Hi ,

I have some single cell ATAC seq data that I want to analyze using Signac. I want to add gene annotations using Annotation Hub. But I keep getting this error

library(AnnotationHub)
ah <- AnnotationHub()

# Search for the Ensembl 98 EnsDb for Homo sapiens on AnnotationHub
query(ah, "EnsDb.Hsapiens.v98")

ensdb_v98 <- ah[["AH75011"]]

loading from cache
Error: failed to load resource
  name: AH75011
  title: Ensembl 98 EnsDb for Homo sapiens
  reason: database disk image is malformed
In addition: Warning message:
Couldn't set synchronous mode: database disk image is malformed
Use `synchronous` = NULL to turn off this warning.

I uninstalled and reinstall the package. Didn't work. I guess this is a problem with the file in the database. Any thoughts or suggestions?

Thanks, AB

What is your sessionInfo()? I just tried locally and it works fine so there might have been a bad or interrupted download when initially retrieving the file.

> ensdb_v98 <- ah[["AH75011"]]
downloading 1 resources
retrieving 1 resource
  |======================================================================| 100%

loading from cache
require("ensembldb")

This should only be done once or it defeats the point of caching, and will incur a cost to the project each time something is downloaded, but can you try force re-downloading the file using the following syntax. There is an issue open suggesting a safe guard against this that I hope to look into soon.

library(AnnotationHub)
ah <- AnnotationHub()
ensdb_v98 <- ah[["AH75011", force=TRUE]]