Problems running Humann

Microbial community profiling HUMAnN
1

Hi - I am trying to run Humann on a new machine. Initially I tried to download humann fresh using conda (conda install bioconda::humann), but ran into errors (which I can make a separate post about). I have successfully run Humann before on another machine, so I recreated the environment by building from a config yaml (humann=3.9, metaphlan=4.1.1).

I downloaded the following dbs:


humann_databases --download chocophlan full chocophlan --update-config yes
humann_databases --download uniref uniref90_diamond uniref --update-config yes
humann_databases --download utility_mapping full utility --update-config yes
metaphlan --install --bowtie2db /db/location

I am running a test with just one fastq file, and got this far:

humann \
        --input merged_reads/test_reads.fastq.gz \
        --output /data/test_data/humann_output/test/ \
        --verbose \
        --metaphlan-options "--bowtie2db /data/metaphlan_db --index mpa_vJan25_CHOCOPhlAnSGB_202503"
Output files will be written to: /data/test_data/humann_output/test

Writing temp files to directory: /data/test_data/humann_output/test/test_reads_humann_temp

File ( /data/test_data/merged_reads/test_reads.fastq.gz ) is of format:  fastq.gz

Decompressing gzipped file ...


Running metaphlan ........


/data/miniconda3/envs/humann39/bin/metaphlan /data/test_data/humann_output/test/test_reads_humann_temp/tmpcia1okap/tmppo6x56_a --bowtie2db /data/metaphlan_db --index mpa_vJan25_CHOCOPhlAnSGB_202503 -o /data/test_data/humann_output/test/test_reads_humann_temp/test_reads_metaphlan_bugs_list.tsv --input_type fastq --bowtie2out /data/test_data/humann_output/test/test_reads_humann_temp/test_reads_metaphlan_bowtie2.txt


TIMESTAMP: Completed prescreen : 2683 seconds



ERROR: The MetaPhlAn taxonomic profile provided was not generated with the database version v3 or vJun23 . Please update your version of MetaPhlAn to at least v3.0 or if you are using MetaPhlAn v4 please use the database vJun23.

I’m not sure how best to proceed - any guidance would be helpful. I can try and figure out how to download the vJun23 database if that’s the answer, but these downloads take a long time.

Thanks!