(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.
uh.