I am new to mothur and I am doing the analysis example MySeq SOP (http://www.mothur.org/wiki/MiSeq_SOP), using the example data in the tutorial. Up till now, I was able to run it properly, and even solve some minor problems I encountered. However, now, when I was using the summary.shared command in the beta diversity measurement section (section 8.2), there is a problem in the output that I don’t know how to fix. The command is:
summary.shared(calc=sharedchao, groups= F3D0-F3D1-F3D2-F3D3, all=T)
And the Terminal tells me: F3D0 is not a valid group, and will be disregarded.
When I open the generated files, I observe that sample F3D0 has, indeed, not been included in the analysis. How can I fix this?
I am using a MacBook Pro (Retina, 15-inch, Mid 2015). Let me know if you need more info on my system or whatever.
Thanks a lot for your help.