Apologies in advance as I am very new to Mothur. I completed the classify otu command and I made a design file with my groups and treatments (made in excel, saved as tab-delimited). I am trying to run the get.groups command before I proceed with alpha/beta diversity, pcoa, and nmds, but I keep on getting these error messages:
“Unable to open final.design” “You must provide a design file when using the sets parameter”. The design file is saved in the correct working directory.
Hi - this generally means that final.design is not in your working directory. Can you make sure its in the same place as all of your other files? Alternatively, final.design might have an extension at the end of it like .tsv. You’ll need to include the entire file name. You can double check both of these from within mothur by running system(ls) if you’re on Mac/Linux or system(dir) if you’re on windows.