Error during summarize_taxa_through_plots.py

[Vanessa V.]

Hi all, 

I'm getting an error (or errors) when I run summarize_taxa_through_plots.py.  Workflow error and Run time error, Invalid display variable.  I'm not working on a virtual machine; instead I am working with QIIME recently installed on our HPCC at my institution.  It seems like some type of site package is not correct?  It's hard for me to discern from this error exactly what needs to be changed/updated?

Thanks for your help in advance, 

Vanessa

summarize_taxa_through_plots.py -i otu_table_mc2_w_tax.biom -o taxonomy_summaries_plots/

Traceback (most recent call last):

  File "/opt/qiime/1.9.1/bin/summarize_taxa_through_plots.py", line 4, in <module>

    __import__('pkg_resources').run_script('qiime==1.9.1', 'summarize_taxa_through_plots.py')

  File "/gpfs0/export/opt/anaconda-2.3.0/lib/python2.7/site-packages/setuptools-17.1.1-py2.7.egg/pkg_resources/__init__.py", line 735, in run_script

  File "/gpfs0/export/opt/anaconda-2.3.0/lib/python2.7/site-packages/setuptools-17.1.1-py2.7.egg/pkg_resources/__init__.py", line 1652, in run_script

  File "/gpfs0/export/opt/qiime/1.9.1/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg/EGG-INFO/scripts/summarize_taxa_through_plots.py", line 143, in <module>

    main()

  File "/gpfs0/export/opt/qiime/1.9.1/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg/EGG-INFO/scripts/summarize_taxa_through_plots.py", line 140, in main

    status_update_callback=status_update_callback)

  File "/opt/qiime/1.9.1/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg/qiime/workflow/downstream.py", line 711, in run_summarize_taxa_through_plots

    close_logger_on_success=close_logger_on_success)

  File "/opt/qiime/1.9.1/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg/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 taxonomy_summaries_plots/otu_table_mc2_w_tax_L2.txt,taxonomy_summaries_plots/otu_table_mc2_w_tax_L3.txt,taxonomy_summaries_plots/otu_table_mc2_w_tax_L4.txt,taxonomy_summaries_     plots/otu_table_mc2_w_tax_L5.txt,taxonomy_summaries_plots/otu_table_mc2_w_tax_L6.txt -o taxonomy_summaries_plots//taxa_summary_plots/

Command returned exit status: 1

Stdout:

Stderr

Traceback (most recent call last):

  File "/opt/qiime/1.9.1/bin/plot_taxa_summary.py", line 4, in <module>

    __import__('pkg_resources').run_script('qiime==1.9.1', 'plot_taxa_summary.py')

  File "/gpfs0/export/opt/anaconda-2.3.0/lib/python2.7/site-packages/setuptools-17.1.1-py2.7.egg/pkg_resources/__init__.py", line 735, in run_script

  File "/gpfs0/export/opt/anaconda-2.3.0/lib/python2.7/site-packages/setuptools-17.1.1-py2.7.egg/pkg_resources/__init__.py", line 1652, in run_script

  File "/gpfs0/export/opt/qiime/1.9.1/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg/EGG-INFO/scripts/plot_taxa_summary.py", line 278, in <module>

    main()

  File "/gpfs0/export/opt/qiime/1.9.1/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg/EGG-INFO/scripts/plot_taxa_summary.py", line 274, in main

    resize_nth_label, label_type, include_html_legend)

  File "/opt/qiime/1.9.1/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg/qiime/plot_taxa_summary.py", line 1138, in make_all_charts

    resize_nth_label, label_type, include_html_legend))

  File "/opt/qiime/1.9.1/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg/qiime/plot_taxa_summary.py", line 1073, in get_counts

    label_type, include_html_legend))

  File "/opt/qiime/1.9.1/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg/qiime/plot_taxa_summary.py", line 861, in make_HTML_table

    props={'title': title})

  File "/opt/qiime/1.9.1/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg/qiime/plot_taxa_summary.py", line 466, in make_area_bar_chart

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

  File "/gpfs0/export/opt/anaconda-2.3.0/lib/python2.7/site-packages/matplotlib/pyplot.py", line 435, in figure

    **kwargs)

  File "/gpfs0/export/opt/anaconda-2.3.0/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 "/gpfs0/export/opt/anaconda-2.3.0/lib/python2.7/site-packages/matplotlib/backends/backend_qt4agg.py", line 54, in new_figure_manager_given_figure

    canvas = FigureCanvasQTAgg(figure)

  File "/gpfs0/export/opt/anaconda-2.3.0/lib/python2.7/site-packages/matplotlib/backends/backend_qt4agg.py", line 72, in __init__

    FigureCanvasQT.__init__(self, figure)

  File "/gpfs0/export/opt/anaconda-2.3.0/lib/python2.7/site-packages/matplotlib/backends/backend_qt4.py", line 68, in __init__

    _create_qApp()

  File "/gpfs0/export/opt/anaconda-2.3.0/lib/python2.7/site-packages/matplotlib/backends/backend_qt5.py", line 138, in _create_qApp

    raise RuntimeError('Invalid DISPLAY variable')

RuntimeError: Invalid DISPLAY variable

[Greg Caporaso]

Hi Vanessa,

This may be a server configuration issue. Can you please run the following two commands for me and reply with the output:

echo $DISPLAY

python -c "import matplotlib; print(matplotlib.get_backend())"

Thanks!

Greg

[Vanessa V.]

Hi Greg, 

Here is the output: 

[vav002@qmaster01 qiime_NEC]$ echo $DISPLAY

[vav002@qmaster01 qiime_NEC]$ python -c "import matplotlib; print(matplotlib.get_backend())"

Qt4Agg

[Vanessa V.]

Is there anything I can do to get around this?  I also cannot get the core diversity analyses to run either.  I get an error that again says Invalid DISPLAY variable.

Thanks for your help,

Vanessa

[Greg Caporaso]

Hi Vanessa,

This is a configuration issue with matplotlib, the library that QIIME uses for generating plots. You might want to work with your system administrator on this, as I'm not sure if there is a specific reason for this configuration. Your current matplotlib backend is set to qt4agg, which requires there to be an active display, but you don't have an active display (as indicated by there being no result when you called echo $DISPLAY). 

To get around this, you should first check if you have a matplotlibrc file. You can do this by running:

python -c "import matplotlib; print(matplotlib.matplotlib_fname())"

If that returns a filepath, you'll want to look for a line in that file that contains this:

backend : qt4agg

I would created a backup of that file, and then (in the original copy) replace that line with:

backend : agg

If you don't already have a matplotlibrc file, you can create one at $HOME/.matplotlib/matplotlibrc. That file should contain only the line:

backend : agg

As I mentioned, you might want to talk with your system administrator about this before making any changes. 

Sorry for the trouble - I realize this is a bit of a complicated fix, but it does seem to be a server/matplotlib configuration issue, not an issue that is specific to QIIME. 

If you could get back to me to let me know if that works, that would be very useful in case other users run into this in the future.

Best,

Greg

[Greg Caporaso]

Vanessa,

Following on your other post, I can see from the output the backend is still qtagg. 

Can you please run:

python -c "import matplotlib; print(matplotlib.matplotlib_fname())"

that will tell you where your matplotlibrc file is. If you could then attach that file, that will let me see if your backend is set incorrectly. If you don't get anything back from the above command, you'll need to work through the steps I suggested again to create the matplotlibrc file. If you don't have write access to your matplotlibrc file (e.g., it's in a centralized location for many users on your server), you can create a local matplotlibrc (at $HOME/.matplotlib/matplotlibrc), and that will take precedence.

Greg

[Greg Caporaso]

Hi Vanessa,

I also just noticed that you may not have been able to reply to this topic earlier, since it had been marked as a duplicate, so that may be why you created the new topic. Sorry about that - you should be able to reply here now. 

Greg

[Vanessa V.]

Hi Greg, 

I've been working on this the past day or so before I saw your recent responses here!  Thanks for the help.  As an update, I have been working with my system administrator and installed X-11 forwarding with Xming.  It works now with 'summarize taxa through plots' (whereas previously it did not) but it still has an issue with 'core diversity' analyses.  At the rarefaction plotting step, it errors out and reads that it cannot connect to X server local host 12.0.  I am running this script directly after the summarize taxa through plots step (same terminal) and Xming is indeed still in my tool bar.

This is now what I get from the following commands that you mentioned above.  I do not see   backend : agg   Sorry if I am missing something here?

[vav002@qmaster01 ~]$ echo $DISPLAY

localhost:12.0

[vav002@qmaster01 ~]$ python -c "import matplotlib; print(matplotlib.matplotlib_fname())"

/usr/lib64/python2.6/site-packages/matplotlib/mpl-data/matplotlibrc

[Greg Caporaso]

Hi Vanessa,

From that output, it looks like you're using a system-wide matplotlibrc. Can you try the following steps?

First, confirm that the $HOME/.matplotlib/matplotlibrc file doen't exist - this command should tell you "No such file or directory.":

ls $HOME/.matplotlib/matplotlibrc

If that file doesn't exist, try the following:

mkdir $HOME/.matplotlib

echo "backend : agg" > $HOME/.matplotlib/matplotlibrc

Then try re-running your QIIME commands.

If the $HOME/.matplotlib/matplotlibrc file does exist, don't run those second commands, but rather send that file to me. 

Greg

[Vanessa V.]

Hi Greg, 

Here's what happened: 

[vav002@qmaster01 ~]$ ls $HOME/.matplotlib/matplotlibrc

ls: cannot access /gpfs0/home/resgoodman/vav002/.matplotlib/matplotlibrc: No such file or directory

[vav002@qmaster01 ~]$ mkdir $HOME/.matplotlib

mkdir: cannot create directory `/gpfs0/home/resgoodman/vav002/.matplotlib': File exists

It wouldn't let me make the directory because it says the file exists.  When I look in vav002 I do not see a matplotlib file??  However, I am able to access it by cd $HOME/.matplotlib and when I open the .matplotlib directory, it's empty.  Sorry if I'm misunderstanding this, should I still go ahead and run echo "backend : agg" > $HOME/.matplotlib?

Thanks, 

Vanessa

[Greg Caporaso]

Hi Vanessa,

Sorry, I had a typo in my previous instructions, which I've corrected now. Could you run this command:

echo "backend : agg" > $HOME/.matplotlib/matplotlibrc

Then try re-running your QIIME commands.

Thanks!

Greg

[Vanessa V.]

Hi Greg, 

Unfortunately, it still didn't work but I'll explain why.  The scripts (e.g. for plots, core diversity analyses) all seem like they are working if I run them interactively on the login node or by requesting a computer node and SSHing in directly.  What doesn't work (even with trying your matplotlib suggestion above with the typo corrected) is when I submit the jobs via our workload scheduler SLURM.  For some reason it will not recognize the local host when I submit the scripts as a batch script through SLURM.  We're trying to troubleshoot this - as of now, we're stumped.  We tried including a few different different #SBATCH commands to recognize the DISPLAY or get the environmental variable, but none worked.  So for now I'm working directly on a himem node but SLURM doesn't know I'm there and it's not ideally the way the managers of the cluster want things to be run, but they are letting me run like that for now.  If you have any insights regarding that, that would be great!  Sorry for all of the confusion on this.

Thanks, 

Vanessa

[Colin Brislawn]

OK, so you've got the right software versions locally, but the remote worker machines have other versions which cause errors. I've run into this issue before, but relied heavily on the server admins to fix these issue.

Using conda environments may be a good way to handle this. Have you tried deploying qiime with conda? The idea here is that you could tell the worker node to load your own conda environment, that way is uses the right software, instead of using the (wrong) local copies. 

Colin

PS As far as I know, this error happens mostly on this script. Because other scripts work OK, your short term solution of 'sneaking into' the himem node could work fine. 

[Vanessa V.]

Thanks!  I'll inquire about conda!

[Colin Brislawn]

One of the cool things about conda, is that is designed to run without any admin or sudo rights. So you can run the real thing, without admins:

http://conda.pydata.org/miniconda.html 

Colin

[Vanessa V.]

Awesome, thank you!

[Vanessa V.]

Hi Colin, 

I haven't tried conda yet, as I'm still learning how work my way around in Linux/HPCC and I've been running through the core diversity analyses without any problems (until today!).  I did just run into this error regarding the matplotlib during core diversity analyses.  Any suggestions or quick fixes?  Just thought I'd ask.

  File "/gpfs0/export/opt/anaconda-2.3.0/lib/python2.7/site-packages/matplotlib/backends/backend_agg.py", line 94, in __init__

    self._renderer = _RendererAgg(int(width), int(height), dpi, debug=False)

ValueError: width and height must each be below 32768

[Colin Brislawn]

I have not seen that error, unfortunately. 

Sorry,

Colin 

[SAMIK]

Hello All, 

I had similar issue with the cluster environment. I installed qiime 1.9.1 using conda and had display issue. my matplotlibrc file is in  /home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc. I changed the backend : qt4agg with backend : agg as suggested in the post, the script running fine, but with every command giving me warning as below wich is just annoying. Can you suggest how to fix the warning message: 

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #369

""#path.simplify : True   # When True, simplify paths by removing ""invisible"""

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #375

""#path.snap : True # When True, rectilinear axis-aligned paths will be snapped to"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #376

""                  # the nearest pixel when certain criteria are met.  When False,"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #378

""#path.sketch : None # May be none, or a 3-tuple of the form (scale, length,"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #387

""# e.g., you may want a higher resolution, or to make the figure"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #392

""#savefig.format      : png      # png, ps, pdf, svg"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #396

""                                # e.g. setting animation.writer to ffmpeg will not work,"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #399

""#savefig.jpeg_quality: 95       # when a jpeg is saved, the default quality parameter."

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #400

""#savefig.directory   : ~        # default directory in savefig dialog box,"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #409

""#ps.papersize      : letter   # auto, letter, legal, ledger, A0-A10, B0-B10"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #410

""#ps.useafm         : False    # use of afm fonts, results in small files"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #411

""#ps.usedistiller   : False    # can be: None, ghostscript or xpdf"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #413

""                                          # xpdf intended for production of publication quality files,"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #414

""                                          # but requires ghostscript, xpdf and ps2eps"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #429

""#    'svgfont': Embed characters as SVG fonts -- supported only by Chrome,"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #437

""# levels are: silent, helpful, debug, debug-annoying.  Any level is"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #438

""# inclusive of all the levels below it.  If your setting is ""debug"","

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #440

""# problems to the mailing-list, please set verbose to ""helpful"" or ""debug"""

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #443

""# The ""fileo"" gives the destination for any calls to verbose.report."

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #444

""# These objects can a filename, or a filehandle like sys.stdout."

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #448

""# levels, e.g., --verbose-helpful."

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #452

""#verbose.level  : silent      # one of silent, helpful, debug, debug-annoying"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #453

""#verbose.fileo  : sys.stdout  # a log filename, sys.stdout or sys.stderr"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #457

""# Leave the field(s) empty if you don't need a key-map. (i.e., fullscreen : '')"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #460

""#keymap.home : h, r, home            # home or reset mnemonic"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #461

""#keymap.back : left, c, backspace    # forward / backward keys to enable"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #462

""#keymap.forward : right, v           #   left handed quick navigation"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #466

""#keymap.quit : ctrl+w, cmd+w         # close the current figure"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #469

""#keymap.xscale : L, k                # toggle scaling of x-axes ('log'/'linear')"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc

[s068b830@submit2 ~]$ ls $HOME/.matplotlib/matplotlibrc

ls: cannot access /home/s068b830/.matplotlib/matplotlibrc: No such file or directory

[s068b830@submit2 ~]$ python -c "import matplotlib; print(matplotlib.matplotlib_fname())"

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #6

""# there, please note that it will be overwritten in your next install."

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #8

""# overwritten, place it in the following location:"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #19

""# syntax highlighting. Blank lines, or lines starting with a comment"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #20

""# symbol, are ignored, as are trailing comments.  Other lines must"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #24

""# Colors: for the color values below, you can either use - a"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #25

""# matplotlib color string, such as r, k, or b - an rgb tuple, such as"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #26

""# (1.0, 0.5, 0.0) - a hex string, such as ff00ff or #ff00ff - a scalar"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #27

""# grayscale intensity such as 0.75 - a legal html color name, e.g., red,"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #28

""# blue, darkslategray"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #40

""# If you are using the Qt4Agg backend, you can choose here"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #47

""# ""pyqt"" and ""pyside"".  The ""pyqt"" setting has the side effect of"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #53

""# If webagg.port is unavailable, a number of other random ports will"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #57

""# When True, open the webbrowser to the plot that is shown"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #60

""# When True, the figures rendered in the nbagg backend are created with"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #65

""# conflicts, we will automatically try to find a compatible one for"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #70

""#toolbar      : toolbar2   # None | toolbar2  (""classic"" is deprecated)"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #71

""#timezone     : UTC        # a pytz timezone string, e.g., US/Central or Europe/Paris"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #74

""# location.  This is where the matplotlib fonts, bitmaps, etc reside"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #86

""#lines.markersize  : 6            # markersize, in points"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #94

""# Patches are graphical objects that fill 2D space, like polygons or"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #110

""# The font.family property has five values: 'serif' (e.g., Times),"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #111

""# 'sans-serif' (e.g., Helvetica), 'cursive' (e.g., Zapf-Chancery),"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #112

""# 'fantasy' (e.g., Western), and 'monospace' (e.g., Courier).  Each of"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #114

""# order of priority associated with them.  When text.usetex is False,"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #117

""# The font.style property has three values: normal (or roman), italic"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #118

""# or oblique.  The oblique style will be used for italic, if it is not"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #122

""# TrueType fonts, which are scalable fonts, small-caps is equivalent"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #123

""# to using a font size of 'smaller', or about 83% of the current font"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #126

""# The font.weight property has effectively 13 values: normal, bold,"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #127

""# bolder, lighter, 100, 200, 300, ..., 900.  Normal is the same as"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #128

""# 400, and bold is 700.  bolder and lighter are relative values with"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #131

""# The font.stretch property has 11 values: ultra-condensed,"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #132

""# extra-condensed, condensed, semi-condensed, normal, semi-expanded,"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #133

""# expanded, extra-expanded, ultra-expanded, wider, and narrower.  This"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #136

""# The font.size property is the default font size for text, given in pts."

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #145

""# special text sizes tick labels, axes, labels, title, etc, see the rc"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #147

""# relative to font.size, using the following values: xx-small, x-small,"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #148

""# small, medium, large, x-large, xx-large, larger, or smaller"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #150

""#font.serif          : Bitstream Vera Serif, New Century Schoolbook, Century Schoolbook L, Utopia, ITC Bookman, Bookman, Nimbus Roman No9 L, Times New Roman, Times, Palatino, Charter, serif"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #151

""#font.sans-serif     : Bitstream Vera Sans, Lucida Grande, Verdana, Geneva, Lucid, Arial, Helvetica, Avant Garde, sans-serif"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #152

""#font.cursive        : Apple Chancery, Textile, Zapf Chancery, Sand, cursive"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #153

""#font.fantasy        : Comic Sans MS, Chicago, Charcoal, Impact, Western, fantasy"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #154

""#font.monospace      : Bitstream Vera Sans Mono, Andale Mono, Nimbus Mono L, Courier New, Courier, Fixed, Terminal, monospace"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #166

""                              # new century schoolbook, bookman, times, palatino,"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #167

""                              # zapf chancery, charter, serif, sans-serif, helvetica,"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #168

""                              # avant garde, courier, monospace, computer modern roman,"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #169

""                              # computer modern sans serif, computer modern typewriter"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #171

""                              # LaTeX \usepackage command, please inquire at the"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #173

""#text.latex.unicode : False # use ""ucs"" and ""inputenc"" LaTeX packages for handling"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #181

""                            # text.latex.preamble : \usepackage{bm},\usepackage{euler}"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #182

""                            # The following packages are always loaded with usetex, so"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #183

""                            # beware of package collisions: color, geometry, graphicx,"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #184

""                            # type1cm, textcomp. Adobe Postscript (PSSNFS) font packages"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #185

""                            # may also be loaded, depending on your font settings"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #198

""                       #             font file, if available, and if your"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #200

""                       #   'either': Use the native hinting information,"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #202

""                       # For backward compatibility, this value may also be"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #208

""#text.antialiased : True # If True (default), the text will be antialiased."

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #214

""# Note that this ""custom"" mode is unsupported and may go away in the"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #222

""#mathtext.fontset : cm # Should be 'cm' (Computer Modern), 'stix',"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #224

""#mathtext.fallback_to_cm : True  # When True, use symbols from the Computer Modern"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #229

""                       # Can be any of the LaTeX font names, including"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #230

""                       # the special name ""regular"" for the same font"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #234

""# default face and edge color, default tick sizes,"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #235

""# default fontsizes for ticklabels, and so on.  See"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #247

""                               # the axes elements (lines, text, etc)"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #249

""#axes.formatter.limits : -7, 7 # use scientific notation if log10"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #252

""#axes.formatter.use_locale : False # When True, format tick labels"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #254

""                                   # For example, use ',' as a decimal"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #256

""#axes.formatter.use_mathtext : False # When True, use mathtext for scientific"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #258

""#axes.formatter.useoffset      : True    # If True, the tick label formatter"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #267

""#axes.color_cycle    : b, g, r, c, m, y, k  # color cycle for plot lines"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #269

""                                            # single letter, long name, or"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #287

""#xtick.direction      : in     # direction: in, out, or inout"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #297

""#ytick.direction      : in     # direction: in, out, or inout"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #304

""#grid.alpha       :   1.0     # transparency, between 0.0 and 1.0"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #307

""#legend.fancybox      : False  # if True, use a rounded box for the"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #308

""                               # legend, else a rectangle"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #328

""#figure.figsize   : 8, 6    # figure size in inches"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #332

""#figure.autolayout : False  # When True, automatically adjust subplot"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #359

""### Warning: experimental, 2008/10/10"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #363

""                                  # when plotting very large data sets,"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #365

""                                  # It may cause minor artifacts, though."

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #369

""#path.simplify : True   # When True, simplify paths by removing ""invisible"""

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #375

""#path.snap : True # When True, rectilinear axis-aligned paths will be snapped to"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #376

""                  # the nearest pixel when certain criteria are met.  When False,"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #378

""#path.sketch : None # May be none, or a 3-tuple of the form (scale, length,"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #387

""# e.g., you may want a higher resolution, or to make the figure"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #392

""#savefig.format      : png      # png, ps, pdf, svg"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #396

""                                # e.g. setting animation.writer to ffmpeg will not work,"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #399

""#savefig.jpeg_quality: 95       # when a jpeg is saved, the default quality parameter."

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #400

""#savefig.directory   : ~        # default directory in savefig dialog box,"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #409

""#ps.papersize      : letter   # auto, letter, legal, ledger, A0-A10, B0-B10"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #410

""#ps.useafm         : False    # use of afm fonts, results in small files"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #411

""#ps.usedistiller   : False    # can be: None, ghostscript or xpdf"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #413

""                                          # xpdf intended for production of publication quality files,"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #414

""                                          # but requires ghostscript, xpdf and ps2eps"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #429

""#    'svgfont': Embed characters as SVG fonts -- supported only by Chrome,"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #437

""# levels are: silent, helpful, debug, debug-annoying.  Any level is"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #438

""# inclusive of all the levels below it.  If your setting is ""debug"","

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #440

""# problems to the mailing-list, please set verbose to ""helpful"" or ""debug"""

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #443

""# The ""fileo"" gives the destination for any calls to verbose.report."

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #444

""# These objects can a filename, or a filehandle like sys.stdout."

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #448

""# levels, e.g., --verbose-helpful."

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #452

""#verbose.level  : silent      # one of silent, helpful, debug, debug-annoying"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #453

""#verbose.fileo  : sys.stdout  # a log filename, sys.stdout or sys.stderr"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #457

""# Leave the field(s) empty if you don't need a key-map. (i.e., fullscreen : '')"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #460

""#keymap.home : h, r, home            # home or reset mnemonic"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #461

""#keymap.back : left, c, backspace    # forward / backward keys to enable"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #462

""#keymap.forward : right, v           #   left handed quick navigation"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #466

""#keymap.quit : ctrl+w, cmd+w         # close the current figure"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/__init__.py:1004: UserWarning: Illegal line #469

""#keymap.xscale : L, k                # toggle scaling of x-axes ('log'/'linear')"

"

in file "/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc"

  warnings.warn('Illegal %s' % error_details)

/home/s068b830/.conda/envs/qiime1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc

[Jai Ram Rideout]

Hello,

It's possible your matplotlibrc file is corrupted after editing it. Can you send me the file so I can take a look? Please post the file as an attachment instead of pasting it into your post.

Best,

Jai

[SAMIK]

Hi Jai, 

I realized that and now reinstalled conda again and build my qiime env there. Everything is working fine now. 

Thank you

Samik

[Jai Ram Rideout]

Great, glad you got it working with a reinstall!

Jai