WordPress loses database connection after some time?

Hi all,
I have a problem: I have a script which makes thumbnails from pdf for preview in a slideshow. It uses imagemagick’s convert command, and sometimes takes some 10 minutes to finish.
After converting I have to run the update_post_meta, beause I store the filenames in a custom meta tag.
Sometimes I don’t have any problem, but sometimes (when the convert command runs long), it seems that the php code loses connection with the database, not just the update_post_meta fails with false return, but I also can’t get the next post data, which post is clearly available in normal case.
What should I do?
Thanks!