only few genes detected with Busco-trained augustus

Hi,

I'm annotating a genome and I trained augustus with Busco3 and --long option as usual. However, when running augustus within Maker, it only detects 207 genes compared to 15-20k from the other gene predictors.

I redid the training and changed augustus versions a few times but the result is always the same. Have you seen this problem before?

Cheers, Xabi

EDIT: forgot to mention that the completeness report looks normal with completeness close to 90%.