I am following the MiSeq_SOP on the mothur wiki page. I have downloaded all the fastq files in the example dataset. When I run make.file(inputdir=~/MiSeq_SOP, type=fastq, prefix=stability) the stability.files that is created is not correct: for every line in the first column I just have 'MiSeq' instead of the sample group names as should be the case.

I cannot understand why this is, since I have just copy and pasted the command from the wiki page, with the only difference being '~/' in front of the the folder specified by the inputdir argument. I would be grateful if someone could shed some light on why this is happening.