[EMBOSS] Problem with showdb and seqret

[Mohd Noor Mat Isa]

Dear Mohd Afiq,

I'm not an expert also on EMBOSS installation but I can give you some clues
on your problems:

First, showdb does not give you any db list as you need to index all the
databases that you requires to show. You can get further info here
http://emboss.sourceforge.net/docs/adminguide/node56.html on how to index
databases.

as for seqret you should tell the seqret you input format as *embl::xlrhodop
* not embl*:*xlrhodop.

Regards
Mohd Noor
Malaysia Genome Institute

On Tue, Feb 24, 2009 at 9:28 AM, Mohd Afiq Hazlami <afikolami at gmail.com>wrote:

> Hello,
> I'm new to EMBOSS and I have a problem that I can't figure out. I have
> configured and installed EMBOSS-6.0.1 on my Ubuntu machine and I tried
> doing
> the exercises according to the tutorial. There's nothing wrong when I typed
> 'wossname' and the program works fine, just like in the tutorial. But when
> it comes to 'showdb' tutorial, the program returns this:
>


>
> afiq at peregrin:~/EMBOSS-6.0.1$ showdb
> Displays information on configured databases
> # Name         Type  ID  Qry All Comment
> # ============ ==== ==  === === =======
> afiq at peregrin:~/EMBOSS-6.0.1$
>
> which is totally different from the tutorial where it shows some database
> names. Is this normal?
>
> Then, when I tried to use seqret as in the tutorial given (using xlrhodop),
> the program returns this:
>
> afiq at peregrin:~/EMBOSS-6.0.1$ seqret
> Reads and writes (returns) sequences
> Input (gapped) sequence(s): embl:xlrhodop
> Error: Failed to open filename 'embl'
> Error: Unable to read sequence 'embl:xlrhodop'
> Input (gapped) sequence(s):
>
> which is really confusing. Can anybody tell me what's wrong?
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