Gneiss "Maximum Recursion Depth" Error

[cks (Caroline)]

Hi there,

I am new to Qiime2 but am trying to run a Gneiss balance analysis on OTU data. I have successfully imported my read counts by OTU (.biom file) and my taxonomy (.tsv) to form .qza objects, I have added pseudocounts, clustered via correlation-clustering and calculated the log ratios. My clustering took about a day, but I thought that was due to the fact that I am working with 275 samples and 26000 OTUs. Now, when I try to either visualize the balances as a dendrogram or run the multivariate linear regression, I receive the error: "maximum recursion depth exceeded"

My error log reads:
FutureWarning: '.reindex_axis' is deprecated and will be removed in a future version. Use '.reindex' instead.
Traceback (most recent call last):
File "/Users/cks/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/q2cli/commands.py", line 274, in call
results = action(**arguments)
File "", line 2, in dendrogram_heatmap
File "/Users/cks/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/sdk/action.py", line 232, in bound_callable
output_types, provenance)
File "/Users/cks/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/sdk/action.py", line 429, in callable_executor
ret_val = self._callable(output_dir=temp_dir, **view_args)
File "/Users/cks/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/q2_gneiss/plot/_plot.py", line 370, in dendrogram_heatmap
highlight_width=0.01, figsize=(12, 8))
File "/Users/cks/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/gneiss-0.4.4-py3.5.egg/gneiss/plot/_heatmap.py", line 69, in heatmap
t = SquareDendrogram.from_tree(tree)
File "/Users/cks/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/gneiss-0.4.4-py3.5.egg/gneiss/plot/_dendrogram.py", line 406, in from_tree
tree.update_geometry(use_lengths=False)
File "/Users/cks/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/gneiss-0.4.4-py3.5.egg/gneiss/plot/_dendrogram.py", line 81, in update_geometry
c.update_geometry(use_lengths, self.depth)

It then repeats the last line over and over.

Any suggestions on how I could debug this?

Thanks so much.

[mortonjt (Jamie Morton)]

Crap - that this happening because Python cannot properly handle recursion.

Short term solution, need to trim down those OTUs -- 26k OTUs is a lot for this renderer.

Long term solution, we need to decouple the phylogenetics visualization from the regression summaries. We are currently working on a scalable phylogenetics visualization that can handle over 200k tips, will give more updates on that once we figure out how to interface this with q2.