[Bioclusters] Details on a local blast cluster question

[Tim Harsch]

Also for the record.  I've found that splitting a database in this way has
the extremely beneficial side effect of reducing the total RAM required by
BLAST (over blasting against a single database of the exact same sequences).
It seems to scale with the number of databases created.  Though I've not
verified with any rigorous testing, so reader beware.


----- Original Message -----
From: "Wim Glassee" <wim.glassee@ua.ac.be>
To: <bioclusters@bioinformatics.org>
Sent: Tuesday, January 21, 2003 12:54 AM
Subject: RE: [Bioclusters] Details on a local blast cluster question


Hi Joe,

Just for the record,

In the new version of formatdb the -v parameter takes MB's in stead of
bytes. So the command would be:

formatdb -v 100 -p T -o T -i nr

> -----Original Message-----
> From: bioclusters-admin@bioinformatics.org [mailto:bioclusters-
> admin@bioinformatics.org] On Behalf Of Joe Landman
> Sent: maandag 20 januari 2003 23:57
> To: bioclusters@bioinformatics.org
> Subject: Re: [Bioclusters] Details on a local blast cluster question
>
> Hi Tracy:
>
>   Look at the -v switch on formatdb.  The -v switch breaks the database
> into volumes and preserves the complete database size (so you do not
> have to recalculate the size-dependent quantities upon completion).
>
> For exanple, to split a recent nr into several volumes of at most 100M
> letters
>
>         formatdb -v 100000000 -p T -o T -i nr
>
> yields
>
>         [root@frontend-0 db2]# ls -alF
>         total 1507984
>         drwxr-xr-x    2 root     root         4096 Jan 20 22:53 ./
>         drwxr-xr-x   10 root     root         4096 Jan 20 22:43 ../
>         -rw-r--r--    1 root     root          405 Jan 20 22:53
> formatdb.log
>         -rw-r--r--    1 root     root     589765675 Jan 20 22:44 nr
>         -rw-r--r--    1 root     root     190609908 Jan 20 22:49 nr.00.phr
>         -rw-r--r--    1 root     root      6949984 Jan 20 22:51 nr.00.pin
>         -rw-r--r--    1 root     root     12565120 Jan 20 22:49 nr.00.pnd
>         -rw-r--r--    1 root     root        49132 Jan 20 22:49 nr.00.pni
>         -rw-r--r--    1 root     root     173748036 Jan 20 22:50 nr.00.psd
>         -rw-r--r--    1 root     root      3804603 Jan 20 22:51 nr.00.psi
>         -rw-r--r--    1 root     root     277315926 Jan 20 22:49 nr.00.psq
>         -rw-r--r--    1 root     root     82065838 Jan 20 22:53 nr.01.phr
>         -rw-r--r--    1 root     root      2997568 Jan 20 22:53 nr.01.pin
>         -rw-r--r--    1 root     root      5409488 Jan 20 22:53 nr.01.pnd
>         -rw-r--r--    1 root     root        21180 Jan 20 22:53 nr.01.pni
>         -rw-r--r--    1 root     root     74213127 Jan 20 22:53 nr.01.psd
>         -rw-r--r--    1 root     root      1658969 Jan 20 22:53 nr.01.psi
>         -rw-r--r--    1 root     root     119641224 Jan 20 22:53 nr.01.psq
>         -rw-r--r--    1 root     root          106 Jan 20 22:53 nr.pal
>
> To run the code, simply use the normal methods.  Use nr as the database
> (-d nr)
>
> Joe
>
> --
> Joseph Landman, Ph.D
> Scalable Informatics LLC,
> email: landman@scalableinformatics.com
> web  : http://scalableinformatics.com
> phone: +1 734 612 4615
>
> _______________________________________________
> Bioclusters maillist  -  Bioclusters@bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters


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