John Urban

@Dooozy Check out the error messages I received when using STAR BAMs (even after including `--outSAMstrandField intronMotif` ) posted on issue #589 Do you think we are dealing with the...

Update: providing a raw fastq, instead of a STAR produced BAM, solved GeneMark-ETP issues we were having. See #582.

If Braker3 is only using the RNA-seq data to produce a StringTie assembly, then an option to just pass Braker3 the StringTie assembly (or any reference-guided transcriptome assembly) would be...

I am currently debugging. The problem seems to be in `gmetp.pl` at this line: ``` PrepareGenomeTraining($proc) if 1; ``` (I know this is technically not a Braker problem at this...

And specifically at this line in `PrepareGenomeTraining` inside the if statement: ``` if ( CreateThis("hc_regions.gtf")) { ## breaks with the following line system( "$bin/create_regions.pl --hcc $hcc_genes --hcp $hcp_genes --out hc_regions.gtf...

I have a valid license for GeneMark-ES/ET/EP ver 4.71_lic. It works for both Braker1 and Braker2 runs. It does not work for Braker3 runs. Perhaps that is b/c that license...

Is there a way to get GeneMark-ETP if one is not using the container?

Uh oh - time to learn Docker.

Got it! Thanks! ``` wget http://topaz.gatech.edu/GeneMark/etp.for_braker.tar.gz && \ tar -xzf etp.for_braker.tar.gz && \ mv etp.for_braker ETP && \ chmod a+x /opt/ETP/bin/*py /opt/ETP/bin/*pl /opt/ETP/tools/* ```

Well, I gave Braker3 a try with the GeneMark-ETP copy found here http://topaz.gatech.edu/GeneMark/etp.for_braker.tar.gz -- but `gmetp.pl` gives the same error that I opened up this thread with -- essentially `complete.gtf`...