TreeKnit/TreeKnit.jl/src/cli.jl:76 [Info] [15:24] - Treeknit: 
TreeKnit/TreeKnit.jl/src/cli.jl:77 [Info] [15:24] - Input trees: examples/tree_h3n2_ha.nwk  examples/tree_h3n2_na.nwk  
TreeKnit/TreeKnit.jl/src/cli.jl:78 [Info] [15:24] - Results directory: treeknit_results
TreeKnit/TreeKnit.jl/src/cli.jl:79 [Info] [15:24] - γ: 2
TreeKnit/TreeKnit.jl/src/cli.jl:82 [LogLevel(-1)] [15:24] - Reading trees...
TreeKnit/TreeKnit.jl/src/cli.jl:218 [Info] [15:24] - 
TreeKnit/TreeKnit.jl/src/cli.jl:219 [Info] [15:24] - Setting up parameters of the TreeKnit run
TreeKnit/TreeKnit.jl/src/cli.jl:235 [Info] [15:24] - Using the `--better-MCCs` method by default for 2 trees
TreeKnit/TreeKnit.jl/src/cli.jl:257 [Info] [15:24] - .. Will perform 1 rounds of TreeKnit
TreeKnit/TreeKnit.jl/src/cli.jl:258 [Info] [15:24] - .. Will preresolve all trees before MCC inference
TreeKnit/TreeKnit.jl/src/cli.jl:260 [Info] [15:24] - .. Will resolve trees during MCC inference (change with `--no-resolve`)
TreeKnit/TreeKnit.jl/src/cli.jl:262 [Info] [15:24] - .. Will Only resolve unambiguous splits (change with `--liberal-resolve`)
TreeKnit/TreeKnit.jl/src/cli.jl:135 [LogLevel(-1)] [15:24] - Parameters: OptArgs
  γ: Int64 2
  itmax: Int64 15
  likelihood_sort: Bool true
  resolve: Bool true
  strict: Bool true
  seq_lengths: Array{Int64}((2,)) [1, 1]
  pre_resolve: Bool true
  rounds: Int64 1
  final_no_resolve: Bool false
  parallel: Bool false
  nMCMC: Int64 50
  sa_rep: Int64 1
  Tmin: Float64 0.05
  Tmax: Float64 1.0
  nT: Int64 100
  cooling_schedule: Symbol geometric
  Trange: Array{Float64}((101,)) [1.0, 0.9704869503929601, 0.9418449208830277, 0.9140482050108684, 0.8870718549931568, 0.8608916593317348, 0.8354841210835904, 0.8108264367721563, 0.7868964759210002, 0.7636727611915388  …  0.06547306980281228, 0.0635407598457967, 0.061665478248398686, 0.059845541929811855, 0.058079317482077134, 0.05636521970408557, 0.05470171017884719, 0.053087295892748944, 0.05152052789556264, 0.05000000000000002]



TreeKnit/TreeKnit.jl/src/cli.jl:138 [Info] [15:24] - Inferring MCCs...

TreeKnit/TreeKnit.jl/src/main.jl:29 [LogLevel(-1)] [15:24] - ROUND: 1


TreeKnit/TreeKnit.jl/src/main.jl:39 [LogLevel(-1)] [15:24] - Infering MCCs for trees: tree_h3n2_na and tree_h3n2_ha


TreeKnit/TreeKnit.jl/src/main.jl:189 [LogLevel(-1)] [15:24] - Initial state: 41 naive MCCs
TreeKnit/TreeKnit.jl/src/main.jl:194 [LogLevel(-1)] [15:24] - --- Iteration 1 (max. 15) - 100 leaves remaining ---

TreeKnit/TreeKnit.jl/src/main.jl:197 [LogLevel(-1)] [15:24] - Running optimization to find MCCs...
TreeKnit/TreeKnit.jl/src/main.jl:198 [LogLevel(-1)] [15:24] - Cooling schedule: geometric / Temperature values: 101 / Total of MCMC steps: 5000
TreeKnit/TreeKnit.jl/src/SplitGraph/SplitGraph.jl:56 [LogLevel(-1)] [15:24] - Sorting 4 topologically equivalent configurations.
TreeKnit/TreeKnit.jl/src/main.jl:212 [LogLevel(-1)] [15:24] - Found 10 new mccs.
TreeKnit/TreeKnit.jl/src/main.jl:216 [LogLevel(-1)] [15:24] - Proceeding based on newly found MCCs...
TreeKnit/TreeKnit.jl/src/main.jl:267 [LogLevel(-1)] [15:24] - Found mccs do not cover all leaves. Pruning them from trees.
TreeKnit/TreeKnit.jl/src/main.jl:286 [LogLevel(-1)] [15:24] - Resulting trees have incompatibilities (11 naive mccs left). Continuing.


TreeKnit/TreeKnit.jl/src/main.jl:194 [LogLevel(-1)] [15:24] - --- Iteration 2 (max. 15) - 70 leaves remaining ---

TreeKnit/TreeKnit.jl/src/main.jl:197 [LogLevel(-1)] [15:24] - Running optimization to find MCCs...
TreeKnit/TreeKnit.jl/src/main.jl:198 [LogLevel(-1)] [15:24] - Cooling schedule: geometric / Temperature values: 101 / Total of MCMC steps: 3500
TreeKnit/TreeKnit.jl/src/SplitGraph/SplitGraph.jl:56 [LogLevel(-1)] [15:24] - Sorting 3 topologically equivalent configurations.
TreeKnit/TreeKnit.jl/src/main.jl:212 [LogLevel(-1)] [15:24] - Found 4 new mccs.
TreeKnit/TreeKnit.jl/src/main.jl:216 [LogLevel(-1)] [15:24] - Proceeding based on newly found MCCs...
TreeKnit/TreeKnit.jl/src/main.jl:267 [LogLevel(-1)] [15:24] - Found mccs do not cover all leaves. Pruning them from trees.
TreeKnit/TreeKnit.jl/src/main.jl:277 [LogLevel(-1)] [15:24] - Resulting trees are compatible: final decomposition found. Stopping.

TreeKnit/TreeKnit.jl/src/main.jl:46 [LogLevel(-1)] [15:24] - found MCCs for trees: tree_h3n2_na and tree_h3n2_ha
TreeKnit/TreeKnit.jl/src/main.jl:50 [LogLevel(-1)] [15:24] - ladderized and sorted trees: tree_h3n2_na and tree_h3n2_ha
TreeKnit/TreeKnit.jl/src/cli.jl:144 [Info] [15:24] - Found [15] MCCs (runtime 9.053259659)

TreeKnit/TreeKnit.jl/src/cli.jl:147 [Info] [15:24] - Writing results in treeknit_results
TreeKnit/TreeKnit.jl/src/cli.jl:165 [LogLevel(-1)] [15:24] - Building ARG from trees and MCCs...
TreeKnit/TreeKnit.jl/src/cli.jl:167 [LogLevel(-1)] [15:24] - Found 14 reassortments in the ARG.

