[EMBOSS] whichdb error

[Peter Rice]

Veronique.Martin at jouy.inra.fr wrote:
> I have this error with whichdb command:

Whichdb will search for L07770 by ID and by accession in all the 
databases you have defined. The outputn will show a list of all the 
databases it tests, which will be defined in your emboss.defaults file 
and perhaps in your personal ~/.embossrc file

> -----------
> whichdb -showall
> Search all sequence databases for an entry and retrieve it
> ID or Accession number: L07770
> Output file [stdout]:
> # Trying 'gb_rod:l07770'
> # Failed 'gb_rod:l07770'
> # Trying 'gb_pln:l07770'
> # Failed 'gb_pln:l07770'
> # Trying 'gp_syn:l07770'
> # Failed 'gp_syn:l07770'
> # Trying 'gb_pri:l07770'
> # Failed 'gb_pri:l07770'
> # Trying 'genbankwgs:l07770'
> # Failed 'genbankwgs:l07770'
> # Trying 'nr80:l07770'
> # Failed 'nr80:l07770'
> # Trying 'PRINTS:l07770'
> Warning: Cannot open division file '<null>' for database 'PRINTS'
> Warning: seqCdQry failed

This suggests you have PRINTS defined as a sequence database. Prints is 
a pattern database and does not need to be defined in emboss.defaults of 
~/.embossrc

> # Failed 'PRINTS:l07770'
> # Trying 'opsdw:l07770'
> # Failed 'opsdw:l07770'
> # Trying 'emblwgs_hum:l07770'
> 
>    EMBOSS An error in ajindex.c at line 2429:
> GetKeys: No keys in node
> ------------


and this suggests a problem with the indexing of your emblwgs_hum 
database. You need to check the status of this database and correct it.

Meanwhile, perhaps we can persuade whichdb to continue checking the 
remaining databases. You failed to find L07770 because it stopped at 
this point.

> However, it's ok for this ID, because for example,
> infoseq or other commands (seqret...) runs correctly, as you can see 
> bellow:
> -------------
> infoseq genbank:l07770
> Display basic information about sequences
> USA                      Database  Name           Accession      Type 
> Length %GC    Description
> genbank-id:XELRHODOP     genbank        XELRHODOP      L07770         N 
> 1684   45.72  Xenopus laevis rhodopsin mRNA, complete cds.

So whichdb will find the entry when it reaches genbank and searched by 
accession.

I hope this helps. Let us know (mail to emboss-bug at emboss.open-bio.org) 
if you need help in correcting your databases.

regards,

Peter Rice