--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out.log	Wed Apr 13 15:03:31 2022 +0000
@@ -0,0 +1,62 @@
+
+================== ASTRAL ===================== 
+
+This is ASTRAL version 5.7.8
+Gene trees are treated as unrooted
+424 trees read from test-data/song_mammals.424.gene.tre
+index0
+All output trees will be *arbitrarily* rooted at Chicken
+
+======== Running the main analysis
+Number of taxa: 37 (37 species)
+Taxa: [Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby]
+Taxon occupancy: {Rat=424, Tarsier=424, Dolphin=424, Rabbit=424, Macaque=424, Pika=424, Alpaca=424, Shrew=424, Sloth=424, Tree_Shrew=424, Kangaroo_Rat=424, Armadillos=424, Chimpanzee=424, Horse=424, Dog=424, Human=424, Lesser_Hedgehog_Tenrec=424, Microbat=424, Platypus=424, Wallaby=424, Cow=424, Pig=424, Marmoset=424, Megabat=424, Hedgehog=424, Mouse=424, Guinea_Pig=424, Mouse_Lemur=424, Cat=424, Hyrax=424, Elephant=424, Chicken=424, Orangutan=424, Opossum=424, Galagos=424, Squirrel=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: 1933
+Number of Clusters after addition by distance: 1933
+calculating extra bipartitions to be added at level 1 ...
+Adding to X using resolutions of greedy consensus ...
+Limit for sigma of degrees:975
+polytomy size limit : 4
+discarded polytomies:  [3, 3, 4, 4]
+Threshold 0.0:
+Threshold 0.01:
+Threshold 0.02:
+Threshold 0.05:
+Threshold 0.1:
+Threshold 0.2:
+polytomy of size 4; rounds with additions with at least 5 support: 0; clusters: 1933
+Threshold 0.3333333333333333:
+polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 1933
+polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 1933
+polytomy of size 4; rounds with additions with at least 5 support: 0; clusters: 1933
+max k is :0
+Number of Clusters after addition by greedy: 1933
+gradient0 in heuristiic: 1933
+partitions formed in 0.638 secs
+Dynamic Programming starting after 0.638 secs
+Using tree-based weight calculation.
+Using polytree-based weight calculation.
+Polytree max score: 28003080
+Polytree building time: 0.191 seconds.
+Number of quartet trees in the gene trees: 28003080
+Size of largest cluster: 37
+Greedy score: 24862814
+estimationFactor: 1.1263037241078182
+Sub-optimal score: 25489533
+Total Number of elements weighted: 3372
+Normalized score (portion of input quartet trees satisfied before correcting for multiple individuals): 0.9115752624354179
+Optimization score: 25526915
+Optimal tree inferred in 1.287 secs.
+(Chimpanzee,(Human,(Gorilla,(Orangutan,(Macaque,(Marmoset,(Tarsier,((Galagos,Mouse_Lemur),((Tree_Shrew,((Rabbit,Pika),(Squirrel,(Guinea_Pig,(Kangaroo_Rat,(Mouse,Rat)))))),((((Chicken,Platypus),(Opossum,Wallaby)),((Sloth,Armadillos),(Lesser_Hedgehog_Tenrec,(Hyrax,Elephant)))),((Shrew,Hedgehog),((Microbat,Megabat),((Horse,(Dog,Cat)),(Alpaca,(Pig,(Dolphin,Cow))))))))))))))));
+Final quartet score is: 25526915
+Final normalized quartet score is: 0.9115752624354179
+Extended species tree:
+(Chicken,(Platypus,((Opossum,Wallaby)N0'[pp1=1;pp2=0;pp3=0]':4.04422017503953,(((Sloth,Armadillos)N1'[pp1=1;pp2=0;pp3=0]':3.748755962145693,(Lesser_Hedgehog_Tenrec,(Hyrax,Elephant)N2'[pp1=1;pp2=0;pp3=0]':1.4675747778148045)N3'[pp1=1;pp2=0;pp3=0]':2.8408725661075143)N4'[pp1=1;pp2=0;pp3=0]':0.11272139311072937,(((Shrew,Hedgehog)N5'[pp1=1;pp2=0;pp3=0]':0.9911063406548961,((Microbat,Megabat)N6'[pp1=1;pp2=0;pp3=0]':1.5111714492447694,((Horse,(Dog,Cat)N7'[pp1=1;pp2=0;pp3=0]':2.7358873553893504)N8'[pp1=0.89;pp2=0.06;pp3=0.05]':0.05992302074136598,(Alpaca,(Pig,(Dolphin,Cow)N9'[pp1=1;pp2=0;pp3=0]':1.3217644299037643)N10'[pp1=1;pp2=0;pp3=0]':0.6263941421637529)N11'[pp1=1;pp2=0;pp3=0]':3.259811403201244)N12'[pp1=1;pp2=0;pp3=0]':0.11044150209434113)N13'[pp1=1;pp2=0;pp3=0]':0.42171242314482726)N14'[pp1=1;pp2=0;pp3=0]':1.9051712317138048,((Tree_Shrew,((Rabbit,Pika)N15'[pp1=1;pp2=0;pp3=0]':3.168751437685628,(Squirrel,(Guinea_Pig,(Kangaroo_Rat,(Mouse,Rat)N16'[pp1=1;pp2=0;pp3=0]':4.080152184265601)N17'[pp1=1;pp2=0;pp3=0]':0.6030253811559223)N18'[pp1=1;pp2=0;pp3=0]':0.14397458523452245)N19'[pp1=1;pp2=0;pp3=0]':1.61126493088363)N20'[pp1=1;pp2=0;pp3=0]':0.8259790342993206)N21'[pp1=0.9;pp2=0.01;pp3=0.1]':0.08166400531937129,((Galagos,Mouse_Lemur)N22'[pp1=1;pp2=0;pp3=0]':2.3122034886710434,(Tarsier,(Marmoset,(Macaque,(Orangutan,(Gorilla,(Human,Chimpanzee)N23'[pp1=1;pp2=0;pp3=0]':0.6305518601232605)N24'[pp1=1;pp2=0;pp3=0]':2.2394148609781763)N25'[pp1=1;pp2=0;pp3=0]':2.457113083090445)N26'[pp1=1;pp2=0;pp3=0]':2.550229319109434)N27'[pp1=1;pp2=0;pp3=0]':3.756538102587758)N28'[pp1=1;pp2=0;pp3=0]':0.6381142252128742)N29'[pp1=1;pp2=0;pp3=0]':2.0440320320838024)N30'[pp1=1;pp2=0;pp3=0]':2.239479484018153)N31'[pp1=1;pp2=0;pp3=0]':1.5208686854769229)N32'[pp1=1;pp2=0;pp3=0]':3.0967076693654274)N33'[pp1=1;pp2=0;pp3=0]':0.9068831258917384)N34)N35;
+Weight calculation took 0.332760708 secs
+ASTRAL finished in 1.713 secs