# Plugin error from alpha diversity
**URL:** https://forum.qiime2.org/t/plugin-error-from-alpha-diversity/27105
**Category:** User Support
**Tags:** alpha
**Created:** [July 18, 2023, 8:11pm UTC](https://forum.qiime2.org/t/plugin-error-from-alpha-diversity/27105 "2023-07-18T20:11:58Z")
**Posts on this page:** 11
**Page:** 1
### Author:  [@deepak](https://forum.qiime2.org/u/deepak)
#### Post date: [July 18, 2023, 8:11pm UTC](https://forum.qiime2.org/t/plugin-error-from-alpha-diversity/27105/1 "2023-07-18T20:11:58Z")
I was analyzing alpha diversity of my data through following command:
**qiime diversity alpha --i-table feature-table-otu-input.qza --p-metric ace --o-alpha-diversity observed\_otus\_vector\_alpha\_ace\_evenness.qza**
Further I am getting following error. I have also done the Chao1 but I am curious how to resolve this Ace metric issue.
Plugin error from diversity:
The only rare OTUs are singletons, so the ACE metric is undefined. EstimateS suggests using bias-corrected Chao1 instead.
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### Author:  [@lizgehret](https://forum.qiime2.org/u/lizgehret)
#### Post date: [July 19, 2023, 4:12pm UTC](https://forum.qiime2.org/t/plugin-error-from-alpha-diversity/27105/2 "2023-07-19T16:12:11Z")
Hi @deepak,
Can you re-run your command with the `--verbose` flag and copy/paste the entire traceback in your response? This will help us to better determine where exactly this error is coming from. Thanks! 🦎
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### Author:  [@deepak](https://forum.qiime2.org/u/deepak)
#### Post date: [July 19, 2023, 4:32pm UTC](https://forum.qiime2.org/t/plugin-error-from-alpha-diversity/27105/3 "2023-07-19T16:32:03Z")
Hi, following is the log of the command:
(qiime2-2023.5) dve@CRB:/mnt/f/c/alpha$ qiime diversity alpha --i-table motu-table.qza --p-metric ace --o-alpha-diversity observed\_otus\_vector\_alpha\_ace\_evenness.qza --verbose
Traceback (most recent call last):
File "/home/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2cli/commands.py", line 473, in **call**
results = action(\*\*arguments)
File "", line 2, in alpha
File "/home/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/sdk/action.py", line 274, in bound\_callable
outputs = self._callable\_executor_(
File "/home/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/sdk/action.py", line 590, in _callable\_executor_
outputs = self.\_callable(scope.ctx, \*\*view\_args)
File "/home/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2\_diversity/\_alpha/\_pipeline.py", line 28, in alpha
vector, = action(table=table, metric=metric)
File "/home/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/sdk/context.py", line 140, in deferred\_action
return action\_obj.\_bind(
File "", line 2, in alpha\_passthrough
File "/home/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/sdk/action.py", line 274, in bound\_callable
outputs = self._callable\_executor_(
File "/home/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/sdk/action.py", line 509, in _callable\_executor_
output\_views = self.\_callable(\*\*view\_args)
File "", line 2, in alpha\_passthrough
File "/home/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2\_diversity\_lib/\_util.py", line 69, in \_disallow\_empty\_tables
return wrapped\_function(\*args, \*\*kwargs)
File "/home/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2\_diversity\_lib/alpha.py", line 108, in alpha\_passthrough
results.append(skbio.diversity.alpha\_diversity(metric=metric,
File "/home/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/skbio/diversity/\_driver.py", line 181, in alpha\_diversity
results = [metric(c, \*\*kwargs) for c in counts]
File "/home/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/skbio/diversity/\_driver.py", line 181, in
results = [metric(c, \*\*kwargs) for c in counts]
File "/home/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/skbio/diversity/alpha/\_ace.py", line 93, in ace
raise ValueError("The only rare OTUs are singletons, so the ACE "
ValueError: The only rare OTUs are singletons, so the ACE metric is undefined. EstimateS suggests using bias-corrected Chao1 instead.
Plugin error from diversity:
The only rare OTUs are singletons, so the ACE metric is undefined. EstimateS suggests using bias-corrected Chao1 instead.
See above for debug info.
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### Author:  [@colinvwood](https://forum.qiime2.org/u/colinvwood)
#### Post date: [July 19, 2023, 4:51pm UTC](https://forum.qiime2.org/t/plugin-error-from-alpha-diversity/27105/4 "2023-07-19T16:51:36Z")
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### Author:  [@lizgehret](https://forum.qiime2.org/u/lizgehret)
#### Post date: [July 19, 2023, 6:19pm UTC](https://forum.qiime2.org/t/plugin-error-from-alpha-diversity/27105/5 "2023-07-19T18:19:41Z")
Hi @deepak,
Thanks for sharing that traceback! It looks like this is coming directly from the diversity package within scikitbio - I've never seen this error before, but based on what it says it seems like you might not be able to use this metric on your data.
Can you tell us a bit more about your data and why you chose this specific metric? This might better inform your next steps and why this didn't work for your analysis.
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### Author:  [@lizgehret](https://forum.qiime2.org/u/lizgehret)
#### Post date: [July 19, 2023, 6:19pm UTC](https://forum.qiime2.org/t/plugin-error-from-alpha-diversity/27105/6 "2023-07-19T18:19:43Z")
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### Author:  [@deepak](https://forum.qiime2.org/u/deepak)
#### Post date: [July 19, 2023, 6:59pm UTC](https://forum.qiime2.org/t/plugin-error-from-alpha-diversity/27105/7 "2023-07-19T18:59:29Z")
Hi, thank you so much @lizgehret for prompt response
I analyzed my shotgun sequencing data through mOTU plugin and performed downstream analysis. Here I tried to analyze alpha diversity in multiple ways so that I can compare the outputs. I analyzed all the methods for alpha diversity but only this one was giving this error.
I have results of other methods, but I was curious why this error was coming.
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### Author:  [@colinvwood](https://forum.qiime2.org/u/colinvwood)
#### Post date: [July 19, 2023, 7:03pm UTC](https://forum.qiime2.org/t/plugin-error-from-alpha-diversity/27105/8 "2023-07-19T19:03:34Z")
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### Author:  [@lizgehret](https://forum.qiime2.org/u/lizgehret)
#### Post date: [July 20, 2023, 9:11pm UTC](https://forum.qiime2.org/t/plugin-error-from-alpha-diversity/27105/9 "2023-07-20T21:11:14Z")
Hi @deepak,
Thanks for sharing that context!
So for full disclosure, I'm not super familiar with the ACE metric in particular, but I did find [this forum post](https://forum.qiime2.org/t/alpha-diversity-after-filtering/8927) which discusses how the ACE metric (and other similar diversity metrics) are calculated, along with their limitations. Hopefully this will help contextualize this error a bit, based on the dataset you're working with. Cheers 🦎
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### Author:  [@lizgehret](https://forum.qiime2.org/u/lizgehret)
#### Post date: [July 20, 2023, 9:11pm UTC](https://forum.qiime2.org/t/plugin-error-from-alpha-diversity/27105/10 "2023-07-20T21:11:16Z")
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### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [August 21, 2023, 3:11am UTC](https://forum.qiime2.org/t/plugin-error-from-alpha-diversity/27105/11 "2023-08-21T03:11:53Z")
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