You can generate a separate output file each time the Integration Service starts a new transaction. You can dynamically name each target flat file.

To generate a separate output file for each transaction, add a FileName port to the flat file target definition. When you connect the FileName port in the mapping, the Integration Service creates a separate target file at each commit. The Integration Service names the output file based on the FileName port value from the first row in each transaction. By default, the Integration Service writes output files to $PMTargetFileDir.