Zero community-level pathways detected despite gene families present

Microbial community profiling HUMAnN
1

Hi,

I’m running HUMAnN 3.9 on my samples and want to confirm my understanding of the pathway output on five of the samples.

My command:

humann \
	-i "${local_work_dir}/${base}"_host_rm_combined.fq.gz \
	-o ${local_work_dir} \
	--threads 8 \
	--taxonomic-profile "${local_work_dir}/${base}"_profile_abs.forHUMAnN.txt \
	--memory-use minimum \
	--output-basename ${base}

Observed pattern across the five samples:

  • genefamilies.tsv: contains data

  • pathabundance.tsv and pathcoverage.tsv: only show:

  UNMAPPED      0.0000000000  
  UNINTEGRATED  0.0000000000

Sample breakdown:

  • Four samples: Relatively small-sized FASTQ (~0.2 Mb) + 100% unclassified MetaPhlAn profiles

  • One sample: Relatively normal-sized FASTQ (~15 Mb) + valid MetaPhlAn profile (contains taxonomic classifications)

My understanding from the documentation:

  • Pathways can be detected at both species-level and community-level

  • With 100% unclassified profiles, I wouldn’t expect species-specific pathways (it was mentioned in HUMAnN log as well)

  • However, community-level pathways should still be possible if the detected gene families form complete pathway structures

My question:

Does my output simply mean that no community-level pathways were detected across any of these samples? Meaning the gene families present don’t satisfy criteria for any pathways, regardless of whether there’s taxonomic classification?

Or is there something else I should investigate, particularly for the sample with valid taxonomic information?

Thanks!