Merge.files fails every time

Whenever I try merge.files, I get an error that the input files cannot be found. Running 1.33.3 on CentOS 6.x.

Cat from the command line works just fine to merge the same files. Minor problem, but annoying.

If you run:


Do you see the files you want? I suspect you’re running mothur from a different folder than you suspect.


No, I don’t see the file in the folder the mothur executable lives in - I set a different default working directory for each run. It seems reasonable to expect merge.files to obey set.dir like all of the other commands … but I know what is reasonable isn’t always practical.