search

shz9 / viprs

Variational Inference of Polygenic Risk Scores
https://shz9.github.io/viprs/
MIT License
18 stars 1 forks source link

No valid LD matrix files were found at: data/ld/ #8

Open MuhammadMuneeb007 opened 1 month ago

MuhammadMuneeb007 commented 1 month ago

When I executed

python viprs/bin/viprs_fit -l data/ld/ -s /path/to/sumstats/ --output-dir /

Code did not execute and said

FileNotFoundError: No valid LD matrix files were found at: data/ld/

python viprs/bin/viprsfit -l data/ld/chr* -s S/X.txt --output-dir /S

also produced error.

opened viprs/bin/viprs_fit line 43 change the following.

ld_store_files = get_filenames(args.ld_dir, extension='.zgroup')

ld_store_files = get_filenames(args.ld_dir, extension='.zarray')

opened site-packages/magenpy/GWADataLoader.py:600: ld_store_files = get_filenames(ld_store_paths, extension='.zgroup')

ld_store_files = get_filenames(ld_store_paths, extension='.zarray')

but error is the same. The new versions use zarr group rather than zarr array.. when LD matrices are extracted ig contains .zarry

chr_1]$ ls -a . .. 0 1 10 11 2 3 4 5 6 7 8 9 .zarray .zattrs

shz9 commented 1 month ago

Which versions of magenpy and viprs are you using in this example? Also, are those your own LD matrices or the ones that we published on Zenodo?

The published LD matrices on Zenodo only work with magenpy<0.1 (e.g. v0.0.12) and viprs<0.1 (e.g. v 0.0.4). I'm working on getting matrices with the new format published as soon as possible, just finalizing some crucial tests.