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I am running snakemake on a SGE cluster, and I have problems with the submission of jobs involving the activation of a conda environment. The jobs start and I get the message "Activating conda environment". But then they keep running forever doing nothing and without error messages.

The envs get correctly activated on the login nodes, so I think the problem is with qsub. I tried to use the -V option as suggested here Using Conda enviroment in SnakeMake on SGE cluster problem but it does not seem to work for me.

This is what I use for submission:

snakemake -j 2 --use-conda --cluster-config cluster.json --cluster "{cluster.qsub} -l virtual_free={cluster.ram},h_rt={cluster.time},disk={cluster.disk} -q {cluster.queue}" --keep-going --latency-wait 100

And these are the configurations in my cluster.json file:

{
  "__default__" :
  {
  "qsub" : "qsub -cwd -V -o logs/{rule}.{wildcards}.$$.out -e logs/{rule}.{wildcards}.$$.out",
  "ram" : "4G",
  "time" : "01:00:00",
  "disk" : "2G",
  "queue" : "short-sl7"
  }
}

The point is that submitted jobs work fine when no environment activation is needed.

Does anyone have any suggestion?

Federica Mantica
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    Can you also add your conda environment file? Also, have you tried using qsub in interactive mode and try to activate the environment in `.snakemake/conda/$hash` and see how long it takes? – JohnnyBD Nov 20 '18 at 12:59

0 Answers0