Here is my run:
mothur > read.otu(list=threesamples.fn.list,group=threesamples.group)
Your group file contains sequences and list file contains sequences. Please correct.
For a list of names that are in your list file and not in your group file, please refer to threesamples.fn.missing.group.
However, the file threesamples.fn.missing.group. turns out an empty file.
I’ve checked the group file"threesamples.group" carefully and there are 468 lines, with one group-name of a sequence each line. There seems no reason for this error.