Tomáš Brůna

Hi @Aled32, take a look at this issue, it could help: https://github.com/Gaius-Augustus/BRAKER/issues/222 Tomas

Hello @claumer, you mentioned that you had no luck with the bioconda braker2 package. The `sortGeneMark.py` is a new script but it should be a part of the latest bioconda...

Hi Parul, did you try running the example in [test1.sh](https://github.com/Gaius-Augustus/BRAKER/blob/master/example/tests/test1.sh) and did that run without issues? Can you also share the full `braker.log` file? Best, Tomas

Hi Parul, is your genome repeat masked? I see that you are working with a rice genome (based on the file `rice_introns.f.gff`). GeneMark and other _ab initio_ gene predictors struggle...

Hi @Fu-Yin, in your case, almost no predicted introns are supported by RNA-Seq. This is causing the error. Are you working with Giardia? The cause of the problem could actually...

You can try running BRAKER in the `--esmode` (as illustrated in [test8.sh](https://github.com/Gaius-Augustus/BRAKER/blob/master/example/tests/test8.sh)). This could work because the `--esmode` does not rely on evidence-supported introns.

Hi @shoriri, the `-gff3` should not affect the `prothint.py` run, I do not understand what is causing this error... Can you please share the full `braker.log` file?

Hi @shoriri, > I want to know why BUSCO's rating differs between the protein file braker made and gffread made. Is there any trouble with my gtf file ?? The...

Hi @marchoeppner, thanks for reporting this problem! It indeed looks like that with GenomeThreader, the code is currently using the `mRNA` feature, but with Spaln, it's failing as you described....

From the error logs, it seems that BRAKER failed while running `etraining`, which is a part of AUGUSTUS: ``` 22837 Segmentation fault /work/nitinr/perl_env/bin/etraining ... ``` Please try updating your AUGUSTUS...