[BiO BB] FW: [blast-help] formatdbrc is now required?

Amir Karger 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
Harvard University

-----Original Message-----
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.

Best regards,
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] 
> FileOpen("/n/compbio/users/akarger/.formatdbrc","r")
> fai
> led
> 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
> -------------------
> As you can see, I'm getting warning messages for not having a 
> .formatdbrc.
> 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?
> Thanks,
> - Amir Karger
> Computational Biology Group
> Bauer Center for Genomics Research
> Harvard University
> 617-496-0626
> 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 #2 SMP 
> Wed May 25
> 10:52:09
>  EDT 2005 i686 unknown

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