Issue with reference URL

[seanken]

Hey,

Great tool! Sorry to bother you, I am trying to run Azimuth locally (something that has worked well for me many times in the past), but when I try to load any preexisting references from a URL (such as reference <- LoadReference(path = "https://seurat.nygenome.org/azimuth/references/v1.0.0/human_pbmc") though I have tried other references as well) I get the error:

Error in LoadReference(path = "https://seurat.nygenome.org/azimuth/references/v1.0.0/human_pbmc") : 
  Cannot find the following files at the site given: ref.Rds and idx.annoy

Looking at https://seurat.nygenome.org/azimuth/references/v1.0.0/human_pbmc with my browser get a 404 error, and at least one other member of our group has the same issue with LoadReference. Just checking if the references have been moved, this is a temporary outage, something wrong on my end (though this exact same code has worked for us many times), etc. Any pointers would be great!

Best wishes and thanks,

Sean

[AustinHartman]

Hi, thanks for pointing this out, I'll look into it. For now, you can load the reference with the following code: SeuratData::InstallData("pbmcref") followed by ref <- SeuratData::LoadData("pbmcref", type="azimuth")

[federicogiorgi]

Hi I have the same issue but with a different reference, the mouse_motorcortex, and I don't seem to find it in SeuratData.

Any workaround? Thanks!

> reference <- LoadReference(path = "https://azimuth.hubmapconsortium.org/references/mouse_motorcortex/")
Error in LoadReference(path = "https://azimuth.hubmapconsortium.org/references/mouse_motorcortex/") : 
  Cannot find the following files at the site given: ref.Rds and idx.annoy

EDIT: I answer myself, I can also use the SeuratData workaround

SeuratData::InstallData("mousecortexref")
ref<-SeuratData::LoadData("mousecortexref", type="azimuth")

[hildejl]

Hi!

I have had the same issue as mentioned here. Until now I have been able to use the SeuratData workaround. Now however, I get a warning:  > reference <- SeuratData::LoadData("pbmcref", type="azimuth") Warning: Overwriting miscellanous data for model Warning: Adding a dimensional reduction (refUMAP) without the associated assay being present Warning: Adding a dimensional reduction (refUMAP) without the associated assay being present

I have tried to reinstall everything in a clean R environment, on a different computer and with the newest version of r and seurat/azimuth and still get the same error.

I also get this warning for SeuratData:

> library(SeuratData) ── Installed datasets ─────────────────────────── SeuratData v0.2.2.9001 ── pbmc3k 3.1.4 tonsilref 1.0.0 pbmcref 1.0.0 ─────────────── Key ──────────────────── Dataset loaded successfully ❯ Dataset built with a newer version of Seurat than installed Unknown version of Seurat installed

Any ideas or pointers as to how I can solve this? Thanks in advance!