Loading Chado with "Gene Ontology", infinite loop or is it normal?

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Loading Chado with "Gene Ontology", infinite loop or is it normal?

dahlbma
Hello, I just installed Gbrowse2 and Chado and it seem to work. But
when I try to load the "Gene Ontology" into Chado it just keep running
forever (if more than an hour is forever).

I first loaded "Relationship Ontology", "Sequence Ontology" and
"Chado Feature Properties" and those only took a few seconds to load.
But the "Gene Ontology" seem to be stuck. Here is the trace of what I
have done with the ontologies:

[matsda@databases chado-1.2]# make ontologies
./Build ontologies
Available ontologies:
[1] Relationship Ontology
[2] Sequence Ontology
[3] Gene Ontology
[4] Chado Feature Properties
[5] Plant Ontology

Which ontologies would you like to load (Comma delimited)? [0]  1,2
fetching files for Relationship Ontology
  +http://www.obofoundry.org/ro/ro.obo
    updated
    loading...done!
fetching files for Sequence Ontology
  +http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo
    updated
    loading...done!
[matsda@databases chado-1.2]# make ontologies
./Build ontologies
Available ontologies:
[1] Relationship Ontology
[2] Sequence Ontology
[3] Gene Ontology
[4] Chado Feature Properties
[5] Plant Ontology

Which ontologies would you like to load (Comma delimited)? [0]  4
fetching files for Chado Feature Properties
  +load/etc/feature_property.obo
    loading...done!
[matsda@databases chado-1.2]# make ontologies
./Build ontologies
Available ontologies:
[1] Relationship Ontology
[2] Sequence Ontology
[3] Gene Ontology
[4] Chado Feature Properties
[5] Plant Ontology

Which ontologies would you like to load (Comma delimited)? [0]  3
fetching files for Gene Ontology
  +http://www.geneontology.org/ontology/gene_ontology.obo
    updated
    loading...



It ends with saying "loading..." and it has been stuck there now for
more than an hour. Is this normal or is the loading stuck in an
infinite loop? If I run the top-command I see that a process named
xsltproc is using 100% of the CPU.


All the best,
Mats

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Re: Loading Chado with "Gene Ontology", infinite loop or is it normal?

Scott Cain
Hi Mats,

It can take a few hours to load GO. It is significantly larger that the other Obo files and so both the conversion step (which uses xsltproc) and the loading step (which uses perl/stag-storenode.pl) will take a while.

Scott


Sent from my iPhone

On Feb 11, 2013, at 6:20 AM, Mats Dahlberg <[hidden email]> wrote:

> Hello, I just installed Gbrowse2 and Chado and it seem to work. But
> when I try to load the "Gene Ontology" into Chado it just keep running
> forever (if more than an hour is forever).
>
> I first loaded "Relationship Ontology", "Sequence Ontology" and
> "Chado Feature Properties" and those only took a few seconds to load.
> But the "Gene Ontology" seem to be stuck. Here is the trace of what I
> have done with the ontologies:
>
> [matsda@databases chado-1.2]# make ontologies
> ./Build ontologies
> Available ontologies:
> [1] Relationship Ontology
> [2] Sequence Ontology
> [3] Gene Ontology
> [4] Chado Feature Properties
> [5] Plant Ontology
>
> Which ontologies would you like to load (Comma delimited)? [0]  1,2
> fetching files for Relationship Ontology
>  +http://www.obofoundry.org/ro/ro.obo
>    updated
>    loading...done!
> fetching files for Sequence Ontology
>  +http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo
>    updated
>    loading...done!
> [matsda@databases chado-1.2]# make ontologies
> ./Build ontologies
> Available ontologies:
> [1] Relationship Ontology
> [2] Sequence Ontology
> [3] Gene Ontology
> [4] Chado Feature Properties
> [5] Plant Ontology
>
> Which ontologies would you like to load (Comma delimited)? [0]  4
> fetching files for Chado Feature Properties
>  +load/etc/feature_property.obo
>    loading...done!
> [matsda@databases chado-1.2]# make ontologies
> ./Build ontologies
> Available ontologies:
> [1] Relationship Ontology
> [2] Sequence Ontology
> [3] Gene Ontology
> [4] Chado Feature Properties
> [5] Plant Ontology
>
> Which ontologies would you like to load (Comma delimited)? [0]  3
> fetching files for Gene Ontology
>  +http://www.geneontology.org/ontology/gene_ontology.obo
>    updated
>    loading...
>
>
>
> It ends with saying "loading..." and it has been stuck there now for
> more than an hour. Is this normal or is the loading stuck in an
> infinite loop? If I run the top-command I see that a process named
> xsltproc is using 100% of the CPU.
>
>
> All the best,
> Mats
>
> ------------------------------------------------------------------------------
> Free Next-Gen Firewall Hardware Offer
> Buy your Sophos next-gen firewall before the end March 2013
> and get the hardware for free! Learn more.
> http://p.sf.net/sfu/sophos-d2d-feb
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema

------------------------------------------------------------------------------
Free Next-Gen Firewall Hardware Offer
Buy your Sophos next-gen firewall before the end March 2013
and get the hardware for free! Learn more.
http://p.sf.net/sfu/sophos-d2d-feb
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema