[EMBOSS] Cannot open division file

[ajb at ebi.ac.uk]

Hi,

The line in the debug output:

namVarResolve 'emboss_tempdata' = '/usr/local/share/EMBOSS/test'

implies that you've set emboss_tempdata incorrectly in emboss.default.
It should be /usr/local/emboss/share/EMBOSS/test according to
the rest of the information you give.

HTH

Alan

> 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
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at emboss.open-bio.org
> http://newportal.open-bio.org/mailman/listinfo/emboss
>