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Code Block
languagebash
cd $SCRATCH/core_ngs/align2
$path_code/script/align/align_bwa_illumina.sh

Run the pipeline. By piping the output to tee <filename> we can see the script's progress at the terminal, and it also is written to <filename>.

Code Block
languagebash
$path_code/script/align/align_bwa_illumina.sh ./fastq/Sample_Yeast_L005_R1.cat.fastq.gz yeast_chip sacCer3 1 2>&1 | tee aln.yeast_chip.log