I am running Mothur v. 1.39.1 and if I follow the MiSeq SOP and run the following command:

rename.file(input=silva.nr_v123.pcr.align, new= silva.v4.fasta)

I get an error stating this is an invalid command. Can anyone help?

I just realized I was on a server that had an old version of Mothur so the command was not recognized.