[BioSQL-l] load_ncbi_taxonomy.pl error

[aaron.j.mackey at gsk.com]

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
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