Error in X[, index] : subscript out of bounds

[njrob25]

Hello,

I am receiving this error message. When I try traceback, my R is not returning any information. My myGD has 41528 obs. of 7703 variables, my myGM has 7703 obs. of 3 variables, and my myY has 41528 obs. of 2 variables.

GenoPhenoGAPIT <- GAPIT(Y=myY,

•                     GD = myGD,
  

•                     GM = myGM,
  

•                     PCA.total = 3,
  

•                     model=c("GLM","MLM","MLMM","FarmCPU","Blink"),
  

•                     SNP.MAF = 0.05,
  

•                     Multiple_analysis = TRUE)
  

[1] "--------------------- Welcome to GAPIT ----------------------------"
[1] "GLM" "MLM" "MLMM" "FarmCPU" "Blink"
[1] "--------------------Processing traits----------------------------------"
[1] "Phenotype provided!"
[1] "The 1 model in all."
[1] "GLM"
[1] "GAPIT.DP in process..."
[1] "GAPIT will filter marker with MAF setting !!"
[1] "The markers will be filtered by SNP.MAF: 0.05"
maf_index
FALSE TRUE
209 7493
[1] "Calculating kinship..."
[1] "Number of individuals and SNPs are 24181 and 7493"
[1] "Calculating ZHANG relationship defined by Zhiwu Zhang..."
[1] "substracting mean..."
[1] "Getting X'X..."
[1] "Adjusting..."
[1] "Adjustment by the minimum diagonal"
[1] "Calculating kinship with Zhang method: done"
[1] "kinship calculated"
[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"
Error in X[, index] : subscript out of bounds