count is not a valid parameter

Commands in mothur
1

Hi,
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!

Phil

2

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.

3

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()