need help

Peter Rice pmr at sanger.ac.uk
Tue Jan 5 04:35:28 EST 1999

Jean-Marc Plaza <plaza at infobiogen.fr> writes:

> hello,
> I find a problem when indexing embl 57 in srs
> for the feature PID only(ftpid).
> The srsbuild crashes with the -m option which Merge index partitions
> to a single index:
> ....
> + time srsbuild EMBL -c -f  pid -xdir SRSINX: -odir SRSINX:
> ...wrote IDs file "/env/lovelace/env_ibg/pack/srs5/index/embl_pid_1.ids"
>          size: 1 kbytes, IDs: 0
> + time srsbuild EMBL -m -f  pid -xdir SRSINX: -odir SRSINX:
> time: command terminated abnormally.
> Could someone give me a clue?

The "IDs: 0" is the clue.

SRS has big problems when the first section of the index has no data.
The empty file breaks the merge. Thure knows about it. I guess there
will be a fix in SRS 6 :-)

You can get "Ids: 0" for the PID index if you start with ESTs because
there are no CDS features in the EST entries.

Change the order of the EMBL files to have something else first.
I currently use "pro" (flatfile). EBI uses "em_ba" (GCG).

Sorry, but if you change the order of the files you have to rebuild *all*
the indices.

There are SRS index files at the EBI FTP server - but the
filenames are only for GCG format. I have a version at Sanger that
worked with the FTP index files for flat files (I had to add the
filenames in the right order) and also has NID indexed.

Peter Rice                | Informatics Division, The Sanger Centre,
E-mail: pmr at sanger.ac.uk  | Wellcome Trust Genome Campus,
Tel: (44) 1223 494967     | Hinxton, Cambridge, CB10 1SA, England
Fax: (44) 1223 494919     | URL: http://www.sanger.ac.uk/Users/pmr/

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