timetree plots before using config

docs/results/latest/timetree/timetree_skyline.tsv

@@ -1,22 +1,22 @@
 #Skyline assuming 50 gen/year and approximate confidence bounds (+/- 2.000000 standard deviations of the LH)
 #date 	N_e 	lower 	upper
--4050.2	54662.3	21498.4	138985.9
--3731.0	72609.6	36465.9	144577.7
--3411.7	84927.8	42083.0	171392.8
--3092.4	95497.6	49881.9	182827.7
--2773.1	104575.6	54083.5	202207.0
--2453.9	108235.1	54608.4	214524.6
--2134.6	111388.4	56034.7	221423.1
--1815.3	116952.6	60148.0	227404.4
--1496.0	164859.1	83897.9	323947.7
--1176.8	215252.6	107564.8	430751.2
--857.5	227198.9	112024.6	460785.4
--538.2	238314.5	117078.8	485090.5
--218.9	233798.3	124454.9	439208.4
-100.3	208103.5	111609.0	388024.8
-419.6	175466.5	98531.0	312475.2
-738.9	195741.5	113781.5	336739.9
-1058.2	364609.0	237098.3	560694.6
-1377.4	401926.6	277600.9	581932.4
-1696.7	1492569.7	1268088.2	1756789.8
-2016.0	333742.9	265046.2	420244.8
+-4099.1	54948.0	21617.7	139667.1
+-3777.3	73439.3	36905.9	146137.5
+-3455.4	84625.6	41915.4	170856.1
+-3133.6	92668.6	47488.8	180831.6
+-2811.7	100853.8	52340.1	194334.7
+-2489.9	103940.7	52869.2	204347.3
+-2168.0	108865.8	54957.9	215651.3
+-1846.2	115549.3	59578.9	224100.2
+-1524.3	158918.1	81090.7	311440.8
+-1202.5	212256.4	106308.2	423794.0
+-880.6	224023.8	110459.1	454346.1
+-558.8	235308.1	115802.4	478141.1
+-236.9	237632.0	127532.5	442781.2
+84.9	212406.6	112966.2	399380.9
+406.8	163381.3	90236.4	295816.8
+728.6	183921.3	106554.7	317461.8
+1050.5	364005.3	235907.3	561660.6
+1372.3	387311.1	266057.1	563825.8
+1694.2	1461916.4	1241603.0	1721322.8
+2016.0	338408.1	269647.8	424702.3

docs/results/latest/timetree/timetree_{}.log

@@ -0,0 +1,170 @@
+
+107.09	-TreeTime._set_branch_length_mode: maximum branch length is 3.648e-05,
+      	 using branch length mode joint
+
+107.09	-TreeAnc.optimize_tree: sequences...
+
+107.09	-TreeAnc.infer_ancestral_sequences with method: probabilistic, joint
+
+107.09	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`.
+107.09	--TreeAnc._ml_anc_joint: type of reconstruction: Joint
+107.09	---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods...
+110.91	---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum
+      	   likelihood sequences...
+111.04	---TreeAnc._ml_anc_joint: ...done
+111.04	--TreeAnc.infer_gtr: counting mutations...
+112.11	---TreeAnc.infer_gtr: counting mutations...done
+
+112.11	-GTR: with alphabet: ['A', 'C', 'G', 'T', '-']
+112.11	--GTR: ambiguous character: N
+112.11	---GTR: init with dummy values!
+
+112.11	-GTR: model inference
+112.11	---GTR inference iteration 0 change: 0.447213595499958
+112.11	---GTR inference iteration 1 change: 0.24246907925186573
+112.11	---GTR inference iteration 2 change: 0.000509782157875719
+112.11	---GTR inference iteration 3 change: 5.105228329868478e-05
+112.11	---GTR inference iteration 4 change: 4.234818529391279e-05
+112.12	--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
+112.12	--TreeAnc.infer_gtr: setting overall rate to 1.0...
+112.12	--TreeAnc._ml_anc_joint: type of reconstruction: Joint
+112.12	---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods...
+115.64	---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum
+      	   likelihood sequences...
+115.80	---TreeAnc._ml_anc_joint: ...done
+
+115.81	-TreeAnc.optimize_branch_length: running branch length optimization using
+      	 jointML ancestral sequences
+
+118.99	-TreeAnc.prune_short_branches: pruning short branches (max prob at
+      	 zero)...
+
+119.18	-TreeAnc.infer_ancestral_sequences with method: probabilistic, joint
+119.18	--TreeAnc._ml_anc_joint: type of reconstruction: Joint
+119.18	---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods...
+122.68	---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum
+      	   likelihood sequences...
+122.77	---TreeAnc._ml_anc_joint: ...done
+122.78	--TreeAnc.optimize_tree: Iteration 1. #Nuc changed since prev
+      	  reconstructions: 87
+
+122.78	-TreeAnc.optimize_branch_length: running branch length optimization using
+      	 jointML ancestral sequences
+125.74	--TreeAnc.optimize_tree: Unconstrained sequence LH:-6571129.681030
+
+125.75	-TreeAnc.optimize_tree: sequences...
+
+125.75	-TreeAnc.infer_ancestral_sequences with method: probabilistic, joint
+125.75	--TreeAnc._ml_anc_joint: type of reconstruction: Joint
+125.75	---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods...
+129.20	---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum
+      	   likelihood sequences...
+129.30	---TreeAnc._ml_anc_joint: ...done
+
+129.31	-TreeAnc.optimize_branch_length: running branch length optimization using
+      	 jointML ancestral sequences
+
+131.93	-TreeAnc.infer_ancestral_sequences with method: probabilistic, joint
+131.93	--TreeAnc._ml_anc_joint: type of reconstruction: Joint
+131.93	---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods...
+135.48	---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum
+      	   likelihood sequences...
+135.58	---TreeAnc._ml_anc_joint: ...done
+135.59	--TreeAnc.optimize_tree: Iteration 1. #Nuc changed since prev
+      	  reconstructions: 7
+
+135.59	-TreeAnc.optimize_branch_length: running branch length optimization using
+      	 jointML ancestral sequences
+138.12	--TreeAnc.optimize_tree: Unconstrained sequence LH:-6571090.016708
+
+138.12	###TreeTime.run: INITIAL ROUND
+
+138.12	-ClockTree: Maximum likelihood tree optimization with temporal
+      	 constraints
+138.12	--ClockTree.init_date_constraints...
+138.12	---ClockTree.init_date_constraints: Initializing branch length
+      	   interpolation objects...
+148.53	--ClockTree.date2dist: Setting new molecular clock. rate=8.969e-09,
+      	  R^2=0.2650
+148.56	--ClockTree - Joint reconstruction:  Propagating leaves -> root...
+173.56	--ClockTree - Joint reconstruction:  Propagating root -> leaves...
+
+173.62	###TreeTime.run: ITERATION 1 out of 3 iterations
+
+173.62	-TreeTime.run: adding coalescent prior with Tc=const
+177.26	--optimized Tc to 0.000127
+relaxed_clock {'slack': 1.0, 'coupling': 0}
+177.59	--TreeTime.relaxed_clock: slack=1.000000, coupling=0.000000
+
+177.60	-ClockTree: Maximum likelihood tree optimization with temporal
+      	 constraints
+177.60	--ClockTree.init_date_constraints...
+177.60	---ClockTree.init_date_constraints: Initializing branch length
+      	   interpolation objects...
+188.71	--ClockTree.date2dist: Setting new molecular clock. rate=8.969e-09,
+      	  R^2=0.2650
+188.73	--ClockTree - Joint reconstruction:  Propagating leaves -> root...
+229.47	--ClockTree - Joint reconstruction:  Propagating root -> leaves...
+
+229.73	-TreeAnc.infer_ancestral_sequences with method: ml, joint
+229.73	--TreeAnc._ml_anc_joint: type of reconstruction: Joint
+229.73	---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods...
+233.82	---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum
+      	   likelihood sequences...
+233.89	---TreeAnc._ml_anc_joint: ...done
+
+234.00	###TreeTime.run: ITERATION 2 out of 3 iterations
+
+234.01	-TreeTime.run: adding coalescent prior with Tc=const
+237.47	--optimized Tc to 0.000119
+relaxed_clock {'slack': 1.0, 'coupling': 0}
+237.82	--TreeTime.relaxed_clock: slack=1.000000, coupling=0.000000
+
+237.84	-ClockTree: Maximum likelihood tree optimization with temporal
+      	 constraints
+237.84	--ClockTree.init_date_constraints...
+237.84	---ClockTree.init_date_constraints: Initializing branch length
+      	   interpolation objects...
+248.76	--ClockTree.date2dist: Setting new molecular clock. rate=8.969e-09,
+      	  R^2=0.2650
+248.79	--ClockTree - Joint reconstruction:  Propagating leaves -> root...
+286.87	--ClockTree - Joint reconstruction:  Propagating root -> leaves...
+
+287.00	-TreeAnc.infer_ancestral_sequences with method: ml, joint
+287.00	--TreeAnc._ml_anc_joint: type of reconstruction: Joint
+287.00	---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods...
+289.86	---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum
+      	   likelihood sequences...
+289.93	---TreeAnc._ml_anc_joint: ...done
+
+290.04	###TreeTime.run: ITERATION 3 out of 3 iterations
+
+290.04	-TreeTime.run: adding coalescent prior with Tc=skyline
+290.19	--Coalescent:optimize_skyline:... current LH: 6455.234887
+341.39	--Coalescent:optimize_skyline:...done. new LH: 7054.589370
+341.39	--optimized a skyline
+relaxed_clock {'slack': 1.0, 'coupling': 0}
+341.77	--TreeTime.relaxed_clock: slack=1.000000, coupling=0.000000
+
+341.80	-ClockTree: Maximum likelihood tree optimization with temporal
+      	 constraints
+341.80	--ClockTree.init_date_constraints...
+341.80	---ClockTree.init_date_constraints: Initializing branch length
+      	   interpolation objects...
+356.69	--ClockTree.date2dist: Setting new molecular clock. rate=8.969e-09,
+      	  R^2=0.2650
+356.72	--ClockTree - Joint reconstruction:  Propagating leaves -> root...
+401.36	--ClockTree - Joint reconstruction:  Propagating root -> leaves...
+
+401.57	-TreeAnc.infer_ancestral_sequences with method: ml, joint
+401.57	--TreeAnc._ml_anc_joint: type of reconstruction: Joint
+401.57	---TreeAnc._ml_anc_joint: Walking up the tree, computing likelihoods...
+404.97	---TreeAnc._ml_anc_joint: Walking down the tree, computing maximum
+      	   likelihood sequences...
+405.04	---TreeAnc._ml_anc_joint: ...done