Mismatched feature IDs

User Support
7

Good evening!
I just finished updating my pipeline to the November release of qiime2! To be sure I repeated every step of the analysis to completely flush out all the files that were generated using the February release.

My pipeline looks like this:

  1. qiime tools import
  2. qiime cutadapt trim-paired
  3. qiime vsearch join-pairs
  4. qiime quality-filter q-score-joined
  5. qiime vsearch dereplicate-sequences
  6. importing silva as reference...
  7. qiime vsearch uchime-ref
  8. qiime feature-classifier classify-consensus-vsearch

Then I used:

  1. qiime feature-table filter-features and qiime taxa barplot
    I checked if the annotation work > it did very well! However I do not understand the filtering well. I am still trying to understand it using the docs and this answer.
  2. qiime feature-table summarize and qiime feature-table tabulate-seqs
    I have nice results, worked like a charm.
  3. qiime phylogeny align-to-tree-mafft-fasttree
    I get my rooted, unrooted tree and also the alingment and masked alignment.

However when I call:

qiime diversity core-metrics-phylogenetic
--i-table out5-derep-filtered_table.qza
--i-phylogeny out5-derep-seq_rooted-tree.qza
--p-sampling-depth 50000 \ (checked this with the exported table)
--m-metadata-file metadata_sheet.tsv
--p-n-jobs 16
--output-dir core-metrics-phylogenetic-output

Now I get the same error as earlier. I export the rooted tree (qiime tools export) and again the feature_ids were appended with the filenames. So at some point I must have made a mistake.

I will try to figure it out on my own, but I am thankful for every hint I can get! The update did not change the problem I have. I think that I made a mistake somewhere.

Thank you!

P.S.: Here is the errorlog:

/usr/appli/freeware/miniconda/3.6/envs/qiime2-2018.11/lib/python3.5/site-packages/sklearn/utils/validation.py:475
: DataConversionWarning: Data with input dtype float64 was converted to bool by check_pairwise_arrays.
warnings.warn(msg, DataConversionWarning)
Traceback (most recent call last):
File "/usr/appli/freeware/miniconda/3.6/envs/qiime2-2018.11/lib/python3.5/site-packages/q2_diversity/_alpha/_me
thod.py", line 46, in alpha_phylogenetic
tree=phylogeny)
File "/usr/appli/freeware/miniconda/3.6/envs/qiime2-2018.11/lib/python3.5/site-packages/skbio/diversity/driver
.py", line 170, in alpha_diversity
counts, otu_ids, tree, validate, single_sample=False)
File "/usr/appli/freeware/miniconda/3.6/envs/qiime2-2018.11/lib/python3.5/site-packages/skbio/diversity/alpha/
faith_pd.py", line 136, in _setup_faith_pd
_validate_otu_ids_and_tree(counts[0], otu_ids, tree)
File "/usr/appli/freeware/miniconda/3.6/envs/qiime2-2018.11/lib/python3.5/site-packages/skbio/diversity/_util.p
y", line 104, in _validate_otu_ids_and_tree
" ".join(missing_tip_names)))
skbio.tree._exception.MissingNodeError: All otu_ids must be present as tip names in tree. otu_ids not
corresponding to tip names (n=20624): c4446b4a7ecb9ecca5747fe65dd9c941f21c4a37 [and another20.000 features]