Clearcut output files

I’m running MOTHUR on a MAC 10.6.4

When I run the clearcut command the output files aren’t in the specified folder, and I’m not sure if they were created at all . Interestingly, I have received one output file in the same folder that the original fasta file was in by running the same command. I have the MOTHUR.exe and Clearcut.exe in the same folder, named “clearcut” which is in the “bioinformatic” folder. Any thoughts on this issue?

mothur > clearcut(kimura, fasta=6p1-21.fas_NAST.fasta, DNA=T)

sh: /Users/TRW/desktop/bioinformatic/clearcut/clearcut/clearcut: Not a directory

Output File Names:

Nevermind. The problem was I had the Mothur.exe and clearcut.exe in the same folder. I took the mothur.exe up one folder and there was no directory failure. The file still comes out where my input file originated, but that’s OK with me.
I also noticed, as is stated elsewhere on these boards, that with two terminal windows open the output files aren’t created.