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Error with GeneralPloidySNP

freeseekfreeseek Member
edited August 2012 in Ask the GATK team

I have been using successfully before the UnifiedGenotyper with the following argument: "-glm POOLSNP -pnrm POOL -ploidy 4". Now I changed that to "-glm GeneralPloidySNP -ploidy 4" as I understand the model names have changed. Though, I get the following error:

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

java.lang.IllegalArgumentException: No enum const class org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel$Model.GENERALPLOIDYSNP
at java.lang.Enum.valueOf(Enum.java:214)
at org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel$Model.valueOf(GenotypeLikelihoodsCalculationModel.java:59)
at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.getGLModelsToUse(UnifiedGenotyperEngine.java:682)
at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.calculateLikelihoodsAndGenotypes(UnifiedGenotyperEngine.java:179)
at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:354)
at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:119)
at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:65)
at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:18)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:62)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:265)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:93)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.1-4-ge32f61d):
ERROR
ERROR Please visit the wiki to see if this is a known problem
ERROR If not, please post the error, 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 enum const class org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel$Model.GENERALPLOIDYSNP
ERROR ------------------------------------------------------------------------------------------

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