Fix for NULL feature.gene_order

SELECT o.id, count(f.id) FROM organisms o JOIN features f ON o.id=f.organism_id JOIN organisms_projects op ON o.id=op.organism_id JOIN projects p ON op.project_id = p.id WHERE p.id=[PROJECT_ID] AND f.gene_order IS NULL GROUP BY o.id;

To assess such a problem site wide:

SELECT o.id, count(f.id) FROM features f JOIN organisms o ON o.id = f.organism_id WHERE f.gene_order IS NULL GROUP BY o.id;

Fix

Once you have identify the problem organisms. Get the list of organism ids in comma separated format, and then you can update the gene_order with the following SQL query by replacing [ORGANISM_IDS], ex: 1,2,3,4:

Update features f, (
SELECT @rn:= (IF(@prev_contig=t1.contig_id, @rn+1, 1)) AS row_num,
t1.id,
t1.name,
c.name AS contig_name,
t1.contig_id,
t1.organism_id,
t1.gene_order,
@prev_contig := t1.contig_id
FROM (features t1, (SELECT @rn:=0) t2, (SELECT @prev_contig := '') t3)
INNER JOIN contigs c ON c.id = t1.contig_id
WHERE t1.organism_id in ([ORGANISM_IDS])
ORDER BY t1.contig_id, t1.`from`
) AS f2
SET f.gene_order = f2.row_num
WHERE f.id = f2.id;