# What to do about a single non-corresponding tree tip?
**URL:** https://forum.qiime2.org/t/what-to-do-about-a-single-non-corresponding-tree-tip/5364
**Category:** User Support
**Tags:** taxonomy, diversity, tree, feature-table
**Created:** [August 1, 2018, 4:37pm UTC](https://forum.qiime2.org/t/what-to-do-about-a-single-non-corresponding-tree-tip/5364 "2018-08-01T16:37:50Z")
**Posts on this page:** 7
**Page:** 1
### Author:  [@EmerickL](https://forum.qiime2.org/u/EmerickL)
#### Post date: [August 1, 2018, 4:37pm UTC](https://forum.qiime2.org/t/what-to-do-about-a-single-non-corresponding-tree-tip/5364/1 "2018-08-01T16:37:50Z")
Greetings Qiime community, I typically do analysis in R after classification, tree building and BIOM exporting but am giving QIIME2's other features a go.
I am starting with alpha and beta diversity metrics but have run into the following error:
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All `feature_ids` must be present as tip names in `phylogeny`. `feature_ids` not corresponding to tip names (n=1): 429b5b12899efa00c5d61dc11c424c7f
* * *
I could not find this feature ID in my table.qza after performing a search.
I am not sure how to remedy this. My next approach was to go into the tree.nwk, which is upstream in the pipeline of the midpoint rTree (rooted-tree-filtered.qza) being used in the diversity commands. I opened the .nwk in a text editor and searched there. Still didnt find this missing tip/feature ID.
Here are the scripts I'm running on my University's cluster.
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**Import:**
```
# ----------------Load Modules--------------------
module load qiime2/2018.4
# ----------------Housekeeping---------------------
#rm -r demux*.q*
cd data
# ----------------Commands------------------------
#Import Data in qiime2 artifact
qiime tools import \
--type 'SampleData[PairedEndSequencesWithQuality]' \
--input-path /ufrc/strauss/emerickl/WCT/data/raw_data \
--source-format CasavaOneEightSingleLanePerSampleDirFmt \
--output-path demux-paired-end.qza
qiime demux summarize \
--i-data demux-paired-end.qza \
--o-visualization demux-paired-end.qzv
```
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**DADA**
```
cp data/demux-paired-end.qza features/dada2input.qza
qiime dada2 denoise-paired \
--i-demultiplexed-seqs dada2input.qza \
--output-dir output \
--p-n-threads 14 \
--o-table table.qza \
--o-representative-sequences rep-seqs.qza \
--p-trunc-len-f 251 --p-trunc-len-r 250
```
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**Feature table**
```
qiime feature-table summarize \
--i-table table.qza \
--o-visualization table.qzv \
--m-sample-metadata-file #PATH TO VALIDATED MAPPING FILE
qiime feature-table tabulate-seqs \
--i-data rep-seqs.qza \
--o-visualization rep-seqs.qzv
qiime diversity alpha-rarefaction \
--i-table table.qza \
--o-visualization alpha-rarefaction.qzv \
--p-max-depth 8200
--p-metrics chao1,simpson,shannon
--m-metadata-file #PATH TO VALIDATED MAPPING FILE
```
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**Taxonomy** (classifier trainer at bottom)
```
qiime feature-classifier classify-sklearn \
--i-reads rep-seqs.qza \
--o-classification taxonomy.qza \
--i-classifier /ufrc/strauss/emerickl/SILVA_nb_99_V3-V4.qza
qiime metadata tabulate \
--m-input-file taxonomy.qza \
--o-visualization taxonomy.qzv
qiime taxa barplot \
--i-table table.qza \
--i-taxonomy taxonomy.qza \
--o-visualization taxa-bar-plots.qzv \
--m-metadata-file WCTmetaData.tsv
```
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**BIOM export and other stuff**
```
qiime tools export \
table.qza \
--output-dir ../biom
qiime tools export \
taxonomy.qza \
--output-dir ../biom
module load qiime/1.9.1
cd ../biom
biom convert \
-i feature-table.biom \
-o feature-json.biom \
--table-type="OTU table" \
--to-json
sed -i s/Taxon/taxonomy/ taxonomy.tsv | sed -i s/Feature\ ID/FeatureID/ taxonomy.tsv
biom add-metadata \
-i feature-json.biom \
-o feature_w_tax.biom \
--observation-metadata-fp taxonomy.tsv \
--observation-header FeatureID,taxonomy,Confidence \
--sc-separated taxonomy --float-fields Confidence
filter_samples_from_otu_table.py \
-i feature_w_tax.biom \
-o filtered-table.biom \
-n 5000 #Pay attention to this number, change it according to the table visualization
filter_taxa_from_otu_table.py \
-i filtered-table.biom \
-o table_wo_chl_mit.biom \
-n D_2 __Chloroplast,D_4__ Mitochondria
normalize_table.py \
-i table_wo_chl_mit.biom \
-a DESeq2 \
--DESeq_negatives_to_zero \
-o DESeq2_table.biom
biom add-metadata \
-i DESeq2_table.biom \
-o DESeq2_w_tax.biom \
--observation-metadata-fp taxonomy.tsv \
--observation-header FeatureID,taxonomy,Confidence \
--sc-separated taxonomy --float-fields Confidence
normalize_table.py \
-i table_wo_chl_mit.biom \
-a CSS \
-o CSS_table.biom
biom convert \
-i table_wo_chl_mit.biom \
-o feature-table.tsv \
--to-tsv \
--table-type "OTU table"
sed -i s/"#OTU ID"/FeatureID/ feature-table.tsv
sed -i '1d' feature-table.tsv
```
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**Build Trees**
```
qiime feature-table filter-seqs \
--i-data ../features/rep-seqs.qza \
--m-metadata-file feature-table.tsv \
--p-no-exclude-ids \
--o-filtered-data rep-seqs-filtered.qza
qiime alignment mafft \
--i-sequences rep-seqs-filtered.qza \
--p-n-threads 12 \
--o-alignment aligned-rep-seqs-filtered.qza
qiime alignment mask \
--i-alignment aligned-rep-seqs-filtered.qza \
--o-masked-alignment masked-aligned-rep-seqs-filtered.qza
qiime phylogeny fasttree \
--i-alignment masked-aligned-rep-seqs-filtered.qza \
--o-tree unrooted-tree-filtered.qza
qiime phylogeny midpoint-root \
--i-tree unrooted-tree-filtered.qza \
--o-rooted-tree rooted-tree-filtered.qza
qiime tools export \
rooted-tree-filtered.qza \
--output-dir .
```
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**SciKit train**
```
qiime tools import \
--type 'FeatureData[Sequence]' \
--input-path SILVA_132_QIIME_release/rep_set/rep_set_16S_only/99/silva_132_99_16S.fa \
--output-path SILVA_132_99_otus.qza
qiime tools import \
--type 'FeatureData[Taxonomy]' \
--source-format HeaderlessTSVTaxonomyFormat \
--input-path SILVA_132_QIIME_release/taxonomy/16S_only/99/consensus_taxonomy_7_levels.txt \
--output-path SILVA_132_99_tax.qza
qiime feature-classifier extract-reads \
--i-sequences SILVA_132_99_otus.qza \
--p-f-primer GTGYCAGCMGCCGCGGTAA \
--p-r-primer GGACTACNVGGGTWTCTAAT \
--p-trunc-len 300 \
--o-reads SILVA_132_99_otus_515-926.qza
qiime feature-classifier fit-classifier-naive-bayes \
--i-reference-reads SILVA_132_99_otus_515-926.qza \
--i-reference-taxonomy SILVA_132_99_tax.qza \
--o-classifier SILVA_nb_99_V3-V4.qza
```
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---
### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [August 1, 2018, 4:42pm UTC](https://forum.qiime2.org/t/what-to-do-about-a-single-non-corresponding-tree-tip/5364/2 "2018-08-01T16:42:26Z")
---
### Author:  [@EmerickL](https://forum.qiime2.org/u/EmerickL)
#### Post date: [August 3, 2018, 1:14am UTC](https://forum.qiime2.org/t/what-to-do-about-a-single-non-corresponding-tree-tip/5364/3 "2018-08-03T01:14:48Z")
I wasnt sure how to search for the id directly in the feature\_table.BIOM inside the table.qza compressed archive, so I converted it to a .tsv and still did not find this missing id.
---
### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [August 3, 2018, 4:28am UTC](https://forum.qiime2.org/t/what-to-do-about-a-single-non-corresponding-tree-tip/5364/4 "2018-08-03T04:28:36Z")
> [@EmerickL](#):
>
> --i-data ../features/rep-seqs.qza
Where is this file coming from? This looks different than the `--o-representative-sequences rep-seqs.qza` from your DADA2 step. Did you filter these seqs? If so, then your tree will be constructed using fewer features than your table, which would clarify the cause of this error message. You can [filter your table](https://docs.qiime2.org/2018.6/tutorials/filtering/#filtering-feature-tables) down to match the features present in your rep-seqs.
---
### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [August 3, 2018, 4:28am UTC](https://forum.qiime2.org/t/what-to-do-about-a-single-non-corresponding-tree-tip/5364/5 "2018-08-03T04:28:45Z")
---
### Author:  [@EmerickL](https://forum.qiime2.org/u/EmerickL)
#### Post date: [August 3, 2018, 1:20pm UTC](https://forum.qiime2.org/t/what-to-do-about-a-single-non-corresponding-tree-tip/5364/6 "2018-08-03T13:20:27Z")
I ran:
```
qiime feature-table filter-features \
--i-table features/table.qza \
--m-metadata-file biom/feature-table.tsv \
--o-filtered-table filtered-table.qza
```
after making sure featuretable.tsv (extracted from the table.qza) didnt have the 1 feature id not in the tree, I was able to successfully run:
```
qiime diversity core-metrics-phylogenetic \
--i-phylogeny biom/rooted-tree-filtered.qza \
--i-table features/table.qza \
--p-sampling-depth 5590 \
--m-metadata-file features/WCTmetaDataQ2.tsv \
--output-dir core-metrics-results
```
---
### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [September 3, 2018, 7:28pm UTC](https://forum.qiime2.org/t/what-to-do-about-a-single-non-corresponding-tree-tip/5364/7 "2018-09-03T19:28:10Z")
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