Trouble with Arguments and Time it Takes to Make Tree

Microbial community profiling PhyloPhlAn
1

Hello, I recently started using PhyloPhlAn. I have 500 strains of interest that I want to make the tree with. To do so I uploaded the nucelotide WGS sequences for them, and ran PhyloPhlAn.

phylophlan \
    -i key_genomes\
    -d phylophlan \
    -f supertree_aa.cfg \
    --force_nucleotides \
    --diversity high \
    --accurate \
    -o phylophlan_output\
    --nproc 32\
    --verbose \
    --maas phylophlan.tsv
    2>&1 | tee logs/phylophlan.log

I added the --maas as troubleshooting board reccomended this. It is now day 3 and lines are being generated with different versions of this

"Refining gene tree "phylophlan key_genomes/tmp/trim_not_variant/p0318.aln" "p0101.tre" generated in 9444s"

I have two major concerns:

1. Did I specify the right arguments given that I have 500 nucleotide genomes? If not what corrections do I need, I kept on getting errors until I used the above code. I recognzie PhyloPhlAn tends to take in a proteomic upload, so its this the cause of the issue?
2. Is the 3-4 days time window to be expected? I’m concerned about it running for a while on errenous arguments and that’s why it’s taking so long, I have 32CPU dedciated per the code for refernece.