GATK4: an error with VariantRecalibrator

Question

[tongshiyuan]

Hi,

I use the VariantRecalibrator with GATK-4.0.10.1, and my sample is WGS data. I use CombineGVCFs with trio. it make an error:

18:19:38.004 WARN  VariantDataManager - WARNING: Very large training set detected. Downsampling to 2500000 training variants.  
18:19:38.150 INFO  GaussianMixtureModel - Initializing model with 100 k-means iterations...  
18:23:57.006 INFO  VariantRecalibratorEngine - Finished iteration 0.  
18:25:35.317 INFO  VariantRecalibratorEngine - Finished iteration 5.    Current change in mixture coefficients = 2.18508  
18:27:22.226 INFO  VariantRecalibratorEngine - Finished iteration 10.   Current change in mixture coefficients = 2.44691  
18:29:11.724 INFO  VariantRecalibratorEngine - Finished iteration 15.   Current change in mixture coefficients = 0.45284  
18:31:01.478 INFO  VariantRecalibratorEngine - Finished iteration 20.   Current change in mixture coefficients = 0.14604  
18:32:51.452 INFO  VariantRecalibratorEngine - Finished iteration 25.   Current change in mixture coefficients = 0.07146  
18:34:40.870 INFO  VariantRecalibratorEngine - Finished iteration 30.   Current change in mixture coefficients = 0.04044  
18:36:30.225 INFO  VariantRecalibratorEngine - Finished iteration 35.   Current change in mixture coefficients = 0.03140  
18:38:20.063 INFO  VariantRecalibratorEngine - Finished iteration 40.   Current change in mixture coefficients = 0.03935  
18:40:07.539 INFO  VariantRecalibratorEngine - Finished iteration 45.   Current change in mixture coefficients = 0.02160  
18:41:56.840 INFO  VariantRecalibratorEngine - Finished iteration 50.   Current change in mixture coefficients = 0.00508  
18:43:43.879 INFO  VariantRecalibratorEngine - Finished iteration 55.   Current change in mixture coefficients = 0.00669  
18:45:33.833 INFO  VariantRecalibratorEngine - Finished iteration 60.   Current change in mixture coefficients = 0.02022  
18:47:22.956 INFO  VariantRecalibratorEngine - Finished iteration 65.   Current change in mixture coefficients = 0.01239  
18:49:12.972 INFO  VariantRecalibratorEngine - Finished iteration 70.   Current change in mixture coefficients = 0.00722  
18:51:02.744 INFO  VariantRecalibratorEngine - Finished iteration 75.   Current change in mixture coefficients = 0.00462  
18:52:52.044 INFO  VariantRecalibratorEngine - Finished iteration 80.   Current change in mixture coefficients = 0.00322  
18:54:40.463 INFO  VariantRecalibratorEngine - Finished iteration 85.   Current change in mixture coefficients = 0.00239  
18:56:07.809 INFO  VariantRecalibratorEngine - Convergence after 89 iterations!  
18:56:23.014 INFO  VariantRecalibratorEngine - Evaluating full set of 5415683 variants...  
18:56:23.014 WARN  VariantRecalibratorEngine - Evaluate datum returned a NaN.  
18:56:23.244 INFO  VariantDataManager - Selected worst 0 scoring variants --> variants with LOD <= -5.0000.  
18:56:23.247 INFO  VariantRecalibrator - Shutting down engine  
[April 3, 2019 6:56:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 43.62 minutes.  
Runtime.totalMemory()=13087801344 
java.lang.IllegalArgumentException: No data found.  
        at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibratorEngine.generateModel(VariantRecalibratorEngine.java:34)  
        at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.onTraversalSuccess(VariantRecalibrator.java:656)  
        at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:968)  
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)  
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)  
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)  
        at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)  
        at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)  
        at org.broadinstitute.hellbender.Main.main(Main.java:289)

and my command line is :

gatk VariantRecalibrator -R /my/path/of/reference/ucsc.hg19.fasta -V /my/path/of/familymerge/vcf/W007.HC.vcf.gz  
--resource hapmap,known=false,training=true,truth=true,
prior=15.0:$GATK_bundle/hg19/hapmap_3.3.hg19.sites.vcf  
--resource omini,known=false,training=true,truth=false,prior=12.0:$GATK_bundle/hg19/1000G_omni2.5.hg19.sites.vcf  
--resource 1000G,known=false,training=true,truth=false,prior=10.0:$GATK_bundle/hg19/1000G_phase1.snps.high_confidence.hg19.sites.vcf  
--resource dbsnp,known=true,training=false,truth=false,prior=6.0:$GATK_bundle/hg19/dbsnp_138.hg19.vcf  
-an DP -an QD -an FS -an SOR -an ReadPosRankSum -an MQRankSum -mode SNP -tranche 100.0 -tranche 99.9 -tranche
 99.0 -tranche 95.0 -tranche 90.0  
--rscript-file /my/path/of/outdir/W007.HC.snps.plots.R  
--tranches-file /my/path/of/outdir/W007.HC.snps.tranches  
-O /my/path/of/outdir/W007.HC.snps.recal `

[finswimmer]

Hello and welcome to biostars tongshiyuan ,

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Thank you!