Hi, have you seen if the header is the same (.fsa and .gff)? Looks like the error msg is talking about it: your .fsa is Contig002 and the GFF lcl|Contig002.

Usually when I send the genome to Genbank I prefer to use the table2asn with the tbl format.

https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/

You should convert the GFF into TBL before using the table2asn.

You can use this tool: https://genomeannotation.github.io/GAG/

gag.py --fasta organism.fasta --gff organism.gff --out gag_output (tbl)

When you convert the GFF to TBL the probability of error is reduced.

Thank you Juliana for your reply!

In the meanwhile I have tried to use the GAG script, but somehow something goes wrong. The gff table is completely ok, since it gives no errors at NCBI when running their scripts, but when I use it as input for the GAG tool, it somehow does not detect the CDS features.

To give you an idea of how the file looks, I have attached part of it here. Maybe you can see what went wrong?

Hi!

Your file is missing the mRNA and Exon feature. 

You can add the mRNA feature

##gff-version 3 ##gff-version 3

Hi Guillaume,

I am trying to run the tool but unable to do so. How did you install it? chmod +x doesn't work for me. Can you please comment. Thanks

Arslan