Hi Andrea, Biomart doesn't support materialize data into different servers. The source data and the mart have to be in the same machine. You cannot do the materialize unless your have the write permit with ensembldb.ensembl.org.
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
