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:
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.
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
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
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:
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!