[EMBOSS] Cannot open division file

[Tim Troup]

Hi,

I corrected the path emboss_tempdata variable in the emboss.default  
file and all now works smoothly.

Thanks, Tim


On 4 Nov 2005, at 14:02, ajb at ebi.ac.uk wrote:

> 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
>>
>
>