AttributeError: 'DataFrame' object has no attribute 'to_dense'

[eliscar]

Hi,

I'm trying to do correlation analysis with SCNIC but I'm stacked at this point.

qiime SCNIC calculate-correlations
--i-table fake_data-filtered.qza
--p-method sparcc
--o-correlation-table fake_correls.qza

I received this error: "Plugin error from SCNIC:

'DataFrame' object has no attribute 'to_dense'

Debug info has been saved to /tmp/qiime2-q2cli-err-8mn7co9c.log"

The debug info is this:
Correlating with sparcc
Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/q2cli/commands.py", line 329, in call
results = action(**arguments)
File "", line 2, in calculate_correlations
File "/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/sdk/action.py", line 244, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/sdk/action.py", line 390, in callable_executor
output_views = self._callable(**view_args)
File "/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/q2_SCNIC/_SCNIC_methods.py", line 29, in calculate_correlations
correls = ca.fastspar_correlation(table, verbose=True, nprocs=n_procs)
File "/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/SCNIC/correlation_analysis.py", line 77, in fastspar_correlation
table.to_dataframe().to_dense().to_csv(path.join(temp, 'otu_table.tsv'), sep='\t', index_label='#OTU ID')
File "/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/pandas/core/generic.py", line 5465, in getattr
return object.getattribute(self, name)
AttributeError: 'DataFrame' object has no attribute 'to_dense'

I understood that 'to_dense' is something related to pandas, so I try to install pandas but still, the error remains.

Someone could help me fixing it?

Thank you

[weedcentipede]

Hi, I have the exact same issue, in the same Qiime2 version (2021.4) and other env versions (2020.8 and 2020.11).

Thanks in advance,
Luis Alfonso.

[timyerg]

For me worked chanding pandas version:
pip install pandas==0.25
After the analysis change it back to newer version to avoid further issues