Can you try to change the line:
file=$(ls -1 *.fastq | tail -n +${SGE_TASK_ID}| head -1)
to be :
file=$(ls -1 *.fastq | tail -${SGE_TASK_ID}| head -1)
On Wed, Sep 2, 2015 at 1:17 PM, VG <[email protected]> wrote:
> HI everyone,
>
> I am trying to make a job array script. I have 2 files in my working
> directory namely abc.fastq and def.fastq
>
> I want to run one command on these 2 files(later on I will include more
> .fastq files) on different compute nodes. So I made this array script, but
> it only produces output for abc.fastq.
>
> Here is the script:
>
> #!/bin/bash
>
> file=$(ls -1 *.fastq | tail -n +${SGE_TASK_ID}| head -1)
> filename=${file%.fastq}
> awk 'NR % 2 == 0{print substr($1,7,100)};NR % 2 ==1' $file >
> ${filename}_BR.fastq
>
>
> I submit it as qsub -cwd -j y -t 1-2 -N testjob ./script.sh
>
> But only abc.fastq file gets processed?:
>
> What am I doing wrong here?
>
> Hope to hear sonn from you guys.
>
> Thanks
>
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--
Best,
Feng
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