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!