I’m totaly new in the mothur environment, just to be clear.
Nevertheless i’m using tutorials from mothur wiki, and i cannot read any file under Mac environment
From mothur i write;
mothur > read.dist(phylip=den.dist, cutoff=0.1)
and i get “Could not open den.dist”
same thing when i change name to den.dst (i thought maybe extension issue)
i even tried both versions of compiled mothur on the page, and i’ve compiled one myself (still cannot read)
to have more fun, i’ve run the same thing under windows (using paralel desktop) and it read the file (?)
but under windows i cannot create groups:
mothur > read.dist(phylip=den.dist, cutoff=0.1, name=den.names)
and i get “Could not read den.names”
and later when i want to determine OTU’s:
mothur > read.otu(list=den.fn.list, group=den.groups, label=unique-0.03-0.05-0.10)
and i get “Could not read den.groups”
so at this point i was out of ideas…
I suspect the problem is that the files aren’t where you think they are. You have to be very specific about where things are.
At the prompt type (in mac): system(ls)
At the prompt type (in win): system(dir)
Does the output contain the distance file? You need to use the command line tools to navigate to the correct folder and put the files in that folder.
Well files were there
When i’ve opened mothur from terminal from folder in which dst file was it worked.
But opening it by double-clicking and loading file gave an error. Anyway, problem 1 solved.
Still i have same issues with name= and group= as in win
When you double click on the file it think it’s in the folder where the executable is located, not the data. Move the executable into the same folder as the data and try. Note - this is not the best way to do it. Rather, open Terminal.app, and navigate to the folder with the data and call mothur from wherever it’s located.
Sure, got that working.
Still cannot create groups.
Anyway i’ve been also using phylotype command, and still i don;t know how to view files which were created using it. (i mean, i have a DEN50_NAST.silva.slv.tx.list file, but i don;t know how to open it - i cannot find it in Your wiki)
every file used and created in mothur is a text file. if you’ve got a mac you can open it in a free program called textwrangler.