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Old 06-27-2011, 03:03 PM   #1
Location: boston

Join Date: Jun 2011
Posts: 27
Default Save error report as text file in BWA

Hi I'm using SUN Grid Engine to submit BWA jobs, written by shell script like this:


#$ -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/

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
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.

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