[EMBOSS] embl and dbxflat segmentation fault

[ajb at ebi.ac.uk]

Hi,

You should upgrade to EMBOSS 5.0.0. Make sure you apply the
patch in the pub/EMBOSS/fixes/patches/ directory before
configuring. Both 5.0.0 and the patch contain indexing
fixes.

HTH

Alan

> Hello, and happy 2008.
>
> When I index the embl database with dbxflat, a segmentation fault occurs:
>
> $ dbxflat -dbname embl -dbresource embl -idformat EMBL -filenames
> "*.dat" -directory . -fields id,acc -release 93.0 -date 08/01/08
> Database b+tree indexing for flat file databases
> Processing file ./rel_ann_env_01_r93.dat
> ...
> Processing file ./wgs_aahc_inv.dat
> Segmentation fault
>
> The "embl" database is defined in emboss.default, also the "embl"
> resource with default values. The embl release is 93, and  the
> segmentation fault seems to happen in the file wgs_aahc_inv.dat. I
> downloaded it again, it seems ok, but still same error happens.
>
> When I index only that file, i.e dbxflat -filenames "wgs_aahc_inv.dat"
> etc etc, it works ok.
>
> What could be the problem?
>
> I have emboss 4.1 on linux on IA64 with enough disk space.
>
> Thank you very much!
>
> --
> Hernández Alvarez Alfredo José
> Unidad de Administración de Tecnologías de Información
> Licenciatura en Ciencias Genómicas
> Centro de Ciencias Genómicas UNAM
> Ext. 38221 Red UNAM / Tel. (01) 777 3290821
> ajhernan at lcg.unam.mx / ajhernan at ccg.unam.mx
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