No SGBs in humann3.9 genefamily.tsv

Microbial community profiling HUMAnN
1

Hi there,

after updating humann to 3.9, I still failed to find any genefamilies belonging to SGBs in my huamnn output *.humann_genefamilies.txt file. May I ask what could be the reason?

To be more specific, I have this taxa k__Bacteria|p__Firmicutes|c__CFGB10477|o__OFGB10477|f__FGB10477|g__GGB9345|s__GGB9345_SGB14311 annotated from metaphlan 4.1.0 with database version mpa_vJun23_CHOCOPhlAnSGB_202307. And I ran humann 3.9 with database v201901_v31 after that with command: humann --input $TEMPDIR/sample_concat.fq.gz --output $TEMPDIR --nucleotide-database /hm3/chocophlan/ --protein-database /hm3/uniref/ --output-basename sample --metaphlan-options "--bowtie2db /db/mph4/ -x mpa_vJun23_CHOCOPhlAnSGB_202307 --offline".

Was this about the compatibility between metaphlan and humann or I need to use both humann4 and metaphlan4 to get the dabundance of genefamilies belonging to SGBs?

Merry Xmas,

ben

2

When using HUMAnN 3 with MetaPhlAn 4 (and SGBs), the HUMAnN outputs are in terms of species in the HUMAnN 3 database that correspond to SGBs in the MetaPhlAn 4 output (on the basis of overlapping reference genomes). I believe the HUMAnN 3 log file includes the details of how SGBs and v3 species were linked to help your determine equivalences?

4

Thanks! I found the corresponding species in the log. It’s s__Clostridium_sp_CAG_138.