Bug in retraining step with Augustus - affects genome mode for Eukaryotes
Unfortunately fixing some bugs in the latest releases broke the retraining step of Augustus.
This will affect all the runs in genome mode for all Eukaryotes. So observations in issues #177 #181 (closed) are likely due to this bug.
BUSCO cannot find the retraining files for the second run of Augustus. Thus the scores you get in the short_summary.txt only derive from the first round of Augustus and are preliminary.
The bug is easy to fix and we’ll get this done on Monday.
Thank you for your patience.