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Unknown problem whilst running Variant Recalibrator

jparker4jparker4 Member
edited February 6 in Ask the GATK team
Hi, whilst running Variant Recalibrator this error was thrown:

```
INFO 12:20:52,023 VariantRecalibratorEngine - Convergence after 70 iterations!
INFO 12:20:52,379 VariantRecalibratorEngine - Evaluating full set of 657697 variants...
WARN 12:20:52,380 VariantRecalibratorEngine - Evaluate datum returned a NaN.
INFO 12:20:52,409 VariantDataManager - Selected worst 0 scoring variants --> variants with LOD <= -5.0000.
##### 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:536)
at org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:191)
at org.broadinstitute.gatk.engine.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:115)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:323)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.8-0-ge9d806836):
##### 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
##### ERROR MESSAGE: No data found.
##### ERROR ------------------------------------------------------------------------------------------
```

The statement I am running is:

```
java -Xmx20G -Djava.io.tmpdir=/fastdata/mbp15jdp/tmp -jar ~/Downloads/GenomeAnalysisTK-3.8-0-ge9d806836/GenomeAnalysisTK.jar
-T VariantRecalibrator
-R hg38_noalt_sorted.fa
-input genotyped_gVCFs.dir/R55E.genotyped_combined.g.vcf -resource:hapmap,known=false,training=true,truth=true,prior=15.0 /shared/sudlab1/General/mirror/snp_sets/hapmap/resources_broad_hg38_v0_hapmap_3.3.hg38.vcf.gz -resource:omni,known=false,training=true,truth=true,prior=12.0 /shared/sudlab1/General/mirror/snp_sets/omni/resources_broad_hg38_v0_1000G_omni2.5.hg38.vcf.gz -resource:1000G,known=false,training=true,truth=false,prior=10.0 /shared/sudlab1/General/mirror/snp_sets/1000_genomes/ALL.1000genomes_numerical.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 /shared/sudlab1/General/mirror/snp_sets/dbsnp/dbSNP-All.chr_format.vcf
-an DP
-an QD
-an FS
-an SOR
-an MQ
-an ReadPosRankSum
-mode SNP
-tranche 100.0
-tranche 99.9
-tranche 99.0
-tranche 90.0
-recalFile variant_recalibration.dir/R55E.recalibrate_SNP.recal
-tranchesFile variant_recalibration.dir/R55E_recalibrate_SNP.tranches
-rscriptFile variant_recalibration.dir/R55E_recalibrate_SNP_plots.R
```

Strangely, even though this throws an error, running it still gives me an indexed .recal file and both the .R and .tranches files and their respective .pdfs. Any help on the cause of this and whether the output files are likely to be incomplete would be much appreciated.

Many thanks

Jacob

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