>Note: For some reason, I seem to remember needing to put a >"Data=/path/to/scoring/matrices" as the third line in mpiblast.conf. I >make sure this is a shared path. > I put that in there as the 3rd line, it worked, but then I removed it and it still works. Not sure what is going on, but it seems to find the PAM matrices now. Can anybody else here testify as to whether they put it in the last line of mpiblast.conf? >What was your original mpiformatdb line? mpiformatdb -f /usr/local/bioinformatics/etc/mpiblast.conf -N 20 -i /scratch/data/nr -o T -p T My mpiblast.conf still has just the two lines pointing to the shared and local storage. It was run from a bash shell script, and the offending null filled file was located where I ran the bash script from. -John