Gneiss ZeroDivisionError

Hello all!

I have been attempting to learn more about Gneiss, and apply it to my own project. However, I have run into an error while attempting to do so. I have attached the log file that reports the error, and my code is written below.

qiime gneiss add-pseudocount \
  --i-table table10.qza \
  --p-pseudocount 1 \
  --o-composition-table GWG_Gneiss/composition.qza
qiime gneiss correlation-clustering \
  --i-table GWG_Gneiss/composition.qza \
  --o-clustering GWG_Gneiss/hierarchy.qza
qiime gneiss ilr-transform \
  --i-table GWG_Gneiss/composition.qza \
  --i-tree GWG_Gneiss/hierarchy.qza \
  --o-balances GWG_Gneiss/balances.qza
qiime gneiss ols-regression \
  --p-formula "GWG_Category" \
  --i-table GWG_Gneiss/balances.qza \
  --i-tree GWG_Gneiss/hierarchy.qza \
  --m-metadata-file GWG_metadata.tsv \
  --o-visualization GWG_Gneiss/regression_summary.qzv
qiime gneiss dendrogram-heatmap \
  --i-table GWG_Gneiss/composition.qza \
  --i-tree GWG_Gneiss/hierarchy.qza \
  --m-metadata-file GWG_metadata.tsv \
  --m-metadata-category GWG_Category \
  --p-color-map seismic \
  --o-visualization GWG_Gneiss/heatmap.qzv

Gneiss_Error.txt (2.4 KB)

I ran a similar simple regression using a different variable, but I did not get any errors from that run, so I am quite confused by this. Any help is much appreciated!

  • Sirtaj Singh

@Sirtaj-Singh can you print out some of the dimensions of your tables?
Looking at the error messages, you may be feeding in an empty table.

@mortonjt do you mean the dimensions of my metadata file? It should have 318 rows (one for each sample), and 2655 columns. Furthermore, there are no NA or empty values for the covariate of interest (GWG_Category).

Ok - how have you FeatureTable? How many samples are in there?

Could you upload you qza files so that we could reproduce this error?

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