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Error creating conda environment #651

@stolpeo

Description

@stolpeo

Describe the bug
I'm not very sure if this only a local problem with my setup. But maybe somebody encounters the same error. Running the varfish_annotator wrapper (from the wgs_cnv_export workflow), it fails to create the conda environment.

03-30 14:37 snakemake.logging WARNING  Downloading and installing remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /home/users/stolpeo/dragen-workflow/snappy-pipeline/snappy_wrappers/wrappers/varfish_annotator/annotate_svs/environment.yaml:
Command:
mamba env create --quiet --file "/project1/GRCh37/wgs_cnv_export_external/.snakemake/conda/727e3d1495c1a04cf82b74272ffe51d5_.yaml" --prefix "/project1/GRCh37/wgs_cnv_export_external/.snakemake/conda/727e3d1495c1a04cf82b74272ffe51d5_"
Output:
error    libmamba Non-conda folder exists at prefix
critical libmamba Aborting.

Submitting the failed command manually on the command line worked though.

mamba env create --quiet --file "/project1/GRCh37/wgs_cnv_export_external/.snakemake/conda/727e3d1495c1a04cf82b74272ffe51d5_.yaml" --prefix "/project1/GRCh37/wgs_cnv_export_external/.snakemake/conda/727e3d1495c1a04cf82b74272ffe51d5_"

(The prefixes of the paths have been shortened, but the paths are legit from the relevant folder on downwards.)

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