There are three key configuration properties that must be set so MySQL can handle the size of data you are using.

They are:
  myisam_max_sort_file_size
  myisam_sort_buffer_size
  read_buffer_size

* If you are using an existing MySQL database, login to it and run these commands to see the current values of these properties:
   
                 mysql> show variables LIKE 'myisam_max_sort_file_size';
               
                 mysql> show variables LIKE 'myisam_sort_buffer_size';

                 mysql> show variables LIKE 'read_buffer_size';     

         
          NOTE: These values will display in bytes, i.e. a value of
                2147479552 for read_buffer_size is equivalent to 2 Gigabytes.

If these values are less than what you will need, as described below, contact your mysql administrator (provide this file for reference).


* If you are installing your own mysql, edit these properties in the mysql.cnf file.


* Suggested settings

       a) set myisam_sort_buffer_size= to 50% of available ram
           - to find out how much ram you have:
                dmesg | grep Memory
           - it gives you a report in kilobytes.  divide by 1000000 to get a number of Gs.

       b) set myisam_max_sort_file_size= to 5 x the size of the file made by orthomclBlastParser.
           - (revisit this after you have run orthomclBlastParser)

       c) set read_buffer_size= to ???