[BiO BB] formatdb now requires .formatdbrc?
Pamela Culpepper
pculpep at hotmail.com
Fri Jan 27 12:28:35 EST 2006
Amir,
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.
Pam
>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
>blah
>
>========================[ 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]
>FileOpen("/n/compbio/users/akarger/.formatdbrc","r")
>failed
>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.
>Ignoring
>Formatted 2 sequences in volume 0
>
>
>I believe this started occurring when we upgraded from blast 2.2.10 to
>2.2.13.
>
>Normally, I wouldn't complain, but I've got a script parsing the output
>from
>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?
>
>Thanks,
>
>- Amir Karger
>Computational Biology Group
>Bauer Center for Genomics Research
>Harvard University
>617-496-0626
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