Error in curl; timeout when using biomaRt
Entering edit mode
nlin0907 • 0
Last seen 9 weeks ago

I am currently trying to run biomaRt as a qsub job on a node, and I keep getting the error below:

> library(biomaRt)
> ensembl = useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl", host="")
Ensembl site unresponsive, trying useast mirror
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [] Connection timed out after 10000 milliseconds
Calls: useMart ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted

The code works fine on RStudio on my local computer, but on the node in the cluster, I get the error above. Is there any way I can fix this? Is this because the node has no internet connection so it cannot retrieve data from

biomaRt curl timeout getBM Bioconductor • 183 views
Entering edit mode
swbarnes2 ▴ 890
Last seen 2 hours ago
San Diego

That is the error you get when you can't connect. So yes, if the cluster can't get to the internet, it won't be able to reach ensembl.


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