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.
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!

"No data found" error came up when performing VQSR on SNPs

EmmaDanEmmaDan ChinaMember


I am doing VQSR with -mode SNP, and it came up with a error saying "No data found". Here is my command line:

/path/to/java -Xmx7g -Djava.io.tmpdir=pwd/tmp -jar /path/to/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar -T VariantRecalibrator -R /path/to/Data/bundle_2.8_hg19/ucsc.hg19.fasta -input /path/to/VQSR_0722/All8sample.vcf -resource:hapmap,known=false,training=true,truth=true,prior=15.0 /path/to/Data/bundle_2.8_hg19/hapmap_3.3.hg19.vcf -resource:omni,known=false,training=true,truth=false,prior=12.0 /path/to/Data/bundle_2.8_hg19/1000G_omni2.5.hg19.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=6.0 /ifshk1/BC_MD/GROUP/Workflow/Data/bundle_2.8_hg19/dbsnp_138.hg19.vcf -an QD -an FS -an SOR -an MQ -an MQRankSum -an ReadPosRankSum -mode SNP -tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 -recalFile /path/to/VQSR_0722/All8sample.snp.VQSR.recal -tranchesFile /path/to/VQSR_0722/All8sample.snp.VQSR.tranches -rscriptFile /path/to/VQSR_0722/All8sample.snp.VQSR.plot.R

I noticed a line in the log file that saying "INFO 08:08:09,495 VariantDataManager - Training with worst 0 scoring variants --> variants with LOD <= -5.0000.". This is followed by the error message given below:

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

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.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:116)
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)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.3-0-g37228af):
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: No data found.

I used to have error message of "No data found" when performing VQSR with -mode INDEL, and I know it was due to the fact that there were not enough indel variants overlapped with the training data. But this time the mode is SNP. I counted the total for SNPs in my dataset (awk 'length ($4)==1 && length ($5)==1' /path/to/VQSR_0722/All8sample.vcf | wc -l) and there are 184,540 SNPs. I wonder if it is the same cause as that for INDEL VQSR error?

Thank you!




  • SheilaSheila Broad InstituteMember, Broadie admin

    Hi Emma,

    I am assuming you have 8 samples in you input VCF. VQSR requires at least 30 exome samples to build a good model. You can either do hard filtering or add in data from 1000Genomes samples.


  • tommycarstensentommycarstensen United KingdomMember ✭✭✭

    @EmmaDan Perhaps you can try with --maxGaussians 4 as suggested here?

    P.S. Your awk command is not correct in the case of multiallelic SNPs. As far as I recall GATK can count and return statistics. I use another competing tool myself, that I will not advertise for here.

    P.P.S. The latest version of GATK is 3.4.

Sign In or Register to comment.