Bgen file not being opened by PRSice

Question

[Varsha]

I used the following command to calculate PRS of a sequenced file coming from a collaborator. I imputed the vcf file which gave me separate vcf files for each chromosome. I then converted them to bgen and generated bgi and sample files too.

Rscript ../PRSice/PRSice.R --base ../ukb_prs/PGS000785.txt --target ../tempus_files/202030905/207532750086_R08C02/#,../tempus_files/202030905/207532750086_R08C02/1.sample --type bgen --snp SNP --chr CHR --bp BP --A1 A1 --A2 A2 --stat BETA --pvalue P --binary-target T --no-clump --fastscore --ignore-fid --pheno ../tempus_files/202030905/207532750086_R08C02/207532750086_R08C02_pheno.txt --out 207532750086_R08C02_results --prsice ../PRSice/PRSice_linux

But I get the following error: Error: Cannot open bgen file ../tempus_files/202030905/207532750086_R08C02/1.bgen

The paths are all correct, but I cannot identify what the problem is. Please help me figure this out.

[Jeremy Leipzig]

you might be a directory up or down from where you think you should be. add some debugging statements in PRSice.R (yes, modify it)

paste("hey I am looking here is this where I thought it was?", paste(list.files(path = "../"),collapse=" "))