[Bioperl-l] Loading taxonomy data into BioSQL

[SG Edwards]

I have been trying:

perl load_ncbi_taxonomy.pl -dbname milk -driver Pg -dbuser s0460205 -dbpass
password -download

and this gave me the error message below.
If I download the ncbi_taxonomy data manually it and direct the perl script to
this using:

perl load_ncbi_taxonomy.pl -dbname milk -driver Pg -dbuser s0460205 -dbpass
password -directory /home/s0460205/

This seems to get a bit further but still results in error,

"loading NCBI taxon database in /home/s0460205:
   ... 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

It seems to be choking on finding the nodes.dmp but I'm not sure why?!


Quoting Brian Osborne <brian_osborne at cognia.com>:

> SG,
>
> =head1 DESCRIPTION
>
> 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
>
>
>
>
> 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
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