Comments (4)
Hi Luis, I'm not sure what the problem might be here other than an issue I had a while ago after updating Snakemake. Are you using a profile to run on the cluster? if so can you show me your profile config?
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HI Mike,
Here the profile config file.
Thank you,
Luis
config.txt
from hecatomb.
Hi Luis,
Yes I see the problem. I've run into this before but forgot to update the example profile with Hecatomb. You need to add --parsable
to the sbatch command following a Snakemake update. Try this:
cluster:
mkdir -p logs/{rule}/ &&
sbatch
--cpus-per-task={threads}
--mem={resources.mem_mb}
--time={resources.time}
--job-name=smk-{rule}
--parsable
--output=logs/{rule}/{jobid}.out
--error=logs/{rule}/{jobid}.err
default-resources:
- mem_mb=2000
- time=1440
jobs: 100
latency-wait: 50
local-cores: 8
restart-times: 1
max-jobs-per-second: 20
keep-going: True
rerun-incomplete: True
printshellcmds: True
scheduler: greedy
use-conda: True
conda-frontend: mamba
cluster-status: ~/.config/snakemake/slurm/slurm-status.py
max-status-checks-per-second: 10
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Now it's working!
Thanks a lot Mike.
Luis
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