[BiO BB] formatdb now requires .formatdbrc?

Pamela Culpepper pculpep at hotmail.com
Fri Jan 27 12:28:35 EST 2006


I have used formatdb and have not encountered any problems.  However, I 
compiled formatdb from scratch using the NCBI Toolkit.

Go to http://www.lifeformulae.com/local_blast_graphics/index.html

and get the HOW_TO.txt and blastall_diff.txt files.

They will enable you to compile the NCBI toolkit (with blastall, formatdb, 
etc.) for the Linux environment.

This is the formatdb I used.  As an aside, blastall will now product a local 
BLAST alignment gif for both the old and new BLAST engines.


>From: Amir Karger <akarger at CGR.Harvard.edu>
>Reply-To: "The general forum at Bioinformatics.Org" 
><bio_bulletin_board at bioinformatics.org>
>To: "'bio_bulletin_board at bioinformatics.org'" 
><bio_bulletin_board at bioinformatics.org>
>Subject: [BiO BB] formatdb now requires .formatdbrc?
>Date: Fri, 27 Jan 2006 11:51:19 -0500
>I'm seeing new behavior when I run formatdb:
>testportal:play/recip_blast/t2>formatdb -o T -i Hinf.faa -l stdout -p T -t
>========================[ Jan 27, 2006 11:40 AM ]========================
>Version 2.2.13 [Nov-27-2005]
>Started database file "Hinf.faa"
>NOTE: CoreLib [002.003] FileOpen(".formatdbrc","r") failed
>NOTE: CoreLib [002.003] 
>NOTE: [000.000] No number of link bits used found in config  file. Ignoring
>NOTE: [000.000] No number of membership bits used found in config file.
>Formatted 2 sequences in volume 0
>I believe this started occurring when we upgraded from blast 2.2.10 to
>Normally, I wouldn't complain, but I've got a script parsing the output 
>formatdb, which is now breaking. The docs to formatdb still say in the
>formatdbrc section that "These features are still under development and
>useful within NCBI only." Have they automatically put this feature into the
>binaries now, such that everyone needs a .formatdbrc?
>- Amir Karger
>Computational Biology Group
>Bauer Center for Genomics Research
>Harvard University
>Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org

More information about the BBB mailing list