[BiO BB] formatdb now requires .formatdbrc?

Amir Karger akarger at CGR.Harvard.edu
Fri Jan 27 11:51:19 EST 2006

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] FileOpen("/n/compbio/users/akarger/.formatdbrc","r")
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 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?


- Amir Karger
Computational Biology Group
Bauer Center for Genomics Research
Harvard University

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