I am following the MiSeq_SOP on the Mothur wiki page. I have downloaded all the datasets and set up the directories as described. I have copy and pasted all the command, so it should be word-for-word correct. However, on a number of commands such as get.groups when I pass in groups=Mock I get the error message as described below in the output. If anyone could suggest what is causing this and how to resolve it that would be a great help.

mothur > get.groups(count=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.count_table, fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta, groups=Mock)

Mock is not a valid group, and will be disregarded. You provided no valid groups. I will run the command using all the groups in your file. Selected 1328 sequences from your fasta file. Selected 117919 sequences from your count file.