Hello,
I am working my way through the Moving Pictures Tutorial and came across the following error in the “Alpha and beta diversity analysis” bit. I am using the dataset provided (I am new to Qiime2) and have kept the same names as suggested for any generated artifacts. I entered the following which gave me an error:
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
Plugin error from diversity:
[(’/tmp/qiime2-archive-tgx4o53g/43e587a3-c7ae-4e3f-95bc-8dccd7ec651e/data/feature-table.biom’, ‘/tmp/qiime2-archive-tb06inr8/a05018db-a322-419e-a766-ded3ffff98f0/data/feature-table.biom’, “[Errno 13] Permission denied: ‘/tmp/qiime2-archive-tgx4o53g/43e587a3-c7ae-4e3f-95bc-8dccd7ec651e/data/feature-table.biom’ -> ‘/tmp/qiime2-archive-tb06inr8/a05018db-a322-419e-a766-ded3ffff98f0/data/feature-table.biom’”)]
I have pasted the error log below and wondered if anyone could lend a hand?
Thanks in advance!
/home/sanch/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/sklearn/metrics/pairwise.py:1761: DataConversionWarning: Data was converted to boolean for metric jaccard
warnings.warn(msg, DataConversionWarning)
/home/sanch/miniconda3/envs/qiime2-2020.6/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 -0.012336187183218527 and the largest is 3.5587658825312127.
RuntimeWarning
/home/sanch/miniconda3/envs/qiime2-2020.6/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 -0.008486462219123376 and the largest is 2.359849122691839.
RuntimeWarning
/home/sanch/miniconda3/envs/qiime2-2020.6/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 -0.018817617413132804 and the largest is 3.15369980093899.
RuntimeWarning
Traceback (most recent call last):
File “/home/sanch/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2cli/commands.py”, line 329, in call
results = action(**arguments)
File “”, line 2, in core_metrics_phylogenetic
File “/home/sanch/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 245, in bound_callable
output_types, provenance)
File “/home/sanch/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 512, in callable_executor
aliased_result = output._alias(prov)
File “/home/sanch/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/sdk/result.py”, line 163, in _alias
self.type, self.format, clone_original, provenance_capture)
File “/home/sanch/miniconda3/envs/qiime2-2020.6/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/sanch/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/core/archive/format/v5.py”, line 21, in write
provenance_capture)
File “/home/sanch/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/core/archive/format/v1.py”, line 19, in write
provenance_capture)
File “/home/sanch/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/core/archive/format/v0.py”, line 62, in write
data_initializer(data_dir)
File “/home/sanch/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/sdk/result.py”, line 158, in clone_original
copy_function=os.link) # Use hardlinks
File “/home/sanch/miniconda3/envs/qiime2-2020.6/lib/python3.6/shutil.py”, line 365, in copytree
raise Error(errors)
shutil.Error: [(’/tmp/qiime2-archive-gk2uwpub/556ec736-b092-46c8-9142-22219368f529/data/feature-table.biom’, ‘/tmp/qiime2-archive-xfbix150/31775e82-6e55-4b23-910f-2995f339cc4d/data/feature-table.biom’, “[Errno 13] Permission denied: ‘/tmp/qiime2-archive-gk2uwpub/556ec736-b092-46c8-9142-22219368f529/data/feature-table.biom’ -> ‘/tmp/qiime2-archive-xfbix150/31775e82-6e55-4b23-910f-2995f339cc4d/data/feature-table.biom’”)]
forum!