Ensemble site connection error
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Makoto ▴ 10
@bbe45128
Last seen 19 days ago
Japan

Dear all,

Hi. I've been trying to query gene name using biomaRt, but connection to ensemble site was failed as follows:


ensembl <- useEnsembl(biomart = "ENSEMBL_MART_FUNCGEN", 
+                       dataset = "hsapiens_regulatory_feature")

Ensembl site unresponsive, trying uswest mirror
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [uswest.ensembl.org:8443] Connection timed out after 10002 milliseconds

Here is my session info: R version 4.0.5 (2021-03-31) biomaRt version: 2.46.3 Platform: Ubuntu20.04 on Windows 10 Pro Build21359.co_release.210409-1536 (WSL2)

I tried restarting but I still got the same error. Does anyone have the same problem? I will appreciate if you could help to solve the problem.

Thanks

biomaRt • 81 views
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@kevin
Last seen 4 hours ago
United States

Hi,

The Ensembl servers can become quite overloaded. Please re-try the command —possibly a few times, even more than 10— and it should eventually be able to create the connection object. I have just verified this.

Kevin

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Hi Kevin,

Thank you for your quick and polite response. I'm quite new in bioinformatics, so sorry to ask such a basic question. I could successfully connected by repeatedly retrying to query. I'm really appreciate your kind support, again.

Makoto

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No problem, Makoto, and your question was no problem at all. Thank you for using Bioconductor.

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