Hi, I'm trying to do downstream analysis of picrust2 ouput with aldex2 in qiime2-2019.7 on linux, but have error from this command:
qiime aldex2 aldex2
--i-table q2-picrust2_output/pathway_abundance.qza
--m-metadata-file metadata.tsv
--m-metadata-column Type
--output-dir q2-picrust2_output/aldex2_pathabun
the error log is this:
[1] "aldex.clr: generating Monte-Carlo instances and clr values"
[1] "operating in serial mode"
Error in aldex.clr.function(as.data.frame(reads), conds, mc.samples, denom, :
not all reads are integers
Calls: aldex -> aldex.clr -> aldex.clr -> aldex.clr.function
Execution halted
Complete error log:aldex2_error_1.txt (2.4 KB)
But no error if the input is the asv feature table.
Thanks.
Hi @didietkeren,
I have moved this topic to "community plugin support" because it concerns q2-picrust2 and q2-aldex2, both of which are community plugins.
The error message is quite clear:
aldex2 is looking for integer counts, but picrust2 can output non-integer values as described here:
This is why an ASV table works (all values are integers) but picrust2 output does not. Looks like you will need to round those results somehow before passing to aldex2.