[EMBOSS] Cannot open division file
ajb at ebi.ac.uk
ajb at ebi.ac.uk
Thu Oct 25 20:22:18 UTC 2007
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
>
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