Plugin error from composition

Technical Support
1

To Whom It May Concern,

I am trying to analyze my data with ANCOM. I have no problem constructing the feature tables and then turning them into composition artifacts. When I try to run ANCOM on certain columns of my data, however, I get the following error:

Plugin error from composition:

Debug info has been saved to /tmp/qiime2-q2cli-err-emv3dvou.log

I am using QIIME2-2018.11 and I believe it is installed on conda. The command that I am trying to run is as follows:

(qiime2-2018.11) rblucas@qps01:~/Desktop/2017RyanSamples/westchester-2017-sequences/Ryan_test$ qiime composition ancom --i-table comp-westchester-table.qza --m-metadata-file Ryan_2017_Map_2.tsv --m-metadata-column SampleType --o-visualization ancom-westchester.qzv

Here is the command run with the --verbose flag:

(qiime2-2018.11) rblucas@qps01:~/Desktop/2017RyanSamples/westchester-2017-sequences/Ryan_test$ qiime composition ancom --i-table comp-westchester-table.qza --m-metadata-file Ryan_2017_Map_2.tsv --m-metadata-column SampleType --o-visualization ancom-westchester.qzv --verbose
Traceback (most recent call last):
File “/usr/local/bin/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/q2cli/commands.py”, line 274, in call
results = action(**arguments)
File “”, line 2, in ancom
File “/usr/local/bin/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/usr/local/bin/miniconda3/envs/qiime2-2018.11/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 “/usr/local/bin/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/q2_composition/_ancom.py”, line 56, in ancom
significance_test=f_oneway)
File “/usr/local/bin/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/skbio/stats/composition.py”, line 971, in ancom
_logratio_mat = _log_compare(mat.values, cats.values, significance_test)
File “/usr/local/bin/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/skbio/stats/composition.py”, line 1073, in _log_compare
log_ratio = np.zeros((c, c))
MemoryError

Plugin error from composition:

See above for debug info.

Any help with this issue would be greatly appreciated.

Thank you,

Ryan

2

Hi @Rblucas,
See the last line of that error message: you are running out of memory! I would recommend filtering out any features that are very rare (unless if you are specifically interested in these). That should probably be good enough — if you keep running into this issue, though, you will need to move to a more powerful machine.

Good luck!

3

Thank you Nicholas! I will give that a try.