Weighted UniFrac is not parallelizable

I’m using q2cli version 2017.10.0 on Ubuntu 16.04.3 and run the following command:

qiime diversity core-metrics-phylogenetic   --i-phylogeny rooted-tree.qza   --i-table tabl.qza   --m-metadata-file metadata.txt   --output-dir core_metrics_output   --p-sampling-depth 1000 --p-n-jobs 20

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-ohnrm9rv.log

I do not get the same error when using the same command but leaving out --p-n-jobs 20

This appears to be a bug, where qiime diversity core-metrics-phylogenetic is trying to provide the weighted unifrac function with multiple threads, but the function throws an error.


Thanks for the bug report @nick-youngblut! We recently refactored the core-metrics* methods to become pipelines, and looks like this regression crept in!

I have opened an issue on the relevant issue tracker. Stay tuned!


Have you looked at qiime diversity beta-phylogenetic-alt? That definitely as a parallelizable option and is freaking fast!


QIIME 2 2017.12 is now out, and it includes a fix for this bug. Thanks for reporting it! :bug:

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