log文件很长你用less 打开查看
老师好,课程上讲的是打开log文件看best-fit model但是我打开我的log文件后没看到这几个单词,您可以帮我看一下我这个结果里面哪个代表了最佳模型吗,谢谢老师
结果如下:
1 IQ-TREE multicore version 2.2.2.2 COVID-edition for Linux 64-bit built Nov 16 2022
2 Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
3 Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
4
5 Host: 9c55ccc77b4f (AVX2, FMA3, 5 GB RAM)
6 Command: iqtree2 -s HSP90_pep_final_aligned_trimed.fasta -m MFP -B 1000 --bnni -T 2 --prefix iqtree2.pep.fullLength
7 Seed: 322460 (Using SPRNG - Scalable Parallel Random Number Generator)
8 Time: Sun Dec 3 19:46:41 2023
9 Kernel: AVX+FMA - 2 threads (2 CPU cores detected)
10
11 Reading alignment file HSP90_pep_final_aligned_trimed.fasta ... Fasta format detected
12 Reading fasta file: done in 0.0003235 secs using 19.78% CPU
13 Alignment most likely contains protein sequences
14 Constructing alignment: done in 0.000678 secs using 115.5% CPU
15 Alignment has 20 sequences with 614 columns, 608 distinct patterns
16 398 parsimony-informative, 155 singleton sites, 61 constant sites
17 Gap/Ambiguity Composition p-value
18 Analyzing sequences: done in 2.9e-05 secs using 37.93% CPU
19 1 Glyma.02G124500.Wm82.a2.v1 2.93% passed 80.70%
20 2 Glyma.08G332900.Wm82.a2.v1 1.79% passed 99.93%
21 3 Glyma.01G068000.Wm82.a2.v1 2.93% passed 86.78%
22 4 Glyma.17G220000.Wm82.a2.v1 51.14% passed 5.30%
23 5 Glyma.02G305600.Wm82.a2.v1 1.95% passed 65.74%
24 6 Glyma.11G227000.Wm82.a2.v1 55.37% failed 1.43%
25 7 Glyma.09G131500.Wm82.a2.v1 1.63% passed 99.98%
26 8 Glyma.03G114400.Wm82.a2.v1 9.77% failed 2.36%
27 9 Glyma.17G258700.Wm82.a2.v1 2.12% passed 96.78%
28 10 Glyma.16G178800.Wm82.a2.v1 1.63% passed 99.99%
29 11 Glyma.14G011600.Wm82.a2.v1 1.79% passed 99.96%
30 12 Glyma.10G098300.Wm82.a2.v1 57.49% passed 72.36%
31 13 Glyma.18G074100.Wm82.a2.v1 1.79% passed 99.89%
32 14 Glyma.14G219700.Wm82.a2.v1 2.12% passed 97.52%
33 15 Glyma.02G302500.Wm82.a2.v1 1.79% passed 99.94%
34 16 Glyma.07G207600.Wm82.a2.v1 57.17% passed 68.22%
35 17 Glyma.08G032900.Wm82.a2.v1 9.12% passed 99.58%
36 18 Glyma.17G182500.Wm82.a2.v1 44.95% passed 45.15%
37 19 Glyma.19G098200.Wm82.a2.v1 52.77% passed 9.65%
38 20 Glyma.14G007700.Wm82.a2.v1 2.12% passed 69.11%
39 WARNING: 5 sequences contain more than 50% gaps/ambiguity
40 **** TOTAL 18.12% 2 sequences failed composition chi2 test (p-value<5%; df=19)
41 Checking for duplicate sequences: done in 6.5e-05 secs using 69.23% CPU
42
43
44 Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.004 seconds
45 Perform fast likelihood tree search using LG+I+G model...
46 Estimate model parameters (epsilon = 5.000)
47 Perform nearest neighbor interchange...
48 Optimizing NNI: done in 0.266794 secs using 196.5% CPU
49 Estimate model parameters (epsilon = 1.000)
50 1. Initial log-likelihood: -8620.850
51 Optimal log-likelihood: -8620.640
52 Proportion of invariable sites: 0.021
53 Gamma shape alpha: 7.556
54 Parameters optimization took 1 rounds (0.100 sec)