Aldex2 error when processing picrust2 output

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.

Good luck!

cc: @dgiguer and @gmdouglas in case you have anything to add.

2 Likes

thanks… now it can be done after rounding the numbers… but is it have no significant effects to the results?

See the topic I linked to above for relevant discussion on this. Good luck!