It would be so amazing if the mother logfiles were named after the job/project you just ran. If you are running each script separately each resulting mothur logfile would mirror that job, i.e., mothur.classify.logfile. If you run jobs serially you could designate a project name and then the resulting mothur logfile would be mothur.project.logfile. For any repeating logfiles you could add a number, mothur classify2.logfile. I don’t know if this is feasible or even worth your time, but I would be so happy if I didn’t have to rename every logfile lest I have to weed through a million to find the right one later.
It’s not automatic, but within a mothur session you can use the set.logfile command to change the name of your logfile when mothur exits. It saves having to look through a bunch of logfiles to find the correct one.