Hi PICRUSt community,
I am just working through the revision of my manuscript and got into PICRUSt to spice up the data analysis and discussion. However, I came across some serious (?) issue which I cannot solve despite many attempts.
I run pathway pipeline including –per_sequence_contrib function to get the ASVs contribution to the pathway function:
pathway_pipeline.py -i EC_metagenome_out/pred_metagenome_unstrat.tsv.gz \
> -o pathways_out \
> --intermediate minpath_working \
> --per_sequence_abun EC_metagenome_out/seqtab_norm.tsv.gz \
> --per_sequence_function EC_predicted.tsv.gz \
> --per_sequence_contrib \
> -p 1
In the output file (path_abun_contrib.tsv.gz) the norm_taxon_function_contrib column has roughly 90% values denoted as NAs while some of the functions seems to be calcualted completely. Could you please let me know what could be the problem? I have tried also running the pathway pipeline with the input of EC stratified file but the result was the same.
Best regards
Franek