Question about --genemodel=complete option of Augustus

[evolver]

Hi all,

I am afraid I have a silly question but I am really confused.

I am now trying to construct a de novo gene model for my species using augustus.

I ran augustus with "--genemodel=complete" option as below:
augustus --species=mySpecies --exonnames=on --codingseq=on --protein=on --extrinsicCfgFile=extrinsic.M.RM.E.W.cfg --alternatives-from-evidence=true --hintsfile=hint.gff --allow_hinted_splicesites=atac --genemodel=complete genome.fa > aug.out

ant then, used getAnnoFasta.pl to extract amino acid sequences in fasta format.
However, I found in aug.out.aa file that some predicted proteins do not start with methionine(Met).

Does this kind of thing occur commonly or can it be attribute to my fault at any steps of augustus?

Best,
evolver

[WhatsOEver]

As far as I know, "complete" means just "not partial". With the default settings, augustus predicts incomplete gene models at the sequence boundaries. This makes sense because the program will be used mainly on draft genomes which consist of a lot of contigs. Besides that, there are also mature proteins that do not start with a Met, so making this a prerequisite might sometimes also be wrong.