c++ exception (unknown reason)

[gblokland]

Hi,

I'm running the following code from Rstudio:

ld_folder="~/data/dms-gwas/opt/gctb_refs/LD_Reference/ukbEUR_Imputed"

for (pheno in c("test")) { ma_file=paste0("~/data/dms-gwas/sumstats/Biomarkers/", pheno, "/", pheno, "_sumstats_COJO.tsv")
out_prefix=paste0("~/data/dms-gwas/data/prs/SBayesRC/sbayesrcprs", pheno)
SBayesRC::tidy(mafile=ma_file, LDdir=ld_folder, output=paste0(out_prefix, "_tidy.ma"), log2file=TRUE)

SBayesRC::impute(mafile=paste0(out_prefix, "_tidy.ma"), LDdir=ld_folder, output=paste0(out_prefix, "_imp.ma"), log2file=TRUE) }

and get this error:

Impute the summary data by LD |--------------------------------------------------| |==================================================| 3754019 SNPs in common between GWAS summary and LD 428984 SNPs set from summary data 3325035 SNPs flipped alleles 3754019 SNPs are typed SNPs Start summary imputation... ==========1========= Imputing... Read error (m) Error in impGa(info$template, idxBlk, info$type, ma_exist$z, idxtt, m, : c++ exception (unknown reason)

Could you please help identify what the issue could be?

Thanks, Gabriëlla

[gblokland]

P.S.: it does seem to work when I call the code with Rscript from the bash command line.