pick_open_reference_otus.py Error: No script named 'pyqi'

[Vini Salazar]

Hello,

I'm trying to run the pick_open_reference_otus.py script but I'm constantly getting the following error:

h184-72:teste viniciusWS$ pick_open_reference_otus.py -o otus/ -i split_libraries/seqs.fna -r /anaconda/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta

Traceback (most recent call last):

  File "//anaconda/bin/pick_open_reference_otus.py", line 4, in <module>

    __import__('pkg_resources').run_script('qiime==1.9.1', 'pick_open_reference_otus.py')

  File "//anaconda/lib/python2.7/site-packages/setuptools-20.2.2-py2.7.egg/pkg_resources/__init__.py", line 726, in run_script

   

  File "//anaconda/lib/python2.7/site-packages/setuptools-20.2.2-py2.7.egg/pkg_resources/__init__.py", line 1484, in run_script

   

  File "/anaconda/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg-info/scripts/pick_open_reference_otus.py", line 453, in <module>

    main()

  File "/anaconda/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg-info/scripts/pick_open_reference_otus.py", line 432, in main

    minimum_failure_threshold=minimum_failure_threshold)

  File "//anaconda/lib/python2.7/site-packages/qiime/workflow/pick_open_reference_otus.py", line 1045, in pick_subsampled_open_reference_otus

    close_logger_on_success=False)

  File "//anaconda/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: Add taxa to OTU table

Command run was:

 biom add-metadata -i otus//otu_table_mc2.biom --observation-metadata-fp otus//uclust_assigned_taxonomy/rep_set_tax_assignments.txt -o otus//otu_table_mc2_w_tax.biom --sc-separated taxonomy --observation-header OTUID,taxonomy

Command returned exit status: 1

Stdout:

Stderr

Traceback (most recent call last):

  File "//anaconda/bin/pyqi", line 4, in <module>

    __import__('pkg_resources').run_script('pyqi==0.3.2', 'pyqi')

  File "//anaconda/lib/python2.7/site-packages/setuptools-20.2.2-py2.7.egg/pkg_resources/__init__.py", line 726, in run_script

  File "//anaconda/lib/python2.7/site-packages/setuptools-20.2.2-py2.7.egg/pkg_resources/__init__.py", line 1476, in run_script

pkg_resources.ResolutionError: No script named 'pyqi'

I have checked my pyqi version and all looks fine. I'm a bit confused because when I try to navigate to the path indicated in the error ("//anaconda/lib/python2.7/site-packages/setuptools-20.2.2-py2.7.egg/pkg_resources/__init__.py") I can't find a FOLDER named "setuptools-20.2.2-py2.7.egg/", only a FILE named so, and therefore can't find the __init__.py script in which the line 1476 error occurs. I found a pyqi script file in a few other folders, maybe it's placed in the incorrect directory?

I think pyqi is installed correctly as it is located in the following path:

h184-72:~ viniciusWS$ which pyqi

//anaconda/bin/pyqi

I have found this topic which seems related:

https://github.com/biocore/pyqi/issues/266

It suggests installing a virtual env and installing pyqi there, but I can't see how this might work in my case, would I need to redirect qiime's pyqi import requests to the virtual env? I don't know how to do this.

I'm fairly new to command line tools and python so I feel like I'm missing something obvious here... Please let me know how I could improve my explanation of the problem.

Thank you!

[Vini Salazar]

Apparently I have solved this by pip uninstall pyqi && conda install pyqi

But I will test better and return here to post the results so people having the same problem can see.