[Bioperl-l] Loading taxonomy data into BioSQL

Brian Osborne brian_osborne at cognia.com
Fri Mar 18 08:18:31 EST 2005



This script loads or updates a biosql schema with the NCBI Taxon
Database. There are a number of options to do with where the biosql
database is (i.e., database name, hostname, user for database,
password, database name).

This script may download the NCBI Taxon Database from the NCBI FTP
server on-the-fly (ftp://ftp.ncbi.nih.gov/pub/taxonomy/). Otherwise it
expects the files to be downloaded already.

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of SG Edwards
Sent: Friday, March 18, 2005 6:45 AM
To: bioperl-l at portal.open-bio.org
Subject: [Bioperl-l] Loading taxonomy data into BioSQL


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
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
Use of uninitialized value in concatenation (.) or string at
load_ncbi_taxonomy.pl line 820.
rollback failed
Bioperl-l mailing list
Bioperl-l at portal.open-bio.org

More information about the Bioperl-l mailing list