[BioSQL-l] load_ncbi_taxonomy.pl error

[Hilmar Lapp]

Well I don't know about your systems but as a matter of fact it is a  
mysql error that is reported here, so it is clearly the mysql server  
which is causing the issue.

When you say you've tried on different platforms, did you only run  
the script on different platforms or did you also install and set up  
and use the mysql server on the different (local) platforms?

	-hilmar

On Sep 13, 2006, at 1:43 PM, Seth Johnson wrote:

> That would be strange since I've tried it on Sun Solaris and  
> Windows XP
> (with gigs of free space) with same exact results.
>
> On 9/13/06, aaron.j.mackey at gsk.com <aaron.j.mackey at gsk.com> wrote:
>>
>> Most likely you've run out of space in /var/tmp ...
>>
>> -Aaron
>>
>> biosql-l-bounces at lists.open-bio.org wrote on 09/13/2006 11:06:28 AM:
>>
>>> Hello,
>>> I'm a newbie to BioSQl, trying to set it up on mySQL server  
>>> following
>> the
>>> installation directions and ran into a problem.  When trying to  
>>> load the
>>> taxonomic info, I get an error at 230000+ line.  Progress dump  
>>> follows.
>>> Have I missed anything???
>>> =======================================
>>> # perl load_ncbi_taxonomy.pl -dbname BioSQL_1 -host localhost - 
>>> port 3306
>>> -dbuser root -dbpass xxxxx -verbose=2 -download
>>> Loading NCBI taxon database in taxdata:
>>>         ... retrieving all taxon nodes in the database
>>>         ... reading in taxon nodes from nodes.dmp
>>>         ... insert / update / delete taxon nodes
>>>                 10000/324120 done (in 15 secs, 666.7 rows/s)
>>>                 20000/324120 done (in 15 secs, 666.7 rows/s)
>>>                 30000/324120 done (in 15 secs, 666.7 rows/s)
>>>                 40000/324120 done (in 15 secs, 666.7 rows/s)
>>>                 50000/324120 done (in 15 secs, 666.7 rows/s)
>>>                 60000/324120 done (in 14 secs, 714.3 rows/s)
>>>                 70000/324120 done (in 15 secs, 666.7 rows/s)
>>>                 80000/324120 done (in 14 secs, 714.3 rows/s)
>>>                 90000/324120 done (in 15 secs, 666.7 rows/s)
>>>                 100000/324120 done (in 14 secs, 714.3 rows/s)
>>>                 110000/324120 done (in 16 secs, 625.0 rows/s)
>>>                 120000/324120 done (in 15 secs, 666.7 rows/s)
>>>                 130000/324120 done (in 14 secs, 714.3 rows/s)
>>>                 140000/324120 done (in 15 secs, 666.7 rows/s)
>>>                 150000/324120 done (in 15 secs, 666.7 rows/s)
>>>                 160000/324120 done (in 14 secs, 714.3 rows/s)
>>>                 170000/324120 done (in 14 secs, 714.3 rows/s)
>>>                 180000/324120 done (in 15 secs, 666.7 rows/s)
>>>                 190000/324120 done (in 15 secs, 666.7 rows/s)
>>>                 200000/324120 done (in 14 secs, 714.3 rows/s)
>>>                 210000/324120 done (in 15 secs, 666.7 rows/s)
>>>                 220000/324120 done (in 14 secs, 714.3 rows/s)
>>>                 230000/324120 done (in 15 secs, 666.7 rows/s)
>>> failed to insert node (281015;281015;3817;species;1;1): Error  
>>> writing
>> file
>>> '/var/tmp/MLtydiOb' (Errcode: 28) at load_ncbi_taxonomy.pl line 545.
>>> #
>>> ===================================================
>>>
>>>
>>> --
>>> Best Regards,
>>>
>>>
>>> Seth Johnson
>>> Senior Bioinformatics Associate
>>>
>>> Ph: (202) 470-0900
>>> Fx: (775) 251-0358
>>> _______________________________________________
>>> BioSQL-l mailing list
>>> BioSQL-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biosql-l
>>>
>>
>>
>>
>
>
> -- 
> Best Regards,
>
>
> Seth Johnson
> Senior Bioinformatics Associate
>
> Ph: (202) 470-0900
> Fx: (775) 251-0358
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biosql-l
>

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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