First look in the all open and closed issues for the error message you got.
As atlas is based on snakemake, check if you find a similar bug already discussed for other snakemake-workflows.
If you don't find any help. Submit a issue:
- specify the system you are working on: linux, cluster, shared filesystem?
- copy the error message
- add the log file of the rule, which produced the error.
- If you run the atlas on a cluster join also the log file of the cluster.
I hope we can help you...