Hi there,

I have encountered an error that I have been unable to troubleshoot using the gneiss workflow.

`qiime gneiss correlation-clustering \ --i-table $input_table \ --o-clustering hierarchy.qza`

`qiime gneiss ilr-hierarchical \ --i-table $input_table \ --i-tree hierarchy.qza \ --o-balances balances.qza`

Both of these work and generate balances and heirarchy files.

`qiime gneiss ols-regression \ --p-formula "Sample_type" \ --i-table balances.qza \ --i-tree hierarchy.qza \ --m-metadata-file $metadatapath \ --verbose \ --o-visualization regression_summary_Sample_type.qzv`

However, this command fails with the error below.

I thought maybe this was because there were some 0 balances, however when I run:

qiime tools export --input-path balances.qza --output exportbalances

biom summarize-table -i exportbalances/feature-table.biom -o exportbalances/summarized.txt

/local/one/CSTAIRS/CONDA/env/qiime2-2018.8/lib/python3.5/site-packages/gneiss-0.4.4-py3.5.egg/gneiss/regression/_ols.py:192: RuntimeWarning: invalid value encountered in sqrt

/local/one/CSTAIRS/CONDA/env/qiime2-2018.8/lib/python3.5/site-packages/gneiss-0.4.4-py3.5.egg/gneiss/regression/_ols.py:193: RuntimeWarning: invalid value encountered in true_divide

/local/one/CSTAIRS/CONDA/env/qiime2-2018.8/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater

return (self.a < x) & (x < self.b)

/local/one/CSTAIRS/CONDA/env/qiime2-2018.8/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less

return (self.a < x) & (x < self.b)

/local/one/CSTAIRS/CONDA/env/qiime2-2018.8/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1818: RuntimeWarning: invalid value encountered in less_equal

cond2 = cond0 & (x <= self.a)

/local/one/CSTAIRS/CONDA/env/qiime2-2018.8/lib/python3.5/site-packages/gneiss-0.4.4-py3.5.egg/gneiss/regression/_ols.py:206: RuntimeWarning: invalid value encountered in double_scalars

/local/one/CSTAIRS/CONDA/env/qiime2-2018.8/lib/python3.5/site-packages/statsmodels/stats/multitest.py:320: RuntimeWarning: invalid value encountered in less_equal

reject = pvals_sorted <= ecdffactor*alpha

Traceback (most recent call last):

File “/local/one/CSTAIRS/CONDA/env/qiime2-2018.8/lib/python3.5/site-packages/q2cli/commands.py”, line 274, in **call**

results = action(**arguments)

File “”, line 2, in ols_regression

File “/local/one/CSTAIRS/CONDA/env/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable

output_types, provenance)

File “/local/one/CSTAIRS/CONDA/env/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 424, in *callable_executor*

ret_val = self._callable(output_dir=temp_dir, **view_args)

File “/local/one/CSTAIRS/CONDA/env/qiime2-2018.8/lib/python3.5/site-packages/q2_gneiss/regression/_regression.py”, line 34, in ols_regression

ols_summary(output_dir, res, tree)

File “/local/one/CSTAIRS/CONDA/env/qiime2-2018.8/lib/python3.5/site-packages/gneiss-0.4.4-py3.5.egg/gneiss/plot/_regression_plot.py”, line 302, in ols_summary

hm_p = _heatmap_summary(model.pvalues.T, model.coefficients().T)

File “/local/one/CSTAIRS/CONDA/env/qiime2-2018.8/lib/python3.5/site-packages/gneiss-0.4.4-py3.5.egg/gneiss/plot/_regression_plot.py”, line 186, in _heatmap_summary

ind = int(np.floor((x - _min) / (_max - _min) * (N - 1)))

ValueError: cannot convert float NaN to integer

Plugin error from gneiss:

cannot convert float NaN to integer

See above for debug info.