CDS not contained within cross-referenced mRNA FEATURE

Question

[sandra.hilario]

Dear all,

I am trying to submit a genome annotation to NCBI, but I am having some issues. I used AGAT command lines to merge my gff files, and I am now using the table2asn program to create the .asn file to submit my annotation. However, I got some errors regarding the CDS and mRNA. It seems that the first interval of my mRNA is not is not coincident with the one from CDS. For instance, take a look at what I obtained:

mRNA            join(228..230,376..955,1006..1050,1105..1412,1478..1580,
                     1629..1735,1799..2024,2080..2417,2544..2676)
                     /locus_tag="JT55_005876"
                     /product="hypothetical protein M431DRAFT_106171"
 CDS            join(228..322,376..955,1006..1050,1105..1412,1478..1580,
                     1629..1735,1799..2024,2080..2417,2544..2676)
                     /locus_tag="JT55_005876"
                     /codon_start=1
                     /product="hypothetical protein M431DRAFT_106171"
                     /protein_id="JT55:cds-1"

Did you ever come across with errors like this? I am not sure why this is happening, but I got this error almost in each line I have a CDA. Do you know if there is any way to span the CDS across the same range of mRNA?

Thank you all Sandra

[lieven.sterck]

Hello sandra.hilario ,

Welcome!

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Thank you!

[lieven.sterck]

For some reason there seems to be an invalid 'end coordinate' for the first CDS part ... strange.

Can you perhaps post the lines from the original files for that gene? (so before running AGAT on it)

[Juke34]

Yes please provide the output from AGAT for the JT55_005876 locus to check if the problem comes from AGAT