CondaMemoryError when creating conda envs in cluster about grenepipe HOT 3 CLOSED

Hi @orangelc1221,

the error that you are seeing is one of the reasons why we recommend to use mamba. The picard environment somehow seems to be causing trouble for conda, no idea why, and it works fine with mamba. Hence, I recommend that you use conda to install mamba :-) You can for example add it to the grenepipe environment itself, that you already created. That way, you can use mamba even on a cluster that does not yet have it.

As for your second issue with the cluster script run.slurm: I have no idea what the rest of these guidelines say, or what that script contains, so I cannot really comment on that without further knowledge of the situation. However, we do provide our own guide for running snakemake and grenepipe in cluster environments. In particular relevant seems to be the part on what you described as "just run on the terminal": That usually won't work, as the snakemake command will then inevitably stop once you want to close that terminal. At the least, you will have to run snakemake from within screen or tmux, see above guide.

Hope that helps, so long
Lucas

from grenepipe.

Thank you!

from grenepipe.

You're welcome! For future reference: Did this solve all issues you had, and is it working now?

from grenepipe.