While running the ANCOM analysis on my 16S data set I get the following error when running
qiime composition ancom --i-table Year1_ANCOM/comp_tax_level6_Year1_Merged_table.qza --m-metadata-file turf_metadata3.tsv --m-metadata-column grouping --o-visualization Year1_ANCOM/comp_tax_level6_Year1_Merged_table.qzv --verbose
/home/dcurtis/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/scipy/stats/sta ts.py:3235: RuntimeWarning: invalid value encountered in double_scalars
f = msb / msw
While qiime composition ancom does produce a result, I am curious as to the reason behind this. While searching the forums I came across this explanation. Does this apply to my data? There are low abundance features and I want to make sure I understand what is going on.
I’ve attached the .tsv output from comp_tax_level6_Year1_Merged_table.qza which has pseudocounts and the .tsv version without pseudocounts. I’ve also attached the qiime composition ancom .qzv file for your reference.
Appreciate your help troubleshooting.