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
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