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| 5.11 -TreeTime._set_branch_length_mode: maximum branch length is 3.716e-05, | ||
| 5.41 -TreeTime._set_branch_length_mode: maximum branch length is 3.716e-05, | ||
| using branch length mode joint | ||
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| 5.11 -TreeAnc.optimize_tree: sequences... | ||
| 5.41 -TreeAnc.optimize_tree: sequences... | ||
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| 5.11 -TreeAnc.infer_ancestral_sequences with method: probabilistic, joint | ||
| 5.41 -TreeAnc.infer_ancestral_sequences with method: probabilistic, joint | ||
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| 5.11 WARNING: Previous versions of TreeTime (<0.7.0) RECONSTRUCTED sequences of | ||
| 5.41 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`. | ||
| 5.11 --TreeAnc._ml_anc_joint: type of reconstruction: Joint | ||
| 5.11 ---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods... | ||
| 10.88 ---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum | ||
| 5.41 --TreeAnc._ml_anc_joint: type of reconstruction: Joint | ||
| 5.41 ---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods... | ||
| 11.89 ---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum | ||
| likelihood sequences... | ||
| 11.09 ---TreeAnc._ml_anc_joint: ...done | ||
| 11.10 --TreeAnc.infer_gtr: counting mutations... | ||
| 12.49 ---TreeAnc.infer_gtr: counting mutations...done | ||
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| 12.49 -GTR: with alphabet: ['A', 'C', 'G', 'T', '-'] | ||
| 12.49 --GTR: ambiguous character: N | ||
| 12.49 ---GTR: init with dummy values! | ||
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| 12.49 -GTR: model inference | ||
| 12.49 ---GTR inference iteration 0 change: 0.447213595499958 | ||
| 12.49 ---GTR inference iteration 1 change: 0.2417647365143318 | ||
| 12.50 ---GTR inference iteration 2 change: 0.0007800149839042479 | ||
| 12.50 ---GTR inference iteration 3 change: 6.374148089767242e-05 | ||
| 12.50 ---GTR inference iteration 4 change: 7.153405244601736e-05 | ||
| 12.50 ---GTR inference iteration 5 change: 3.054919302593857e-05 | ||
| 12.50 --The model allows for gaps which are estimated to occur at a low fraction | ||
| 12.14 ---TreeAnc._ml_anc_joint: ...done | ||
| 12.15 --TreeAnc.infer_gtr: counting mutations... | ||
| 13.71 ---TreeAnc.infer_gtr: counting mutations...done | ||
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| 13.71 -GTR: with alphabet: ['A', 'C', 'G', 'T', '-'] | ||
| 13.71 --GTR: ambiguous character: N | ||
| 13.71 ---GTR: init with dummy values! | ||
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| 13.71 -GTR: model inference | ||
| 13.71 ---GTR inference iteration 0 change: 0.447213595499958 | ||
| 13.71 ---GTR inference iteration 1 change: 0.2417647365143318 | ||
| 13.71 ---GTR inference iteration 2 change: 0.0007800149839042479 | ||
| 13.71 ---GTR inference iteration 3 change: 6.374148089767242e-05 | ||
| 13.71 ---GTR inference iteration 4 change: 7.153405244601736e-05 | ||
| 13.71 ---GTR inference iteration 5 change: 3.054919302593857e-05 | ||
| 13.71 --The model allows for gaps which are estimated to occur at a low fraction | ||
| of 6.123e-04 this can potentially result in artificats. gap fraction | ||
| will be set to 0.0100 | ||
| 12.50 --TreeAnc.infer_gtr: setting overall rate to 1.0... | ||
| 12.50 --TreeAnc._ml_anc_joint: type of reconstruction: Joint | ||
| 12.50 ---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods... | ||
| 17.84 ---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum | ||
| 13.71 --TreeAnc.infer_gtr: setting overall rate to 1.0... | ||
| 13.71 --TreeAnc._ml_anc_joint: type of reconstruction: Joint | ||
| 13.71 ---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods... | ||
| 19.47 ---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum | ||
| likelihood sequences... | ||
| 18.09 ---TreeAnc._ml_anc_joint: ...done | ||
| 19.71 ---TreeAnc._ml_anc_joint: ...done | ||
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| 18.10 -TreeAnc.optimize_branch_length: running branch length optimization using | ||
| 19.72 -TreeAnc.optimize_branch_length: running branch length optimization using | ||
| jointML ancestral sequences | ||
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| 23.44 -TreeAnc.prune_short_branches: pruning short branches (max prob at | ||
| 24.90 -TreeAnc.prune_short_branches: pruning short branches (max prob at | ||
| zero)... | ||
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| 23.81 -TreeAnc.infer_ancestral_sequences with method: probabilistic, joint | ||
| 23.81 --TreeAnc._ml_anc_joint: type of reconstruction: Joint | ||
| 23.81 ---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods... | ||
| 28.36 ---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum | ||
| 25.27 -TreeAnc.infer_ancestral_sequences with method: probabilistic, joint | ||
| 25.27 --TreeAnc._ml_anc_joint: type of reconstruction: Joint | ||
| 25.28 ---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods... | ||
| 30.36 ---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum | ||
| likelihood sequences... | ||
| 28.49 ---TreeAnc._ml_anc_joint: ...done | ||
| 28.50 --TreeAnc.optimize_tree: Iteration 1. #Nuc changed since prev | ||
| 30.53 ---TreeAnc._ml_anc_joint: ...done | ||
| 30.54 --TreeAnc.optimize_tree: Iteration 1. #Nuc changed since prev | ||
| reconstructions: 139 | ||
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| 28.50 -TreeAnc.optimize_branch_length: running branch length optimization using | ||
| 30.54 -TreeAnc.optimize_branch_length: running branch length optimization using | ||
| jointML ancestral sequences | ||
| 33.27 --TreeAnc.optimize_tree: Unconstrained sequence LH:-6607581.176202 | ||
| 33.66 --ClockTree.date2dist: Setting new molecular clock. rate=8.764e-09, | ||
| 35.35 --TreeAnc.optimize_tree: Unconstrained sequence LH:-6607581.176202 | ||
| 35.72 --ClockTree.date2dist: Setting new molecular clock. rate=8.764e-09, | ||
| R^2=0.2682 | ||
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| 33.80 -TreeAnc.optimize_tree: sequences... | ||
| 35.90 -TreeAnc.optimize_tree: sequences... | ||
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| 33.80 -TreeAnc.infer_ancestral_sequences with method: probabilistic, joint | ||
| 33.80 --TreeAnc._ml_anc_joint: type of reconstruction: Joint | ||
| 33.80 ---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods... | ||
| 38.87 ---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum | ||
| 35.90 -TreeAnc.infer_ancestral_sequences with method: probabilistic, joint | ||
| 35.90 --TreeAnc._ml_anc_joint: type of reconstruction: Joint | ||
| 35.90 ---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods... | ||
| 41.65 ---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum | ||
| likelihood sequences... | ||
| 39.00 ---TreeAnc._ml_anc_joint: ...done | ||
| 41.78 ---TreeAnc._ml_anc_joint: ...done | ||
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| 39.01 -TreeAnc.optimize_branch_length: running branch length optimization using | ||
| 41.80 -TreeAnc.optimize_branch_length: running branch length optimization using | ||
| jointML ancestral sequences | ||
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| 44.00 -TreeAnc.infer_ancestral_sequences with method: probabilistic, joint | ||
| 44.00 --TreeAnc._ml_anc_joint: type of reconstruction: Joint | ||
| 44.00 ---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods... | ||
| 48.71 ---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum | ||
| 46.67 -TreeAnc.infer_ancestral_sequences with method: probabilistic, joint | ||
| 46.67 --TreeAnc._ml_anc_joint: type of reconstruction: Joint | ||
| 46.67 ---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods... | ||
| 52.44 ---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum | ||
| likelihood sequences... | ||
| 48.84 ---TreeAnc._ml_anc_joint: ...done | ||
| 48.85 --TreeAnc.optimize_tree: Iteration 1. #Nuc changed since prev | ||
| 52.59 ---TreeAnc._ml_anc_joint: ...done | ||
| 52.60 --TreeAnc.optimize_tree: Iteration 1. #Nuc changed since prev | ||
| reconstructions: 6 | ||
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| 48.85 -TreeAnc.optimize_branch_length: running branch length optimization using | ||
| 52.60 -TreeAnc.optimize_branch_length: running branch length optimization using | ||
| jointML ancestral sequences | ||
| 53.36 --TreeAnc.optimize_tree: Unconstrained sequence LH:-6607522.247063 | ||
| 57.80 --TreeAnc.optimize_tree: Unconstrained sequence LH:-6607522.247063 | ||
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| 53.36 ###TreeTime.run: INITIAL ROUND | ||
| 57.80 ###TreeTime.run: INITIAL ROUND | ||
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| 53.36 -ClockTree: Maximum likelihood tree optimization with temporal constraints | ||
| 53.36 --ClockTree.init_date_constraints... | ||
| 53.36 ---ClockTree.init_date_constraints: Initializing branch length | ||
| 57.80 -ClockTree: Maximum likelihood tree optimization with temporal constraints | ||
| 57.80 --ClockTree.init_date_constraints... | ||
| 57.80 ---ClockTree.init_date_constraints: Initializing branch length | ||
| interpolation objects... | ||
| 76.48 --ClockTree.date2dist: Setting new molecular clock. rate=8.726e-09, | ||
| 82.73 --ClockTree.date2dist: Setting new molecular clock. rate=8.726e-09, | ||
| R^2=0.2666 | ||
| 76.53 --ClockTree - Joint reconstruction: Propagating leaves -> root... | ||
| 119.90 --ClockTree - Joint reconstruction: Propagating root -> leaves... | ||
| 82.77 --ClockTree - Joint reconstruction: Propagating leaves -> root... | ||
| 128.79 --ClockTree - Joint reconstruction: Propagating root -> leaves... | ||
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| 120.12 ###TreeTime.run: ITERATION 1 out of 3 iterations | ||
| 128.96 ###TreeTime.run: ITERATION 1 out of 3 iterations | ||
| relaxed_clock {'slack': 5.0, 'coupling': 0} | ||
| 120.12 --TreeTime.relaxed_clock: slack=5.000000, coupling=0.000000 | ||
| 128.96 --TreeTime.relaxed_clock: slack=5.000000, coupling=0.000000 | ||
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| 120.16 -ClockTree: Maximum likelihood tree optimization with temporal | ||
| 129.00 -ClockTree: Maximum likelihood tree optimization with temporal | ||
| constraints | ||
| 120.16 --ClockTree.init_date_constraints... | ||
| 120.16 ---ClockTree.init_date_constraints: Initializing branch length | ||
| 129.00 --ClockTree.init_date_constraints... | ||
| 129.00 ---ClockTree.init_date_constraints: Initializing branch length | ||
| interpolation objects... | ||
| 143.41 --ClockTree.date2dist: Setting new molecular clock. rate=8.726e-09, | ||
| 154.57 --ClockTree.date2dist: Setting new molecular clock. rate=8.726e-09, | ||
| R^2=0.2666 | ||
| 143.45 --ClockTree - Joint reconstruction: Propagating leaves -> root... | ||
| 185.39 --ClockTree - Joint reconstruction: Propagating root -> leaves... | ||
| 154.62 --ClockTree - Joint reconstruction: Propagating leaves -> root... | ||
| 201.47 --ClockTree - Joint reconstruction: Propagating root -> leaves... | ||
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| 185.55 -TreeAnc.infer_ancestral_sequences with method: ml, joint | ||
| 185.55 --TreeAnc._ml_anc_joint: type of reconstruction: Joint | ||
| 185.55 ---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods... | ||
| 190.16 ---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum | ||
| 201.64 -TreeAnc.infer_ancestral_sequences with method: ml, joint | ||
| 201.64 --TreeAnc._ml_anc_joint: type of reconstruction: Joint | ||
| 201.64 ---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods... | ||
| 206.68 ---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum | ||
| likelihood sequences... | ||
| 190.29 ---TreeAnc._ml_anc_joint: ...done | ||
| 206.81 ---TreeAnc._ml_anc_joint: ...done | ||
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| 190.30 ###TreeTime.run: ITERATION 2 out of 3 iterations | ||
| 206.82 ###TreeTime.run: ITERATION 2 out of 3 iterations | ||
| relaxed_clock {'slack': 5.0, 'coupling': 0} | ||
| 190.30 --TreeTime.relaxed_clock: slack=5.000000, coupling=0.000000 | ||
| 206.82 --TreeTime.relaxed_clock: slack=5.000000, coupling=0.000000 | ||
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| 190.33 -ClockTree: Maximum likelihood tree optimization with temporal | ||
| 206.86 -ClockTree: Maximum likelihood tree optimization with temporal | ||
| constraints | ||
| 190.33 --ClockTree.init_date_constraints... | ||
| 190.33 ---ClockTree.init_date_constraints: Initializing branch length | ||
| 206.86 --ClockTree.init_date_constraints... | ||
| 206.86 ---ClockTree.init_date_constraints: Initializing branch length | ||
| interpolation objects... | ||
| 215.09 --ClockTree.date2dist: Setting new molecular clock. rate=8.726e-09, | ||
| 237.34 --ClockTree.date2dist: Setting new molecular clock. rate=8.726e-09, | ||
| R^2=0.2666 | ||
| 215.13 --ClockTree - Joint reconstruction: Propagating leaves -> root... | ||
| 258.85 --ClockTree - Joint reconstruction: Propagating root -> leaves... | ||
| 237.39 --ClockTree - Joint reconstruction: Propagating leaves -> root... | ||
| 282.41 --ClockTree - Joint reconstruction: Propagating root -> leaves... | ||
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| 259.02 -TreeAnc.infer_ancestral_sequences with method: ml, joint | ||
| 259.02 --TreeAnc._ml_anc_joint: type of reconstruction: Joint | ||
| 259.02 ---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods... | ||
| 263.71 ---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum | ||
| 282.59 -TreeAnc.infer_ancestral_sequences with method: ml, joint | ||
| 282.59 --TreeAnc._ml_anc_joint: type of reconstruction: Joint | ||
| 282.59 ---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods... | ||
| 288.47 ---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum | ||
| likelihood sequences... | ||
| 263.83 ---TreeAnc._ml_anc_joint: ...done | ||
| 288.61 ---TreeAnc._ml_anc_joint: ...done | ||
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| 263.84 ###TreeTime.run: ITERATION 3 out of 3 iterations | ||
| 288.62 ###TreeTime.run: ITERATION 3 out of 3 iterations | ||
| relaxed_clock {'slack': 5.0, 'coupling': 0} | ||
| 263.84 --TreeTime.relaxed_clock: slack=5.000000, coupling=0.000000 | ||
| 288.62 --TreeTime.relaxed_clock: slack=5.000000, coupling=0.000000 | ||
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| 263.88 -ClockTree: Maximum likelihood tree optimization with temporal | ||
| 288.66 -ClockTree: Maximum likelihood tree optimization with temporal | ||
| constraints | ||
| 263.88 --ClockTree.init_date_constraints... | ||
| 263.88 ---ClockTree.init_date_constraints: Initializing branch length | ||
| 288.66 --ClockTree.init_date_constraints... | ||
| 288.66 ---ClockTree.init_date_constraints: Initializing branch length | ||
| interpolation objects... | ||
| 288.80 --ClockTree.date2dist: Setting new molecular clock. rate=8.726e-09, | ||
| 316.24 --ClockTree.date2dist: Setting new molecular clock. rate=8.726e-09, | ||
| R^2=0.2666 | ||
| 288.85 --ClockTree - Joint reconstruction: Propagating leaves -> root... | ||
| 335.93 --ClockTree - Joint reconstruction: Propagating root -> leaves... | ||
| 316.28 --ClockTree - Joint reconstruction: Propagating leaves -> root... | ||
| 363.20 --ClockTree - Joint reconstruction: Propagating root -> leaves... | ||
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| 336.17 -TreeAnc.infer_ancestral_sequences with method: ml, joint | ||
| 336.17 --TreeAnc._ml_anc_joint: type of reconstruction: Joint | ||
| 336.17 ---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods... | ||
| 341.50 ---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum | ||
| 363.44 -TreeAnc.infer_ancestral_sequences with method: ml, joint | ||
| 363.44 --TreeAnc._ml_anc_joint: type of reconstruction: Joint | ||
| 363.44 ---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods... | ||
| 368.50 ---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum | ||
| likelihood sequences... | ||
| 341.65 ---TreeAnc._ml_anc_joint: ...done | ||
| 368.63 ---TreeAnc._ml_anc_joint: ...done | ||
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| 341.66 ###TreeTime.run: FINAL ROUND - confidence estimation via marginal | ||
| 368.64 ###TreeTime.run: FINAL ROUND - confidence estimation via marginal | ||
| reconstruction | ||
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| 341.66 -ClockTree: Maximum likelihood tree optimization with temporal | ||
| 368.64 -ClockTree: Maximum likelihood tree optimization with temporal | ||
| constraints | ||
| 341.66 --ClockTree.init_date_constraints... | ||
| 341.66 ---ClockTree.init_date_constraints: Initializing branch length | ||
| 368.64 --ClockTree.init_date_constraints... | ||
| 368.64 ---ClockTree.init_date_constraints: Initializing branch length | ||
| interpolation objects... | ||
| 367.31 --ClockTree.date2dist: Setting new molecular clock. rate=8.726e-09, | ||
| 394.41 --ClockTree.date2dist: Setting new molecular clock. rate=8.726e-09, | ||
| R^2=0.2666 | ||
| 367.35 --ClockTree - Marginal reconstruction: Propagating leaves -> root... | ||
| 447.66 --ClockTree - Marginal reconstruction: Propagating root -> leaves... | ||
| 394.46 --ClockTree - Marginal reconstruction: Propagating leaves -> root... | ||
| 480.03 --ClockTree - Marginal reconstruction: Propagating root -> leaves... |
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