Takes too long

[Juan David Tovar Duran]

Hi all.

I'm using the following lines of code, but I am not getting any results despite setting it to run only once.

using PhyloNetworks
trees=readMultiTopology("\\path\\raxml_trees.treefile")  
q,t = countquartetsintrees(trees)
df = writeTableCF(q,t)
astralCF = readTableCF(df)
tre=readTopology("\\path\\ASTRAL_quartet_support.tree") 

net0 = snaq!(tre, astralCF, hmax=0, filename="snaq\\net0_astral", seed=123, runs=1)

My dataset contains 254 trees with 86 tips, resulting in 2,123,555 quartets. I've run this script both locally and on a cluster, but no results are printed in the snaq folder. Any suggestions?  Is it normal that it takes so long just for one run?

Thanks.

J.

[Cécile Ané]

It takes too long indeed for 86 tips. Something like 25 tips is around the maximum that snaq can handle (with patience).

This conversation is relevant.

If some of your tips are individuals from the same species, then you could group them to reduce the number of tips in the network (see the documentation on "multiple alleles").

Cecile.