Meaning of 'Processed Reads' in Metaphlan4


I have a question related to Metaphlan’ output:

At the top of every .txt files, there’s three lines of commentaries beginning with #. One of them tell us the database used, the next one is the command line, but the final one give the number of “reads processed”.

#1311986 reads processed

I know Metaphlan give relative abundances for each clades. What are those lines resuming ? I couldn’t find information about it online, or in the questions here, so I was left wondering:

  • is it stricly the number of reads that have a match in the database ?
  • is it the number of reads that Metaphlan used for its statistics, whether or not they are counted as contaminant ?
  • something else entirely ?

So, more simply put, my question is: What is the definition of “reads processed” in the context of Metaphlan ?

Thank you and regards,