Error in curl; timeout when using biomaRt
1
0
Entering edit mode
nlin0907 • 0
@baa3c012
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="http://useast.ensembl.org")
Ensembl site unresponsive, trying useast mirror
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [useast.ensembl.org:80] 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 http://useast.ensembl.org?

biomaRt curl timeout getBM Bioconductor • 183 views
ADD COMMENT
1
Entering edit mode
swbarnes2 ▴ 890
@swbarnes2-14086
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.

ADD COMMENT

Login before adding your answer.

Traffic: 332 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6