PolyPred not recognizing my bed file

[bcoombes]

I am running this code

python polypred.py \ --combine-betas \ --betas $projdir/polyfun_susie_hrc_allelesaligned.txt, $projdir/prsweights_allelesaligned.txt \ --pheno $projdir/gainpheno.txt \ --output-prefix polypredout \ --extract $projdir/extractsnps.txt \ --plink-exe plink \ $beddir/GENO.bed

where I have confirmed that the pheno file has the correct headers FID IID PHENO and I have made sure my betas are all corresponding to the same A1 allele. However, I am getting this error:

polypred.py: error: unrecognized arguments: [insert file path]/GENO.bed

I have also tried running this using the bed files provided in the example and it tells me it doesn't recognize that list of 1000G.subset bed files. If I remove the last line (providing no bed file), I get this error:

Traceback (most recent call last): File "/research/bsi/tools/biotools/polyfun/1.0.0/polyfun/polypred.py", line 430, in estimate_mixing_weights(args) File "/research/bsi/tools/biotools/polyfun/1.0.0/polyfun/polypred.py", line 283, in estimate_mixing_weights df_prs_sum = computs_prs_all_files(args, betas_file, disable_jackknife=True, keep_file=args.pheno) File "/research/bsi/tools/biotools/polyfun/1.0.0/polyfun/polypred.py", line 213, in computs_prs_all_files raise ValueError('File suffix must be either .bed or .pgen') ValueError: File suffix must be either .bed or .pgen

So the script is looking for a bed file but doesn't recognize bed files. Any help you can provide is appreciated. Thanks!

[bcoombes]

It was the space between the beta weights files.