Hi Richard, To add to what Syed wrote one thing that sometimes can happen is you forget to create an necessary index during mart creation and for a large dataset when you run a query BioMart will seem to hang when in actuality it is waiting for the DBMS to return the results and the DBMS is going slowly because it is missing the index and having to do a table scan.
Take the SQL queries that you see BioMart running and with the MySQL or Pg client put EXPLAIN in front of the query and execute it, then it will show you what the DBMS is trying to do and you will see quickly if an index is missing. -Leandro On Tue, Dec 14, 2010 at 1:17 PM, Syed Haider <syed.hai...@oicr.on.ca> wrote: > Hi Richard, > > please modify the file biomart-perl/conf/log4perl.conf > > and change it as shown below: > > log4perl.logger = DEBUG,Screen > > then redo perl bin/configure.pl -r conf/yourRegistry.xml --clean > > kill/restart apache. > > now all the sql queries will appear in logs/error_log file. > > HTH, > Syed > > On 10/12/2010 11:11, Richard Cote wrote: > >> Hi mart-dev >> >> Is there a way to access the raw sql queries that are being generated by a >> biomart? I have a problem where the data is in the right place in the >> database, >> the filters and attributes seem ok, but no data is coming out, which is >> very >> frustrating and any help would be appreciated. >> >> Cheers, >> Rc >> >>
