Weighted UniFrac is not parallelizable

User Support
1

Hello Qiimers
I’m using qiime2-2018.8 on Ubuntu 16.04 and run the following command:

!qiime diversity beta-phylogenetic \
  --i-table table.qza \
  --i-phylogeny rooted-tree.qza \
  --p-metric weighted_unifrac \
  --o-distance-matrix weighted_unifrac_distance_matrix.qza \
  --p-n-jobs 16

I’m getting the following error:
Plugin error from diversity:

  Weighted UniFrac is not parallelizable

Debug info has been saved to /tmp/qiime2-q2cli-err-mdv4gvps.log

Traceback (most recent call last):
  File "/home/amir/anaconda2/envs/qiime2-2018.8/lib/python3.5/site-packages/q2cli/commands.py", line 274, in __call__
    results = action(**arguments)
  File "<decorator-gen-348>", line 2, in beta_phylogenetic
  File "/home/amir/anaconda2/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
    output_types, provenance)
  File "/home/amir/anaconda2/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py", line 362, in _callable_executor_
    output_views = self._callable(**view_args)
  File "/home/amir/anaconda2/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_diversity/_beta/_method.py", line 59, in beta_phylogenetic
    raise ValueError("Weighted UniFrac is not parallelizable")
ValueError: Weighted UniFrac is not parallelizable

note: when i use the same command with UNweighted_unifrac i dont get any errors.

2

Hi @Yos.Dos,

That means that you cannot parallelize this command for weighted unifrac... you have two options:

  1. remove this line from your command: --p-n-jobs 16
  2. use beta-phylogenetic-alt instead, which can be run in parallel.
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