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[tberthelier]

Hello,
I ran a Braker annotation on a plant genome and there is one issue that I didn't get with my other genomes (my script works fine for my other genomes). In fact, it is the same issue that #14. I tried to solve the issue by locating the stuck Spaln process with the command "ps aux | grep spaln" but I have no result.
So I do not know how to resolve that issue and I'm asking for your help.
Many thanks in advance,
Thomas.

[tomasbruna]

I can try debugging this if the problem still persists. Can you share the genome.fasta, protein.fasta, and the genemark.gtf (predicted by genemark-ES)? You can send me an email at bruna.tomas@gmail.com if you don't want to share publicly.

[MFSeidl]

Hello, I would like to follow up on this point. I also experience this issue with multiple genomes. I am trying to annotate ~10k fungal genomes and it doesn't seem that the processes that get stuck (not all) have issues with the same protein in the protein database (I use fungi.odb10). it would be great if there would be some timeout, as proposed in #14, to continue with the overall process. Fetching out these by hand is not feasible given the number of genomes. Thank you very much!

[tomasbruna]

Hi @MFSeidl,

Agreed, I'll look into this!

Cheers,
Tomas

[MFSeidl]

Awesome, Thank you!