ortholog spawning an error that I can't figure out

[pombase-admin]

mRNA SPCC24B10.08c.1: failed to create ortholog relation from SPCC24B10.08c to TADA2B: DBIx::Class::ResultSet::create(): DBI Exception: DBD::Pg::st execute failed: ERROR: duplicate key value violates unique constraint "feature_relationship_c1"

looks OK in the contig file?

Original comment by: ValWood

[pombase-admin]

another error the actual ortholog file contains SPBC17G9.09 EIF2S3|EIF2S3L; with a trailing semi colon, but the input is compara_orths.tsv:SPBC17G9.09 ENSG00000180574,ENSG00000130741

so I con't figure out where the semi-colon is coming from?

Original comment by: ValWood

[pombase-admin]

the contig one has TADA2B twice:

FT /controlled_curation="term=human TADA2B and TADA2B FT ortholog; date=20141020"

Original comment by: mah11

[pombase-admin]

OK that fixes SPCC24B10.08c

Original comment by: ValWood

[pombase-admin]

so I con't figure out where the semi-colon is coming from?

Me neither until I checked what Ensembl is sending us. Although it's fine on the web page for that gene, the Ensembl API is returning: "ENSG00000180574 EIF2S3L;". There are 13 other genes with a semi-colon at the end of the gene name. I'll report it. In the mean time the Ensembl gene reader now removes any trailing semi-colons on name.

Original comment by: kimrutherford

[pombase-admin]

I'll report it.

I reported the semi-colon in the Ensembl gene name. The got back to me to say thanks and it will be fixed in the next release.

The Chado load with the local fix is still running.

Original comment by: kimrutherford

[pombase-admin]

• Description has changed:

Diff:

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+++ new
@@ -1,4 +1,3 @@
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 mRNA SPCC24B10.08c.1:   failed to create ortholog relation from SPCC24B10.08c to TADA2B: DBIx::Class::ResultSet::create(): DBI Exception: DBD::Pg::st execute failed: ERROR:  duplicate key value violates unique constraint "feature_relationship_c1"

• status: open --> closed-fixed

Original comment by: kimrutherford