Missing samples in PICRUSt2 output files


I am new to PICRUSt2 analysis. After completing the pipeline and observing the predictive results in the output folder, particularly the EC_metagenome_out/pred_metagenome_contrib.tsv file - I found that most of my samples are missing from the output file.

I have a total of 56 samples in my dataset (.biom file) - I can see predictive results for only 16 of my samples. Has this happened to anybody else? How can I fix this? I wonder if I am missing out on something really important?

I followed the tutorial from Github. While performing the pipeline on command line, I also got a note that all of my samples had no noise (NSTI <2.0) and hence retained for analysis. I am not sure if this is related to the final output in any way, but just thought of mentioning it, if that helps anybody decode what might be going on here.

I eagerly look forward to advice and input on this at the earliest. I am trying to put my results together for an upcoming manuscript.

Thank you so much in advance.

Best wishes,