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, [EMAIL PROTECTED] 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. >> >> [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 >> > > _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
