Found problems when running qiime diversity beta-phylogenetic

Hi! I'm trying to run qiime diversity beta-phylogenetic in a conda environment installed qiime2-amplicon-2024.2.

I have seen a thread about it (i find ERROR in qiime diversity core-metrics-phylogenetic - #3 by linke0909) , but it is closed. They suggest that there is a problem with the GPU, but my computer has no GPU.

I have the same issue than in the previous thread:

> (qiime2-amplicon-2024.2) pgen@pgen:/media/pgen/Disco_2/GEN00497_Pichel_16S/9_Sample_Analisis/Analisis1_Modelo_IGF1/1A1_WTvsKO_3mss/core_metrics/beta-div$ qiime diversity beta-phylogenetic --i-table ../../table_1A1.qza --i-phylogeny ../../phylogeny/rooted-tree.qza --p-metric unweighted_unifrac --o-distance-matrix UU_distance_matrix.qza --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:
> 
> ssu -i /tmp/qiime2/pgen/data/951f679d-bbd7-4a85-b799-26f737173d90/data/feature-table.biom -t /tmp/qiime2/pgen/data/99d2aecf-0f13-4ebd-95e8-880a2c994783/data/tree.nwk -m unweighted -o /tmp/q2-LSMatFormat-8wkehd64
> 
> Failing in Thread:0
> call to cuInit returned error 804: Other
> 
> Traceback (most recent call last):
>   File "/home/pgen/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2cli/commands.py", line 520, in __call__
>     results = self._execute_action(
>   File "/home/pgen/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2cli/commands.py", line 586, in _execute_action
>     results = action(**arguments)
>   File "<decorator-gen-147>", line 2, in beta_phylogenetic
>   File "/home/pgen/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 "/home/pgen/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 "/home/pgen/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2_diversity/_beta/_pipeline.py", line 31, in beta_phylogenetic
>     dm, = action(table, phylogeny, threads=threads,
>   File "<decorator-gen-818>", line 2, in unweighted_unifrac
>   File "/home/pgen/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 "<decorator-gen-819>", line 2, in unweighted_unifrac
>   File "/home/pgen/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 "/home/pgen/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 "<decorator-gen-143>", line 2, in unweighted_unifrac
>   File "/home/pgen/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 "<decorator-gen-142>", line 2, in unweighted_unifrac
>   File "/home/pgen/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 "/home/pgen/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2_diversity_lib/beta.py", line 220, in unweighted_unifrac
>     _omp_cmd_wrapper(threads, cmd)
>   File "/home/pgen/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 "/home/pgen/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 "/home/pgen/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/subprocess.py", line 516, in run
>     raise CalledProcessError(retcode, process.args,
> subprocess.CalledProcessError: Command '['ssu', '-i', '/tmp/qiime2/pgen/data/951f679d-bbd7-4a85-b799-26f737173d90/data/feature-table.biom', '-t', '/tmp/qiime2/pgen/data/99d2aecf-0f13-4ebd-95e8-880a2c994783/data/tree.nwk', '-m', 'unweighted', '-o', '/tmp/q2-LSMatFormat-8wkehd64']' returned non-zero exit status 1.
> 
> Plugin error from diversity:
> 
>   Command '['ssu', '-i', '/tmp/qiime2/pgen/data/951f679d-bbd7-4a85-b799-26f737173d90/data/feature-table.biom', '-t', '/tmp/qiime2/pgen/data/99d2aecf-0f13-4ebd-95e8-880a2c994783/data/tree.nwk', '-m', 'unweighted', '-o', '/tmp/q2-LSMatFormat-8wkehd64']' returned non-zero exit status 1.
> 
> See above for debug info.

I've tried to deactivate GPU usage as mentioned (export UNIFRAC_USE_GPU=N) but it does not work.

Thanks
María

Hi @matoro

I am alittle confused about your computer not having a GPU. Could you provide more information about the computer you are running?

:turtle: