Core-metrics-phylogenetic - error report

Hi, everyone,
I got an error log of “core-metrics-phylogenetic” step.
Command lines below:
time qiime diversity core-metrics-phylogenetic
–i-phylogeny rooted-tree.qza
–i-table table.qza
–p-sampling-depth 2000
–m-metadata-file sample-metadata.tsv
–output-dir core-metrics-results

The error log listed below:
> /opt/conda/envs/qiime2-2018.8/lib/python3.5/site-packages/sklearn/utils/ DataConversionWarning: Data with input dtype float64 was converted to bool by check_pairwise_arrays.
> warnings.warn(msg, DataConversionWarning)
> Traceback (most recent call last):
> File “/opt/conda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_diversity/_alpha/”, line 46, in alpha_phylogenetic
> tree=phylogeny)
> File “/opt/conda/envs/qiime2-2018.8/lib/python3.5/site-packages/skbio/diversity/”, line 170, in alpha_diversity
> counts, otu_ids, tree, validate, single_sample=False)
> File “/opt/conda/envs/qiime2-2018.8/lib/python3.5/site-packages/skbio/diversity/alpha/”, line 136, in _setup_faith_pd
> _validate_otu_ids_and_tree(counts[0], otu_ids, tree)
> File “/opt/conda/envs/qiime2-2018.8/lib/python3.5/site-packages/skbio/diversity/”, 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=1235): 30367346d3ef5faacb273c932af1521a 1e5661205de138910d7d431f55199ba6 46e257ad64dd633dbdacdc6d06cd0f2c e454e6b6d7c5bd4c9a4101bd09190c8e 3708bd4ac07188d79db4ba8e0a62f0e3

Could you help me with that?
Actually, I run this before, it could generate the folder, and this time it is not working.
Thank you for helping me.
Best regards,

I could not see the reply from @thermokarst.
What could I do now?
Thank you for your reply, I could see the information “last reply 1h”.
Thank you.

I haven’t replied yet — please stay tuned.

Hey there @doudou2047!

This error message is telling you that 1235 features in your phylogenetic tree are not present in your feature table. This pipeline requires that the features present in both of those inputs be identical. Can you tell us a bit about these data? How did you get your tree and table? :t_rex:

Hi, @thermokarst,
Thank you so much for your reply. I tested 16S (v3-v4) data analysis for 3 young / 3 old mice fecal sample.
I totally understand your suggestion.
The problem is I did twice, so probably I using the table.qza and tree.qza from different test pipelines, I will double check that.
Here is the code I get table & tree file.
time qiime diversity alpha-rarefaction
–i-table table.qza
–i-phylogeny rooted-tree.qza
–p-max-depth 2000
–m-metadata-file sample-metadata.tsv
–o-visualization alpha-rarefaction.qzv

time qiime feature-classifier classify-sklearn
–i-classifier /home/mengq3/microbiome/qiime_Jobs/classifier-16S-341F-805R-dada2-forum-2017qiime.qza
–i-reads rep-seqs.qza
–o-classification taxonomy.qza
time qiime metadata tabulate
–m-input-file taxonomy.qza
–o-visualization taxonomy.qzv

time qiime demux summarize
–i-data paired-end-demux.qza
–o-visualization paired-end-demux.qzv
time qiime taxa barplot
–i-table table.qza
–i-taxonomy taxonomy.qza
–m-metadata-file sample-metadata.tsv
–o-visualization taxa-bar-plots.qzv

time qiime tools import
–type ‘SampleData[PairedEndSequencesWithQuality]’
–input-path pe-33-manifest
–output-path paired-end-demux.qza
–input-format PairedEndFastqManifestPhred33
time qiime quality-filter q-score
–i-demux paired-end-demux.qza
–o-filtered-sequences demux-filtered.qza
–o-filter-stats demux-filter-stats.qza
time qiime deblur denoise-16S
–i-demultiplexed-seqs demux-filtered.qza
–p-trim-length 290
–o-representative-sequences rep-seqs-deblur.qza
–o-table table-deblur.qza
–o-stats deblur-stats.qza
time qiime metadata tabulate
–m-input-file demux-filter-stats.qza
–o-visualization demux-filter-stats.qzv
time qiime deblur visualize-stats
–i-deblur-stats deblur-stats.qza
–o-visualization deblur-stats.qzv
mv rep-seqs-deblur.qza rep-seqs.qza
mv table-deblur.qza table.qza

time qiime feature-table summarize
–i-table table.qza
–o-visualization table.qzv \

time qiime feature-table tabulate-seqs
–i-data rep-seqs.qza
–o-visualization rep-seqs.qzv


time qiime alignment mafft
–i-sequences rep-seqs.qza
–o-alignment aligned-rep-seqs.qza

alignment mask

time qiime alignment mask
–i-alignment aligned-rep-seqs.qza
–o-masked-alignment masked-aligned-rep-seqs.qza
time qiime phylogeny fasttree
–i-alignment masked-aligned-rep-seqs.qza
–o-tree unrooted-tree.qza
time qiime phylogeny midpoint-root
–i-tree unrooted-tree.qza
–o-rooted-tree rooted-tree.qza

Thank you so much for your help.
And I still have a question related to trunc size and trim size, I need to ask separately, right?
Thank you.

I suspect this is the problem — mixed up input files. Let us know!

Yes please — that makes it easier (and faster) for us to reply, and much easier for other users to search and discover your questions.


This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.