Hello,
I hope this isn’t a silly question, but I am trying to run an amova test on my data and it is saying that my .design file is unable to be opened. I’ve ensured that my .design file is in the same operating file as mothur (the ./ on the stability file results from making contigs from a folder of zipped files at the beginning of my analysis).
I’ve made my design file in both excel (.csv) and in texwranger (.txt) and I feel like I’m missing something simple to be able to get the file to read. The file does have 4 treatments (instead of the two, Early and Late, in the example), but I didn’t think that should be a problem for the amova…
mothur > amova(phylip=./stability.an.jclass.0.03.lt.ave.dist, design=trt.design) Unable to open trt.design. Trying default ./trt.design Unable to open ./trt.design. Trying mothur's location ./trt.design Unable to open ./trt.design [ERROR]: did not complete amova.
The file looks like this:
group trt
I1A FF
I1B L
I1C FF
I1D SG
I1E FF
I2A FF
I2B L
I2C FF
I2D SG
I2E FF
I3A FF
I3B L
I3C FF
I3D SG
I3E SG
II1A FF
II1B L
II1C FF
II1D SG
II1E FF
II2A FF
II2B L
II2C FF
II2D SG
II2E FF
II3A FF
II3B L
II3C FF
II3D SG
II3E SG
Control1 C
Control2 C
Any help or guidance would be greatly appreciated.
Thank you!