error while running ancom-bc

[JiaqianLi]

Hi,
Thanks for sharing! I tried to use same command as you but I recieved the :"Error: Detected invalid character in: “label”"
Could you please give me any suggestion for that? I'm appreciate for that

[gregcaporaso]

Hi @JiaqianLi, Can you please re-run your command including the --verbose parameter, and post the command and the error message here? Thank you!

[JiaqianLi]

Hi @gregcaporaso thanks a lot for your concern! Following are information I got with putting --vrebose:

Traceback (most recent call last):
File "/home/haichao/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/pandas/core/indexes/base.py", line 2897, in get_loc
return self._engine.get_loc(key)
File "pandas/_libs/index.pyx", line 107, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/index.pyx", line 131, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 1607, in pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas/_libs/hashtable_class_helper.pxi", line 1614, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'label'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/haichao/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2cli/commands.py", line 329, in call
results = action(**arguments)
File "", line 2, in ancombc
File "/home/haichao/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
output_types, provenance)
File "/home/haichao/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/sdk/action.py", line 390, in callable_executor
output_views = self._callable(**view_args)
File "/home/haichao/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2_ancombc/_method.py", line 56, in ancombc
for var in variables
File "/home/haichao/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2_ancombc/_method.py", line 56, in
for var in variables
File "/home/haichao/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/pandas/core/frame.py", line 2995, in getitem
indexer = self.columns.get_loc(key)
File "/home/haichao/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/pandas/core/indexes/base.py", line 2899, in get_loc
return self._engine.get_loc(self._maybe_cast_indexer(key))
File "pandas/_libs/index.pyx", line 107, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/index.pyx", line 131, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 1607, in pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas/_libs/hashtable_class_helper.pxi", line 1614, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'label'

Plugin error from ancombc:

'label'

See above for debug info.

[lizgehret]

Hi @JiaqianLi,

It looks like you're using the ancom-bc community plugin, which is no longer actively maintained. I would recommend using the ancom-bc method that I've implemented within q2-composition. Here's a link to our docs with details on this method and the available parameters/outputs: ancombc: Analysis of Composition of Microbiomes with Bias Correction — QIIME 2 2023.5.1 documentation

I see that you're using QIIME 2 2020.6 - in order to use the ancom-bc method mentioned above, you'll need to install a new QIIME 2 environment (either 2023.2 or 2023.5).

Hope this helps! Cheers