Error in Snp set analysis using MetaSKAT

Question

[NB]

Hello,

I am trying to run MetaSkat on three cohorts and get the following error

EX.set.bed<-"file1.bed"
EX.set.bim<-"cohort1.bim"
EX.set.fam<-"cohort1.fam"
EX.set.setid<-"cohort1.SETID"
EX.set.Mat<-"cohort1.MSSD"
EX.set.Info<-"cohort1.SSD.MInfo"
FAM_Cov<-Read_Plink_FAM_Cov(EX.set.fam,"Covariates_cohort1.cov" , Is.binary=TRUE, flag1=0, cov_header=FALSE)
y<-FAM_Cov$Phenotype
N.Sample<-length(y)
X1<-FAM_Cov$COV1
obj <-SKAT_Null_Model(y ~ X1, out_type="D")
v1.0<-Generate_Meta_Files(obj, EX.set.bed, EX.set.bim, EX.set.setid, EX.set.Mat, EX.set.Info,N.Sample)

Read SetID file
SetID file has 1 sets
Read Bim file
Bim file has 4784 markers
Merge datasets and get set info
Error in Print_Error_CODE(err_code) : Error code = 9
Calls: Generate_Meta_Files -> Check_Saved -> Print_Error_CODE
Execution halted

However, the same code works just fine on a set with markers up to 3500. Is there a way to run MetaSkat with a large number of markers ? Or an alternative tool that accepts plink files and a covariate file?

Many thanks