On Wed, 8 Sep 2004, Joe Landman wrote: >Dan Bolser wrote: > >> >>Basically I would like to know if I am or could be running mpiBLAST >>without knowing it, and all these bugs traceback to mpiBLAST, or if >>mpiBLAST is reporting (in the web page above) a bug which traces back to >>BLAST on multi CPU archetecture. >> >> > >It is highly unlikely you are running mpiBLAST without knowing it. What >does your command line look like? This looks like it is a translation >bug in the lower reaches of the blast code. mpiBLAST hits those code >sections, so it sees the bug more often than not. The notes indicate >that it is related to using one of the -m options (for output >translation). What does the rest of your command line look like? That is what I guessed (I didn't ever knowingly install mpiBLAST). formatdb -i sequences.fa -o T blastall -d sequences.fa -p blastp -i domain_sequences.fa -m 8 -a4 > results > >>I get "blastall 2.2.8". >> >> >>Anybody know if this 'bug' is serious? Can I ignore it? >> >> > >Hmm. Does it impact the output data you need (actual alignment >information), or are you after parameters and computational "side >effects" (bit scores, E-values,...) I haven't looked in detail yet. I am interested in the similarity of these sequences to themselves (hence blastall). I want to make my own clusters of these sequences / compare clusterings. I use -m 8 because I don't care about the alignment, but perhaps that would give clues to the error. If you like I can re-run the problem sequences with -m 7 and send along some results. Cheers, Dan. > > >