[BioSQL-l] load_ncbi_taxonomy.pl error

[aaron.j.mackey at gsk.com]

strange or not, that is exactly what MySQL error 28 means: no space left 
on device.

-Aaron

"Seth Johnson" <johnson.biotech at gmail.com> wrote on 09/13/2006 01:43:45 
PM:

> 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