Throttling mysql command line

[Eric Cope]

Hello all,
I have a nightly script that executes a mysql batch file that takes
approximately 8 minutes to run. Unfortunately it makes my web server
unresponsive for all 8 minutes. I've tried ionice and nice to lower
the priority, but it still seems to consume all resources. The weird
thing is "top" and "iostat" look like nothing is running. Any ideas?

Its mysql 5.1.x

Thanks,
Eric