[Bioclusters] mpiBLAST

Osborne, John bioclusters@bioinformatics.org
Wed, 14 May 2003 16:46:30 -0400


>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