[ssml] copymat-rpsblast

Dan Bolser dmb at mrc-dunn.cam.ac.uk
Mon May 2 12:43:59 EDT 2005


On Mon, 2 May 2005, Mensur Dlakic wrote:

>
>If you are using recent RPS-Blast databases (say Pfam or larger, which would 
>be CDD), 512Mb will probably be insufficient. I was struggling with these 
>databases even when my computer had 1Gb, though it worked after taking an 
>overnight to execute the program. I would recommend 2Gb RAM for comfortable 
>work with present RPS-Blast databases. There are experts at NCBI to ask about 
>this as well, though they are not always speedy when responding.


I think that address is;

mailto:toolbox at ncbi.nlm.nih.gov 

Another problem with asking questions at that address is that the answers
are not archived in a public place, although the NCBI do run public
mailing lists related to blast, etc.;

http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit.section.mailing_lists

And I really like their 'bookshelf' in general... 

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=books


Anyway, my point was that if you want to ask for technical assistance with
largescale searches and performance issues you can get great feedback from
the following (open archive) list...

mailto:bioclusters at bioinformatics.org

You can search the archive here (which is always a good first step)...

http://bioinformatics.org/pipermail/bioclusters/



>
>Take care,
>
>Mensur
>
>
>On Mon, 2 May 2005, Ratna Rajesh Thangudu wrote:
>
>|>Dear all,
>|>
>|>While trying to create a rpsblast searchable profile database, I am facing 
>|>problems with  Secondary preprocessing of the files with copymat.
>|>It is throwing the following error - 
>|>
>|>[copymat] FATAL ERROR: Failed to allocate -1554705136 bytes
>|>
>|>
>|>How to solve this memory problem. I tried running this on a P4 with 512 MB RAM 
>|>also.
>|>
>|>Thanks in advance.
>|>
>|>best
>|>
>|>Rajesh
>
>==========================================================================
>| Mensur Dlakic, Ph.D.              | Tel: (406) 994-6576                |
>| Department of Microbiology        | Fax: (406) 994-4926                |
>| Montana State University          |                                    |
>| 109 Lewis Hall, P.O. Box 173520   | http://myprofile.cos.com/mensur    |
>| Bozeman, MT 59717-3520            | E-mail: mdlakic at montana.edu        |
>==========================================================================
>
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