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Gaius-Augustus / Augustus

Genome annotation with AUGUSTUS
http://bioinf.uni-greifswald.de/webaugustus/
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Empty genbank produced by gff2gbSmallDNA.pl #419

Open katharinedickson opened 1 month ago

katharinedickson commented 1 month ago

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

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 commented 3 weeks ago

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.