Hello.
Maybe I'm missing something, but I don't know why.
I am currently using the qiime2 2022.2 version (VMware).
First, a core-diversity guide was formed using qiime diversity core-metrics-phylogenetic in all samples to create a core-diversity directory.
This time it went well with no problems.
Afterward, among the samples obtained, what used the qiime taxa filter table to filter the specific taxon.
Who used the qiime feature-table filter samples to remove the samples in a particular column.
The sequence was also purified and separated based on the table obtained in this way.
Who rebuilt the tree with the filtered sequence.
And I tried to form the core-diversity directory by running qiime diversity core-metrics-phylogenetic, but the below error is displayed.
/home/qiime2/miniconda/envs/qiime2-2022.2/lib/python3.8/site-packages/sklearn/metrics/pairwise.py:1776: DataConversionWarning: Data was converted to boolean for metric jaccard
warnings.warn(msg, DataConversionWarning)
/home/qiime2/miniconda/envs/qiime2-2022.2/lib/python3.8/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:143: 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 -0.1374879396965191 and the largest is 5.560571462721946.
warn(
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command:
faithpd -i /tmp/qiime2-archive-n1z8qqz6/5a12baa0-ae23-447d-b4ff-04be11b3a17e/data/feature-table.biom -t /tmp/qiime2-archive-356vybcy/1702cbb8-0f7d-491f-9ef3-f39270452896/data/tree.nwk -o /tmp/q2-AlphaDiversityFormat-f1u2nod8
Compute failed in faith_pd_one_off: Table observation IDs are not a subset of the tree tips. This error can also be triggered if a node name contains a single quote (this is unlikely).
Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/commands.py", line 339, in __call__
results = action(**arguments)
File "<decorator-gen-96>", line 2, in core_metrics_phylogenetic
File "/home/qiime2/miniconda/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
outputs = self._callable_executor_(scope, callable_args,
File "/home/qiime2/miniconda/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 485, in _callable_executor_
outputs = self._callable(scope.ctx, **view_args)
File "/home/qiime2/miniconda/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_diversity/_core_metrics.py", line 62, in core_metrics_phylogenetic
faith_pd_vector, = faith_pd(table=cr.rarefied_table,
File "<decorator-gen-457>", line 2, in faith_pd
File "/home/qiime2/miniconda/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
outputs = self._callable_executor_(scope, callable_args,
File "/home/qiime2/miniconda/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 391, in _callable_executor_
output_views = self._callable(**view_args)
File "<decorator-gen-26>", line 2, in faith_pd
File "/home/qiime2/miniconda/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_diversity_lib/_util.py", line 59, in _disallow_empty_tables
return wrapped_function(*args, **kwargs)
File "<decorator-gen-25>", line 2, in faith_pd
File "/home/qiime2/miniconda/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_diversity_lib/_util.py", line 102, in _validate_requested_cpus
return wrapped_function(*bound_arguments.args, **bound_arguments.kwargs)
File "/home/qiime2/miniconda/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_diversity_lib/alpha.py", line 53, in faith_pd
_omp_cmd_wrapper(threads, cmd)
File "/home/qiime2/miniconda/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_diversity_lib/_util.py", line 118, in _omp_cmd_wrapper
return _run_external_cmd(cmd, verbose=verbose, env=env)
File "/home/qiime2/miniconda/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_diversity_lib/_util.py", line 112, in _run_external_cmd
return subprocess.run(cmd, check=True, env=env)
File "/home/qiime2/miniconda/envs/qiime2-2022.2/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['faithpd', '-i', '/tmp/qiime2-archive-n1z8qqz6/5a12baa0-ae23-447d-b4ff-04be11b3a17e/data/feature-table.biom', '-t', '/tmp/qiime2-archive-356vybcy/1702cbb8-0f7d-491f-9ef3-f39270452896/data/tree.nwk', '-o', '/tmp/q2-AlphaDiversityFormat-f1u2nod8']' returned non-zero exit status 1.
Plugin error from diversity:
Command '['faithpd', '-i', '/tmp/qiime2-archive-n1z8qqz6/5a12baa0-ae23-447d-b4ff-04be11b3a17e/data/feature-table.biom', '-t', '/tmp/qiime2-archive-356vybcy/1702cbb8-0f7d-491f-9ef3-f39270452896/data/tree.nwk', '-o', '/tmp/q2-AlphaDiversityFormat-f1u2nod8']' returned non-zero exit status 1.
See above for debug info.
Can you guess the cause?
Or, is it correct to draw PCoA by applying the tree for the entire sample to the filter-applied table without modification?
I have put the executable code below.
Please review.
$time qiime diversity core-metrics-phylogenetic \
--i-table uchime-denovo-out/uchime-denovo-outtable-nonchimer-filtered-nounassign-Arthropoda-Chordata-noFelis_63ea.qza \
--i-phylogeny tree-noUnassign-Arthropoda-Chordata-noFelis_63ea/rooted_tree.qza \
--p-sampling-depth 500 \
--m-metadata-file metadata-noFelis_63ea.tsv \
--output-dir diversity-filtered-nounassign-Arthropoda-Chordata-noFelis_63ea-depth500-1 \
--verbose