[EMBOSS] Problems indexing with dbxfasta

[simon andrews (BI)]

On 13 Apr 2006, at 10:19, ajb at ebi.ac.uk wrote:

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

Yes.  All patched with the latest fixes as of last week.

> If you are using the latest fixes (check file sizes) and it is still
> failing then let me know.

It is still failing.  I'll have a go at generating a .dbg file if you 
think it'll help, but given how verbose those tend to be, and how long 
it takes to fail I was a bit concerned at the size of file it was 
likely to generate.

Simon.

>
>
> 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
>>
>> _______________________________________________
>> EMBOSS mailing list
>> EMBOSS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/emboss
>>
>
>
>
-- 
Simon Andrews PhD
Bioinformatics Dept.
The Babraham Institute

simon.andrews at bbsrc.ac.uk
+44 (0) 1223 496463