[EMBOSS] Problems indexing with dbxfasta

[ajb at ebi.ac.uk]

Hello Simon,

Did you pick up the latest set of patches from:
  ftp://emboss.open-bio.org/pub/EMBOSS/fixes/
?

The indexing system was rewritten a few months ago to fix this. See
the README in that directory.
If you are using the latest fixes (check file sizes) and it is still
failing then let me know.


HTH

Alan

> I'm trying to use dbxfasta to index one of the WGS trace databases.
> Unfortunately dbxfasta is falling over on me.  The session looks like
> this:
>
> $ dbxfasta
> Database b+tree indexing for fasta file databases
> Basename for index files: traces_oanatinus
> Resource name: all
>     simple : >ID
>      idacc : >ID ACC
>      gcgid : >db:ID
>   gcgidacc : >db:ID ACC
>       dbid : >db ID
>       ncbi : | formats
> ID line format [idacc]: simple
> Database directory [.]:
> Wildcard database filename [*.dat]: *.fasta
> Release number [0.0]:
> Index date [00/00/00]:
> Processing file ./nisc-platypus-shotgun-1048960391.fasta
> Processing file ./nisc-platypus-shotgun-1071756042.fasta
> Processing file ./nisc-platypus-shotgun-1080815515.fasta
> Processing file ./nisc-platypus-shotgun-1102160893.fasta
> Processing file ./nisc-platypus-shotgun-1104879084.fasta
> Processing file ./nisc-platypus-shotgun-1109000445.fasta
> Processing file ./nisc-platypus-shotgun-1110804272.fasta
> Processing file ./nisc-platypus-shotgun-1116844699.fasta
> Processing file ./nisc-platypus-shotgun-1142973027.fasta
> Processing file
> ./wugsc-ornithorhynchus_anatinus-cloneEnd-1113828608.fasta
> Processing file
> ./wugsc-ornithorhynchus_anatinus-cloneEnd-1115655383.fasta
> Processing file
> ./wugsc-ornithorhynchus_anatinus-cloneEnd-1119433885.fasta
>
>    EMBOSS An error in ajindex.c at line 615:
> Maximum retries (100) reached in btreeCacheFetch for page 14240710656
>
> The same files have indexed OK with formatdb.  I havent' tried with
> dbifasta as I'm trying to move everything over to the new dbx system
> (and the rest of our databases have processed OK with dbx(fasta|flat)).
>
> Anyone have any ideas about how to debug this?
>
> Cheers
>
> Simon.
>
> --
> Simon Andrews PhD
> Bioinformatics Group
> The Babraham Institute
>
> simon.andrews at bbsrc.ac.uk
> +44 (0) 1223 496463
>
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