Hello,
This is the first time I am running an Amova test. I have tried running
amova(phylip=pipeall.final.an.thetayc.0.03.lt.dist, design=pipeallbydate.design) but MOTHUR always gives an error that:
[ERROR]: K13.530F is not in your design file, please correct.
[ERROR]: K14.530F is not in your design file, please correct.
[ERROR]: K15.530F is not in your design file, please correct.
[ERROR]: K16.530F is not in your design file, please correct.
[ERROR]: K17.530F is not in your design file, please correct.
[ERROR]: K18.530F is not in your design file, please correct.
[ERROR]: K7.530F is not in your design file, please correct.
[ERROR]: K8.530F is not in your design file, please correct.
[ERROR]: K9.530F is not in your design file, please correct.
[ERROR]: N1 is not in your design file, please correct.
[ERROR]: N2 is not in your design file, please correct.
[ERROR]: N3 is not in your design file, please correct.
I made the design file as instructed and it looks like this:
K7.530F D
K8.530F D
K9.530F D
K13.530F M
K14.530F M
K15.530F M
K16.530F J
K17.530F J
K18.530F J
N1 A
N2 A
N3 A
I am trying to compare my samples by sampling time so D=December M=March J=July A=August.
I have no idea what I am doing wrong I would love some help!
What version of mothur are you using? It seems like mothur is not reading your design file properly. You can see what mothur is reading by setting the debug flag. Run set.dir(debug=t) then the amova command.
Thank you westcot for replying.
I am using MOTHUR v. 1.25.1. I tired running just what you said and this is what I got
mothur > set.dir(debug=t)
Setting [DEBUG] flag.
mothur > amova(phylip=pipeall.final.an.thetayc.0.03.lt.dist, design=pipeallbydate.design)
[ERROR]: K13.530F is not in your design file, please correct.
[ERROR]: K14.530F is not in your design file, please correct.
[ERROR]: K15.530F is not in your design file, please correct.
[ERROR]: K16.530F is not in your design file, please correct.
[ERROR]: K17.530F is not in your design file, please correct.
[ERROR]: K18.530F is not in your design file, please correct.
[ERROR]: K7.530F is not in your design file, please correct.
[ERROR]: K8.530F is not in your design file, please correct.
[ERROR]: K9.530F is not in your design file, please correct.
[ERROR]: N1 is not in your design file, please correct.
[ERROR]: N2 is not in your design file, please correct.
[ERROR]: N3 is not in your design file, please correct.
westcot I found the error with my design file. I had it in a word document and it worked when I put it in notepad. t
Thank you so much for your help!
I am glad you were able to resolve the problem. Our current version is 1.31, and it includes many new commands, feature updates and bug fixes. You can download it at, http://www.mothur.org/wiki/Download_mothur.