Faith pd in the context of continuous metadata

User Support
1

Hi!
I'm working on the alpha diversity analysis, the alpha-group significance worked fine (although it did´t use one of the categorical variables in my metadata sheet).
When running the alpha-correlation i get the error below.

  • If 3 of my columns in my sample metadata are numerical, could it be that it´s treating them as discrete variables and that´s why it does´t run?

  • Are spaces allowed when naming the sample metadata columns? Or any character restriction?

Thanks in advance :slight_smile:

(qiime2-2017.2) MacBook-Pro-de-Malena-2:Secondtrial mae$ qiime diversity alpha-correlation --i-alpha-diversity cm48000/faith_pd_vector.qza --m-metadata-file sample-metadata.tsv --o-visualization cm48000/faith-pd-correlation.qzv --verbose
/Users/mae/Desktop/Shell/ENTER/envs/qiime2-2017.2/lib/python3.5/site-packages/numpy/lib/function_base.py:2569: RuntimeWarning: invalid value encountered in true_divide
  c /= stddev[:, None]
/Users/mae/Desktop/Shell/ENTER/envs/qiime2-2017.2/lib/python3.5/site-packages/numpy/lib/function_base.py:2570: RuntimeWarning: invalid value encountered in true_divide
  c /= stddev[None, :]
/Users/mae/Desktop/Shell/ENTER/envs/qiime2-2017.2/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:875: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/Users/mae/Desktop/Shell/ENTER/envs/qiime2-2017.2/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:875: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/Users/mae/Desktop/Shell/ENTER/envs/qiime2-2017.2/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1814: RuntimeWarning: invalid value encountered in less_equal
  cond2 = cond0 & (x <= self.a)
Traceback (most recent call last):
  File "/Users/mae/Desktop/Shell/ENTER/envs/qiime2-2017.2/lib/python3.5/site-packages/q2cli-2017.2.0-py3.5.egg/q2cli/commands.py", line 217, in __call__
    results = action(**arguments)
  File "<decorator-gen-174>", line 2, in alpha_correlation
  File "/Users/mae/Desktop/Shell/ENTER/envs/qiime2-2017.2/lib/python3.5/site-packages/qiime2-2017.2.0-py3.5.egg/qiime2/sdk/action.py", line 171, in callable_wrapper
    output_types, provenance)
  File "/Users/mae/Desktop/Shell/ENTER/envs/qiime2-2017.2/lib/python3.5/site-packages/qiime2-2017.2.0-py3.5.egg/qiime2/sdk/action.py", line 305, in _callable_executor_
    ret_val = callable(output_dir=temp_dir, **view_args)
  File "/Users/mae/Desktop/Shell/ENTER/envs/qiime2-2017.2/lib/python3.5/site-packages/q2_diversity-2017.2.0-py3.5.egg/q2_diversity/_alpha/_visualizer.py", line 175, in alpha_correlation
    with open(os.path.join(output_dir, filename), 'w') as fh:
FileNotFoundError: [Errno 2] No such file or directory: '/var/folders/n3/hytr03qx30v_r4kr_g2z6n840000gn/T/qiime2-temp-0z0zcdco/category-Batch%20Glycerol%20%28g/L%29.jsonp'

Plugin error from diversity:

  [Errno 2] No such file or directory: '/var/folders/n3/hytr03qx30v_r4kr
  _g2z6n840000gn/T/qiime2-temp-0z0zcdco/category-
  Batch%20Glycerol%20%28g/L%29.jsonp'

See above for debug info.
2

Hi @malenaamer! I think metadata category names containing spaces is the issue, as you suspected. I created a bug report so we can fix this in an upcoming release. In the meantime, can you try renaming your category and rerunning the command?

If you're wondering why certain metadata categories are being excluded by alpha-group-significance or alpha-correlation, there will be messages at the top of the HTML page describing why these categories were excluded. Take a look at those messages and get in touch if you need clarification on that (screenshots would be helpful).

2 Likes
3

It worked!
I eliminated spaces and special characters like ( / ).
Thanks!

1 Like