# Adonis run error
**URL:** https://forum.qiime2.org/t/adonis-run-error/8877
**Category:** Technical Support
**Created:** [March 20, 2019, 5:03pm UTC](https://forum.qiime2.org/t/adonis-run-error/8877 "2019-03-20T17:03:06Z")
**Posts on this page:** 6
**Page:** 1
### Author:  [@bsen2018](https://forum.qiime2.org/u/bsen2018)
#### Post date: [March 20, 2019, 5:03pm UTC](https://forum.qiime2.org/t/adonis-run-error/8877/1 "2019-03-20T17:03:06Z")
Hi,
**We stumbled upon an error message while running the following codes for "Adonis" on a Jupyter notebook:**
> from qiime2.plugins.diversity.visualizers import adonis
> adonis = adonis(beta\_diversity\_dist, metadata, formula = "Temp+pH")
> adonis.visualization
**And here is the error message:**
> Running external command line application. This may print messages to stdout and/or stderr.
> The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
>
> Command: run\_adonis.R /tmp/tmpmhqfyrnm/dm.tsv /tmp/tmpmhqfyrnm/md.tsv Temp+pH 999 1 /tmp/qiime2-temp-a7ugxr7p/adonis.tsv
>
> * * *
>
> CalledProcessError Traceback (most recent call last)
> in
> 1 from qiime2.plugins.diversity.visualizers import adonis
> ----\> 2 adonis = adonis(beta\_diversity\_dist, metadata, formula = "Temp+pH")
> 3 adonis.visualization
>
> \ in adonis(distance\_matrix, metadata, formula, permutations, n\_jobs)
>
> ~/anaconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py in bound\_callable(\*args, \*\*kwargs)
> 229 # Execute
> 230 outputs = self._callable\_executor_(scope, callable\_args,
> --\> 231 output\_types, provenance)
> 232
> 233 if len(outputs) != len(self.signature.outputs):
>
> ~/anaconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py in _callable\_executor_(self, scope, view\_args, output\_types, provenance)
> 425 # will also need to be updated to support OutPath instead of str.
> 426 with tempfile.TemporaryDirectory(prefix='qiime2-temp-') as temp\_dir:
> --\> 427 ret\_val = self.\_callable(output\_dir=temp\_dir, \*\*view\_args)
> 428 if ret\_val is not None:
> 429 raise TypeError(
>
> ~/anaconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2\_diversity/\_beta/\_visualizer.py in adonis(output\_dir, distance\_matrix, metadata, formula, permutations, n\_jobs)
> 363 cmd = ['run\_adonis.R', dm\_fp, md\_fp, formula, str(permutations),
> 364 str(n\_jobs), results\_fp]
> --\> 365 \_run\_command(cmd)
> 366
> 367 # Visualize results
>
> ~/anaconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2\_diversity/\_beta/\_visualizer.py in \_run\_command(cmd, verbose)
> 389 print("\nCommand:", end=' ')
> 390 print(" ".join(cmd), end='\n\n')
> --\> 391 subprocess.run(cmd, check=True)
>
> ~/anaconda3/envs/qiime2-2019.1/lib/python3.6/subprocess.py in run(input, timeout, check, \*popenargs, \*\*kwargs)
> 416 if check and retcode:
> 417 raise CalledProcessError(retcode, process.args,
> --\> 418 output=stdout, stderr=stderr)
> 419 return CompletedProcess(process.args, retcode, stdout, stderr)
> 420
>
> CalledProcessError: Command '['run\_adonis.R', '/tmp/tmpmhqfyrnm/dm.tsv', '/tmp/tmpmhqfyrnm/md.tsv', 'Temp+pH', '999', '1', '/tmp/qiime2-temp-a7ugxr7p/adonis.tsv']' returned non-zero exit status 1.
**System specification: Qiime2.2019.1, Windows-subsystem-Linux.**
Any solution, pl.
Thanks in advance!
---
### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [March 20, 2019, 10:25pm UTC](https://forum.qiime2.org/t/adonis-run-error/8877/2 "2019-03-20T22:25:23Z")
It looks like the underlying adonis call failed here - would you be able to share download links to these data, that way we can reproduce locally and look more closely at the issue? Thanks! :qiime2: 🦖
---
### Author:  [@bsen2018](https://forum.qiime2.org/u/bsen2018)
#### Post date: [March 21, 2019, 1:37am UTC](https://forum.qiime2.org/t/adonis-run-error/8877/3 "2019-03-21T01:37:41Z")
Hi Matthew,
Here are the [beta-dist.qza](https://cdck-file-uploads-global.s3.dualstack.us-west-2.amazonaws.com/flex002/uploads/qiime21/original/2X/6/6415221b8adfc539079d47bdf539613331c7676a.qza) (43.6 KB)
(Bray-Curtis distance matrix) and [metadata.txt](https://cdck-file-uploads-global.s3.dualstack.us-west-2.amazonaws.com/flex002/uploads/qiime21/original/2X/9/9199acc2a45c5ffb4f37070e8696b8076a9430a5.txt) (462 Bytes)
files, which we linked to the `Adonis` code described in my initial post. Thanks for your time! :qiime2: 🧐
---
### Author:  [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [March 21, 2019, 1:14pm UTC](https://forum.qiime2.org/t/adonis-run-error/8877/5 "2019-03-21T13:14:45Z")
---
### Author:  [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [March 21, 2019, 1:23pm UTC](https://forum.qiime2.org/t/adonis-run-error/8877/6 "2019-03-21T13:23:18Z")
Thank you for sharing your data, @bsen2018.
[This is a bug that we previously caught and have already fixed](https://forum.qiime2.org/t/adonis-not-recognizing-metadata-columns-in-formula/8314/11). The fix will be available in next month's release of QIIME 2. For now, the easiest thing to do is just change the header ID from `#SampleID` to `sample-id`.
Good luck!
---
### Author:  [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [March 21, 2019, 1:23pm UTC](https://forum.qiime2.org/t/adonis-run-error/8877/7 "2019-03-21T13:23:20Z")