The current GATK version is 3.8-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Get notifications!

You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements, by following the instructions given here.

Got a problem?

1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

Did we ask for a bug report?

Then follow instructions in Article#1894.

Formatting tip!

Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block as demonstrated here.

Jump to another community
Download the latest Picard release at
GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

error while running VariantRecalibrator

xiaojunzhaoxiaojunzhao Member
edited November 2012 in Ask the GATK team

experiment: target enrichment and sequencing using Illumina platform

raw VCF file from UnifiedGenotyper -> Variantrecalibrator

I got the following error, any potential explanation? Thanks

##### **ERROR MESSAGE: Bad input: Error during negative model training. Minimum number of variants to use in training is larger than the whole call set. One can attempt to lower the --minNumBadVariants arugment but this is unsafe.**

I tried to lower this number, but different error message came up.

script used:

java -Xmx4g -jar GenomeAnalysisTK.jar -T VariantRecalibrator \
-mode BOTH -nt 4 \
-R hg19_all_MT.fasta \
-input \
-resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.b37.sites.fy_left.vcf \
-resourcemni,known=false,training=true,truth=false,prior=12.0 \
-resource:dbsnp,known=true,training=false,truth=false,prior=8.0 dbsnp137_sort_fy_left.vcf \
-recalFile \
-tranchesFile \
-rscriptFile \
-tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 -tranche 85.0 -tranche 80.0 \
-an QD -an HaplotypeScore -an MQRankSum -an ReadPosRankSum -an MQ -an FS -an HRun 
Post edited by Geraldine_VdAuwera on

Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Your first error means what it says: you don't have enough variants to train the recalibration model. This is explained in the documentation on variant recalibration.

    What is the second error message?

    By the way, if the command you copied here is copied exactly from what you used, I can tell you there's a problem at the line that starts with -resourcemni.

  • Hi, Geraldine,

    Sorry, it was my typo when I posted code. In my code, it was "resource:omni,"

    After I get this error, I added
    "--minNumBadVariants 1500"

    I get the following errors:

    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 --percentBadVariants 0.05, for example) or lowering the maximum number of Gaussians to use in the model (via --maxGaussians 4, for example)

    Is it due to my incorrect "resource" file?

Sign In or Register to comment.