gg2 taxonomic annotation

Community Plugin Support
1
  1. Hello, I am getting a error while performing taxonomy annotation ussing gg2
    qiime greengenes2 taxonomy-from-table
    --i-reference-taxonomy 2022.10.taxonomy.asv.nwk.qza
    --i-table feature-table89.qza
    --o-classification taxonomy.qza
    Plugin error from greengenes2:

No requested tips found

Debug info has been saved to /tmp/qiime2-q2cli-err-ukm0hqjb.log

this is the debug info:
Traceback (most recent call last):
File "/home/temp/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2cli/commands.py", line 478, in call
results = self._execute_action(
File "/home/temp/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2cli/commands.py", line 539, in _execute_action
results = action(**arguments)
File "", line 2, in taxonomy_from_table
File "/home/temp/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self.callable_executor(
File "/home/temp/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/sdk/action.py", line 566, in callable_executor
output_views = self._callable(**view_args)
File "/home/temp/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2_gg2/_methods.py", line 778, in taxonomy_from_table
tree = _load_tree_and_cache(open(str(reference_taxonomy)), features)
File "/home/temp/miniconda3/envs/qiime2-2023.7/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

I previously used this classifier: gg-13-8-99-nb-classifier.qza
it worked fine. My primer sequnces were V3-V4 specific.
My upstream commands were

qiime dada2 denoise-paired \

--i-demultiplexed-seqs paired-end-demux 89 .qza \

--p-trunc-len-f 2 68 \

--p-trim-left-r 1 8 \

--p-trim-left- f 1 8 `` \

--p-trunc-len-r 2 21 \

--o-representative-sequences asv-sequences 89 .qza \

--o-table feature-tabl e89 .qza \

--o-denoising-stats dada2-stats 89 .qza \

I tried suggestions on one of the post (Greengenes2 taxonomy-from-table error - #8 by wasade) with same error, unable to access the link provided there

2

Hi @komal,

The phylogenetic taxonomy which leverages existing placements in the tree works on exact match of identifiers. We primarily only placed 515F-806R ASVs with the majority being length 90, 100 and 150nt. For V3 data, I recommend using the Naive Bayes classifier (available on the QIIME 2 Resources page), or perform closed reference clustering using the non-v4-16s action.

A TODO item is to improve the error output here, as what you've encountered is not very user friendly, see this issue.

Best,
Daniel