Problems with BLAST formatdb

Gary Williams gwilliam at hgmp.mrc.ac.uk
Mon Nov 15 05:39:21 EST 1999

I wonder if anyone can help me:

We format our own BLAST databases and are interested in working with formatdb's
new '-v' option.

It is not clear what number should be used for the -v option.  With a
database of about 4 Mb, any number greater than 1 seems to produce one

What should the number be?

The greater problem is that when I try to use formatdb on a database of
size greater than 2 Gb (actually 2.1 Gb) it gives the following report
in formatdb.log and the index files are created with zero size.

Version 2.0.10 [Aug-26-1999]
Started database file "htg"
NOTE: CoreLib [002.003] FileOpen("htg","r") failed

I am using the executable for Solaris (version 2.0.10), as provided on
NCBI's FTP site, on a SUN Enterprise 6000 running Solaris 2.7

Has anyone has any success in using formatdb on SUNs with files over 2 Gb?

Many thanks,

Gary Williams               Tel: +44 1223 494522  Fax: +44 1223 494512
mailto:G.Williams at hgmp.mrc.ac.uk            http://www.hgmp.mrc.ac.uk/
Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK

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