Install version issue - Metaphlan4

Microbial community profiling MetaPhlAn
1

I followed conda installation instructions (MetaPhlAn 4 · biobakery/MetaPhlAn Wiki · GitHub) to install metaphlan4 but when i check the version it appears to be v3.

I have tried to follow other discussions to fix the issue and have not had any luck.

$ metaphlan --version
MetaPhlAn version 3.0.7 (09 Dec 2020)

Any input would be appreciated.

2

Hi @fsaravia
You can try to force the installation of the new version by running:
conda install -c bioconda metaphlan=4.0.1

3

Hi @aitor.blancomiguez

Unfortunately the force install doesn’t work. Here is my issue:

(metaphlan4) fatimas@alustt129 PROD$ metaphlan --version
MetaPhlAn version 3.0.7 (09 Dec 2020)

(metaphlan4) fatimas@alustt129 PROD$ conda install -c bioconda metaphlan=4.0.1
Collecting package metadata: done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.6.14
latest version: 4.14.0
Please update conda by running
$ conda update -n base -c defaults conda

Package Plan

environment location: /home/fatimas/.conda/envs/metaphlan4
added / updated specs:
- metaphlan=4.0.1
The following packages will be downloaded:
package | build
---------------------------|-----------------
ca-certificates-2022.9.14 | ha878542_0 152 KB conda-forge

certifi-2022.9.14          |     pyhd8ed1ab_0         156 KB  conda-forge
------------------------------------------------------------
                                     Total:         308 KB

The following packages will be UPDATED:
ca-certificates pkgs/main::ca-certificates-2022.07.19~ → conda-forge::ca-certificates-2022.9.14-ha878542_0
certifi 2022.6.15.1-pyhd8ed1ab_0 → 2022.9.14-pyhd8ed1ab_0

Proceed ([y]/n)? y

Downloading and Extracting Packages
ca-certificates-2022 | 152 KB | ####################################################################################################################################### | 100%

certifi-2022.9.14 | 156 KB | ####################################################################################################################################### | 100%

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

(metaphlan4) fatimas@alustt129 PROD$ metaphlan --version

MetaPhlAn version 3.0.7 (09 Dec 2020)

4

That is really odd, maybe try to add the --upgrade flag to the command ?