No pathways identified after HUMAnN


I have shotgun metagenomic data and ran HUMAnN on it. After tweaking with available protein and nucleotide databases, I was able to get “Gene families and their abundance” table showing a lot identified genes (code mentioned at the end). However, “pathways and their abundance” table does not show any pathways (screenshot attached).

My questions:

  1. Is it normal to have only gene families and no pathways? Should I fix something?
  2. Is it reasonable to take only gene families and go through with the downstream analyses?
  3. Is it possible to use the gene families (GO:terms and their abudances) and construct the pathways using some other tools?

code for humann:

humann --input '/data/dnb09/galaxy_db/files/3/8/b/dataset_38b82fd0-9435-4483-9b72-870fb08df232.dat' --input-format fasta -o 'output' --bypass-prescreen  --nucleotide-database '/data/db/data_managers/humann/data/nucleotide_database/chocophlan-full-3.6.0-29032023' --nucleotide-identity-threshold 0.0 --nucleotide-subject-coverage-threshold 50.0 --nucleotide-query-coverage-threshold 90.0   --translated-alignment 'diamond' --protein-database '/data/db/data_managers/humann/data/protein_database/uniref-uniref90_diamond-3.0.0-13052021' --search-mode 'uniref90' --evalue 1.0 --translated-subject-coverage-threshold 50.0 --translated-query-coverage-threshold 90.0  --gap-fill 'on' --minpath 'on' --pathways 'metacyc' --xipe 'off' --annotation-gene-index 3 --log-level 'DEBUG' --o-log '/data/jwd05e/main/067/779/67779456/outputs/dataset_f849d124-f8cf-4bd9-93af-440aa2e0f1f7.dat' --output-basename 'humann' --output-format 'tsv' --output-max-decimals 10   --threads "${GALAXY_SLOTS:-4}" --memory-use minimum