Error while setting up NF_MGIllumina_1.0.0

Open ankurnaqib opened this issue 4 months ago • 1 comments

Hi. I have been using the SW_MGIllumina_2.0.3 for a long time now. I thought of updating to the NF_MGIllumina_1.0.0 also because I want to be able to use the parameter -t rel_ab_w_read_stats option while running metaphlan to get the estimated absolute read counts. While trying to test the nextflow pipeline with just two samples, I got the following error. Would someone be able to please help me resolve this error? Thank you.

ERROR ~ Error executing process > 'run_read_based_analysis:read_based:HUMANN (1)'

Caused by: Failed to create Conda environment command: conda env create --prefix /home/anaqib/Projects/Robin_MIND_Test_NF/conda/env-d6245bd79df04395-6d2125640955ec84dff04c408b9c21b8 --file /home/anaqib/NF_MGIllumina_1.0.0/envs/humann3.yaml status : 1 message: Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... failed

  ResolvePackageNotFound:
    - metaphlan=4.10

Oct 05 '25 20:10 ankurnaqib

There is a typo in the NF_MGIllumina_1.0.0/envs/humann3.yaml file. The MetaPhlAn version should be 4.1.0 (as specified in the GL-DPPD-7107-A pipeline document) not 4.10 . An updated version of the environment file has been added to the master branch of the repository and will be incorporated into the next Metagenomics workflow release. In the meantime, please download the fixed version of the file and replace the incorrect file in the NF_MGIllumina_1.0.0 release package (or edit the file directly).

Nov 04 '25 18:11 bnovak32