DBIBLAST error when creating blast database

Marcus Claesson marcus at chah.ucc.ie
Mon Dec 2 15:45:53 UTC 2002


> Your wildcard filename fails to find any files. 
> If you still had the ecoli.aa fasta file (the one formatdb was used on) 
> this would work - the wildcard filename check finds that file and then 
> tries the formatdb index extensions.
> 
> You should specify ecoli.aa.* (in quotes if on the command line because of 
> the '*')
> 

Tried it, but it will still not fully work.
Looks like this now:

[marcus at nsfm39 db]$ ls -l ecoli.aa.*
-rw-------    1 marcus   marcus    1774183 Dec  2 14:15 ecoli.aa.fasta
-rw-rw-r--    1 marcus   marcus     563415 Nov 11 17:08 ecoli.aa.phr
-rw-rw-r--    1 marcus   marcus      34376 Nov 11 17:08 ecoli.aa.pin
-rw-rw-r--    1 marcus   marcus      34312 Nov 11 17:08 ecoli.aa.pnd
-rw-rw-r--    1 marcus   marcus        180 Nov 11 17:08 ecoli.aa.pni
-rw-rw-r--    1 marcus   marcus     354726 Nov 11 17:08 ecoli.aa.psd
-rw-rw-r--    1 marcus   marcus       8287 Nov 11 17:08 ecoli.aa.psi
-rw-rw-r--    1 marcus   marcus    1363280 Nov 11 17:08 ecoli.aa.psq
[marcus at nsfm39 db]$ dbiblast
Index a BLAST database
Database name: ecoli.aa
Database directory [.]:
Wildcard database filename [ecoli.aa]: ecoli.aa.*
Release number [0.0]:
Index date [00/00/00]:
         N : nucleic
         P : protein
         ? : unknown
Sequence type [unknown]: P
         1 : wublast and setdb/pressdb
         2 : formatdb
         0 : unknown
Blast index version [unknown]:2
Warning: Duplicate ID skipped: '0?0???7(AE000312)' All hits will point to
first ID found
Warning: Duplicate ID skipped: '0?0???7(AE000312)' All hits will point to
first ID found
Warning: Duplicate ID skipped: '0?0???7(AE000312)' All hits will point to
first ID found
Warning: Duplicate ID skipped: '0?0???7(AE000312)' All hits will point to
first ID found
Warning: Duplicate ID skipped: '0?0???7(AE000314)' All hits will point to
first ID found
..
..
..
and so on...

Am I almost there?

Regards
Marcus




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