Hi, i have 96 interleaved fasta files of approx 9.5 GB each (Chicken fecal metagenome).
My server has 1Tb memory and 48 cpus with 12 core per socket. I have already run metaphlan.
The command i am running is
humann3 --input input_interleaved.fa --taxonomic-profile metaphlan_output.txt --output output_name --nucleotide-database path/to/chocophlan --protein-database path/to/uniref --threads 48
(i have both uniref50 and uniref90 in the database folder).
each sample is taking more than 10 days to complete. Is there a way to speed this up. or am i doing something wrong here. Running multiple commands parallel using python scripts doesn’t help either.
Metaphlan was run with CHOCOPhlan_201901 database
I am unable to figure it out.
Deeply appreciate any help