Maximum recursion depth exceeded

[justinshaffer]

Hello,

I am receiving a plugin error from deicode when using in QIIME2:

"maximum recursion depth exceeded"

This is from running this code:

qiime deicode rpca \
  --i-table ~/danone/data/deblur_agp_danone_merged_150nt_sub3_sepp_only_noChl_noMit_fecal.qza \
  --p-min-feature-count 10 \
  --p-min-sample-count 500 \
  --o-biplot ~/danone/data/deblur_agp_danone_merged_150nt_sub3_sepp_only_noChl_noMit_fecal_rpca.qza \
  --o-distance-matrix ~/danone/data/deblur_agp_danone_merged_150nt_sub3_sepp_only_noChl_noMit_fecal_rpca_dist.qza

I'm using QIIME2 2018.11.

There are about 5000 samples in the data.

Thanks in advance for any insight.

[cameronmartino]

@justinshaffer Thank you for reporting this! Could you post the full traceback so I can see where exactly the recursion limit is being violated? Thanks again!

[justinshaffer]

@cameronmartino Sure thing. Thanks for taking a look!

`Traceback (most recent call last): File "/home/jpshaffer/software/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/q2cli/commands.py", line 274, in call results = action(arguments) File "", line 2, in rpca File "/home/jpshaffer/software/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/action.py", line 231, in bound_callable output_types, provenance) File "/home/jpshaffer/software/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/action.py", line 362, in _callableexecutor output_views = self._callable(view_args) File "/home/jpshaffer/software/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/deicode/q2/_method.py", line 20, in rpca table = table.to_dataframe().T.drop_duplicates() File "/home/jpshaffer/software/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/pandas/core/frame.py", line 3535, in drop_duplicates duplicated = self.duplicated(subset, keep=keep) File "/home/jpshaffer/software/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/pandas/core/frame.py", line 3584, in duplicated ids = get_group_index(labels, shape, sort=False, xnull=False) File "/home/jpshaffer/software/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/pandas/core/sorting.py", line 95, in get_group_index return loop(list(labels), list(shape)) File "/home/jpshaffer/software/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/pandas/core/sorting.py", line 86, in loop return loop(labels, shape) ...(above three lines repeat many times)... File "/home/jpshaffer/software/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/pandas/core/sorting.py", line 86, in loop return loop(labels, shape) File "/home/jpshaffer/software/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/pandas/core/sorting.py", line 60, in loop stride = np.prod(shape[1:nlev], dtype='i8') File "/home/jpshaffer/software/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/numpy/core/fromnumeric.py", line 2498, in prod out=out, **kwargs) RecursionError: maximum recursion depth exceeded

Plugin error from deicode:

maximum recursion depth exceeded

See above for debug info. QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment. Usage: qiime emperor biplot [OPTIONS] Try "qiime emperor biplot --help" for help.`

[cameronmartino]

@justinshaffer see this pull request in pandas. Try updating to greater or equal to pandas 0.23.2 and see if that fixes the problem. Additionally, I have removed the bit of code causing this error in pull request #29 so that should also solve the problem.

[justinshaffer]

@cameronmartino Thanks! The old version of Pandas is an artifact of my using an old QIIME2 build (2018.11) without updated dependencies. Upon using build 2019.1 things seem to work.

[cameronmartino]

@justinshaffer Great! I am going to close this issue then. If you see the issue again feel free to reopen it.