core-metrics-phylogenetic error - Plugin error from diversity

Hello,

I got an error when I was running core-metrics-phylogenetic. Here are the commands and the error I got. I'm using MacBook for QIIME2. Any suggestions would be appreciated.
rooted-tree-renamed.qza (1.8 MB)
table-filtered-genus-level6.qza (904.7 KB)
Mapping_file.tsv (62.9 KB)

qiime feature-table filter-seqs --i-data representative_sequences.qza --i-table table-no-mitochondria-no-chloroplast-renamed.qza --o-filtered-data sequences-no-mitochondria-no-chloroplast-renamed.qza

qiime feature-classifier classify-sklearn \
  --i-classifier silva-138-99-515-806-nb-classifier.qza \
  --i-reads sequences-no-mitochondria-no-chloroplast-renamed.qza \
  --o-classification taxonomy-no-mitochondria-no-chloroplast.qza

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

qiime taxa collapse \
--i-table table-no-mitochondria-no-chloroplast-renamed.qza \
--i-taxonomy taxonomy-no-mitochondria-no-chloroplast.qza \
--p-level 6 \
--o-collapsed-table table-filtered-genus-level6.qza

 qiime diversity core-metrics-phylogenetic \
  --i-phylogeny rooted-tree-renamed.qza \
  --i-table table-filtered-genus-level6.qza \
  --p-sampling-depth 3000 \
  --m-metadata-file Mapping_file.tsv \
  --output-dir core-metrics-results-phylogenetic-genus-6

Plugin error from diversity:

  Command '['faithpd', '-i', '/var/folders/lz/940kw0q15cd0p1r3mm2wkpdr0000gn/T/qiime2/busihan/data/affd05ea-bb0d-4b53-b932-cdbf8f427fd1/data/feature-table.biom', '-t', '/var/folders/lz/940kw0q15cd0p1r3mm2wkpdr0000gn/T/qiime2/busihan/data/17c0e862-839f-4815-88bb-5334191bd3b0/data/tree.nwk', '-o', '/var/folders/lz/940kw0q15cd0p1r3mm2wkpdr0000gn/T/q2-AlphaDiversityFormat-afcknxpt']' returned non-zero exit status 1.

Debug info has been saved to /var/folders/lz/940kw0q15cd0p1r3mm2wkpdr0000gn/T/qiime2-q2cli-err-7301iqj2.log

1 Like

Hello!

Looks like you are trying to calculate core-metrics based on:

  • rooted tree created at the ASV level
  • feature table collapsed to genus level

Mismatched IDs will cause an error.

Unless intended, core-metrics are recommended to be calculated at ASV/OTU level.

Still, one can calculate non-phylogenetic metrics with collapsed table.

Best,

2 Likes

Thank you so much. It worked!

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