Running Mothur in command line mode

I am installing Mothur v1.43 in macOS, but it only works in interactive mode. How can I activate command line mode?

After conclude installation, ./mothur only open the interactive mode at Mothur directory, but the command mothur is not found from any directory, including Mothur directory.

I’ll be very grateful for help.


Welcome to mothur. You need to open your terminal/command prompt and use cd to move to the directory containing your data and mothur. From there you can type mothur.exe (windows) or ./mothur (mac/linux) to start the interactive mode. I suspect you’re double clicking on the icon - that causes problems down the pipeline. For the command line mode instead of launching mothur, you would do ./mothur "#summary.seqs(fasta=my_sequences.fasta)" to run a mothur command from the command line.


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