Paired-end reads in MetaPhlAn3

HI @fbeghini
I have total 300 fastq.gz files from 150 samples (one forward-end and one reverse-end read each sample). I want to profile them samplwise with MetaphlAn3. I will run them using for loop. Is there any problem if I first, concatenate the forward and the reverse files of each of the sample and get 150 fastq.gz files. And, then run these 150 fastq.gz files with MetaPhlAn3?

Thanks and regards,

It would be the same as running MetaPhlAn by feeding it with a comma-separated list of file names, eventually they are sequentially piped to bowtie2