core-metrics-phylogenetic: returned non-zero exit status 1._v1_220713

Hello.

Maybe I'm missing something, but I don't know why.

I am currently using the qiime2 2022.2 version (VMware).

First, a core-diversity guide was formed using qiime diversity core-metrics-phylogenetic in all samples to create a core-diversity directory.

This time it went well with no problems.

Afterward, among the samples obtained, what used the qiime taxa filter table to filter the specific taxon.

Who used the qiime feature-table filter samples to remove the samples in a particular column.

The sequence was also purified and separated based on the table obtained in this way.

Who rebuilt the tree with the filtered sequence.

And I tried to form the core-diversity directory by running qiime diversity core-metrics-phylogenetic, but the below error is displayed.

/home/qiime2/miniconda/envs/qiime2-2022.2/lib/python3.8/site-packages/sklearn/metrics/pairwise.py:1776: DataConversionWarning: Data was converted to boolean for metric jaccard
  warnings.warn(msg, DataConversionWarning)
/home/qiime2/miniconda/envs/qiime2-2022.2/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 -0.1374879396965191 and the largest is 5.560571462721946.
  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-archive-n1z8qqz6/5a12baa0-ae23-447d-b4ff-04be11b3a17e/data/feature-table.biom -t /tmp/qiime2-archive-356vybcy/1702cbb8-0f7d-491f-9ef3-f39270452896/data/tree.nwk -o /tmp/q2-AlphaDiversityFormat-f1u2nod8

Compute failed in faith_pd_one_off: Table observation IDs are not a subset of the tree tips. This error can also be triggered if a node name contains a single quote (this is unlikely).
Traceback (most recent call last):
  File "/home/qiime2/miniconda/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/commands.py", line 339, in __call__
    results = action(**arguments)
  File "<decorator-gen-96>", line 2, in core_metrics_phylogenetic
  File "/home/qiime2/miniconda/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
    outputs = self._callable_executor_(scope, callable_args,
  File "/home/qiime2/miniconda/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 485, in _callable_executor_
    outputs = self._callable(scope.ctx, **view_args)
  File "/home/qiime2/miniconda/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_diversity/_core_metrics.py", line 62, in core_metrics_phylogenetic
    faith_pd_vector, = faith_pd(table=cr.rarefied_table,
  File "<decorator-gen-457>", line 2, in faith_pd
  File "/home/qiime2/miniconda/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
    outputs = self._callable_executor_(scope, callable_args,
  File "/home/qiime2/miniconda/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 391, in _callable_executor_
    output_views = self._callable(**view_args)
  File "<decorator-gen-26>", line 2, in faith_pd
  File "/home/qiime2/miniconda/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_diversity_lib/_util.py", line 59, in _disallow_empty_tables
    return wrapped_function(*args, **kwargs)
  File "<decorator-gen-25>", line 2, in faith_pd
  File "/home/qiime2/miniconda/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_diversity_lib/_util.py", line 102, in _validate_requested_cpus
    return wrapped_function(*bound_arguments.args, **bound_arguments.kwargs)
  File "/home/qiime2/miniconda/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_diversity_lib/alpha.py", line 53, in faith_pd
    _omp_cmd_wrapper(threads, cmd)
  File "/home/qiime2/miniconda/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_diversity_lib/_util.py", line 118, in _omp_cmd_wrapper
    return _run_external_cmd(cmd, verbose=verbose, env=env)
  File "/home/qiime2/miniconda/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_diversity_lib/_util.py", line 112, in _run_external_cmd
    return subprocess.run(cmd, check=True, env=env)
  File "/home/qiime2/miniconda/envs/qiime2-2022.2/lib/python3.8/subprocess.py", line 516, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['faithpd', '-i', '/tmp/qiime2-archive-n1z8qqz6/5a12baa0-ae23-447d-b4ff-04be11b3a17e/data/feature-table.biom', '-t', '/tmp/qiime2-archive-356vybcy/1702cbb8-0f7d-491f-9ef3-f39270452896/data/tree.nwk', '-o', '/tmp/q2-AlphaDiversityFormat-f1u2nod8']' returned non-zero exit status 1.

Plugin error from diversity:

  Command '['faithpd', '-i', '/tmp/qiime2-archive-n1z8qqz6/5a12baa0-ae23-447d-b4ff-04be11b3a17e/data/feature-table.biom', '-t', '/tmp/qiime2-archive-356vybcy/1702cbb8-0f7d-491f-9ef3-f39270452896/data/tree.nwk', '-o', '/tmp/q2-AlphaDiversityFormat-f1u2nod8']' returned non-zero exit status 1.

See above for debug info.

Can you guess the cause?

Or, is it correct to draw PCoA by applying the tree for the entire sample to the filter-applied table without modification?

I have put the executable code below.

Please review.

$time qiime diversity core-metrics-phylogenetic \
    --i-table uchime-denovo-out/uchime-denovo-outtable-nonchimer-filtered-nounassign-Arthropoda-Chordata-noFelis_63ea.qza \
    --i-phylogeny tree-noUnassign-Arthropoda-Chordata-noFelis_63ea/rooted_tree.qza \
    --p-sampling-depth 500 \
    --m-metadata-file metadata-noFelis_63ea.tsv \
    --output-dir diversity-filtered-nounassign-Arthropoda-Chordata-noFelis_63ea-depth500-1 \
    --verbose

Hi @Jun_ho_Choi,

Welcome back to the :qiime2: forum!

From the command you provided, it looks like you included the --verbose flag - but the additional log details weren't included in your post above. Can you please re-run your command (still including the --verbose flag) and copy/paste the entire terminal output in your response? This will help us to better determine what the source of this issue is. Thanks! :lizard:

1 Like

Thank you. As you said, I uploaded the entire log. Please review.

Hi @Jun_ho_Choi,

Thanks for your patience here, and for providing that updated error log!

This is the source of the issue:

This essentially means that your tree and your feature table don't contain the same IDs (i.e. tree tips). This is almost certainly a result of these steps in your analysis:

Because you've done additional filtering on the tree, all of the feature IDs won't match up with what is present in your feature table. If you'd like to run this analysis on this filtered subset of your data, you'll need to modify your feature table to match the remaining samples that are present in your filtered tree.

Hope this helps!

Cheers :lizard:

1 Like

Thank you for your kind reply. I still don't know the exact cause, but I'll try as you said. First, we are analyzing the entire sample. Rather than collecting only the necessary pieces and proceeding, we approach the approach by analyzing all models and adjusting the sampling depth.