ah okay, it works big thanks Stefan
2013/5/30 Steffen Durinck <[email protected]> > 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 >> >> >> _______________________________________________ >> Users mailing list >> [email protected] >> https://lists.biomart.org/mailman/listinfo/users >> > >
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