From metagenome whole shotgun sequencing (*fastq.gz) to generate count matrix table

I wanted to use MSPminer, which needs a tab-separated values matrix giving the number of reads mapped on genes (rows) across metagenomic samples (columns). ((namely count table))

Recently, I used metawibele, a software also helping preprocessing the fastq.gz files, but the program frequently crushing in the ”prokka” step.
Then I tried to use NGLess from embl to generate that count matrix, but I only got the single colum table according the human-gut.ngl (predefined pipeline)……..I think I have to modified the script from NGLess, but didn’t know how.

I am not familiar with metagenomic WGS data (I used to deal with 16S amplicon data), and don’t know how to generate the count table required by MSPminer.