QIIME2 2025.7
Conda installation on Linux Ubuntu 22.04
qiime diversity core-metrics-phylogenetic errors:
qiime parameters:
qiime diversity core-metrics-phylogenetic
--i-table table.qza
--i-phylogeny rooted_tree.qza
--p-sampling-depth 39544
--m-metadata-file metadata.tsv
--output-dir diversity
--verbose
Verbose mode & error messages:
/home/bioinfo/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/unifrac/init.py:9: UserWarning: pkg_resources is deprecated as an API. See Package Discovery and Resource Access using pkg_resources - setuptools 80.9.0 documentation . The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
import pkg_resources
/home/bioinfo/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/skbio/util/_warning.py:60: UserWarning: observed_otus is deprecated as of 0.6.0.
warn(f"{func.name} is deprecated as of {ver}.")
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/bioinfo/processes/7280-1756906848.9@bioinfo/tmp/q2-OutPath-9j0b78i1 -t /tmp/qiime2/bioinfo/data/f593a058-7a2c-4186-a832-d821f1c64543/data/tree.nwk -o /tmp/qiime2/bioinfo/processes/7280-1756906848.9@bioinfo/tmp/q2-OutPath-7gfqsd5u
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:
ssu -i /tmp/qiime2/bioinfo/data/84a57cbe-8e93-47c1-80c8-c8f51ff1e058/data/feature-table.biom -t /tmp/qiime2/bioinfo/data/f593a058-7a2c-4186-a832-d821f1c64543/data/tree.nwk -m unweighted -o /tmp/qiime2/bioinfo/processes/7280-1756906848.9@bioinfo/tmp/q2-OutPath-obbmr5cp
Failing in Thread:0
call to cuInit returned error 999: Unknown
Traceback (most recent call last):
File "/home/bioinfo/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/q2cli/commands.py", line 529, in call
results = self._execute_action(
File "/home/bioinfo/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/q2cli/commands.py", line 607, in _execute_action
results = action(**arguments)
File "", line 2, in core_metrics_phylogenetic
File "/home/bioinfo/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/qiime2/sdk/action.py", line 221, in bound_callable
outputs = self.callable_executor(
File "/home/bioinfo/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/qiime2/sdk/action.py", line 443, in callable_executor
outputs = self._callable(ctx, **view_args)
File "/home/bioinfo/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/q2_diversity/_core_metrics.py", line 77, in core_metrics_phylogenetic
dms += unweighted_unifrac(table=cr.rarefied_table, phylogeny=phylogeny,
File "", line 2, in unweighted_unifrac
File "/home/bioinfo/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/qiime2/sdk/context/base.py", line 90, in callable_action
return self.dispatch(args, kwargs)
File "/home/bioinfo/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/qiime2/sdk/context/base.py", line 45, in dispatch
results = exe(*args, **kwargs)
File "", line 2, in unweighted_unifrac
File "/home/bioinfo/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/qiime2/sdk/action.py", line 221, in bound_callable
outputs = self.callable_executor(
File "/home/bioinfo/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/qiime2/sdk/action.py", line 362, in callable_executor
output_views = self._callable(**view_args)
File "", line 2, in unweighted_unifrac
File "/home/bioinfo/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/q2_diversity_lib/_util.py", line 75, in _validate_tables
return wrapped_function(*args, **kwargs)
File "", line 2, in unweighted_unifrac
File "/home/bioinfo/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/q2_diversity_lib/_util.py", line 118, in _validate_requested_cpus
return wrapped_function(*bound_arguments.args, **bound_arguments.kwargs)
File "/home/bioinfo/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/q2_diversity_lib/beta.py", line 220, in unweighted_unifrac
_omp_cmd_wrapper(threads, cmd)
File "/home/bioinfo/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/q2_diversity_lib/_util.py", line 134, in _omp_cmd_wrapper
return _run_external_cmd(cmd, verbose=verbose, env=env)
File "/home/bioinfo/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/q2_diversity_lib/_util.py", line 128, in _run_external_cmd
return subprocess.run(cmd, check=True, env=env)
File "/home/bioinfo/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/subprocess.py", line 526, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['ssu', '-i', '/tmp/qiime2/bioinfo/data/84a57cbe-8e93-47c1-80c8-c8f51ff1e058/data/feature-table.biom', '-t', '/tmp/qiime2/bioinfo/data/f593a058-7a2c-4186-a832-d821f1c64543/data/tree.nwk', '-m', 'unweighted', '-o', '/tmp/qiime2/bioinfo/processes/7280-1756906848.9@bioinfo/tmp/q2-OutPath-obbmr5cp']' returned non-zero exit status 1.
Plugin error from diversity:
Command '['ssu', '-i', '/tmp/qiime2/bioinfo/data/84a57cbe-8e93-47c1-80c8-c8f51ff1e058/data/feature-table.biom', '-t', '/tmp/qiime2/bioinfo/data/f593a058-7a2c-4186-a832-d821f1c64543/data/tree.nwk', '-m', 'unweighted', '-o', '/tmp/qiime2/bioinfo/processes/7280-1756906848.9@bioinfo/tmp/q2-OutPath-obbmr5cp']' returned non-zero exit status 1.
See above for debug info.
——
Can anybody help ? Thanks