Plugin error from diversity Command '[ 'faithpd'...

Hello QIIME 2 Community,

I am encountering an issue while running the core-metrics-phylogenetic command in QIIME 2. Below are the details of the command I executed and the error message received:

Command executed:
qiime diversity core-metrics-phylogenetic
--i-phylogeny "/Volumes/Andrea 16GB/Qiime RP/rooted-tree-15426_200cat2.qza"
--i-table "/Volumes/Andrea 16GB/Qiime RP/15426_200cat2_otu_table.qza"
--p-sampling-depth 500
--m-metadata-file "/Volumes/Andrea 16GB/Rio Piedras/15426_cat2_sampleinfo_27052024.txt"
--output-dir "/Volumes/Andrea 16GB/Qiime RP/core-metrics-results-15426_200cat2_rar500"
--verbose

Error message:
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 /var/folders/lv/plvslxfx66qcd78k7wv8x2qm0000gn/T/qiime2/megl10/data/485dc347-44a4-4509-8e21-ce63ffe38fe1/data/feature-table.biom -t /var/folders/lv/plvslxfx66qcd78k7wv8x2qm0000gn/T/qiime2/megl10/data/2d8aa9aa-32cf-4a96-9590-1f243c174316/data/tree.nwk -o /var/folders/lv/plvslxfx66qcd78k7wv8x2qm0000gn/T/q2-AlphaDiversityFormat-qjjxsc7u

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 "/Users/megl10/anaconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2cli/commands.py", line 478, in call
results = self._execute_action(
File "/Users/megl10/anaconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2cli/commands.py", line 544, in _execute_action
results = action(**arguments)
File "", line 2, in core_metrics_phylogenetic
File "/Users/megl10/anaconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self.callable_executor(
File "/Users/megl10/anaconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/sdk/action.py", line 647, in callable_executor
outputs = self._callable(scope.ctx, **view_args)
File "/Users/megl10/anaconda3/envs/qiime2-2023.7/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 "/Users/megl10/anaconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/sdk/context.py", line 140, in deferred_action
return action_obj._bind(
File "", line 2, in faith_pd
File "/Users/megl10/anaconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self.callable_executor(
File "/Users/megl10/anaconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/sdk/action.py", line 566, in callable_executor
output_views = self._callable(**view_args)
File "", line 2, in faith_pd
File "/Users/megl10/anaconda3/envs/qiime2-2023.7/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 "/Users/megl10/anaconda3/envs/qiime2-2023.7/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 "/Users/megl10/anaconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2_diversity_lib/alpha.py", line 53, in faith_pd
_omp_cmd_wrapper(threads, cmd)
File "/Users/megl10/anaconda3/envs/qiime2-2023.7/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 "/Users/megl10/anaconda3/envs/qiime2-2023.7/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 "/Users/megl10/anaconda3/envs/qiime2-2023.7/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['faithpd', '-i', '/var/folders/lv/plvslxfx66qcd78k7wv8x2qm0000gn/T/qiime2/megl10/data/485dc347-44a4-4509-8e21-ce63ffe38fe1/data/feature-table.biom', '-t', '/var/folders/lv/plvslxfx66qcd78k7wv8x2qm0000gn/T/qiime2/megl10/data/2d8aa9aa-32cf-4a96-9590-1f243c174316/data/tree.nwk', '-o', '/var/folders/lv/plvslxfx66qcd78k7wv8x2qm0000gn/T/q2-AlphaDiversityFormat-qjjxsc7u']' returned non-zero exit status 1.

Plugin error from diversity:

Command '['faithpd', '-i', '/var/folders/lv/plvslxfx66qcd78k7wv8x2qm0000gn/T/qiime2/megl10/data/485dc347-44a4-4509-8e21-ce63ffe38fe1/data/feature-table.biom', '-t', '/var/folders/lv/plvslxfx66qcd78k7wv8x2qm0000gn/T/qiime2/megl10/data/2d8aa9aa-32cf-4a96-9590-1f243c174316/data/tree.nwk', '-o', '/var/folders/lv/plvslxfx66qcd78k7wv8x2qm0000gn/T/q2-AlphaDiversityFormat-qjjxsc7u']' returned non-zero exit status 1.

See above for debug info.

Any help will be greatly appreciated

Hi @abpirivera
The helpful part of the error is here:

This forum post suggests that this could be happening because you may have features in your table that are not present in your phylogeny:

Try what they suggest there and the run it again. If it throws the same error check out some of these other forum posts where people were able to resolve a similar issue. If you are still stuck reply here and we can figure it out together.
--Hannah

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