[EMBOSS] Warning: Cannot open division file '<null>' for database 'swissprot'
Joanne Fox
joanne at bioinformatics.ubc.ca
Mon Mar 6 22:51:00 UTC 2006
Hello EMBOSS community,
I used dbiflat to index the latest flatfile distribution of swissprot
(uniprot_sprot.dat). Now I am trying to use this database with the
EMBOSS patmatdb program and I'm encountering an error that reads,
"Warning: Cannot open division file '<null>' for database 'swissprot'".
I searched the mailing list archives and I see others with this same
problem that boil down to permissions and/or path problems. However, I
still can't figure out what's going wrong on my system. I've put more
detailed information below. I'm new to the world of configuring EMBOSS
so if anyone has any ideas about what might be going wrong, I'd really
appreciate the advice.
Thanks,
Joanne.
--
| Joanne Fox
| http://bioinformatics.ubc.ca/people/joanne
~> showdb
Displays information on the currently available databases
# Name Type ID Qry All Comment
# ==== ==== == === === =======
swissprot P OK OK OK Swissprot Release 7.1, 2/21/2006
~> patmatdb
Search a protein sequence with a motif
Input sequence(s): swissprot
Warning: Cannot open division file '<null>' for database 'swissprot'
Error: Unable to read sequence 'swissprot'
Input sequence(s): swissprot:*
Warning: Cannot open division file '<null>' for database 'swissprot'
Error: Unable to read sequence 'swissprot:*'
Died: patmatdb terminated: Bad value for '-sequence' and no more retries
contents of .embossrc file:
set emboss_logfile /usr/local/software/bioinformatics/emboss/log/emboss.log
set emboss_database_dir /raid1/bioinformatics/data
DB swissprot [
type: P
method: emblcd
format: swissprot
dir: \$emboss_database_dir/swissprot/swissprot_V7_1
file: "*.dat"
release: "7.1"
comment: "Swissprot Release 7.1, 2/21/2006"
]
contents of the /raid1/bioinformatics/data/swissprot/swissprot_V7_1/
directory:
-rw-r--r-- 1 bin bin 1165524 Mar 6 12:37 acnum.hit
-rw-r--r-- 1 bin bin 3899118 Mar 6 12:37 acnum.trg
-rw-r--r-- 1 bin bin 322 Mar 6 12:37 division.lkp
-rw-r--r-- 1 bin bin 4368405 Mar 6 12:37 entrynam.idx
-rw-r--r-- 1 bin bin 802445434 Mar 6 12:23 uniprot_sprot.dat
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