Hi Andrea, Why you want to materialize ensembl data? If you just want to query the data, you can deploy your server and query through virtual mart. Or you can add a mart from martdb.ensembl.org, or URL.
Hope this helps. Yong On 11-03-25 5:22 PM, "Andrea Edwards" <[email protected]> wrote: > Hi > > I am trying to materialize a dataset based on the ensembl core database. > It doesn't seem to be working. > I have called the dataset gene. This is what happens when i click > materialize > > target database: gene > target_schema: gene > martrunner host:localhost > port: 9005 > database server: ensembldb.ensembl.org > database port: 5306 > > > NOthing seems to happen. When i click refresh the job is still pink but > the 'start job' button is active again. If i look in the terminal where > martrunner is running there is this error > > [Thread-3] ERROR martrunner - > com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Access denied > for user 'anonymous'@'%' to database 'gene' > ERROR [Thread-3] (Log.java:197) - > com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Access denied > for user 'anonymous'@'%' to database 'gene' > > > I have created a database called gene and given the anonymous user full > access to this database on the local server. > > andrea@oscar:~/biomart/release-0_8-candidate_5/dist/scripts$ mysql -u > anonymous > > > mysql> show databases; > +--------------------+ > | Database | > +--------------------+ > | information_schema | > | gene | > +--------------------+ > 2 rows in set (0.00 sec) > > mysql> use gene; > Database changed > > > I thought perhaps there might be some confusion because my database is > called gene and I was using gene as the main table in the ensembl core > database so i renamed my local database to gene_test and then i got this > error instead > > andrea@oscar:~/biomart/release-0_8-candidate_5/dist/scripts$ > ./martrunner.sh 9005 > Starting MartRunner please wait .... > ...martrunner started. > [Thread-3] ERROR martrunner - > com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Unknown > database 'gene_test' > ERROR [Thread-3] (Log.java:197) - > com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Unknown > database 'gene_test' > > > but the database does exist > > > mysql> show databases; > +--------------------+ > | Database | > +--------------------+ > | information_schema | > | gene_test | > +--------------------+ > 2 rows in set (0.00 sec) > > mysql> use gene_test; > Database changed > > thanks a lot > > > _______________________________________________ > Users mailing list > [email protected] > https://lists.biomart.org/mailman/listinfo/users _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
