Humann3 intermediate output file (sam) for strainphlan

Hi all, I ran humann3 in the following manner:

humann3 --input “$0” --output “$1”_humann3_out --input-format fastq --nucleotide-database /data/databases/Humann3/chocophlan/ --protein-database /data/databases/Humann3/uniref/ --diamond /install/software/anaconda3.6.a/bin/ --metaphlan /install/software/mincondas/3.7/instance2/bin/metaphlan --metaphlan-options “–bowtie2db /data/databases/MetaPhlAn3/ --index mpa_v30_CHOCOPhlAn_201901” --search-mode uniref90 --threads 9 --memory-use maximum"

The intermediate output folder thus formed has an aligned sam file. Can this file be used to produce consensus marker sequences and run strainphlan? Or will I have to run metaphlan again as described in the tutorial and generate a sam file and run strainphlan? Will these 2 files be different?

Apologies for the basic question, any help would be appreciated.
Thank you