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titleClick here for commands file example and launcher_creator.py generator
Code Block
titleExample commands file
breseq -j 12 -r NC_012967.1.gbk -o output_00K SRR030252_1.fastq SRR030252_2.fastq &> 00K.log.txt
breseq -j 12 -r NC_012967.1.gbk -o output_02K SRR030253_1.fastq SRR030253_2.fastq &> 02K.log.txt
breseq -j 12 -r NC_012967.1.gbk -o output_05K SRR030254_1.fastq SRR030254_2.fastq &> 05K.log.txt
breseq -j 12 -r NC_012967.1.gbk -o output_10K SRR030255_1.fastq SRR030255_2.fastq &> 10K.log.txt
breseq -j 12 -r NC_012967.1.gbk -o output_15K SRR030256_1.fastq SRR030256_2.fastq &> 15K.log.txt
breseq -j 12 -r NC_012967.1.gbk -o output_20K SRR030257_1.fastq SRR030257_2.fastq &> 20K.log.txt
breseq -j 12 -r NC_012967.1.gbk -o output_40K SRR030258_1.fastq SRR030258_2.fastq &> 40K.log.txt
Code Block
launcher_creator.py -q normal -t 3:00:00 -n launcher -a "UT-2015-05-18" -m "module load bowtie/2.1.0"
qsub launcher.sge

This will likely sit for some time in the launcher que, making it a good opportunity to work through the interrogating launcher queue portion of our linux tutorial if you didn't get the opportunity to earlier.

 

Examining breseq results

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