[Bioclusters] Details on a local blast cluster question

[andy law (RI)]

... and also for the record on our RedHat 7.2 based system (kernel 2.4.2-2smp?), files greater than 2GB have to be piped into formatdb, rather than supplied as an argument

Later,

Andy

-------------
Yada, yada, yada...

The information contained in this e-mail (including any attachments) is confidential and is intended for the use of the addressee only.   The opinions expressed within this e-mail (including any attachments) are the opinions of the sender and do not necessarily constitute those of Roslin Institute (Edinburgh) ("the Institute") unless specifically stated by a sender who is duly authorised to do so on behalf of the Institute.


> -----Original Message-----
> From: Wim Glassee [mailto:wim.glassee@ua.ac.be]
> Sent: 21 January 2003 08:54
> To: bioclusters@bioinformatics.org
> 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
> 
> 
> _______________________________________________
> Bioclusters maillist  -  Bioclusters@bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters
>