"GD does not mach GM in Manhattan !!!" Error in `[.data.frame`(GD, , !is.na(GI.MP[, 3])) :

[zhaohy1208]

Hello, I encountered an error while generating a Manhattan map while doing association analysis with multiple models in GAPIT3. I cannot run the GLM model, MLM model, and FarmCPU model, and the error message says that the GD and GP files do not match. But the gBLUP and CBLUP models work smoothly, with no Manhattan map output in the result. Can you tell me how to adjust it to ensure smooth analysis? Thank you very much!
The commands I use and the error messages are as follows:

library(multtest)
library(gplots)
library(LDheatmap)
library(genetics)
library(ape)
library(EMMREML)
library(compiler)
library(scatterplot3d)
library(grid)
library(bigmemory)
library(nloptr)
library(snpStats)
library(Matrix)
library(lme4)
library(rgl)
library(GAPIT)

myY <- read.table("gapit_traits.txt", head = TRUE)
myG <- read.table("filtered_removed.hmp.txt", head = FALSE)
myKI <- read.table("gapit.kinship.txt", head = FALSE)
myCV <- read.table("GAPIT_CV.txt", head = TRUE)

#Step 2: Run GAPIT
myGAPIT <- GAPIT(
Y=myY,
G=myG,
KI=myKI,
CV=myCV,
model=c("MLM","FarmCPU","Blink","gBLUP","CBLUP"),#c("GLM", "MLM", "CMLM",
Multiple_analysis=TRUE)

[jiabowang]

Please check your genotype data, and whether there are duplicated positions in the genotype map file.