<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Under what circumstances will maker not include a gene model from the model_gff file in its final output? It was my understanding from this post:<div> <a href="https://groups.google.com/d/topic/maker-devel/Y5jSdZ1Olcc/discussion">https://groups.google.com/d/topic/maker-devel/Y5jSdZ1Olcc/discussion</a></div><div><br></div><div>That maker will keep or replace models in model_gff and never remove them. I'm reannotating a fungal genome and in model_gff I'm providing the gene models originally made by the sequencing center. I have 12006 models in the file I specify in model_gff but maker's final annotation has only 10727 models in it. </div><div>-Mike</div><div><br></div></body></html>