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SNP Recalibration Model

I am trying to run a SNP Recalibration model with the procedure explained here: https://www.broadinstitute.org/gatk/guide/article?id=2805
I'm currently running STEP 2: Build a SNP recalibration model.
For my -resource sets, I am using a truth set that I developed my multiple SNP callers (This will be both a truth and training set) and for another -resource set, I have subset my input file and using that as my training set only.

Here is my command line:

java -jar "$GATK" \
-T VariantRecalibrator \
-R "$iREF" \
-input "$input_file" \
-resource:truthset,known=false,training=true,truth=true,prior=12.0 "$truth" \
-resource:trainset,known=false,training=true,truth=false,prior=2.0 "$train" \
-an DP \
-an QD \
-an FS \
-an SOR \
-an MQ \
-an MQRankSum \
-an ReadPosRankSum \
-an InbreedingCoeff \
-mode SNP \
-tranche 99.9 -tranche 90.0 \
-recalFile recalibrate_SNP.recal \
-tranchesFile recalibrate_SNP.tranches \
-rscriptFile recalibrate_SNP_plots.R

This is the error that I got:

INFO 00:42:05,938 VariantRecalibratorEngine - Finished iteration 40. Current change in mixture coefficients = 0.00393
INFO 00:42:05,984 VariantRecalibratorEngine - Convergence after 43 iterations!
INFO 00:42:06,046 VariantRecalibratorEngine - Evaluating full set of 224012 variants...
INFO 00:42:06,060 VariantDataManager - Training with worst 0 scoring variants --> variants with LOD <= -5.0000.
INFO 00:42:16,371 GATKRunReport - Uploaded run statistics report to AWS S3

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
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 ------------------------------------------------------------------------------------------

Could you please help resolve this issue?

Thanks

Answers

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