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PhyNEST_sa.log
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PhyNEST: Phylogenetic Network Estimation using SiTe patterns
Analysis start: 2024-06-02 at 20:03:58
Input file: example/sample_n5h1.txt
Number of sequences: 5
Sequence length: 1000000
Starting Topology: (5,(2,(3,(4,1))));
Outgroup specified for rooting: 5
Number of maximum reticulation(s): 1
The maximum number of iterations for each optimization: 1000
Search algorithm selected: Simulated annealing with alpha=0.5; c=0.5
The maximum number of steps during search: 250000
The maximum number of consecutive failures: 50 (computed using probN=9.5e-45 provided.)
Output file store directory: /Users/khaosan/Dropbox/PhyNESTp.jl
The number of processors for this analysis: 1
(1/2) Searching for the best network using the simulated annealing algorithm; 2024-06-02 at 20:03:59
Starting topology remains unchanged
Running 25 burn-ins...
Burn in complete. At most -log likelihood value can change 253831.89630290028 at a single step.
Showing 10 best topologies found in this run:
Rank Composite Likelihood Network
1 4.74134463406e6 (5:9.873,(4:4.979,((3:1.57,(2:1.43)#H6:0.14::0.525):1.427,(1:1.43,#H6:0.0::0.475):1.567):1.981):4.894);
2 4.74134463406e6 (5:9.873,(4:4.979,((3:1.57,(2:1.43)#H6:0.14::0.525):1.427,(#H6:0.0::0.475,1:1.43):1.567):1.981):4.894);
3 4.74134463406e6 (5:9.873,(4:4.979,((3:1.57,(2:1.43)#H6:0.14::0.525):1.427,(1:1.43,#H6:0.0::0.475):1.567):1.981):4.894);
4 4.74135224735e6 (5:10.27,(4:5.197,((3:2.358,(2:0.38,#H6:0.0::0.62):1.978):1.273,(1:0.38)#H6:3.25::0.38):1.566):5.073);
The total length of best trees is shorter than k.
Speciation times for some newicks may not have updated if estimates are weird (e.g., NaN).
The search terminated at step 585 and at 50th consecutive failures and (Cooling schedule)ci=2154.7764941621217.
Summary of each move:
Insertion of reticulation edge: 2 proposed, 1 accepted.
Tail move of reticulation edge: 165 proposed, 106 accepted.
Head move of reticulation edge: 133 proposed, 44 accepted.
Change the direction of reticulation edge: 122 proposed, 37 accepted.
Deletion of reticulation edge: 0 proposed, 0 accepted.
Nearest-neighbor interchange (NNI): 163 proposed, 9 accepted.
On the current topology, 68 moves were made, including 18 unsuccessful moves.
Terminated because it reached the maximum number of failures (current maximum_number_of_failures=50).
(1/2) Estimated topology in this run: (5:9.873,(4:4.979,((3:1.57,(2:1.43)#H6:0.14::0.525):1.427,(1:1.43,#H6:0.0::0.475):1.567):1.981):4.894);
(1/2) Composite likelihood of the estimated topology in this run: 4.741344634057322e6
(2/2) Searching for the best network using the simulated annealing algorithm; 2024-06-02 at 20:05:13
Starting topology remains unchanged
Running 25 burn-ins...
Burn in complete. At most -log likelihood value can change 276213.0673120329 at a single step.
Showing 10 best topologies found in this run:
Rank Composite Likelihood Network
1 4.74134463406e6 (5:9.873,(4:4.979,((1:1.43,(2:1.43)#H6:0.0::0.475):1.567,(3:1.57,#H6:0.14::0.525):1.427):1.981):4.894);
2 4.74134463406e6 (5:9.873,(((1:1.43,(2:1.43)#H6:0.0::0.475):1.567,(#H6:0.14::0.525,3:1.57):1.427):1.981,4:4.979):4.894);
3 4.74134463406e6 (5:9.873,(4:4.979,((3:1.57,(2:1.43)#H6:0.14::0.525):1.427,(1:1.43,#H6:0.0::0.475):1.567):1.981):4.894);
4 4.74134463406e6 (5:9.873,(4:4.979,((1:1.43,#H6:0.0::0.525):1.567,((2:1.43)#H6:0.14::0.475,3:1.57):1.427):1.981):4.894);
5 4.74134463406e6 (5:9.873,(4:4.979,((#H6:0.0::0.525,1:1.43):1.567,((2:1.43)#H6:0.14::0.475,3:1.57):1.427):1.981):4.894);
6 4.74134463406e6 (5:9.873,(4:4.979,((3:1.57,(2:1.43)#H6:0.14::0.525):1.427,(#H6:0.0::0.475,1:1.43):1.567):1.981):4.894);
The total length of best trees is shorter than k.
Speciation times for some newicks may not have updated if estimates are weird (e.g., NaN).
The search terminated at step 910 and at 50th consecutive failures and (Cooling schedule)ci=1512.6720311686329.
Summary of each move:
Insertion of reticulation edge: 1 proposed, 1 accepted.
Tail move of reticulation edge: 251 proposed, 131 accepted.
Head move of reticulation edge: 228 proposed, 69 accepted.
Change the direction of reticulation edge: 216 proposed, 95 accepted.
Deletion of reticulation edge: 0 proposed, 0 accepted.
Nearest-neighbor interchange (NNI): 214 proposed, 14 accepted.
On the current topology, 66 moves were made, including 16 unsuccessful moves.
Terminated because it reached the maximum number of failures (current maximum_number_of_failures=50).
(2/2) Estimated topology in this run: (5:9.873,(4:4.979,((1:1.43,#H6:0.0::0.475):1.567,(3:1.57,(2:1.43)#H6:0.14::0.525):1.427):1.981):4.894);
(2/2) Composite likelihood of the estimated topology in this run: 4.741344634057322e6
Summary:
Run Composite likelihood Network estimated
1 4.7413446e6 (5:9.873,(4:4.979,((3:1.57,(2:1.43)#H6:0.14::0.525):1.427,(1:1.43,#H6:0.0::0.475):1.567):1.981):4.894);
2 4.7413446e6 (5:9.873,(4:4.979,((1:1.43,#H6:0.0::0.475):1.567,(3:1.57,(2:1.43)#H6:0.14::0.525):1.427):1.981):4.894);
Best topology: (5:9.873,(4:4.979,((3:1.57,(2:1.43)#H6:0.14::0.525):1.427,(1:1.43,#H6:0.0::0.475):1.567):1.981):4.894);)
End;