How can I specify an email address in the SLURM snakemake json configuration file?

Question

I am working on a SLURM-based cluster. I am currently using the following slurm json file:

{
    "__default__" :
    {
        "A" : "overall",
        "time" : "96:00:00",
        "nodes": 1,
        "ntasks": 1,
        "cpus" : 24,
        "p" : "LONG",
        "mem": 16G,
        "output": "snakemake%A.out",
        "error": "snakemake%A.err"
    }
}

along with the following command:

snakemake --jobs 200 --use-conda --printshellcmds  --cluster-config slurm.json --cluster "sbatch -A {cluster.A} -p {cluster.p} -t {cluster.time} --output {cluster.output} --error {cluster.error} --ntasks {cluster.ntasks} --cpus-per-task {cluster.cpus} --mem {cluster.mem}"

I would like to be able to specify my email and receive an email when a job finishes. I have tried adding a line in the json file with "email": my@email.com and an option to the sbatch command --email {cluster.email} but that did not work.

Anyone knows how to do it?

Answer 1

As noted by the comments and the SLURM manual (not so much bioinformatics related?)

You need the following terms in your batch/queuing command:

--mail-type=ALL
--mail-user=you@email.com

I used "ALL" which will send you all reports. If you just want the finish message then you would use "END" and "FAIL" like such:

--mail-type=END,FAIL

Here are the specifics from the manual if you wish to make a different selection:

--mail-type=

Notify user by email when certain event types occur. Valid type values are NONE, BEGIN, END, FAIL, REQUEUE, ALL (equivalent to BEGIN, END, FAIL, REQUEUE, and STAGE_OUT), STAGE_OUT (burst buffer stage out and teardown completed), TIME_LIMIT, TIME_LIMIT_90 (reached 90 percent of time limit), TIME_LIMIT_80 (reached 80 percent of time limit), TIME_LIMIT_50 (reached 50 percent of time limit) and ARRAY_TASKS (send emails for each array task). Multiple type values may be specified in a comma separated list. The user to be notified is indicated with --mail-user. Unless the ARRAY_TASKS option is specified, mail notifications on job BEGIN, END and FAIL apply to a job array as a whole rather than generating individual email messages for each task in the job array.

--mail-user=

User to receive email notification of state changes as defined by --mail-type. The default value is the submitting user.