Could the humann2_split_stratified_table script simply be replace with the command:

grep -v “|” input > output

yes and no, that’s also what I used to do before discovering that script existed, but it only creates one “community-level” file, whereas the split_stratified creates 2 files : ones with only the startified read counts, and one with only non-stratified read counts (community level read counts)

Confirmed on this. You would have to use a slightly fancier grep command to isolate only the stratified rows because just grepping on | would exclude the headers. And you would need to run two greps if you wanted separate files for totals + stratified.