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.