AnnotationHub data for Mus musculus seems to be missing, while previously it was there
1
0
Entering edit mode
Thon • 0
@1917db9e
Last seen 4 months ago
United States

I have been using tximeta to get the annotation data for my RNAseq data, created by salmon. I was previously able to get the annotations for the mouse genome it was using and it had successfully downloaded the Ensembl data needed for DESeq2. But I recently deleted the .cache data for the annotaitonhub, but it now no longer is able to load the annotaiton data and produces the error shown below.

It seems resource "AH73905" is incomplete? It seems to "know" it, since it downloads some of the annotationhub data, but fails after that.


library(tximeta)
library(BiocFileCache)
library(DESeq2)
bfc <- BiocFileCache(ask = FALSE)
cache <- slot(bfc, "cache")
setTximetaBFC(cache)
r_design_matrix <- read.csv("/home/tdeboer/CODE/rnayx/rnayx/design_matrix.csv")
r_design_matrix[] <- lapply(r_design_matrix, factor)
se_full <- tximeta(r_design_matrix, useHub = TRUE)

And that produces this output.

importing quantifications
reading in files with read_tsv
1 2 3 4 5 6 7 8 9 10 11 12 
found matching transcriptome:
[ Ensembl - Mus musculus - release 97 ]
useHub=TRUE: checking for EnsDb via 'AnnotationHub'
/home/rstudio/.cache/R/AnnotationHub
  does not exist, create directory? (yes/no): yes
  |========================================================================================================================================================================================================================================================================================| 100%

snapshotDate(): 2023-04-25
found matching EnsDb via 'AnnotationHub'
downloading 1 resources
retrieving 1 resource
  |========================================================================================================================================================================================================================================================================================| 100%

Error: failed to load resource
  name: AH73905
  title: Ensembl 97 EnsDb for Mus musculus
  reason: 1 resources failed to download
In addition: Warning messages:
1: download failed
  web resource path: 'https://annotationhub.bioconductor.org/fetch/80651'
  local file path: '/home/rstudio/.cache/R/AnnotationHub/2085491c3_80651'
  reason: Conflict (HTTP 409). 
2: bfcadd() failed; resource removed
  rid: BFC3
  fpath: 'https://annotationhub.bioconductor.org/fetch/80651'
  reason: download failed 
3: download failed
  hub path: 'https://annotationhub.bioconductor.org/fetch/80651'
  cache resource: 'AH73905 : 80651'
  reason: bfcadd() failed; see warnings()
tximeta AnnotationHub AnnotationHubData • 461 views
ADD COMMENT
1
Entering edit mode
shepherl 3.8k
@lshep
Last seen 2 days ago
United States

This should be resolved now. The hubs were down unexpectedly yesterday. I'm sorry I didn't post an announcement here but will if it happens in the future. https://stat.ethz.ch/pipermail/bioc-devel/2023-October/019953.html .

ADD COMMENT
0
Entering edit mode

I can confirm it is working for me again. Thanks for the great service you provide here.

ADD REPLY

Login before adding your answer.

Traffic: 622 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6