Dear All,
thanks in advance for your attention and help.
I merged my samples batch following the FMT tutorial and using a tex tool to make a new samples-metadata.tsv
I first run the qiime phylogeny align-to-tree-mafft-fasttree and everything worked well.
Then, I run the qiime diversity core-metrics-phylogenetic and I received the following error:
Plugin error from diversity:
All feature_ids must be present as tip names in phylogeny. feature_ids not corresponding to tip names (n=342): d64ae243450f88d63658c28c3a7ec5b (more features id)
Debug info has been saved to /scratch_local/slurm_job.4876860/qiime2-q2cli-err-20taa38n.log
May I lost some features in the merging process?
Can anyone understand how to overcome this issue and what does cause it?
You should not have lost ant features after the merging.
Just to double-check few points, did you use the same denoising parameters for both runs?
Did you use the merged sequence file for the align-to-tree-mafft-fastree step?
Did you filter the table/sequences before the diversity analysis?
Dear Luca,
thank you very much for your reply.
Following the FMT tutorial I merged the rep-seqs as follow:
qiime feature-table merge
--i-tables table-1.qza
--i-tables table-2.qza
--o-merged-table table.qza
qiime feature-table merge-seqs
--i-data rep-seqs-1.qza
--i-data rep-seqs-2.qza
--o-merged-data rep-seqs.qza
then I have used the output to make the phylogeny
qiime phylogeny align-to-tree-mafft-fasttree
--i-sequences rep-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
