根据log文件判断进化树最佳模型

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)

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omicsgene - 生物信息
擅长:重测序,遗传进化,转录组,GWAS

log文件很长你用less 打开查看

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  • 提出于 2023-12-03 20:03

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