issues with qiime2-amplicon-2024.2 for core-metrics-phylogenetic

(qiime2-amplicon-2024.2) [XYB@Dulab fastq]$ qiime diversity core-metrics-phylogenetic --i-phylogeny rooted-tree-withoutPRJNA445346.qza --i-table table-filter-contam-no-archaea-eukaryota-withouPRJNA445346.qza --p-sampling-depth 60000 --m-metadata-file paired_metadata_without_PRJNA445346.tsv --output-dir core-metric-results --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/XYB/data/e1bfdd46-1e1c-44d3-8de5-cd2e09813951/data/feature-table.biom -t /tmp/qiime2/XYB/data/2d5ad368-de70-45ea-9869-a890013a3200/data/tree.nwk -o /tmp/q2-AlphaDiversityFormat-113rtk76

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 "/data/home/XYB/01.software/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2cli/commands.py", line 520, in call
results = self._execute_action(
File "/data/home/XYB/01.software/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2cli/commands.py", line 586, in _execute_action
results = action(**arguments)
File "", line 2, in core_metrics_phylogenetic
File "/data/home/XYB/01.software/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self.callable_executor(
File "/data/home/XYB/01.software/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 647, in callable_executor
outputs = self._callable(scope.ctx, **view_args)
File "/data/home/XYB/01.software/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2_diversity/_core_metrics.py", line 65, in core_metrics_phylogenetic
faith_pd_vector, = faith_pd(table=cr.rarefied_table,
File "", line 2, in faith_pd
File "/data/home/XYB/01.software/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/context.py", line 143, in deferred_action
return action_obj._bind(
File "", line 2, in faith_pd
File "/data/home/XYB/01.software/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self.callable_executor(
File "/data/home/XYB/01.software/miniconda3/envs/qiime2-amplicon-2024.2/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 "/data/home/XYB/01.software/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2_diversity_lib/_util.py", line 75, in _validate_tables
return wrapped_function(*args, **kwargs)
File "", line 2, in faith_pd
File "/data/home/XYB/01.software/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2_diversity_lib/_util.py", line 118, in _validate_requested_cpus
return wrapped_function(*bound_arguments.args, **bound_arguments.kwargs)
File "/data/home/XYB/01.software/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2_diversity_lib/alpha.py", line 54, in faith_pd
_omp_cmd_wrapper(threads, cmd)
File "/data/home/XYB/01.software/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2_diversity_lib/_util.py", line 134, in _omp_cmd_wrapper
return _run_external_cmd(cmd, verbose=verbose, env=env)
File "/data/home/XYB/01.software/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2_diversity_lib/_util.py", line 128, in _run_external_cmd
return subprocess.run(cmd, check=True, env=env)
File "/data/home/XYB/01.software/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['faithpd', '-i', '/tmp/qiime2/XYB/data/e1bfdd46-1e1c-44d3-8de5-cd2e09813951/data/feature-table.biom', '-t', '/tmp/qiime2/XYB/data/2d5ad368-de70-45ea-9869-a890013a3200/data/tree.nwk', '-o', '/tmp/q2-AlphaDiversityFormat-113rtk76']' returned non-zero exit status 1.

Plugin error from diversity:

Command '['faithpd', '-i', '/tmp/qiime2/XYB/data/e1bfdd46-1e1c-44d3-8de5-cd2e09813951/data/feature-table.biom', '-t', '/tmp/qiime2/XYB/data/2d5ad368-de70-45ea-9869-a890013a3200/data/tree.nwk', '-o', '/tmp/q2-AlphaDiversityFormat-113rtk76']' returned non-zero exit status 1.

See above for debug info.

Hello!

Here is a key part. Looks like you have some features in the table that are missing in the tree you provided. Double check your filtering steps to make sure that all features from the table are present in tree.

Best,

1 Like

Dear timanix,
Thanks for your help! I checked the filter steps and figured out the mistakes since I did not keep the same conditions for the feature table and feature sequences :sweat_smile: uh.