using AMOVA

Commands in mothur
1

I am a first time using of Mothur. In attempt to use the AMOVA command I get the following error message for about 50% of my dataset:
e.g. “[Error]: AU8932 is not in your design file, please correct”
I checked the design file and found that during the analysis only every other sample is recognized, i.e. sample 1, sample 3, sample5 …etc are recognized but not sample 2, sample 4, sample 6 …etc. What could be the problem?
Thanks
James. :slight_smile:

2

Do you have extra spaces in the design file? Mothur expects a tab delimited two column file. If you want to send your design file to mothur.bugs@gmail.com, I can take a look for you?

3

Thanks, Westcott.
I will send you the file.
James. :slight_smile:

4

Here’s a link to what a design file should look like, http://www.mothur.org/wiki/Design_File.

5

how do you get a .design file as an output?

6

You have to create it.

7

how does it differ from the .groups file?

8

I am trying to compare winter (W) and summer (S) bacterial communities and my .groups file is tab delimited and looks like this:
DMUD15 W
ENUA15 W
etc.
DMUA15 S
GN-2A15 S
etc.
I renamed the tab delimited .groups file as a .design file and I am getting this an an output:

not found Among Within Total
SS 0 0 0
df 0 194 194
MS nan 0
Fs: nan
p-value: <0.001*

Why is mothur not recognizing the W-S comparison?

9

James - do you have spaces between sample and the number? That would be a big problem and explain what you’re seeing. Also, everyone should keep in mind that these commands are really intended for use to compare groups of samples, not groups of sequences.