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</home/bsen/anaconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/decorator.py:decorator-gen-427> 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)
420CalledProcessError: 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!