database problem

Thomas Keller kellert at
Wed Apr 30 21:45:26 UTC 2003

I just ran dbigcg on the nsf directory mounted on my machine, it 
contains the GCG GenBank database. I had to create the index in a 
different directory, cause the data is read only. It took about 2.5 
hours to finish indexing, and gave a bunch of warnings about ajStrFixI 
called with length 2048 for string with size 2048. And it warned about 
one accession number that it expected, but couldn't find. However, it 
make the correct files and they are of substantial size. But I seem to 
have a problem though:
kellert% seqret
Reads and writes (returns) sequences
Input sequence(s): mygenbank:L42450
Segmentation fault
This sounds like a RAM issue to me, but I have 768 MB on this machine, 
which seems adequate to me.

Here's the DB definition in ~/.embossrc:
DB mygenbank [
         type: N
         method: gcg
         format: GenBank
         fields: "acnum seqvn des keywords taxon"
         dir: $emboss_db_dir/gcggenbank
         indexdir: $emboss_indices/gcggenbank
         file: "*.seq"
         release: "133.0"
         comment: "GCG genbank db from dna2 mounted locally: 

Any suggestions?
Tom K.
Thomas J. Keller, Ph.D.
Director, MMI Core Facility
Oregon Health & Science University
3181 SW Sam Jackson Park Rd.
Portland, OR, USA,   97239

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