core_diversity_analyses.py error

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Muhammad Afiq

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Oct 26, 2017, 4:19:32 AM10/26/17
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Hi,

Can someone help me with this error?

Command returned exit status: 1
Stdout:

Stderr
Traceback (most recent call last):
  File "/root/miniconda2/bin/make_rarefaction_plots.py", line 4, in <module>
    __import__('pkg_resources').run_script('qiime==1.9.1', 'make_rarefaction_plots.py')
  File "/root/miniconda2/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/__init__.py", line 744, in run_script

  File "/root/miniconda2/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/__init__.py", line 1499, in run_script

  File "/root/miniconda2/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg-info/scripts/make_rarefaction_plots.py", line 229, in <module>
    main()
  File "/root/miniconda2/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 "/root/miniconda2/lib/python2.7/site-packages/qiime/make_rarefaction_plots.py", line 667, in make_averages
    metric_name, output_type)
  File "/root/miniconda2/lib/python2.7/site-packages/qiime/make_rarefaction_plots.py", line 36, in save_ave_rarefaction_plots
    plt.clf()
  File "/root/miniconda2/lib/python2.7/site-packages/matplotlib/pyplot.py", line 673, in clf
    gcf().clf()
  File "/root/miniconda2/lib/python2.7/site-packages/matplotlib/pyplot.py", line 586, in gcf
    return figure()
  File "/root/miniconda2/lib/python2.7/site-packages/matplotlib/pyplot.py", line 535, in figure
    **kwargs)
  File "/root/miniconda2/lib/python2.7/site-packages/matplotlib/backends/backend_qt4agg.py", line 46, in new_figure_manager
    return new_figure_manager_given_figure(num, thisFig)
  File "/root/miniconda2/lib/python2.7/site-packages/matplotlib/backends/backend_qt4agg.py", line 53, in new_figure_manager_given_figure
    canvas = FigureCanvasQTAgg(figure)
  File "/root/miniconda2/lib/python2.7/site-packages/matplotlib/backends/backend_qt4agg.py", line 76, in __init__
    FigureCanvasQT.__init__(self, figure)
  File "/root/miniconda2/lib/python2.7/site-packages/matplotlib/backends/backend_qt4.py", line 63, in __init__
    _create_qApp()
  File "/root/miniconda2/lib/python2.7/site-packages/matplotlib/backends/backend_qt5.py", line 136, in _create_qApp
    raise RuntimeError('Invalid DISPLAY variable')
RuntimeError: Invalid DISPLAY variable


Thank you.

Colin Brislawn

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Oct 26, 2017, 1:40:24 PM10/26/17
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Hello Muhammad,

This is caused by a newer version of matplotlib which does not like qiime 1.9.1. If you install a specific version of matplotlib, this should solve the problem:

conda install matplotlib=1.4.3

Let me know how well that works for you!
Colin

Muhammad

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Oct 26, 2017, 7:39:19 PM10/26/17
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Hi Colin,

Thank you for your reply. I tried the command, but somehow it has a conflict. Below is the error:

# conda install matplotlib=1.4.3
Fetching package metadata .................
Solving package specifications: .

UnsatisfiableError: The following specifications were found to be in conflict:
  - libgd
  - matplotlib 1.4.3*
Use "conda info <package>" to see the dependencies for each package.

Thank you.

zech xu

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Oct 26, 2017, 9:02:34 PM10/26/17
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Hello Muhammad,

You can also try to change the matplotlib backend to "agg". Please see https://matplotlib.org/1.3.1/users/customizing.html on how to do that.
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