Errno 13 - Permission Denied

Hi all,

I’ve just started using QIIME2 on my home computer and am currently working my way through the ‘Moving Pictures’ tutorial. I’m trying to run one of the steps and I keep getting the same Errno 13 message. Below is the debug info. I’m running Ubuntu as admin and it still isn’t working! Any help would be greatly appreciated!

James H

/home/james/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/sklearn/metrics/pairwise.py:1761: DataConversionWarning: Data was converted to boolean for metric jaccard
  warnings.warn(msg, DataConversionWarning)
/home/james/anaconda3/envs/qiime2-2020.8/lib/python3.6/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 -0.009921666875883169 and the largest is 3.282046672169648.
  RuntimeWarning
/home/james/anaconda3/envs/qiime2-2020.8/lib/python3.6/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 -0.00838042021567985 and the largest is 2.5787674525060686.
  RuntimeWarning
/home/james/anaconda3/envs/qiime2-2020.8/lib/python3.6/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 -0.016742395472169422 and the largest is 2.3800660955056223.
  RuntimeWarning
Traceback (most recent call last):
  File "/home/james/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2cli/commands.py", line 329, in __call__
    results = action(**arguments)
  File "<decorator-gen-421>", line 2, in core_metrics_phylogenetic
  File "/home/james/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
    output_types, provenance)
  File "/home/james/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/sdk/action.py", line 512, in _callable_executor_
    aliased_result = output._alias(prov)
  File "/home/james/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/sdk/result.py", line 163, in _alias
    self.type, self.format, clone_original, provenance_capture)
  File "/home/james/anaconda3/envs/qiime2-2020.8/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/james/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/core/archive/format/v5.py", line 21, in write
    provenance_capture)
  File "/home/james/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/core/archive/format/v1.py", line 19, in write
    provenance_capture)
  File "/home/james/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/core/archive/format/v0.py", line 62, in write
    data_initializer(data_dir)
  File "/home/james/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/sdk/result.py", line 158, in clone_original
    copy_function=os.link)  # Use hardlinks
  File "/home/james/anaconda3/envs/qiime2-2020.8/lib/python3.6/shutil.py", line 365, in copytree
    raise Error(errors)
shutil.Error: [('/tmp/qiime2-archive-z8eu8kc6/2736550c-92f5-4656-922a-a6f75e50f653/data/feature-table.biom', '/tmp/qiime2-archive-xztkdfhs/9e0cb922-432d-430c-97e4-8a3a63cdf75c/data/feature-table.biom', "[Errno 13] Permission denied: '/tmp/qiime2-archive-z8eu8kc6/2736550c-92f5-4656-922a-a6f75e50f653/data/feature-table.biom' -> '/tmp/qiime2-archive-xztkdfhs/9e0cb922-432d-430c-97e4-8a3a63cdf75c/data/feature-table.biom'")]

Hi @jameshorn0 :wave:

This is a common issue which has been discussed before, e.g.:

Please familiarize yourself with the search functionality and take the time to explore if your questions have been asked before.

Thanks for the question and welcome to the forum. Cheers! :slight_smile:

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