Error in rule
Closed this issue · 2 comments
I'm trying to run atlas on SGE. I added the SGE options in the ~/.config/snakemake/cluster/key_mapping.yaml so they look like this:
# only parameters defined in key_mapping (see below) are passed to the command in the order specified.
system: "SGE" #check if system is defined below
SGE:
command: 'qsub'
key_mapping:
name: "-N"
threads: "-pe smp {}"
mem_mb: "-l m_mem_free={}M"
account: "-A {}"
queue: "-q {}"
time_min: "-l h_rt={}"
but I get following errors:
CLUSTER: 2023-07-26 17:47:24 Automatically choose best queue to submit
CLUSTER: 2023-07-26 17:47:25 Choose queue: longrun
CLUSTER: 2023-07-26 17:47:25 submit command: qsub -N -pe smp 4 -l h_rt=5760 -l m_mem_free=1000M -q longrun /data/study/fastq_files/.snakemake/tmp.xne35nac/snakejob.initialize_qc.202.sh
CLUSTER: 2023-07-26 17:47:25 Job can't be submitted
Unable to read script file because of error: error opening smp: No such file or directory
The submit command looks right, but I don't understand the issue with -pe smp {}, as this is the way I usually request the number of cores.
I also would like to omit the -q option, as the scheduler in the cluster does this automatically depending on the resources. How can I do this?
Not sure if this is relevant, but the directory ~/.config/snakemake/cluster that I created with
cookiecutter --output-dir ~/.config/snakemake https://github.com/metagenome-atlas/clusterprofile.git
cluster
SGE
contains two files: pbs_status.py and slurm_status.py, but nothing called SGE_status.py, although ~/.config/snakemake/cluster/config.yaml contains the line
cluster-status: "SGE_status.py" #
I suggest you to look at the profile for sge.
https://github.com/Snakemake-Profiles/sge/tree/master/
It has already rhe sge submit, status and cancel script.
You might need to modify it a little bit but I think it should be easier than with my profile..