Qiime diversity alpha-rarefaction tmp directory error

Hi, I am trying to run alpha rarefaction script with qiime2-2018.6 but I keep getting the following error.


export TMPDIR=/rhome/hkiss001/qiime2-tmp

qiime diversity alpha-rarefaction \
  --i-table ~/shared/LakeRing/analysis-results/16SEMP/featureTABLE/feature-table-2.qza \
  --i-phylogeny ~/shared/LakeRing/analysis-results/16SEMP/tree/reference-hit-seqs-aligned_masked-rooted-tree.qza \
  --p-max-depth 18431 \
  --p-min-depth 245 \
  --m-metadata-file ~/shared/LakeRing/qiime-files/mapping-files/mapping-file.tsv \
  --o-visualization ~/shared/LakeRing/analysis-results/16SEMP/diversityMETRICS/alpha-rarefaction.qzv \


Traceback (most recent call last):
  File "/rhome/hkiss001/.conda/envs/qiime2-2018.6/lib/python3.5/site-packages/q2cli/commands.py", line 274, in __call__
    results = action(**arguments)
  File "<decorator-gen-355>", line 2, in alpha_rarefaction
  File "/rhome/hkiss001/.conda/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/sdk/action.py", line 232, in bound_callable
    output_types, provenance)
  File "/rhome/hkiss001/.conda/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/sdk/action.py", line 429, in _callable_executor_
    ret_val = self._callable(output_dir=temp_dir, **view_args)
  File "/rhome/hkiss001/.conda/envs/qiime2-2018.6/lib/python3.5/site-packages/q2_diversity/_alpha/_visualizer.py", line 368, in alpha_rarefaction
    metric_name, c_df, column)
  File "/rhome/hkiss001/.conda/envs/qiime2-2018.6/lib/python3.5/site-packages/q2_diversity/_alpha/_visualizer.py", line 262, in _alpha_rarefaction_jsonp
    with open(os.path.join(output_dir, filename), 'w') as fh:
FileNotFoundError: [Errno 2] No such file or directory: '/bigdata/biklab/shared/tmp/qiime2-temp-e189kn4j/observed_otus-Alona_rectangula/guttata.jsonp'

Plugin error from diversity:

  [Errno 2] No such file or directory: '/bigdata/biklab/shared/tmp/qiime2-temp-e189kn4j/observed_otus-Alona_rectangula/guttata.jsonp'

See above for debug info.

To prevent the possible deletion of this file in the /tmp directory, I have set the TMPDIR to a permanent directory where space is not an issue with ‘export TMPDIR=’, but it results in the same error.

Do you have any suggestions on how to solve this error?


1 Like

It looks like you have bumped into a known issue related to forward slashes / in metadata column names: Alona_rectangula/guttata. Drop the slash and you should be good to go.


Thank you @thermokarst! The alpha rarefaction script was successful.


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