annotate test-data/out_primates.log @ 0:66ebc4b19d6c draft default tip

"planemo upload for repository https://github.com/smirarab/ASTRAL commit 0f93f327c49e93d6af057973d68ba772ba5715dc-dirty"

================== ASTRAL ===================== 

This is ASTRAL version 5.7.8
Gene trees are treated as unrooted
424 trees read from test-data/song_primates.424.gene.tre
index0
All output trees will be *arbitrarily* rooted at Marmoset

======== Running the main analysis
Number of taxa: 14 (14 species)
Taxa: [Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galago, Mouse_Lemur, Tree_Shrew, Rat, Tarsier, Rabbit, Horse, Sloth]
Taxon occupancy: {Human=424, Rat=424, Tarsier=424, Galago=424, Rabbit=424, Macaque=424, Sloth=424, Marmoset=424, Tree_Shrew=424, Chimpanzee=424, Mouse_Lemur=424, Horse=424, Orangutan=424, Gorilla=424}
Number of gene trees: 424
0 trees have missing taxa
Calculating quartet distance matrix (for completion of X)
Species tree distances calculated ...
Building set of clusters (X) from gene trees 
------------------------------
gradient0: 339
Number of Clusters after addition by distance: 339
calculating extra bipartitions to be added at level 1 ...
Adding to X using resolutions of greedy consensus ...
Limit for sigma of degrees:400
polytomy size limit : 3
discarded polytomies:  [3]
Threshold 0.0:
Threshold 0.01:
Threshold 0.02:
Threshold 0.05:
Threshold 0.1:
Threshold 0.2:
Threshold 0.3333333333333333:
polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 339
max k is :0
Number of Clusters after addition by greedy: 339
gradient0 in heuristiic: 339
partitions formed in 0.192 secs
Dynamic Programming starting after 0.192 secs
Using tree-based weight calculation.
Using polytree-based weight calculation.
Polytree max score: 424424
Polytree building time: 0.052 seconds.
Number of quartet trees in the gene trees: 424424
Size of largest cluster: 14
Greedy score: 389226
estimationFactor: 1.090430752313566
Sub-optimal score: 389226
Total Number of elements weighted: 452
Normalized score (portion of input quartet trees satisfied before correcting for multiple individuals): 0.9182656965675834
Optimization score: 389734
Optimal tree inferred in 0.319 secs.
(Gorilla,((Human,Chimpanzee),(Orangutan,(Macaque,(Marmoset,(Tarsier,((Galago,Mouse_Lemur),((Horse,Sloth),(Tree_Shrew,(Rat,Rabbit))))))))));
Final quartet score is: 389734
Final normalized quartet score is: 0.9182656965675834
Weight calculation took 0.027776492 secs
ASTRAL finished in 0.438 secs