DBIBLAST error when creating blast database

[Marcus Claesson]

 > The latest formatdb from NCBI creates "version 4" blast index files. NCBI 
> have not provided any documentation on this format, so it is not supported 
> by EMBOSS. To produce the 'old' (non-ASN.1) index files, use:
>
> formatdb -A F
>
> That should fix it. 

Not fully, but at least I don't get any error messages. The ecoli.aa db
won't show up when I run 'showdb'. Here's what I did:

[marcus at nsfm39 db]$ formatdb -A F -i ecoli.aa -p T -o T
[marcus at nsfm39 db]$ ll|grep "Dec  2"
-rw-------    1 marcus   marcus    1774183 Dec  2 14:15 ecoli.aa
-rw-rw-r--    1 marcus   marcus     387530 Dec  2 15:29 ecoli.aa.phr
-rw-rw-r--    1 marcus   marcus      34372 Dec  2 15:29 ecoli.aa.pin
-rw-rw-r--    1 marcus   marcus      34312 Dec  2 15:29 ecoli.aa.pnd
-rw-rw-r--    1 marcus   marcus        180 Dec  2 15:29 ecoli.aa.pni
-rw-rw-r--    1 marcus   marcus     354726 Dec  2 15:29 ecoli.aa.psd
-rw-rw-r--    1 marcus   marcus       8287 Dec  2 15:29 ecoli.aa.psi
-rw-rw-r--    1 marcus   marcus    1363280 Dec  2 15:29 ecoli.aa.psq
-rw-rw-r--    1 marcus   marcus     642786 Dec  2 15:29 formatdb.log
[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
[marcus at nsfm39 db]$ showdb
Displays information on the currently available databases
# Name        Type ID  Qry All Comment
# ====        ==== ==  === === =======
tpir          P    OK  OK  OK  PIR using NBRF access for 4 files
tsw           P    OK  OK  OK  Swissprot native format with EMBL CD-ROM
index
tswnew        P    OK  OK  OK  Swissnew as 3 files in native format with
EMBL CD-ROM index
twp           P    OK  OK  OK  EMBL new in native format with EMBL CD-ROM
index
gb            N    OK  -   -   Genbank IDs
gba           N    OK  -   -   Genbank ACs
tembl         N    OK  OK  OK  EMBL in native format with EMBL CD-ROM
index
tgb           N    OK  -   -   Genbank IDs
tgenbank      N    OK  OK  OK  GenBank in native format with EMBL CD-ROM 
index
[marcus at nsfm39 db]$ ll|grep "Dec  2"
-rw-rw-r--    1 marcus   marcus        300 Dec  2 15:30 acnum.hit
-rw-rw-r--    1 marcus   marcus        300 Dec  2 15:30 acnum.trg
-rw-rw-r--    1 marcus   marcus        322 Dec  2 15:30 division.lkp
-rw-------    1 marcus   marcus    1774183 Dec  2 14:15 ecoli.aa
-rw-rw-r--    1 marcus   marcus     387530 Dec  2 15:29 ecoli.aa.phr
-rw-rw-r--    1 marcus   marcus      34372 Dec  2 15:29 ecoli.aa.pin
-rw-rw-r--    1 marcus   marcus      34312 Dec  2 15:29 ecoli.aa.pnd
-rw-rw-r--    1 marcus   marcus        180 Dec  2 15:29 ecoli.aa.pni
-rw-rw-r--    1 marcus   marcus     354726 Dec  2 15:29 ecoli.aa.psd
-rw-rw-r--    1 marcus   marcus       8287 Dec  2 15:29 ecoli.aa.psi
-rw-rw-r--    1 marcus   marcus    1363280 Dec  2 15:29 ecoli.aa.psq
-rw-rw-r--    1 marcus   marcus      86080 Dec  2 15:30 entrynam.idx
-rw-rw-r--    1 marcus   marcus     642786 Dec  2 15:29 formatdb.log

Thus, nothing new in showdb...

Thanks for helping me Peter!

/Marcus