[Bioclusters] Details on a local blast cluster question

[Joe Landman]

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