[BioSQL-l] First download of ncbi_taxonomy

[SG Edwards]

Hi,

Can you please help me with an error message? I have just installed a BioSQL
database and am trying to run the load_ncbi_taxonomy.pl script to get taxonomy
data into my database before I start to load sequences in. The database has
been created and is empty, however, I get the following error message:


Cannot open Local file taxdata/taxdump.tar.gz: No such file or directory at
load_ncbi_taxonom.pl line 628
gunzip: taxdata/taxdump.tar.gz: No such file or directory
sh: line 1: cd: taxdata: No such file or directory
tar: taxdump.tar: cannot open: No such file or directory
tar: error is not recoverable: exiting now
loading NCBI taxon database in taxdata:
       ... retrieving all taxon nodes in the database
       ... reading in taxon nodes from nodes.dmp
Couldn't open data file taxdata/nodes.dmp: No such file or directory
rollback ineffective with AutoCommit enabled at load_ncbi_taxonomy.pl line 818.
Use of uninitialized value in concatenation (.) or string at
load_ncbi_taxonomy.pl line 820.
rollback failed