Alpha and beta diversity analysis plugin error from diversity feature_ids must be present as tip names

using qiime2-2019.1

When running Alpha and beta diversity analysis I received the following plugin error from diversity:

All feature_ids must be present as tip names in phylogeny. feature_ids not corresponding to tip names (n=87):

any thoughts on why I am receiving this error? I generated a tree for phylogenetic diversity analysis prior to attempting the alpha and beta analysis.

Hi @mudbugecology,

I think the error has to do with the way your tree and feature table are named. Could you describe the steps you used to get to the tree and table?

Best,
Justine

Thanks! Here is my error message: Debug info has been saved to /var/folders/6w/6zjxtzz12y5dkn40sxjg9mbm0000gn/T/qiime2-q2cli-err-zsre7t99.log

Plugin error from diversity:

All feature_ids must be present as tip names in phylogeny. feature_ids not corresponding to tip names (n=316):

I also received this error message this morning: Error: --output-dir directory already exists, won’t overwrite. so I added the various outputs as follows and still received the above error message:

(qiime2-2019.1) Kyles-MacBook-Pro:~ kyleharris$ qiime diversity core-metrics-phylogenetic --i-phylogeny /Users/kyleharris/Desktop/crayfishmicrobiome2018/rooted-tree.qza --i-table /Users/kyleharris/Desktop/crayfishmicrobiome2018/table.qza --p-sampling-depth 8000 --m-metadata-file /Users/kyleharris/Desktop/crayfishmicrobiome2018/Metadata\ ocreek\ January\ 29\ 2019.txt --o-faith-pd-vector core-metrics-results/faith-pd-vector-qza --o-unweighted-unifrac-distance-matrix core-metrics-results/unweighted-unifrac-distance-matrix.qza --o-bray-curtis-pcoa-results core-metrics-results/bray-curtis-pcoa-results.qza --o-shannon-vector core-metrics-results/shannon-vector.qza --o-rarefied-table core-metrics-results/rarefied-table.qza --o-weighted-unifrac-distance-matrix core-metrics-results/weighted-unifrac-distance-matrix.qza --o-jaccard-pcoa-results core-metrics-results/jaccard-pcoa-results.qza --o-observed-otus-vector core-metrics-results/observed-otus-vector.qza --o-weighted-unifrac-pcoa-results core-metrics-results/weighted-unifrac-pcoa-results.qza --o-jaccard-distance-matrix core-metrics-results/jaccard-distance-matrix.qza --o-evenness-vector core-metrics-results/evenness-vector.qza --o-bray-curtis-distance-matrix core-metrics-results/bray-curtis-distance-matrix.qza --o-unweighted-unifrac-pcoa-results core-metrics-results/unweighted-unifrac-pcoa-results.qza --o-unweighted-unifrac-emperor core-metrics-results/unweighted-unifrac-emperor.qzv --o-jaccard-emperor core-metrics-results/jaccard-emperor.qzv --o-bray-curtis-emperor core-metrics-results/bray-curtis-emperor.qzv --o-weighted-unifrac-emperor core-metrics-results/weighted-unifrac-emperor.qzv

Hi @mudbugecology,

The command that generated the errors is really helpful, but it doesn’t answer my question. Could you tell me which commands you used to generate your tree and table?

Best,
Justine

Kyles-MacBook-Pro:crayfishmicrobiome2018 kyleharris$ qiime demux emp-paired --m-barcodes-file /Users/kyleharris/Desktop/crayfishmicrobiome2018/metadatafile\ ocreek\ microbial\ community\ assembly\ barcode\ corrected.txt.txt --m-barcodes-column BarcodeSequence --i-seqs emp-paired-end-sequences.qza --o-per-sample-sequences demux.qza

-bash: syntax error near unexpected token `Kyles-MacBook-Pro:crayfishmicrobiome2018’

(qiime2-2018.11) Kyles-MacBook-Pro:crayfishmicrobiome2018 kyleharris$ qiime dada2 denoise-paired --i-demultiplexed-seqs demux.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 250 --p-trunc-len-r 250 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza

Saved FeatureTable[Frequency] to: table.qza

Saved FeatureData[Sequence] to: rep-seqs.qza

Saved SampleData[DADA2Stats] to: denoising-stats.qza

(qiime2-2018.11) Kyles-MacBook-Pro:crayfishmicrobiome2018 kyleharris$

(qiime2-2018.11) Kyles-MacBook-Pro:crayfishmicrobiome2018 kyleharris$ qiime feature-table summarize --i-table table.qza --o-visualization table.qzv --m-/Users/kyleharris/Desktop/crayfishmicrobiome2018/metadatafile\ ocreek\ microbial\ community\ assembly\ barcode\ corrected.txt.txt qiime feature-table tabulate-seqs --i-data rep-seqs.qza --o-visualization rep-seqs.qzv

Usage: qiime feature-table summarize [OPTIONS]

Try "qiime feature-table summarize --help" for help.

Error: no such option: --m-/Users/kyleharris/Desktop/crayfishmicrobiome2018/metadatafile ocreek microbial community assembly barcode corrected.txt.txt

(qiime2-2018.11) Kyles-MacBook-Pro:crayfishmicrobiome2018 kyleharris$

(qiime2-2018.11) Kyles-MacBook-Pro:crayfishmicrobiome2018 kyleharris$ qiime feature-table summarize --i-table table.qza --o-visualization table.qzv --m-sample-metadata-file /Users/kyleharris/Desktop/crayfishmicrobiome2018/metadatafile\ ocreek\ microbial\ community\ assembly\ barcode\ corrected.txt.txt qiime feature-table tabulate-seqs --i-data rep-seqs.qza --o-visualization rep-seqs.qzv

Usage: qiime feature-table summarize [OPTIONS]

Try "qiime feature-table summarize --help" for help.

Error: no such option: --i-data

(qiime2-2018.11) Kyles-MacBook-Pro:crayfishmicrobiome2018 kyleharris$ qiime feature-table summarize --i-table table.qza --o-visualization table.qzv --m-sample-metadata-file /Users/kyleharris/Desktop/crayfishmicrobiome2018/metadatafile\ ocreek\ microbial\ community\ assembly\ barcode\ corrected.txt.txt

Saved Visualization to: table.qzv

(qiime2-2018.11) Kyles-MacBook-Pro:crayfishmicrobiome2018 kyleharris$ qiime feature-table tabulate-seqs --i-data rep-seqs.qza --o-visualization rep-seqs.qzv

Saved Visualization to: rep-seqs.qzv

(qiime2-2018.11) Kyles-MacBook-Pro:crayfishmicrobiome2018 kyleharris$ qiime metadata tabulate --m-input-file denoising-stats.qza --o-visualization denoising-stats.qzv

Saved Visualization to: denoising-stats.qzv

(qiime2-2018.11) Kyles-MacBook-Pro:crayfishmicrobiome2018 kyleharris$

[Restored Jan 28, 2019, 10:33:32 PM]

Last login: Fri Jan 25 18:31:53 on console

Kyles-MacBook-Pro:crayfishmicrobiome2018 kyleharris$

HI @mudbugecology,

Thanks. Could you give me the commands you used to build your tree?

Best,
Justine

qiime phylogeny align-to-tree-mafft-fasttree --i-sequences rep-seqs–no-mitochondria-no-chloroplast.qza --o-alignment aligned-rep-seqs–no-mitochondria-no-chloroplast.qza --o-masked-alignment masked-aligned-rep-seqs–no-mitochondria-no-chloroplast --o-tree unrooted-tree.qza --o-rooted-tree rooted-tree.qza

thank you for looking at this, Justine!

Where did this file come from? The filename suggests that you have filtered features from these sequences --- did you forget to perform similar filtering on your feature table?

1 Like

Thank you all for the replies! Your advice helped and it worked.

1 Like

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