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| 29.20 -TreeTime._set_branch_length_mode: maximum branch length is 3.648e-05, | ||
| using branch length mode joint | ||
| 2.60 -TreeTime._set_branch_length_mode: maximum branch length is 3.648e-05, | ||
| using branch length mode joint | ||
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| 2.60 -TreeAnc.optimize_tree: sequences... | ||
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| 2.60 -TreeAnc.infer_ancestral_sequences with method: probabilistic, joint | ||
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| 2.60 WARNING: Previous versions of TreeTime (<0.7.0) RECONSTRUCTED sequences of | ||
| tips at positions with AMBIGUOUS bases. This resulted in unexpected | ||
| behavior is some cases and is no longer done by default. If you want to | ||
| replace those ambiguous sites with their most likely state, rerun with | ||
| `reconstruct_tip_states=True` or `--reconstruct-tip-states`. | ||
| 2.60 --TreeAnc._ml_anc_joint: type of reconstruction: Joint | ||
| 2.60 ---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods... | ||
| 5.79 ---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum | ||
| likelihood sequences... | ||
| 5.89 ---TreeAnc._ml_anc_joint: ...done | ||
| 5.89 --TreeAnc.infer_gtr: counting mutations... | ||
| 6.68 ---TreeAnc.infer_gtr: counting mutations...done | ||
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| 6.68 -GTR: with alphabet: ['A', 'C', 'G', 'T', '-'] | ||
| 6.68 --GTR: ambiguous character: N | ||
| 6.68 ---GTR: init with dummy values! | ||
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| 6.68 -GTR: model inference | ||
| 6.68 ---GTR inference iteration 0 change: 0.447213595499958 | ||
| 6.68 ---GTR inference iteration 1 change: 0.24246874204285596 | ||
| 6.68 ---GTR inference iteration 2 change: 0.0005098535209121346 | ||
| 6.68 ---GTR inference iteration 3 change: 5.105020464037095e-05 | ||
| 6.68 ---GTR inference iteration 4 change: 4.235336051547948e-05 | ||
| 6.68 --The model allows for gaps which are estimated to occur at a low fraction | ||
| of 5.321e-04 this can potentially result in artificats. gap fraction will | ||
| be set to 0.0100 | ||
| 6.68 --TreeAnc.infer_gtr: setting overall rate to 1.0... | ||
| 6.68 --TreeAnc._ml_anc_joint: type of reconstruction: Joint | ||
| 6.68 ---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods... | ||
| 9.78 ---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum | ||
| likelihood sequences... | ||
| 9.91 ---TreeAnc._ml_anc_joint: ...done | ||
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| 9.92 -TreeAnc.optimize_branch_length: running branch length optimization using | ||
| jointML ancestral sequences | ||
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| 12.44 -TreeAnc.prune_short_branches: pruning short branches (max prob at | ||
| zero)... | ||
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| 12.60 -TreeAnc.infer_ancestral_sequences with method: probabilistic, joint | ||
| 12.60 --TreeAnc._ml_anc_joint: type of reconstruction: Joint | ||
| 12.60 ---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods... | ||
| 15.43 ---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum | ||
| likelihood sequences... | ||
| 15.50 ---TreeAnc._ml_anc_joint: ...done | ||
| 15.51 --TreeAnc.optimize_tree: Iteration 1. #Nuc changed since prev | ||
| reconstructions: 88 | ||
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| 15.51 -TreeAnc.optimize_branch_length: running branch length optimization using | ||
| jointML ancestral sequences | ||
| 17.97 --TreeAnc.optimize_tree: Unconstrained sequence LH:-6571129.399010 | ||
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| 29.20 -TreeAnc.optimize_tree: sequences... | ||
| 17.98 -TreeAnc.optimize_tree: sequences... | ||
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| 17.98 -TreeAnc.infer_ancestral_sequences with method: probabilistic, joint | ||
| 17.98 --TreeAnc._ml_anc_joint: type of reconstruction: Joint | ||
| 17.98 ---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods... | ||
| 21.71 ---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum | ||
| likelihood sequences... | ||
| 21.81 ---TreeAnc._ml_anc_joint: ...done | ||
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| 29.20 -TreeAnc.infer_ancestral_sequences with method: probabilistic, joint | ||
| 21.82 -TreeAnc.optimize_branch_length: running branch length optimization using | ||
| jointML ancestral sequences | ||
|
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| 29.20 WARNING: Previous versions of TreeTime (<0.7.0) RECONSTRUCTED sequences of | ||
| tips at positions with AMBIGUOUS bases. This resulted in unexpected | ||
| behavior is some cases and is no longer done by default. If you want to | ||
| replace those ambiguous sites with their most likely state, rerun with | ||
| `reconstruct_tip_states=True` or `--reconstruct-tip-states`. | ||
| 29.20 --TreeAnc._ml_anc_joint: type of reconstruction: Joint | ||
| 29.20 ---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods... | ||
| 63.89 ---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum | ||
| 24.45 -TreeAnc.infer_ancestral_sequences with method: probabilistic, joint | ||
| 24.45 --TreeAnc._ml_anc_joint: type of reconstruction: Joint | ||
| 24.45 ---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods... | ||
| 27.28 ---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum | ||
| likelihood sequences... | ||
| 64.79 ---TreeAnc._ml_anc_joint: ...done | ||
| 64.89 --TreeAnc.infer_gtr: counting mutations... | ||
| 75.40 ---TreeAnc.infer_gtr: counting mutations...done | ||
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| 75.40 -GTR: with alphabet: ['A', 'C', 'G', 'T', '-'] | ||
| 75.40 --GTR: ambiguous character: N | ||
| 75.40 ---GTR: init with dummy values! | ||
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| 75.40 -GTR: model inference | ||
| 75.40 ---GTR inference iteration 0 change: 0.447213595499958 | ||
| 75.40 ---GTR inference iteration 1 change: 0.24246907925186573 | ||
| 75.40 ---GTR inference iteration 2 change: 0.000509782157875719 | ||
| 75.40 ---GTR inference iteration 3 change: 5.105228329868478e-05 | ||
| 75.40 ---GTR inference iteration 4 change: 4.234818529391279e-05 | ||
| 75.40 --The model allows for gaps which are estimated to occur at a low fraction | ||
| of 5.320e-04 this can potentially result in artificats. gap fraction | ||
| will be set to 0.0100 | ||
| 75.40 --TreeAnc.infer_gtr: setting overall rate to 1.0... | ||
| 75.40 --TreeAnc._ml_anc_joint: type of reconstruction: Joint | ||
| 75.40 ---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods... | ||
| 110.30 ---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum | ||
| likelihood sequences... | ||
| 111.40 ---TreeAnc._ml_anc_joint: ...done | ||
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| 111.50 -TreeAnc.optimize_branch_length: running branch length optimization using | ||
| jointML ancestral sequences | ||
|
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| 138.60 -TreeAnc.prune_short_branches: pruning short branches (max prob at | ||
| zero)... | ||
|
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| 140.39 -TreeAnc.infer_ancestral_sequences with method: probabilistic, joint | ||
| 140.39 --TreeAnc._ml_anc_joint: type of reconstruction: Joint | ||
| 140.39 ---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods... | ||
| 169.30 ---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum | ||
| likelihood sequences... | ||
| 169.99 ---TreeAnc._ml_anc_joint: ...done | ||
| 170.00 --TreeAnc.optimize_tree: Iteration 1. #Nuc changed since prev | ||
| reconstructions: 87 | ||
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| 170.00 -TreeAnc.optimize_branch_length: running branch length optimization using | ||
| jointML ancestral sequences | ||
| 192.49 --TreeAnc.optimize_tree: Unconstrained sequence LH:-6571129.681030 | ||
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| 192.50 -TreeAnc.optimize_tree: sequences... | ||
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| 192.50 -TreeAnc.infer_ancestral_sequences with method: probabilistic, joint | ||
| 192.50 --TreeAnc._ml_anc_joint: type of reconstruction: Joint | ||
| 192.50 ---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods... | ||
| 224.30 ---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum | ||
| likelihood sequences... | ||
| 225.09 ---TreeAnc._ml_anc_joint: ...done | ||
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| 225.10 -TreeAnc.optimize_branch_length: running branch length optimization using | ||
| jointML ancestral sequences | ||
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| 247.49 -TreeAnc.infer_ancestral_sequences with method: probabilistic, joint | ||
| 247.49 --TreeAnc._ml_anc_joint: type of reconstruction: Joint | ||
| 247.49 ---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods... | ||
| 276.79 ---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum | ||
| likelihood sequences... | ||
| 277.40 ---TreeAnc._ml_anc_joint: ...done | ||
| 277.49 --TreeAnc.optimize_tree: Iteration 1. #Nuc changed since prev | ||
| reconstructions: 7 | ||
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| 277.49 -TreeAnc.optimize_branch_length: running branch length optimization using | ||
| jointML ancestral sequences | ||
| 300.00 --TreeAnc.optimize_tree: Unconstrained sequence LH:-6571090.016708 | ||
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| 300.00 ###TreeTime.run: INITIAL ROUND | ||
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| 300.00 -ClockTree: Maximum likelihood tree optimization with temporal | ||
| constraints | ||
| 300.00 --ClockTree.init_date_constraints... | ||
| 300.00 ---ClockTree.init_date_constraints: Initializing branch length | ||
| interpolation objects... | ||
| 314.30 --ClockTree.date2dist: Setting new molecular clock. rate=8.969e-09, | ||
| R^2=0.2650 | ||
| 314.32 --ClockTree - Joint reconstruction: Propagating leaves -> root... | ||
| 334.95 --ClockTree - Joint reconstruction: Propagating root -> leaves... | ||
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| 335.00 ###TreeTime.run: ITERATION 1 out of 3 iterations | ||
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| 335.00 -TreeTime.run: adding coalescent prior with Tc=const | ||
| 338.22 --optimized Tc to 0.000127 | ||
| relaxed_clock {'slack': 1.0, 'coupling': 0} | ||
| 338.48 --TreeTime.relaxed_clock: slack=1.000000, coupling=0.000000 | ||
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| 338.50 -ClockTree: Maximum likelihood tree optimization with temporal | ||
| constraints | ||
| 338.50 --ClockTree.init_date_constraints... | ||
| 338.50 ---ClockTree.init_date_constraints: Initializing branch length | ||
| interpolation objects... | ||
| 347.23 --ClockTree.date2dist: Setting new molecular clock. rate=8.969e-09, | ||
| R^2=0.2650 | ||
| 347.25 --ClockTree - Joint reconstruction: Propagating leaves -> root... | ||
| 379.10 --ClockTree - Joint reconstruction: Propagating root -> leaves... | ||
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| 379.22 -TreeAnc.infer_ancestral_sequences with method: ml, joint | ||
| 379.22 --TreeAnc._ml_anc_joint: type of reconstruction: Joint | ||
| 379.22 ---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods... | ||
| 381.92 ---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum | ||
| likelihood sequences... | ||
| 381.98 ---TreeAnc._ml_anc_joint: ...done | ||
|
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| 382.06 ###TreeTime.run: ITERATION 2 out of 3 iterations | ||
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| 382.06 -TreeTime.run: adding coalescent prior with Tc=const | ||
| 384.84 --optimized Tc to 0.000119 | ||
| relaxed_clock {'slack': 1.0, 'coupling': 0} | ||
| 385.10 --TreeTime.relaxed_clock: slack=1.000000, coupling=0.000000 | ||
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| 385.11 -ClockTree: Maximum likelihood tree optimization with temporal | ||
| constraints | ||
| 385.11 --ClockTree.init_date_constraints... | ||
| 385.11 ---ClockTree.init_date_constraints: Initializing branch length | ||
| interpolation objects... | ||
| 394.03 --ClockTree.date2dist: Setting new molecular clock. rate=8.969e-09, | ||
| R^2=0.2650 | ||
| 394.04 --ClockTree - Joint reconstruction: Propagating leaves -> root... | ||
| 423.58 --ClockTree - Joint reconstruction: Propagating root -> leaves... | ||
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| 423.71 -TreeAnc.infer_ancestral_sequences with method: ml, joint | ||
| 423.71 --TreeAnc._ml_anc_joint: type of reconstruction: Joint | ||
| 423.71 ---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods... | ||
| 426.47 ---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum | ||
| likelihood sequences... | ||
| 426.53 ---TreeAnc._ml_anc_joint: ...done | ||
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| 426.61 ###TreeTime.run: ITERATION 3 out of 3 iterations | ||
|
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| 426.61 -TreeTime.run: adding coalescent prior with Tc=skyline | ||
| 426.69 --Coalescent:optimize_skyline:... current LH: 6455.234887 | ||
| 464.99 --Coalescent:optimize_skyline:...done. new LH: 7054.589370 | ||
| 464.99 --optimized a skyline | ||
| relaxed_clock {'slack': 1.0, 'coupling': 0} | ||
| 465.27 --TreeTime.relaxed_clock: slack=1.000000, coupling=0.000000 | ||
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| 465.29 -ClockTree: Maximum likelihood tree optimization with temporal | ||
| constraints | ||
| 465.29 --ClockTree.init_date_constraints... | ||
| 465.29 ---ClockTree.init_date_constraints: Initializing branch length | ||
| interpolation objects... | ||
| 474.47 --ClockTree.date2dist: Setting new molecular clock. rate=8.969e-09, | ||
| R^2=0.2650 | ||
| 474.49 --ClockTree - Joint reconstruction: Propagating leaves -> root... | ||
| 504.05 --ClockTree - Joint reconstruction: Propagating root -> leaves... | ||
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| 504.18 -TreeAnc.infer_ancestral_sequences with method: ml, joint | ||
| 504.18 --TreeAnc._ml_anc_joint: type of reconstruction: Joint | ||
| 504.18 ---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods... | ||
| 506.92 ---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum | ||
| likelihood sequences... | ||
| 506.97 ---TreeAnc._ml_anc_joint: ...done | ||
| 27.34 ---TreeAnc._ml_anc_joint: ...done | ||
| 27.34 --TreeAnc.optimize_tree: Iteration 1. #Nuc changed since prev | ||
| reconstructions: 7 | ||
|
|
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| 27.34 -TreeAnc.optimize_branch_length: running branch length optimization using | ||
| jointML ancestral sequences | ||
| 29.27 --TreeAnc.optimize_tree: Unconstrained sequence LH:-6571119.293822 | ||
|
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| 29.27 ###TreeTime.run: INITIAL ROUND | ||
|
|
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| 29.27 -ClockTree: Maximum likelihood tree optimization with temporal constraints | ||
| 29.27 --ClockTree.init_date_constraints... | ||
| 29.27 ---ClockTree.init_date_constraints: Initializing branch length | ||
| interpolation objects... | ||
| 37.85 --ClockTree.date2dist: Setting new molecular clock. rate=8.791e-09, | ||
| R^2=0.2319 | ||
| 37.87 --ClockTree - Joint reconstruction: Propagating leaves -> root... | ||
| 56.21 --ClockTree - Joint reconstruction: Propagating root -> leaves... |
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