Issue in GAPIT run stuck on "Calling prcomp..."

[akhtarmzn2010]

Dear Sir,

I am running GAPIT with multiple analysis function, run is stuck on "Calling prcomp..." step.

My gapit function:

for(i in 2:ncol(myY)) { myGAPIT <- GAPIT( Y=myY[,c(1,i)], GD=myGD, GM=myGM, model=c("GLM","MLM","MLMM","FarmCPU","Blink"), PCA.total=3,
NJtree.group=3,

QTN.position=mysimulation$QTN.position,

Geno.View.output=F, Inter.Plot=FALSE,
Multiple_analysis=TRUE,
PCA.3d=FALSE,
file.output=T ) }

Run stuck on: [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..."

Please help to solve this.

[jiabowang]

Could you introduce the size of your data? In the R, the huge genotype data may make computing problem.

[akhtarmzn2010]

Hello Sir, I'm using 93249 SNPs data for 103 genotype.
I have already use genotypic data upto 300000 SNPs, but this time i got above error .

Kindly help me. Javed

[jiabowang]

Sounds not a huge dataset. Generally speaking, more than 1 M markers should make a computing burden. How many individuals in your genotype file?

[akhtarmzn2010]

Yes sir, Dateset not a huge. These is only 103 individuals are using for gwas. After re-installation GAPIT, still got same problem, stuck on [1] "Calling prcomp..." step.

[jiabowang]

how much memory is there in your computer? Or could you send your data to me? I can help with figuring out the reason.

[liuye2024]

Hello, how did you solve this problem? I've encountered the same issue，there are over 300 individuals and more than 8 million SNP sites.. My email is liuye2019@outlook.com. Thank you for your help.

[jiabowang]

@liuye2024 8M markers will make computing problems with PCA in R. Please use other C software to calculate PCA, such as PLINK. Then, put PCs into GAPIT as CV file to perform GWAS.

[liuye2024]

Thanks a lot , wish you have a good day!