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/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 “/opt/conda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_diversity/_alpha/_method.py”, line 46, in alpha_phylogenetic
> tree=phylogeny)
> File “/opt/conda/envs/qiime2-2018.8/lib/python3.5/site-packages/skbio/diversity/_driver.py”, 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/_faith_pd.py”, 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/_util.py”, 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,
Q
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?
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
