[EMBOSS] dbxflat problem

ajb at ebi.ac.uk ajb at ebi.ac.uk
Tue Aug 31 10:52:20 UTC 2010

Hi Aengus,

Are you saying that it's restricted to RHEL5 or that it's the only
platform you've tried it on.

Assuming it's not restricted to RHEL5 then first check your RES
definitions in your emboss.default (or .embossrc) to verify that
the field lengths are not set too small.

If they look OK then you'd need to post us:

  a) Your RES definitions
  b) A URL/site and specify where we can get exactly the source
     data you are trying to index. Tell us of any modifications
     made to the data.
  c) The command lines used (already given below), plus any responses
     to any further prompts.

We could then attempt to reproduce the error.



> Hi folks,
> Not sure if I am doing something wrong but I am getting an error from
> 6.3.1 on Redhat EL5
> dbxflat -verbose -idformat swiss -directory . -filenames "*.dat" -dbname
> trembl -dbresource trembl
> -release - -date 29/08/10 -fields id,acc,sv,des,key,org -outfile
> emboss.index.log
> Index a flat file database using b+tree indices
>     EMBOSS An error in ajindex.c at line 702:
> Maximum retries (100) reached in btreeCacheFetch for page 1069056
> Actually I am getting the same error with dbiflat as well.
> dbxfasta -idformat gcgidacc -directory /data/INCOMING/nrprot -filenames
> nrprot.fasta -dbname nrprot
> -dbresource nrprot -release "-" -date 29/08/10 -fields "acc,sv,des"
> -outfile emboss.index.log
> Index a fasta file database using b+tree indices
>     EMBOSS An error in ajindex.c at line 702:
> Maximum retries (100) reached in btreeCacheFetch for page 2774040576
> Aengus
> --
> -----------------------------------------------------------------------
> Aengus Stewart                                 Tel: +44 (0)20 7269 3679
> Head of Bioinformatics and BioStatistics
> CRUK London Research Institute
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