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Many bioinformatics workflows run the same command on multiple files. When the file sizes are small, the command could only take a few seconds to finish.If you submit the processing of each file as a job often causes the job scheduler to complain of short-running jobs.
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Create a working directory on scratch3 scratch and change into the newly-created directory. For example, for user abc123, the working directory will be
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srun --pty -p interactive -t 0-12:0:0 --mem 2000M -n 1 /bin/bash mkdir /n/scratch3scratch/users/a/abc123/testBatchJob cd /n/scratch3scratch/users/a/abc123/testBatchJob |
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