Question

AnnotationHub Server denied you to change the given directory

1

Entering edit mode

bastien.ducreux ▴ 10

@bastienducreux-20715

Last seen 5.7 years ago

Dear everyone,

I'm currently having an issue with AnnotationHub package as I can't manage to have access to url linked to the database I need to use. Would anyone have some guidance regarding this problem ?

Thank you in advance, Regards.

Bastien

> ah <- AnnotationHub() 
> query(ah, c("Gencode", "gff", "human"))
> ah["AH49556"] 

AnnotationHub with 1 record
# snapshotDate(): 2018-10-24 
# names(): AH49556
# $dataprovider: Gencode
# $species: Homo sapiens
# $rdataclass: GRanges
# $rdatadateadded: 2015-08-14
# $title: gencode.v23.basic.annotation.gff3.gz
# $description: Gene annotations on reference chromosomes from Gencode
# $taxonomyid: 9606
# $genome: GRCh38
# $sourcetype: GFF
# $sourceurl: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_23/gencode....
# $sourcesize: 29841317
# $tags: c("gencode", "v23", "basic", "annotation", "gff3") 
# retrieve record with 'object[["AH49556"]]'

> gc <- ah[["AH49556"]]

downloading 1 resources
retrieving 1 resource
Error: failed to load resource
  name: AH49556
  title: gencode.v23.basic.annotation.gff3.gz
  reason: 1 resources failed to download
In addition: Warning message:
download failed
  hub path: ‘https://annotationhub.bioconductor.org/fetch/56276’
  cache path: ‘C:/.../AppData/.AnnotationHub/56276’
  reason: Server denied you to change to the given directory

annotation annotationhub • 1.5k views

ADD COMMENT • link updated 5.7 years ago by shepherl 4.1k • written 5.7 years ago by bastien.ducreux ▴ 10

0

Entering edit mode

Could you please provide your sessionInfo()?

ADD REPLY • link 5.7 years ago shepherl 4.1k

0

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Looks like the endpoint has changed -- following https://annotationhub.bioconductor.org/fetch/56276%E2%80%99 leads a file-not-found error and navigating up to ftp://ftp.sanger.ac.uk/pub/gencode/ leads to a README with

The GENCODE data can now be found at ftp://ftp.ebi.ac.uk/pub/databases/gencode/

this will require an update to the AnnotationHub database.

ADD REPLY • link 5.7 years ago Martin Morgan 25k

0

Entering edit mode

I'll look into adjusting the endpoint.

ADD REPLY • link 5.7 years ago shepherl 4.1k

score 0 · Answer 1 · 2019-05-07

Thank you for bringing this to our attention and thank you for the catch on the endpoint change Martin. The issue has been resolved, Upon reload of AnnotationHub, you should be able to access the resource

> ah = AnnotationHub()
snapshotDate(): 2019-05-07
> gc <- ah[["AH49556"]]
downloading 1 resources
retrieving 1 resource
  |======================================================================| 100%

loading from cache 
    'AH49556 : 56276'
require("rtracklayer")
>