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. [EMAIL PROTECTED]/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: [EMAIL PROTECTED]: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 [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
