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The breseq_commands file
As already noted above, the run will still take ~1 hour to runwill take ~3 hours to complete. Making this a great opportunity to use the job queue system rather than interactively on an idev session. As we will discuss on Friday, the job queue system is the common way you will use TACC to analyze your own data. For now we will be ignoring the theory and practice of how to use the system and instead focus on getting our analysis into the queue system so it can run overnight before tomorrow's class. As you will be reminded it is recommended that you start Thursday's class with evaluating this job submission in case you choose to make use of it during Thursday's class.
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As the file provided is generic you will need to make a few changes to the file. Note that most of these lines have additional text to the right of the line. This commented text is present to help remind you what goes on each line, leaving it alone will not hurt anything, removing it may make it more difficult for you to remember what the purpose of the line is
| Line number | As is | To be |
|---|---|---|
| 16 | #SBATCH -J jobName | #SBATCH -J D3Breseq |
| 21 | #SBATCH -t 12:00:00 | #SBATCH -t 4:00:00 |
| 22 | ##SBATCH --mail-user=ADD | #SBATCH --mail-user=<YourEmailAddress> |
| 23 | ##SBATCH --mail-type=all | #SBATCH --mail-type=all |
| 27 | conda activate GVA2021 | conda activate GVA-breseq |
| 31 | export LAUNCHER_JOB_FILE=commands | export LAUNCHER_JOB_FILE=breseq_commands |
The changes to lines 22 and 23 are optional but will give you an idea of what types of email you could expect from TACC if you choose to use these options. Just be sure to pay attention to these 2 lines starting with a single # symbol after editing them.
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