Invalid DISPLAY variable Error

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Vanessa V.

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May 18, 2016, 1:47:32 PM5/18/16

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Hi there,

I am reposting this as a new question as I have tried testing things from a previous linked post but I'm still having no luck. I'm running into an Invalid DISPLAY variable error - I am using QIIME remotely on our cluster. When I run the print qiime config as described, my matplotlib version is indeed 1.4.3. See below. I'm running into issues as I'm unable to run summarize taxa through plots or any of the core diversity analyses --- the latter is what I really want to focus on. I tried python -c 'import matplotlib; print matplotlib.matplotlib_fname()' which seemed like it worked (I did not get an error after I did this) but I still get an error (Invalid DISPLAY variable) when I run a plot or diversity related script through QIIME. Example of error from running one of these scripts is after the print_qiime_config information below.

I also checked echo $DISPLAY and it said localhost:11.0. I tried to use this to sign in with PuTTY with X-11 forwarding (I selected enable X-11 forwarding) and X display location localhost:11.0 and also tried localhost:0.0, but neither worked. I get an error each time that says it cannot connect to X server localhost.

If anyone has any suggestions, I would really appreciate it!

Thanks,

Vanessa

print_qiime_config.py -t

System information

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

Platform: linux2

Python version: 2.7.10 |Anaconda 2.3.0 (64-bit)| (default, May 28 2015, 17:02:03) [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]

Python executable: /gpfs0/export/opt/anaconda-2.3.0/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: 1.9.2

SciPy version: 0.15.1

pandas version: 0.16.2

matplotlib version: 1.4.3

biom-format version: 2.1.5

h5py version: 2.5.0 (HDF5 version: 1.8.15)

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 [Feb 23 2016 12:35:53]

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: /opt/blast/2.2.22/data

pick_otus_reference_seqs_fp: /opt/qiime/1.9.1/lib/python2.7/site-pack ages/qiime_default_reference-0.1.3-py2.7.egg/qiime_default_reference/gg_13_8_otu s/rep_set/97_otus.fasta

sc_queue: all.q

topiaryexplorer_project_dir: None

pynast_template_alignment_fp: /opt/qiime/1.9.1/lib/python2.7/site-pack ages/qiime_default_reference-0.1.3-py2.7.egg/qiime_default_reference/gg_13_8_otu s/rep_set_aligned/85_otus.pynast.fasta

cluster_jobs_fp: start_parallel_jobs.py

pynast_template_alignment_blastdb: None

assign_taxonomy_reference_seqs_fp: /opt/qiime/1.9.1/lib/python2.7/site-pack ages/qiime_default_reference-0.1.3-py2.7.egg/qiime_default_reference/gg_13_8_otu s/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: /opt/qiime/1.9.1/lib/python2.7/site-pack ages/qiime_default_reference-0.1.3-py2.7.egg/qiime_default_reference/gg_13_8_otu s/taxonomy/97_otu_taxonomy.txt

temp_dir: /tmp/

slurm_memory: None

slurm_queue: None

blastall_fp: /opt/blast/2.2.22/bin/blastall

seconds_to_sleep: 1

QIIME base install test results

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

.........

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

Ran 9 tests in 0.169s

*** 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

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May 19, 2016, 10:35:37 AM5/19/16

to Qiime 1 Forum

Hi Vanessa,

It's helpful for future users if we can keep all of the discussion in a single thread. I'm going to follow up there. Let consolidate discussion there please.