I've just experienced this same problem; awstats was correctly looking
at my conf file /etc/awstats/awstats.my.domain.conf and then it stopped
working -- turning on -debug=2 (easier than strace!) shows that awstats
started looking in /usr/lib/cgi-bin for the conf file. I'd changed
various things about my awstats conf, so I don't know what I did that
tripped the problem. I have worked around it by explicitly specifying
the whole path to the conf file, so "awstats -config
/etc/awstats/awstats.my.domain.conf -update", which works. Quite why
"-config my.domain" now does not work is baffling. I can confirm that
the problem is not about user permissions on files: awstats is
explicitly looking in /usr/lib/cgi-bin for conf files, and I run the
command as root.

** Changed in: awstats (Ubuntu)
       Status: Expired => New

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https://bugs.launchpad.net/bugs/1181790

Title:
  looking in /usr/lib/cgi-bin instead of /etc/awstats

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