Hey guys,
Im trying to run the feature volatility command and Im getting an error message and cant get it to work; all other longitudinal commands work fine:
qiime longitudinal feature-volatility
–i-table …/collapsed_taxa/"$comp"-table-pruned-filtered-genus.qza
–m-metadata-file $map
–p-state-column sample_time
–p-individual-id-column tree
–p-n-estimators 10
–p-random-state 100
–output-dir “$comp”-taxa_volatility_genus
“$comp” is just a variable, and entering the precise path doesnt change the outcome. Heres the error message:
Plugin error from longitudinal:
Value must have type '<class 'int'>'
Debug info has been saved to /tmp/qiime2-q2cli-err-cbu1r1no.log
and here the logfile:
Traceback (most recent call last):
File “/home/mfbeuq/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/q2cli/commands.py”, line 329, in call
results = action(**arguments)
File “”, line 2, in feature_volatility
File “/home/mfbeuq/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 245, in bound_callable
output_types, provenance)
File “/home/mfbeuq/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 484, in callable_executor
outputs = self._callable(scope.ctx, **view_args)
File “/home/mfbeuq/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/q2_longitudinal/_longitudinal.py”, line 648, in feature_volatility
missing_samples=missing_samples)
File “”, line 2, in regress_samples
File “/home/mfbeuq/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 245, in bound_callable
output_types, provenance)
File “/home/mfbeuq/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 484, in callable_executor
outputs = self._callable(scope.ctx, **view_args)
File “/home/mfbeuq/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/q2_sample_classifier/classify.py”, line 220, in regress_samples
summary, = summarize_estimator(sample_estimator)
File “”, line 2, in summarize
File “/home/mfbeuq/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 245, in bound_callable
output_types, provenance)
File “/home/mfbeuq/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 452, in callable_executor
ret_val = self._callable(output_dir=temp_dir, **view_args)
File “/home/mfbeuq/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/q2_sample_classifier/classify.py”, line 383, in summarize
_summarize_estimator(output_dir, sample_estimator)
File “/home/mfbeuq/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/q2_sample_classifier/utilities.py”, line 532, in _summarize_estimator
title=‘Estimator Summary’)
File “/home/mfbeuq/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/q2_sample_classifier/utilities.py”, line 538, in _visualize
pd.set_option(‘display.max_colwidth’, None)
File “/home/mfbeuq/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/pandas/_config/config.py”, line 233, in call
return self.func(*args, **kwds)
File “/home/mfbeuq/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/pandas/_config/config.py”, line 127, in _set_option
o.validator(v)
File “/home/mfbeuq/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/pandas/_config/config.py”, line 772, in inner
raise ValueError(msg.format(typ=_type))
ValueError: Value must have type ‘<class ‘int’>’
Thanks in advance!
Max