[EMBOSS] Cannot open division file

Thu Oct 25 22:06:01 UTC 2007

Hello Alan,

Thank you so much for fast response! It seems that this backslash  
cause me all the problems. Once I removed them, the program works  
flawlessly. :)

Kann

PS. I can find the document and will mail you once I know the version  
of this emboss tutorial.

On Oct 25, 2007, at 3:22 PM, ajb at ebi.ac.uk wrote:

> Dear Kann,
>
> One major problem is your DB entry:
>
> DB gbmam [
> # required parameters
>     method: "emblcd"
>     format: "GB"
>     type: "N"
>     dir: "\$emboss_database_dir/genbank"
>     file: "gbmam*.seq"
> # optional parameters
>     fields: "sv des key org"
>     release: "161.0"
>     comment: "Genbank database for mam sequences"
>     indexdir: "\$emboss_index_dir/genbank/mam"
> ]
>
> You should remove the two backquote characters before the '$'
> characters. I believe they mistakenly appeared in some documentation
> in the past (possibly as a result of some automatic formatting).
> It'd be useful if you'd email me off-list and tell me which  
> documentation
> contained the error (if my guess is correct).
>
>
> Alan
>
>
>> Hello everyone,
>>
>> I just finish indexing a genbank database for my lab using dbiflat
>> command. I set up an emboss.default file referenced from
>> emboss.default.template as it was provided. "seqret" is a command
>> that is used to test the system, and it seems that EMBOSS could not
>> find the division file.
>>
>> I can see from the archive that there was this kind of problem with
>> test database provided from emboss as well. (http://emboss.open-
>> bio.org/pipermail/emboss/2005-November/002323.html). However, I am
>> pretty sure that I correctly pointed the path to my database.
>> However, here is my configuration.
>>
>> The system is Mac OS 10.4
>>
>> 1. Emboss was installed from fink at /sw/share/EMBOSS
>>
>> 2. All database was installed in /lab/data/databases/genbank/*.seq
>>
>> 3. Index files are in /lab/data/indices/genbank/??? Here is an
>> example of one of the index directory from my lab.
>>
>> xxx at yyy/lab/data/indices/genbank/mam:
>> acnum.hit     des.trg       keyword.hit   seqvn.hit     taxon.trg
>> acnum.trg     division.lkp  keyword.trg   seqvn.trg
>> des.hit       entrynam.idx  mam.dbiflat   taxon.hit
>>
>> 4. Here is a fraction from my emboss.default file:
>>
>> # Set location of acd files that describe each program
>> SET emboss_acdroot /sw/share/EMBOSS/acd
>>
>>
>> # Set location of Genbank flatfiles in protein
>> SET  emboss_database_dir /lab/data/databases
>>
>> # Set location of Genbank flatfiles indices in protein
>> set emboss_index_dir /lab/data/indices
>>
>> # Set a log file that user can append their records and EMBOSS
>> automatically write log information
>> SET emboss_logfile /sw/share/EMBOSS/log/log
>>
>> # Set Paper size of disc page and is required by the 'dbx' indexing
>> program and 'method: "emblcd" emboss'
>> # Recommended value is 2048
>> SET PAGESIZE 2048
>>
>> # Set Caches size required for 'dbx' indexing and 'method emboss'.
>> # It is a page size number to cache. Recommended value is 200
>> SET CACHESIZE 200
>>
>> # Set parameter for flat file indices that we have created in
>> # /lab/data/indices/genbank
>> .
>> .
>> .
>> .
>> .
>> DB gbmam [
>> # required parameters
>>     method: "emblcd"
>>     format: "GB"
>>     type: "N"
>>     dir: "\$emboss_database_dir/genbank"
>>     file: "gbmam*.seq"
>> # optional parameters
>>     fields: "sv des key org"
>>     release: "161.0"
>>     comment: "Genbank database for mam sequences"
>>     indexdir: "\$emboss_index_dir/genbank/mam"
>> ]
>>
>> 5. I run this seqret command to test the system, but it throw error
>> and you can see:
>>
>> xxx at yyy~:seqret gbmam:BC102801
>> Reads and writes (returns) sequences
>> Warning: Cannot open division file '<null>' for database 'gbmam'
>> Warning: seqCdQry failed
>> Error: Unable to read sequence 'gbmam:BC102801'
>> Died: seqret terminated: Bad value for '-sequence' and no prompt
>>
>> 6. I also run the seqret command in debug mode and this is its log
>> from the command.
>>
>> Debug file seqret.dbg buffered:No
>> ajAcdInitP pgm 'seqret' package ''
>> ajFileNewIn '/sw/share/EMBOSS/acd/seqret.acd'
>> EOF ajFileGetsL file /sw/share/EMBOSS/acd/seqret.acd
>> closing file '/sw/share/EMBOSS/acd/seqret.acd'
>> ajFileNewIn '/sw/share/EMBOSS/acd/codes.english'
>> EOF ajFileGetsL file /sw/share/EMBOSS/acd/codes.english
>> closing file '/sw/share/EMBOSS/acd/codes.english'
>> ajTableNewFunctionLen hint 25 size 251
>> ajTableNewFunctionLen hint 25 size 251
>> ajTableNewFunctionLen hint 25 size 251
>> ajFileNewIn '/sw/share/EMBOSS/acd/knowntypes.standard'
>> EOF ajFileGetsL file /sw/share/EMBOSS/acd/knowntypes.standard
>> closing file '/sw/share/EMBOSS/acd/knowntypes.standard'
>> Set acdprotein value '$(sequence.protein)'
>> ajSeqinClear called
>> ++seqUsaProcess 'gbmam:BC102801' 0..0(N) '' 0
>> USA to test: 'gbmam:BC102801'
>>
>> format regexp: No list:No
>> no format specified in USA
>>
>> ...input format not set
>> dbname dbexp: Yes
>> found dbname 'gbmam' level: '<null>' qry->QryString: 'BC102801'
>> seqQueryFieldC usa 'sv' fields 'sv des key org'
>> seqQueryField test 'sv'
>> seqQueryField match 'sv'
>> ajSeqQueryWild id 'BC102801' acc 'BC102801' sv 'BC102801' gi '' des
>> '' org '' key ''
>> wild (has) query Sv 'BC102801'
>> database type: 'N' format 'GB'
>> use access method 'emblcd'
>> Matched seqAccess[2] 'emblcd'
>> seqAccessEmblcd type 2
>> directory '\$emboss_index_dir/genbank/mam' entry 'BC102801' acc
>> 'BC102801' hasacc:Yes
>> ajFileNewIn '\$emboss_index_dir/genbank/mam/division.lkp'
>> Database 'gbmam' : access method 'emblcd' failed
>> ajSeqinClear called
>> ++seqUsaProcess 'gbmam:BC102801' 0..0(N) '' 0
>> USA to test: 'gbmam:BC102801'
>>
>> format regexp: No list:No
>> no format specified in USA
>>
>> ...input format not set
>> dbname dbexp: Yes
>> found dbname 'gbmam' level: '<null>' qry->QryString: 'BC102801'
>> seqQueryFieldC usa 'sv' fields 'sv des key org'
>> seqQueryField test 'sv'
>> seqQueryField match 'sv'
>> ajSeqQueryWild id 'BC102801' acc 'BC102801' sv 'BC102801' gi '' des
>> '' org '' key ''
>> wild (has) query Sv 'BC102801'
>> database type: 'N' format 'GB'
>> use access method 'emblcd'
>> Matched seqAccess[2] 'emblcd'
>> seqAccessEmblcd type 2
>> directory '\$emboss_index_dir/genbank/mam' entry 'BC102801' acc
>> 'BC102801' hasacc:Yes
>> ajFileNewIn '\$emboss_index_dir/genbank/mam/division.lkp'
>> Database 'gbmam' : access method 'emblcd' failed
>>
>> It seems that the emboss could not find the division file. I still
>> don't know what the problem is. Do you have any recommendation?
>>
>> Thank you so much in advance for any help!
>>
>> Kann
>>
>> _______________________________________________
>> EMBOSS mailing list
>> EMBOSS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/emboss
>>
>
>