I have already run the following codes for v3-v4 of 16s data analysis.
1.5 De novo clustering
qiime vsearch cluster-features-de-novo
--i-table 1_4_table.qza
--i-sequences 1_4_rep-seqs.qza
--p-perc-identity 0.99
--p-threads 36
--o-clustered-table 1_5_table-dn-99.qza
--o-clustered-sequences 1_5_rep-seqs-dn-99.qza
(qiime2-amplicon-2024.10) sujan@DESKTOP-VKEBCR4:~/practice/test-run$ qiime feature-classifier extract-reads \
--i-sequences 2022.10.backbone.full-length.fna.qza
--p-f-primer CCTACGGGNGGCWGCAG
--p-r-primer GACTACHVGGGTATCTAATCC
--p-min-length 300
--p-max-length 500
--o-reads 3_3_ref-seqs.qza
/home/sujan/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/numpy/core/getlimits.py:542: UserWarning: Signature b'\x00\xd0\xcc\xcc\xcc\xcc\xcc\xcc\xfb\xbf\x00\x00\x00\x00\x00\x00' for <class 'numpy.longdouble'> does not match any known type: falling back to type probe function.
This warnings indicates broken support for the dtype!
machar = _get_machar(dtype)
Saved FeatureData[Sequence] to: 3_3_ref-seqs.qza
(qiime2-amplicon-2024.10) sujan@DESKTOP-VKEBCR4:~/practice/test-run$ qiime feature-classifier fit-classifier-naive-bayes \
--i-reference-reads 3_3_ref-seqs.qza
--i-reference-taxonomy 2022.10.backbone.tax.qza
--o-classifier 3_4_classifier.qza
/home/sujan/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/numpy/core/getlimits.py:542: UserWarning: Signature b'\x00\xd0\xcc\xcc\xcc\xcc\xcc\xcc\xfb\xbf\x00\x00\x00\x00\x00\x00' for <class 'numpy.longdouble'> does not match any known type: falling back to type probe function.
This warnings indicates broken support for the dtype!
machar = _get_machar(dtype)
Saved TaxonomicClassifier to: 3_4_classifier.qza
(qiime2-amplicon-2024.10) sujan@DESKTOP-VKEBCR4:~/practice/test-run$ qiime feature-classifier classify-sklearn \
--i-classifier 3_4_classifier.qza
--i-reads 1_7b_rep-seqs-dn-99.qza
--o-classification 3_5a_taxonomy.qza
/home/sujan/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/numpy/core/getlimits.py:542: UserWarning: Signature b'\x00\xd0\xcc\xcc\xcc\xcc\xcc\xcc\xfb\xbf\x00\x00\x00\x00\x00\x00' for <class 'numpy.longdouble'> does not match any known type: falling back to type probe function.
This warnings indicates broken support for the dtype!
machar = _get_machar(dtype)
Saved FeatureData[Taxonomy] to: 3_5a_taxonomy.qza
(qiime2-amplicon-2024.10) sujan@DESKTOP-VKEBCR4:~/practice/test-run$ qiime metadata tabulate \
--m-input-file 3_5a_taxonomy.qza
--o-visualization 3_5b_taxonomy.qzv
/home/sujan/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/numpy/core/getlimits.py:542: UserWarning: Signature b'\x00\xd0\xcc\xcc\xcc\xcc\xcc\xcc\xfb\xbf\x00\x00\x00\x00\x00\x00' for <class 'numpy.longdouble'> does not match any known type: falling back to type probe function.
This warnings indicates broken support for the dtype!
machar = _get_machar(dtype)
Saved Visualization to: 3_5b_taxonomy.qzv
(qiime2-amplicon-2024.10) sujan@DESKTOP-VKEBCR4:~/practice/test-run$ qiime taxa barplot \
--i-table 1_7a_table-dn-99.qza
--i-taxonomy 3_5a_taxonomy.qza
--m-metadata-file metadata.tsv
--o-visualization 3_6_taxa-bar-plots.qzv
/home/sujan/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/numpy/core/getlimits.py:542: UserWarning: Signature b'\x00\xd0\xcc\xcc\xcc\xcc\xcc\xcc\xfb\xbf\x00\x00\x00\x00\x00\x00' for <class 'numpy.longdouble'> does not match any known type: falling back to type probe function.
This warnings indicates broken support for the dtype!
machar = _get_machar(dtype)
Saved Visualization to: 3_6_taxa-bar-plots.qzv
My queries are:
- Does these codes run properly??
- How can I understand or find out the percentage of OTU used here?