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"planemo upload for repository https://github.com/smirarab/ASTRAL commit 0f93f327c49e93d6af057973d68ba772ba5715dc-dirty"
author padge
date Wed, 13 Apr 2022 15:03:31 +0000
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-1:000000000000 0:66ebc4b19d6c
1
2 ================== ASTRAL =====================
3
4 This is ASTRAL version 5.7.8
5 Gene trees are treated as unrooted
6 424 trees read from test-data/song_mammals.424.gene.tre
7 index0
8 All output trees will be *arbitrarily* rooted at Chicken
9
10 ======== Running the main analysis
11 Number of taxa: 37 (37 species)
12 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]
13 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}
14 Number of gene trees: 424
15 0 trees have missing taxa
16 Calculating quartet distance matrix (for completion of X)
17 Species tree distances calculated ...
18 Building set of clusters (X) from gene trees
19 ------------------------------
20 gradient0: 1933
21 Number of Clusters after addition by distance: 1933
22 calculating extra bipartitions to be added at level 1 ...
23 Adding to X using resolutions of greedy consensus ...
24 Limit for sigma of degrees:975
25 polytomy size limit : 4
26 discarded polytomies: [3, 3, 4, 4]
27 Threshold 0.0:
28 Threshold 0.01:
29 Threshold 0.02:
30 Threshold 0.05:
31 Threshold 0.1:
32 Threshold 0.2:
33 polytomy of size 4; rounds with additions with at least 5 support: 0; clusters: 1933
34 Threshold 0.3333333333333333:
35 polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 1933
36 polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 1933
37 polytomy of size 4; rounds with additions with at least 5 support: 0; clusters: 1933
38 max k is :0
39 Number of Clusters after addition by greedy: 1933
40 gradient0 in heuristiic: 1933
41 partitions formed in 0.638 secs
42 Dynamic Programming starting after 0.638 secs
43 Using tree-based weight calculation.
44 Using polytree-based weight calculation.
45 Polytree max score: 28003080
46 Polytree building time: 0.191 seconds.
47 Number of quartet trees in the gene trees: 28003080
48 Size of largest cluster: 37
49 Greedy score: 24862814
50 estimationFactor: 1.1263037241078182
51 Sub-optimal score: 25489533
52 Total Number of elements weighted: 3372
53 Normalized score (portion of input quartet trees satisfied before correcting for multiple individuals): 0.9115752624354179
54 Optimization score: 25526915
55 Optimal tree inferred in 1.287 secs.
56 (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))))))))))))))));
57 Final quartet score is: 25526915
58 Final normalized quartet score is: 0.9115752624354179
59 Extended species tree:
60 (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;
61 Weight calculation took 0.332760708 secs
62 ASTRAL finished in 1.713 secs