make.file requires write permission in input directory


Quite new to this, so apologies if I get anything wrong. I’m trying to create a ‘stability.files’ file using make.file(inputdir=unwriteable/place, outdir=writeable/place, type=gz) and I’m getting an error that ‘unwritable/place’ does not exist or is unwriteable. If I chmod it, everything is ok, in the sense that the it produces the output in the outdir, but the modification date of the inputdir gets changed. Even if I change the tempdefault directory prior to the make.file.

It doesn’t change if I uncompress the fasta files and point to them instead, and the actual directory contents of the inputdir don’t look different before and after, as the stability.files is getting put somewhere entirely different. I’d prefer to keep the permissions on the fasta directory as they are (a nextflow workflow will be able to cache things better, amongst other reasons). Any ideas?
Thanks - Gavin


When you set the input directory, mothur checks it by trying to create a file in the location. Since your directory is not writable, that fails and the input directory can not be set. Sorry for the inconvenience.