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

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out_primates.log	Wed Apr 13 15:03:31 2022 +0000
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+
+================== 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