<div dir="ltr">Hi,<br><br>I am trying to upload my organism data to CHADO and I am stuck in a error.<br>I have downloaded a GenBank formatted file, used the suggested transformation to GFF3:<br><br><pre><font size="4">bp_genbank2gff3.pl -noCDS -s -o . temp.txt<br>
<br><br>After, I have used this sintax for gmod_bulk_load:<br><br><br>gmod_bulk_load_gff3.pl --dbname XXX --dbxref GeneID --organism XXX --gff temp.gff<br><br><br>Preparing data for inserting into the CruziGeneDB database<br>
(This may take a while ...)<br><br>no parent Tc00.1047053508153.20;<br>you probably need to rerun the loader with the --recreate_cache option<br><br>Well, the Tc00.1047053508153.20 ID is in the GFF file and is before the entry that references it as Parent.<br>
<br>I have followed the suggestion, and ran the same command line above, but including --recreate_cache.<br><br>The script runs for a long time and then the following error appears.<br><br>DBD::Pg::db pg_endcopy failed: ERROR: invalid input syntax for integer: ""<br>
CONTEXT: COPY feature_relationship, line 1, column type_id: "" at /opt/coolstack/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 2723, <$fh> line 64298.<br><br><br>Then I tried to run gmod_bulk_load with --noload --inserts --save_tmpfiles.<br>
<br>When inspecting the chado-feature_relationshipXXX file, I have found that Features having a Parent= delimiter in the GFF file have a empty field in the INSERT statement for type_id. As an example:<br><br>INSERT INTO feature_relationship (feature_relationship_id,subject_id,object_id,type_id) VALUES (15,190738,190737,);<br>
INSERT INTO feature_relationship (feature_relationship_id,subject_id,object_id,type_id) VALUES (16,190739,190738,53);<br><br>The first line is from a feature containing a Parent delimiter. It has a empty value for type_id<br>
The second line is from a feature containing a derived_from delimiter. It has the correct cvterm_id for type_id.<br><br>So, the OBO relationship of the Parent Delimiter is not being correctly identified. <br><br>I have tried to found 'part_of' in the cvterm table, and found only entries related to the cv 'Gene Ontology' and 'Plant Ontology'.<br>
The 'derives_from' term, in the cvterm table, is mapped to the 'relationship' cv, but I have no 'part_of' mapped to 'relationship' cv. Is that a possible source for this error? Anyway, if you could help me in any <br>
sense, I would be very glad.<br><br>Thanks in advance.<br><br>Christian M. Probst<br><br></font></pre><br></div>