[EMBOSS] New and confusing problem with infoseq!

Peter Rice pmr at ebi.ac.uk
Tue Sep 23 12:34:48 UTC 2008

michael watson (IAH-C) wrote:
> Confusing because this didn't happen before and I haven't changed
> anything!
> EMBOSS 5.0.0 on RHEL 4.
> Why is infoseq complaining about a database?  Has my environment changed
> because this used to work exactly how I wanted it to!
> Mick
> -bash-3.00$ infoseq 
> Displays some simple information about sequences
> Input (gapped) sequence(s):  Contig0.1399.fasta
> Died: Qualifier '-database' not found

Yes, your environment has changed. EMBOSS 5.0.0 does have a -database 
qualifier, but the infoseq.acd file that was used does not have one.

The -database qualifier was new in 5.0.0 and controls whether the 
database column appears in the output.

If you run infoseq with the command line option -debug it will write a 
file infoseq.dbg that will include the full path the the infoseq.acd 
file that it used.

If you need more help working out why the wrong file is used, please 
send the infoseq.dbg file to emboss-bug at emboss.open-bio.org and we will 
try to help.


Peter Rice

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