'qiime diversity alpha-rarefaction' consume too much cpus and run weird slow

[bayegy]

Hi, there
I am experiencing a strange problem. My qiime run weird slow and was consuming all my CPUs.

My qiime2 version: qiime2-2021.11

The command I used:

qiime diversity alpha-rarefaction --i-table table.qza --i-phylogeny rooted-tree.qza --p-max-depth 825 --m-metadata-file mapping_file.xls --p-steps 5 --o-visualization alpha-rarefaction-Qiime2.qzv

When I switched to qiime2-2019.10, this command finished in no time.

Any idea for this problem? I am glad to provide more information.

Thanks!

[thermokarst]

Hi there @bayegy!

This is the first report of this I have heard - I don't think we have made any changes to that visualizer in several years, so it is possible that a dependency has changed/regressed, causing an issue. Can you confirm for me that this is using the same data in both environments? Are you comfortable sharing these data with me? If so, feel free to send me a link here or in a DM, I will attempt to diagnose there.

Thanks!

:qiime2:

[bayegy]

Many thanks for your reply!

Can you confirm for me that this is using the same data in both environments?

Yes, I used the same data in both environments.

Are you comfortable sharing these data with me?

Of course! Here It is:
table.qza (41.4 KB) rooted-tree.qza (76.2 KB) mapping_file.txt (4.1 KB)

Looking forward to your reply.

Best regards！

[thermokarst]

Thanks for sharing @bayegy, and yes, I can confirm the slowdown. I totally forgot about this, but we refactored part of that viz to allow for more transparent code-reuse, I suspect the slowdown is related to that, and I'm not sure if there is much for us to do about it at this point. As far as resource consumption, this visualizer has no concept of parallelism or concurrency, so you shouldn't see any change in the number of CPUs working.