how to access hsapiens_gene_ensembl or whatever has replaced it? listDatasets does not show "human" in it on ensembl.org or on uswest.ensembl.org. Worked yesterday.... ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl") waits a long long time and come back with a response of no such data set
Any clues what's causing the malfunction? metazoa.ensemble.org also appears to be failing intermittently and giving strange errors (see below). The code I'm using is the same one as Error in useMart while using a dataset in biomaRt. I've run my script a few times, with failures about 50% of the time.
I.e:Add comment
Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database metazoa_mart_38: DBI connect('database=metazoa_mart_38;host=hh-mysql-eg-mart-web.ebi.ac.uk;port=4599','ensro',...) failed: Lost connection to MySQL server at 'reading authorization packet', system error: 0 at /nfs/public/release/ensweb/live/eg_mart/www_91/metazoa/lib/BioMart/Configuration/DBLocation.pm line 98.
I don't know any details, only that the Ensembl team are aware of it (https://twitter.com/ensembl/status/956216658007388162)