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.
Notice:
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.
Attention:
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!

VariantRecalibrator error

Dear GATK Team,

I'm trying to perform variant recalibration on 3 WGS sequencing data. I am following the pipeline described in Best Practices. I have generated individual g.vcf files for each patient and used GenotypeGVCFs to obtain multisample vcf for the three samples. But then I got stuck at the VQSR step. The VariantRecalibration tool throws the following error:
INFO 08:01:34,635 VariantRecalibratorEngine - Convergence after 49 iterations!
INFO 08:01:44,150 VariantRecalibratorEngine - Evaluating full set of 6602089 variants...
INFO 08:01:51,139 VariantDataManager - Training with worst 28183 scoring variants --> variants with LOD <= -5.0000.
INFO 08:01:51,140 GaussianMixtureModel - Initializing model with 100 k-means iterations...
INFO 08:01:51,535 VariantRecalibratorEngine - Finished iteration 0.
INFO 08:01:51,744 VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.13136
INFO 08:01:51,876 VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.03466
INFO 08:01:52,005 VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 0.02910
INFO 08:01:52,131 VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 0.01388
INFO 08:01:52,256 VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.00651
INFO 08:01:52,382 VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.00323
INFO 08:01:52,483 VariantRecalibratorEngine - Convergence after 34 iterations!
INFO 08:01:52,652 VariantRecalibratorEngine - Evaluating full set of 6602089 variants...

ERROR ------------------------------------------------------------------------------------------
ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.7-0-gcfedb67):
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 https://software.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: NaN LOD value assigned. Clustering with this few variants and these annotations is unsafe. Please consider raising the number of variants used to train the negative model (via --minNumBadVariants 5000, for example).
ERROR -------------------------

The command I used:
java -Djava.io.tmpdir=./tmp -XX:ParallelGCThreads=1 -jar GenomeAnalysisTK.jar \
-T VariantRecalibrator \
-R GRCh37-lite.fa \
-input germline10.vcf \
-resource:hapmap,known=false,training=true,truth=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 \
-resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.b37.vcf \
-an MQ -MQCap 70 -an DP -an QD -an FS -an SOR -an MQRankSum -an ReadPosRankSum \
-mode SNP -tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 \
-recalFile recalibrate_SNP.recal -tranchesFile recalibrate_SNP.tranches -rscriptFile recalibrate_SNP_plots.R

-maxNumTrainingData 4000000 \

--minNumBadVariants 5000 \

There are more than 6million variants. Even after adjusted maxNumTrainingData and minNumBadVariants, I kept getting this message. I searched the forum and I am not sure If I need more samples or if I have a problem in my command.

Thanks a lot!

Chunxu

Tagged:

Best Answer

Answers

Sign In or Register to comment.