AleRax average run time

[Sawsan Wehbi]

Hello Benoit,

Hope you're doing well.

I recently started using AleRax to reconcile a tree distribution for a single pfam generated from IQ-Tree's ultrafast bootstrap process.

I have had no issues so far other than noticing a particularly long run time.

I have a single family gene tree with 400 taxa and 1000 trees in the input distribution ( gene tree sample option is set at 100). 

Its been running on the HPC for 6 days now and it seems to be stuck at the optimizing model rates step '[Species search] Optimizing model rates (light)'.

Ive also tried it using your primates sample data with two families and gene tree sample set at 10 and that is also still running ( for over a day).

I just wanted to check if this is normal or do you think there might be some other underlying problem.

Thank you as always.

Sawsan

[Benoit Morel]

Hi Sawsan,
I guess it's not surprising because 400 taxa is quite high already.
But for the primates sample, that's weird. Did you just run the example script?

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