EMBOSS - Indexing breaks on large databases

Len F. Zaifman leonardz at bioinfo.sickkids.on.ca
Thu Feb 8 14:51:44 UTC 2001

ableasby at hgmp.mrc.ac.uk wrote:
> You should indeed be worried about the duplicate entries
> (normally caused by indexing the database and updates
> at the same time) as you'll never be certain which one is
> retrieved. It is best to index them separately.
> wrt the 64-bit thing on this same thread. Coincidentally
> I'm working on this at the moment. The compilation flags
> are not the only concern. There's ftell64's, ftello's
> [and fseeks] and, of course, the indexing. That's not
> even mentioning ajints and ajlongs :-)
> Alan

Thanks Alan but I think I may not have been clear enough:

I don't think that dbiflat it self has the problem (although I could be
I think the problem comes from:
 >  the indexing breaks due to sort running out of memory:  << my
>         UX:sort: ERROR: Out of memory before merge: Not enough space  << the error reported

So I believe it is a system issue where my resident memory set size
needs to be increased. I was hoping someone had a workaround to get sort
to work within available memory, and not request the an amount beyond
the limit.

Having said that, geeting a 64 bit clean emboss would be great.

Thanks to the others who responded as well.
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