Here is the full output-
(qiime2-2023.2) omic@omic-world-001:~/Downloads/16S_Data_plant_current/plant_data_untouched1$ qiime diversity alpha-rarefaction --i-table table.qza --i-phylogeny rooted-tree.qza --p-max-depth 4000 --m-metadata-file sample-metadata.tsv --o-visualization alpha-rarefaction.qzv --verbose
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/omic/data/37d24100-d122-49a9-956c-273188c71205/data/feature-table.biom -t /tmp/qiime2/omic/data/021eb7b4-36f1-4e9f-b9a8-79488418dc10/data/tree.nwk -o /tmp/q2-AlphaDiversityFormat-q1k7bswk
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/omic/data/e42260f1-bb5d-480f-8b5c-eeb71e54ac31/data/feature-table.biom -t /tmp/qiime2/omic/data/021eb7b4-36f1-4e9f-b9a8-79488418dc10/data/tree.nwk -o /tmp/q2-AlphaDiversityFormat-0q9vdvyu
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/omic/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2cli/commands.py", line 352, in call
results = action(**arguments)
File "", line 2, in alpha_rarefaction
File "/home/omic/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 234, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/home/omic/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 443, in callable_executor
ret_val = self._callable(output_dir=temp_dir, **view_args)
File "/home/omic/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py", line 375, in alpha_rarefaction
data = _compute_rarefaction_data(table, min_depth, max_depth,
File "/home/omic/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py", line 306, in _compute_rarefaction_data
vector, = alpha_phylo(table=rt, metric=metric,
File "", line 2, in alpha_phylogenetic
File "/home/omic/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 234, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/home/omic/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 475, in callable_executor
outputs = self._callable(scope.ctx, **view_args)
File "/home/omic/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_diversity/_alpha/_pipeline.py", line 16, in alpha_phylogenetic
vector, = action(table, phylogeny)
File "", line 2, in faith_pd
File "/home/omic/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 234, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/home/omic/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 381, in callable_executor
output_views = self._callable(**view_args)
File "", line 2, in faith_pd
File "/home/omic/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_diversity_lib/_util.py", line 69, in _disallow_empty_tables
return wrapped_function(*args, **kwargs)
File "", line 2, in faith_pd
File "/home/omic/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_diversity_lib/_util.py", line 112, in _validate_requested_cpus
return wrapped_function(*bound_arguments.args, **bound_arguments.kwargs)
File "/home/omic/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_diversity_lib/alpha.py", line 53, in faith_pd
_omp_cmd_wrapper(threads, cmd)
File "/home/omic/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_diversity_lib/_util.py", line 128, in _omp_cmd_wrapper
return _run_external_cmd(cmd, verbose=verbose, env=env)
File "/home/omic/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_diversity_lib/_util.py", line 122, in _run_external_cmd
return subprocess.run(cmd, check=True, env=env)
File "/home/omic/miniconda3/envs/qiime2-2023.2/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['faithpd', '-i', '/tmp/qiime2/omic/data/e42260f1-bb5d-480f-8b5c-eeb71e54ac31/data/feature-table.biom', '-t', '/tmp/qiime2/omic/data/021eb7b4-36f1-4e9f-b9a8-79488418dc10/data/tree.nwk', '-o', '/tmp/q2-AlphaDiversityFormat-0q9vdvyu']' returned non-zero exit status 1.
Plugin error from diversity:
Command '['faithpd', '-i', '/tmp/qiime2/omic/data/e42260f1-bb5d-480f-8b5c-eeb71e54ac31/data/feature-table.biom', '-t', '/tmp/qiime2/omic/data/021eb7b4-36f1-4e9f-b9a8-79488418dc10/data/tree.nwk', '-o', '/tmp/q2-AlphaDiversityFormat-0q9vdvyu']' returned non-zero exit status 1.
See above for debug info.