Can you help me understand these lines in the completed braker.log

Question

[Vijith]

The braker run has been over, and I went through the braker.log file. Here are some details that I wish I understood quite well.

# Fri Nov 22 05:59:51 2024: Setting value of "stopCodonExcludedFromCDS" ... to "true"
grep -c "exon doesn't end in stop codon" /media/.../errors/firstetraining.stderr
# Fri Nov 22 05:59:58 2024: Error rate of missing stop codon is 0.94985590778098
# Fri Nov 22 05:59:58 2024: The appropriate value for "stopCodonExcludedFromCDS" seems to be "false".
# Fri Nov 22 05:59:58 2024: Setting value of "stopCodonExcludedFromCDS" in /media/.../new_species_t1_parameters.cfg to "false"

So, here I understand when stopCodonExcludedFromCDS is set to True, the augustus checks each exon only up to the stop codon. The grep command with "exon doesn't end in a stop codon" has returned an error rate of ~95%; does that mean the remaining 5% exons are the last ones in the gene structure? In this case, what is the logic behind setting the parameter value to false? Is it because of the 5% exons with stop codons?

[lieven.sterck]

I could give you an answer of what I think it means or does but you're likely better of asking this to the people involved in the BRAKER project.

I advise to post a question on their github issue tracker: https://github.com/Gaius-Augustus/BRAKER

We would appreciate if you come back and let us know what their answer to your issue is.

[Vijith]

lieven.sterck, thank you for this suggestion. I will definitely update it if I get an answer to this issue.