Can't load databases

Microbial community profiling HUMAnN
1

Hi,

see error below. I followed the conda install instructions here exactly:

and downloaded the databases as per that page without any errors. I alto ran the test with no errors.

I am running humann on an HPC job node with no internet access, so it seems humann will not run? Is this correct? Is there any way to force it to use the databases which were already downloaded? The configuration file shows the correct locations where I downloaded them:

database_folders : nucleotide = /g/data/dy44/db/humann/chocophlan
database_folders : protein = /g/data/dy44/db/humann/uniref

So I’m very confused why it is trying to download.

Thanks.

2

CRITICAL ERROR: Error executing: /g/data/nm31/bin/conda/biobakery/bin/metaphlan /g/data/nm31/d/r18_elcho/test/endia50.fastq -t rel_ab -o /g/data/nm31/d/r18_elcho/humann/endia50_humann_temp/endia50_metaphlan_bugs_list.tsv --input_type fastq --mapout /g/data/nm31/d/r18_elcho/humann/endia50_humann_temp/endia50_metaphlan_bowtie2.txt --nproc 48

Error message returned from metaphlan :
Wed Sep 3 15:24:21 2025: [Warning] It seems that you do not have Internet access.
Wed Sep 3 15:24:21 2025: [Warning] Cannot connect to the database server. The latest available local database will be used.
Wed Sep 3 15:24:21 2025: MetaPhlAn database not present or partially present in /g/data/nm31/bin/conda/biobakery/lib/python3.7/site-packages/metaphlan/metaphlan_databases.
Downloading database
Please note due to the size this might take a few minutes.
Wed Sep 3 15:24:21 2025: Downloading and uncompressing bowtie2 indexes
Wed Sep 3 15:24:21 2025: [Warning] File /g/data/nm31/bin/conda/biobakery/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_vJan25_CHOCOPhlAnSGB_202503_bt2.tar already present!
Wed Sep 3 15:24:21 2025: Downloading http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/bowtie2_indexes/mpa_vJan25_CHOCOPhlAnSGB_202503_bt2.md5
Wed Sep 3 15:24:21 2025: [Error] EnvironmentError “<urlopen error [Errno 101] Network is unreachable>”
Unable to download http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/bowtie2_indexes/mpa_vJan25_CHOCOPhlAnSGB_202503_bt2.md5
Wed Sep 3 15:24:21 2025: Stop execution.

This is not spam.. please stop flagging my questions as spam?

4

Why have you flagged this as spam?

6

The internet connection seems required only because you are missing a metaphlan db, which is required by default to run humann. You therefore have two options: (1) turn off metaphlan, or (2) get the db and point humann to it.

I assume you want the metaphlan database.
#starting in desired location, or move tar/outputs to it after
wget http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/bowtie2_indexes/[pick the right version]
tar xvf [right version]_bt2.tar

Then, with that database

humann --input reads.fq --output humannoutput --metaphlan-options “--bowtie2db /path/to/metaphlandatabase --index [right version]”

the “right version” depends on your version of humann and metaphlan