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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