Taxa barplot plugin error

User Support
,
1

Hello! I am having a similar issue to a few other threads, but I still can't quite figure out what is wrong. I am trying to use the QIIME2 pipeline on ITS2 amplicons for the algae Symbiodinium (found in corals). There is a small Symbiodinium database that is available for this, which I have used to run closed-reference feature clustering at 97% (I first tried using a naive-bayes trained classifier, but with such a small database, my final taxa barplots did not give enough resolution, I believe due to the high number of single variant differences/features that were found that could not match the database).

From the clustering, I have been trying to create barplots using my clustered feature table and a taxonomy file that mirrors the features in the table, but have had some difficulty. I continue to get the following error:

Plugin error from taxa:

'float' object has no attribute 'split'

My command line is as follows:

qiime taxa barplot
--i-table table_cr_97.qza
--i-taxonomy tax_97.qza
--m-metadata-file ITS2_metadata.txt
--o-visualization ITS2_taxa-bar-plots_97.qzv

Traceback is:

Traceback (most recent call last):
File "/usr/local/miniconda/envs/qiime2-2017.10/lib/python3.5/site-packages/q2cli/commands.py", line 218, in call
results = action(**arguments)
File "", line 2, in barplot
File "/usr/local/miniconda/envs/qiime2-2017.10/lib/python3.5/site-packages/qiime2/sdk/action.py", line 220, in bound_callable
output_types, provenance)
File "/usr/local/miniconda/envs/qiime2-2017.10/lib/python3.5/site-packages/qiime2/sdk/action.py", line 416, in callable_executor
ret_val = self._callable(output_dir=temp_dir, **view_args)
File "/usr/local/miniconda/envs/qiime2-2017.10/lib/python3.5/site-packages/q2_taxa/_visualizer.py", line 29, in barplot
collapsed_tables = _extract_to_level(taxonomy, table)
File "/usr/local/miniconda/envs/qiime2-2017.10/lib/python3.5/site-packages/q2_taxa/_util.py", line 30, in _extract_to_level
max_obs_lvl = _get_max_level(taxonomy)
File "/usr/local/miniconda/envs/qiime2-2017.10/lib/python3.5/site-packages/q2_taxa/_util.py", line 11, in _get_max_level
return taxonomy.apply(lambda x: len(x.split(';'))).max()
File "/usr/local/miniconda/envs/qiime2-2017.10/lib/python3.5/site-packages/pandas/core/series.py", line 2355, in apply
mapped = lib.map_infer(values, f, convert=convert_dtype)
File "pandas/_libs/src/inference.pyx", line 1574, in pandas._libs.lib.map_infer (pandas/_libs/lib.c:66645)
File "/usr/local/miniconda/envs/qiime2-2017.10/lib/python3.5/site-packages/q2_taxa/_util.py", line 11, in
return taxonomy.apply(lambda x: len(x.split(';'))).max()
AttributeError: 'float' object has no attribute 'split'

I have attached my input files here:

table_cr_97.qza (94.5 KB)
tax_97.qza (3.2 KB)
ITS2_metadata.txt (49.7 KB)

Any help with how I might be able to move forward with this would be greatly appreciated! Thank you so much :slight_smile:

3

Hi @hannah_eps!

I think there's a missing value in your taxonomy for feature GS_C1, which is probably being loaded as np.NaN (a floating point number).

If you add an annotation for that and it fixes the problem, let us know. I'll see about filing a bug-report to give a better error when a taxonomy file is missing annotations.

5

Hi @ebolyen, thanks for the response!

It's all fixed, but not quite what I expected! I had a look at the tax_97.qzv and you're right, there was no annotation for GS_C1. The weird thing is that there is no feature called GS_C1. Turns out, I had a feature called GS_C1# that QIIME was reading of course as just GS_C1, and then leaving out the annotation that was there for it. Once I changed the feature name, it all worked perfectly. Thank you so much for your help!!

6

Ah! That makes sense. If you update to 2018.2, problems like that shouldn't come up anymore as comments (# like these) can only appear at the beginning of a line now.

Glad we could help!

7

Ran across an existing issue for this.