[Bioperl-l] BlastPlus usage inquiry

[Mark A. Jensen]

Hi Ross --
Add the following option:

-num_threads 7

and see if it picks up the other CPUs--
cheers Mark
----- Original Message ----- 
From: "Ross KK Leung" <ross at cuhk.edu.hk>
To: "'Janine Arloth'" <janine.arloth at googlemail.com>; 
<bioperl-l at lists.open-bio.org>
Sent: Wednesday, March 31, 2010 5:28 PM
Subject: [Bioperl-l] BlastPlus usage inquiry


> Dear all,
>
> I know it is inappropriate to raise this question in bioperl but as I
> received no better response from NCBI and so have to ask in this group
> (because finally I'll use bioperl to call blastplus). I have already been
> using the latest blastplus (the command is blastn directly) and found the
> problem of running slow and inability to run in a parallel/multithread
> manner.
>
>
> Previously I was using non blastplus version 2.2.22 with the command
> blastall -p blastn -a 8 etc.
>
> With similar arguments as below except the word size was 12, my shell script
> for the same input and database finishes almost instantly. I notice that
> except word size and min raw gapped score were changed by me, nothing
> appears to differ from the previous version parameters. Moreover, when I top
> my process, I find it uses only one CPU instead of 7.
>
> What may be the problem for the script that makes the job running for a day
> and still hasn't finished?
>
> blastn -query $1 -db $2 -out $1_$2.xml -num_threads 7 -word_size 4 -gapopen
> 3 -gapextend 1 -penalty -2 -outfmt 5 -xdrop_ungap 30 -xdrop_gap 30
> -xdrop_gap_final 30 -min_raw_gapped_score 10
>
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