Hello. I was trying to find out the features differ in abundance across different groups. I followed the three steps (shown below) mentioned in the Tutorial and got an error that I dont know how to deal with. Please give me some advices. Thank you all.
The three steps are:
"qiime taxa collapse
--i-table gut-table.qza
--i-taxonomy taxonomy.qza
--p-level 6
--o-collapsed-table gut-table-l6.qza
qiime composition add-pseudocount
--i-table gut-table-l6.qza
--o-composition-table comp-gut-table-l6.qza
qiime composition ancom
--i-table comp-gut-table-l6.qza
--m-metadata-file sample-metadata.tsv
--m-metadata-column subject
--o-visualization l6-ancom-subject.qzv"
qiime composition ancom \
--i-table comp-gut-table-l6.qza
--m-metadata-file sow.meta.qiime2.tsv
--m-metadata-column Stage
--verbose
--o-visualization l6-ancom-subject.qzv"
My errors are:
/share/apps/python/anaconda3-3.6.0/envs/qiime2-2018.4/lib/python3.5/site-packages/scipy/stats/stats.py:2968: RuntimeWarning: invalid value encountered in double_scalars
f = msb / msw
Traceback (most recent call last):
File "/share/apps/python/anaconda3-3.6.0/envs/qiime2-2018.4/lib/python3.5/site-packages/q2cli/commands.py", line 274, in call
results = action(**arguments)
File "", line 2, in ancom
File "/share/apps/python/anaconda3-3.6.0/envs/qiime2-2018.4/lib/python3.5/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/share/apps/python/anaconda3-3.6.0/envs/qiime2-2018.4/lib/python3.5/site-packages/qiime2/sdk/action.py", line 428, in callable_executor
ret_val = self._callable(output_dir=temp_dir, **view_args)
File "/share/apps/python/anaconda3-3.6.0/envs/qiime2-2018.4/lib/python3.5/site-packages/q2_composition/_ancom.py", line 75, in ancom
transform_function, difference_function)
File "/share/apps/python/anaconda3-3.6.0/envs/qiime2-2018.4/lib/python3.5/site-packages/q2_composition/_ancom.py", line 147, in _volcanoplot
fold_change = transformed_table.apply(diff_func, axis=0)
File "/share/apps/python/anaconda3-3.6.0/envs/qiime2-2018.4/lib/python3.5/site-packages/pandas/core/series.py", line 3192, in apply
mapped = lib.map_infer(values, f, convert=convert_dtype)
File "pandas/_libs/src/inference.pyx", line 1472, in pandas._libs.lib.map_infer
File "/share/apps/python/anaconda3-3.6.0/envs/qiime2-2018.4/lib/python3.5/site-packages/pandas/core/series.py", line 3179, in
f = lambda x: func(x, *args, **kwds)
TypeError: diff_func() got an unexpected keyword argument 'axis'
Plugin error from composition:
diff_func() got an unexpected keyword argument 'axis'
See above for debug info.