We read every piece of feedback, and take your input very seriously.
To see all available qualifiers, see our documentation.
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
I created a cluster.json file to use exclusive nodes on lsf cluster:
{ "__default__": { "queue": "normal", "nodes": "lz-gpu lf-gpu ln-gpu lx-gpu ly-gpu ll-gpu", "extra": "", "threads": 4 # Default thread count, can be overridden per rule } }
Snakemake version 7.32.4
Please only report bugs of the latest stable release of Snakemake. raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command 'bsub -M 200 -n 1 -R 'select[mem>200] rusage[mem=200] span[hosts=1]' -W 300 -o "logs/cluster/patch_segmentation_baysor/index=53/jobid55_6637d0e7-670b-4ba2-ad88-3580dba86228.out" -e "logs/cluster/patch_segmentation_baysor/index=53/jobid55_6637d0e7-670b-4ba2-ad88-3580dba86228.err" -J "patch_segmentation_baysor.index=53" -q normal /lila/data/chanjlab/ryanr2/sopa/workflow/.snakemake/tmp.5z0azw4k/snakejob.patch_segmentation_baysor.55.sh' returned non-zero exit status 255.
raise BsubInvocationError(error) main.BsubInvocationError: Command 'bsub -M 200 -n 1 -R 'select[mem>200] rusage[mem=200] span[hosts=1]' -W 300 -o "logs/cluster/patch_segmentation_baysor/index=53/jobid55_6637d0e7-670b-4ba2-ad88-3580dba86228.out" -e "logs/cluster/patch_segmentation_baysor/index=53/jobid55_6637d0e7-670b-4ba2-ad88-3580dba86228.err" -J "patch_segmentation_baysor.index=53" -q normal /lila/data/chanjlab/ryanr2/sopa/workflow/.snakemake/tmp.5z0azw4k/snakejob.patch_segmentation_baysor.55.sh' returned non-zero exit status 255. Error submitting jobscript (exit code 1):
Describe the bug its an error in the lsf_submit. Do I need to change the snakefile as well?
The text was updated successfully, but these errors were encountered:
Should this rather be addressed in the corresponding profiles repo? see https://github.com/Snakemake-Profiles/lsf
Sorry, something went wrong.
No branches or pull requests
I created a cluster.json file to use exclusive nodes on lsf cluster:
Snakemake version
7.32.4
Please only report bugs of the latest stable release of Snakemake.
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command 'bsub -M 200 -n 1 -R 'select[mem>200] rusage[mem=200] span[hosts=1]' -W 300 -o "logs/cluster/patch_segmentation_baysor/index=53/jobid55_6637d0e7-670b-4ba2-ad88-3580dba86228.out" -e "logs/cluster/patch_segmentation_baysor/index=53/jobid55_6637d0e7-670b-4ba2-ad88-3580dba86228.err" -J "patch_segmentation_baysor.index=53" -q normal /lila/data/chanjlab/ryanr2/sopa/workflow/.snakemake/tmp.5z0azw4k/snakejob.patch_segmentation_baysor.55.sh' returned non-zero exit status 255.
raise BsubInvocationError(error)
main.BsubInvocationError: Command 'bsub -M 200 -n 1 -R 'select[mem>200] rusage[mem=200] span[hosts=1]' -W 300 -o "logs/cluster/patch_segmentation_baysor/index=53/jobid55_6637d0e7-670b-4ba2-ad88-3580dba86228.out" -e "logs/cluster/patch_segmentation_baysor/index=53/jobid55_6637d0e7-670b-4ba2-ad88-3580dba86228.err" -J "patch_segmentation_baysor.index=53" -q normal /lila/data/chanjlab/ryanr2/sopa/workflow/.snakemake/tmp.5z0azw4k/snakejob.patch_segmentation_baysor.55.sh' returned non-zero exit status 255.
Error submitting jobscript (exit code 1):
Describe the bug
its an error in the lsf_submit. Do I need to change the snakefile as well?
The text was updated successfully, but these errors were encountered: