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.)
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_annotatorwrapper (from thewgs_cnv_exportworkflow), it fails to create the conda environment.Submitting the failed command manually on the command line worked though.
(The prefixes of the paths have been shortened, but the paths are legit from the relevant folder on downwards.)