sfffile not working

I’m trying to merge sff files by typing:
sfffile -o combined.sff CC2.sff CC7.sff CA2.sff

Mothur is outputting:
[ERROR] you are missing (

What am I doing wrong? Is there another way to merge sff files?

You want to enter that at the command prompt, not within mothur.

Actually this format "sfffile -o combined.sff infile1.sff infile2.sff"is not executable in cmd.I tried “sfffile -o combined.sff infile1.sff infile2.sff” and “E:>mothur(sfffile -o combined.sff file1.sff file2.sff”, but both failed. Could you tell me what excatly the format should be? Thank you!

sfffile is not a mothur command - so you will not run it from within mothur. It looks as though you perhaps have a windows machine, and I’m not sure that any of 454’s tools can be run in windows, which is likely your problem since they’re unix tools.