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

This is ASTRAL version 5.6.3
Gene trees are treated as unrooted
4 trees read from /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_astral/pargenes/astral_run/gene_trees.newick
All output trees will be *arbitrarily* rooted at taxa_0

======== Running the main analysis
Number of taxa: 10 (10 species)
Taxa: [taxa_0, taxa_1, taxa_3, taxa_2, taxa_7, taxa_9, taxa_6, taxa_5, taxa_4, taxa_8]
Taxon occupancy: {taxa_9=1, taxa_0=4, taxa_2=4, taxa_1=4, taxa_4=1, taxa_3=4, taxa_6=1, taxa_5=1, taxa_8=1, taxa_7=1}
Number of gene trees: 4
3 trees have missing taxa
Calculating quartet distance matrix (for completion of X)
Species tree distances calculated ...
Will attempt to complete bipartitions from X before adding using a distance matrix.
Building set of clusters (X) from gene trees 
------------------------------
gradient0: 43
Number of Clusters after addition by distance: 43
calculating extra bipartitions to be added at level 1 ...
Adding to X using resolutions of greedy consensus ...
Limit for sigma of degrees:300
polytomy size limit : 3
discarded polytomies:  []
Threshold 0.0:
Threshold 0.01:
Threshold 0.02:
Threshold 0.05:
Threshold 0.1:
Threshold 0.2:
Threshold 0.3333333333333333:
max k is :0
Number of Clusters after addition by greedy: 43
gradient0 in heuristiic: 43
partitions formed in 0.052 secs
Dynamic Programming starting after 0.052 secs
Using tree-based weight calculation.
Using polytree-based weight calculation.
Polytree max score: 213
Polytree building time: 0.004 seconds.
Number of quartet trees in the gene trees: 213
Size of largest cluster: 10
Greedy score: 210
estimationFactor: 1.0142857142857142
Sub-optimal score: 210
Total Number of elements weighted: 32
Normalized score (portion of input quartet trees satisfied before correcting for multiple individuals): 0.9859154929577465
Optimization score: 210
Optimal tree inferred in 0.088 secs.
(taxa_1,((taxa_2,taxa_7),(taxa_9,(taxa_6,((taxa_5,taxa_4),(taxa_0,(taxa_3,taxa_8)))))));
Final quartet score is: 210
Final normalized quartet score is: 0.9859154929577465
You may want to ignore posterior probabilities and other statistics related to the following branch branch because the effective number of genes impacting it is only 1:
	{taxa_3, taxa_8}
You may want to ignore posterior probabilities and other statistics related to the following branch branch because the effective number of genes impacting it is only 1:
	{taxa_5, taxa_4}
You may want to ignore posterior probabilities and other statistics related to the following branch branch because the effective number of genes impacting it is only 1:
	{taxa_2, taxa_7}
You may want to ignore posterior probabilities and other statistics related to the following branch branch because the effective number of genes impacting it is only 1:
	{taxa_1, taxa_2, taxa_7}
You may want to ignore posterior probabilities and other statistics related to the following branch branch because the effective number of genes impacting it is only 1:
	{taxa_1, taxa_2, taxa_7, taxa_9}
You may want to ignore posterior probabilities and other statistics related to the following branch branch because the effective number of genes impacting it is only 1:
	{taxa_1, taxa_2, taxa_7, taxa_9, taxa_6}
You may want to ignore posterior probabilities and other statistics related to the following branch branch because the effective number of genes impacting it is only 1:
	{taxa_1, taxa_2, taxa_7, taxa_9, taxa_6, taxa_5, taxa_4}
(taxa_0,((taxa_3,taxa_8)0.67:0.2876820724517809,((taxa_5,taxa_4)0.67:0.2876820724517809,(taxa_6,(taxa_9,((taxa_2,taxa_7)0.67:0.2876820724517809,taxa_1)0.67:0.2876820724517809)0.67:0.2876820724517809)0.67:0.2876820724517809)0.67:0.2876820724517809));
Weight calculation took 7.95642E-4 secs
ASTRAL finished in 0.155 secs
