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6i.ASTRAL_PRO_species_tree_node_annotations.log
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6i.ASTRAL_PRO_species_tree_node_annotations.log
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================== ASTRAL-Pro =====================
This is ASTRAL-Pro (A-Pro) version 1.1.6
Using native AVX batch computing.
Gene trees are treated as unrooted
There are 48 threads used to run.
ti: 3
tx: 3
pw: 4
The number of input tree read is 10
194 trees read from 6f.ASTRAL_PRO_input_gene_trees.tre
22 extra trees.
All output trees will be *arbitrarily* rooted at S0306
======== Running the main analysis
Number of taxa: 10 (10 species)
Taxa: [S0306, S0896, S0741, S0895, S0435, S0509, S0728sl, S0285, S0941, S0946]
Taxon occupancy: {S0896=146, S0435=194, S0941=113, S0306=91, S0728sl=139, S0946=145, S0509=175, S0285=126, S0741=189, S0895=176}
Using polytree-based weight calculation.
Number of gene trees: 194
188 trees have missing taxa
Calculating distance matrix (for completion of X) ....with 4 distance matrices in parallel
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
------------------------------
Number of Clusters after addition by distance: 211
Adding to X using resolutions of greedy consensus ...
Computing greedy consensus took 0 seconds
Limit for sigma of degrees:300
polytomy size limit : > 4
[4]
discarded polytomies:
Threshold 0.0:
Threshold 0.01:
Threshold 0.02:
Threshold 0.05:
Threshold 0.1:
Threshold 0.2:
Threshold 0.3333333333333333:
polytomy of size 4; rounds with additions with at least 5 support: 0; clusters: 211
Number of Clusters after addition by greedy: 211
calculating extra bipartitions from extra input trees ...
Number of Clusters after additions from extra trees: 211
partitions formed in 4.445 secs
Dynamic Programming starting after 4.445 secs
Polytree max score: 1484
Polytree building time: 0.202 seconds.
Number of quartet trees in the gene trees: 1484
Computing hash values took 0 seconds
Size of largest cluster: 10
Total Number of elements: 372
Final optimization score: 0
Size of largest cluster: 10
373 0 372
Total Number of elements: 372
Normalized score (portion of input quartet trees satisfied before correcting for multiple individuals): 0.6475741239892183
Final optimization score: 961
Optimal tree inferred in 6.048 secs.
Weight calculation cumulatively took 0.019080014 secs
(S0306,(S0946,(S0895,(S0741,(S0285,(S0896,(S0728sl,(S0509,(S0435,S0941)))))))));
Final quartet score is: 961
Final normalized quartet score is: 0.6475741239892183
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 8:
{S0435, S0509, S0941}
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 7:
{S0435, S0509, S0728sl, S0941}
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 8:
{S0896, S0435, S0509, S0728sl, S0285, S0941}
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 7:
{S0435, S0941}
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 6:
{S0896, S0435, S0509, S0728sl, S0941}
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 9:
{S0896, S0741, S0435, S0509, S0728sl, S0285, S0941}
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 4:
{S0896, S0741, S0895, S0435, S0509, S0728sl, S0285, S0941}
(S0306,(S0946,(S0895,(S0741,(S0285,(S0896,(S0728sl,(S0509,(S0435,S0941)'[q1=0.4339622641509434;q2=0.22641509433962265;q3=0.339622641509434;f1=3.2857142857142856;f2=1.7142857142857142;f3=2.5714285714285716;pp1=0.4953134628138401;pp2=0.19683245377693492;pp3=0.307854083409225;QC=7;EN=7.571428571428571]':0.0779615414697118)'[q1=0.7395833333333334;q2=0.11458333333333333;q3=0.14583333333333334;f1=5.916666666666667;f2=0.9166666666666666;f3=1.1666666666666667;pp1=0.9645238581952132;pp2=0.01693555178624325;pp3=0.01854059001854352;QC=12;EN=8.0]':0.665748206371831)'[q1=0.4622641509433962;q2=0.29245283018867924;q3=0.2452830188679245;f1=3.2666666666666666;f2=2.066666666666667;f3=1.7333333333333334;pp1=0.5488687630120682;pp2=0.2451501875715018;pp3=0.20598104941643003;QC=15;EN=7.066666666666667]':0.11365931847252136)'[q1=0.5377358490566038;q2=0.330188679245283;q3=0.1320754716981132;f1=3.5625;f2=2.1875;f3=0.875;pp1=0.6601461864845882;pp2=0.22416602751263182;pp3=0.11568778600278008;QC=16;EN=6.625]':0.22416866672945499)'[q1=0.5166666666666667;q2=0.3;q3=0.18333333333333332;f1=4.133333333333334;f2=2.4;f3=1.4666666666666666;pp1=0.669914822094028;pp2=0.2000497049421838;pp3=0.13003547296378834;QC=15;EN=8.0]':0.20935022918187393)'[q1=0.47706422018348627;q2=0.19266055045871563;q3=0.3302752293577982;f1=4.333333333333333;f2=1.75;f3=3.0;pp1=0.604187786348127;pp2=0.14347132665722248;pp3=0.25234088699465024;QC=12;EN=9.083333333333332]':0.1562189328913174)'[q1=1.0;q2=0.0;q3=0.0;f1=4.285714285714286;f2=0.0;f3=0.0;pp1=0.9880811681950253;pp2=0.00595941590248734;pp3=0.00595941590248734;QC=7;EN=4.285714285714286]':1.259542655480747));
ASTRAL-Pro finished in 7.657 secs