"ImportError: No module named dateutil.rrule" from beta_diversity_through_plots.py

[Daniel Smith]

Whenever I run beta_diversity_through_plots.py, I get the following error output:

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

*** ERROR RAISED DURING STEP: Make 2D plots (continuous coloring, weighted_unifrac)

Command run was:

 /usr/local/bin/qiime-1.6.0/python-2.7.3-release/bin/python /usr/local/bin/qiime-1.6.0/qiime-1.6.0-release/bin/make_2d_plots.py -p 09_beta_diversity/prefs.txt -i 09_beta_diversity/weighted_unifrac_pc.txt -o 09_beta_diversity/weighted_unifrac_2d_continuous/ -m MappingFile.txt 

Command returned exit status: 1

Stdout:

Stderr

Traceback (most recent call last):

  File "/usr/local/bin/qiime-1.6.0/qiime-1.6.0-release/bin/make_2d_plots.py", line 22, in <module>

    from qiime.make_2d_plots import generate_2d_plots

  File "/usr/local/bin/qiime-1.6.0/qiime-1.6.0-release/lib/qiime/make_2d_plots.py", line 17, in <module>

    from matplotlib.pylab import *

  File "/usr/local/bin/qiime-1.6.0/matplotlib-1.1.0-release/lib/python2.7/site-packages/matplotlib/pylab.py", line 221, in <module>

    from matplotlib import mpl  # pulls in most modules

  File "/usr/local/bin/qiime-1.6.0/matplotlib-1.1.0-release/lib/python2.7/site-packages/matplotlib/mpl.py", line 3, in <module>

    from matplotlib import axes

  File "/usr/local/bin/qiime-1.6.0/matplotlib-1.1.0-release/lib/python2.7/site-packages/matplotlib/axes.py", line 19, in <module>

    import matplotlib.dates as mdates

  File "/usr/local/bin/qiime-1.6.0/matplotlib-1.1.0-release/lib/python2.7/site-packages/matplotlib/dates.py", line 119, in <module>

    from dateutil.rrule import rrule, MO, TU, WE, TH, FR, SA, SU, YEARLY, \

ImportError: No module named dateutil.rrule

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

I tried running "sudo apt-get install python-dateutil" to no avail (the library was already installed and up to date)

The following parameters were in the log file generated by beta_diversity_through_plots.py:

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

QIIME version: 1.6.0

qiime_config values:
blastmat_dir	/usr/local/bin/qiime-1.6.0/blast-2.2.22-release/data
sc_queue	all.q
pynast_template_alignment_fp	/usr/local/bin/qiime-1.6.0/core_set_aligned.fasta.imputed
cluster_jobs_fp	/usr/local/bin/qiime-1.6.0/qiime-1.6.0-release/bin/start_parallel_jobs.py
assign_taxonomy_reference_seqs_fp	/usr/local/bin/qiime-1.6.0/gg_otus-12_10-release/rep_set/97_otus.fasta
torque_queue	friendlyq
template_alignment_lanemask_fp	/usr/local/bin/qiime-1.6.0/lanemask_in_1s_and_0s
jobs_to_start	1
cloud_environment	False
qiime_scripts_dir	/usr/local/bin/qiime-1.6.0/qiime-1.6.0-release/bin
denoiser_min_per_core	50
working_dir	/tmp/
python_exe_fp	/usr/local/bin/qiime-1.6.0/python-2.7.3-release/bin/python
temp_dir	/tmp/
blastall_fp	/usr/local/bin/qiime-1.6.0/blast-2.2.22-release/bin/blastall
seconds_to_sleep	60
assign_taxonomy_id_to_taxonomy_fp	/usr/local/bin/qiime-1.6.0/gg_otus-12_10-release/taxonomy/97_otu_taxonomy.txt

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

Any ideas?

Thanks,

   -Dan

[Daniel Smith]

I'm seeing the exact same error message when running summarize_taxa_through_plots.py, if that help narrow things down.

[Tony Walters]

Hello Daniel,

Jai had a solution for this (https://groups.google.com/forum/?fromgroups=#!topic/qiime-forum/GRkmnT6NXWQ), you may need to install pip to follow these instructions though.

-Tony

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[Daniel Smith]

Hi Tony,

Jai's solution isn't working for me:

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

bash$ pip install python-dateutil

Requirement already satisfied (use --upgrade to upgrade): python-dateutil in /usr/local/lib/python2.7/dist-packages

Requirement already satisfied (use --upgrade to upgrade): six in /usr/local/lib/python2.7/dist-packages (from python-dateutil)

Cleaning up...

bash$ pip install --upgrade python-dateutil

Requirement already up-to-date: python-dateutil in /usr/local/lib/python2.7/dist-packages

Requirement already up-to-date: six in /usr/local/lib/python2.7/dist-packages (from python-dateutil)

Cleaning up...

bash$ sudo pip install python-dateutil

Requirement already satisfied (use --upgrade to upgrade): python-dateutil in /usr/local/lib/python2.7/dist-packages

Requirement already satisfied (use --upgrade to upgrade): six in /usr/local/lib/python2.7/dist-packages (from python-dateutil)

Cleaning up...

bash$ sudo pip install --upgrade python-dateutil

Requirement already up-to-date: python-dateutil in /usr/local/lib/python2.7/dist-packages

Requirement already up-to-date: six in /usr/local/lib/python2.7/dist-packages (from python-dateutil)

Cleaning up...

bash$ beta_diversity_through_plots.py -i 06_otu_table/otu_table_even.biom -t 08_phylogeny/rep_set.tre -m MappingFile.txt -o 09_beta_diversity

Traceback (most recent call last):

  File "/usr/local/bin/qiime-1.6.0/qiime-1.6.0-release/bin/beta_diversity_through_plots.py", line 165, in <module>

    main()

  File "/usr/local/bin/qiime-1.6.0/qiime-1.6.0-release/bin/beta_diversity_through_plots.py", line 162, in main

    status_update_callback=status_update_callback)

  File "/usr/local/bin/qiime-1.6.0/qiime-1.6.0-release/lib/qiime/workflow.py", line 867, in run_beta_diversity_through_plots

    close_logger_on_success=close_logger_on_success)

  File "/usr/local/bin/qiime-1.6.0/qiime-1.6.0-release/lib/qiime/workflow.py", line 135, in call_commands_serially

    raise WorkflowError, msg

qiime.workflow.WorkflowError: 

[Tony Walters]

Hello Daniel,

You may have to try installing this manually (https://pypi.python.org/pypi/python-dateutil/), and then open a new terminal and see if that fixes the error.  What versions of the software are you using btw (output of print_qiime_config.py)?

[Daniel Smith]

Hi Tony,

Thanks for the suggestion. I'll try re-installing dateutil and see what happens.

Here is the output of print_qiime_config.py:

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

bash$ print_qiime_config.py

System information

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

         Platform:      linux2

   Python version:      2.7.3 (default, Dec 20 2012, 19:37:26)  [GCC 4.6.3]

Python executable:      /usr/local/bin/qiime-1.6.0/python-2.7.3-release/bin/python

Dependency versions

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

                     PyCogent version:  1.5.3

                        NumPy version:  1.5.1

                   matplotlib version:  1.1.0

                  biom-format version:  1.1.1

                QIIME library version:  1.6.0

                 QIIME script version:  1.6.0

        PyNAST version (if installed):  1.2

RDP Classifier version (if installed):  rdp_classifier-2.2.jar

          Java version (if installed):  1.6.0_27

QIIME config values

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

                     blastmat_dir:      /usr/local/bin/qiime-1.6.0/blast-2.2.22-release/data

                         sc_queue:      all.q

      topiaryexplorer_project_dir:      None

     pynast_template_alignment_fp:      /usr/local/bin/qiime-1.6.0/core_set_aligned.fasta.imputed

                  cluster_jobs_fp:      /usr/local/bin/qiime-1.6.0/qiime-1.6.0-release/bin/start_parallel_jobs.py

pynast_template_alignment_blastdb:      None

assign_taxonomy_reference_seqs_fp:      /usr/local/bin/qiime-1.6.0/gg_otus-12_10-release/rep_set/97_otus.fasta

                     torque_queue:      friendlyq

              qiime_test_data_dir:      None

   template_alignment_lanemask_fp:      /usr/local/bin/qiime-1.6.0/lanemask_in_1s_and_0s

                    jobs_to_start:      1

                cloud_environment:      False

                qiime_scripts_dir:      /usr/local/bin/qiime-1.6.0/qiime-1.6.0-release/bin

            denoiser_min_per_core:      50

                      working_dir:      /tmp/

                    python_exe_fp:      /usr/local/bin/qiime-1.6.0/python-2.7.3-release/bin/python

                         temp_dir:      /tmp/

                      blastall_fp:      /usr/local/bin/qiime-1.6.0/blast-2.2.22-release/bin/blastall

                 seconds_to_sleep:      60

assign_taxonomy_id_to_taxonomy_fp:      /usr/local/bin/qiime-1.6.0/gg_otus-12_10-release/taxonomy/97_otu_taxonomy.txt

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

[Jai Ram Rideout]

Hi Daniel,

This is likely installing python-dateutil using a different python executable than the one that's being used for QIIME. Can you try running the following command:

which pip

This will show you where your pip executable is. Then:

sudo /usr/local/bin/qiime-1.6.0/python-2.7.3-release/bin/python /path/to/your/pip/executable install python-dateutil

where you've replaced /path/to/your/pip/executable with the path given by the 'which pip' command. Not sure if this will do the trick, but it's worth a shot.

-Jai

[Daniel Smith]

Hi Jai and Tony,

Thanks for all your help. The manual re-install of dateutil didn't work, but while I was poking around I noticed this:

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

bash$ locate rrule.py

/usr/local/bin/qiime-1.5.0/matplotlib-1.1.0-release/lib/python2.7/site-packages/dateutil/rrule.py

/usr/local/bin/qiime-1.5.0/matplotlib-1.1.0-release/lib/python2.7/site-packages/dateutil/rrule.pyc

/usr/share/pyshared/dateutil/rrule.py

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

That is, these is no rrule.py in my qiime-1.6.0 directory, though there is one in my prior 1.5.0 installation of QIIME.

So, I tried this:

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

mv /usr/local/bin/qiime-1.6.0/matplotlib-1.1.0-release /usr/local/bin/qiime-1.6.0/matplotlib-1.1.0-release_backup

ln -s /usr/local/bin/qiime-1.5.0/matplotlib-1.1.0-release /usr/local/bin/qiime-1.6.0/matplotlib-1.1.0-release

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

And now beta_diversity_through_plots.py run perfectly. Not an ideal solution, but hey if it works, it works.

I think I'm good to go, but if you want more info about the contents of the qiime-1.6.0/matplotlib-1.1.0-release just let me know.

Thanks!

   -Dan