I figured out my issues getting mgcluster to run on my data so now have the list file. My next step was to read that in using the read.otu command, correct? I have multiple samples that I clustered so was trying to use group to generate the shared otu file. But I’m getting the following error. It seems to me that mothur is reading a space as a sequence name? I haven’t done anything to the list file and since it’s so huge I can’t open it with a text editor to see what’s wrong with the file. There weren’t any errors when I ran mgcluster.
mothur > read.otu(list=j_LP_HOT_SI_aa.fas.fn.list, group=j_LP_HOT_SI_aa.group, label=0.2-0.4-0.6) Error: Sequence '' was not found in the group file, please correct.