nf-core
Termination of the sarek process without any output
I tried to run sarek with Human WGS data, but the process ended within 5 minutes and there is no output. Is this a problem caused by insufficient computing resources?Any suggestions on how to set up computing resources? Slurm job scheduling system was used, settings: --ntasks-per-node 16 -c 8
params_2025-02-19_21-16-01.json
execution_trace_2025-02-19_21-15-43.txt
Hey can you also provide the command you used to run the pipeline?
You are using v3.5.0 of the pipeline and N E X T F L O W ~ version 24.10.4, right? Maybe you can try with the latest release 3.5.1 and see if the error persists? Just add -r 3.5.1 to your nextflow run command.
To help you debug could you please provide the custom config file (/dssg/home/acct-sjtuei/sjtuei-lxb/nfcore/nf-core-sarek_3.5.0/workflow/slurm.config) that you used? Based on the error message in the nextflow log file, it looks like there might be a syntax error:
groovy.lang.MissingMethodException: No signature of method: java.util.LinkedList.getFileSystem() is applicable for argument types: () values: []
Are you running this pipeline on a single node or are you using the slurm executor?
