Description
- run humann
https://github.com/biobakery/humann#standard-workflow
(find the option to provide metaphlan output files, since humann wants to run metaphlan first but you will already have done this)
output data: /projects/rps/emh9/henafflab/2025-Gowanus_Biofilm_BioBAT/data/humann4_all
- renormalize to cpm
https://github.com/biobakery/humann#humann_renorm_table
merged and normalized to cpm tables: /projects/rps/emh9/henafflab/2025-Gowanus_Biofilm_BioBAT/data/humann4_merged
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output data: /projects/rps/emh9/henafflab/2025-Gowanus_Biofilm_BioBAT/data/humann4_all
(without HaoWei samples)
Internal thoughts:
Dear Bioinformatics Diary
- Setting up HumanN environment on Toarch:
- We experienced some workblocks. New HumanN 4 has some weird databases compatibility issues that we were trying to resolve today with Sheglong. And he also was confused.
- Torch went down @April 30, 2026 so the work is delayed
Lab databses:
cd /projects/rps/emh9/henafflab/cb_database
#where installed recommended databases for the new version HumanN4
cd /projects/rps/emh9/henafflab/cb_database/DB