Created
February 9, 2016 15:59
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SGE job array for submitting imputation interval jobs
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| #!/bin/bash | |
| #$ -S /bin/bash | |
| ## | |
| ## Inherit user environment from the login node | |
| #$ -V | |
| ## | |
| ## Use the current directory as the working directory for SGE output and determining paths to files | |
| #$ -cwd | |
| ## | |
| ## Redirect std out/err | |
| #$ -o /mnt/iusers01/jw01/mdeasjdb/scratch/impute_practice/std_out | |
| #$ -e /mnt/iusers01/jw01/mdeasjdb/scratch/impute_practice/std_err | |
| ## | |
| ## Set array parameters. | |
| #$ -t 1-551 | |
| INTERVAL_LIST='/mnt/iusers01/jw01/jw01-shared-resources/impute2/interval_list/hg19.impute2.interval.qc.list' | |
| INTERVAL=$(sed -n -e "$SGE_TASK_ID p" $INTERVAL_LIST) | |
| sh imputation/scripts/impute2_job.sh $INTERVAL |
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Hi, any chance you could share your hg19.impute2.interval.qc.list ?