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
