I have installed q2-greengenes2 and tested it with V4 sequences obtained after cutadapt / dada2 steps.
These sequences can be classified by q2 feature-classifier classify-sklearn using the pretrained 2022.10.backbone.v4.nb.qza classifier.
In order to get used to this new plugin, I started q2 greengenes2 taxonomy-from-features or taxonomy-from-table commands, but get a plugin error from gereengenes2: No requested tips found
The debug info showed this:
Traceback (most recent call last):
File "/home/bt140047/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2cli/commands.py", line 352, in call
results = action(**arguments)
File "", line 2, in taxonomy_from_features
File "/home/bt140047/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 234, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/home/bt140047/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 381, in callable_executor
output_views = self._callable(**view_args)
File "/home/bt140047/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_gg2/_methods.py", line 771, in taxonomy_from_features
tree = _load_tree_and_cache(open(str(reference_taxonomy)), features)
File "/home/bt140047/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_gg2/_methods.py", line 543, in _load_tree_and_cache
tree = tree.shear(names & features)
File "bp/_bp.pyx", line 758, in bp._bp.BP.shear
File "bp/_bp.pyx", line 800, in bp._bp.BP.shear
ValueError: No requested tips found
The greengenes2 tutorial on github does not contain the qiime greengenes2 filter-features step as on the tutorial in this forum. I tried also the filter step before, but got the same error.
Is this due to the md5 hash created from the representative sequences by dada2, which do not fit if the query and reference sequences are not exactly the same (length, sequence)?
Does anybody have an advice to me how to solve this issue?
I would appreciate any suggestion how to solve this issue.