diversity core-metrics-phylogenetic Alpha & beta diversity

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.

Hi @saitha,

Welcome back to the :qiime2: forum!

Apologies for the delay in response on this - I am looking into this error, and will follow up shortly. Thanks!

Hi @saitha,

Thanks again for your patience here! Can you share with me how you're running QIIME 2 (conda, virtual machine, etc), and what operating system you are using? Is this a single user machine, or a cluster, etc?

Thanks! :lizard:

Thank you
Running Qiime2 in conda
OS - Centos 7
Yes it is single user

Hi @saitha,

Thanks so much for your patience here! Can you please try deleting and re-installing QIIME 2 2022.8, and let me know if that resolves the issue? You can do this with the following commands:

This first step is only necessary if you still have this environment activated.

conda deactivate

You'll need to replace $ENV_NAME with your conda environment name for QIIME 2 2022.8

conda env remove -n $ENV_NAME

Then you can just follow the install guide here to re-install QIIME 2 2022.8 via conda for linux.

Cheers :lizard:

1 Like

Thank you
Sure I will do it and run again & get back to you

Hi Lizgehret

even after re install QIIME 2 2022-8 the same error appears

Plugin error from diversity:

Command '['ssu', '-i', '/tmp/qiime2/uid=#0/data/6d50a52b-8f1a-4919-91dc-11df3b6636a2/data/feature-table.biom', '-t', '/tmp/qiime2/uid=#0/data/96e1c288-0033-4761-b621-117642b0576b/data/tree.nwk', '-m', 'unweighted', '-o', '/tmp/q2-LSMatFormat-sp6vgdxz']' returned non-zero exit status 1.

Debug info has been saved to /tmp/qiime2-q2cli-err-aoh43jbr.log

Hi @saitha,

Thanks for following up and giving that a try - it seems like this may be an issue related to the following packages installed on your machine:

Can you give this command a try and see if it resolves the issue?

export UNIFRAC_USE_GPU=N

Thanks! :lizard: