Core-metrics plugin error from diversity

[jllowell (Jennifer Lowell)]

Hello everyone,

I am running qiime2-amplicon-2023.9 on a Mac in conda environment. I installed this according to the qiime2 install page and ran through the Moving Pictures tutorial without errors. Today I updated conda.

Currently I am trying to run qiime diversity core-metrics-using my own data with the following:

qiime diversity core-metrics-phylogenetic
--i-phylogeny rooted-tree.qza
--i-table merged-table.qza
--p-sampling-depth 1292
--m-metadata-file combmeta.tsv
--output-dir COcore-metrics-results
--verbose

I am getting the following returned:

faithpd -i /var/folders/cf/gyj42fxx1d305q4vgzfzc04jjszt4h/T/qiime2/jllowell/data/130c2596-4900-40da-9529-c19daacaaf84/data/feature-table.biom -t /var/folders/cf/gyj42fxx1d305q4vgzfzc04jjszt4h/T/qiime2/jllowell/data/640d7c6c-2dbd-4414-8239-197b14c5dc3d/data/tree.nwk -o /var/folders/cf/gyj42fxx1d305q4vgzfzc04jjszt4h/T/q2-AlphaDiversityFormat-onnd2ks7

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 "/opt/anaconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/q2cli/commands.py", line 520, in call
results = self._execute_action(
File "/opt/anaconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/q2cli/commands.py", line 586, in _execute_action
results = action(**arguments)
File "", line 2, in core_metrics_phylogenetic
File "/opt/anaconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self.callable_executor(
File "/opt/anaconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/qiime2/sdk/action.py", line 647, in callable_executor
outputs = self._callable(scope.ctx, **view_args)
File "/opt/anaconda3/envs/qiime2-amplicon-2023.9/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 "/opt/anaconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/qiime2/sdk/context.py", line 140, in deferred_action
return action_obj._bind(
File "", line 2, in faith_pd
File "/opt/anaconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self.callable_executor(
File "/opt/anaconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/qiime2/sdk/action.py", line 566, in callable_executor
output_views = self._callable(**view_args)
File "", line 2, in faith_pd
File "/opt/anaconda3/envs/qiime2-amplicon-2023.9/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 faith_pd
File "/opt/anaconda3/envs/qiime2-amplicon-2023.9/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 "/opt/anaconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/q2_diversity_lib/alpha.py", line 53, in faith_pd
_omp_cmd_wrapper(threads, cmd)
File "/opt/anaconda3/envs/qiime2-amplicon-2023.9/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 "/opt/anaconda3/envs/qiime2-amplicon-2023.9/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 "/opt/anaconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['faithpd', '-i', '/var/folders/cf/gyj42fxx1d305q4vgzfzc04jjszt4h/T/qiime2/jllowell/data/130c2596-4900-40da-9529-c19daacaaf84/data/feature-table.biom', '-t', '/var/folders/cf/gyj42fxx1d305q4vgzfzc04jjszt4h/T/qiime2/jllowell/data/640d7c6c-2dbd-4414-8239-197b14c5dc3d/data/tree.nwk', '-o', '/var/folders/cf/gyj42fxx1d305q4vgzfzc04jjszt4h/T/q2-AlphaDiversityFormat-onnd2ks7']' returned non-zero exit status 1.

Plugin error from diversity:

Command '['faithpd', '-i', '/var/folders/cf/gyj42fxx1d305q4vgzfzc04jjszt4h/T/qiime2/jllowell/data/130c2596-4900-40da-9529-c19daacaaf84/data/feature-table.biom', '-t', '/var/folders/cf/gyj42fxx1d305q4vgzfzc04jjszt4h/T/qiime2/jllowell/data/640d7c6c-2dbd-4414-8239-197b14c5dc3d/data/tree.nwk', '-o', '/var/folders/cf/gyj42fxx1d305q4vgzfzc04jjszt4h/T/q2-AlphaDiversityFormat-onnd2ks7']' returned non-zero exit status 1.

I found a similar post at the link below and tried the solution although the post was regarding Linux. It did not work for me on my Mac.

Core-metrics (Plugin error from diversity)

hi everyone, Im trying to make alpha and beta diversity but when i run the following : qiime diversity core-metrics-phylogenetic --i-phylogeny Lombok_v9_18-rooted-tree.qza --i-table Lombok_v9_18_table.qza --p-sampling-depth 11358 --m-metadata-file Metadata_Lombok02_v9_18.tsv --output-dir core-metrics-results --verbose it delivers the following: faithpd -i /tmp/qiime2/carolline/data/f98e6d82-b833-443d-8921-556872735626/data/feature-table.biom -t /tmp/qiime2/carolline/data/f968ca8b-7…

Thank you for any insight and solutions.

[timanix (Timur Yergaliyev)]

Hello and welcome to the forum!

Thank you for using search on the forum before asking questions!

Even if the errors look similar, there is a key difference:

@jllowell

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).

It looks like not all features from your table are present in a tree. I noticed that your feature table has "merged" in the name. Does it mean that you merged several tables from different runs? If yes, did you merge rep-seqs.qza files as well before tree construction? If not, then definitely it may cause the error you are facing.

Best,

[jllowell (Jennifer Lowell)]

Hello and thank you for the reply. Yes, feature tables and rep-seqs were merged after dada2 denoising and prior to tree construction.

[timanix (Timur Yergaliyev)]

Did you find an error then?
From data you provided, it can be that one of the following reasons may cause an issue you are facing:

1. You didn't merge all rep-seqs.qza files
2. You used not merged rep-seqs.qza for tree construction.
3. You filtered your final rep-seqs.qza at some point but didn't filter feature table
4. You used tree that was constructed based on other dataset
5. You used feature table from another dataset
6. You altered features in feature table, for example, by collapsing it to taxonomy level
7. You clustered sequences from rep-seqs.qza to OTUs.

[jllowell (Jennifer Lowell)]

@timanix Thank you for these suggestions! We went back and took at the rep-seqs and table file generation, and indeed there was an error in the merged rep seqs. So, I think now I will be good to go.

Kindly,

Jen