i’m a new learner of qiime. i just found problem while learning from qiimedocs( “Moving Pictures” tutorial), here is the situation:
1. i’m running my code on the Windows10 Subsystem for Linux, and the version is qiime2-2020.8
2. It is normal before running the following code for " Alpha and beta diversity analysis":
*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*
3. the system error is as follows：
Plugin error from diversity:
[(’/tmp/qiime2-archive-jv7791rr/72c02275-ba2e-45a1-9ca5-62d646d23967/data/feature-table.biom’, ‘/tmp/qiime2-archive-dlrb3r44/c47e3c32-b838-4815-a54e-cc14edf61c4b/data/feature-table.biom’, “[Errno 13] Permission denied: ‘/tmp/qiime2-archive-jv7791rr/72c02275-ba2e-45a1-9ca5-62d646d23967/data/feature-table.biom’ -> ‘/tmp/qiime2-archive-dlrb3r44/c47e3c32-b838-4815-a54e-cc14edf61c4b/data/feature-table.biom’”)]
Debug info has been saved to /tmp/qiime2-q2cli-err-pbhwynd4.log
4. and the debug info metioned as follow:
/home/lt/miniconda3/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/lt/miniconda3/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 -0.013263207656646254 and the largest is 2.9535509581978907.
RuntimeWarning
/home/lt/miniconda3/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 -0.20706786265277805 and the largest is 8.051840306115771.
RuntimeWarning
/home/lt/miniconda3/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 -0.04126958327046105 and the largest is 1.984254569409116.
RuntimeWarning
/home/lt/miniconda3/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 -0.31357092629584016 and the largest is 5.842112557386606.
RuntimeWarning
Traceback (most recent call last):
File “/home/lt/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2cli/commands.py”, line 329, in call
“qiime2-q2cli-err-pbhwynd4.log” 34L, 4600C
