MetaPhlAn 4.2.2 work with humann v3.0.1

Microbial community profiling HUMAnN
1

I used MetaPhlAn version 4.2.2 to run the alignment successfully and generated an abundance file. Now, I hope to use this file as input and run humann v3.0.1 to obtain the correspondence between species, abundance, and functional profiles. However, I have been unable to achieve this. My codes were as follows:

/datapool/software/anaconda3/envs/phylophlan/bin/humann3 -i B38_03.merge.fq.gz -o B38_03.hum --threads 20 --metaphlan /datapool/software/anaconda3/bin/metaphlan --metaphlan-options “–index mpa_vJan25_CHOCOPhlAnSGB_202503 -t rel_ab --mapout B38_03.merge_metaphlan_bowtie2.txt --db_dir /datapool/software/anaconda3/lib/python3.7/site-packages/metaphlan/metaphlan_databases” --diamond /datapool/software/anaconda3/envs/phylophlan/bin/diamond

The above didn’t work. So I try to run the MetaPhlAn firstly, and put the output to humann3 as input.
/datapool/software/anaconda3/envs/phylophlan/bin/humann3 -i B38_03.merge.fq.gz -o B38_03.hum --threads 20 --taxonomic-profile B38_03.mp --metaphlan /datapool/software/anaconda3/bin/metaphlan --metaphlan-options “–index mpa_vJan25_CHOCOPhlAnSGB_202503 --db_dir /datapool/software/anaconda3/lib/python3.7/site-packages/metaphlan/metaphlan_databases”

But the codes also failed. The errors as follows:
ERROR: The MetaPhlAn2 taxonomic profile provided was not generated with the database version v30 . Please update your version of MetaPhlAn2 to v3.0.

Thank you.

2 Likes
2

I met same problem to be solved, my problem is that humann database could not use the metaphlan_bug_list.tsv file as input.

3

Sorry that that error message is not very informative. HUMAnN 4.0.0.alpha.1 is currently configured to work with the Oct22 SGB set. By default MetaPhlAn 4.2 is now profiling the Jan25 SGB set, so HUMAnN is not able to work with the corresponding profile. The post-alpha release of HUMAnN 4.0 will support the Jan25 SGBs.

4

I had this issue, and I was going crazy. I was able to fix it by downgrading my metaphlan from 4.22 to 3.9. Then re-running with humann v3.9 worked perfectly. So basically metaphlan 4.22 isn’t compatible with humann3.9. That is the issue

5

I have this problem. How do you downgrade metaphlan in the conda environment? Thanks.

6

run this in linux, it creates a new humann3 directory:
fresh env (recommended)

mamba create -n humann3 -c bioconda -c conda-forge humann=3.9 metaphlan=3.1.0
conda activate humann3

verify

humann --version
metaphlan -v

1 Like
7

Once you are in the new humann3 enviroment and you rereun metaphlan, it automatically downloads an old database

1 Like
8

Hi,

Sorry, I already posted this question before. But I am just trying to get it working. I have HUMAnN 4.0.0.alpha.1 and MetaPhlAn version 4.0.6 (1 Mar 2023) installed. I also downloaded the database mpa_vOct22_CHOCOPhlAnSGB_202403. However, every time I tried to run humann “humann -i demo.fastq -o sample_results”, metaphlan automatically starts to download the database mpa_vJan25_CHOCOPhlAnSGB_202503, and I get an incompatibility error.

How to prevent Metaphlan from downloading the vJan25 DB while using humann?

Thanks

9

I guess the –-offline flags does the trick.