[BiO BB] FW: [blast-help] formatdbrc is now required?
akarger at CGR.Harvard.edu
Mon Jan 30 16:13:48 EST 2006
Here's the email I got from NCBI. I didn't hear quite as much "Sorry for
breaking your script without changing the formatdb docs." as I would like,
but it is free software after all. (It falls under the "paid for by my tax
dollars" definition of free.)
- Amir Karger
Computational Biology Group
Bauer Center for Genomics Research
From: Matten, Wayne (NIH/NLM) [C] [mailto:matten at ncbi.nlm.nih.gov]
Sent: Monday, January 30, 2006 3:54 PM
To: Amir Karger; NLM/NCBI List blast-help
Subject: RE: [blast-help] formatdbrc is now required?
You can ignore those messages. No .formatdbrc file is needed.
Wayne Matten, PhD
NCBI Service Desk
> -----Original Message-----
> From: Amir Karger [mailto:akarger at CGR.Harvard.edu]
> Sent: Monday, January 30, 2006 9:53 AM
> To: NLM/NCBI List blast-help
> Subject: [blast-help] formatdbrc is now required?
> I'm getting warning messages from the new formatdb.
> I used a file Hinf.faa with two protein sequences in it, and did:
> testportal>formatdb -o T -p T -i Hinf.faa more formatdb.log
> ========================[ Jan 30, 2006 9:47 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
> As you can see, I'm getting warning messages for not having a
> Unfortunately, this is breaking a script I have which runs
> formatdb every night and looks for errors in the log. Of
> course, I can change it to skip these lines, but I'm still curious.
> The formatdb docs say "These features are still under
> development and useful within NCBI only." Do I (and everyone
> in my building who uses formatdb) need to create a
> formatdbrc? What should I put in there?
> - Amir Karger
> Computational Biology Group
> Bauer Center for Genomics Research
> Harvard University
> ps I'm using the blast-2.2.13-ia32-linux.tar:
> The executable files were built on Tue Dec 6 10:23:48 EST
> 2005 The version number of each individual application may be
> found in the appropriate documentation files in ./ncbi/doc/
> uname -a ouput is: Linux icoremake0 126.96.36.199-III-64G #2 SMP
> Wed May 25
> EDT 2005 i686 unknown
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