RunAzimuth ATAC working for BMMC but not for PBMC atlas

[rauldiul]

Hi!

Thanks for your great software.

I'm using Azimuth locally, with RunAzimuthATAC and having downloaded the PBMC and the BMMC reference ext.Rds objects from the Zenodos (https://zenodo.org/record/7770374, https://zenodo.org/records/7770389).

Using these files I can succesfully run Azimuth with the BMMC reference as such:

Azimuth::RunAzimuthATAC(query = foo, reference = file.path(root_drive,"DATABASES/AZIMUTH/ATAC_HUMAN_BMMC"))

But using the PBMC reference gives this error:

foo <- Azimuth::RunAzimuthATAC(query = foo, reference = file.path(root_drive,"DATABASES/AZIMUTH/ATAC_HUMAN_PBMC"))

Warning: Overwriting miscellanous data for model
Extracting reads overlapping genomic regions
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=05m 55s
Performing TF-IDF normalization
Projecting new data onto SVD
Error in GetIndexFile(fragment = path, verbose = verbose) : 
  Fragment file is not indexed.

I don't think there's anything wrong with my fragments index or anything because it works with the BMMC reference. I also tried re-indexing the fragments tbi (as suggested in this issue) but got the same error.

Thanks for your help!