If the long-running process needs those handles (as it apparently does), try re-opening them to some file (before running the subprocess).

In some more detail, the undelying problem is that the implicitly forked subprocess running under nohup is getting duplicates of the file handles of the parent process (your main script) at the time of the fork, and all "instances" of those file handles - which are connected via pipes to the web server - will need to be closed (or re-opened to elsewhere), before the web server considers the CGI job completed.

-The other Anonymous Monk

In reply to Re^4: exec command taking ages by Anonymous Monk
in thread exec command taking ages by pmcilfatrick

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