Run snakemake on Cluster about grenepipe HOT 3 CLOSED

Update: I tried to change the setting of --conda-prefix, i.e. I created a new folder for the new project to save the environments, and it started to run without the "ModuleNotFoundError" shown above. Could this be the issue? So we have to create the environments again for different projects?

from grenepipe.

Hey @orangelc1221,

this sounds to me like an issue with some of the nodes of the cluster being set up differently from others, or some issue with conda not being properly set up. I've had an issue a while ago on our cluster that would also come and go "randomly", but it turned out that it always was the same node that caused trouble, because it had some broken config script or something, that IT was then able to fix.

For that particular reason, the grenepipe log at the very start of a run prints out all kind of information, so that we can debug these kinds of issues. Can you check the output or log files of runs, and see if the conda/python/snakemake versions are what you expect them to be?

Also, are you using the grenepipe conda environment when starting snakemake, as described in the wiki here? Basically, what you want to do in order to run the pipeline is

conda activate grenepipe 
snakemake ...

to make sure that the correct conda version is used.

Let me know if that helps. If it doesn't, I'd suggest to talk with IT again ;-)

Cheers
Lucas

from grenepipe.

Hey @orangelc1221,

it seems you solved the issue? Would you mind sharing how, so that users with the same issue in the future can learn from your solution as well?

Cheers and thanks
Lucas

from grenepipe.