I am getting following error while using imputVCF function:
Exception in thread "main" java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at ngsep.NGSEPcore.main(NGSEPcore.java:58)
Caused by: java.lang.NullPointerException
at ngsep.variants.imputation.GenotypeImputationHMM.runBaumWelchStep(GenotypeImputationHMM.java:281)
at ngsep.variants.imputation.GenotypeImputationHMM.train(GenotypeImputationHMM.java:234)
at ngsep.variants.imputation.GenotypeImputationHMM.imputeGenotypes(GenotypeImputationHMM.java:198)
at ngsep.variants.imputation.GenotypeImputer.imputeGenotypesHMM(GenotypeImputer.java:261)
at ngsep.variants.imputation.GenotypeImputer.imputeGenotypes(GenotypeImputer.java:246)
at ngsep.variants.imputation.GenotypeImputer.impute(GenotypeImputer.java:207)
at ngsep.variants.imputation.GenotypeImputer.main(GenotypeImputer.java:102)
... 5 more
Please help
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I am getting following error while using imputVCF function:
Exception in thread "main" java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at ngsep.NGSEPcore.main(NGSEPcore.java:58)
Caused by: java.lang.NullPointerException
at ngsep.variants.imputation.GenotypeImputationHMM.runBaumWelchStep(GenotypeImputationHMM.java:281)
at ngsep.variants.imputation.GenotypeImputationHMM.train(GenotypeImputationHMM.java:234)
at ngsep.variants.imputation.GenotypeImputationHMM.imputeGenotypes(GenotypeImputationHMM.java:198)
at ngsep.variants.imputation.GenotypeImputer.imputeGenotypesHMM(GenotypeImputer.java:261)
at ngsep.variants.imputation.GenotypeImputer.imputeGenotypes(GenotypeImputer.java:246)
at ngsep.variants.imputation.GenotypeImputer.impute(GenotypeImputer.java:207)
at ngsep.variants.imputation.GenotypeImputer.main(GenotypeImputer.java:102)
... 5 more
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Please find attached the log file
May I ask, which version of NGSEP are you using?