biomart hangs

I am trying to run the following:

genome = useMart(biomart="ENSEMBL_MART_ENSEMBL",                                                                  
      host = "https://www.ensembl.org",                                                                               
      dataset="hsapiens_gene_ensembl")

Sometimes it works, other times I get

Error in req_perform(): ! HTTP 500 Internal Server Error. Run rlang::last_trace() to see where the error occurred.

"Error in .getAttributes(mart, verbose = verbose) : biomaRt error: looks like we're connecting to incompatible version of BioMart."

Error: Your query has been redirected to http://status.ensembl.org indicating this Ensembl service is currently unavailable. Look at ?useEnsembl for details on how to try a mirror site.

This used to work perfectly in the past. I am using biomaRt_2.60.1

Any help appreciated

biomart

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updated 9 months ago by Kevin Blighe

• written 1.7 years ago by ramiro.barrantes •

I have been having problems connecting to various Ensembl sites for the past week or two. I think maybe they're experiencing some issues.

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written 1.7 years ago by Dave Carlson

Agreed with Dave, 500 is server error.

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written 1.7 years ago by Mark

1 answer

The errors you encounter indicate server-side issues at Ensembl, which align with reports from other users experiencing intermittent connection problems over recent weeks. The HTTP 500 error signifies an internal server failure, while the incompatible version message and redirection to the status page suggest temporary unavailability or maintenance. Ensembl services, including BioMart, have faced disruptions in 2025, such as timeouts and planned downtimes, and the status page itself is currently inaccessible.

To resolve this, switch to an Ensembl mirror site, as recommended in the biomaRt documentation. Replace your host parameter with one of the following alternatives:

genome <- useMart(biomart = "ENSEMBL_MART_ENSEMBL",
                  dataset = "hsapiens_gene_ensembl",
                  host = "uswest.ensembl.org")

genome <- useMart(biomart = "ENSEMBL_MART_ENSEMBL",
                  dataset = "hsapiens_gene_ensembl",
                  host = "useast.ensembl.org")

genome <- useMart(biomart = "ENSEMBL_MART_ENSEMBL",
                  dataset = "hsapiens_gene_ensembl",
                  host = "asia.ensembl.org")

Test these sequentially until a stable connection is established. If the problem persists across mirrors, verify your biomaRt installation by reinstalling the package:

BiocManager::install("biomaRt", force = TRUE)

Ensure your R session has no proxy or firewall restrictions blocking the connection.

Kevin

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written 9 months ago by Kevin Blighe