[Bioperl-l] Loading taxonomy data into BioSQL

[Hilmar Lapp]

Why do you believe the script thinks that taxon_id is a varchar? It 
doesn't AFAIK.

Also, not sure why your Pg (you are using PostgreSQL, right?) is in 
auto-commit mode. That doesn't sound right.

	-hilmar

On Friday, March 18, 2005, at 06:05  AM, SG Edwards wrote:

> 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
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at portal.open-bio.org
>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>>
>>>
>>
>>
>>
>
>
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-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------