I am following : Analyses of metagenomics data - The global picture
But I stuck on HUMAnN2 input sequence file step
I dont know which file i need to upload?SAM File or FASTA File?
Agree, that part is a bit confusing! This step uses the same input file as the prior step. So, scroll up a bit in the tutorial to the prior Data Upload step to find it. It is probably already loaded in your history if you are following the full tutorial.
Right now, that file is exactly this one.
https://zenodo.org/record/815875/files/SRR606451_pampa.fasta
warning for others reading: which file to use at any step, in any tutorial, can change over time. So, double check against the tutorial you are following for the exact data to use 
Hope that helps!