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LSF job parameter error #192
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Please add this to your
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I made that change to ~/.caper/default.conf (attached) Now the leader job seems to be put in the queue without error, but simply and immediately disappears. I can't find error logs about why it crashed. |
I get the same situation too. I think is the some problem in caper. usually we submit job in lsf ,the command should be quote, but cap submit like 'bsub -M 10G -env all -J CAPER_SNPCalling /public/home/al9nwn5e.sh'. it will go wrong "/.lsbatch/1688980273.3800411: line 8: al9nwn5e.sh: command not found" |
When I submit an lsf hpc job I get an error because the bsub memory parameter isn't in the form that my system expects. It should get ... "-M 4000" but instead it's getting "-M 4g"
Here is the command that I'm using (default test json) and the error:
$ caper -v
2.2.3
$ echo $INPUT_JSON
https://storage.googleapis.com/encode-pipeline-test-samples/encode-atac-seq-pipeline/ENCSR356KRQ_subsampled.json
$ caper hpc submit atac.wdl -i "${INPUT_JSON}" --singularity --leader-job-name JWT_Leader
2023-04-06 10:12:03,243|caper.hpc|INFO| Running shell command: bsub -W 2880 -M 4g -env all -J CAPER_JWT_Leader /home/jtobias/y3v9bq3x.sh
4g: MEMLIMT value should be a positive integer. Job not submitted.
I've also attached my backend conf file which I recovered from a temp directory.
Please let me know what I should modify to work around this problem.
Many thanks!
orig.backend.conf.zip
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