Troubleshooting humann in 2026 CE

Microbial community profiling HUMAnN
3

working install

installed early Oct '26.

h4ref=/path/to/db/folder
h4=/path/to/humann4_work/with_demo_fastq_file

## min hacks for min paths  -  mamba+pip, what could go wrong
mamba create -n h4p311 python=3.11 -y ; mamba activate h4p311
conda config --add channels defaults 
conda config --add channels bioconda 
conda config --add channels conda-forge 
conda config --add channels biobakery 

# note custom versions for MP4, BT2, D
pip install humann==4.0.0a1 --no-binary :all:
mamba install metaphlan=4.1.1 -y
mamba install bowtie2=2.5.4 -y
# Minpath 1.12 builtin , stays as it it.

# run & then get lunch
humann_databases --download chocophlan full $h4ref --update-config yes &
humann_databases --download uniref uniref90_ec_filtered_diamond $h4ref --update-config yes &
humann_databases --download utility_mapping full $h4ref --update-config yes &
metaphlan --install --index mpa_vOct22_CHOCOPhlAnSGB_202403

humann --input $h4/demo.fastq --output $h4/demo_mamb --threads 40 --metaphlan-options "-t rel_ab_w_read_stats"

Gives fully sane output. Final sanity - version checks:

head -20 ~/bin/MinPath/MinPath.py ; bowtie2 --version ; diamond --version ; metaphlan --version ; humann --version

# dross removed 
# >  MinPath built into H4, v. 1.12
# >  /home/user/bin/miniforge3/envs/h4u/bin/bowtie2-align-s version 2.5.4
# >  diamond version 2.0.15
# >  MetaPhlAn version 4.1.1 (11 Mar 2024)
# >  humann v4.0.0.alpha.1

  • CRITICAL ERROR: Can not call software version for metaphlan was ~solved by specifying MP4.1.1 when creating/installing the env. As mentioned above, it can also be patched by setting "line" : 0 for metaphlan_version, circa line #373 of humann_config after installation.

  • miniforge3/envs/h4u/lib/python3.12/site-packages/humann/quantify/MinPath12hmp.py:804: SyntaxWarning: invalid escape sequence '\\d' addressed by setting python=3.11 as >recommended here<


    Happy hunting!

Humann=4.0.0a1 : MinPath12hmp.py:804: SyntaxWarning