"Can not put single artist in more than one figure" Error with print_qiime

André Soares

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Mar 3, 2016, 12:42:26 PM3/3/16

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Hello there,

I get the following with: summarize_taxa_through_plots.py -i lala.biom -o./plots -m /home/andre/Desktop/PRJEB0000/map_SraRunTable3.txt -f
A .pdf and a .png still come up in ./tax, properly identified by sample, but with no legend...

Help?

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 ./plots/lala_L2.txt,./plots/lala_L3.txt,./plots/lala_L4.txt,./plots/lala_L5.txt,./plots/lala_L6.txt -o ./plots/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 662, in make_area_bar_chart
    background_color, img_abs, generate_image_type, dpi)
File "/usr/local/lib/python2.7/dist-packages/qiime/plot_taxa_summary.py", line 187, in make_legend
    shadow=False, fancybox=False)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/figure.py", line 1277, in legend
    l = Legend(self, handles, labels, *args, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/legend.py", line 385, in __init__
    self._init_legend_box(handles, labels, markerfirst)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/legend.py", line 654, in _init_legend_box
    fontsize, handlebox))
File "/usr/local/lib/python2.7/dist-packages/matplotlib/legend_handler.py", line 119, in legend_artist
    fontsize, handlebox.get_transform())
File "/usr/local/lib/python2.7/dist-packages/matplotlib/legend_handler.py", line 252, in create_artists
    self.update_prop(p, orig_handle, legend)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/legend_handler.py", line 78, in update_prop
    legend._set_artist_props(legend_handle)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/legend.py", line 401, in _set_artist_props
    a.set_figure(self.figure)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/artist.py", line 640, in set_figure
    raise RuntimeError("Can not put single artist in "
RuntimeError: Can not put single artist in more than one figure

print_qiime_config.py output:
System information
==================
         Platform:    linux2
   Python version:    2.7.6 (default, Jun 22 2015, 17:58:13) [GCC 4.8.2]
Python executable:    /usr/bin/python

QIIME default reference information
===================================
For details on what files are used as QIIME's default references, see here:
https://github.com/biocore/qiime-default-reference/releases/tag/0.1.3

Dependency versions
===================
          QIIME library version:    1.9.1
           QIIME script version:    1.9.1
qiime-default-reference version:    0.1.3
                  NumPy version:    1.10.4
                  SciPy version:    0.17.0
                 pandas version:    0.17.1
             matplotlib version:    1.5.1
            biom-format version:    2.1.5
                   h5py version:    2.5.0 (HDF5 version: 1.8.11)
                   qcli version:    0.1.1
                   pyqi version:    0.3.2
             scikit-bio version:    0.2.3
                 PyNAST version:    1.2.2
                Emperor version:    0.9.51
                burrito version:    0.9.1
       burrito-fillings version:    0.1.1
              sortmerna version:    SortMeRNA version 2.0, 29/11/2014
              sumaclust version:    SUMACLUST Version 1.0.00
                  swarm version:    Swarm 1.2.19 [Oct 15 2015 08:21:24]
                          gdata:    Installed.

QIIME config values
===================
For definitions of these settings and to learn how to configure QIIME, see here:
http://qiime.org/install/qiime_config.html
http://qiime.org/tutorials/parallel_qiime.html

                     blastmat_dir:    None
      pick_otus_reference_seqs_fp:    /usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
                         sc_queue:    all.q
      topiaryexplorer_project_dir:    None
     pynast_template_alignment_fp:    /usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set_aligned/85_otus.pynast.fasta
                  cluster_jobs_fp:    start_parallel_jobs.py
pynast_template_alignment_blastdb:    None
assign_taxonomy_reference_seqs_fp:    /usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
                     torque_queue:    friendlyq
                    jobs_to_start:    1
                       slurm_time:    None
            denoiser_min_per_core:    50
assign_taxonomy_id_to_taxonomy_fp:    /usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
                         temp_dir:    /tmp/
                     slurm_memory:    None
                      slurm_queue:    None
                      blastall_fp:    blastall
                 seconds_to_sleep:    1

QIIME base install test results
===============================
.........
----------------------------------------------------------------------
Ran 9 tests in 0.023s

OK

Jamie Morton

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Mar 3, 2016, 5:06:53 PM3/3/16

to Qiime 1 Forum

Hi Andre,

That is actually a bug related to matplotlib. I'd try installing another version of matplotlib.

Best,

Jamie

André Soares

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Mar 4, 2016, 3:17:51 AM3/4/16

to Qiime 1 Forum

Hey again,

With maplotlib 1.4.3 I get this, although all the outputs come out as usual:
/usr/local/lib/python2.7/dist-packages/matplotlib/collections.py:590: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
if self._edgecolors == str('face'):

Thanks for this!

Alex Koeppel

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Dec 13, 2016, 11:52:01 AM12/13/16

to Qiime 1 Forum

I'm getting this same error with summarize_taxa_through_plots.py

I found in this thread and others that the solution is to downgrade matplotlib to 1.4.3, however, I installed matplotlib 1.4.3 with conda (conda install 'matplotlib==1.4.3') and while the install appears to have been successful, Qiime doesn't seem to recognize it, as print_qiime_config still shows matplotlib 1.5.1.

Is there a field in the config file or elsewhere that I can use to direct Qiime to a particular install of matplotlib?

Any help would be appreciated.

print_qiime_config.py -t

System information

==================

Platform: linux2

Python version: 2.7.12 | packaged by conda-forge | (default, Sep 8 2016, 14:22:31) [GCC 4.8.2 20140120 (Red Hat 4.8.2-15)]

Python executable: /home/afk2s/Software_alex/Anaconda_Install/bin/python

QIIME default reference information

===================================

For details on what files are used as QIIME's default references, see here:

https://github.com/biocore/qiime-default-reference/releases/tag/0.1.3

Dependency versions

===================

QIIME library version: 1.9.1

QIIME script version: 1.9.1

qiime-default-reference version: 0.1.3

NumPy version: 1.11.2

SciPy version: 0.18.1

pandas version: 0.19.0

matplotlib version: 1.5.1

biom-format version: 2.1.4

h5py version: 2.3.1 (HDF5 version: 1.8.13)

qcli version: 0.1.1

pyqi version: 0.3.2

scikit-bio version: 0.2.3

PyNAST version: 1.2.2

Emperor version: 0.9.51

burrito version: 0.9.1

burrito-fillings version: 0.1.1

sortmerna version: SortMeRNA version 2.0, 29/11/2014

sumaclust version: SUMACLUST Version 1.0.00

swarm version: Swarm 1.2.19 [Aug 17 2015 13:55:05]

gdata: Installed.

QIIME config values

===================

For definitions of these settings and to learn how to configure QIIME, see here:

http://qiime.org/install/qiime_config.html

http://qiime.org/tutorials/parallel_qiime.html

blastmat_dir: None

pick_otus_reference_seqs_fp: /home/afk2s/Software_alex/Anaconda_Install/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta

sc_queue: all.q

topiaryexplorer_project_dir: None

pynast_template_alignment_fp: /home/afk2s/Software_alex/Anaconda_Install/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set_aligned/85_otus.pynast.fasta

cluster_jobs_fp: start_parallel_jobs.py

pynast_template_alignment_blastdb: None

assign_taxonomy_reference_seqs_fp: /home/afk2s/Software_alex/Anaconda_Install/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta

torque_queue: friendlyq

jobs_to_start: 1

slurm_time: None

denoiser_min_per_core: 50

assign_taxonomy_id_to_taxonomy_fp: /home/afk2s/Software_alex/Anaconda_Install/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt

temp_dir: /home/afk2s/projects/gilchrist/cryptosporidium/otu_picking/otu_tmp/

slurm_memory: None

slurm_queue: None

blastall_fp: blastall

seconds_to_sleep: 1

QIIME base install test results

===============================

.........

----------------------------------------------------------------------

Ran 9 tests in 0.029s

OK

Alex Koeppel

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Dec 13, 2016, 1:23:55 PM12/13/16

to Qiime 1 Forum

Disregard the above. I sourced a new conda environment with the correct version of matplotlib loaded and that solved the problem. Sorry.

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André Soares

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