Hi
I am new to qiime
There was no error untill build phylogenetic tree for diversity analysis
I am receiving an error while running alpha and beta diversity analysis , please guide me how to rectify , I installed qiime2 2022.8 version.
I am herewith enclosing the error
Thanks in advance
Sabitha
qiime diversity core-metrics-phylogenetic
--i-phylogeny rooted-tree.qza
--i-table filtered-table2.qza
--p-sampling-depth 100
--m-metadata-file sample-metadata.tsv
--output-dir diversity-metrices-results
--verbose
/home/wia/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/sklearn/metrics/pairwise.py:1776: DataConversionWarning: Data was converted to boolean for metric jaccard
warnings.warn(msg, DataConversionWarning)
/home/wia/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:143: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.006677676131540084 and the largest is 1.4114280839765325.
warn(
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/wia/data/961a15cd-2e5b-4d84-94d9-5e2f9d960b1a/data/feature-table.biom -t /tmp/qiime2/wia/data/b3a7dc27-3dd3-48b5-aa2f-6dde6d92615d/data/tree.nwk -o /tmp/q2-AlphaDiversityFormat-al_37fw7
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/wia/data/961a15cd-2e5b-4d84-94d9-5e2f9d960b1a/data/feature-table.biom -t /tmp/qiime2/wia/data/b3a7dc27-3dd3-48b5-aa2f-6dde6d92615d/data/tree.nwk -m unweighted -o /tmp/q2-LSMatFormat-21ficw8c
Failing in Thread:0
call to cuInit returned error 34: Other
Traceback (most recent call last):
File "/home/wia/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2cli/commands.py", line 339, in __call__
results = action(**arguments)
File "<decorator-gen-268>", line 2, in core_metrics_phylogenetic
File "/home/wia/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/action.py", line 234, in bound_callable
outputs = self._callable_executor_(scope, callable_args,
File "/home/wia/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/action.py", line 475, in _callable_executor_
outputs = self._callable(scope.ctx, **view_args)
File "/home/wia/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2_diversity/_core_metrics.py", line 66, in core_metrics_phylogenetic
dms += unweighted_unifrac(table=cr.rarefied_table, phylogeny=phylogeny,
File "<decorator-gen-470>", line 2, in unweighted_unifrac
File "/home/wia/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/action.py", line 234, in bound_callable
outputs = self._callable_executor_(scope, callable_args,
File "/home/wia/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/action.py", line 381, in _callable_executor_
output_views = self._callable(**view_args)
File "<decorator-gen-238>", line 2, in unweighted_unifrac
File "/home/wia/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2_diversity_lib/_util.py", line 69, in _disallow_empty_tables
return wrapped_function(*args, **kwargs)
File "<decorator-gen-237>", line 2, in unweighted_unifrac
File "/home/wia/miniconda3/envs/qiime2-2022.8/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/wia/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2_diversity_lib/beta.py", line 221, in unweighted_unifrac
_omp_cmd_wrapper(threads, cmd)
File "/home/wia/miniconda3/envs/qiime2-2022.8/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/wia/miniconda3/envs/qiime2-2022.8/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/wia/miniconda3/envs/qiime2-2022.8/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['ssu', '-i', '/tmp/qiime2/wia/data/961a15cd-2e5b-4d84-94d9-5e2f9d960b1a/data/feature-table.biom', '-t', '/tmp/qiime2/wia/data/b3a7dc27-3dd3-48b5-aa2f-6dde6d92615d/data/tree.nwk', '-m', 'unweighted', '-o', '/tmp/q2-LSMatFormat-21ficw8c']' returned non-zero exit status 1.
Plugin error from diversity:
Command '['ssu', '-i', '/tmp/qiime2/wia/data/961a15cd-2e5b-4d84-94d9-5e2f9d960b1a/data/feature-table.biom', '-t', '/tmp/qiime2/wia/data/b3a7dc27-3dd3-48b5-aa2f-6dde6d92615d/data/tree.nwk', '-m', 'unweighted', '-o', '/tmp/q2-LSMatFormat-21ficw8c']' returned non-zero exit status 1.
See above for debug info.
