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comparison test-data/files/clsReps.aln.log @ 0:9a3a2e04f47a draft default tip

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author dave
date Mon, 10 Jun 2019 16:04:10 -0400
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-1:000000000000 0:9a3a2e04f47a
1 IQ-TREE multicore version 1.6.10 for Linux 64-bit built Mar 21 2019
2 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor,
3 Heiko Schmidt, Dominik Schrempf, Michael Woodhams.
4
5 Host: gaius (AVX2, FMA3, 15 GB RAM)
6 Command: iqtree -s clsReps.aln -m GTR+R4 -nt 1
7 Seed: 50990 (Using SPRNG - Scalable Parallel Random Number Generator)
8 Time: Tue May 28 13:09:57 2019
9 Kernel: AVX+FMA - 1 threads (8 CPU cores detected)
10
11 HINT: Use -nt option to specify number of threads because your CPU has 8 cores!
12 HINT: -nt AUTO will automatically determine the best number of threads to use.
13
14 Reading alignment file clsReps.aln ... Fasta format detected
15 Alignment most likely contains DNA/RNA sequences
16 Alignment has 84 sequences with 305 columns, 301 distinct patterns
17 238 parsimony-informative, 52 singleton sites, 15 constant sites
18 WARNING: Some sequence names are changed as follows:
19 K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1_1_0 -> K03455_HIVHXB2CG_1286_1769_0_0_0_4_0_0_0_1_1_0
20 K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1_2_1 -> K03455_HIVHXB2CG_5977_6467_2_0_0_2_0_0_1_1_2_1
21 K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1_3_2 -> K03455_HIVHXB2CG_6040_6545_1_0_0_0_0_0_2_1_3_2
22 K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1_1_3 -> K03455_HIVHXB2CG_3580_4035_1_0_0_0_0_0_3_1_1_3
23 K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1_2_4 -> K03455_HIVHXB2CG_5251_5720_0_0_0_1_0_0_4_1_2_4
24 K03455|HIVHXB2CG_5574_6092_2_0_0_1_0_0_5/1_1_5 -> K03455_HIVHXB2CG_5574_6092_2_0_0_1_0_0_5_1_1_5
25 K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1_1_6 -> K03455_HIVHXB2CG_7273_7731_1_0_0_5_0_0_6_1_1_6
26 K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1_1_7 -> K03455_HIVHXB2CG_5438_5909_1_0_0_4_0_0_7_1_1_7
27 K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1_2_8 -> K03455_HIVHXB2CG_4165_4569_2_0_0_3_0_0_8_1_2_8
28 K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1_1_9 -> K03455_HIVHXB2CG_2832_3397_3_0_0_2_0_0_9_1_1_9
29 K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1_2_10 -> K03455_HIVHXB2CG_1312_1798_2_0_0_1_0_0_a_1_2_10
30 K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1_2_11 -> K03455_HIVHXB2CG_6501_7035_0_0_0_0_0_0_b_1_2_11
31 K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1_1_12 -> K03455_HIVHXB2CG_2252_2786_0_0_0_0_0_0_c_1_1_12
32 K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1_1_13 -> K03455_HIVHXB2CG_7972_8486_1_0_0_0_0_0_e_1_1_13
33 K03455|HIVHXB2CG_368_934_2_0_0_3_0_0_f/1_1_14 -> K03455_HIVHXB2CG_368_934_2_0_0_3_0_0_f_1_1_14
34 K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1_1_15 -> K03455_HIVHXB2CG_8446_8894_4_0_0_3_0_0_10_1_1_15
35 K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1_2_16 -> K03455_HIVHXB2CG_6869_7379_1_0_0_3_0_1_11_1_2_16
36 K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1_1_17 -> K03455_HIVHXB2CG_5034_5548_1_0_0_4_0_0_13_1_1_17
37 K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1_1_18 -> K03455_HIVHXB2CG_418_930_3_0_0_1_0_0_14_1_1_18
38 K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1_1_19 -> K03455_HIVHXB2CG_8325_8818_2_0_0_2_0_0_15_1_1_19
39 K03455|HIVHXB2CG_673_1207_2_0_0_2_0_0_16/1_2_20 -> K03455_HIVHXB2CG_673_1207_2_0_0_2_0_0_16_1_2_20
40 K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1_1_21 -> K03455_HIVHXB2CG_7932_8405_1_0_0_1_0_0_17_1_1_21
41 K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1_1_22 -> K03455_HIVHXB2CG_2894_3537_2_0_0_0_0_0_18_1_1_22
42 K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1_1_23 -> K03455_HIVHXB2CG_5989_6545_2_0_0_1_0_0_19_1_1_23
43 K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/1_1_24 -> K03455_HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b_1_1_24
44 K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1_1_25 -> K03455_HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d_1_1_25
45 K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1_1_26 -> K03455_HIVHXB2CG_7_537_2_0_0_1_0_0_1e_1_1_26
46 K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1_1_27 -> K03455_HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f_1_1_27
47 K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1_1_28 -> K03455_HIVHXB2CG_5516_5958_3_0_0_2_0_0_20_1_1_28
48 K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1_2_29 -> K03455_HIVHXB2CG_8434_8946_0_0_0_1_0_0_21_1_2_29
49 K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1_1_30 -> K03455_HIVHXB2CG_2808_3255_0_0_0_1_0_0_22_1_1_30
50 K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1_1_31 -> K03455_HIVHXB2CG_5108_5621_3_0_0_2_0_0_23_1_1_31
51 K03455|HIVHXB2CG_3875_4298_2_0_0_1_0_0_24/1_1_32 -> K03455_HIVHXB2CG_3875_4298_2_0_0_1_0_0_24_1_1_32
52 K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1_1_33 -> K03455_HIVHXB2CG_8231_8877_0_0_0_3_0_0_25_1_1_33
53 K03455|HIVHXB2CG_7126_7621_1_1_1_3_1_0_26/1_1_34 -> K03455_HIVHXB2CG_7126_7621_1_1_1_3_1_0_26_1_1_34
54 K03455|HIVHXB2CG_3672_4151_0_0_0_1_0_0_27/1_1_35 -> K03455_HIVHXB2CG_3672_4151_0_0_0_1_0_0_27_1_1_35
55 K03455|HIVHXB2CG_4642_5125_0_0_0_3_0_0_28/1_1_36 -> K03455_HIVHXB2CG_4642_5125_0_0_0_3_0_0_28_1_1_36
56 K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1_1_37 -> K03455_HIVHXB2CG_8349_8802_1_0_0_0_0_0_29_1_1_37
57 K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1_2_38 -> K03455_HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a_1_2_38
58 K03455|HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b/1_2_39 -> K03455_HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b_1_2_39
59 K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1_2_40 -> K03455_HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d_1_2_40
60 K03455|HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e/1_1_41 -> K03455_HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e_1_1_41
61 K03455|HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f/1_1_42 -> K03455_HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f_1_1_42
62 K03455|HIVHXB2CG_3823_4361_1_0_0_0_0_0_30/1_1_43 -> K03455_HIVHXB2CG_3823_4361_1_0_0_0_0_0_30_1_1_43
63 K03455|HIVHXB2CG_4420_4903_1_0_0_1_0_0_31/1_1_44 -> K03455_HIVHXB2CG_4420_4903_1_0_0_1_0_0_31_1_1_44
64 K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1_1_45 -> K03455_HIVHXB2CG_1739_2301_2_0_0_2_0_0_33_1_1_45
65 K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1_1_46 -> K03455_HIVHXB2CG_756_1235_2_0_0_1_0_0_34_1_1_46
66 K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1_1_47 -> K03455_HIVHXB2CG_217_724_2_1_0_2_0_0_36_1_1_47
67 K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/1_1_48 -> K03455_HIVHXB2CG_8069_8641_1_0_0_0_0_0_38_1_1_48
68 K03455|HIVHXB2CG_1786_2269_1_0_0_1_0_0_39/1_1_49 -> K03455_HIVHXB2CG_1786_2269_1_0_0_1_0_0_39_1_1_49
69 K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1_1_50 -> K03455_HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a_1_1_50
70 K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1_2_51 -> K03455_HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b_1_2_51
71 K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1_1_52 -> K03455_HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c_1_1_52
72 K03455|HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d/1_1_53 -> K03455_HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d_1_1_53
73 K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1_1_54 -> K03455_HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e_1_1_54
74 K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1_1_55 -> K03455_HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f_1_1_55
75 K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1_1_56 -> K03455_HIVHXB2CG_8342_8779_1_0_0_2_0_0_40_1_1_56
76 K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/1_1_57 -> K03455_HIVHXB2CG_6619_7094_0_0_0_2_0_0_41_1_1_57
77 K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1_1_58 -> K03455_HIVHXB2CG_5150_5584_1_0_0_2_0_0_42_1_1_58
78 K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1_1_59 -> K03455_HIVHXB2CG_5329_5821_2_0_0_2_0_0_43_1_1_59
79 K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/1_1_60 -> K03455_HIVHXB2CG_4457_4958_4_0_0_0_0_0_44_1_1_60
80 K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1_1_61 -> K03455_HIVHXB2CG_906_1404_1_0_0_3_0_0_45_1_1_61
81 K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1_1_62 -> K03455_HIVHXB2CG_2685_3250_0_0_0_0_0_0_46_1_1_62
82 K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1_1_63 -> K03455_HIVHXB2CG_6045_6577_2_0_0_1_0_0_47_1_1_63
83 K03455|HIVHXB2CG_1707_2205_1_0_0_3_0_0_48/1_2_64 -> K03455_HIVHXB2CG_1707_2205_1_0_0_3_0_0_48_1_2_64
84 K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/1_1_65 -> K03455_HIVHXB2CG_4939_5430_1_0_0_0_0_0_49_1_1_65
85 K03455|HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a/1_1_66 -> K03455_HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a_1_1_66
86 K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1_1_67 -> K03455_HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e_1_1_67
87 K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1_1_68 -> K03455_HIVHXB2CG_2700_3243_0_0_0_3_1_0_51_1_1_68
88 K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1_2_69 -> K03455_HIVHXB2CG_3027_3517_0_0_0_6_0_0_53_1_2_69
89 K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1_1_70 -> K03455_HIVHXB2CG_313_880_0_0_0_2_0_0_54_1_1_70
90 K03455|HIVHXB2CG_1938_2460_2_0_0_0_0_0_55/1_1_71 -> K03455_HIVHXB2CG_1938_2460_2_0_0_0_0_0_55_1_1_71
91 K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1_1_72 -> K03455_HIVHXB2CG_1235_1682_3_0_0_0_0_0_56_1_1_72
92 K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1_1_73 -> K03455_HIVHXB2CG_1835_2322_3_0_0_1_0_0_57_1_1_73
93 K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1_1_74 -> K03455_HIVHXB2CG_2276_2810_0_0_0_0_0_0_58_1_1_74
94 K03455|HIVHXB2CG_3596_4110_1_0_0_2_0_0_59/1_1_75 -> K03455_HIVHXB2CG_3596_4110_1_0_0_2_0_0_59_1_1_75
95 K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1_1_76 -> K03455_HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a_1_1_76
96 K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1_1_77 -> K03455_HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b_1_1_77
97 K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1_1_78 -> K03455_HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d_1_1_78
98 K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1_1_79 -> K03455_HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e_1_1_79
99 K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/1_1_80 -> K03455_HIVHXB2CG_121_652_1_0_0_0_0_0_5f_1_1_80
100 K03455|HIVHXB2CG_5585_6024_1_0_0_0_0_0_60/1_1_81 -> K03455_HIVHXB2CG_5585_6024_1_0_0_0_0_0_60_1_1_81
101 K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1_1_82 -> K03455_HIVHXB2CG_7976_8475_3_0_0_1_0_0_61_1_1_82
102 K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1_1_83 -> K03455_HIVHXB2CG_6322_6838_1_0_0_0_1_0_63_1_1_83
103
104 Gap/Ambiguity Composition p-value
105 1 K03455_HIVHXB2CG_1286_1769_0_0_0_4_0_0_0_1_1_0 77.05% passed 19.90%
106 2 K03455_HIVHXB2CG_5977_6467_2_0_0_2_0_0_1_1_2_1 77.05% failed 4.53%
107 3 K03455_HIVHXB2CG_6040_6545_1_0_0_0_0_0_2_1_3_2 77.05% failed 1.21%
108 4 K03455_HIVHXB2CG_3580_4035_1_0_0_0_0_0_3_1_1_3 77.05% passed 25.36%
109 5 K03455_HIVHXB2CG_5251_5720_0_0_0_1_0_0_4_1_2_4 77.05% passed 55.86%
110 6 K03455_HIVHXB2CG_5574_6092_2_0_0_1_0_0_5_1_1_5 77.05% passed 35.72%
111 7 K03455_HIVHXB2CG_7273_7731_1_0_0_5_0_0_6_1_1_6 77.05% failed 0.71%
112 8 K03455_HIVHXB2CG_5438_5909_1_0_0_4_0_0_7_1_1_7 77.05% passed 85.58%
113 9 K03455_HIVHXB2CG_4165_4569_2_0_0_3_0_0_8_1_2_8 77.05% passed 7.28%
114 10 K03455_HIVHXB2CG_2832_3397_3_0_0_2_0_0_9_1_1_9 77.05% passed 23.71%
115 11 K03455_HIVHXB2CG_1312_1798_2_0_0_1_0_0_a_1_2_10 77.05% failed 4.76%
116 12 K03455_HIVHXB2CG_6501_7035_0_0_0_0_0_0_b_1_2_11 77.05% passed 36.06%
117 13 K03455_HIVHXB2CG_2252_2786_0_0_0_0_0_0_c_1_1_12 77.05% failed 0.72%
118 14 K03455_HIVHXB2CG_7972_8486_1_0_0_0_0_0_e_1_1_13 77.05% failed 0.74%
119 15 K03455_HIVHXB2CG_368_934_2_0_0_3_0_0_f_1_1_14 77.05% failed 0.54%
120 16 K03455_HIVHXB2CG_8446_8894_4_0_0_3_0_0_10_1_1_15 77.05% failed 1.66%
121 17 K03455_HIVHXB2CG_6869_7379_1_0_0_3_0_1_11_1_2_16 77.05% passed 88.47%
122 18 K03455_HIVHXB2CG_5034_5548_1_0_0_4_0_0_13_1_1_17 77.05% failed 0.11%
123 19 K03455_HIVHXB2CG_418_930_3_0_0_1_0_0_14_1_1_18 77.05% passed 36.61%
124 20 K03455_HIVHXB2CG_8325_8818_2_0_0_2_0_0_15_1_1_19 77.05% passed 81.18%
125 21 K03455_HIVHXB2CG_673_1207_2_0_0_2_0_0_16_1_2_20 77.05% failed 0.00%
126 22 K03455_HIVHXB2CG_7932_8405_1_0_0_1_0_0_17_1_1_21 77.05% passed 14.75%
127 23 K03455_HIVHXB2CG_2894_3537_2_0_0_0_0_0_18_1_1_22 77.05% passed 65.23%
128 24 K03455_HIVHXB2CG_5989_6545_2_0_0_1_0_0_19_1_1_23 77.05% passed 15.67%
129 25 K03455_HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b_1_1_24 77.05% failed 0.02%
130 26 K03455_HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d_1_1_25 77.05% passed 56.52%
131 27 K03455_HIVHXB2CG_7_537_2_0_0_1_0_0_1e_1_1_26 77.05% passed 26.05%
132 28 K03455_HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f_1_1_27 77.05% failed 1.57%
133 29 K03455_HIVHXB2CG_5516_5958_3_0_0_2_0_0_20_1_1_28 77.05% passed 10.98%
134 30 K03455_HIVHXB2CG_8434_8946_0_0_0_1_0_0_21_1_2_29 77.05% passed 27.02%
135 31 K03455_HIVHXB2CG_2808_3255_0_0_0_1_0_0_22_1_1_30 77.05% passed 13.08%
136 32 K03455_HIVHXB2CG_5108_5621_3_0_0_2_0_0_23_1_1_31 77.05% failed 0.03%
137 33 K03455_HIVHXB2CG_3875_4298_2_0_0_1_0_0_24_1_1_32 77.05% passed 12.47%
138 34 K03455_HIVHXB2CG_8231_8877_0_0_0_3_0_0_25_1_1_33 77.05% passed 7.89%
139 35 K03455_HIVHXB2CG_7126_7621_1_1_1_3_1_0_26_1_1_34 77.05% passed 25.36%
140 36 K03455_HIVHXB2CG_3672_4151_0_0_0_1_0_0_27_1_1_35 77.05% failed 0.48%
141 37 K03455_HIVHXB2CG_4642_5125_0_0_0_3_0_0_28_1_1_36 77.05% passed 7.92%
142 38 K03455_HIVHXB2CG_8349_8802_1_0_0_0_0_0_29_1_1_37 77.05% passed 41.51%
143 39 K03455_HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a_1_2_38 77.05% failed 0.24%
144 40 K03455_HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b_1_2_39 77.05% passed 41.06%
145 41 K03455_HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d_1_2_40 77.05% passed 62.06%
146 42 K03455_HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e_1_1_41 77.05% failed 0.00%
147 43 K03455_HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f_1_1_42 77.05% passed 94.90%
148 44 K03455_HIVHXB2CG_3823_4361_1_0_0_0_0_0_30_1_1_43 77.05% passed 21.68%
149 45 K03455_HIVHXB2CG_4420_4903_1_0_0_1_0_0_31_1_1_44 77.05% passed 22.88%
150 46 K03455_HIVHXB2CG_1739_2301_2_0_0_2_0_0_33_1_1_45 77.05% passed 32.28%
151 47 K03455_HIVHXB2CG_756_1235_2_0_0_1_0_0_34_1_1_46 77.05% passed 14.89%
152 48 K03455_HIVHXB2CG_217_724_2_1_0_2_0_0_36_1_1_47 77.05% failed 3.69%
153 49 K03455_HIVHXB2CG_8069_8641_1_0_0_0_0_0_38_1_1_48 77.05% passed 19.81%
154 50 K03455_HIVHXB2CG_1786_2269_1_0_0_1_0_0_39_1_1_49 77.05% passed 8.95%
155 51 K03455_HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a_1_1_50 77.05% passed 15.20%
156 52 K03455_HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b_1_2_51 77.05% passed 16.44%
157 53 K03455_HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c_1_1_52 77.05% passed 72.71%
158 54 K03455_HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d_1_1_53 77.05% passed 46.60%
159 55 K03455_HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e_1_1_54 77.05% failed 2.49%
160 56 K03455_HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f_1_1_55 77.05% passed 25.92%
161 57 K03455_HIVHXB2CG_8342_8779_1_0_0_2_0_0_40_1_1_56 77.05% passed 36.75%
162 58 K03455_HIVHXB2CG_6619_7094_0_0_0_2_0_0_41_1_1_57 77.05% passed 12.72%
163 59 K03455_HIVHXB2CG_5150_5584_1_0_0_2_0_0_42_1_1_58 77.05% passed 33.57%
164 60 K03455_HIVHXB2CG_5329_5821_2_0_0_2_0_0_43_1_1_59 77.05% passed 89.40%
165 61 K03455_HIVHXB2CG_4457_4958_4_0_0_0_0_0_44_1_1_60 77.05% passed 20.77%
166 62 K03455_HIVHXB2CG_906_1404_1_0_0_3_0_0_45_1_1_61 77.05% passed 20.83%
167 63 K03455_HIVHXB2CG_2685_3250_0_0_0_0_0_0_46_1_1_62 77.05% failed 0.48%
168 64 K03455_HIVHXB2CG_6045_6577_2_0_0_1_0_0_47_1_1_63 77.05% passed 16.69%
169 65 K03455_HIVHXB2CG_1707_2205_1_0_0_3_0_0_48_1_2_64 77.05% passed 24.64%
170 66 K03455_HIVHXB2CG_4939_5430_1_0_0_0_0_0_49_1_1_65 77.05% failed 1.23%
171 67 K03455_HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a_1_1_66 77.05% failed 0.65%
172 68 K03455_HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e_1_1_67 77.05% passed 68.90%
173 69 K03455_HIVHXB2CG_2700_3243_0_0_0_3_1_0_51_1_1_68 77.05% passed 51.19%
174 70 K03455_HIVHXB2CG_3027_3517_0_0_0_6_0_0_53_1_2_69 77.05% failed 0.60%
175 71 K03455_HIVHXB2CG_313_880_0_0_0_2_0_0_54_1_1_70 77.05% failed 0.10%
176 72 K03455_HIVHXB2CG_1938_2460_2_0_0_0_0_0_55_1_1_71 77.05% passed 5.03%
177 73 K03455_HIVHXB2CG_1235_1682_3_0_0_0_0_0_56_1_1_72 77.05% passed 33.28%
178 74 K03455_HIVHXB2CG_1835_2322_3_0_0_1_0_0_57_1_1_73 77.05% passed 50.17%
179 75 K03455_HIVHXB2CG_2276_2810_0_0_0_0_0_0_58_1_1_74 77.05% failed 0.26%
180 76 K03455_HIVHXB2CG_3596_4110_1_0_0_2_0_0_59_1_1_75 77.05% passed 6.77%
181 77 K03455_HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a_1_1_76 77.05% failed 2.37%
182 78 K03455_HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b_1_1_77 77.05% passed 10.04%
183 79 K03455_HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d_1_1_78 77.05% failed 3.16%
184 80 K03455_HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e_1_1_79 77.05% passed 32.98%
185 81 K03455_HIVHXB2CG_121_652_1_0_0_0_0_0_5f_1_1_80 77.05% passed 51.70%
186 82 K03455_HIVHXB2CG_5585_6024_1_0_0_0_0_0_60_1_1_81 77.05% passed 14.88%
187 83 K03455_HIVHXB2CG_7976_8475_3_0_0_1_0_0_61_1_1_82 77.05% passed 82.25%
188 84 K03455_HIVHXB2CG_6322_6838_1_0_0_0_1_0_63_1_1_83 77.05% passed 68.89%
189 WARNING: 84 sequences contain more than 50% gaps/ambiguity
190 **** TOTAL 77.05% 26 sequences failed composition chi2 test (p-value<5%; df=3)
191
192 Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.017 seconds
193
194 NOTE: 3 MB RAM (0 GB) is required!
195 Estimate model parameters (epsilon = 0.100)
196 1. Initial log-likelihood: -7393.152
197 2. Current log-likelihood: -6850.590
198 3. Current log-likelihood: -6814.795
199 4. Current log-likelihood: -6812.204
200 5. Current log-likelihood: -6811.732
201 6. Current log-likelihood: -6811.618
202 Optimal log-likelihood: -6811.491
203 Rate parameters: A-C: 1.16582 A-G: 3.17373 A-T: 0.69428 C-G: 1.33012 C-T: 3.22998 G-T: 1.00000
204 Base frequencies: A: 0.281 C: 0.222 G: 0.210 T: 0.287
205 Site proportion and rates: (0.080,0.274) (0.303,0.606) (0.379,0.714) (0.238,2.200)
206 Parameters optimization took 6 rounds (0.508 sec)
207 Computing ML distances based on estimated model parameters... 0.032 sec
208 WARNING: Some pairwise ML distances are too long (saturated)
209 Computing BIONJ tree...
210 0.003 seconds
211 Log-likelihood of BIONJ tree: -6859.680
212 --------------------------------------------------------------------
213 | INITIALIZING CANDIDATE TREE SET |
214 --------------------------------------------------------------------
215 Generating 98 parsimony trees... 1.076 second
216 Computing log-likelihood of 98 initial trees ... 1.196 seconds
217 Current best score: -6803.399
218
219 Do NNI search on 20 best initial trees
220 Estimate model parameters (epsilon = 0.100)
221 BETTER TREE FOUND at iteration 1: -6746.667
222 Estimate model parameters (epsilon = 0.100)
223 BETTER TREE FOUND at iteration 4: -6743.453
224 Estimate model parameters (epsilon = 0.100)
225 BETTER TREE FOUND at iteration 8: -6739.399
226 Iteration 10 / LogL: -6755.382 / Time: 0h:0m:8s
227 Iteration 20 / LogL: -6783.485 / Time: 0h:0m:12s
228 Finish initializing candidate tree set (20)
229 Current best tree score: -6739.399 / CPU time: 11.455
230 Number of iterations: 20
231 --------------------------------------------------------------------
232 | OPTIMIZING CANDIDATE TREE SET |
233 --------------------------------------------------------------------
234 Estimate model parameters (epsilon = 0.100)
235 BETTER TREE FOUND at iteration 24: -6738.697
236 Estimate model parameters (epsilon = 0.100)
237 BETTER TREE FOUND at iteration 25: -6730.006
238 Estimate model parameters (epsilon = 0.100)
239 BETTER TREE FOUND at iteration 27: -6728.392
240 Estimate model parameters (epsilon = 0.100)
241 BETTER TREE FOUND at iteration 29: -6725.172
242 Iteration 30 / LogL: -6728.632 / Time: 0h:0m:15s (0h:0m:53s left)
243 Estimate model parameters (epsilon = 0.100)
244 BETTER TREE FOUND at iteration 31: -6723.283
245 Estimate model parameters (epsilon = 0.100)
246 BETTER TREE FOUND at iteration 37: -6720.321
247 Estimate model parameters (epsilon = 0.100)
248 BETTER TREE FOUND at iteration 39: -6717.689
249 Iteration 40 / LogL: -6719.783 / Time: 0h:0m:19s (0h:0m:48s left)
250 Estimate model parameters (epsilon = 0.100)
251 BETTER TREE FOUND at iteration 41: -6717.333
252 Estimate model parameters (epsilon = 0.100)
253 BETTER TREE FOUND at iteration 44: -6715.754
254 Iteration 50 / LogL: -6716.133 / Time: 0h:0m:21s (0h:0m:42s left)
255 Estimate model parameters (epsilon = 0.100)
256 BETTER TREE FOUND at iteration 56: -6714.598
257 Estimate model parameters (epsilon = 0.100)
258 BETTER TREE FOUND at iteration 59: -6714.257
259 Iteration 60 / LogL: -6715.774 / Time: 0h:0m:25s (0h:0m:42s left)
260 Estimate model parameters (epsilon = 0.100)
261 BETTER TREE FOUND at iteration 66: -6713.872
262 Iteration 70 / LogL: -6714.239 / Time: 0h:0m:28s (0h:0m:39s left)
263 Iteration 80 / LogL: -6714.049 / Time: 0h:0m:30s (0h:0m:33s left)
264 Iteration 90 / LogL: -6716.076 / Time: 0h:0m:33s (0h:0m:28s left)
265 Iteration 100 / LogL: -6715.577 / Time: 0h:0m:36s (0h:0m:24s left)
266 BETTER TREE FOUND at iteration 105: -6713.864
267 Iteration 110 / LogL: -6715.309 / Time: 0h:0m:39s (0h:0m:34s left)
268 Iteration 120 / LogL: -6713.877 / Time: 0h:0m:42s (0h:0m:30s left)
269 Estimate model parameters (epsilon = 0.100)
270 BETTER TREE FOUND at iteration 123: -6712.300
271 Estimate model parameters (epsilon = 0.100)
272 BETTER TREE FOUND at iteration 126: -6710.985
273 Estimate model parameters (epsilon = 0.100)
274 BETTER TREE FOUND at iteration 127: -6710.445
275 Estimate model parameters (epsilon = 0.100)
276 BETTER TREE FOUND at iteration 130: -6709.739
277 Iteration 130 / LogL: -6709.739 / Time: 0h:0m:45s (0h:0m:35s left)
278 Estimate model parameters (epsilon = 0.100)
279 BETTER TREE FOUND at iteration 136: -6709.364
280 Iteration 140 / LogL: -6710.807 / Time: 0h:0m:48s (0h:0m:33s left)
281 Estimate model parameters (epsilon = 0.100)
282 BETTER TREE FOUND at iteration 142: -6709.294
283 Estimate model parameters (epsilon = 0.100)
284 BETTER TREE FOUND at iteration 147: -6708.895
285 Iteration 150 / LogL: -6712.081 / Time: 0h:0m:51s (0h:0m:33s left)
286 Estimate model parameters (epsilon = 0.100)
287 BETTER TREE FOUND at iteration 160: -6708.749
288 Iteration 160 / LogL: -6708.749 / Time: 0h:0m:54s (0h:0m:34s left)
289 Estimate model parameters (epsilon = 0.100)
290 BETTER TREE FOUND at iteration 163: -6708.686
291 Iteration 170 / LogL: -6710.289 / Time: 0h:0m:57s (0h:0m:31s left)
292 Estimate model parameters (epsilon = 0.100)
293 BETTER TREE FOUND at iteration 173: -6708.554
294 Estimate model parameters (epsilon = 0.100)
295 BETTER TREE FOUND at iteration 180: -6708.518
296 Iteration 180 / LogL: -6708.518 / Time: 0h:1m:0s (0h:0m:33s left)
297 Iteration 190 / LogL: -6709.408 / Time: 0h:1m:3s (0h:0m:30s left)
298 Estimate model parameters (epsilon = 0.100)
299 BETTER TREE FOUND at iteration 193: -6705.296
300 BETTER TREE FOUND at iteration 200: -6705.295
301 Iteration 200 / LogL: -6705.295 / Time: 0h:1m:6s (0h:0m:33s left)
302 Estimate model parameters (epsilon = 0.100)
303 BETTER TREE FOUND at iteration 202: -6705.270
304 Iteration 210 / LogL: -6705.378 / Time: 0h:1m:8s (0h:0m:30s left)
305 Iteration 220 / LogL: -6708.516 / Time: 0h:1m:11s (0h:0m:26s left)
306 Iteration 230 / LogL: -6705.293 / Time: 0h:1m:14s (0h:0m:23s left)
307 Iteration 240 / LogL: -6707.618 / Time: 0h:1m:17s (0h:0m:20s left)
308 Iteration 250 / LogL: -6705.961 / Time: 0h:1m:20s (0h:0m:16s left)
309 Iteration 260 / LogL: -6705.327 / Time: 0h:1m:22s (0h:0m:13s left)
310 Iteration 270 / LogL: -6705.292 / Time: 0h:1m:25s (0h:0m:10s left)
311 Iteration 280 / LogL: -6707.215 / Time: 0h:1m:28s (0h:0m:6s left)
312 Iteration 290 / LogL: -6705.310 / Time: 0h:1m:31s (0h:0m:3s left)
313 BETTER TREE FOUND at iteration 293: -6705.270
314 BETTER TREE FOUND at iteration 295: -6705.269
315 Iteration 300 / LogL: -6705.416 / Time: 0h:1m:33s (0h:0m:29s left)
316 Iteration 310 / LogL: -6708.491 / Time: 0h:1m:36s (0h:0m:26s left)
317 Iteration 320 / LogL: -6705.394 / Time: 0h:1m:39s (0h:0m:23s left)
318 UPDATE BEST LOG-LIKELIHOOD: -6705.269
319 Iteration 330 / LogL: -6707.929 / Time: 0h:1m:41s (0h:0m:20s left)
320 Iteration 340 / LogL: -6705.373 / Time: 0h:1m:44s (0h:0m:16s left)
321 Iteration 350 / LogL: -6706.548 / Time: 0h:1m:47s (0h:0m:13s left)
322 Iteration 360 / LogL: -6705.366 / Time: 0h:1m:50s (0h:0m:10s left)
323 Iteration 370 / LogL: -6708.694 / Time: 0h:1m:52s (0h:0m:7s left)
324 Iteration 380 / LogL: -6707.358 / Time: 0h:1m:55s (0h:0m:4s left)
325 Iteration 390 / LogL: -6705.825 / Time: 0h:1m:58s (0h:0m:1s left)
326 TREE SEARCH COMPLETED AFTER 396 ITERATIONS / Time: 0h:1m:59s
327
328 --------------------------------------------------------------------
329 | FINALIZING TREE SEARCH |
330 --------------------------------------------------------------------
331 Performs final model parameters optimization
332 Estimate model parameters (epsilon = 0.010)
333 1. Initial log-likelihood: -6705.269
334 Optimal log-likelihood: -6705.266
335 Rate parameters: A-C: 1.13682 A-G: 3.52293 A-T: 0.74232 C-G: 0.82784 C-T: 3.38691 G-T: 1.00000
336 Base frequencies: A: 0.281 C: 0.222 G: 0.210 T: 0.287
337 Site proportion and rates: (0.052,0.226) (0.340,0.517) (0.301,0.517) (0.307,2.143)
338 Parameters optimization took 1 rounds (0.062 sec)
339 BEST SCORE FOUND : -6705.266
340 Total tree length: 81.560
341
342 Total number of iterations: 396
343 CPU time used for tree search: 114.612 sec (0h:1m:54s)
344 Wall-clock time used for tree search: 119.058 sec (0h:1m:59s)
345 Total CPU time used: 115.545 sec (0h:1m:55s)
346 Total wall-clock time used: 120.013 sec (0h:2m:0s)
347
348 Analysis results written to:
349 IQ-TREE report: clsReps.aln.iqtree
350 Maximum-likelihood tree: clsReps.aln.treefile
351 Likelihood distances: clsReps.aln.mldist
352 Screen log file: clsReps.aln.log
353
354 Date and Time: Tue May 28 13:11:57 2019