Core-metrics-phylogenetic: Plugin error from Diversity returned non-zero exit status 1

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1

I am currently running 2023.7 and am getting a non-zero exit status I don't understand. I had run core metrics on this same dataset in 2020.11 and didn't have an issue.

qiime diversity core-metrics-phylogenetic --i-table removed_samples/1_filtered_table.qza --i-phylogeny removed_samples/fastree/rooted_tree.qza --p-sampling-depth 5200 --m-metadata-file new_newt_metadata.tsv --output-dir removed_samples/core_metrics/alpha_5200/ --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/tally/data/daaf3539-e49b-4550-8732-571d2e261089/data/feature-table.biom -t /tmp/qiime2/tally/data/09d3e619-41d2-4b68-ba12-1f863faefc34/data/tree.nwk -o /tmp/q2-AlphaDiversityFormat-q7lo6k4k

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/tally/data/daaf3539-e49b-4550-8732-571d2e261089/data/feature-table.biom -t /tmp/qiime2/tally/data/09d3e619-41d2-4b68-ba12-1f863faefc34/data/tree.nwk -m unweighted -o /tmp/q2-LSMatFormat-ajbrgr90

Failing in Thread:0
call to cuInit returned error 999: Unknown

Traceback (most recent call last):
File "/home/tally/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2cli/commands.py", line 478, in call
results = self._execute_action(
File "/home/tally/miniconda3/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 "/home/tally/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self.callable_executor(
File "/home/tally/miniconda3/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 "/home/tally/miniconda3/envs/qiime2-2023.7/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 "/home/tally/miniconda3/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 unweighted_unifrac
File "/home/tally/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self.callable_executor(
File "/home/tally/miniconda3/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 unweighted_unifrac
File "/home/tally/miniconda3/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 unweighted_unifrac
File "/home/tally/miniconda3/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 "/home/tally/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2_diversity_lib/beta.py", line 221, in unweighted_unifrac
_omp_cmd_wrapper(threads, cmd)
File "/home/tally/miniconda3/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 "/home/tally/miniconda3/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 "/home/tally/miniconda3/envs/qiime2-2023.7/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['ssu', '-i', '/tmp/qiime2/tally/data/daaf3539-e49b-4550-8732-571d2e261089/data/feature-table.biom', '-t', '/tmp/qiime2/tally/data/09d3e619-41d2-4b68-ba12-1f863faefc34/data/tree.nwk', '-m', 'unweighted', '-o', '/tmp/q2-LSMatFormat-ajbrgr90']' returned non-zero exit status 1.

Plugin error from diversity:

Command '['ssu', '-i', '/tmp/qiime2/tally/data/daaf3539-e49b-4550-8732-571d2e261089/data/feature-table.biom', '-t', '/tmp/qiime2/tally/data/09d3e619-41d2-4b68-ba12-1f863faefc34/data/tree.nwk', '-m', 'unweighted', '-o', '/tmp/q2-LSMatFormat-ajbrgr90']' returned non-zero exit status 1.

See above for debug info.
(qiime2-2023.7) tally@tally-MS-7C75:~/Desktop/final_qiime$ qiime diversity core-metrics-phylogenetic --i-table removed_samples/1_filtered_table.qza --i-phylogeny removed_samples/fastree/rooted_tree.qza --p-sampling-depth 5200 --m-metadata-file new_newt_metadata.tsv --output-dir removed_samples/core_metrics/alpha_5200/ --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/tally/data/daaf3539-e49b-4550-8732-571d2e261089/data/feature-table.biom -t /tmp/qiime2/tally/data/09d3e619-41d2-4b68-ba12-1f863faefc34/data/tree.nwk -o /tmp/q2-AlphaDiversityFormat-0ewhgz8d

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/tally/data/daaf3539-e49b-4550-8732-571d2e261089/data/feature-table.biom -t /tmp/qiime2/tally/data/09d3e619-41d2-4b68-ba12-1f863faefc34/data/tree.nwk -m unweighted -o /tmp/q2-LSMatFormat-ehq39mok

Failing in Thread:0
call to cuInit returned error 999: Unknown

Traceback (most recent call last):
File "/home/tally/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2cli/commands.py", line 478, in call
results = self._execute_action(
File "/home/tally/miniconda3/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 "/home/tally/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self.callable_executor(
File "/home/tally/miniconda3/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 "/home/tally/miniconda3/envs/qiime2-2023.7/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 "/home/tally/miniconda3/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 unweighted_unifrac
File "/home/tally/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self.callable_executor(
File "/home/tally/miniconda3/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 unweighted_unifrac
File "/home/tally/miniconda3/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 unweighted_unifrac
File "/home/tally/miniconda3/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 "/home/tally/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2_diversity_lib/beta.py", line 221, in unweighted_unifrac
_omp_cmd_wrapper(threads, cmd)
File "/home/tally/miniconda3/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 "/home/tally/miniconda3/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 "/home/tally/miniconda3/envs/qiime2-2023.7/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['ssu', '-i', '/tmp/qiime2/tally/data/daaf3539-e49b-4550-8732-571d2e261089/data/feature-table.biom', '-t', '/tmp/qiime2/tally/data/09d3e619-41d2-4b68-ba12-1f863faefc34/data/tree.nwk', '-m', 'unweighted', '-o', '/tmp/q2-LSMatFormat-ehq39mok']' returned non-zero exit status 1.

Plugin error from diversity:

Command '['ssu', '-i', '/tmp/qiime2/tally/data/daaf3539-e49b-4550-8732-571d2e261089/data/feature-table.biom', '-t', '/tmp/qiime2/tally/data/09d3e619-41d2-4b68-ba12-1f863faefc34/data/tree.nwk', '-m', 'unweighted', '-o', '/tmp/q2-LSMatFormat-ehq39mok']' returned non-zero exit status 1.

I have never had this issue appear in any of my previous workflows using QIIME. sorry for the bad formatting.

3

Hello @UnevenCuttlefish. Do you have an Nvidia GPU in your system? The error you are seeing

appears to be an Nvidia related issue. Based on this thread on their forum it appears to happen when Nvidia drivers attempt to invoke the GPU but can't find it. The command that is failing for you

is running unifrac which will attempt to use an Nvidia GPU if it finds one. It would appear as though unifrac is seeing your Nvidia drivers and attempting to use your GPU but your drivers are failing to find and invoke your GPU.

Unfortunately, I can't provide much support for this since it's outside the scope of QIIME 2, but I would start by looking at posts about that particular error on the Nvidia user forum and maybe reinstalling your drivers.

1 Like
4

@Oddant1 I do have an NVIDIA GPU, an interesting error considering it happened within the same session where I ran core-metrics earlier that day. Thank you for your help!

2 Likes
5

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