Some help required.

Peter Rice peter.rice at
Tue Jul 30 15:00:06 UTC 2002

Alex Brown wrote:

> In order to get the 'showdb' command to list the available databases, I
> uncommented the first line of the emboss.default.template file (SET
> emboss_tempdata path_to_directory_$EMBOSS/test) and copied this to
> emboss.default. The command 'showdb' results in the following output:
> indicating the databases in the /local/share/EMBOSS/test directory.
> So far so good.
> However, attempting to work through the tutorial on the EMBOSS web-site,
> I find that I am unable to access the databases: for example
> [xxxxxx:~] me% seqret
> Reads and writes (returns) sequences
> Input sequence(s): tembl:hs*
> Warning: Cannot open division file '<null>'
> Warning: seqCdQry failed
> Error: Unable to read sequence 'tembl:hs*'
> Input sequence(s):

First, I assume your emboss.default file has:

SET emboss_tempdata /local/share/EMBOSS/test

Next, you can try:

seqret -debug

This will write a file seqret.dbg  where I would expect lines like this:

directory '/local/share/EMBOSS/test/embl' entry 'hs*' acc 'hs*'
ajFileNewIn '/local/share/EMBOSS/test/embl/division.lkp'
ajNamResolve of '/local/share/EMBOSStest/embl/division.lkp'

This is the division file which it says cannot be opened.

If you see what appears to be the right filename, check file (and
directory) protection.

If you see something else, it may give a clue to where the setup is wrong,
or you can get help from emboss-bug at


Peter Rice

Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at +44 1223 224723

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