model selection error

[sebranham]

Running the following code with model selection = true gives the following errors and does not produce the BIC files. The same input files will produce output without model selection = true for the multiple analysis option. Any advice would be appreciated.

myGAPIT <- GAPIT(Y=myY,G=myG,PCA.total=5,Model.selection = TRUE)
[1] "--------------------- Welcome to GAPIT ----------------------------"
[1] "MLM"
[1] "--------------------Processing traits----------------------------------"
[1] "Phenotype provided!"
[1] "The 1 model in all."
[1] "MLM"
[1] "GAPIT.DP in process..."
[1] "Converting genotype..."
[1] "Converting HapMap format to numerical under model of Middle"
[1] "Perform numericalization"
[1] "Succesfuly finished converting HapMap which has bits of 2"
[1] "Converting genotype done."
[1] "GAPIT will filter marker with MAF setting !!"
[1] "The markers will be filtered by SNP.MAF: 0"
maf_index
TRUE
44830
[1] "Calculating kinship..."
[1] "Number of individuals and SNPs are 125 and 44830"
[1] "Calculating ZHANG relationship defined by Zhiwu Zhang..."
[1] "substracting mean..."
[1] "Getting X'X..."
[1] "Adjusting..."
[1] "Adjustment by the minimum diagonal"
[1] "Adjustment by the minimum off diagonal"
[1] "Calculating kinship with Zhang method: done"
[1] "kinship calculated"
[1] "Creating heat map for kinship..."
[1] "Kinship heat map created"
[1] "Adding IDs to kinship..."
[1] "Writing kinship to file..."
[1] "Kinship save as file"
[1] "Kinship created!"
[1] "Calling prcomp..."
[1] "Creating PCA graphs..."
[1] "Joining taxa..."
[1] "Exporting PCs..."
[1] "PC created"
[1] "Filting marker for GAPIT.Genotype.View function ..."
[1] "GAPIT.Genotype.View . pdfs generate.successfully!"
[1] 125 6
[1] "GAPIT.DP accomplished successfully for multiple traits. Results are saved"
[1] "Processing trait: flesh_color"
[1] "GAPIT.Phenotype.View in press..."
[1] "GAPIT.Phenotype.View output pdf has been generated successfully!"
[1] "--------------------Phenotype and Genotype ----------------------------------"
[1] "Zhang"
[1] TRUE
[1] "There are 1 traits in phenotype data."
[1] "There are 125 individuals in phenotype data."
[1] "There are 44830 markers in genotype data."
[1] "Phenotype and Genotype are test OK !!"
[1] "--------------------GAPIT Logical Done----------------------------------"
[1] "GAPIT.IC in process..."
[1] "There is 0 Covarinces."
[1] "There are 80 common individuals in genotype , phenotype and CV files."
[1] "The dimension of total CV is "
[1] 80 6
[1] "GAPIT.IC accomplished successfully for multiple traits. Results are saved"
[1] "GAPIT.SS in process..."
[1] "GAPIT will be into GWAS approach..."
[1] "Zhang"
[1] "The GAPIT would go into Main..."
[1] "------------Examining data (QC)------------------------------------------"
[1] "Try to group from and to were set to 1"
[1] "------------Examining data (QC) done-------------------------------------"
[1] "-------------------Sandwich burger and dressing------------------------"
The upper bound of groups is too high. It was set to the size of kinship!
The lower bound of groups is too high. It was set to the size of kinship!
[1] "-------------------------Iteration in process--------------------------"
[1] "Total iterations: 1"
[1] "-------Mixed model with Kinship-----------------------------"
Error in diag(1/ves, nrow(K)) : 'x' must have positive length
In addition: There were 16 warnings (use warnings() to see them)
warnings()
Warning messages:
1: In order(as.numeric(as.character(chor_taxa))) : NAs introduced by coercion
2: In log(colSums(Etasq/Lambdas)) : NaNs produced
3: In log(Lambdas) : NaNs produced
4: In log(lambda + delta) : NaNs produced
5: In log(sum(etas * etas/(lambda + delta))) : NaNs produced
6: In log(lambda + delta) : NaNs produced
7: In log(lambda + delta) : NaNs produced
8: In min(LL[!index]) : no non-missing arguments to min; returning Inf
9: In log(colSums(Etasq/Lambdas)) : NaNs produced
10: In log(Lambdas) : NaNs produced
11: In log(lambda + delta) : NaNs produced
12: In log(sum(etas * etas/(lambda + delta))) : NaNs produced
13: In log(lambda + delta) : NaNs produced
14: In log(lambda + delta) : NaNs produced
15: In min(LL[!index]) : no non-missing arguments to min; returning Inf
16: In rm(eig.R) : object 'eig.R' not found

[Lightoscope]

I'm getting the same error with the most recent version of GAPIT.