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comparison fasttree/test-data/log.txt @ 0:b2b9795cc862 draft

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author qfab
date Thu, 29 May 2014 23:53:21 -0400
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-1:000000000000 0:b2b9795cc862
1 FastTree Version 2.1.7 SSE3
2 Alignment: standard input
3 Nucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 1000
4 Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
5 TopHits: 1.00*sqrtN close=default refresh=0.80
6 ML Model: Jukes-Cantor, CAT approximation with 20 rate categories
7 Ignored unknown character K (seen 1 times)
8 Ignored unknown character R (seen 4 times)
9 Ignored unknown character S (seen 5 times)
10 Ignored unknown character X (seen 240 times)
11 Ignored unknown character Y (seen 2 times)
12 1.46 seconds: Top hits for 399 of 533 seqs (at seed 200)
13 1.69 seconds: Top hits for 459 of 533 seqs (at seed 300)
14 1.87 seconds: Top hits for 498 of 533 seqs (at seed 400)
15 2.06 seconds: Top hits for 526 of 533 seqs (at seed 500)
16 3.31 seconds: Joined 100 of 530
17 4.88 seconds: Joined 200 of 530
18 6.11 seconds: Joined 300 of 530
19 7.43 seconds: Joined 400 of 530
20 8.67 seconds: Joined 500 of 530
21 Initial topology in 8.86 seconds
22 Refining topology: 36 rounds ME-NNIs, 2 rounds ME-SPRs, 18 rounds ML-NNIs
23 8.86 seconds: ME NNI round 1 of 36, 1 of 531 splits
24 9.05 seconds: ME NNI round 1 of 36, 201 of 531 splits, 40 changes (max delta 0.029)
25 9.23 seconds: ME NNI round 1 of 36, 401 of 531 splits, 71 changes (max delta 0.029)
26 9.36 seconds: ME NNI round 2 of 36, 1 of 531 splits
27 9.54 seconds: ME NNI round 2 of 36, 201 of 531 splits, 19 changes (max delta 0.013)
28 9.73 seconds: ME NNI round 2 of 36, 401 of 531 splits, 40 changes (max delta 0.016)
29 9.85 seconds: ME NNI round 3 of 36, 1 of 531 splits
30 10.04 seconds: ME NNI round 3 of 36, 201 of 531 splits, 17 changes (max delta 0.003)
31 10.19 seconds: ME NNI round 4 of 36, 1 of 531 splits
32 10.38 seconds: ME NNI round 4 of 36, 201 of 531 splits, 10 changes (max delta 0.005)
33 10.52 seconds: ME NNI round 5 of 36, 101 of 531 splits, 5 changes (max delta 0.003)
34 10.65 seconds: SPR round 1 of 2, 1 of 1064 nodes
35 12.20 seconds: SPR round 1 of 2, 101 of 1064 nodes
36 13.72 seconds: SPR round 1 of 2, 201 of 1064 nodes
37 15.33 seconds: SPR round 1 of 2, 301 of 1064 nodes
38 16.82 seconds: SPR round 1 of 2, 401 of 1064 nodes
39 18.48 seconds: SPR round 1 of 2, 501 of 1064 nodes
40 19.91 seconds: SPR round 1 of 2, 601 of 1064 nodes
41 21.36 seconds: SPR round 1 of 2, 701 of 1064 nodes
42 23.06 seconds: SPR round 1 of 2, 801 of 1064 nodes
43 24.59 seconds: SPR round 1 of 2, 901 of 1064 nodes
44 26.04 seconds: SPR round 1 of 2, 1001 of 1064 nodes
45 27.28 seconds: ME NNI round 13 of 36, 1 of 531 splits
46 27.46 seconds: ME NNI round 13 of 36, 201 of 531 splits, 1 changes (max delta 0.007)
47 27.64 seconds: ME NNI round 13 of 36, 401 of 531 splits, 2 changes (max delta 0.007)
48 27.76 seconds: ME NNI round 14 of 36, 1 of 531 splits
49 27.94 seconds: ME NNI round 14 of 36, 201 of 531 splits, 1 changes (max delta 0.003)
50 28.11 seconds: ME NNI round 14 of 36, 401 of 531 splits, 1 changes (max delta 0.003)
51 28.23 seconds: ME NNI round 15 of 36, 1 of 531 splits
52 29.84 seconds: SPR round 2 of 2, 101 of 1064 nodes
53 31.44 seconds: SPR round 2 of 2, 201 of 1064 nodes
54 33.04 seconds: SPR round 2 of 2, 301 of 1064 nodes
55 34.51 seconds: SPR round 2 of 2, 401 of 1064 nodes
56 36.07 seconds: SPR round 2 of 2, 501 of 1064 nodes
57 37.52 seconds: SPR round 2 of 2, 601 of 1064 nodes
58 38.98 seconds: SPR round 2 of 2, 701 of 1064 nodes
59 40.71 seconds: SPR round 2 of 2, 801 of 1064 nodes
60 42.29 seconds: SPR round 2 of 2, 901 of 1064 nodes
61 43.91 seconds: SPR round 2 of 2, 1001 of 1064 nodes
62 45.04 seconds: ME NNI round 25 of 36, 1 of 531 splits
63 45.22 seconds: ME NNI round 25 of 36, 201 of 531 splits, 1 changes (max delta 0.000)
64 45.40 seconds: ME NNI round 25 of 36, 401 of 531 splits, 1 changes (max delta 0.000)
65 45.51 seconds: ME NNI round 26 of 36, 1 of 531 splits
66 45.70 seconds: ME NNI round 26 of 36, 201 of 531 splits, 0 changes
67 45.88 seconds: ME NNI round 26 of 36, 401 of 531 splits, 0 changes
68 Total branch-length 34.168 after 46.56 sec
69 46.66 seconds: ML Lengths 1 of 531 splits
70 47.64 seconds: ML Lengths 101 of 531 splits
71 48.63 seconds: ML Lengths 201 of 531 splits
72 49.59 seconds: ML Lengths 301 of 531 splits
73 50.54 seconds: ML Lengths 401 of 531 splits
74 51.50 seconds: ML Lengths 501 of 531 splits
75 51.81 seconds: ML NNI round 1 of 18, 1 of 531 splits
76 54.77 seconds: ML NNI round 1 of 18, 101 of 531 splits, 15 changes (max delta 19.328)
77 57.67 seconds: ML NNI round 1 of 18, 201 of 531 splits, 36 changes (max delta 19.328)
78 60.58 seconds: ML NNI round 1 of 18, 301 of 531 splits, 52 changes (max delta 19.328)
79 63.61 seconds: ML NNI round 1 of 18, 401 of 531 splits, 72 changes (max delta 28.170)
80 66.61 seconds: ML NNI round 1 of 18, 501 of 531 splits, 83 changes (max delta 28.170)
81 ML-NNI round 1: LogLk = -287815.653 NNIs 89 max delta 28.17 Time 67.75
82 68.12 seconds: Site likelihoods with rate category 1 of 20
83 68.50 seconds: Site likelihoods with rate category 2 of 20
84 68.87 seconds: Site likelihoods with rate category 3 of 20
85 69.25 seconds: Site likelihoods with rate category 4 of 20
86 69.62 seconds: Site likelihoods with rate category 5 of 20
87 70.00 seconds: Site likelihoods with rate category 6 of 20
88 70.37 seconds: Site likelihoods with rate category 7 of 20
89 70.75 seconds: Site likelihoods with rate category 8 of 20
90 71.12 seconds: Site likelihoods with rate category 9 of 20
91 71.50 seconds: Site likelihoods with rate category 10 of 20
92 71.87 seconds: Site likelihoods with rate category 11 of 20
93 72.25 seconds: Site likelihoods with rate category 12 of 20
94 72.62 seconds: Site likelihoods with rate category 13 of 20
95 72.99 seconds: Site likelihoods with rate category 14 of 20
96 73.36 seconds: Site likelihoods with rate category 15 of 20
97 73.74 seconds: Site likelihoods with rate category 16 of 20
98 74.11 seconds: Site likelihoods with rate category 17 of 20
99 74.49 seconds: Site likelihoods with rate category 18 of 20
100 74.86 seconds: Site likelihoods with rate category 19 of 20
101 75.24 seconds: Site likelihoods with rate category 20 of 20
102 Switched to using 20 rate categories (CAT approximation)
103 Rate categories were divided by 0.780 so that average rate = 1.0
104 CAT-based log-likelihoods may not be comparable across runs
105 Use -gamma for approximate but comparable Gamma(20) log-likelihoods
106 75.44 seconds: ML NNI round 2 of 18, 1 of 531 splits
107 77.30 seconds: ML NNI round 2 of 18, 101 of 531 splits, 6 changes (max delta 8.408)
108 79.63 seconds: ML NNI round 2 of 18, 201 of 531 splits, 16 changes (max delta 11.916)
109 81.66 seconds: ML NNI round 2 of 18, 301 of 531 splits, 26 changes (max delta 12.582)
110 83.77 seconds: ML NNI round 2 of 18, 401 of 531 splits, 37 changes (max delta 12.582)
111 85.45 seconds: ML NNI round 2 of 18, 501 of 531 splits, 45 changes (max delta 12.582)
112 ML-NNI round 2: LogLk = -243521.538 NNIs 47 max delta 12.58 Time 86.22
113 86.22 seconds: ML NNI round 3 of 18, 1 of 531 splits
114 87.60 seconds: ML NNI round 3 of 18, 101 of 531 splits, 2 changes (max delta 2.600)
115 89.51 seconds: ML NNI round 3 of 18, 201 of 531 splits, 10 changes (max delta 3.628)
116 90.90 seconds: ML NNI round 3 of 18, 301 of 531 splits, 12 changes (max delta 3.628)
117 ML-NNI round 3: LogLk = -243454.047 NNIs 17 max delta 4.33 Time 92.41
118 92.40 seconds: ML NNI round 4 of 18, 1 of 531 splits
119 93.59 seconds: ML NNI round 4 of 18, 101 of 531 splits, 0 changes
120 94.89 seconds: ML NNI round 4 of 18, 201 of 531 splits, 4 changes (max delta 8.267)
121 ML-NNI round 4: LogLk = -243401.668 NNIs 8 max delta 15.05 Time 95.80
122 95.79 seconds: ML NNI round 5 of 18, 1 of 531 splits
123 97.12 seconds: ML NNI round 5 of 18, 101 of 531 splits, 1 changes (max delta 5.470)
124 ML-NNI round 5: LogLk = -243385.290 NNIs 5 max delta 5.47 Time 97.70
125 97.69 seconds: ML NNI round 6 of 18, 1 of 531 splits
126 ML-NNI round 6: LogLk = -243379.465 NNIs 0 max delta 0.00 Time 98.56
127 Turning off heuristics for final round of ML NNIs (converged)
128 98.55 seconds: ML NNI round 7 of 18, 1 of 531 splits
129 101.64 seconds: ML NNI round 7 of 18, 101 of 531 splits, 3 changes (max delta 5.543)
130 104.85 seconds: ML NNI round 7 of 18, 201 of 531 splits, 4 changes (max delta 5.543)
131 107.89 seconds: ML NNI round 7 of 18, 301 of 531 splits, 8 changes (max delta 5.543)
132 111.07 seconds: ML NNI round 7 of 18, 401 of 531 splits, 9 changes (max delta 5.543)
133 114.20 seconds: ML NNI round 7 of 18, 501 of 531 splits, 12 changes (max delta 20.657)
134 ML-NNI round 7: LogLk = -243045.843 NNIs 13 max delta 20.66 Time 115.43 (final)
135 115.43 seconds: ML Lengths 1 of 531 splits
136 116.25 seconds: ML Lengths 101 of 531 splits
137 117.06 seconds: ML Lengths 201 of 531 splits
138 117.84 seconds: ML Lengths 301 of 531 splits
139 118.68 seconds: ML Lengths 401 of 531 splits
140 119.49 seconds: ML Lengths 501 of 531 splits
141 Optimize all lengths: LogLk = -243039.348 Time 120.01
142 129.12 seconds: ML split tests for 100 of 530 internal splits
143 138.49 seconds: ML split tests for 200 of 530 internal splits
144 148.16 seconds: ML split tests for 300 of 530 internal splits
145 156.37 seconds: ML split tests for 400 of 530 internal splits
146 165.18 seconds: ML split tests for 500 of 530 internal splits
147 Total time: 167.98 seconds Unique: 533/533 Bad splits: 5/530 Worst delta-LogLk 10.254