It would be totally killer if mothur could accept a log=logfile.pathname parameter for each command.
If the parameter is not specified, then mothur.##########.logfile (s) could be generated as usual.
Since I typically call multiple mothur commands in a bash script, and most everything else in the script is a bash variable,
it would be easy to name the log files and much more easy to come in and the morning and try to figure out what happened.
Anyway, not a critical feature, but I figure it would be (possibly/hopefully) easy to implement.
(A sign of good software when this is the kind of crap people ask for 
)