8000 No module named bioconda::fq · Issue #1555 · nf-core/rnaseq · GitHub
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bk1n opened this issue May 21, 2025 · 3 comments
Open

No module named bioconda::fq #1555

bk1n opened this issue May 21, 2025 · 3 comments
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@bk1n
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bk1n commented May 21, 2025 •
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Description of the bug

Get error when trying to run from conda:
No module named bioconda::fq

This only happens with 3.18.0 - when I try 3.17.0 I don't get this error.

Config contains the temporary fix found in #1554

Command used and terminal output

nextflow run nf-core/rnaseq --input fastq/sample_sheet.csv --outdir nfout --gtf reference/Homo_sapiens.GRCh38.113.gtf --fasta reference/Homo_sapiens.GRCh38.dna.primary_assembly.fa --email <myemail> -c nf_config_fix.config -r 3.18.0 -with-conda -profile test



nf-core/rnaseq execution completed unsuccessfully!
The exit status of the task that caused the workflow execution to fail was: null.

The full error message was:

Error executing process > 'NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (7)'

Caused by:
  Failed to create Conda environment
    command: conda env create --prefix /exports/eddie/scratch/s1754085/arid1a_rnaseq/work/conda/env-d44174e8314b7d21-16bfc74f50473b17f7bf05d44dde0205 --file /home/s1754085/.nextflow/assets/nf-core/rnaseq/modules/nf-core/fq/lint/environment.yml
    status : 1
    message:
      Channels:
       - conda-forge
       - bioconda
       - defaults
      Platform: linux-64
      Collecting package metadata (repodata.json): ...working... done
      Solving environment: ...working... failed
      
      PackagesNotFoundError: The following packages are not available from current channels:
      
        - bioconda::fq==0.12.0
      
      Current channels:
      
        - https://conda.anaconda.org/conda-forge/linux-64
        - https://conda.anaconda.org/bioconda/linux-64
        - https://repo.anaconda.com/pkgs/main/linux-64
        - https://repo.anaconda.com/pkgs/r/linux-64
        - https://conda.anaconda.org/bioconda
      
      To search for alternate channels that may provide the conda package you're
      looking for, navigate to
      
          https://anaconda.org
      
      and use the search bar at the top of the page.

Relevant files

No response

System information

HPC, Rocky Linux 9.4, Nextflow 25.04.2, nf-core/rnaseq 3.18.0
@bk1n bk1n added the bug Something isn't working label May 21, 2025
@bk1n
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bk1n commented May 21, 2025

Actually, same bug occurred with 3.17.0

nextflow run nf-core/rnaseq --input fastq/sample_sheet.csv --outdir nfout --gtf reference/Homo_sapiens.GRCh38.113.gtf --fasta reference/Homo_sapiens.GRCh38.dna.primary_assembly.fa --email myemail -c nf_config_fix.config -r 3.17.0 -with-conda -profile test

@nttg8100
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nttg8100 commented May 21, 2025 •
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For anyone who wants to have a quick fix, I used this to avoid creating additional config

nextflow run nf-core/rnaseq -r 3.18.0 -profile singularity,test --outdir result -process.shell bash

@bk1n
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bk1n commented May 21, 2025 •
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For anyone who wants to have a quick fix, I used this to avoid creating additional config

nextflow run nf-core/rnaseq -r 3.18.0 -profile singularity,test --outdir result -process.shell bash

I think you maybe meant to put this in #1554? It does work though thanks 👍

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