[Bioperl-l] Loading taxonomy data into BioSQL

[SG Edwards]

I find that if I manually gunzip and tar the download from ncbi then the script
finds the file nodes.dmp (N.B not sure if this is a fault with
load_ncbi_taxonomy.pl or something with my system?!)

The script then tries to load the data into the taxon table but the column
"taxon_id" type is INTEGER but the script thinks it is varchar. So either need
to change the database column to varchar or change the perl script to INTEGER.

Has anyone had this problem?!


Quoting s0460205 at sms.ed.ac.uk:

> 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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> >
> >
> >
> >
>
>
>