Spaln not completing in resonable amount of time and thus annotation is stuck.

[KPapac]

Hey there,

I am using the singularity image of braker3 to annotate my genomes. To annotate I use RNA and protein data from orthodb v11. For some of the genomes, braker is stuck when running gmetp at one Spaln process on a protein that seems highly repetitive in sequence. I attach the from orthodb that is tried to be aligned on the genome.

mucin2.txt

The Spaln process stays like this for days, whereas other genomes from the same species finish the whole braker3 annotation within half a day. If I kill that Spaln process, then the pipeline continues on and on the braker.log file it tells me that the run finished successfully. I get the final gff file.

So, me stopping this process, is it going to have any negative effects on the results?

Can I do anything about this, so that the Spaln process is completed?

[tomasbruna]

I'm closing this as a duplicate of Gaius-Augustus/BRAKER#912