I am trying to do diversity analyses using qiime diversity core-metrics-phylogenetic. This used to work perfectly with 2017:9. I am getting “QIIME 2 plugin ‘diversity’ has no action ‘core-metrics-pylogenetic’” error message when I tried running it in 2017:10.
Could anyone help?
I found that the other diversity plugin “qiime diversity core-metrics” does all the core diversity metrics including the phylogenetic analysis (at least this was the case in 2017-9).
It looks like your command has a typo, you want
@lvandiep, I think you might have the wrong version there, we renamed
core-metrics-phylogenetic in 2017.9 (and used
core-metrics for the non-phylogenetic version). But what you are saying is true for 2017.8
Yes, you are correct the version I was using was the 2017.8.
I noticed the typo in my command, and I have corrected it but, it is still not working. Has anyone managed to get it to work?
In order for us to help you, can you please provide the following information:
- What was the exact command you ran? Copy-and-paste please.
- What was the exact error you observed? Please either copy-and-paste the detailed results when run with the
--verbose flag, or attach the error log that is referenced at the end of the error.
I tried the command again and it seemed to have worked this time. No idea what was going wrong previously.
Thanks for the response all the same.
Hello! I have the same problem:
qiime diversity core-metrics-phylogenetic --i-phylogeny rooted-tree.qza --i-table table.qza --p-sampling-depth 1109 --m-metadata-file /home/comi/vjera.kovacevic/qiime2-moving-pictures-tutorial/sample-metadata.tsv --output-dir core-metrics-results
Error: QIIME 2 plugin ‘diversity’ has no action ‘core-metrics-phylogenetic’.
Python version: 3.6.2
QIIME 2 release: 2017.7
QIIME 2 version: 2017.7.0
q2cli version: 2017.7.0
Thanks in advance!
Your installation is older than
core-metrics-phylogenetic. As indicated earlier in this thread, you’ll need to install the latest release to see that action.
Hope that helps!
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