Hi I'm using SUN Grid Engine to submit BWA jobs, written by shell script like this:
Just as shown at the end of script, I want to save the error report as .txt file; actually -o $HOME/sge_jobs_output/sge_job.$JOB_ID.out -j y has done similar thing; but what I want is variable SAM_NAME instead of JOB_ID.
I tried using '>', like : /share/bin/bwa aln hg19_index "$SAM_NAME_1".recal.fastq.gz > "$SAM_NAME_1".sai 2> "$SAM_NAME_1".txt
But this doesn't work. Seems all .sai file information rather than error report will be stored in .txt.
Thanks
Code:
#!/bin/bash #$ -pe single 24 #$ -V #$ -cwd #$ -o $HOME/sge_jobs_output/sge_job.$JOB_ID.out -j y #$ -S /bin/bash #$ -l mem_free=8G cd $HOME/scratch/bwa2/ job_number=$SGE_TASK_ID SAM_NAME_1=`head -"$job_number" master_list_1|tail -1` /share/bin/bwa aln hg19_index "$SAM_NAME_1".recal.fastq.gz > "$SAM_NAME_1".sai #Do sth. here to save the output as text file. Here by output I don't mean # .sai file, but the error report like "10000000 sequences have been processed", #And text file name is SAM_NAME_1, which is a variable
I tried using '>', like : /share/bin/bwa aln hg19_index "$SAM_NAME_1".recal.fastq.gz > "$SAM_NAME_1".sai 2> "$SAM_NAME_1".txt
But this doesn't work. Seems all .sai file information rather than error report will be stored in .txt.
Thanks