Hello, I got this message after running picrust2 full pipeline, I have matched the IDs from the input files and reached 99.9% the only mismatch is the #OTUID part
28 of 31952 ASVs were above the max NSTI cut-off of 2.0 and were removed from the downstream analyses.
Warning: fewer than half of the sequence ids overlap between the input files.
Hello @fikri,
Welcome to the forums! 
This is a warning (helpful alert/notification of possible problems), not an error (something is broken and must be fixed), so you can safely continue with analysis.
Here's a little more context:
PICRUSt2 works by comparing your ASVs to known sequence in a database.
As part of this process, it calculates the Nearest Sequenced Taxon Index (NSTI) for each ASV, which shows if the database has a close hit for this ASV making it. If there is no close matches for an ASV in the database, then the PICRUSt2 prediction might not be reliable so this ASV is filtered out of downstream PICRUSt2 predictions.
Matching 28 ASVs out of 32k ASVs is pretty good!
This is more concerning! If 99.9% match, maybe this line of the warning is wrong?
There's more discussion of this error on GitHub: The new version seems to have some problem about the --min_align option · Issue #122 · picrust/picrust2 · GitHub
Thank you for your answer, it is very helpful
This is actually just an extra line in the sample ID, so it still says 100% match but with 1 mismatch, after I checked there was indeed 1 line that didn't match, namely the #OTUID section
Hey @fikri,
Just to qiime in on this - while I'm not too familiar with using picrust2 myself, if you have any further questions, I'd recommend either reaching out to the developers of that tool or posting on the picrust google group. Here are some quick references that may be of use!
Cheers 