Plugin Error in `qiime diversity core-metrics-phylogenetic` Command (Exit Status 126)**

User Support
1

I am encountering an issue while running the following command in QIIME 2:

qiime diversity core-metrics-phylogenetic
--i-phylogeny rooted-tree.qza
--i-table table-with-phyla.qza
--p-sampling-depth 17360
--m-metadata-file metadata.tsv
--output-dir core-metrics-results

The error message is as follows:
/home/jaishi452/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/numpy/core/getlimits.py:542: UserWarning: Signature b'\x00\xd0\xcc\xcc\xcc\xcc\xcc\xcc\xfb\xbf\x00\x00\x00\x00\x00\x00' for <class 'numpy.longdouble'> does not match any known type: falling back to type probe function.
This warning indicates broken support for the dtype!
machar = _get_machar(dtype)

Plugin error from diversity:

Command '['faithpd', '-i', '/tmp/qiime2/jaishi452/data/981fea5a-d12d-4c90-83db-4441fa1194d4/data/feature-table.biom', '-t', '/tmp/qiime2/jaishi452/data/d59a75c9-04e5-4b15-a5e6-9ac72767fbb5/data/tree.nwk', '-o', '/tmp/qiime2/jaishi452/processes/6570-1737136226.2@jaishi452/tmp/q2-OutPath-4apqbvij']' returned non-zero exit status 126.

Debug info has been saved to /tmp/qiime2-q2cli-err-8mk5k8uq.log


I am running QIIME 2 on an Ubuntu environment within Windows (via WSL), with 16GB RAM.

* The error message points to an issue with the `faithpd` command and indicates that a binary file cannot be executed.
* I have already checked if `faithpd` is executable and attempted reinstalling it, but the error persists. I updated coda , re-install QIIME 2 but the issue still exists.


Thank you in advance for any guidance!
Best,
Namraj
2

Hey @Namraj_Jaishi,

Can you re-run this command with the --verbose flag enabled and copy/paste the entire error traceback in your reply (with full page screenshots of your command line as well, if possible)? This will help us to better identify where the error is coming from. Thanks! :lizard:

3

Hello @lizgehret
Here is the full command:
(qiime2-amplicon-2024.10) jaishi452@TSU102911:~/18Ssoil/train18S$ qiime diversity core-metrics-phylogenetic
--i-phylogeny rooted-tree.qza
--i-table table-with-phyla.qza
--p-sampling-depth 17360
--m-metadata-file metadata.tsv
--output-dir core-metrics-results
--verbose
/home/jaishi452/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/numpy/core/getlimits.py:542: UserWarning: Signature b'\x00\xd0\xcc\xcc\xcc\xcc\xcc\xcc\xfb\xbf\x00\x00\x00\x00\x00\x00' for <class 'numpy.longdouble'> does not match any known type: falling back to type probe function.
This warnings indicates broken support for the dtype!
machar = _get_machar(dtype)
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/jaishi452/data/981fea5a-d12d-4c90-83db-4441fa1194d4/data/feature-table.biom -t /tmp/qiime2/jaishi452/data/68b6f821-9521-4b30-97e5-97650dceaeac/data/tree.nwk -o /tmp/qiime2/jaishi452/processes/18346-1737154973.42@jaishi452/tmp/q2-OutPath-89awoh8m

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/jaishi452/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2cli/commands.py", line 530, in call
results = self._execute_action(
File "/home/jaishi452/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2cli/commands.py", line 608, in _execute_action
results = action(**arguments)
File "", line 2, in core_metrics_phylogenetic
File "/home/jaishi452/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/sdk/action.py", line 299, in bound_callable
outputs = self.callable_executor(
File "/home/jaishi452/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/sdk/action.py", line 651, in callable_executor
outputs = self._callable(ctx, **view_args)
File "/home/jaishi452/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity/_core_metrics.py", line 65, in core_metrics_phylogenetic
faith_pd_vector, = faith_pd(table=cr.rarefied_table,
File "", line 2, in faith_pd
File "/home/jaishi452/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/sdk/context.py", line 125, in deferred_action
return action_obj._bind(
File "", line 2, in faith_pd
File "/home/jaishi452/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/sdk/action.py", line 299, in bound_callable
outputs = self.callable_executor(
File "/home/jaishi452/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/sdk/action.py", line 570, in callable_executor
output_views = self._callable(**view_args)
File "", line 2, in faith_pd
File "/home/jaishi452/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity_lib/_util.py", line 75, in _validate_tables
return wrapped_function(*args, **kwargs)
File "", line 2, in faith_pd
File "/home/jaishi452/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity_lib/_util.py", line 118, in _validate_requested_cpus
return wrapped_function(*bound_arguments.args, **bound_arguments.kwargs)
File "/home/jaishi452/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity_lib/alpha.py", line 63, in faith_pd
_omp_cmd_wrapper(threads, cmd)
File "/home/jaishi452/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity_lib/_util.py", line 134, in _omp_cmd_wrapper
return _run_external_cmd(cmd, verbose=verbose, env=env)
File "/home/jaishi452/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_diversity_lib/_util.py", line 128, in _run_external_cmd
return subprocess.run(cmd, check=True, env=env)
File "/home/jaishi452/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/subprocess.py", line 526, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['faithpd', '-i', '/tmp/qiime2/jaishi452/data/981fea5a-d12d-4c90-83db-4441fa1194d4/data/feature-table.biom', '-t', '/tmp/qiime2/jaishi452/data/68b6f821-9521-4b30-97e5-97650dceaeac/data/tree.nwk', '-o', '/tmp/qiime2/jaishi452/processes/18346-1737154973.42@jaishi452/tmp/q2-OutPath-89awoh8m']' returned non-zero exit status 1.

Plugin error from diversity:

Command '['faithpd', '-i', '/tmp/qiime2/jaishi452/data/981fea5a-d12d-4c90-83db-4441fa1194d4/data/feature-table.biom', '-t', '/tmp/qiime2/jaishi452/data/68b6f821-9521-4b30-97e5-97650dceaeac/data/tree.nwk', '-o', '/tmp/qiime2/jaishi452/processes/18346-1737154973.42@jaishi452/tmp/q2-OutPath-89awoh8m']' returned non-zero exit status 1.

See above for debug info.
(qiime2-amplicon-2024.10) jaishi452@TSU102911:~/18Ssoil/train18S$.

Thank you for looking.
Best,
Namraj

1 Like
4

Hi @Namraj_Jaishi,

Thanks for providing that full traceback! Here's where the issue is coming from:

This error indicates that you have some features in the table that are missing in the tree you provided. Double check your filtering steps to make sure that all features from the table are present in the tree.

If you're still unsure of how to proceed, I'd recommend reviewing these related forum posts on the same error you've received.

Let us know if you're still stuck and we can dig in further. Cheers :lizard:

1 Like
5

@lizgehret
Yes, there was a filtering error in my pipeline. It was resolved now.
But before running the core metric phylogenetic, I run this
export UNIFRAC_MAX_CPU=basic.
If not it also brings errors.
Thank you for your insights.

Best,
Namraj

2 Likes