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Code Block
titlePrepare to align yeast data
cd $SCRATCH/core_ngs/alignment
ln -s $WORK/core_ngs/references/bwa/sacCer3
ls sacCer3

As our workflow indicated, we first use bwa aln on the R1 and R2 FASTQs, producing a BWA-specific .sai intermediate binary files. Since these alignments are completely independent, we can execute them in parallel in a batch job.


Create the batch submission script specifying a wayness of 2 (2 tasks per node) on the normal queue and a time of 1 hour10 minutes, then submit the job and monitor the queue:

Code Block
titleSubmit BWA alignment job
launcher_creator.py -n aln -j aln.cmds -t 0100:0010:00 -q normal -w 2
sbatch aln.slurm
showq -u