Question: Error when calling AnnotationHub()
0
gravatar for albadrs.93
25 days ago by
albadrs.9310
albadrs.9310 wrote:

Hii,

I am getting use to the Seurat scRNA seq pipeline and as I am trying to obtain gene names for cell cycle genes from Ensembl IDs, I have tried to use Annotation Hub R package to query Ensembl using the ensembldb R package All of the cell cycle genes are Ensembl IDs, but our gene IDs are the gene names. To score the genes in our count matrix for cell cycle, we need to obtain the gene names for the cell cycle genes.

We can use annotation databases to acquire these IDs. While there are many different options, including BioMart, AnnotationDBI, and AnnotationHub. We will use the AnnotationHub R package to query Ensembl using the ensembldb R package.

I get the following error when I try to connect:

> AnnotationHub()
Error in .util_download(x, rid[i], proxy, config, "bfcadd()", ...) : 
  bfcadd() failed; see warnings()
In addition: Warning messages:
1: download failed
  web resource path: ‘https://annotationhub.bioconductor.org/metadata/annotationhub.sqlite3’
  local file path: ‘C:\Users\delriosa\AppData\Local\AnnotationHub\AnnotationHub\Cache/fc476662152_annotationhub.sqlite3’
  reason: Failed to connect to annotationhub.bioconductor.org port 443: Connection refused 
2: bfcadd() failed; resource removed
  rid: BFC11
  fpath: ‘https://annotationhub.bioconductor.org/metadata/annotationhub.sqlite3’
  reason: download failed 

I tried uninstalling and reinstalling, but can´t make it work.

Thanks in advance!

annotation • 57 views
ADD COMMENTlink written 25 days ago by albadrs.9310
1

Are you behind a proxy? The proxy will need to be set if so. This can be done by passing as an argument directly in the constructor AnnotationHub(proxy=<value>) or though setAnnotationHubOptions("PROXY", <value>) before running the constructor.

ADD REPLYlink modified 25 days ago • written 25 days ago by shepherl ♦♦ 1.7k
1

That was indeed the problem!

Thanks a lot

ADD REPLYlink written 11 days ago by albadrs.9310
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