I’ve wanted to use Mothur for my 454 sequencing data. Downloaded 64-bit mac executable version but mother doesn’t want to run any commands even summar.seqs.
What might be the problem?
Thanks,
Fey
Could you post the error message you are receiving?
It is
Unable to open holme.fas
[ERROR]: did not complete summary.seqs.
The most common cause of mothur not finding a file is because you double clicked on the mothur executable to run mothur. This will open a terminal or command prompt window in your home directory. Mothur will then look for the input files in the home directory instead of in the directory where mothur’s executable is located. If this is the cause, you either put the input files in your home directory, give complete file names, or open a terminal or command prompt window, cd into the directory where the mothur executable is located and run mothur by using “./mothur” for mac or “mothur” for windows.
It works! Thanks, you are really helpful 
Fey
Hi,
I wanted to run align.seqs command (using silva template), but getting this error message;
Unable to open silva.bacteria.fasta
[ERROR]: did not complete align.seqs.
All the files related to mothur are in the home directory…
Thanks in advance,
Fey
Sorry this looks like a very old message that we missed - are you sure that silva.bacteria.fasta is in the same folder as your data and where you are running the program from?