...
and submit it using qsub:
qsub bwa_test.sge
Check that it's in the queue:
qstat
When the job finishes, you should have four SAM files that contain the alignment information: test0*.sam. They have header lines. To combine them using cat, we want to get rid of the headers. (The proper way of combining them would be to use samtools sort and merge, but that's just barely beyond our scope today.)
awk '! /^@/' test00.sam > test_noheader-00.sam
cat test_noheader*.sam