# qiime diversity alpha-group-significance All numbers are identical in kruskal
**URL:** https://forum.qiime2.org/t/qiime-diversity-alpha-group-significance-all-numbers-are-identical-in-kruskal/32070
**Category:** User Support
**Tags:** alpha
**Created:** [December 5, 2024, 11:43pm UTC](https://forum.qiime2.org/t/qiime-diversity-alpha-group-significance-all-numbers-are-identical-in-kruskal/32070 "2024-12-05T23:43:41Z")
**Posts on this page:** 5
**Page:** 1
### Author:  [@tinoracha](https://forum.qiime2.org/u/tinoracha)
#### Post date: [December 5, 2024, 11:43pm UTC](https://forum.qiime2.org/t/qiime-diversity-alpha-group-significance-all-numbers-are-identical-in-kruskal/32070/1 "2024-12-05T23:43:41Z")
Hi Qiime folks!
I am having an issue with using the qiime diversity alpha-group-significance function.
_Here is my input:_
qiime diversity alpha-group-significance
--i-alpha-diversity diversity/shannon\_vector.qza
--m-metadata-file $METADATA2
--verbose
--o-visualization diversity/shannon\_compare\_groups.qzv
_Here's the output:_
**Plugin error from diversity:**
**All numbers are identical in kruskal**
_And here's the debug info:_
/Users/s.d./miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2\_types/sample\_data/\_transformer.py:27: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to\_numeric without passing `errors` and catch exceptions explicitly instead
df[cols] = df[cols].apply(pd.to\_numeric, errors='ignore')
Traceback (most recent call last):
File "/Users/s.d./miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2cli/commands.py", line 520, in **call**
results = self.\_execute\_action(
File "/Users/s.d./miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2cli/commands.py", line 581, in \_execute\_action
results = action(\*\*arguments)
File "", line 2, in alpha\_group\_significance
File "/Users/s.d./miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/action.py", line 342, in bound\_callable
outputs = self._callable\_executor_(
File "/Users/s.d./miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/action.py", line 625, in _callable\_executor_
ret\_val = self.\_callable(output\_dir=temp\_dir, \*\*view\_args)
File "/Users/s.d./miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2\_diversity/\_alpha/\_visualizer.py", line 97, in alpha\_group\_significance
kw\_H\_all, kw\_p\_all = scipy.stats.mstats.kruskalwallis(\*groups)
File "/Users/s.d./miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/scipy/stats/\_mstats\_basic.py", line 1649, in kruskal
raise ValueError('All numbers are identical in kruskal')
ValueError: All numbers are identical in kruskal
My metadata file seems correct, I ran **qiime metadata tabulate** just to be sure. I can provide the TSV too if that would be useful.
Thanks for the help!
---
### Author:  [@timanix](https://forum.qiime2.org/u/timanix)
#### Post date: [December 6, 2024, 5:26am UTC](https://forum.qiime2.org/t/qiime-diversity-alpha-group-significance-all-numbers-are-identical-in-kruskal/32070/2 "2024-12-06T05:26:08Z")
Hello,
This error arises when all numerical values to be compared are identical.
I guess that something went wrong at the diversity metrics calculation step.
I would export / extract the tsv file from the shannon\_entropy\_vector.qza file and manually inspect it to see if all values are identical, at least within one group. Double check the command you run for core-metrics.
Best,
---
### Author:  [@tinoracha](https://forum.qiime2.org/u/tinoracha)
#### Post date: [December 6, 2024, 10:31pm UTC](https://forum.qiime2.org/t/qiime-diversity-alpha-group-significance-all-numbers-are-identical-in-kruskal/32070/3 "2024-12-06T22:31:43Z")
Thank you! Yes, the core metrics were generated incorrectly. using a sampling depth of 1000 I got much better results. Is there a good rule of thumb for choosing a sampling depth for calculating these metrics?
---
### Author:  [@timanix](https://forum.qiime2.org/u/timanix)
#### Post date: [December 6, 2024, 10:47pm UTC](https://forum.qiime2.org/t/qiime-diversity-alpha-group-significance-all-numbers-are-identical-in-kruskal/32070/4 "2024-12-06T22:47:58Z")
Welcome!
This value is a compromise between the number of samples you want to keep (all samples with lower depth are removed) and the number of features you want to use for diversity metrics calculation.
---
### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [January 7, 2025, 4:48am UTC](https://forum.qiime2.org/t/qiime-diversity-alpha-group-significance-all-numbers-are-identical-in-kruskal/32070/5 "2025-01-07T04:48:47Z")
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