David.Bauer at SCHERING.DE David.Bauer at SCHERING.DE
Tue Jul 9 06:00:22 UTC 2002

Hi Qingjuan,

I know this problem.
dbiblast expects to find the source fasta file which was used for formating the
BLAST databases in the same directory.
The 'Wildcard database filename' is used as base and then the .nin etc. are
appended to this name.
So the error says that dbiblast thinks 'ecoli.nt.nhr' is the fasta file and
looks for a BLAST index file 'ecoli.nt.nhr.nin'.
Either copy the fasta file in the same directory or create a symbolic link
Then specify "ecoli.nt" as "Wildcard database filename" which in this case is
not a wildcard.

Peter, what about changing "Wildcard database filename" to "Filename of fasta
source file" in dbiblast ?


 I am configuring emboss for blast database. I copied part of database from
balst formatted database into my test directory. Here is the files:

 # ls -l
total 1308
-rwxr--r--   1 root     system     11306 Jul  8 13:52 alu.n.nhr
-rwxr--r--   1 root     system      3988 Jul  8 13:52 alu.n.nin
-rwxr--r--   1 root     system     16640 Jul  8 13:52 alu.n.nsd
-rwxr--r--   1 root     system       411 Jul  8 13:52 alu.n.nsi
-rwxr--r--   1 root     system     20336 Jul  8 13:52 alu.n.nsq
-rwxr--r--   1 nobody   blast      41492 Feb 27 22:15 ecoli.nt.nhr
-rwxr--r--   1 nobody   blast       4864 Feb 27 22:15 ecoli.nt.nin
-rwxr--r--   1 nobody   blast       3200 Feb 27 22:15 ecoli.nt.nnd
-rwxr--r--   1 nobody   blast         60 Feb 27 22:15 ecoli.nt.nni
-rwxr--r--   1 nobody   blast      58320 Feb 27 22:15 ecoli.nt.nsd
-rwxr--r--   1 nobody   blast       1264 Feb 27 22:15 ecoli.nt.nsi
-rwxr--r--   1 nobody   blast    1165813 Feb 27 22:15 ecoli.nt.nsq

When I run dbiblast command, there are some errors:
# dbiblast
Index a BLAST database
Database name: ecoli
Database directory [.]:
Wildcard database filename [ecoli]: ecoli.*
Release number [0.0]:
Index date [00/00/00]: 07/08/02
         N : nucleic
         P : protein
         ? : unknown
Sequence type [unknown]: N
         1 : wublast and setdb/pressdb
         2 : formatdb
         0 : unknown
Blast index version [unknown]: 2

   EMBOSS An error in dbiblast.c at line 640:
 cannot open ./ecoli.nt.nhr table file ./ecoli.nt.nhr.nin

Does anybody have some ideas? Thank you very much in advance.


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