Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

GATK 2.8 variant recalibration code exception

Hi there,

I've a problem running GATK2.8's VariantRecalibrator, I get Code Exception (java.lang.NullPointerException). Below is the error trace:

INFO 17:05:37,528 GenomeAnalysisEngine - Preparing for traversal
INFO 17:14:27,706 VariantDataManager - MQRankSum: mean = -0.09 standard deviation = 0.99
INFO 17:14:27,742 VariantDataManager - ReadPosRankSum: mean = 0.18 standard deviation = 0.96
INFO 17:14:27,820 VariantDataManager - Annotations are now ordered by their information content: [QD, ReadPosRankSum, MQRankSum]
INFO 17:14:27,823 VariantDataManager - Training with 2739 variants after standard deviation thresholding.
INFO 17:14:27,829 GaussianMixtureModel - Initializing model with 100 k-means iterations...
INFO 17:14:28,389 VariantRecalibratorEngine - Finished iteration 0.
INFO 17:14:28,534 VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.20522
INFO 17:14:28,601 VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.46290
INFO 17:14:28,675 VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 9.95604
INFO 17:14:28,759 VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 9.00456
INFO 17:14:28,861 VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.01190
INFO 17:14:28,951 VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.00796
INFO 17:14:29,041 VariantRecalibratorEngine - Finished iteration 35. Current change in mixture coefficients = 0.00546
INFO 17:14:29,131 VariantRecalibratorEngine - Finished iteration 40. Current change in mixture coefficients = 0.00360
INFO 17:14:29,221 VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.00218
INFO 17:14:29,239 VariantRecalibratorEngine - Convergence after 46 iterations!
INFO 17:14:29,276 VariantRecalibratorEngine - Evaluating full set of 13495 variants...
INFO 17:14:29,280 VariantDataManager - Training with worst 0 scoring variants --> variants with LOD <= -5.0000.
INFO 17:14:32,024 GATKRunReport - Uploaded run statistics report to AWS S3

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

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.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: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)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.8-1-g932cd3a):
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 MESSAGE: Code exception (see stack trace for error itself)
ERROR ------------------------------------------------------------------------------------------

And this is the command i used:

java -XX:+UseParallelGC -XX:ParallelGCThreads=8 -Xmx4g -jar ~/genomekey-data/tools/gatk2.jar -T VariantRecalibrator -R ~/genomekey-data/bwa_references/human_g1k_v37.fasta -input ~/simplex/ngs_test/snp_calling/aln.haplotyper.raw.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=8.0 ~/genomekey-data/bundle/current/dbsnp_137.b37.vcf -resource:hapmap,VCF,known=false,training=true,truth=true,prior=15.0 ~/genomekey-data/bundle/current/hapmap_3.3.b37.vcf -resource:omni,VCF,known=false,training=true,truth=false,prior=12.0 ~/genomekey-data/bundle/current/1000G_omni2.5.b37.vcf -an QD -an MQRankSum -an ReadPosRankSum -recalFile ~/simplex/ngs_test/snp_recal/aln.snp.recal -tranche 100 -tranche 99.9 -tranche 99.0 -tranche 90 -tranchesFile ~/simplex/ngs_test/snp_recal/aln.snp.tranches -rscriptFile ~/simplex/ngs_test/snp_recal/aln.snp.plots.R -mode SNP

Please note that i got the same error running GATK 2.6.
Any help or suggestions will be appreciated.



Sign In or Register to comment.