HPC Execution problem when changing to V.1.1.0

[luisalbertoc95]

HPC Execution problem when changing to V.1.1.0

[beardymcjohnface]

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?

[luisalbertoc95]

HI Mike,

Here the profile config file.

Thank you,

Luis
config.txt

[beardymcjohnface]

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

[luisalbertoc95]

Now it's working!

Thanks a lot Mike.

Luis