Plugin error from diversity [Errno 13] Permission denied: ‘/tmp/qiime2-provenance-rdt0o_ri’

Hello,

I was running Qiime2 on WSL(Ubantu 20.04), installed through miniconda3.
Here’s the problem:
when I was running a diversity analysis using

qiime diversity core-metrics-phylogenetic
–i-phylogeny rooted-tree.qza
–i-table table.qza
–p-sampling-depth 1103
–m-metadata-file sample-metadata.tsv
–output-dir core-metrics-results

The plugin error occurred:
'Plugin error from diversity:

  • [Errno 13] Permission denied: ‘/tmp/qiime2-provenance-rdt0o_ri’ → ‘/tmp/qiime2-archive-2awodk99/08363486-57b1-4cd9-953a-8bb5959bbfe8/provenance’*

Debug info has been saved to /tmp/qiime2-q2cli-err-iub1x772.log

Here’s the debug info:

/home/zzbio/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/sklearn/metrics/pairwise.py:1761: DataConversionWarning: Data was converted to boolean for metric jaccard
warnings.warn(msg, DataConversionWarning)
Traceback (most recent call last):
File “/home/zzbio/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/q2cli/commands.py”, line 329, in call
results = action(**arguments)
File “”, line 2, in core_metrics_phylogenetic
File “/home/zzbio/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 245, in bound_callable
output_types, provenance)
File “/home/zzbio/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 484, in callable_executor
outputs = self._callable(scope.ctx, **view_args)
File “/home/zzbio/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/q2_diversity/_core_metrics.py”, line 59, in core_metrics_phylogenetic
metadata=metadata, n_jobs=n_jobs_or_threads)
File “”, line 2, in core_metrics
File “/home/zzbio/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 245, in bound_callable
output_types, provenance)
File “/home/zzbio/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 484, in callable_executor
outputs = self._callable(scope.ctx, **view_args)
File “/home/zzbio/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/q2_diversity/_core_metrics.py”, line 31, in core_metrics
beta_results = metric(table=rarefied_table, n_jobs=n_jobs)
File “”, line 2, in jaccard
File “/home/zzbio/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 245, in bound_callable
output_types, provenance)
File “/home/zzbio/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 418, in callable_executor
spec.qiime_type, output_view, spec.view_type, prov)
File “/home/zzbio/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/qiime2/sdk/result.py”, line 273, in _from_view
provenance_capture=provenance_capture)
File “/home/zzbio/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/qiime2/core/archive/archiver.py”, line 316, in from_data
Format.write(rec, type, format, data_initializer, provenance_capture)
File “/home/zzbio/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/qiime2/core/archive/format/v5.py”, line 21, in write
provenance_capture)
File “/home/zzbio/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/qiime2/core/archive/format/v1.py”, line 26, in write
prov_dir, [root / cls.METADATA_FILE, archive_record.version_fp])
File “/home/zzbio/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/qiime2/core/archive/provenance.py”, line 320, in finalize
self.path.rename(final_path)
File “/home/zzbio/miniconda3/envs/qiime2-2021.2/lib/python3.6/pathlib.py”, line 1309, in rename
self._accessor.rename(self, target)
File “/home/zzbio/miniconda3/envs/qiime2-2021.2/lib/python3.6/pathlib.py”, line 393, in wrapped
return strfunc(str(pathobjA), str(pathobjB), *args)
PermissionError: [Errno 13] Permission denied: ‘/tmp/qiime2-provenance-lojx5l_m’ → ‘/tmp/qiime2-archive-02so3rzw/f9ce3dc9-cca2-415b-8c1b-ece2cada830f/provenance’

Can anyone help please?
Many thanks for the suggestions!

Hi, @Jazzy, and welcome to the forum! :wave:

In WSL, can share the output of ls -lF / | grep tmp? This will show what permissions your /tmp directory has. You can then try running chmod 1777 /tmp to see if that fixes the issue. For details , please see this SO post:

Fingers crossed this is an easy fix :crossed_fingers:

1 Like

Hi Andrew,

Many thanks.

I did try changing the permissions, though I don’t think that’d be the problem because I was using the account that owns /tmp.
I uninstalled WSL and re-installed qiime2 again, run as admin, chown 777 /tmp, none of these works.

I’m still trying, will put up if I’d find any solution.