alpha diversity error

(qiime2-2019.7) [email protected]:~/Desktop/Libraries/Final results for 16S rRNA NaCl.SeaSalt/NaCl12and46/ABCD/Phylogeny$ qiime diversity core-metrics-phylogenetic --i-phylogeny rooted-tree.qza --i-table mergedtableLibABCD.qza --p-sampling-depth 1000 --m-metadata-file metadata2.tsv --output-dir core-metrics-results
Plugin error from diversity:

All feature_ids must be present as tip names in phylogeny. feature_ids not corresponding to tip names (n=541): 7d6a0a97fdf3bf604ac4eef397095b43 879daee9b2b08b7d81ee23da66e35140 b33a982eed43e1331c5e596a35f8b70a 83981b6101859ffe9f1e6311f1d7460a fd46b77358c7789df0c84cd05c5cb64f 5f766bda02a43aab220230b6557183b3 c6a89edad2d0b8c4415ef2ca190ee63d 0f514829eeecdb476673c4fc963d7000 fee569b038475af5a1571e4b58c86b37 522663145f8c9628686890dfebc1b7b2 5537eb7f5c276522553e442e0708442c 20c5931e41677ae6fd0f95cd74ce1a0c a74d17459ca789428dd194c3af0d9ca5 1ef5dd933525af2d23cf96dc67cf0428 bc0a022d2cb1428476cf7641d524113e 6f17ecebcc3e4623fe3358f0b15e0a5a 7ecb36c8dfcf9b00bcb300a7a22584cd cb2b271bb980cfeb4b805b6784a62496 25e4459cab8ab5545ecaa30726772363 ff411135fccfac7e26c7bdac57af69dc f4fc98746b739f61fd708a9a79d52242 edfd7bd0c132dc83bf2677cd74475cd2 104da31bc577ab419b52874a5b04e081 5c7f60f6b159f6d4804e04f06546192f e307f8ae5b3c8bf9c1c500e58c07afa7 98ab60243e0a637b38d3e8ce0e122e6b ea42f5a1d8b4cc2d4fbc4a70a82f0b76 2fa8f9bbb86469bdd813eabd9b4f8b39 c65134a3ab14ae9164b9fefdecd2f544 ab87e71ba6fffb4b887e380df92cc717 abbce5fe324863e1cf9b9d55c5c293f5 39cb9a625b3def1b7c149ce99ffb9624 15cd6eca3f677001b34fda8bda5ebbbf 932439ed05bc7f75b0e882396605db20 bfe946e4036b50aa0cb6aa690b5a7ea7 adc0661412bb5032827139d36413fd04 d1225c1c41002f226e114b2e11d01209 0564b8a36f8b0070bbb3d8a022e51a5f 4129b82cbdf8f171013f946829c216d4 1a8814db6269cddb695f653e5070bed8 c6cf29a84b4d637078f14dcb02015ea5 b617d97f78baac41ffa22c9eb53731e6 ee728fd6cd6f96df73df1e1ba31ee407 80ecb16b1542f846bafe54b2108485d0 a65adf61c1b1c0dd8739345de5533c5b ee793bb9eee4739f91c3affd7d651d9d 1d19b818c8f8c8ff5b8516688e0a1a97 14a246f7442968bdbe227cc08737fc3c 273c57a2472503d06b19a78cc2ee5f6c 2cc214f26d97eb3d8f8bfdb629910dcf 3b812adfbbc4c80d72e4fef20491c5ba 2cb587c3e65b3d0fba6cdc351df17375 532ee516e3501fb1a8abccca43feae29 5fc378819d4ccd0681cb9bac400fbb83 ae234c7395ee78f86cbed80175bdc175 8903cfa93013fe2c704e97b8cede4f8b f3958b61831277504dfcb6b57870da81 786da3a55f780954c11f5790a1a50896 5

could you please to help me to find the error reason?


Hi @TurboQiimer,

It looks like you have a mismatch between your tree and your table. Could you please send the commands you used to generate your table and your tree?


Thanks Justine to reply,
Yes, there you go.

qiime phylogeny align-to-tree-mafft-fasttree
–i-sequences seqs.qza
–o-alignment aligned-rep-seqs.qza
–o-masked-alignment masked-aligned-rep-seqs.qza
–o-tree unrooted-tree.qza
–o-rooted-tree rooted-tree.qza

I think the issue does not lie in this step.

By the way, before the error above I got this error:
(qiime2-2019.7) [email protected]:~/Desktop/Libraries/Final results for 16S rRNA NaCl.SeaSalt/NaCl12and46/ABCD/Phylogeny$ qiime diversity core-metrics-phylogenetic \

–i-phylogeny rooted-tree.qza
–i-table mergedtableLibABCD.qza
–p-sampling-depth 10000
–m-metadata-file metadata.tsv
–output-dir core-metrics-results
Plugin error from diversity:

None of the sample identifiers match between the metadata and the coordinates. Verify that you are using metadata and coordinates corresponding to the same dataset.

Then I tried to change metadata IDs to match. It showed the error i sent to this thread at first. I merged four libraries to each other, made one, then I want to rarefy the joint library (four libraries in a merged table). Should it be problematic? If yes, how to solve it? or I need to rarefy each table individually (before merging)?

mergedtableLibABCD.qza (564.0 KB) metadata.tsv (3.1 KB) mergedtableLibABCD.qza (564.0 KB) metadata.tsv (3.1 KB)

I wanted to share my merged table and metadata files with you, maybe help how to fix the error.

Hi @TurboQiimer,

The issue comes from not having your feature and feature-ids line up. This either means that you built your tree using the wrong rep set or that you somehow filtered your repset before you made the tree. So, I think your tree would also be helpful here.

The metadata mismatch is a different error due to a different mechanism. Let’s solve the tree first then worry about the metadata.


wow … thanks a lot. You reminded me something. I have filtered and merged as well as grouped my libraries.
But beside my seq filtration, I have filtered the table as well. I mean filtered seq and table at the same time. Did you mean they do not match each other; however, both filtered (I have no clue they influence each other while they be filtered from the same stuff)?
Now, do I have to work with my non-manipulated seq-rep? If yes and the issue is that, how about the unassigned taxa which I removed already? They will affect on m result if I use the unmodified seq-rep. Do you have any suggestion?

Thanks for the time


Hi @TurboQiimer,

My suggestion would be to build your tree before filtering. It might take a little bit longer, but at least you’ll know all the sequences are there. Every ASV in your table must be in your tree, but not every tip in your tree has to be in your table.

So, I guess my suggestion there would be to just work with the unfiltered data.


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