Gneiss plugin MemoryError

User Support
1

Hello,

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/commands.py", 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/action.py", line 220, in bound_callable
output_types, provenance)
File "/home/qiime2/miniconda/envs/qiime2-2017.10/lib/python3.5/site-packages/qiime2/sdk/action.py", 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/_composition.py", 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/balances.py", line 121, in balance_basis
basis = clr_inv(basis)
File "/home/qiime2/miniconda/envs/qiime2-2017.10/lib/python3.5/site-packages/skbio/stats/composition.py", line 506, in clr_inv
return closure(np.exp(mat))
MemoryError

Do you know some way to solve this?

Thank you in advance!

3

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?

5

Hey!

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.

Thanks!

9

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!

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11

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