[Bioclusters] Details on a local blast cluster question

[Wim Glassee]

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
>=20
> Hi Tracy:
>=20
>   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).
>=20
> For exanple, to split a recent nr into several volumes of at most 100M
> letters
>=20
>         formatdb -v 100000000 -p T -o T -i nr
>=20
> yields
>=20
>         [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
>=20
> To run the code, simply use the normal methods.  Use nr as the =
database
> (-d nr)
>=20
> Joe
>=20
> --
> Joseph Landman, Ph.D
> Scalable Informatics LLC,
> email: landman@scalableinformatics.com
> web  : http://scalableinformatics.com
> phone: +1 734 612 4615
>=20
> _______________________________________________
> Bioclusters maillist  -  Bioclusters@bioinformatics.org
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