[Bioclusters] Seqret

[simon andrews (BI)]

> -----Original Message-----
> Subject: [Bioclusters] Seqret
> 
> 
> HI All,
> 
> I am having an issue with seqret, and was wondering if any of 
> you have  seen it, or know what may be happening.  Some requests 
> work, and others don't.  For example, a request using the USA 
> nt:L32140 returns the sequence, but when I try, for example, 
> nt:U51243, this is what I get:
>
> -bash-2.05b$ seqret nt:U51243
> Reads and writes (returns) sequences
> Error: Unable to read sequence 'nt:U51243'
> Died: seqret terminated: Bad value for '-sequence' and no prompt

By any chance is the file which contains U51243 > 2Gb in size?  The
current version of dbiflat fails to index any sequences past the 2Gb
limit in any file and just silently drops them.

There is a fix in the works in the next EMBOSS release, but for now the
only fix is to split your database files into <2Gb chunks.

If this isn't it, try running seqret -debug nt:U51243 and look at the
seqret.dbg file for clues as to what's going wrong.

Simon.