=false,prior=10.0 /scratch/ymb-542-aa/pancreas/Genomes/1000G_omni2.5.hg19.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 /scratch/ymb-542-aa/pancreas/Genomes/dbsnp_138.hg19_noXY.vcf -an QD -an DP -an FS -an MQ -tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0
-recalFile /scratch/ymb-542-aa/pancreas/Calling/sub1_focus.snps.recal -tranchesFile /scratch/ymb-542-aa/pancreas/Calling/sub1_focus.snps.tranches -rscriptFile /scratch/ymb-542-aa/pancreas/Calling/sub1_focus.snps.plots.RINFO 20:41:18,337 HelpFormatter - -------------------------------------------------------------------------------- INFO 20:41:18,338 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.8-1-g932cd3a, Compiled 2013/12/06 16:47:15 INFO 20:41:18,339 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 20:41:18,339 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 20:41:18,342 HelpFormatter - Program Args: -nt 8 -et NO_ET -K /rap/ymb-542-aa/utils/tools/dna_tools/post_alignment_tools/GenomeAnalysisTK-2.8-1/raphael.poujol_umontreal.ca.key -T VariantRecalibrator -R /scratch/ymb-542-aa/pancreas/Genomes/hg19.fa -input /scratch/ymb-542-aa/pancreas/Calling/sub1_focus.haplo.vcf -mode SNP -resource:hapmap,known=false,training=true,truth=true,prior=15.0 /scratch/ymb-542-aa/pancreas/Genomes/hapmap_3.3.hg19.vcf -resource:omni,known=false,training=true,truth=false,prior=10.0 /scratch/ymb-542-aa/pancreas/Genomes/1000G_omni2.5.hg19.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 /scratch/ymb-542-aa/pancreas/Genomes/dbsnp_138.hg19_noXY.vcf -an QD -an DP -an FS -an MQ -tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 -recalFile /scratch/ymb-542-aa/pancreas/Calling/sub1_focus.snps.recal -tranchesFile /scratch/ymb-542-aa/pancreas/Calling/sub1_focus.snps.tranches -rscriptFile /scratch/ymb-542-aa/pancreas/Calling/sub1_focus.snps.plots.R INFO 20:41:18,342 HelpFormatter - Date/Time: 2014/03/18 20:41:18 INFO 20:41:18,342 HelpFormatter - -------------------------------------------------------------------------------- INFO 20:41:18,342 HelpFormatter - -------------------------------------------------------------------------------- INFO 20:41:18,367 ArgumentTypeDescriptor - Dynamically determined type of /scratch/ymb-542-aa/pancreas/Calling/sub1_focus.haplo.vcf to be VCF INFO 20:41:18,395 ArgumentTypeDescriptor - Dynamically determined type of /scratch/ymb-542-aa/pancreas/Genomes/hapmap_3.3.hg19.vcf to be VCF INFO 20:41:18,400 ArgumentTypeDescriptor - Dynamically determined type of /scratch/ymb-542-aa/pancreas/Genomes/1000G_omni2.5.hg19.vcf to be VCF INFO 20:41:18,404 ArgumentTypeDescriptor - Dynamically determined type of /scratch/ymb-542-aa/pancreas/Genomes/dbsnp_138.hg19_noXY.vcf to be VCF INFO 20:41:19,154 GenomeAnalysisEngine - Strictness is SILENT INFO 20:41:19,258 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 INFO 20:41:19,313 RMDTrackBuilder - Loading Tribble index from disk for file /scratch/ymb-542-aa/pancreas/Calling/sub1_focus.haplo.vcf INFO 20:41:19,346 RMDTrackBuilder - Loading Tribble index from disk for file /scratch/ymb-542-aa/pancreas/Genomes/hapmap_3.3.hg19.vcf INFO 20:41:19,447 RMDTrackBuilder - Loading Tribble index from disk for file /scratch/ymb-542-aa/pancreas/Genomes/1000G_omni2.5.hg19.vcf INFO 20:41:19,473 RMDTrackBuilder - Loading Tribble index from disk for file /scratch/ymb-542-aa/pancreas/Genomes/dbsnp_138.hg19_noXY.vcf INFO 20:41:19,561 MicroScheduler - Running the GATK in parallel mode with 8 total threads, 1 CPU thread(s) for each of 8 data thread(s), of 8 processors available on this machine INFO 20:41:19,608 GenomeAnalysisEngine - Preparing for traversal INFO 20:41:19,622 GenomeAnalysisEngine - Done preparing for traversal
INFO 20:41:19,622 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 20:41:19,622 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining WARN 20:41:19,637 Utils - ******************************************************************************** WARN 20:41:19,637 Utils - * WARNING: WARN 20:41:19,637 Utils - * WARN 20:41:19,637 Utils - * Rscript not found in environment path. WARN 20:41:19,637 Utils - * /scratch/ymb-542-aa/pancreas/Calling/sub1_focus.snps.plots.R will be WARN 20:41:19,637 Utils - * generated but PDF plots will not. WARN 20:41:19,637 Utils - ******************************************************************************** INFO 20:41:19,640 TrainingSet - Found hapmap track: Known = false Training = true Truth = true Prior = Q15.0 INFO 20:41:19,640 TrainingSet - Found omni track: Known = false Training = true Truth = false Prior = Q10.0 INFO 20:41:19,641 TrainingSet - Found dbsnp track: Known = true Training = false Truth = false Prior = Q2.0 INFO 20:41:19,698 RMDTrackBuilder - Loading Tribble index from disk for file /scratch/ymb-542-aa/pancreas/Calling/sub1_focus.haplo.vcf INFO 20:41:19,705 RMDTrackBuilder - Loading Tribble index from disk for file /scratch/ymb-542-aa/pancreas/Calling/sub1_focus.haplo.vcf INFO 20:41:19,713 RMDTrackBuilder - Loading Tribble index from disk for file /scratch/ymb-542-aa/pancreas/Genomes/hapmap_3.3.hg19.vcf INFO 20:41:19,722 RMDTrackBuilder - Loading Tribble index from disk for file /scratch/ymb-542-aa/pancreas/Calling/sub1_focus.haplo.vcf INFO 20:41:19,726 RMDTrackBuilder - Loading Tribble index from disk for file /scratch/ymb-542-aa/pancreas/Genomes/hapmap_3.3.hg19.vcf INFO 20:41:19,736 RMDTrackBuilder - Loading Tribble index from disk for file /scratch/ymb-542-aa/pancreas/Calling/sub1_focus.haplo.vcf INFO 20:41:19,739 RMDTrackBuilder - Loading Tribble index from disk for file /scratch/ymb-542-aa/pancreas/Genomes/1000G_omni2.5.hg19.vcf INFO 20:41:19,747 RMDTrackBuilder - Loading Tribble index from disk for file /scratch/ymb-542-aa/pancreas/Calling/sub1_focus.haplo.vcf INFO 20:41:19,751 RMDTrackBuilder - Loading Tribble index from disk for file /scratch/ymb-542-aa/pancreas/Genomes/1000G_omni2.5.hg19.vcf INFO 20:41:19,760 RMDTrackBuilder - Loading Tribble index from disk for file /scratch/ymb-542-aa/pancreas/Calling/sub1_focus.haplo.vcf INFO 20:41:19,763 RMDTrackBuilder - Loading Tribble index from disk for file /scratch/ymb-542-aa/pancreas/Genomes/hapmap_3.3.hg19.vcf INFO 20:41:19,772 RMDTrackBuilder - Loading Tribble index from disk for file /scratch/ymb-542-aa/pancreas/Calling/sub1_focus.haplo.vcf INFO 20:41:19,775 RMDTrackBuilder - Loading Tribble index from disk for file /scratch/ymb-542-aa/pancreas/Genomes/dbsnp_138.hg19_noXY.vcf INFO 20:41:19,845 RMDTrackBuilder - Loading Tribble index from disk for file /scratch/ymb-542-aa/pancreas/Genomes/hapmap_3.3.hg19.vcf INFO 20:41:19,856 RMDTrackBuilder - Loading Tribble index from disk for file /scratch/ymb-542-aa/pancreas/Genomes/dbsnp_138.hg19_noXY.vcf INFO 20:41:19,932 RMDTrackBuilder - Loading Tribble index from disk for file /scratch/ymb-542-aa/pancreas/Genomes/hapmap_3.3.hg19.vcf INFO 20:41:19,947 RMDTrackBuilder - Loading Tribble index from disk for file /scratch/ymb-542-aa/pancreas/Genomes/1000G_omni2.5.hg19.vcf INFO 20:41:21,428 RMDTrackBuilder - Loading Tribble index from disk for file /scratch/ymb-542-aa/pancreas/Genomes/hapmap_3.3.hg19.vcf INFO 20:41:21,437 RMDTrackBuilder - Loading Tribble index from disk for file /scratch/ymb-542-aa/pancreas/Genomes/dbsnp_138.hg19_noXY.vcf INFO 20:41:21,492 RMDTrackBuilder - Loading Tribble index from disk for file /scratch/ymb-542-aa/pancreas/Genomes/hapmap_3.3.hg19.vcf INFO 20:41:21,503 RMDTrackBuilder - Loading Tribble index from disk for file /scratch/ymb-542-aa/pancreas/Genomes/1000G_omni2.5.hg19.vcf INFO 20:41:21,514 RMDTrackBuilder - Loading Tribble index from disk for file /scratch/ymb-542-aa/pancreas/Genomes/1000G_omni2.5.hg19.vcf INFO 20:41:21,526 RMDTrackBuilder - Loading Tribble index from disk for file /scratch/ymb-542-aa/pancreas/Genomes/1000G_omni2.5.hg19.vcf INFO 20:41:21,538 RMDTrackBuilder - Loading Tribble index from disk for file /scratch/ymb-542-aa/pancreas/Genomes/dbsnp_138.hg19_noXY.vcf INFO 20:41:21,593 RMDTrackBuilder - Loading Tribble index from disk for file /scratch/ymb-542-aa/pancreas/Genomes/1000G_omni2.5.hg19.vcf INFO 20:41:21,605 RMDTrackBuilder - Loading Tribble index from disk for file /scratch/ymb-542-aa/pancreas/Genomes/dbsnp_138.hg19_noXY.vcf INFO 20:41:21,667 RMDTrackBuilder - Loading Tribble index from disk for file /scratch/ymb-542-aa/pancreas/Genomes/dbsnp_138.hg19_noXY.vcf INFO 20:41:21,859 RMDTrackBuilder - Loading Tribble index from disk for file /scratch/ymb-542-aa/pancreas/Genomes/dbsnp_138.hg19_noXY.vcf INFO 20:41:49,625 ProgressMeter - chr6:33023946 2.48e+07 30.0 s 1.0 s 34.9% 85.0 s 55.0 s INFO 20:42:19,626 ProgressMeter - chr14:38996406 5.30e+07 60.0 s 1.0 s 76.3% 78.0 s 18.0 s INFO 20:42:36,649 VariantDataManager - QD: mean = 16.83 standard deviation = 7.62 INFO 20:42:36,653 VariantDataManager - DP: mean = 19.65 standard deviation = 12.45 INFO 20:42:36,658 VariantDataManager - FS: mean = 0.41 standard deviation = 1.14 INFO 20:42:36,660 VariantDataManager - MQ: mean = 40.98 standard deviation = 2.71 INFO 20:42:36,718 VariantDataManager - Annotations are now ordered by their information content: [MQ, DP, QD, FS] INFO 20:42:36,720 VariantDataManager - Training with 5929 variants after standard deviation thresholding. INFO 20:42:36,729 GaussianMixtureModel - Initializing model with 100 k-means iterations... INFO 20:42:37,020 VariantRecalibratorEngine - Finished iteration 0. INFO 20:42:37,163 VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.32548 INFO 20:42:37,262 VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.40180 INFO 20:42:37,360 VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 0.24424 INFO 20:42:37,459 VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 0.30560 INFO 20:42:37,557 VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.07436 INFO 20:42:37,655 VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.02595 INFO 20:42:37,753 VariantRecalibratorEngine - Finished iteration 35. Current change in mixture coefficients = 0.01395 INFO 20:42:37,851 VariantRecalibratorEngine - Finished iteration 40. Current change in mixture coefficients = 0.01163 INFO 20:42:37,948 VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.01117 INFO 20:42:38,046 VariantRecalibratorEngine - Finished iteration 50. Current change in mixture coefficients = 0.02233 INFO 20:42:38,144 VariantRecalibratorEngine - Finished iteration 55. Current change in mixture coefficients = 0.01832 INFO 20:42:38,242 VariantRecalibratorEngine - Finished iteration 60. Current change in mixture coefficients = 0.01221 INFO 20:42:38,340 VariantRecalibratorEngine - Finished iteration 65. Current change in mixture coefficients = 0.01370 INFO 20:42:38,438 VariantRecalibratorEngine - Finished iteration 70. Current change in mixture coefficients = 0.04717 INFO 20:42:38,536 VariantRecalibratorEngine - Finished iteration 75. Current change in mixture coefficients = 0.01022 INFO 20:42:38,634 VariantRecalibratorEngine - Finished iteration 80. Current change in mixture coefficients = 0.00365 INFO 20:42:38,731 VariantRecalibratorEngine - Finished iteration 85. Current change in mixture coefficients = 0.00875 INFO 20:42:38,829 VariantRecalibratorEngine - Finished iteration 90. Current change in mixture coefficients = 0.00391 INFO 20:42:38,927 VariantRecalibratorEngine - Finished iteration 95. Current change in mixture coefficients = 0.00411 INFO 20:42:39,005 VariantRecalibratorEngine - Convergence after 99 iterations! INFO 20:42:39,037 VariantRecalibratorEngine - Evaluating full set of 12403 variants... INFO 20:42:39,038 VariantDataManager - Training with worst 0 scoring variants --> variants with LOD <= -5.0000.

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

org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Unable to retrieve result at org.broadinstitute.sting.gatk.executive.HierarchicalMicroScheduler.execute(HierarchicalMicroScheduler.java:190) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:313) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91) Caused by: java.lang.NullPointerException at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorEngine.generateModel(VariantRecalibratorEngine.java:83) at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:359) at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:139) at org.broadinstitute.sting.gatk.executive.HierarchicalMicroScheduler.notifyTraversalDone(HierarchicalMicroScheduler.java:226) at org.broadinstitute.sting.gatk.executive.HierarchicalMicroScheduler.execute(HierarchicalMicroScheduler.java:183) ... 5 more

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.8-1-g932cd3a):
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 ------------------------------------------------------------------------------------------

`

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,178Administrator, GATK Developer admin

    Hi there,

    Does this error happen again every time you run it? And does it happen if you deactivate multithreading?

    Geraldine Van der Auwera, PhD

  • raphael123raphael123 MontrealPosts: 3Member

    Your totaly rigth, a new run give me my results.

    I am runing on a little interval so do I increase the probability of such an error with the interval size ?

    Will I change the results for SNPS if I change the interval or run over all genome ?

    thx

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,178Administrator, GATK Developer admin

    It depends. It could be a one-time glitch that won't happen again. Or it could be a compatibility issue between your system and the GATK's multithreading system (which happens sometimes). If so, running on more of the genome will indeed increase the chance that it will happen again. You may want to try using a scatter/gather approach and job management program like Queue (see docs).

    Changing the interval list may cause minor differences in calls between runs due to downsampling effects, but typically the effects are marginal and nothing to worry about.

    Geraldine Van der Auwera, PhD

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