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!

[anglixue]

Hi @rauldiul did you figure out this issue? I met the same issue with RunAzimuthATAC() for PBMC data and confirmed the index file is placed in the reference file path.

[rauldiul]

Hey @anglixue, no, I did not advance with this issue... If you are able to solve it in the future I'd appreciate it if you register it here!

[plbngl]

Hello @anglixue and @rauldiul ! I am stuck with the same issue with the PBMC reference--- which is weird because the same workflow worked a year ago.... Does anybody have updates?

[plbngl]

Update: it worked when I installed a previous version of Seurat (5.0.1) and Signac (1.12.0), but cannot say why. (Azimuth version always 0.5.0)

[bapoorva]

HI. I'm having the same issue. any updates on this ?