# Core-metrics (Plugin error from diversity)
**URL:** https://forum.qiime2.org/t/core-metrics-plugin-error-from-diversity/29402
**Category:** Technical Support
**Tags:** phylogeny, core-metrics, alpha
**Created:** [February 27, 2024, 6:04am UTC](https://forum.qiime2.org/t/core-metrics-plugin-error-from-diversity/29402 "2024-02-27T06:04:15Z")
**Posts on this page:** 12
**Page:** 1
### Author:  [@caca](https://forum.qiime2.org/u/caca)
#### Post date: [February 27, 2024, 6:04am UTC](https://forum.qiime2.org/t/core-metrics-plugin-error-from-diversity/29402/1 "2024-02-27T06:04:15Z")
hi everyone,
Im trying to make alpha and beta diversity but when i run the following :
qiime diversity core-metrics-phylogenetic --i-phylogeny Lombok\_v9\_18-rooted-tree.qza
--i-table Lombok\_v9\_18\_table.qza
--p-sampling-depth 11358
--m-metadata-file Metadata\_Lombok02\_v9\_18.tsv
--output-dir core-metrics-results
--verbose
it delivers the following:
faithpd -i /tmp/qiime2/carolline/data/f98e6d82-b833-443d-8921-556872735626/data/feature-table.biom -t /tmp/qiime2/carolline/data/f968ca8b-7889-42f8-978f-721f522e94b6/data/tree.nwk -o /tmp/q2-AlphaDiversityFormat-c7yzl\_m2
/home/carolline/anaconda3/envs/qiime2-amplicon-2024.2/bin/faithpd: line 43: /home/carolline/anaconda3/envs/qiime2-amplicon-2024.2/bin/faithpd\_nv\_avx2: cannot execute binary file: Exec format error
/home/carolline/anaconda3/envs/qiime2-amplicon-2024.2/bin/faithpd: line 43: /home/carolline/anaconda3/envs/qiime2-amplicon-2024.2/bin/faithpd\_nv\_avx2: Success
Traceback (most recent call last):
File "/home/carolline/anaconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2cli/commands.py", line 520, in **call**
results = self.\_execute\_action(
File "/home/carolline/anaconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2cli/commands.py", line 586, in \_execute\_action
results = action(\*\*arguments)
File "", line 2, in core\_metrics\_phylogenetic
File "/home/carolline/anaconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound\_callable
outputs = self._callable\_executor_(
File "/home/carolline/anaconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 647, in _callable\_executor_
outputs = self.\_callable(scope.ctx, \*\*view\_args)
File "/home/carolline/anaconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2\_diversity/\_core\_metrics.py", line 65, in core\_metrics\_phylogenetic
faith\_pd\_vector, = faith\_pd(table=cr.rarefied\_table,
File "", line 2, in faith\_pd
File "/home/carolline/anaconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/context.py", line 143, in deferred\_action
return action\_obj.\_bind(
File "", line 2, in faith\_pd
File "/home/carolline/anaconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound\_callable
outputs = self._callable\_executor_(
File "/home/carolline/anaconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 566, in _callable\_executor_
output\_views = self.\_callable(\*\*view\_args)
File "", line 2, in faith\_pd
File "/home/carolline/anaconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2\_diversity\_lib/\_util.py", line 75, in \_validate\_tables
return wrapped\_function(\*args, \*\*kwargs)
File "", line 2, in faith\_pd
File "/home/carolline/anaconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2\_diversity\_lib/\_util.py", line 118, in \_validate\_requested\_cpus
return wrapped\_function(\*bound\_arguments.args, \*\*bound\_arguments.kwargs)
File "/home/carolline/anaconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2\_diversity\_lib/alpha.py", line 54, in faith\_pd
\_omp\_cmd\_wrapper(threads, cmd)
File "/home/carolline/anaconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2\_diversity\_lib/\_util.py", line 134, in \_omp\_cmd\_wrapper
return \_run\_external\_cmd(cmd, verbose=verbose, env=env)
File "/home/carolline/anaconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2\_diversity\_lib/\_util.py", line 128, in \_run\_external\_cmd
return subprocess.run(cmd, check=True, env=env)
File "/home/carolline/anaconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['faithpd', '-i', '/tmp/qiime2/carolline/data/f98e6d82-b833-443d-8921-556872735626/data/feature-table.biom', '-t', '/tmp/qiime2/carolline/data/f968ca8b-7889-42f8-978f-721f522e94b6/data/tree.nwk', '-o', '/tmp/q2-AlphaDiversityFormat-c7yzl\_m2']' returned non-zero exit status 126.
Plugin error from diversity:
Command '['faithpd', '-i', '/tmp/qiime2/carolline/data/f98e6d82-b833-443d-8921-556872735626/data/feature-table.biom', '-t', '/tmp/qiime2/carolline/data/f968ca8b-7889-42f8-978f-721f522e94b6/data/tree.nwk', '-o', '/tmp/q2-AlphaDiversityFormat-c7yzl\_m2']' returned non-zero exit status 126.
How can i solve it?
thanks
---
### Author:  [@Oddant1](https://forum.qiime2.org/u/Oddant1)
#### Post date: [February 27, 2024, 5:20pm UTC](https://forum.qiime2.org/t/core-metrics-plugin-error-from-diversity/29402/2 "2024-02-27T17:20:56Z")
---
### Author:  [@Oddant1](https://forum.qiime2.org/u/Oddant1)
#### Post date: [February 27, 2024, 5:21pm UTC](https://forum.qiime2.org/t/core-metrics-plugin-error-from-diversity/29402/3 "2024-02-27T17:21:37Z")
Hello @caca,
The root error here is:
`/home/carolline/anaconda3/envs/qiime2-amplicon-2024.2/bin/faithpd: line 43: /home/carolline/anaconda3/envs/qiime2-amplicon-2024.2/bin/faithpd_nv_avx2: cannot execute binary file: Exec format error`
which means there is some kind of binary incompatibility going on. Of particular interest to me is the `avx2` part in the binary's name.
First of all, what sort of system are you running on? Mac, Linux, WSL? Are you on a local machine or a cluster? Are you sure you followed the correct install instructions for your OS on [this](https://docs.qiime2.org/2024.2/install/native/) page? We have seen a similar error before when people have installed the Linux version on Mac and vice versa.
Assuming you have installed the correct version of QIIME 2 for your system, can you run the command `lscpu` and post the results here?
Thank you.
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### Author:  [@caca](https://forum.qiime2.org/u/caca)
#### Post date: [February 28, 2024, 5:35am UTC](https://forum.qiime2.org/t/core-metrics-plugin-error-from-diversity/29402/4 "2024-02-28T05:35:04Z")
Hello
Thank you for responding. I'm running a Linux system and have followed the installation instructions,
wget [https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.2-py38-linux-conda.yml](https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.2-py38-linux-conda.yml)
conda env create -n qiime2-amplicon-2024.2 --file qiime2-amplicon-2024.2-py38-linux-conda.yml
I run lscpu command and here is the result.
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### Author:  [@Oddant1](https://forum.qiime2.org/u/Oddant1)
#### Post date: [February 28, 2024, 6:17pm UTC](https://forum.qiime2.org/t/core-metrics-plugin-error-from-diversity/29402/5 "2024-02-28T18:17:09Z")
You appear to be following the correct instructions, and your CPU seems to support the avx2 instruction set.
Can you try just running `faithpd` and `faithpd_nv_avx2` and posting the results of those runs here?
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### Author:  [@caca](https://forum.qiime2.org/u/caca)
#### Post date: [February 29, 2024, 6:15am UTC](https://forum.qiime2.org/t/core-metrics-plugin-error-from-diversity/29402/7 "2024-02-29T06:15:01Z")
Hello
Thank you for responding. I ran the commands faithpd and faithpd\_nv\_avx2 and here are the results.
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### Author:  [@wasade](https://forum.qiime2.org/u/wasade)
#### Post date: [February 29, 2024, 4:40pm UTC](https://forum.qiime2.org/t/core-metrics-plugin-error-from-diversity/29402/8 "2024-02-29T16:40:52Z")
Hi @caca,
Could you please try executing `export UNIFRAC_MAX_CPU=basic`, and then running `faithpd`?
Best,
Daniel
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### Author:  [@caca](https://forum.qiime2.org/u/caca)
#### Post date: [March 1, 2024, 2:18am UTC](https://forum.qiime2.org/t/core-metrics-plugin-error-from-diversity/29402/9 "2024-03-01T02:18:09Z")
hello @wasade, Thank you for responding. here are the result.
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### Author:  [@wasade](https://forum.qiime2.org/u/wasade)
#### Post date: [March 1, 2024, 4:27am UTC](https://forum.qiime2.org/t/core-metrics-plugin-error-from-diversity/29402/10 "2024-03-01T04:27:31Z")
Great, thank you! The call to `core-metrics-phylogenetic` should work now. Please note the `export` will need to be done prior to calling `core-metrics-phylogenetic`, and the "exported" variable is does not persist if the terminal is closed and reopened.
What looks to be occurring is your processor has one of the instruction sets we test for, but not all the ones required. We will be switching the library in the future to default to the basic binary to avoid this scenario.
Best,
Daniel
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### Author:  [@caca](https://forum.qiime2.org/u/caca)
#### Post date: [March 1, 2024, 5:33am UTC](https://forum.qiime2.org/t/core-metrics-plugin-error-from-diversity/29402/11 "2024-03-01T05:33:29Z")
Thank you @wasade that helps 😃
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### Author:  [@Oddant1](https://forum.qiime2.org/u/Oddant1)
#### Post date: [March 1, 2024, 4:44pm UTC](https://forum.qiime2.org/t/core-metrics-plugin-error-from-diversity/29402/12 "2024-03-01T16:44:04Z")
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### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [April 1, 2024, 10:44pm UTC](https://forum.qiime2.org/t/core-metrics-plugin-error-from-diversity/29402/13 "2024-04-01T22:44:59Z")
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