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 ?