SLURM Job Array output file in command

Question

I have a command list like this

bedtools intersect -a BED1 -b BED2 >BED1_BED2_overlaps.txt
...

with over 100 files.

Here is the header for my job submission

#SBATCH -t 0-08:00
#SBATCH --job-name=JACCARD_DNase
#SBATCH -o /oasis/scratch/XXX/XXX/temp_project/logs/JACCARD_DNase_%a_out
#SBATCH -e /oasis/scratch/XXX/XXX/temp_project/logs/JACCARD_DNase_%a_err
#SBATCH --array=1-406%50

When I submit the job I get this error

Error: Unable to open file >BED1_BED2_overlaps.txt Exiting.

I tried to pipe an echo command like this

bedtools intersect -a BED1 -b  BED2 | echo "BED1 BED2"

And I got

Error: Unable to open file |. Exiting.

So what gives? How can I submit array jobs with Bash syntax like > output and | pipes?

damienfrancois · Accepted Answer · 2016-07-12 21:04:31Z

3

It looks like you are missing the shebang ; your submission script should start with

#! /bin/bash

or any other shell you like.

answered Jul 12, 2016 at 21:04

damienfrancois

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