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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