Error when using summarize_taxa_through_plots.py

[Luz]

Hi, 

I am getting the error shown below when running summarize_taxa_through_plots.py. I have attached my biom table. 

summarize_taxa_through_plots.py -i Qiime_test4/OTUs/otu_table_mc2_w_tax.biom -o Qiime_test4/summaries

Traceback (most recent call last):

  File "/usr/local/bin/summarize_taxa_through_plots.py", line 143, in <module>

    main()

  File "/usr/local/bin/summarize_taxa_through_plots.py", line 140, in main

    status_update_callback=status_update_callback)

  File "/usr/local/lib/python2.7/dist-packages/qiime/workflow/downstream.py", line 711, in run_summarize_taxa_through_plots

    close_logger_on_success=close_logger_on_success)

  File "/usr/local/lib/python2.7/dist-packages/qiime/workflow/util.py", line 122, in call_commands_serially

    raise WorkflowError(msg)

qiime.workflow.util.WorkflowError:

*** ERROR RAISED DURING STEP: Plot Taxonomy Summary

Command run was:

 plot_taxa_summary.py -i Qiime_test4/summaries/otu_table_mc2_w_tax_L2.txt,Qiime_test4/summaries/otu_table_mc2_w_tax_L3.txt,Qiime_test4/summaries/otu_table_mc2_w_tax_L4.txt,Qiime_test4/summaries/otu_table_mc2_w_tax_L5.txt,Qiime_test4/summaries/otu_table_mc2_w_tax_L6.txt -o Qiime_test4/summaries/taxa_summary_plots/

Command returned exit status: 1

Stdout:

Stderr

Traceback (most recent call last):

  File "/usr/local/bin/plot_taxa_summary.py", line 278, in <module>

    main()

  File "/usr/local/bin/plot_taxa_summary.py", line 274, in main

    resize_nth_label, label_type, include_html_legend)

  File "/usr/local/lib/python2.7/dist-packages/qiime/plot_taxa_summary.py", line 1138, in make_all_charts

    resize_nth_label, label_type, include_html_legend))

  File "/usr/local/lib/python2.7/dist-packages/qiime/plot_taxa_summary.py", line 1073, in get_counts

    label_type, include_html_legend))

  File "/usr/local/lib/python2.7/dist-packages/qiime/plot_taxa_summary.py", line 861, in make_HTML_table

    props={'title': title})

  File "/usr/local/lib/python2.7/dist-packages/qiime/plot_taxa_summary.py", line 466, in make_area_bar_chart

    fig = figure(figsize=(plot_width, plot_height))

  File "/usr/lib/python2.7/dist-packages/matplotlib/pyplot.py", line 535, in figure

    **kwargs)

  File "/usr/lib/python2.7/dist-packages/matplotlib/backends/backend_tkagg.py", line 84, in new_figure_manager

    return new_figure_manager_given_figure(num, figure)

  File "/usr/lib/python2.7/dist-packages/matplotlib/backends/backend_tkagg.py", line 92, in new_figure_manager_given_figure

    window = Tk.Tk()

  File "/usr/lib/python2.7/lib-tk/Tkinter.py", line 1818, in __init__

    self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use)

_tkinter.TclError: no display name and no $DISPLAY environment variable

Thank you for your help! 

[Jai Ram Rideout]

Hi Luz,

Can you try running this command to set a different matplotlib backend? The backend you have set (likely the default) requires a DISPLAY variable but you appear to be in a headless environment.

export MPLBACKEND="Agg"

Once you run that command, try rerunning summarize_taxa_through_plots.py. If the script succeeds, you may want to put the MPLBACKEND command in your .bashrc file so that it is activated whenever you open a new terminal. If you don't put it in your .bashrc file, you'll need to rerun the command each time you open a new terminal.

Best,

Jai

[Luz]

Jai, 

Thank you so much. I will follow up with your recommendations. I was able to make it work using the X2go client instead of Putty. I just finally thought of this after realizing that everyone else in my lab had succeeded with this step, but they were all using X2go. 

Thank you so much, 

Luz

[Jai Ram Rideout]

Thanks for following up with your solution Luz!

Jai