0042-【宏基因组】-qiime1问题列表-make_rarefaction_plots.py无法画图

1.多样性分析的步骤

core_diversity_analyses.py
1. single_rarefaction.py——Rarify the OTU table
2. beta_diversity.py——-beta多样性
3. principal_coordinates.py——PCoA图形化
4. alpha_diversity.py——-Alpha多样性
5. make_rarefaction_plots.py——-稀释曲线
6. summarize_taxa.py——Summarize Taxonomy
7. plot_taxa_summary.py——Taxa summary plots

2.执行命令

core_diversity_analyses.py -o cdout/ -i otus/otu_table_mc2_w_tax_no_pynast_failures.biom -m config/map.txt -t otus/rep_set.tre -e 195965 -p config/diversityParams.txt

3.在执行子程序时

make_rarefaction_plots.py -i cdout//arare_max195965//alpha_div_collated/ -m config/map.txt -o cdout//arare_max195965//alpha_rarefaction_plots/

4.出现错误

Stderr
Traceback (most recent call last):
  File "/home/toucan/miniconda3/envs/qiime1/bin/make_rarefaction_plots.py", line 4, in <module>
    __import__('pkg_resources').run_script('qiime==1.9.1', 'make_rarefaction_plots.py')
  File "/home/toucan/miniconda3/envs/qiime1/lib/python2.7/site-packages/pkg_resources/__init__.py", line 654, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/home/toucan/miniconda3/envs/qiime1/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1434, in run_script
    exec(code, namespace, namespace)
  File "/home/toucan/miniconda3/envs/qiime1/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg-info/scripts/make_rarefaction_plots.py", line 229, in <module>
    main()
  File "/home/toucan/miniconda3/envs/qiime1/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg-info/scripts/make_rarefaction_plots.py", line 219, in main
    generate_average_tables=generate_average_tables)
  File "/home/toucan/miniconda3/envs/qiime1/lib/python2.7/site-packages/qiime/make_rarefaction_plots.py", line 667, in make_averages
    metric_name, output_type)
  File "/home/toucan/miniconda3/envs/qiime1/lib/python2.7/site-packages/qiime/make_rarefaction_plots.py", line 36, in save_ave_rarefaction_plots
    plt.clf()
  File "/home/toucan/miniconda3/envs/qiime1/lib/python2.7/site-packages/matplotlib/pyplot.py", line 547, in clf
    gcf().clf()
  File "/home/toucan/miniconda3/envs/qiime1/lib/python2.7/site-packages/matplotlib/pyplot.py", line 462, in gcf
    return figure()
  File "/home/toucan/miniconda3/envs/qiime1/lib/python2.7/site-packages/matplotlib/pyplot.py", line 435, in figure
    **kwargs)
  File "/home/toucan/miniconda3/envs/qiime1/lib/python2.7/site-packages/matplotlib/backends/backend_qt4agg.py", line 47, in new_figure_manager
    return new_figure_manager_given_figure(num, thisFig)
  File "/home/toucan/miniconda3/envs/qiime1/lib/python2.7/site-packages/matplotlib/backends/backend_qt4agg.py", line 54, in new_figure_manager_given_figure
    canvas = FigureCanvasQTAgg(figure)
  File "/home/toucan/miniconda3/envs/qiime1/lib/python2.7/site-packages/matplotlib/backends/backend_qt4agg.py", line 72, in __init__
    FigureCanvasQT.__init__(self, figure)
  File "/home/toucan/miniconda3/envs/qiime1/lib/python2.7/site-packages/matplotlib/backends/backend_qt4.py", line 68, in __init__
    _create_qApp()
  File "/home/toucan/miniconda3/envs/qiime1/lib/python2.7/site-packages/matplotlib/backends/backend_qt5.py", line 138, in _create_qApp
    raise RuntimeError('Invalid DISPLAY variable')
RuntimeError: Invalid DISPLAY variable

5.然后，在谷歌搜索，qiime2论坛有个相关的帖子

Error in qiime feature-table summarize

https://forum.qiime2.org/t/error-in-qiime-feature-table-summarize/308

大神jairideout也有回答。

The quality score plots are generated using R, which seems to work out-of-the-box on a headless sever. feature-table summarize uses matplotlib (in Python) to generate the visualization. The solution @thermokarst posted instructs matplotlib to use a headless rendering backend (matplotlib’s default backend usually requires a display).

不太懂意思。推测，是否因为使用conda装的qiime1虚拟环境，缺软件之类的事情。要求使用有界面的服务器使用matplotlib。

6.使用桌面的ubuntu 18.04稳定版桌面版，继续执行命令

core_diversity_analyses.py -o cdout2/ -i otus/otu_table_mc2_w_tax_no_pynast_failures.biom -m config/map.txt -t otus/rep_set.tre -e 195965 -p config/diversityParams.txt

7. 显示不同的报错，看来真的缺包和配置之类的

QGtkStyle could not resolve GTK. Make sure you have installed the proper libraries.
/home/toucan/miniconda3/envs/qiime1/lib/python2.7/site-packages/matplotlib/collections.py:590: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
  if self._edgecolors == str('face'):
QGtkStyle could not resolve GTK. Make sure you have installed the proper libraries.
/home/toucan/miniconda3/envs/qiime1/lib/python2.7/site-packages/matplotlib/collections.py:590: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
  if self._edgecolors == str('face'):

8.继续谷歌搜索，发现一个帖子，ubuntu 18.04版本

QGtkStyle could not resolve GTK – Ubuntu 18.04 #1768

https://github.com/ilastik/ilastik/issues/1768

18.04版本缺乏缺少库

跟着他的提示，在qiime1虚拟环境下,追加环境比变量

vim ~/.bashrc

export QT_STYLE_OVERRIDE=gtk2

source ~/.bashrc

9.重新执行core_diversity_analyses.py命令，仍然与，上面相同报错，无效。

10.等待新解决方法，或者使用qiime1 docker的方法，这样的虚拟环境比较健全。