Empty genbank produced by gff2gbSmallDNA.pl

[katharinedickson]

I would like to train Augustus on three eukaryotic genomes. I have the following for each:

• a repeat-masked FASTA
• a GFF file of coding regions, exons, start codons, and stop codons

When I feed the program a command for one of them,
/filepath/gff2gbSmallDNA.pl /filepath/Neolan1_GeneCatalog_genes_20200610.gff /filepath/Neolan1_AssemblyScaffolds_Repeatmasked.fasta 0 /filepath/N_lanati.genbank

I get blank genbank files as output. I have checked and rechecked the filepaths by copy-pasting them from my script into the head command; please assume these are correct.

What is the most likely problem?

[MarioStanke]

That the GFF is not in a suitable format. GFF is not fully specified. It could also be a chromosome name mismatch.
I suggest you try the command with the files genome.fa and traingenes.gff from examples/autoAug/. This should work. And then you can look at the differences between your format and the one from the example and reformat if different.