Probelm with MiSeq SOP summary.shared command

Theory behind mothur
1

Hi,

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.

Best,

Helena

2

Ok, I found the problem. I copied the command from the tutorial and there is a small mistake (a space before F0D3, so it doesn’t recognise that sample):
summary.shared(calc=sharedchao, groups= F3D0-F3D1-F3D2-F3D3, all=T)
It should be:
summary.shared(calc=sharedchao, groups=F3D0-F3D1-F3D2-F3D3, all=T)

Sorry!