[EMBOSS] Cannot open division file

[Tim Troup]

Hi,

> Do you find the database directories under
> /usr/local/emboss/share/EMBOSS/test/ and can you read, for example,  
> the
> swiss/seq.dat file (for tsw) from the account where you are running  
> the
> applications?
>

The database directories are under /usr/local/emboss/share/EMBOSS/ 
test and the files within these directories can be read no problem.



> You can also run with -debug on the command line ... the *.dbg file it
> writes will tell you where is is looking for the files (or, if you  
> send it
> to me, I can find the appropriate lines)
>

I ran seqret again from the command line with the -debug switch as  
follows:

wilkie226:/usr/local/emboss/share/EMBOSS/test troup$ seqret -debug
Reads and writes (returns) sequences
Input sequence(s): tsw:hba_human
Warning: Cannot open division file '<null>' for database 'tsw'
Warning: seqCdQry failed
Error: Unable to read sequence 'tsw:hba_human'
Input sequence(s): tsw:hba_human
Warning: Cannot open division file '<null>' for database 'tsw'
Warning: seqCdQry failed
Error: Unable to read sequence 'tsw:hba_human'
Died: seqret terminated: Bad value for '-sequence' and no more retries

The seqret.dbg file generated is pasted below.

Thanks, Tim



Debug file seqret.dbg buffered:No
ajFileNewIn '/usr/local/emboss/share/EMBOSS/acd/seqret.acd'
EOF ajFileGetsL file /usr/local/emboss/share/EMBOSS/acd/seqret.acd
closing file '/usr/local/emboss/share/EMBOSS/acd/seqret.acd'
Set acdprotein value '$(sequence.protein)'
ajFeatTabInNew 50ba40
ajUserGet buffer len: 0 res: 2048 ptr: 1800a00
ajSeqinClear called
ajFeattabInClear called
++seqUsaProcess 'tsw:hba_human' 0..0(N) '' 0
USA to test: 'tsw:hba_human'

format regexp: No list:No
no format specified in USA

...input format not set
dbname dbexp: Yes
found dbname 'tsw' level: '<null>' qry->QryString: 'hba_human'
namVarResolve 'emboss_tempdata' = '/usr/local/share/EMBOSS/test'
namVarResolve 'emboss_tempdata' = '/usr/local/share/EMBOSS/test'
seqQueryFieldC usa 'sv' fields 'sv des org key'
seqQueryField test 'sv'
seqQueryField match 'sv'
ajSeqQueryWild id 'hba_human' acc 'hba_human' sv 'hba_human' des ''  
org '' key ''
wild (has) query Sv 'hba_human'
database type: 'P' format 'swiss'
use access method 'emblcd'
Matched seqAccess[0] 'emblcd'
seqAccessEmblcd type 2
directory '/usr/local/share/EMBOSS/test/swiss' entry 'hba_human' acc  
'hba_human'
ajFileNewIn '/usr/local/share/EMBOSS/test/swiss/division.lkp'
Database 'tsw' : access method 'emblcd' failed
ajUserGet buffer len: 0 res: 2048 ptr: 1800a00
ajSeqinClear called
ajFeattabInClear called
++seqUsaProcess 'tsw:hba_human' 0..0(N) '' 0
USA to test: 'tsw:hba_human'

format regexp: No list:No
no format specified in USA

...input format not set
dbname dbexp: Yes
found dbname 'tsw' level: '<null>' qry->QryString: 'hba_human'
namVarResolve 'emboss_tempdata' = '/usr/local/share/EMBOSS/test'
namVarResolve 'emboss_tempdata' = '/usr/local/share/EMBOSS/test'
seqQueryFieldC usa 'sv' fields 'sv des org key'
seqQueryField test 'sv'
seqQueryField match 'sv'
ajSeqQueryWild id 'hba_human' acc 'hba_human' sv 'hba_human' des ''  
org '' key ''
wild (has) query Sv 'hba_human'
database type: 'P' format 'swiss'
use access method 'emblcd'
Matched seqAccess[0] 'emblcd'
seqAccessEmblcd type 2
directory '/usr/local/share/EMBOSS/test/swiss' entry 'hba_human' acc  
'hba_human'
ajFileNewIn '/usr/local/share/EMBOSS/test/swiss/division.lkp'
Database 'tsw' : access method 'emblcd' failed