I’m not sure that this is really a bug. But I had some samples slip through with dashes in the names (about ~40 samples out of 190). The logfile was 1.5gb because mothur printed this warning ~9M times. Can this warning just be printed once?
[WARNING]: group deep.water.wm2.Blitz-H2O-51 contains illegal characters in the name. Group names should not include :, -, or / characters. The ':' character is a special character used in trees. Using ':' will result in your tree being unreadable by tree reading software. The '-' character is a special character used by mothur to parse group names. Using the '-' character will prevent you from selecting groups. The '/' character will created unreadable filenames when mothur includes the group in an output filename.