Fail to create conda environment for sourmash_sketch

[buchanri]

After running the pipeline I got this error:

Caused by:
ERROR ~ Error executing process > 'PATHOGENSURVEILLANCE:SKETCH_COMPARISON:SOURMASH_SKETCH_READS (1)'

Caused by:
  Failed to create Conda environment
    command: mamba env create --prefix /nfs7/BPP/Chang_Lab/paradarc/paper3_bra/scripts/pathogensurveillance/work/conda/sourmash_sketch-481c3c545c778fa751538b4cac862f83 --file /nfs7/BPP/Chang_Lab/paradarc/paper3_bra/scripts/pathogensurveillance/./workflows/../subworkflows/local/../../modules/nf-core/sourmash/sketch/environment.yml
    status : 143
    message:
      Channels:
       - conda-forge
       - bioconda
       - defaults
      Platform: linux-64
      Collecting package metadata (repodata.json): ...working... done
      Solving environment: ...working... done



 -- Check '.nextflow.log' file for details
[89/34cffb] Submitted process > PATHOGENSURVEILLANCE:SKETCH_COMPARISON:SUBSET_READS (SZCCHNS3004)
-[nf-core/plantpathsurveil] Sent summary e-mail to [email protected] (sendmail)-
WARN: Access to undefined parameter `outdir` -- Initialise it to a default value eg. `params.outdir = some_value`
-[nf-core/plantpathsurveil] Pipeline completed with errors

 To clean the cache, run the command:
 nextflow clean wise_chandrasekhar -f

WARN: Killing running tasks (48)

I've tried mamba clean --all which has fixed conda environment issues in the past but this time it's not helping. I've also tried to remove the sourmash env it made (if it did make one) to force it to try and make the environment again to reinstall sourmash but no luck. Any ideas?

[zachary-foster]

It looks like one of those intermittent conda errors. Normally I would do what you said, mamba clean --all and deleting /nfs7/BPP/Chang_Lab/paradarc/paper3_bra/scripts/pathogensurveillance/work/conda/sourmash_sketch-481c3c545c778fa751538b4cac862f83. I did see something about anaconda.org doing maintenance recently, so that could be the problem?