Spaln process stays active for long time

[KPapac]

Hey there,

I am using the singularity image of braker3 to annotate my genomes. For some of them, braker is stuck at one Spaln process on a protein that seems highly repetitive in sequence. It stays like this for days, whereas other genomes from the same species finish 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?

[bijendrabio]

@KPapac. Got similar issue #915

[tomasbruna]

Hi @KPapac,

Spaln can occasionally get stuck in an infinite loop while aligning certain proteins. Terminating the stuck Spaln process will only impact the alignment of the specific input protein, so this won't negatively affect the overall results.

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

Besides manually terminating the stuck Spaln process (which will allow BRAKER to continue), you can also remove the problematic protein from your input and re-run BRAKER.

Best,
Tomas