QIIME 2 plugin 'diversity' has no action 'core-metrics-phylogenetic'

[KEDIR_HAMZA]

Hi,
Using your fantastic QIIME2 doc and forum discussion, I have managed to generate rooted tree for phylogenetic diversity analyses.
Once again I have stopped by the following error message.
Error: QIIME 2 plugin ‘diversity’ has no action ‘core-metrics-phylogenetic’.
Below, please find the list of the files that I have generated as well as the command used when I tried to generate the -dir core -metrics-results.

Mode LastWriteTime Length Name

---

d----- 2017-09-28 18:33 casava-18-paired-end-demultiplexed
-a---- 2017-09-30 14:58 165320 aligned-rep-seqs.qza
-a---- 2017-07-03 18:25 3930489494 casava-18-paired-end-demultiplexed.7z
-a---- 2017-09-28 19:44 3948065745 demux-paired-end.qza
-a---- 2017-09-28 19:52 287017 demux-paired-end.qzv
-a---- 2017-09-30 15:02 154665 masked-aligned-rep-seqs.qza
-a---- 2017-09-17 15:56 119108 rep-seqs.qza
-a---- 2017-09-18 13:01 453066 rep-seqs.qzv
-a---- 2017-09-30 15:08 62518 rooted-tree.qza
-a---- 2017-09-28 19:15 565 Sample-metadata.tsv
-a---- 2017-08-14 18:34 5200429568 string
-a---- 2017-09-17 15:56 64574 table.qza
-a---- 2017-09-28 20:02 374498 table.qzv
-a---- 2017-09-30 15:06 61289 unrooted-tree.qza

docker run -t -i -v C:\Users\ha1254ke\KHH006_Analysis_V2:/data qiime2/core:2017.8 qiime diversity core-metrics-phylogenetic --i-phylogeny rooted-tree.qza --i-table table.qza --p-sampling-depth 4197 --output-dir core-metrics-results

[KEDIR_HAMZA]

But When I write the command without -Phylogenetic, I have got the following result.

docker run -t -i -v C:\Users\ha1254ke\KHH006_Analysis_V2:/data qiime2/core:2017.8 qiime diversity core-metrics --i-phylogeny rooted-tree.qza --i-table table.qza --p-sampling-depth 4197 --output-dir core-metrics-results
e[32mSaved SampleData[AlphaDiversity] to: core-metrics-results/faith_pd_vector.qzae[0m
e[32mSaved SampleData[AlphaDiversity] to: core-metrics-results/observed_otus_vector.qzae[0m
e[32mSaved SampleData[AlphaDiversity] to: core-metrics-results/shannon_vector.qzae[0m
e[32mSaved SampleData[AlphaDiversity] to: core-metrics-results/evenness_vector.qzae[0m
e[32mSaved DistanceMatrix to: core-metrics-results/unweighted_unifrac_distance_matrix.qzae[0m
e[32mSaved DistanceMatrix to: core-metrics-results/weighted_unifrac_distance_matrix.qzae[0m
e[32mSaved DistanceMatrix to: core-metrics-results/jaccard_distance_matrix.qzae[0m
e[32mSaved DistanceMatrix to: core-metrics-results/bray_curtis_distance_matrix.qzae[0m
e[32mSaved PCoAResults to: core-metrics-results/unweighted_unifrac_pcoa_results.qzae[0m
e[32mSaved PCoAResults to: core-metrics-results/weighted_unifrac_pcoa_results.qzae[0m
e[32mSaved PCoAResults to: core-metrics-results/jaccard_pcoa_results.qzae[0m
e[32mSaved PCoAResults to: core-metrics-results/bray_curtis_pcoa_results.qzae[0m

PS C:\Users\ha1254ke\KHH006_Analysis_V2> ls

Directory: C:\Users\ha1254ke\KHH006_Analysis_V2

Mode LastWriteTime Length Name

---

d----- 2017-09-28 18:33 casava-18-paired-end-demultiplexed
d----- 2017-10-02 11:20 core-metrics-results
-a---- 2017-09-30 14:58 165320 aligned-rep-seqs.qza
-a---- 2017-07-03 18:25 3930489494 casava-18-paired-end-demultiplexed.7z
-a---- 2017-09-28 19:44 3948065745 demux-paired-end.qza
-a---- 2017-09-28 19:52 287017 demux-paired-end.qzv
-a---- 2017-09-30 15:02 154665 masked-aligned-rep-seqs.qza
-a---- 2017-09-17 15:56 119108 rep-seqs.qza
-a---- 2017-09-18 13:01 453066 rep-seqs.qzv
-a---- 2017-09-30 15:08 62518 rooted-tree.qza
-a---- 2017-09-28 19:15 565 Sample-metadata.tsv
-a---- 2017-08-14 18:34 5200429568 string
-a---- 2017-09-17 15:56 64574 table.qza
-a---- 2017-09-28 20:02 374498 table.qzv
-a---- 2017-09-30 15:06 61289 unrooted-tree.qza

[KEDIR_HAMZA]

Hi again,

I think, the problem seems fixed now!
Since Qiime2 2017.9 is not yet available for windows user, I am still using 2017.8 version.
The above error message is due to the usage of new command ‘core-metrics-phylogenetic’ from Qiime2 2017.9 into the older version 2017.8. Now the problem is fixed by omitting the ’ -phylogenetic’. Hope 2017.9 version will soon be available to windows users.
Please, give me a sign if I am on the right track!!!

Thanks a lot for your unreserved support.
Best,
Kedir

[thermokarst]

Hi @KEDIR_HAMZA — you are right! core-metrics-phylogenetic was added in QIIME 2 2017.9! We are building the Virtual Machine Images as I write this message (!) - keep your eyes peeled on the release announcement - we will follow up there when those images are available. Thanks!

[KEDIR_HAMZA]

Hi @thermokarst- Okay, thanks a lot!