If I'm reading your code correctly, you're doing the following:

• Querying database 1
• Querying database 2
• Writing to file 1 using query 1
• Writing to file 2 using query 2

Also, it looks like your two queries and associated output files are completely independent of each other. In that case, I'd recommend doing the following:

• Connect and query database 1
• Write to file 1
• Use undef on the variables related to database 1
• Repeat above steps for database 2 and file 2

This will limit the amount of data in memory and free up memory once you're done with that data.

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