`ids_to_keep` must contain at least one ID.

User Support
1

Hello there Qiimers!

I am having the following problem when trying to create a feature table:

(qiime2-2020.6) claudiavic@x86_64-apple-darwin13 ~ % qiime feature-table summarize \
  --i-table table.qza \
  --o-visualization table.qzv \
  --m-sample-metadata-file /Users/claudiavic/metadata.tsv --verbose
/Users/claudiavic/opt/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2_feature_table/_summarize/_visualizer.py:122: FutureWarning: The signature of `Series.to_csv` was aligned to that of `DataFrame.to_csv`, and argument 'header' will change its default value from False to True: please pass an explicit value to suppress this warning.
  os.path.join(output_dir, 'sample-frequency-detail.csv'))
/Users/claudiavic/opt/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2_feature_table/_summarize/_visualizer.py:124: FutureWarning: The signature of `Series.to_csv` was aligned to that of `DataFrame.to_csv`, and argument 'header' will change its default value from False to True: please pass an explicit value to suppress this warning.
  os.path.join(output_dir, 'feature-frequency-detail.csv'))
Traceback (most recent call last):
  File "/Users/claudiavic/opt/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2cli/commands.py", line 329, in __call__
    results = action(**arguments)
  File "<decorator-gen-338>", line 2, in summarize
  File "/Users/claudiavic/opt/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
    output_types, provenance)
  File "/Users/claudiavic/opt/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/sdk/action.py", line 452, in _callable_executor_
    ret_val = self._callable(output_dir=temp_dir, **view_args)
  File "/Users/claudiavic/opt/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2_feature_table/_summarize/_visualizer.py", line 156, in summarize
    sample_frequencies
  File "/Users/claudiavic/opt/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2_feature_table/_summarize/_vega_spec.py", line 16, in vega_spec
    sample_frequencies.index)
  File "/Users/claudiavic/opt/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/metadata/metadata.py", line 728, in filter_ids
    ids_to_keep)
  File "/Users/claudiavic/opt/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/metadata/metadata.py", line 184, in _filter_ids_helper
    raise ValueError("`ids_to_keep` must contain at least one ID.")
ValueError: `ids_to_keep` must contain at least one ID.

Plugin error from feature-table:

  `ids_to_keep` must contain at least one ID.

I am using joinedreads already demultiplexed by the sequencing company. I have run Deblur-16S.
Deblur stats seem okay.

Can you please help me?
Thank you very much

3

I have figured out. It was a problem with my trimming.
But still have a question, I have joined reads with a total length around 500. When I apply denoise Deblur 16S with --p-trim-length 150, I loose a lot of reads.

How can I decide the best trimming for my reads?

From raw reads of 47000, I can only get as much as 11000.

Can you please help me?
Thank you.

6

Hi, @CVicent! :wave:

Glad to hear you sorted out the problem with the feature table summary. :+1:

Please search the forum for something like "dada2 trim," using the search bar in the top right corner. You will find lots of discussion about how to select parameters. Please also see these sections of our tutorials for an overview on trimming parameters.

https://docs.qiime2.org/2020.6/tutorials/moving-pictures/#option-1-dada2

https://docs.qiime2.org/2020.6/tutorials/pd-mice/#sequence-quality-control-and-feature-table

If you have more detailed questions unrelated to this topic, please create a new topic.

Thanks!