Hi Reuti,
So basically none of my above script commands runs both of them together.
Only one finishes. But to debug the script , i use $file and $filename and
they got printed out perfectly fine. I STILL DON'T UNDERSTAND WHAT COULD BE
WRONG WITH MY SCRIPT?
On Wed, Sep 2, 2015 at 3:55 PM, Reuti <re...@staff.uni-marburg.de> wrote:
> Hi,
>
> Am 02.09.2015 um 19:17 schrieb VG:
>
> > HI everyone,
> >
> > I am trying to make a job array script. I have 2 files in my working
> directory namely abc.fastq and def.fastq
> >
> > I want to run one command on these 2 files(later on I will include more
> .fastq files) on different compute nodes. So I made this array script, but
> it only produces output for abc.fastq.
> >
> > Here is the script:
> >
> > #!/bin/bash
> >
> > file=$(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 >
> ${filename}_BR.fastq
> >
> >
> > I submit it as qsub -cwd -j y -t 1-2 -N testjob ./script.sh
> >
> > But only abc.fastq file gets processed?:
>
> After the first run the list of files looks different and includes the
> outputfile of the first run. I fear you ended up with an additional file
> abc _BR_BR.fastq.
>
> filename=$(ls *.fastq | sed -n "1~2s/.fastq$//p" | sed -n ${SGE_TASK_ID}p)
>
> -- Reuti
>
> PS: If `ls` doesn't see a TTY, it defaults to single column output.
>
>
> > What am I doing wrong here?
> >
> > Hope to hear sonn from you guys.
> >
> > Thanks
> > _______________________________________________
> > users mailing list
> > users@gridengine.org
> > https://gridengine.org/mailman/listinfo/users
>
>
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