Tomáš Brůna

Hi Tom, I am not sure whether the rest of GeneMark-ET depends on this info. I asked [Alex Lomsadze](http://exon.gatech.edu/GeneMark/contact.html), the original author of GeneMark-ET, whether this would cause any issues....

Hi Tom, can you share the `braker.log` and also a file named `GeneMark-ET.stdout`, if you have it? I'd like to take a look, maybe I'll see something else which is...

Hi Tom, Alex told me that he fixed the overflow error. Can you download the newest GeneMark version from http://exon.gatech.edu/GeneMark/license_download.cgi and test whether it helped? Best, Tomas

Hello, can you share your `braker.gtf` file? I was trying to reproduce this error but the conversion works for me... Until this is fixed, please try converting the `gtf` output...

Hello, this is normal. In the 2.1.4 version, there is some stochasticity in the training of AUGUSTUS. Different training runs (with the same inputs) can result in slightly different statistical...

Hello Siva, please try to re-run with the newest BRAKER (version 2.1.6) and use the `--softmasking` option in your BRAKER call. It might not help, but it will be easier...

Hello Siva, can you also share the following files? * `/mstore/smp/user/siva/braker/errors/gbFilterEtraining.stderr` * `/mstore/smp/user/siva/braker/gbFilterEtraining.stdout` It seems that BRAKER was able to successfully run `gff2gbSmallDNA.pl` (despite all the errors in the log)...

Hello @SchwarzEM, thank you for this report. We've recently made some changes to BRAKER2 code, including the section related to multi-CPU operations. If you have time in the future, could...

Hi Vladislav, I've successfully run BRAKER with modified AUGUSTUS settings before (which were somewhat similar to yours). > I wonder, could it be problem of a memory usage or multi-threading...

Hi Vladislav, the absence of a `.gff3` file is not a concern. We are working on making this better, but in the meantime, you can always convert the `gtf` output...