Hi Steffen Please feel free to post such issues to our "users" mailing list for a quick reply. We have had some problems with the database backend recentlly. Yes you are right, We have migrated to Canada but this is not what was causing the problems. Our servers have been actually performing far better here until very recently but I believe Junjun has restored everything back to normal now so we should expect a smooth service again
a On 2011-02-24, at 1:20, "Steffen Durinck" <<mailto:[email protected]><mailto:[email protected]>[email protected]<mailto:[email protected]>> wrote: Hi Arek, The last couple of days several biomaRt users have been reporting the following issue (I seem to experience it on and of) Any query, e.g. the one below: <?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query><Query virtualSchemaName = 'default' uniqueRows = '1' count = '0' datasetConfigVersion = '0.6' requestid= "biomaRt"> <Dataset name = 'hsapiens_gene_ensembl'><Attribute name = 'ensembl_gene_id'/><Attribute name = 'ensembl_transcript_id'/><Attribute name = 'refseq_dna'/><Attribute name = 'coding'/><Filter name = 'refseq_dna' value = 'NM_198576,NM_032880,NM_173574,NM_001114759,NM_031459,NM_178865,NM_145238,NM_001080850,NM_006369,NM_017768' /></Dataset></Query> Leads to the following error: Error in getBM(c("ensembl_gene_id", "ensembl_transcript_id", "refseq_dna", : Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_61: DBI connect('database=ensembl_mart_61;host=<http://dcc-qa-db.oicr.on.ca><http://dcc-qa-db.oicr.on.ca><http://dcc-qa-db.oicr.on.ca>dcc-qa-db.oicr.on.ca<http://dcc-qa-db.oicr.on.ca>;port=3306','bm_web',...) failed: Can't connect to MySQL server on '<http://dcc-qa-db.oicr.on.ca><http://dcc-qa-db.oicr.on.ca><http://dcc-qa-db.oicr.on.ca>dcc-qa-db.oicr.on.ca<http://dcc-qa-db.oicr.on.ca>' (113) at /srv/biomart_server/<http://biomart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm><http://biomart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm><http://biomart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm>biomart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm<http://biomart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm> line 98 Has the BioMart central portal migrated to canada? Is it possible this switch is causing the problem? Cheers, Steffen
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