ERROR stack trace ; Unable to retrieve result ; A GATK RUNTIME ERROR has occurred

tianmingtianming ChinaPosts: 4Member

Hi, Thanks very much for your answers for my previous questions. It seems that I encountered another difficulties when I run the QVSR steps because some ERROR information was spotted on the screen. These Error info is as follows:

INFO 18:10:01,046 GaussianMixtureModel - Initializing model with 30 k-means iterations... INFO 18:10:01,165 VariantRecalibratorEngine - Finished iteration 0. INFO 18:10:01,186 VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.15059 INFO 18:10:01,196 VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.06115 INFO 18:10:01,206 VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 0.34881 INFO 18:10:01,208 VariantRecalibratorEngine - Convergence after 16 iterations! INFO 18:10:01,211 VariantDataManager - Found 0 variants overlapping bad sites training tracks. INFO 18:10:27,971 ProgressMeter - chr1:249230318 4.34e+06 90.0 s 20.0 s 100.0% 90.0 s 0.0 s

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.VariantDataManager.selectWorstVariants(VariantDataManager.java:278) at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:333) at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:132) 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 2.7-2-g6bda569):
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 think the parameter I set are all right:

java -jar /ifs1/ST_POP/USER/lantianming/HUM/bin/GenomeAnalysisTK-2.7-2-g6bda569/GenomeAnalysisTK.jar -R /ifs1/ST_POP/USER/lantianming/HUM/reference_human/chr1.fa --maxGaussians 4 -numBad 4000 -T VariantRecalibrator -mode SNP
-input /ifs1/ST_POP/USER/lantianming/HUM/align/bwa/split_1_22_X_Y_M/chr1/chr1.recal_10.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=6.0 /nas/RD_09C/resequencing/soft/pipeline/GATK/bundle/2.5/hg19/dbsnp_137.hg19.vcf
-resource:hapmap,known=false,training=true,truth=true,prior=15.0 /nas/RD_09C/resequencing/soft/pipeline/GATK/bundle/2.5/hg19/hapmap_3.3.hg19.vcf -resource:omni,known=false,training=true,truth=false,prior=12.0 /nas/RD_09C/resequencing/soft/pipeline/GATK/bundle/2.5/hg19/1000G_omni2.5.hg19.vcf -an DP -an FS -an HaplotypeScore -an MQ0 -an MQ -an QD -recalFile /ifs1/ST_POP/USER/lantianming/HUM/align/bwa/split_1_22_X_Y_M/chr1/chr1.vcf.snp_11.recal -tranchesFile /ifs1/ST_POP/USER/lantianming/HUM/align/bwa/split_1_22_X_Y_M/chr1/chr1.vcf.snp_11.tranches -rscriptFile /ifs1/ST_POP/USER/lantianming/HUM/align/bwa/split_1_22_X_Y_M/chr1/chr1.vcf.snp_11.plot.R -nt 4 --TStranche 90.0 --TStranche 93.0 --TStranche 95.0 --TStranche 97.0

My input file is chr1 AND the sequencing depth is about 1× AND 4000 snp sites were call out by using UnifiedGenotyper. So what I am not sure is that whether the number of snp sites were enough for doing VQSR? Could you please give me some suggestions? thanks very much!!!

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