matplotlib raise RuntimeError ('Invalid DISPLAY variable')

[xingjianfeng100]

Hi, when plotting the kmer_freq, it reported errors like this:

"23-09-13 23:23:33 [INFO] Plot k15_q200_f2.kmer_freq.pdf
Traceback (most recent call last):
  File "~/.conda/envs/SubPhaser/bin/subphaser", line 33, in <module>
    sys.exit(load_entry_point('subphaser==1.2.6', 'console_scripts', 'subphaser')())
  File "~/.conda/envs/SubPhaser/lib/python3.8/site-packages/subphaser-1.2.6-py3.8.egg/subphaser/__main__.py", line 790, in main
    pipeline.run()
  File "~/.conda/envs/SubPhaser/lib/python3.8/site-packages/subphaser-1.2.6-py3.8.egg/subphaser/__main__.py", line 415, in run
    d_mat = dumps.filter(d_mat, lengths, self.sgs, outfig=histfig, #d_targets=d_targets, 
  File "~/.conda/envs/SubPhaser/lib/python3.8/site-packages/subphaser-1.2.6-py3.8.egg/subphaser/Jellyfish.py", line 504, in filter
    plot_histogram(tot_freqs, outfig, vline=None)
  File "~/.conda/envs/SubPhaser/lib/python3.8/site-packages/subphaser-1.2.6-py3.8.egg/subphaser/Jellyfish.py", line 647, in plot_histogram
    plt.figure(figsize=(7,5), dpi=300, tight_layout=True)
  File "~/.conda/envs/SubPhaser/lib/python3.8/site-packages/matplotlib/pyplot.py", line 797, in figure
    manager = new_figure_manager(
  File "~/.conda/envs/SubPhaser/lib/python3.8/site-packages/matplotlib/pyplot.py", line 316, in new_figure_manager
    return _backend_mod.new_figure_manager(*args, **kwargs)
  File "~/.conda/envs/SubPhaser/lib/python3.8/site-packages/matplotlib/backend_bases.py", line 3545, in new_figure_manager
    return cls.new_figure_manager_given_figure(num, fig)
  File "~/.conda/envs/SubPhaser/lib/python3.8/site-packages/matplotlib/backend_bases.py", line 3550, in new_figure_manager_given_figure
    canvas = cls.FigureCanvas(figure)
  File "~/.conda/envs/SubPhaser/lib/python3.8/site-packages/matplotlib/backends/backend_qt5agg.py", line 21, in __init__
    super().__init__(figure=figure)
  File "~/.conda/envs/SubPhaser/lib/python3.8/site-packages/matplotlib/backends/backend_qt5.py", line 213, in __init__
    _create_qApp()
  File "~/.conda/envs/SubPhaser/lib/python3.8/site-packages/matplotlib/backends/backend_qt5.py", line 108, in _create_qApp
    raise RuntimeError('Invalid DISPLAY variable')
RuntimeError: Invalid DISPLAY variable"

how can I solve it?

[zhangrengang]

It is an issue of interactive backend of matplotlib. Can you find and edit the file ~/.conda/envs/SubPhaser/lib/python3.8/site-packages/matplotlib/mpl-data/matplotlibrc , with setting backend : agg? agg is s a non-interactive backend.

[xingjianfeng100]

It is an issue of interactive backend of matplotlib. Can you find and edit the file ~/.conda/envs/SubPhaser/lib/python3.8/site-packages/matplotlib/mpl-data/matplotlibrc , with setting backend : agg? agg is s a non-interactive backend.

I fixed it after running "bash script" instead of "sh script"; very nice tools, thanks for your response !