core_diversity_analyses.py error in the Illumina Overview Tutorial

[Taruna Aggarwal]

Hello. I'm trying to complete the Illumina Overview Tutorial using Qiime 1.9.1  but am stuck at the following errors. Any suggestions as to how I can fix them? Thanks so much!

Traceback (most recent call last):

  File "/opt/linux/centos/7.x/x86_64/pkgs/python/2.7.12/qiime-env/bin/core_diversity_analyses.py", line 202, in <module>

    main()

  File "/opt/linux/centos/7.x/x86_64/pkgs/python/2.7.12/qiime-env/bin/core_diversity_analyses.py", line 199, in main

    status_update_callback=status_update_callback)

  File "/bigdata/bioinfo/pkgadmin/opt/linux/centos/7.x/x86_64/pkgs/python/2.7.12/qiime-env/lib/python2.7/site-packages/qiime/workflow/core_diversity_anal

yses.py", line 327, in run_core_diversity_analyses

    retain_intermediate_files=False)

  File "/bigdata/bioinfo/pkgadmin/opt/linux/centos/7.x/x86_64/pkgs/python/2.7.12/qiime-env/lib/python2.7/site-packages/qiime/workflow/downstream.py", lin

e 342, in run_alpha_rarefaction

    close_logger_on_success=close_logger_on_success)

  File "/bigdata/bioinfo/pkgadmin/opt/linux/centos/7.x/x86_64/pkgs/python/2.7.12/qiime-env/lib/python2.7/site-packages/qiime/workflow/util.py", line 122,

 in call_commands_serially

    raise WorkflowError(msg)

qiime.workflow.util.WorkflowError:

*** ERROR RAISED DURING STEP: Rarefaction plot: All metrics

Command run was:

 make_rarefaction_plots.py -i /rhome/taruna/shared/learning_qiime/qiime_tutorials/illumina/moving_pictures_tutorial-1.9.0/illumina/cdout//arare_max1114//

alpha_div_collated/ -m /rhome/taruna/shared/learning_qiime/qiime_tutorials/illumina/moving_pictures_tutorial-1.9.0/illumina/map.tsv -o /rhome/taruna/shar

ed/learning_qiime/qiime_tutorials/illumina/moving_pictures_tutorial-1.9.0/illumina/cdout//arare_max1114//alpha_rarefaction_plots/

Command returned exit status: 1

Stdout:

Stderr

Traceback (most recent call last):

  File "/opt/linux/centos/7.x/x86_64/pkgs/python/2.7.12/qiime-env/bin/make_rarefaction_plots.py", line 229, in <module>

    main()

  File "/opt/linux/centos/7.x/x86_64/pkgs/python/2.7.12/qiime-env/bin/make_rarefaction_plots.py", line 219, in main

    generate_average_tables=generate_average_tables)

  File "/bigdata/bioinfo/pkgadmin/opt/linux/centos/7.x/x86_64/pkgs/python/2.7.12/qiime-env/lib/python2.7/site-packages/qiime/make_rarefaction_plots.py",

line 667, in make_averages

    metric_name, output_type)

  File "/bigdata/bioinfo/pkgadmin/opt/linux/centos/7.x/x86_64/pkgs/python/2.7.12/qiime-env/lib/python2.7/site-packages/qiime/make_rarefaction_plots.py",

line 36, in save_ave_rarefaction_plots

    plt.clf()

  File "/bigdata/bioinfo/pkgadmin/opt/linux/centos/7.x/x86_64/pkgs/python/2.7.12/qiime-env/lib/python2.7/site-packages/matplotlib/pyplot.py", line 547, i

n clf

    gcf().clf()

  File "/bigdata/bioinfo/pkgadmin/opt/linux/centos/7.x/x86_64/pkgs/python/2.7.12/qiime-env/lib/python2.7/site-packages/matplotlib/pyplot.py", line 462, i

n gcf

    return figure()

  File "/bigdata/bioinfo/pkgadmin/opt/linux/centos/7.x/x86_64/pkgs/python/2.7.12/qiime-env/lib/python2.7/site-packages/matplotlib/pyplot.py", line 435, i

n figure

    **kwargs)

  File "/bigdata/bioinfo/pkgadmin/opt/linux/centos/7.x/x86_64/pkgs/python/2.7.12/qiime-env/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 "/bigdata/bioinfo/pkgadmin/opt/linux/centos/7.x/x86_64/pkgs/python/2.7.12/qiime-env/lib/python2.7/site-packages/matplotlib/backends/backend_qt4agg

.py", line 54, in new_figure_manager_given_figure

    canvas = FigureCanvasQTAgg(figure)

  File "/bigdata/bioinfo/pkgadmin/opt/linux/centos/7.x/x86_64/pkgs/python/2.7.12/qiime-env/lib/python2.7/site-packages/matplotlib/backends/backend_qt4agg

.py", line 72, in __init__

    FigureCanvasQT.__init__(self, figure)

  File "/bigdata/bioinfo/pkgadmin/opt/linux/centos/7.x/x86_64/pkgs/python/2.7.12/qiime-env/lib/python2.7/site-packages/matplotlib/backends/backend_qt4.py

", line 68, in __init__

    _create_qApp()

  File "/bigdata/bioinfo/pkgadmin/opt/linux/centos/7.x/x86_64/pkgs/python/2.7.12/qiime-env/lib/python2.7/site-packages/matplotlib/backends/backend_qt5.py

", line 138, in _create_qApp

    raise RuntimeError('Invalid DISPLAY variable')

RuntimeError: Invalid DISPLAY variable

[Tomasz]

Hi Taruna,

Are you by any chance running this remotely or in a text-only environment?

The error you're getting is pointing to a problem with printing the results on your screen, i.e. it cannot print graphics.

t.

[Taruna]

Hi Tomasz. I am running the script remotely. So should I contact our system admin regarding this problem if its a server issue not a Qiime issue? 

[Tomasz]

Hi Taruna,

It's not a QIIME or system bug, just that the script tries to print output to your screen which it cannot access, because you're connected remotely. What I'd advise, is that you maybe run this script with `-w` parameter, which prints all of the commands, but does not execute them.

Then, you can run them one by one and execute the one causing an error locally, i.e. on your machine.

t.

[Taruna]

Ah I see. Okay so I should submit my job with the following command? Just want to make sure

core_diversity_analyses.py -w -o cdout/ -i otus/otu_table_mc2_w_tax_no_pynast_failures.biom -m map.tsv -t otus/rep_set.tre -e 1114

[Tomasz]

yes!

apologies for a late response!

t.

[Taruna]

No worries! Thanks very much for your help. I'm already getting errors with the first command. I think it may be how Qiime is installed on our cluster. I have never been able to run anything Qiime related successfully on the cluster.