PICRUST2 output

[Anandi Batabyal]

Hi users,

I am new to PICRUST2. I have used the picrust2_pipeline.py. My script is as follows:

picrust2_pipeline.py \
  -s cleaned_aligned-dna-sequences.fasta \
  -i feature-table.biom \
  -o picrust2_out_pipeline/output \
  -p 8

In my output file, this appears: 

Warning: There was only one file for the function: KO
Maybe that's fine if you used custom traits or there were no sequences matching one of the domains.
Warning: There was only one file for the function: EC
Maybe that's fine if you used custom traits or there were no sequences matching one of the domains.
All ASVs were below the max NSTI cut-off of 2.0 and so all were retained for downstream analyses.

All ASVs were below the max NSTI cut-off of 2.0 and so all were retained for downstream analyses.

Can someone please let me know how to handle the issue of having just one file retained for KO and EC functions?

Thanks in advance,

Anandi
 

-p 8 #--verbose

[Robyn Wright]

Hi Anandi,

That output is basically telling you that all of your sequences were either bacteria or archaea - I don't know which 16S region you have sequenced, but this is most likely fine. Again, I don't know your study, but I would guess that you have only bacteria in your sequences and this is just warning you that there wasn't a second file found for archaea. Unless you were expecting to have both bacteria and archaea in your study sequences, this is fine and you can ignore the warnings. 

Best wishes,

Robyn

[Anandi Batabyal]

Thanks so much! I appreciate it. 

Best,

Anandi