[EMBOSS] dbigcg question
Thomas Keller
kellert at ohsu.edu
Mon Sep 22 22:16:43 UTC 2003
I have the GCG format databases mounted on a read only volume on my
machine. To use these with Embos I made the following entry in my
.embossrc file:
# define dna2.ohsu.edu/gcgdata1 database for EMBOSS
set emboss_db_dir /Volumes/dna2.ohsu.edu
# set location of indices
set emboss_indices /Users/kellert/Emboss_indices
DB myembl [
type: N
format: embl
method: gcg
fields: "id acc sv des org key"
directory: $emboss_db_dir/gcgembl
indexdir: $emboss_indices/gcgembl
comment: "GCG embl db from dna2.ohsu.edu:/gcgdata1 mounted locally"
]
and created an index directory and tried to run dbigcg as follows:
kellert% dbigcg -indexdirectory /Users/kellert/Emboss_indices/gcgembl
Index a GCG formatted database
EMBL : EMBL
SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew
GENBANK : Genbank, DDBJ
PIR : NBRF
Entry format [EMBL]:
Database directory [.]:
Wildcard database filename [*.seq]:
Database name: myembl
Release number [0.0]:
Index date [00/00/00]:
EMBOSS An error in embdbi.c at line 568:
Cannot open myembl001.list for writing
I don't understand why this isn't working. Can someone explain this to
me?
Thanks,
Tom K.
Tom Keller, Ph.D.
http://www.ohsu.edu/core
kellert at ohsu.edu
503-494-2442
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