Plugin error from diversity: Cannot infer number of levels from empty list

[jelly_fan]

New user here. I’ve filtered and clustered my data in DADA2 standalone (my sequencing run had multiple amplicons I needed to handle separately) and imported it into QIIME2 as a BIOM 2.1 file for taxonomic assignment and visualisations. Almost everything is working as expected, However when I enter:

qiime diversity alpha-rarefaction
–i-table table.qza
–i-phylogeny rooted-tree.qza
–p-max-depth 4000
–m-metadata-file test_metadata.tsv
–o-visualization alpha-rarefaction.qzv

I get the following error message message:

Plugin error from diversity: Cannot infer number of levels from empty list

Can someone help me identify (and fix) the problem?

Thanks so much!

[Nicholas_Bokulich]

HI @jelly_fan,
Could you please share the complete error traceback? (you can re-run the command with --verbose added to the end of the command to see the full error)

Please also run qiime feature-table summarize on your feature table and share the results (you can send directly to me if these are sensitive data). I suspect either you may be using a higher max-depth than there are sequences in any single sample or else there is something wrong with the phylogeny.

Let’s start there and see where it takes us!

[jelly_fan]

Thank you for you for the quick response! I really appreciate it.

When I entered the verbose command I didn't get any additional information. However, when I re-ran the command without the verbose command the server logged some debug information to file. Hopefully this is what you need / helps:

Traceback (most recent call last):
File "/gpfs/software/python/anaconda/4.2/anaconda3/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/commands.py", line 246, in call
results = action(**arguments)
File "", line 2, in alpha_rarefaction
File "/gpfs/software/python/anaconda/4.2/anaconda3/envs/qiime2-2018.2/lib/python3.5/site-packages/qiime2/sdk/action.py", line 228, in bound_callable
output_types, provenance)
File "/gpfs/software/python/anaconda/4.2/anaconda3/envs/qiime2-2018.2/lib/python3.5/site-packages/qiime2/sdk/action.py", line 424, in callable_executor
ret_val = self._callable(output_dir=temp_dir, **view_args)
File "/gpfs/software/python/anaconda/4.2/anaconda3/envs/qiime2-2018.2/lib/python3.5/site-packages/q2_diversity/_alpha/_visualizer.py", line 328, in alpha_rarefaction
[(c, '') for c in metadata_df.columns])
File "/gpfs/software/python/anaconda/4.2/anaconda3/envs/qiime2-2018.2/lib/python3.5/site-packages/pandas/core/indexes/multi.py", line 1189, in from_tuples
raise TypeError(msg)
TypeError: Cannot infer number of levels from empty list

I don't think my data is sensitive. (The community data came from wild fish - so no data privacy issues!). Here is the table summary:

table_summary.qzv (360.8 KB)

[thermokarst]

what you need / helps

This error message is pretty helpful, and this is a new error for me — it looks like there is an issue somehow related to your metadata. Can you please send test_metadata.tsv along when you get a chance? Thanks!

[jelly_fan]

Thank you for looking into this further for me.

Glad the output was useful.

Here is the .tsv file. It's the bare minimum, just sample IDs - I wanted to keep everything as simple as possible while running a pilot pipeline.

test_metadata.tsv (2.2 KB)

[thermokarst]

Ah ha! Thanks for the metadata, @jelly_fan! I see the issue — your metadata has no defined metadata columns, effectively it is just a list of IDs, or, empty metadata.

To get you moving forward right now, you can just run this command sans metadata and get the exact same results:

qiime diversity alpha-rarefaction \
  --i-table table.qza \
  --i-phylogeny rooted-tree.qza \
  --p-max-depth 4000 \
  --o-visualization alpha-rarefaction.qzv

I have opened an issue on the relevant bug tracker to make sure that this viz gracefully handles empty metadata in the future.

As well, I would suggest taking a read through the Metadata Tutorial!

Good luck!

[jelly_fan]

Hi,

Just wanted to confirm my rarefaction curves came out nicely with your code, and also when I added in some relevant metadata - the original command started working too.

Thank you for all your help (and developing such a good program).