|   | dbxtax | 
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These indexes allow access of flat files larger than 2Gb.
| 
% dbxtax 
Index NCBI taxonomy using b+tree indices
Basename for index files [taxon]: 
Resource name [taxresource]: 
Database directory [.]: taxonomy
        id : ID
       acc : Synonym
       tax : Scientific name
       rnk : Rank
        up : Parent
        gc : Genetics code
       mgc : Mitochondrial genetic code
Index fields [*]: 
Compressed index files [Y]: 
General log output file [outfile.dbxtax]: 
 | 
Go to the output files for this example
| 
Index NCBI taxonomy using b+tree indices
Version: EMBOSS:6.6.0.0
   Standard (Mandatory) qualifiers:
  [-dbname]            string     [taxon] Basename for index files (Any string
                                  from 2 to 19 characters, matching regular
                                  expression /[A-z][A-z0-9_]+/)
  [-dbresource]        string     [taxresource] Resource name (Any string from
                                  2 to 19 characters, matching regular
                                  expression /[A-z][A-z0-9_]+/)
   -directory          directory  [.] Database directory
   -fields             menu       [*] Index fields (Values: id (ID); acc
                                  (Synonym); tax (Scientific name); rnk
                                  (Rank); up (Parent); gc (Genetics code); mgc
                                  (Mitochondrial genetic code))
   -[no]compressed     boolean    [Y] Compressed index files
   -outfile            outfile    [*.dbxtax] General log output file
   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -release            string     [0.0] Release number (Any string up to 9
                                  characters)
   -date               string     [00/00/00] Index date (Date string dd/mm/yy)
   -indexoutdir        outdir     [.] Index file output directory
   Associated qualifiers:
   "-directory" associated qualifiers
   -extension          string     Default file extension
   "-indexoutdir" associated qualifiers
   -extension          string     Default file extension
   "-outfile" associated qualifiers
   -odirectory         string     Output directory
   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit
 | 
| Qualifier | Type | Description | Allowed values | Default | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||||||||||||||||
| [-dbname] (Parameter 1) | string | Basename for index files | Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/ | taxon | ||||||||||||||
| [-dbresource] (Parameter 2) | string | Resource name | Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/ | taxresource | ||||||||||||||
| -directory | directory | Database directory | Directory | . | ||||||||||||||
| -fields | list | Index fields | 
 | * | ||||||||||||||
| -[no]compressed | boolean | Compressed index files | Boolean value Yes/No | Yes | ||||||||||||||
| -outfile | outfile | General log output file | Output file | <*>.dbxtax | ||||||||||||||
| Additional (Optional) qualifiers | ||||||||||||||||||
| (none) | ||||||||||||||||||
| Advanced (Unprompted) qualifiers | ||||||||||||||||||
| -release | string | Release number | Any string up to 9 characters | 0.0 | ||||||||||||||
| -date | string | Index date | Date string dd/mm/yy | 00/00/00 | ||||||||||||||
| -indexoutdir | outdir | Index file output directory | Output directory | . | ||||||||||||||
| Associated qualifiers | ||||||||||||||||||
| "-directory" associated directory qualifiers | ||||||||||||||||||
| -extension | string | Default file extension | Any string | |||||||||||||||
| "-indexoutdir" associated outdir qualifiers | ||||||||||||||||||
| -extension | string | Default file extension | Any string | |||||||||||||||
| "-outfile" associated outfile qualifiers | ||||||||||||||||||
| -odirectory | string | Output directory | Any string | |||||||||||||||
| General qualifiers | ||||||||||||||||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N | ||||||||||||||
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N | ||||||||||||||
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N | ||||||||||||||
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N | ||||||||||||||
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N | ||||||||||||||
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y | ||||||||||||||
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N | ||||||||||||||
| -warning | boolean | Report warnings | Boolean value Yes/No | Y | ||||||||||||||
| -error | boolean | Report errors | Boolean value Yes/No | Y | ||||||||||||||
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y | ||||||||||||||
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y | ||||||||||||||
| -version | boolean | Report version number and exit | Boolean value Yes/No | N | ||||||||||||||
| Processing directory: /homes/user/test/data/taxonomy/ Processing file: nodes.dmp entries: 41 (41) time: 0.0s (0.0s) Total time: 0.0s Entry idlen 7 OK. Maximum ID length was 6 for '117570'. Field acc acclen 15 OK. Maximum acc term length was 5 for '40673'. Field tax taxlen 120 OK. Maximum tax term length was 23 for 'Pongo abelii x pygmaeus'. Field rnk rnklen 16 OK. Maximum rnk term length was 12 for 'superkingdom'. Field up uplen 7 OK. Maximum up term length was 6 for '131567'. Field gc gclen 2 OK. Maximum gc term length was 1 for '1'. Field mgc mgclen 2 OK. Maximum mgc term length was 1 for '1'. | 
| # Number of files: 1 # Release: 0.0 # Date: 00/00/00 Reference 2 filename database nodes.dmp names.dmp | 
| Type Identifier Compress Yes Pages 3 Secpages 0 Order 71 Fill 46 Level 0 Pagesize 2048 Cachesize 20000 Order2 22 Fill2 24 Secpagesize 512 Seccachesize 20000 Count 1 Fullcount 1 Kwlimit 15 Reffiles 1 | 
| Type Secondary Compress Yes Pages 3 Secpages 1 Order 132 Fill 65 Level 0 Pagesize 2048 Cachesize 20000 Order2 22 Fill2 41 Secpagesize 512 Seccachesize 20000 Count 1 Fullcount 41 Kwlimit 2 Idlimit 7 | 
| Type Identifier Compress Yes Pages 3 Secpages 0 Order 99 Fill 56 Level 0 Pagesize 2048 Cachesize 20000 Order2 22 Fill2 24 Secpagesize 512 Seccachesize 20000 Count 41 Fullcount 41 Kwlimit 7 Reffiles 1 | 
| Type Secondary Compress Yes Pages 3 Secpages 3 Order 132 Fill 65 Level 0 Pagesize 2048 Cachesize 20000 Order2 22 Fill2 41 Secpagesize 512 Seccachesize 20000 Count 3 Fullcount 39 Kwlimit 2 Idlimit 7 | 
| Type Identifier Compress Yes Pages 14 Secpages 6 Order 14 Fill 13 Level 0 Pagesize 2048 Cachesize 20000 Order2 22 Fill2 24 Secpagesize 512 Seccachesize 20000 Count 86 Fullcount 90 Kwlimit 120 Reffiles 1 | 
| Type Secondary Compress Yes Pages 3 Secpages 17 Order 68 Fill 45 Level 0 Pagesize 2048 Cachesize 20000 Order2 22 Fill2 41 Secpagesize 512 Seccachesize 20000 Count 17 Fullcount 41 Kwlimit 16 Idlimit 7 | 
| Type Identifier Compress Yes Pages 3 Secpages 12 Order 99 Fill 56 Level 0 Pagesize 2048 Cachesize 20000 Order2 22 Fill2 24 Secpagesize 512 Seccachesize 20000 Count 33 Fullcount 41 Kwlimit 7 Reffiles 1 | 
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| Program name | Description | 
|---|---|
| dbiblast | Index a BLAST database | 
| dbifasta | Index a fasta file database | 
| dbiflat | Index a flat file database | 
| dbigcg | Index a GCG formatted database | 
| dbxcompress | Compress an uncompressed dbx index | 
| dbxedam | Index the EDAM ontology using b+tree indices | 
| dbxfasta | Index a fasta file database using b+tree indices | 
| dbxflat | Index a flat file database using b+tree indices | 
| dbxgcg | Index a GCG formatted database using b+tree indices | 
| dbxobo | Index an obo ontology using b+tree indices | 
| dbxreport | Validate index and report internals for dbx databases | 
| dbxresource | Index a data resource catalogue using b+tree indices | 
| dbxstat | Dump statistics for dbx databases | 
| dbxuncompress | Uncompress a compressed dbx index | 
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.