[BioBrew Users] : how to run mpiblast

[Glen Otero]

On Jul 15, 2004, at 11:51 PM, kenix y wrote:

> Trying to break
> ecoli.nt (5MB) into 3 fragments of 2MB Executing : formatdb -i
> ecoli.nt -o T -p F -v 2")
>
> What happens when you try to break it into 5 fragments?
> /opt/BioBrew/NCBI/6.1.0/bin/mpiformatdb -f 
> /home/bigcpuguest/mpiblast.conf -N 5 -i ecoli.nt -o T -p F
>
> Trying to break ecoli.nt (5MB) into 5 fragments of 1 MB
> Executing: formatdb -i ecoli.nt -o T -p F -v 1
>
> Moving fragments to /mnt/pvfs
> mv: cannot stat 'ecoli.nt.nal': No such file or directory
> Created and moved 5 fragments.

What happens when you run mpiBLAST against these fragments?
>
> What ecoli.nt.n* files are created?
>
> ecoli.nt.00.nhr
> ecoli.nt.00.nin
> ecoli.nt.00.nnd
> ecoli.nt.00.nni
> ecoli.nt.00.nsd
> ecoli.nt.00.nsi
> ecoli.nt.00.nsq
> . . .
>
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Glen Otero, Ph.D.
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