[email protected] 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 [email protected])
if you need help in correcting your databases.
regards,
Peter Rice
_______________________________________________
EMBOSS mailing list
[email protected]
http://lists.open-bio.org/mailman/listinfo/emboss
