The bioBakery help forum

No MetaPhlAn BowTie2 database found (--index option)!

Hi Biobakery community!

I recently upgraded to HUMAnN v3.0 after having used HUMAnN2, but don’t seem to be able to run the demo because of a recurring error.
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I installed it via conda in a contained environment, as suggested here: humann3 – The Huttenhower Lab

# create env 
conda create --name biobakery3 python=3.7
# activate env
conda activate biobakery3

# update channels
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --add channels biobakery

# install biobakery and metaphlan
conda install -c biobakery human
conda install -c bioconda metaphlan

# test installation

All of the tests seemed to be fine. I then proceeded to run the demo:

humann -i demo.fastq -o demo_outputs

The first time I ran it, it took 4 hours, after which the job was killed on the cluster I was using.

After that, it returned the following errors:

CRITICAL ERROR: Error executing: /data/home/btx143/.conda/envs/biobakery3/bin/metaphlan /data/home/btx143/shotgun2/demo/data/demo.fastq -t rel_ab -o /data/home/btx143/shotgun2/demo/outputs/demo_output/demo_humann_temp/demo_metaphlan_bugs_list.tsv --input_type fastq --bowtie2out /data/home/btx143/shotgun2/demo/outputs/demo_output/demo_humann_temp/demo_metaphlan_bowtie2.txt


Error message returned from metaphlan :
No MetaPhlAn BowTie2 database found (–index option)!
Expecting location /data/home/btx143/.conda/envs/biobakery3/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901

The issue is that when I check in the directory where the database indices should be, then I find the following files:


And the expected “mpa_v30_CHOCOPhlAn_201901” is missing

I found a similar post in this forum and tried the following:

1. manually delete metaphlan/bowtie2 databases and re-run demo

From what I unnderstand, humann (through metaphlan and bowtie2) should automatically

2. manually delete metaphlan/bowtie2 databases, download the files and use bowtie2 to build the databases

tar -xvf mpa_v30_CHOCOPhlAn_201901.tar
bunzip2 *.bz2
bowtie2-build mpa_v30_CHOCOPhlAn_201901.fna mpa_v30_CHOCOPhlAn_201901

And even tried to run humann specifying the databases option:

humann -i demo.fastq -o sample_results --metaphlan-options “–bowtie2db {condapath}/{dbpa} -x mpa_v30_CHOCOPhlAn_201901”

After this, I still get the same annoying error:

No MetaPhlAn BowTie2 database found (–index option)!
Expecting location /data/home/btx143/.conda/envs/biobakery3/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901

Did anyone run into the same or similar error?



Hello, Sorry you are having issues running the demo. Thank you for your detailed and organized post! I think you might have an older version of MetaPhlAn installed. Can you check the version number? If it is an older version if you update to the latest version and then run $ metaphlan --install it should download and install the database. Once you have the database installed, you should hopefully be set! If you still see errors double check you have the latest version of HUMAnN installed. Sometimes conda does not always install the latest version but instead it installs an older version that is compatible with the current conda environment.

Thank you,

Hi Lauren,

Thank you for your reply, and sorry for late answer!
I did have metaphlan v3.0.7 installed already. All it took was to run:

metaphlan --install

(as you sugested)
and the correct databases were installed!

Thank you so much!


Hi Giacomo, Awesome! Thanks for the follow up and glad to hear you are all set! Please post again if you have other issues.

Thank you,