Qiime2-2017:10 QIIME 2 plugin 'diversity' has no action 'core-metrics-pylogenetic'

[Jewelna_Osei-Poku]

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?

[lvandiep]

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).

[ebolyen (Evan Bolyen)]

Hey @Jewelna_Osei-Poku,

@Jewelna_Osei-Poku

I am getting “QIIME 2 plugin ‘diversity’ has no action ‘core-metrics-pylogenetic’” error message when I tried running it in 2017:10.

It looks like your command has a typo, you want phylogenetic not pylogenetic.

---

@lvandiep

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).

@lvandiep, I think you might have the wrong version there, we renamed core-metrics to 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

[lvandiep]

Yes, you are correct the version I was using was the 2017.8.

[Jewelna_Osei-Poku]

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?

[thermokarst]

Hi @Jewelna_Osei-Poku!

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.

Thanks!

[Jewelna_Osei-Poku]

Hello Matthew,
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.

[vjera (Vjera Kovacevic)]

Hello! I have the same problem:

command:
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’.

System versions
Python version: 3.6.2
QIIME 2 release: 2017.7
QIIME 2 version: 2017.7.0
q2cli version: 2017.7.0

Installed plugins
alignment 2017.7.0
composition 2017.7.0
dada2 2017.7.0
deblur 2017.7.0
demux 2017.7.0
diversity 2017.7.0
emperor 2017.7.0
feature-classifier 2017.7.0
feature-table 2017.7.0
gneiss 2017.7.0
metadata 2017.7.0
phylogeny 2017.7.0
quality-filter 2017.7.0
taxa 2017.7.0
types 2017.7.0

Thanks in advance!

[ebolyen (Evan Bolyen)]

Hey @vjera,

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!