Plugin error from diversity - running core metrics in WSL

windows
core-metrics

(Anna Wallis) #1

Hello-

I’m running QIIME 2 2018.11.0 in Windows Subsystem for Linux (the Ubuntu app for Windows 10)

I’m trying to run diversity core metrics.
(Because I’m working on a Windows I’m importing from and exporting to my windows directory, but it creates a long file path):
qiime diversity core-metrics-phylogenetic
–i-phylogeny /mnt/c/Users/aew232/Desktop/q2data/AWAE3/rooted-tree.qza
–i-table /mnt/c/Users/aew232/Desktop/q2data/AWAE3/table.qza
–p-sampling-depth 10000
–m-metadata-file /mnt/c/Users/aew232/Desktop/q2data/AWAE3/AWAE3metadata.txt
–output-dir /mnt/c/Users/aew232/Desktop/q2data/AWAE3/core-metrics-results

I’ve tried with both my own data and with the sample data in the moving pictures tutorial. Both return the same error.

Plugin error from diversity: [Errno 13] Permission denied: ‘/tmp/qiime2-provenance-q0c4w9vi’ -> ‘/tmp/qiime2-archive-sd9ts2w_/0da42ce7-97c6-494b-a900-56f9d67aa7a1/provenance’

Any help would be appreciated. I understand Qiime2 doesn’t currently support the WSL platform, but I’m hoping you might have some advice.

  • Anna

The output is as follows (with verbose flag)
/home/aew232/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/sklearn/utils/validation.py:475: DataConversionWarning: Data with input dtype float64 was converted to bool by check_pairwise_arrays.
warnings.warn(msg, DataConversionWarning)
/home/aew232/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:152: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it’s probably safe to ignore them, but if they are large in magnitude, the results won’t be useful. See the Notes section for more details. The smallest eigenvalue is -0.037165071795644926 and the largest is 2.2413463846073722.
RuntimeWarning
/home/aew232/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:152: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it’s probably safe to ignore them, but if they are large in magnitude, the results won’t be useful. See the Notes section for more details. The smallest eigenvalue is -0.008265865638813498 and the largest is 0.23349356255376896.
RuntimeWarning
/home/aew232/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:152: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it’s probably safe to ignore them, but if they are large in magnitude, the results won’t be useful. See the Notes section for more details. The smallest eigenvalue is -0.05066108233905085 and the largest is 1.650706833932135.
RuntimeWarning
/home/aew232/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:152: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it’s probably safe to ignore them, but if they are large in magnitude, the results won’t be useful. See the Notes section for more details. The smallest eigenvalue is -0.002926958717398591 and the largest is 0.11283504789660662.
RuntimeWarning
Traceback (most recent call last):
File “/home/aew232/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/q2cli/commands.py”, line 274, in call
results = action(**arguments)
File “”, line 2, in core_metrics_phylogenetic
File “/home/aew232/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/home/aew232/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 455, in callable_executor
outputs = self._callable(scope.ctx, **view_args)
File “/home/aew232/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/q2_diversity/_core_metrics.py”, line 65, in core_metrics_phylogenetic
pcoas += pcoa(distance_matrix=dm)
File “”, line 2, in pcoa
File “/home/aew232/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/home/aew232/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 390, in callable_executor
spec.qiime_type, output_view, spec.view_type, prov)
File “/home/aew232/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/result.py”, line 271, in _from_view
provenance_capture=provenance_capture)
File “/home/aew232/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/core/archive/archiver.py”, line 316, in from_data
Format.write(rec, type, format, data_initializer, provenance_capture)
File “/home/aew232/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/core/archive/format/v5.py”, line 21, in write
provenance_capture)
File “/home/aew232/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/core/archive/format/v1.py”, line 26, in write
prov_dir, [root / cls.METADATA_FILE, archive_record.version_fp])
File “/home/aew232/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/core/archive/provenance.py”, line 315, in finalize
self.path.rename(final_path)
File “/home/aew232/miniconda3/envs/qiime2-2018.11/lib/python3.5/pathlib.py”, line 1277, in rename
self.accessor.rename(self, target)
File “/home/aew232/miniconda3/envs/qiime2-2018.11/lib/python3.5/pathlib.py”, line 377, in wrapped
return strfunc(str(pathobjA), str(pathobjB), *args)
PermissionError: [Errno 13] Permission denied: ‘/tmp/qiime2-provenance-q0c4w9vi’ -> '/tmp/qiime2-archive-sd9ts2w
/0da42ce7-97c6-494b-a900-56f9d67aa7a1/provenance’

Plugin error from diversity:

[Errno 13] Permission denied: ‘/tmp/qiime2-provenance-q0c4w9vi’ -> ‘/tmp/qiime2-archive-sd9ts2w_/0da42ce7-97c6-494b-a900-56f9d67aa7a1/provenance’

See above for debug info.


(Fernando Studart) #2

Hi Anna,

I was getting the same error when using WSL. Have you tried to run the app as Administrator? This has worked for me.

Thanks,
FS