Problem with loading ensembl version 105.
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RC • 0
@dca60bb0
Last seen 11 months ago
Germany

Hello there. I am trying to use biomart to load the mouse genes for version M28 (ensembl 105), but I am getting an error:

ensembl_gene_names <- useEnsembl(biomart = 'genes', dataset = 'mmusculus_gene_ensembl', version = 105)

Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [dec2021.archive.ensembl.org:443] Operation timed out after 60001 milliseconds with 0 bytes received

Please note that for other versions this command works just fine. For example, running the following 2 commands does not give an error, these run fine and quickly load an object of class 'Mart'.

ensembl_gene_names <- useEnsembl(biomart = 'genes', dataset = 'mmusculus_gene_ensembl', version = 104)
ensembl_gene_names <- useEnsembl(biomart = 'genes', dataset = 'mmusculus_gene_ensembl', version = 106)

A similar issue occurs for the command

listEnsembl(version = 105)

Which does not occur when using it for version 104 or 106, or any other version I tested for that matter.

biomaRt • 784 views
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@james-w-macdonald-5106
Last seen 1 day ago
United States

You will time out if you try to load that archive using a browser as well. This is not an error with biomaRt, but with EBI's server. You might ask them what's up.

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Yeah I shot them an email, let's see what they say.

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