core_diversity_analyses.py error

[Muhammad Afiq]

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]

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]

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]

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.