I am attempting to filter my sequences using my metadata file but I am getting an error message that says all the features have been filtered out of the data. I have three different study groups composed of about 22 samples each. I want to determine the relative abundance of phyla in each group as opposed to the relative abundance in each individual sample. I might be going about this the wrong way so any feedback is much appreciated.
To filter sequences I used:
qiime feature-table filter-seqs \
–m-metadata-file ‘validatedALLM1 - Sheet3.tsv’
–p-where “‘sample id’=‘C’”
This is the output I get:
(qiime2-2019.1) [email protected]:~/M1alloutput$ qiime feature-table filter-seqs --i-data rep-seqs.qza --m-metadata-file ‘validatedALLM1 - Sheet3.tsv’ --p-where “‘sample id’=‘C’” --o-filtered-data rep-seqsC.qza --verbose
Traceback (most recent call last):
File “/home/ubuntu/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2cli/commands.py”, line 274, in call
results = action(**arguments)
File “</home/ubuntu/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/decorator.py:decorator-gen-318>”, line 2, in filter_seqs
File “/home/ubuntu/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
File “/home/ubuntu/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 365, in callable_executor
output_views = self._callable(**view_args)
File “/home/ubuntu/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_feature_table/_filter.py”, line 112, in filter_seqs
raise ValueError(‘All features were filtered out of the data.’)
ValueError: All features were filtered out of the data.
Plugin error from feature-table:
All features were filtered out of the data.
See above for debug info.
Should I be using a different feature to filter my sequences? Or is there a way I can use the relative abundance data I have already generated for each of my samples to look at the relative abundance of phyla in each of the groups?
Thank you in advance for your help!