Hi Tim,
Thanks for your quick response. I tried to create a new chado database and
load the example data available in the wiki tutorial in to it.
http://gmod.org/wiki/Load_GFF_Into_Chado . I created the database, used the
gmod_bulk_load_gff.pl script to load yeast data into the database.
*This is the terminal output display what i got:*
[r...@agron-90-78 Chadotesting]# gmod_bulk_load_gff3.pl --gfffile
saccharomyces_cerevisiae.gff.sorted --organism yeast --dbname rohit_chado_01
--dbuser rohit --dbpass redearth -dbhost localhost --recreate_cache
(Re)creating the uniquename cache in the database...
Creating table...
Populating table...
Creating indexes...Done.
Preparing data for inserting into the rohit_chado_01 database
(This may take a while ...)
This file was not declared as analysis results (with the --analysis flag,
but this file contains attributes that imply that it is:
* Has a match feature type
You can safely ignore this message if you don't need to access scores
associated with these features.
This GFF file has CDS and/or UTR features that do not belong to a
'central dogma' gene (ie, gene/transcript/CDS). The features of
this type are being stored in the database as is.
There are both CDS and exon features in this file, but
you did not set the --noexon option, which you probably want.
Please see `perldoc gmod_bulk_load_gff3.pl for more information.
Loading data into feature table ...
Loading data into featureloc table ...
Loading data into feature_relationship table ...
Loading data into featureprop table ...
Loading data into feature_cvterm table ...
Loading data into synonym table ...
Loading data into feature_synonym table ...
Loading data into dbxref table ...
Loading data into feature_dbxref table ...
Skipping analysisfeature table since the load file is empty...
Loading data into cvterm table ...
Loading data into db table ...
Skipping cv table since the load file is empty...
Skipping analysis table since the load file is empty...
Skipping organism table since the load file is empty...
Adding cvtermprop=MapReferenceType for 'chromosome' ...
Adding cvtermprop=MapReferenceType to chromosome ...
Loading sequences (if any) ...
Optimizing database (this may take a while) ...
(feature featureloc feature_relationship featureprop feature_cvterm
synonym feature_synonym dbxref feature_dbxref analysisfeature cvterm db cv
analysis organism ) Done.
While this script has made an effort to optimize the database, you
should probably also run VACUUM FULL ANALYZE on the database as well
I think the data is loaded into the tables as I tested for one of the table.
I tried the query that you wrote to me in your previous mail and it fetched
0 rows. I do not know why it is not fetching the any data. I am relatively
new to this field and do not know what the data is and how to analyze the
data. I have no idea of what you meant by "This assumes that the sequence
features have type_id *chromosome*, *sequence*, supercontig, ultra_scaffold,
golden_path_region or contig. If your sequence features do not belong to
that list you can modify it in artemis_sqlmap/Feature.xml. Please let me
know if you think something needs adding to this list." . I could understand
that it is trying to fetch some data which is not available in the database.
Can you please help me understand how this works and how to modify for the
data I loaded in to the database. This data is available in the wiki link
that I gave above and is of the organism "Yeast".
I really appreciate your help.
Thanks and Regards,
Rohit
On Thu, Oct 22, 2009 at 3:11 PM, Tim Carver <t...@sanger.ac.uk> wrote:
> Hi Rohit
>
> The first error suggests a strange character in your cvterm table in the
> column is_relationshiptype. There appears to be a charcter (t?) when the
> mapping is expecting an integer. You should find that and change it to an
> integer.
>
> The second exception looks like it has failed to find the sequences. To
> find the organisms with top level features with residues it runs this query
> which you can try :
>
> SELECT DISTINCT ON( feature.organism_id )
> organism.organism_id AS organismId,
> abbreviation, genus, species, common_name AS commonName, comment
> FROM feature
> join organism using (organism_id)
> join cvterm on feature.type_id = cvterm.cvterm_id
> WHERE residues notnull AND residues != ''
> AND (cvterm.name LIKE '%chromosome%' OR cvterm.name LIKE '%sequence%' OR
> cvterm.name IN ('supercontig', 'ultra_scaffold',
> 'golden_path_region', 'contig'));
>
> This assumes that the sequence features have type_id *chromosome*,
> *sequence*, supercontig, ultra_scaffold, golden_path_region or contig. If
> your sequence features do not belong to that list you can modify it in
> artemis_sqlmap/Feature.xml. Please let me know if you think something needs
> adding to this list.
>
> Regards
> Tim
>
>
> On Thu, 22 Oct 2009, parimi rohit wrote:
>
> Hi All,
>>
>> I am following the wiki page that has the tutorial to integrate Artemis
>> with Chado schema. I have
>> postgres as well as chado schema installed. I used Apollo to annotate data
>> from one of the
>> databases that we created. Now, I am trying to use Artemis on the same
>> data. However I am having
>> problems in running Artemis over the database. I started Artemis with the
>> following command as
>> given in the wiki page:
>>
>> $: ./art -Dchado="localhost:5432/rohit_chado_01?rohit" -Dibatis
>>
>> I entered my credentials in the login window and the Database and File
>> Manager window opened.
>> However I am able to view nothing in the Database part of the window even
>> though there exist
>> many. Also double clicking the folder in the database window is giving an
>> exception in the
>> terminal.
>>
>> I copied the terminal errors in a text file and I am attaching it in this
>> mail. The attachment
>> contains error information for 2 different databases. Please let me know
>> the problem and the way
>> to solve this so that it will work with the data that we have.
>>
>> Regards,
>> Rohit
>>
>>
>>
>>
>>
>>
>
> --
> The Wellcome Trust Sanger Institute is operated by Genome Research Limited,
> a charity registered in England with number 1021457 and a company registered
> in England with number 2742969, whose registered office is 215 Euston Road,
> London, NW1 2BE.
>
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