No MetaPhlAn BowTie2 database found (--index option)! Humann3.6

Hi! I know there are other open questions on this topic, but as I am using the latest version of Humann (3.6) I wanted to open a new issue. I am currently going through the setup process of Humann in a conda environment, and followed the steps on your installation guide and ran the following commands:

conda create --name biobakery3 python=3.7
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --add channels biobakery
conda install humann -c biobakery```

I then downloaded all the databases:

humann_databases --download chocophlan full /scratch4/jsuez1/week12/chocophlan --update-config yes
humann_databases --download uniref uniref90_diamond/scratch4/jsuez1/week12/diamond --update-config yes
humann_databases --download utility_mapping full /scratch4/jsuez1/week12/diamond --update-config yes

Then when I try to run either a sample of mine or the demo.fastq.gz, i get this error:

Running metaphlan ........

CRITICAL ERROR: Error executing: /home/hhallow1/.conda/envs/biobakery3/bin/metaphlan /scratch4/jsuez1/week12_virome/sample_results/demo_humann_temp/tmpm6r5uqir/tmpe2u0gnbk -t rel_ab -o /scratch4/jsuez1/week12_virome/sample_results/demo_humann_temp/demo_metaphlan_bugs_list.tsv --input_type fastq --bowtie2out /scratch4/jsuez1/week12_virome/sample_results/demo_humann_temp/demo_metaphlan_bowtie2.txt

Error message returned from metaphlan :

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

Expecting location bowtie2db


I have tried deleting and re-installing the databases, i’ve tried updating the config file (it was already updated), i’ve tried completely re-installing humann in a new environment and im not sure what else to do. i’ve used humann in the past with no problems at all. any help would be appreciated! Thanks!

Hi! just wanted to update … I still am stuck on this step. It seems that when i download the database using

humann_databases --download chocophlan full /scratch4/jsuez1/week12/chocophlan --update-config yes

The file becomes unzipped. I tried manually combining all files into one .fna by doing this

cat chocophlan/* > mpa_v30_CHOCOPhlAn_201901.fna

then using bowtie-build to build my index

bowtie2-build mpa_v30_CHOCOPhlAn_201901.fna mpa_v30_CHOCOPhlAn_201901

I got about 1000 warnings from bowtie that each reference was empty, i.e contains all Ns rather than ATCG, before i killed the job

So my question is, why is the database unzipping when i download it? what is the correct why to cat these files together to be indexed?

I am running Metaphlan 4.0.2 and Humann 3.6