nasa / nasa/GeneLab_Data_Processing
Error while setting up NF_MGIllumina_1.0.0
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Description
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
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First steps
- Read the whole issue, then the project's contributing guide.
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Research direction
Start with envs/humann3.yaml and the HUMANN process named in the error; inspect the pinned metaphlan=4.10 dependency and the Conda environment creation command. Reproduce the two-sample setup and verify that dependency resolution completes and the read-based analysis can start without ResolvePackageNotFound.
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Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 25/100