Augustus 3.3 stuck run

Discussions about predicting genes with AUGUSTUS. Not covered here: WebAUGUSTUS and BRAKER1

Moderator: bioinf

Post Reply
Posts: 1
Joined: Tue Dec 19, 2017 3:08 pm

Augustus 3.3 stuck run

Post by matsepp »


I am facing infinite runtime when using Augustus 3.3 within our BUSCO tool (
When it is stuck, I have this in the logs:

# Predicted genes for sequence number 1 on both strands
replaced tx with 0 MEA txs

while with 3.2.1 it starts producing output normally, and the run lasts for a few seconds.
# Predicted genes for sequence number 1 on both strands
# start gene g1
NT_033779.5 AUGUSTUS gene 21573855 21577103 0.12 + . g1

The command used is augustus --codingseq=1 --proteinprofile=metazoa_odb9/prfl/EOG091G08VB.prfl --predictionStart=21573855 --predictionEnd=21595101 --species=fly ./tmp/NT_033779.5v3_4200603825_.temp

If needed, I can provide more details, just tell me what.


User avatar
Site Admin
Posts: 530
Joined: Wed Nov 18, 2015 6:14 pm
Location: Greifswald

Re: Augustus 3.3 stuck run

Post by katharina »

Hi Mathieu,

this is an issue that Mario accidentally put into the latest AUGUSTUS release. It has actually been fixed (internally). Please contact me via e-mail in case you need the fixed version. It is not a functional issue, though. It just causes a big output to stderr. katharina dot hoff at uni-greifswald dot de

Post Reply