Hi,

I'm trying to make a shared folder with MOTHUR, and all I get for the moment is this error message. Those are my command lines and error message:

module load apps/mothur/1.38.1
make.shared(biom=example.biom)

-bash: syntax error near unexpected token `biom=example.biom'


Any idea of the problem? Thanks for you help!

P.S. The biom file is found. My mothur installation shows no problem when the module is loaded.

Hi & welcome to LQ! Feel free to introduce yourself (&'distro', hw, goals&interests, etc) here.

I think you need to run/invoke/execute the command/program:
mothur
first. See https://wiki.gacrc.uga.edu/wiki/MOTHUR-Sapelo, which links to http://www.mothur.org/wiki/Command_line_mode

Note that it is the Linux 'bash' (shell/command-interperter) that is complaining about your
make.shared(biom=example.biom)
which is a mothur command (not a bash shell command)!
bash gives similar syntax error IF you enter (at the % or # prompt) something like: man(anything)

Best Wishes... Have a look at some of the linux (&shell) tutorials links here.