[Gmod-schema] a question of loading data into chado database
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[Gmod-schema] a question of loading data into chado database
 
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Re: [Gmod-schema] a question of loading data into chado database
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Re: a question of loading data into chado database
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Re: a question of loading data into chado database
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In reply to this post by zhuang chao
hello , Scott
I downloaded Chado from svn . But the question still exist . The gff file is in the attachment . Here is a history of how I loaded previous data . Thank you very much ! =============================================== root@bnode6:/home/zc/Download# perl /usr/local/bin/gmod_bulk_load_gff3.pl --gfffile NC_001437.gff --organism 'Japanese encephalitis virus' --dbname four_viruses --dbuser zc --dbpass 123456 --dbhost localhost --dbport 5432 --save_tmpfiles Preparing data for inserting into the four_viruses database (This may take a while ...) Dropping cds temp tables... Creating cds temp tables... NOTICE: CREATE TABLE will create implicit sequence "tmp_cds_handler_cds_row_id_seq" for serial column "tmp_cds_handler.cds_row_id" NOTICE: CREATE TABLE / PRIMARY KEY will create implicit index "tmp_cds_handler_pkey" for table "tmp_cds_handler" NOTICE: CREATE TABLE will create implicit sequence "tmp_cds_handler_relationship_rel_row_id_seq" for serial column "tmp_cds_handler_relationship.rel_row_id" NOTICE: CREATE TABLE / PRIMARY KEY will create implicit index "tmp_cds_handler_relationship_pkey" for table "tmp_cds_handler_relationship" 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 ... Skipping feature_cvterm table since the load file is empty... 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... DBD::Pg::db commit failed: ERROR: insert or update on table "feature_relationship" violates foreign key constraint "feature_relationship_subject_id_fkey" DETAIL: Key (subject_id)=(66) is not present in table "feature". at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 3151, <$fh> line 5. commit failed: ERROR: insert or update on table "feature_relationship" violates foreign key constraint "feature_relationship_subject_id_fkey" DETAIL: Key (subject_id)=(66) is not present in table "feature". at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 3151, <$fh> line 5. Abnormal termination, trying to clean up... Attempting to clean up the loader temp table (so that --recreate_cache won't be needed)... Trying to remove the run lock (so that --remove_lock won't be needed)... Exiting... ======================================================= On Tue, 2010-05-18 at 09:07 -0400, Scott Cain wrote: > Hi zhuangchao, > > Are you using Chado from the 1.0 release or from svn? I believe that > people have had that problem with the 1.0 release but it is fixed in > svn. You can get Chado from svn by following these directions and > checking out the schema repository: > > http://gmod.org/wiki/SVN > > (As a side note, I've promised myself to get the 1.1 release out this week.) > > If you are already using Chado from svn, please give us more > information, like a sample of GFF that causes the problem, and perhaps > a history of how you've loaded previous data (if you have). Finally, > you might want to use the option --save_tmpfiles and examine them for > where in the GFF file the missing feature would have occurred that the > database is complaining that it doesn't exist. > > Scott > > > On Tue, May 18, 2010 at 2:54 AM, 庄超 <[hidden email]> wrote: > > When I was loading the gff3 file into chado database using gmod_bulk_load_gff3.pl, I got the errors like this: > > > > DBD::Pg::db commit failed: ERROR: insert or update on table > > "feature_relationship" violates foreign key constraint > > "feature_relationship_subject_id_fkey" > > DETAIL: Key (subject_id)=(31191) is not present in table "feature". > > at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 2651, <$fh> > > line 41. > > > > commit failed: ERROR: insert or update on table "feature_relationship" > > violates foreign key constraint "feature_relationship_subject_id_fkey" > > DETAIL: Key (subject_id)=(31191) is not present in table "feature". > > at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 2651, <$fh> > > line 41. > > > > I don't know why and how to handle. Could you help me? > > I am looking forward to your reply. Thank you very much ! > > > > -------------- > > zhuangchao > > 2010-05-18 > > > > > > > > ------------------------------------------------------------------------------ > > > > _______________________________________________ > > Gmod-schema mailing list > > [hidden email] > > https://lists.sourceforge.net/lists/listinfo/gmod-schema > > > > > ------------------------------------------------------------------------------ _______________________________________________ Gmod-schema mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-schema |
NC_001437.gff (25K)
Re: a question of loading data into chado database
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Re: a question of loading data into chado database
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a question of loading the gff3 file into chado database (1)
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