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Variant Recalibrator Error

cristianro87cristianro87 ArgentinaMember Posts: 10

I am analyzing ION PGM data

i'm getting 25 variants in one individual with the HaplotypeCaller
i try to run the VariantRecalibrator, but i get this error

WARN 18:26:10,578 VariantDataManager - WARNING: Training with very few variant sites! Please check the model reporting PDF to ensure the quality of the model is reliable.
INFO 18:26:10,580 GaussianMixtureModel - Initializing model with 100 k-means iterations...
INFO 18:26:10,636 VariantRecalibratorEngine - Finished iteration 0.
INFO 18:26:10,639 VariantRecalibratorEngine - Convergence after 3 iterations!
INFO 18:26:10,640 VariantDataManager - Training with worst 0 scoring variants --> variants with LOD <= -5.0000.
INFO 18:26:11,854 ProgressMeter - chrM:14784 8.87e+06 30.0 s 3.0 s 100.0% 30.0 s 0.0 s
INFO 18:26:12,444 GATKRunReport - Uploaded run statistics report to AWS S3

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

java.lang.IllegalArgumentException: No data found.
at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorEngine.generateModel(VariantRecalibratorEngine.java:83)
at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:392)
at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:138)
at org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:116)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:313)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:107)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.1-1-g07a4bf8):
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 Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: No data found.
ERROR ------------------------------------------------------------------------------------------

the command line i use was

java -jar /home/horus/Instaladores/GenomeAnalysisTK-3.1-1/GenomeAnalysisTK.jar -T VariantRecalibrator -R /home/horus/Escritorio/PGM/primirna/references/hg19usar.fa -input 1_raw_variants.vcf -resource:hapmap,known=false,training=true,truth=true,prior=15.0 /home/horus/Escritorio/PGM/primirna/references/hapmap_3.3.b37.vcf_nuevo -resource:omni,known=false,training=true,truth=true,prior=12.0 /home/horus/Escritorio/PGM/primirna/references/1000G_omni2.5.b37.vcf_nuevo -resource:1000G,known=false,training=true,truth=false,prior=10.0 /home/horus/Escritorio/PGM/primirna/references/Mills_and_1000G_gold_standard.indels.b37.vcf_nuevo -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 /home/horus/Escritorio/PGM/primirna/references/dbsnp_138.hg19.vcf -an DP -an QD -an FS -an MQRankSum -an ReadPosRankSum -mode SNP -tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 -recalFile 1_recalibrate_SNP.recal -tranchesFile 1_recalibrate_SNP.tranches

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