/home/pierrebc/Documents/julia/dev/TreeKnit/src/cli.jl:64 [Info] Input Newick files: tree_h3n2_ha.nwk 	 tree_h3n2_na.nwk. Reading trees...
/home/pierrebc/Documents/julia/dev/TreeKnit/src/cli.jl:93 [Info] Parameters: OptArgs
  γ: Float64 2.0
  itmax: Int64 15
  likelihood_sort: Bool true
  resolve: Bool true
  seq_lengths: Array{Int64}((2,)) [1, 1]
  nMCMC: Int64 25
  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, 0.05807931748207713, 0.05636521970408557, 0.05470171017884718, 0.053087295892748944, 0.05152052789556264, 0.05000000000000002]
  sa_rep: Int64 1
  verbose: Bool true
  vv: Bool false

/home/pierrebc/Documents/julia/dev/TreeKnit/src/cli.jl:95 [Info] Inferring MCCs...

/home/pierrebc/Documents/julia/dev/TreeKnit/src/main.jl:75 [Info] Initial state: 41 naive MCCs
/home/pierrebc/Documents/julia/dev/TreeKnit/src/main.jl:82 [Info] --- Iteration 1 (max. 15) - 100 leaves remaining ---

/home/pierrebc/Documents/julia/dev/TreeKnit/src/main.jl:85 [Info] Running optimization to find MCCs...
/home/pierrebc/Documents/julia/dev/TreeKnit/src/main.jl:86 [Info] Cooling schedule: geometric / Temperature values: 101 / Total of MCMC steps: 2500
/home/pierrebc/Documents/julia/dev/TreeKnit/src/SplitGraph/SplitGraph.jl:70 [Info] Sorting 2 topologically equivalent configurations.
/home/pierrebc/Documents/julia/dev/TreeKnit/src/SplitGraph/SplitGraph.jl:101 [Info] Comparing 2 configurations using likelihood
/home/pierrebc/Documents/julia/dev/TreeKnit/src/main.jl:95 [Info] Found 9 new mccs.
/home/pierrebc/Documents/julia/dev/TreeKnit/src/main.jl:99 [Info] Proceeding based on newly found MCCs...
/home/pierrebc/Documents/julia/dev/TreeKnit/src/main.jl:152 [Info] Found mccs do not cover all leaves. Pruning them from trees.
/home/pierrebc/Documents/julia/dev/TreeKnit/src/main.jl:174 [Info] Resulting trees have incompatibilities (14 naive mccs left). Continuing.


/home/pierrebc/Documents/julia/dev/TreeKnit/src/main.jl:82 [Info] --- Iteration 2 (max. 15) - 73 leaves remaining ---

/home/pierrebc/Documents/julia/dev/TreeKnit/src/main.jl:85 [Info] Running optimization to find MCCs...
/home/pierrebc/Documents/julia/dev/TreeKnit/src/main.jl:86 [Info] Cooling schedule: geometric / Temperature values: 101 / Total of MCMC steps: 1825
/home/pierrebc/Documents/julia/dev/TreeKnit/src/SplitGraph/SplitGraph.jl:70 [Info] Sorting 3 topologically equivalent configurations.
/home/pierrebc/Documents/julia/dev/TreeKnit/src/SplitGraph/SplitGraph.jl:101 [Info] Comparing 2 configurations using likelihood
/home/pierrebc/Documents/julia/dev/TreeKnit/src/main.jl:95 [Info] Found 1 new mccs.
/home/pierrebc/Documents/julia/dev/TreeKnit/src/main.jl:99 [Info] Proceeding based on newly found MCCs...
/home/pierrebc/Documents/julia/dev/TreeKnit/src/main.jl:152 [Info] Found mccs do not cover all leaves. Pruning them from trees.
/home/pierrebc/Documents/julia/dev/TreeKnit/src/main.jl:174 [Info] Resulting trees have incompatibilities (13 naive mccs left). Continuing.


/home/pierrebc/Documents/julia/dev/TreeKnit/src/main.jl:82 [Info] --- Iteration 3 (max. 15) - 72 leaves remaining ---

/home/pierrebc/Documents/julia/dev/TreeKnit/src/main.jl:85 [Info] Running optimization to find MCCs...
/home/pierrebc/Documents/julia/dev/TreeKnit/src/main.jl:86 [Info] Cooling schedule: geometric / Temperature values: 101 / Total of MCMC steps: 1800
/home/pierrebc/Documents/julia/dev/TreeKnit/src/SplitGraph/SplitGraph.jl:70 [Info] Sorting 2 topologically equivalent configurations.
/home/pierrebc/Documents/julia/dev/TreeKnit/src/main.jl:95 [Info] Found 2 new mccs.
/home/pierrebc/Documents/julia/dev/TreeKnit/src/main.jl:99 [Info] Proceeding based on newly found MCCs...
/home/pierrebc/Documents/julia/dev/TreeKnit/src/main.jl:152 [Info] Found mccs do not cover all leaves. Pruning them from trees.
/home/pierrebc/Documents/julia/dev/TreeKnit/src/main.jl:174 [Info] Resulting trees have incompatibilities (10 naive mccs left). Continuing.


/home/pierrebc/Documents/julia/dev/TreeKnit/src/main.jl:82 [Info] --- Iteration 4 (max. 15) - 67 leaves remaining ---

/home/pierrebc/Documents/julia/dev/TreeKnit/src/main.jl:85 [Info] Running optimization to find MCCs...
/home/pierrebc/Documents/julia/dev/TreeKnit/src/main.jl:86 [Info] Cooling schedule: geometric / Temperature values: 101 / Total of MCMC steps: 1675
/home/pierrebc/Documents/julia/dev/TreeKnit/src/main.jl:95 [Info] Found 3 new mccs.
/home/pierrebc/Documents/julia/dev/TreeKnit/src/main.jl:99 [Info] Proceeding based on newly found MCCs...
/home/pierrebc/Documents/julia/dev/TreeKnit/src/main.jl:152 [Info] Found mccs do not cover all leaves. Pruning them from trees.
/home/pierrebc/Documents/julia/dev/TreeKnit/src/main.jl:163 [Info] Resulting trees are compatible: final decomposition found. Stopping.

/home/pierrebc/Documents/julia/dev/TreeKnit/src/cli.jl:98 [Info] Found 16 MCCs (runtime 4.046723909)

/home/pierrebc/Documents/julia/dev/TreeKnit/src/cli.jl:102 [Info] Resolving trees based on found MCCs...
/home/pierrebc/Documents/julia/dev/TreeKnit/src/cli.jl:106 [Info] Resolved 13 splits in tree_h3n2_ha.nwk and 13 splits in tree_h3n2_na.nwk

/home/pierrebc/Documents/julia/dev/TreeKnit/src/cli.jl:110 [Info] Building ARG from trees and MCCs...
/home/pierrebc/Documents/julia/dev/TreeKnit/src/cli.jl:112 [Info] Found 15 reassortments in the ARG.

/home/pierrebc/Documents/julia/dev/TreeKnit/src/cli.jl:117 [Info] Writing results in treeknit_results
