I tried using qiime 2020.8.0, and I no longer get the same error as when I ran 2019.10. Instead, I get:
/ebio/abt3_projects/software/dev/ll_pipelines/llmgp/.snakemake/conda/d64706f7/lib/python3.6/site-packages/sklearn/metrics/pairwise.py:1761: DataConversionWarning: Data was converted to boolean for metric jaccard
warnings.warn(msg, DataConversionWarning)
More threads were requested than stripes. Using -761554400 threads.
Traceback (most recent call last):
File "/ebio/abt3_projects/software/dev/ll_pipelines/llmgp/.snakemake/conda/d64706f7/lib/python3.6/site-packages/q2cli/commands.py", line 329, in __call__
results = action(**arguments)
File "<decorator-gen-421>", line 2, in core_metrics_phylogenetic
File "/ebio/abt3_projects/software/dev/ll_pipelines/llmgp/.snakemake/conda/d64706f7/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
output_types, provenance)
File "/ebio/abt3_projects/software/dev/ll_pipelines/llmgp/.snakemake/conda/d64706f7/lib/python3.6/site-packages/qiime2/sdk/action.py", line 484, in _callable_executor_
outputs = self._callable(scope.ctx, **view_args)
File "/ebio/abt3_projects/software/dev/ll_pipelines/llmgp/.snakemake/conda/d64706f7/lib/python3.6/site-packages/q2_diversity/_core_metrics.py", line 66, in core_metrics_phylogenetic
threads=n_jobs_or_threads)
File "<decorator-gen-537>", line 2, in unweighted_unifrac
File "/ebio/abt3_projects/software/dev/ll_pipelines/llmgp/.snakemake/conda/d64706f7/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
output_types, provenance)
File "/ebio/abt3_projects/software/dev/ll_pipelines/llmgp/.snakemake/conda/d64706f7/lib/python3.6/site-packages/qiime2/sdk/action.py", line 390, in _callable_executor_
output_views = self._callable(**view_args)
File "<decorator-gen-395>", line 2, in unweighted_unifrac
File "/ebio/abt3_projects/software/dev/ll_pipelines/llmgp/.snakemake/conda/d64706f7/lib/python3.6/site-packages/q2_diversity_lib/_util.py", line 49, in _disallow_empty_tables
return wrapped_function(*args, **kwargs)
File "<decorator-gen-394>", line 2, in unweighted_unifrac
File "/ebio/abt3_projects/software/dev/ll_pipelines/llmgp/.snakemake/conda/d64706f7/lib/python3.6/site-packages/q2_diversity_lib/_util.py", line 92, in _validate_requested_cpus
return wrapped_function(*bound_arguments.args, **bound_arguments.kwargs)
File "/ebio/abt3_projects/software/dev/ll_pipelines/llmgp/.snakemake/conda/d64706f7/lib/python3.6/site-packages/q2_diversity_lib/beta.py", line 159, in unweighted_unifrac
variance_adjusted=False, bypass_tips=bypass_tips)
File "/ebio/abt3_projects/software/dev/ll_pipelines/llmgp/.snakemake/conda/d64706f7/lib/python3.6/site-packages/unifrac/_methods.py", line 103, in unweighted
variance_adjusted, 1.0, bypass_tips, threads)
File "unifrac/_api.pyx", line 102, in unifrac._api.ssu
File "/ebio/abt3_projects/software/dev/ll_pipelines/llmgp/.snakemake/conda/d64706f7/lib/python3.6/site-packages/skbio/stats/distance/_base.py", line 106, in __init__
self._validate(data, ids)
File "/ebio/abt3_projects/software/dev/ll_pipelines/llmgp/.snakemake/conda/d64706f7/lib/python3.6/site-packages/skbio/stats/distance/_base.py", line 873, in _validate
"Data must be symmetric and cannot contain NaNs.")
skbio.stats.distance._base.DistanceMatrixError: Data must be symmetric and cannot contain NaNs.
Maybe it still is a tip-feature matching issue, but there's no indication of that in the warning. The error is really not helpful at all.
When I run core-metrics instead of core-metrics-phylogenetic, there's no such error, and the job completes successfully. Therefore, it's likely a problem with the tree, but how do I figure out the issue?