Fwd: Re: Object method "get_Annotations" error​

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Fwd: Re: Object method "get_Annotations" error​

Scott Cain

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---------- Forwarded message ----------
From: Scott Cain <[hidden email]>
Date: Wed, Jan 8, 2014 at 11:32 AM
Subject: Re: [Gmod-schema] Object method "get_Annotations" error
To: "[hidden email]" <[hidden email]>

Hi Francisco,

The message about not finding part_of is pretty important. Did you load the Relationship Ontology?  If so, what happens when you execute this command:

  Select cvterm.*,cv.name from cvterm join cv using cv_id where cvterm.name = 'part_of';

(I think that SQL is right, but I'm writing it on an iPad without a database to test against, but hopefully you get the idea.)

Scott


Sent from Mailbox for iPad


On Wed, Jan 8, 2014 at 10:42 AM, Francisco García Atienza <[hidden email]> wrote:

Hello,

I'm trying to use the Chado adapter from WebApollo but I get some errors, I've instantiated Chado following your guide at http://gmod.org/wiki/Chado and when I try to load some example in the Chado database doing this:

gmod_bulk_load_gff3.pl --organism yeast  --gfffile saccharomyces_cerevisiae.gff.sorted

(These are my parameters)
GMOD_ROOT=/usr/local/gmod
PERL5LIB=$PERL5LIB:/usr/local/bioperl/bioperl-live
CHADO_DB_NAME=webapollochado
CHADO_DB_USER=web_apollo_users_admin 
CHADO_DB_HOST=localhost
CHADO_DB_PORT=5432

 I get this error 

"WARNING:
Unable to find a 'part_of' term in the relationship ontology;
It's absence indicates that there is something really wrong with the database.
Consider stopping and checking the state of your cvterm table.


Preparing data for inserting into the webapollochado database
(This may take a while ...)
Can't locate object method "get_Annotations" via package "Bio::SeqFeature::Annotated" at /usr/local/share/perl/5.14.2/Bio/SeqFeature/Annotated.pm line 287, <GEN0> line 2.

Abnormal termination, trying to clean up...

Trying to remove the run lock (so that --remove_lock won't be needed)...
Exiting..."


Any ideas what could be wrong? Thank you.

Regards, 

/Francisco.



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