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.
Have you solved the problem yet? I have encountered the exact same issue. I found out that the problem should be from the output of make.file command where it does not add the names of samples to the file.