[Bioclusters] Memory Usage for Blast - question

[Joe Landman]

Dinanath Sulakhe wrote:


> Now the Admin of the Site is asking me if its possible to reduce the 
> amount of memory these blast jobs use? He says these jobs are requesting 
> about 600-700MB of RAM, and he is asking me to reduce it to atmost 500MB.
> 
> Is it possible to reduce the amount of RAM it is requesting by tweaking 
> any of the parameters in blast??

Yes.  Run formatdb similar to this

	formatdb -i $db -o T -p T -v 200

where $db is the name of your db as in your blast line below.  This will 
segment your database down quite a bit.  Note:  there are limits you 
would have to worry about if $db is huge (over 10 GB or so).

> 
> My blast options are :
> 
> blastall -i $input -o $output -d $db -p blastp -m 8 -F F
> 
> Please let me know,
> Thank you,
> Dina
> 
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Joseph Landman, Ph.D
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