GBrowse "Could not open database:"

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GBrowse "Could not open database:"

Samy Jeevan Karloss Antony
Hello,

I am very new to GBrowse.

I have installed Gbrowse, Chado and postgres in Centos.

When I tried to load test yeast data (.gff file) I get this message which I don’t understand “couldn't find GO:0003674 in dbxref for db: (GO)” . Its 1000s of these kind of errors.

"
Skipping organism table since the load file is empty...
Skipping analysis table since the load file is empty...
Skipping db table since the load file is empty...
Skipping dbxref table since the load file is empty...
Skipping cv table since the load file is empty...
Skipping cvterm table since the load file is empty… "


Then, error_log says “ould not open database: Can't call method "new" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm line 42”



My chado_test.conf is below here

[chado:database]
db_adaptor    = Bio::DB::Das::Chado
db_args       = -dsn 'dbi:Pg:dbname=chado;host=localhost'
               -user ‘XXX'
               -pass XXXXX
               -srcfeatureslice 1
               -organism yeast



I dont understand what I am doing wrong.

Thanks,
Jeevan
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Re: GBrowse "Could not open database:"

Michael Dondrup-3
Hi Jeevan,

could you give some details on how you are loading the gff file? (I assume gmod_bulk _oad_ggf3)
Did you run
make prepdb
and  
make ontologies
from the chado directory?

Cheers
Michael

Michael Dondrup
Postdoctoral fellow
Sea Lice Research Centre/Department of Informatics
University of Bergen
Thormøhlensgate 55, N-5008 Bergen,
Norway

On Mar 25, 2014, at 9:50 AM, Samy Jeevan Karloss Antony wrote:

> Hello,
>
> I am very new to GBrowse.
>
> I have installed Gbrowse, Chado and postgres in Centos.
>
> When I tried to load test yeast data (.gff file) I get this message which I don’t understand “couldn't find GO:0003674 in dbxref for db: (GO)” . Its 1000s of these kind of errors.
>
> "
> Skipping organism table since the load file is empty...
> Skipping analysis table since the load file is empty...
> Skipping db table since the load file is empty...
> Skipping dbxref table since the load file is empty...
> Skipping cv table since the load file is empty...
> Skipping cvterm table since the load file is empty… "
>
>
> Then, error_log says “ould not open database: Can't call method "new" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm line 42”
>
>
>
> My chado_test.conf is below here
>
> [chado:database]
> db_adaptor    = Bio::DB::Das::Chado
> db_args       = -dsn 'dbi:Pg:dbname=chado;host=localhost'
>               -user ‘XXX'
>               -pass XXXXX
>               -srcfeatureslice 1
>               -organism yeast
>
>
>
> I dont understand what I am doing wrong.
>
> Thanks,
> Jeevan
> ------------------------------------------------------------------------------
> Learn Graph Databases - Download FREE O'Reilly Book
> "Graph Databases" is the definitive new guide to graph databases and their
> applications. Written by three acclaimed leaders in the field,
> this first edition is now available. Download your free book today!
> http://p.sf.net/sfu/13534_NeoTech
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

------------------------------------------------------------------------------
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/13534_NeoTech
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

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