Mamba fails to create environment because the --yes flag is not supplied.conda.createOptions = '--yes' does not help either.
Failed to create Conda environment
command: mamba env create --prefix ./work/conda/env-961b98c89213eaa1-e6f0bafd6827065b938c2602e5e8feef --file ./envs/seqkit_env.yaml
status : 143
...
─────────────────────────────────────────────────────────────────────────────
Confirm changes: [Y/n]
-- Check '.nextflow.log' file for details
1 Like
yinshiyi
June 23, 2025, 6:19pm
2
My team is dealing with the exact same error.
opened 04:45PM - 23 Dec 24 UTC
closed 02:13PM - 22 Jan 25 UTC
wontfix
## Bug report
If using:
```
conda {
conda.enabled = tr… ue
conda.useMamba = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
```
...the pipeline stalls at creating the conda env `Creating env using mamba` forever (at least >=30 minutes).
If I set `useMamba = false`, the conda env is created within ~1 minute.
So, the issue is caused by mamba.
### Expected behavior and actual behavior
mamba should be creating the conda env rapidly (faster than conda, in most situations).
### Steps to reproduce the problem
See above. I'm using a GCP VM with 8 CPUs, 16 Gb of mem, and Ubuntu 22.04.5.
### Environment
* Nextflow version: 24.10.2
* Java version: 21.0.0
* Operating system: Ubuntu 22.04.5
* Bash version: 5.1.16
### Additional context
```
# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/home/nickyoungblut/miniforge3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
eval "$__conda_setup"
else
if [ -f "/home/nickyoungblut/miniforge3/etc/profile.d/conda.sh" ]; then
. "/home/nickyoungblut/miniforge3/etc/profile.d/conda.sh"
else
export PATH="/home/nickyoungblut/miniforge3/bin:$PATH"
fi
fi
unset __conda_setup
if [ -f "/home/nickyoungblut/miniforge3/etc/profile.d/mamba.sh" ]; then
. "/home/nickyoungblut/miniforge3/etc/profile.d/mamba.sh"
fi
# <<< conda initialize <<<
```