I am using the table2asn and a gff3 to create a .sqn file for a eukaryote genome. And I got this warning (for all of the genes):
SEQ_FEAT.GenCodeMismatch:
After uploading the sqn file to the NCBI, it is considered a FATAL error, and the feedback from the NCBI is not the best (inexistent).
This is the only warning I get, and according to the manual, this warning is related to the genetic code (default=prokaryote) used for the annotation and, it can be ignored if the genome is from a eukaryote
(apparently, it can't be).
If I use the -j "[gcode=1]" (standard code), the warning disappears during the .sqn construction (It confirms the warning is related to the genetic code more than an annotation/format error). However, the "FATAL ERROR" persists after the processing by the NCBI.
Any suggestions?
I'm using mac.table2asn (v1.26.643), and the problem was solved by adding the parent gene to the pseudo genes (I originally submitted just the CDS). The manual says you can submit only CDSs (this is not true at least with the version mentioned before). I also moved the flag 'pseudo=true' to the gene annotation and added a note.