# Troubleshooting humann in 2026 CE

**URL:** <https://forum.biobakery.org/t/troubleshooting-humann-in-2026-ce/9074>\
**Category:** HUMAnN\
**Created:** [October 1, 2026, 12:19pm UTC](https://forum.biobakery.org/t/troubleshooting-humann-in-2026-ce/9074 "2026-10-01T12:19:29Z")\
**Posts on this page:** 1\
**Showing post:** 3

<div class="post-metadata">

**Author:** ![handibles](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/handibles/32/1191_2.png) [@handibles](https://forum.biobakery.org/u/handibles)\
**Post date:** [October 5, 2026, 2:25pm UTC](https://forum.biobakery.org/t/troubleshooting-humann-in-2026-ce/9074/3 "2026-10-05T14:25:12Z")

</div>

## working install

installed early Oct '26.

```auto
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:

```auto
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\<](https://forum.biobakery.org/t/humann-4-0-0a1-minpath12hmp-py-syntaxwarning/8606/2)  
  
  
Happy hunting!

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