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                                            shen

set threads=12 but still submit single cpu job to the cluster

yes. my nextflow.config contains these: singularity.autoMounts = true singularity.enabled = true process { executor='pbs' queue='cal' } And I run CIPHER on the login node.

set threads=12 but still submit single cpu job to the cluster

I can see serveral jobs submiting, but some job should ask the cluster for multi cpus. but all the jobs submit with single cpu: Job ID Username Queue Jobname SessID...

set threads=12 but still submit single cpu job to the cluster

yes, I did add --threads 12 parameter. but it didn't work

set threads=12 but still submit single cpu job to the cluster

no, it submit a job script with 12 threads parameter but without the cluster threads requirement. I think this can be solved by editting your cipher.nf file like this: process...