... 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 >