count is not a valid parameter

So I have just switched to using Mothur on a Mac instead of a PC, and commands which ran perfectly on the PC are bugging out on the Mac i.e.

mothur > summary.seqs(count=stability.trim.contigs.good.count_table)

count is not a valid parameter.
The valid parameters are: fasta, name, processors, inputdir, and outputdir.
Using stability.trim.contigs.good.unique.fasta as input file for the fasta parameter.
[ERROR]: did not complete summary.seqs.

This is from the MiSeq SOP - it works perfectly well on the PC, and other functions are working, help much appreciated!


What version of mothur are you running? I’m not sure when exactly it was added, but count is an accepted parameter for v 1.32.0 or later.

Also - I’m 99% sure you’ll need to provide a fasta file as well. All the sequence metrics (length, ambigs, homopolymers etc) are calculate off your fasta file, and the names/count is just used to scale the abundance of these metrics.

Yeah sounds like you’ve got an old version of mothur. Also, you can leave off the fasta if you already have a file in your “current” list - use get.current()