Entering edit mode
6.4 years ago
tim.ivanov.92
▴
40
Hello!
Does anyone have an experience running grape-nf?
When i'm trying to run it on local machine, i get an error about memory deficiency:
[warm up] executor > local Exception in thread "Task submitter" nextflow.exception.ProcessNotRecoverableException: Process requirement exceed available memory -- req: 62 GB; avail: 16 GB
And when i'm trying to run in on my HPC cluster, i got this java exception:
ERROR ~ Unexpected error [NullPointerException]
I'm trying to make grape-nf work anyhow for some quite time, so if you have ANY ideas or experience, please share, it would really help.
Essentially this is telling you that you don't have the memory available to run the pipeline on your local machine. I'm not entirely sure what's going on with the cluster error. Have you tried posting a GitHub issue?
Shameless plug to my workflow script: https://github.com/c-guzman/cipher-workflow-platform
Can i run it on local machine?
On cluster i have a docker instead of singularity and i'm sure this is replaceable.
Also (since you are advertising) what output/data structures does your pipeline produce? Thank you for the reply!