Gneiss plugin MemoryError


I have been trying to use the ilr-transform function from the Gneiss plugin, but every time I run the following code I obtain the same error.

qiime gneiss ilr-transform --i-table comp-rar.qza --i-tree hierar-cluster-rar.qza --o-balances balance-table.rar

Plugin error from gneiss:
Debug info has been saved to /tmp/qiime2-q2cli-err-kkasuatu.log

I went to check the log file and it indicates that it is a MemoryError:

Traceback (most recent call last):
File “/home/qiime2/miniconda/envs/qiime2-2017.10/lib/python3.5/site-packages/q2cli/”, line 218, in call
results = action(**arguments)
File “”, line 2, in ilr_transform
File “/home/qiime2/miniconda/envs/qiime2-2017.10/lib/python3.5/site-packages/qiime2/sdk/”, line 220, in bound_callable
output_types, provenance)
File “/home/qiime2/miniconda/envs/qiime2-2017.10/lib/python3.5/site-packages/qiime2/sdk/”, line 355, in callable_executor
output_views = self._callable(**view_args)
File “/home/qiime2/miniconda/envs/qiime2-2017.10/lib/python3.5/site-packages/gneiss-0.4.2-py3.5.egg/gneiss/composition/”, line 17, in ilr_transform
basis, _ = balance_basis(_tree)
File “/home/qiime2/miniconda/envs/qiime2-2017.10/lib/python3.5/site-packages/gneiss-0.4.2-py3.5.egg/gneiss/”, line 121, in balance_basis
basis = clr_inv(basis)
File “/home/qiime2/miniconda/envs/qiime2-2017.10/lib/python3.5/site-packages/skbio/stats/”, line 506, in clr_inv
return closure(np.exp(mat))

Do you know some way to solve this?

Thank you in advance!

Interesting - I think this is the first memory that I have seen pop up.

Can you specify how much memory your machine has, and how many features your table has?


My machine is 4GB RAM and the number of features are 16900OTUs (aprox.).
Anyway, looking at the taxonomy classification, I believe I have a problem with the number of OTUs, as several different OTUs have the same taxonomic classification. I’ll try to solve this and I’ll try again.


Hi @mc92! This actually isn’t a problem, and is expected to happen: multiple OTUs or Amplicon Sequence Variants (ASVs) can map to the same taxonomic annotation. You can use qiime taxa collapse to collapse these features (e.g. OTUs or ASVs) at a particular taxonomic level. You can also use qiime taxa barplot to visualize the taxonomic composition of your samples at various taxonomic levels. Hope this helps!


This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.