John Urban

Hey - is Braker3 on the master branch now? I was on `git checkout braker3`. As for singularity, I installed it using conda. So I have I guess I have...

Ok. For the Singularity errors: Command: ``` singularity exec braker3.sif print_braker3_setup.py ``` Error: ``` INFO: Converting SIF file to temporary sandbox... FATAL: while extracting braker3.sif: root filesystem extraction failed: extract...

Ok - I should have mentioned this for the `braker3` branch already, but I didn't want to bombard you with issues (more so than I have). Line `2295` in `braker.pl`...

Alright. I ran Braker3 again with every thing up-to-date -- noting that I did have to change the java version line back to the old approach as described above. I...

It cannot find a file located here: `braker3/GeneMark-ETP/rnaseq/hints/proteins.fa/complete.gtf` So I decided to look at what is there: ``` > ls braker3/GeneMark-ETP/rnaseq/hints/proteins.fa/ log prothint tmp ``` I wonder if the `log`...

And looking more into that, for some reason many of the OrthoDB protein sequences end with a period... e.g.: ``` >307491_0:000000 MLAYADNIVVMGETKDINSTSKLISSNNFKYLGVNINNKIGMHIEINERITNGNSCYFSIIKFLRS. ``` I downloaded orthodb proteins like this: ```...

I re-downloaded the OrthoDB proteins to confirm its not just my copy somehow, and indeed 17014 of the 8266016 metazoan proteins end with a period. But this was still v10...

@Thamos the previous runs with the "dirty" protein sequences did not have that file. Now that I have a "pre-sanitized" protein file, Diamond is happily working at the moment, and...

@Thamos is there a link like `https://v100.orthodb.org/download/odb10_metazoa_fasta.tar.gz` for v11? Else, I could download the whole v11 db here: https://data.orthodb.org/download/ ...do you have any tips on how to filter the entire...

I'm currently running into this issue too, so I appreciate the posted solutions, which I will be trying. I am running `braker.pl version 2.1.6` installed using conda. The command: ```...