I have a genome of a novel fungus. I need to predict the genes in it using Augustus. In the --species flag of augustus, what should I specify, since my fungus is a novel one and does not match any of the identifiers provided in the readme doc in augustus github page.
If none of the available profiles is close enough to your species, then you might consider training Augustus yourself. While this might be a little difficult, I find that using BUSCO v4 (I think newer versions don't use augustus anymore) can make it much easier. BUSCO will automatically train Augustus and make a new profile which you can then use to predict genes.
Another thing you should note is that ab-initio gene prediction (which is what Augustus does) is a noisy and often inaccurate process. It is usually only one step in a large genome annotation pipeline. To get a good annotation, you'd probably want to use evidence such as transcripts, RNA-seq, and protein sequences, in the context of an annotation pipeline like MAKER, PASSA, or EvidenceModeler.