Plugin error from diversity

Hello,

so I got this after running the command:

(qiime2-2017.7) mpbair:~ mpb$ qiime diversity core-metrics --i-phylogeny /rooted-tree.qza  --i-table /otu.table2.silva.filtered.qza --p-sampling-depth 7500 --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=1923): Otu1386
  Otu373 Otu1585 Otu285 Otu1805 Otu2030 Otu1818 Otu1159........

So, the biom table was imported from a qiime1-generated bio file, with no errors. I did a back-export from the .qza to a boom file an then to tab file and the many Otus listed in the error look fine in the table. To generate the tree I actually used qiime2, I imported the fasta file of the OTUs, (I looked dat the headers and are identical to those in the table), did the alignment, masking, unrooted then rooted tree according to the scripts in the tutorial, with no errors. I feels its something to do with the import from the qiime1 boom table (what else could it be?), but I can’t find any differences in the sequence names, and the error refers to n=1923, there are about 2500 OTUs, so some are fine? Thank you in advance for any suggestions!
Mircea Podar

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Hi @mpodar — that error means that your rooted-tree is missing features that are present in your feature table. It might be useful to use feature-table summarize (the third tab, ‘Feature Detail’) and feature-table tabulate-seqs to investigate these data and understand what is going on with your Feature IDs. It looks like you have a filtered dataset you are using in your commands — is it possible you mixed some of these files up while processing? You can try using provenance to help unravel that, if you wish. If those options don’t help, maybe you could share some of the commands that you ran? Thanks!

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Thanks Matthew

no luck yet. I exported the unrooted tree and verified the branches, those taxa are there. They are also there in the biom table after exporting the qza table file. The feature-table plugins you suggested didnt work for me, tried a few options but getting errors like

(qiime2-2017.7) mpbair:~ mpb$ qiime feature-table tabulate-seqs  --i-data /masked-aligned-rep-seqs.qza     --o-visualization /out

Plugin error from feature-table:

  Argument to parameter 'data' is not a subtype of
  FeatureData[Sequence].


The commands I used to generate the various files were:

(qiime2-2017.7) mpbair:~ mpb$ qiime tools import --input-path /otu.table2.silva.filtered.biom --source-format BIOMV210Format --type 'FeatureTable[Frequency]' --output-path /qiime2/otu.table2.silva.filtered.qza

(qiime2-2017.7) mpbair:~ mpb$ qiime tools import  --input-path /qiime2/combined.usf.filt.uniques.denoised_filtered.fna  --output-path /qiime2/combined.usf.filt.uniques.denoised_filtered.qza  --type 'FeatureData[Sequence]'

(qiime2-2017.7) mpbair:~ mpb$ qiime alignment mafft  --i-sequences /qiime2/combined.usf.filt.uniques.denoised_filtered.qza --o-alignment /qiime2/aligned-rep-seqs.qza

(qiime2-2017.7) mpbair:~ mpb$ qiime alignment mask --i-alignment /qiime2/aligned-rep-seqs.qza --o-masked-alignment /qiime2/masked-aligned-rep-seqs.qza

(qiime2-2017.7) mpbair:~ mpb$ qiime phylogeny fasttree --i-alignment /qiime2/masked-aligned-rep-seqs.qza  --o-tree /qiime2/unrooted-tree.qza

(qiime2-2017.7) mpbair:~ mpb$ qiime phylogeny midpoint-root --i-tree /qiime2/unrooted-tree.qza --o-rooted-tree /qiime2/rooted-tree.qza

Thanks!

Mircea

Thanks for the commands @mpodar!

Can you try feature-table tabulate-seqs on the file quoted above? Then you should be able to compare the Feature IDs between you original imported sequences and your original imported feature table!
Thanks!

I did that. The number of sequences is the same between the biom file and the fasta file. The header of the otus is not identical though, in the biome file is

#OTU ID
Otu1
Otu2
etc

In the seq file its

Otu1;uniq=Uniq1;size=462692;
Otu2;uniq=Uniq2;size=265683;

Could that be the issue?

Thanks

Mircea

Yep, looks like we are on the same page!

Your Feature IDs need to be the same in the Feature Table and in your sequences, otherwise these identifiers look completely different when QIIME 2 is working with these data.

It is probably easier to update your sequences to match the feature table’s IDs, but I could be wrong. Let us know if you need some help coming up with a strategy to make this happen!

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