[Bioclusters] help with running mpiBLAST-1.2.0

[Jason Gans]

> Richard Huang wrote:
> 
> Hi,
> 
> I'm trying to run mpiBLAST on the nr peptide database using the first
> entry as the query. I've installed the NCBI toolbox and also MPI. I
> get the following error when I try to run:
> 
> [ryhuang@frontend-0 mpiBLAST-1.2.0]$ mpirun -np 5 -nolocal
> -machinefile machines /home/ryhuang/mpiBLAST-1.2.0/bin/mpiblast
> --debug --log-file=/home/ryhuang/mpiBLAST-1.2.0/log3 -p blastp -d
> nr_092602.fa -i query2.fas -o result.txt
> logging to /home/ryhuang/mpiBLAST-1.2.0/log3.1
> logging to /home/ryhuang/mpiBLAST-1.2.0/log3.2
> logging to logging to /home/ryhuang/mpiBLAST-1.2.0/log3.4
> /home/ryhuang/mpiBLAST-1.2.0/log3.0
> logging to /home/ryhuang/mpiBLAST-1.2.0/log3.3
> [blastall] ERROR: ncbiapi [000.000]  ObjMgrChoice: pointer [0] type
> [1] not found
<snip>

This is a bug in mpiBLAST 1.2.0. Until it is fixed, you should format
the 
database with "-o T" (i.e. Parse SeqId and create indexes) as a work
around.

Regards,

Jason