Error with FarmCPU using Multiple_analysis

[AnthoBdx]

Dear all, First, thank you for your precious help. Unfortunately, the GAPIT forum is not available so I'll explain here the problem.

I try to run this script :

Open the phenotypic and genotypic datasets

myY <-read.table("All_traits_blups.txt", head = TRUE, sep="\t") myG <-read.table("peach_no_filter5%.hmp.txt", head = FALSE)

myGAPIT <- GAPIT::GAPIT( Y=myY[,c(1:14)], G=myG, model=c("MLMM","FarmCPU","Blink"),
PCA.total=0,
Multiple_analysis=TRUE,
)

It worked well for MLMM until the first run of FarmCPU is finished (I mean, first run for my first trait). I get this error message :

[1] "**FarmCPU ACCOMPLISHED SUCCESSFULLY**" [1] "Calculating Orignal GWAS result..." [1] "GAPIT.RandomModel beginning..." [1] FALSE Error: grouping factors must have > 1 sampled level In addition: There were 50 or more warnings (use warnings() to see the first 50)

I spent many hours trying to find what's the issue but... I didn't find! It worked well for MLMM and BLINK... Can someone help me? Thanks a lot in advance,

Anthony

[jiabowang]

Please add Random.model=FALSE to skip PVE estiamted.

[AnthoBdx]

Thanks a lot dear Jiabo Wang, it works perfectly!