I’ve just started using Mothur (using the MiSeq_SOP) and I’ve hit a wall at one of the first steps.
Entering make.contig(file=stability.files, processors=4) gives me an Error message that the file cannot be found in the directory.
This happens with the Mothur executable in the same folder as the stability.files file (and all fastq files).
A thorough googling has found a few approaches to fixing the problem, but none have worked.
One last piece of information: I tried opening the stability.files file in NotePad (to see what was in it), which deleted the .files part of the file name, and the icon changed to the NotePad icon. I set the default program to open the file to Mothur, and re-added the .files to the name. I also tried deleting the whole batch of files and redownloading them, and the stability.files was automatically changed to stability. I’m not sure if any of this even matters, but just in case.
Thanks for the help,