Hi Stefan.
It looks like they are having some issues at the central BioMart service.
You can query ensembl directly doing:
ensembl=useMart("ENSEMBL_MART_ENSEMBL",host="www.ensembl.org
",dataset="mmusculus_gene_ensembl")
Cheers,
Steffen
On Thu, May 30, 2013 at 8:38 AM, Stefan Kroeger <
[email protected]> wrote:
> Hi can anybody confirm my current problems on ensembl biomaRt service?
>
> Executing the following query I get an DB error message.
>
> require(biomaRt)
> ensembl <- useMart("ensembl", dataset = "mmusculus_gene_ensembl")
> biomart_data <- getBM(
> attributes=c("ensembl_gene_id",
> "ensembl_transcript_id",
> "entrezgene",
> "mgi_symbol"),
> filter="entrezgene",
> values=c("1","2"),
> mart=ensembl)
>
> Error in getBM(attributes = c("ensembl_gene_id", "ensembl_transcript_id",
> :
> Query ERROR: caught BioMart::Exception::Database: Could not connect to
> mysql database ensembl_mart_71: DBI
> connect('database=ensembl_mart_71;host=bm_mysql;port=3306','bmweb',...)
> failed: Host '54.225.80.241' is blocked because of many connection errors;
> unblock with 'mysqladmin flush-hosts' at /srv/biomart_server/
> biomart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98
>
>
> --
> Stefan
>
>
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