Hello I have a rather strange observation
I trained Augustus for a new species and was rather successful in my opinion:
75% on the exon level and 45% at the gene level for both sensitivity and specificity. The strange thing though is, that upon prediction I receive all genes without any exons annotated 
E.g. (removed some columns for a better view)
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gene 27294 28002 0.46 - .
transcript 27294 28002 0.46 - .
stop_codon 27294 27296 . - 0
intron 27631 27814 1 - .
CDS 27294 27630 0.96 - 1
CDS 27815 28002 0.48 - 0
start_codon 28000 28002 . - 0
did not realize it immediately.
Any clue what might cause this effect?
My command line was:
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augustus --species=X Contig10.fasta