Hello,
I'm trying to run qiime 1.9.1 but get an error while I'm running this command:
plot_taxa_summary.py -i alpha_diversity/taxonomic_affiliation/otu_normalized_table_L2.txt -l Phylum -t png -x 20 -y 12 -c bar -o alpha_diversity/test
the generated error is:
```
File "/lb/project/mugqic/analyste_dev/software/python/Python-2.7.10/bin/plot_taxa_summary.py", line 4, in <module>
__import__('pkg_resources').run_script('qiime==1.9.1', 'plot_taxa_summary.py')
File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 745, in run_script
File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 1670, in run_script
File "/lb/project/mugqic/analyste_dev/software/python/Python-2.7.10/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 "/lb/project/mugqic/analyste_dev/software/python/Python-2.7.10/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 "/lb/project/mugqic/analyste_dev/software/python/Python-2.7.10/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 "/lb/project/mugqic/analyste_dev/software/python/Python-2.7.10/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 "/lb/project/mugqic/analyste_dev/software/python/Python-2.7.10/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 "/lb/project/mugqic/analyste_dev/software/python/Python-2.7.10/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg/qiime/plot_taxa_summary.py", line 662, in make_area_bar_chart
background_color, img_abs, generate_image_type, dpi)
File "/lb/project/mugqic/analyste_dev/software/python/Python-2.7.10/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg/qiime/plot_taxa_summary.py", line 187, in make_legend
shadow=False, fancybox=False)
File "/lb/project/mugqic/analyste_dev/software/python/Python-2.7.10/lib/python2.7/site-packages/matplotlib-1.5.0-py2.7-linux-x86_64.egg/matplotlib/figure.py", line 1251, in legend
l = Legend(self, handles, labels, *args, **kwargs)
File "/lb/project/mugqic/analyste_dev/software/python/Python-2.7.10/lib/python2.7/site-packages/matplotlib-1.5.0-py2.7-linux-x86_64.egg/matplotlib/legend.py", line 385, in __init__
self._init_legend_box(handles, labels, markerfirst)
File "/lb/project/mugqic/analyste_dev/software/python/Python-2.7.10/lib/python2.7/site-packages/matplotlib-1.5.0-py2.7-linux-x86_64.egg/matplotlib/legend.py", line 654, in _init_legend_box
fontsize, handlebox))
File "/lb/project/mugqic/analyste_dev/software/python/Python-2.7.10/lib/python2.7/site-packages/matplotlib-1.5.0-py2.7-linux-x86_64.egg/matplotlib/legend_handler.py", line 119, in legend_artist
fontsize, handlebox.get_transform())
File "/lb/project/mugqic/analyste_dev/software/python/Python-2.7.10/lib/python2.7/site-packages/matplotlib-1.5.0-py2.7-linux-x86_64.egg/matplotlib/legend_handler.py", line 252, in create_artists
self.update_prop(p, orig_handle, legend)
File "/lb/project/mugqic/analyste_dev/software/python/Python-2.7.10/lib/python2.7/site-packages/matplotlib-1.5.0-py2.7-linux-x86_64.egg/matplotlib/legend_handler.py", line 78, in update_prop
legend._set_artist_props(legend_handle)
File "/lb/project/mugqic/analyste_dev/software/python/Python-2.7.10/lib/python2.7/site-packages/matplotlib-1.5.0-py2.7-linux-x86_64.egg/matplotlib/legend.py", line 401, in _set_artist_props
a.set_figure(self.figure)
File "/lb/project/mugqic/analyste_dev/software/python/Python-2.7.10/lib/python2.7/site-packages/matplotlib-1.5.0-py2.7-linux-x86_64.egg/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
```
From what I understand the function try to overload the legend and matplotlib raise the error.
long story short:
I first get an error with the display that I correct while adding the line
```
backend : agg
```
to ~/.config/matplotlib/matplotlibrc but now this new exception occurs.
Any idea of what is wrong and how I could solve this problem ?
I tried with different input files and different parameters value for -t -x -y and -c but nothing could solve this.
for you information this is the detail of my installation:
print_qiime_config.py -t
System information
==================
Platform: linux2
Python version: 2.7.10 (default, Dec 4 2015, 15:57:27) [GCC 4.4.7 20120313 (Red Hat 4.4.7-11)]
Python executable: /lb/project/mugqic/analyste_dev/software/python/Python-2.7.10/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/0.1.3Dependency versions
===================
QIIME library version: 1.9.1
QIIME script version: 1.9.1
qiime-default-reference version: 0.1.3
NumPy version: 1.10.1
SciPy version: 0.16.1
pandas version: 0.17.1
matplotlib version: 1.5.0
biom-format version: 2.1.5
h5py version: 2.5.0 (HDF5 version: 1.8.5)
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 [Dec 7 2015 10:18:50]
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: /lb/project/mugqic/analyste_dev/software/qiime/qiime-1.9.1/blast-2.2.22-release/data
pick_otus_reference_seqs_fp: /lb/project/mugqic/analyste_dev/software/python/Python-2.7.10/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: /lb/project/mugqic/analyste_dev/software/python/Python-2.7.10/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: /lb/project/mugqic/analyste_dev/software/python/Python-2.7.10/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: /lb/project/mugqic/analyste_dev/software/python/Python-2.7.10/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
temp_dir: /tmp/
slurm_memory: None
slurm_queue: None
blastall_fp: /lb/project/mugqic/analyste_dev/software/qiime/qiime-1.9.1/blast-2.2.22-release/bin/blastall
seconds_to_sleep: 1
QIIME base install test results
===============================
.........
----------------------------------------------------------------------
Ran 9 tests in 0.267s
OK