...
| Code Block | ||||
|---|---|---|---|---|
| ||||
mkdir $SCRATCH/GVA_breseq_lambda_mixed_pop_polymode cp $SCRATCH/GVA_breseq_lambda_mixed_pop/lambda* $SCRATCH/GVA_breseq_lambda_mixed_pop_polymode cd $SCRATCH/GVA_breseq_lambda_mixed_pop_polymode breseq -j 68 -p -r lambda.gbk lambda_mixed_population.fastq |
This time, the run should take ~5 minutes, and again finish with a last line of "+++ SUCCESSFULLY COMPLETED".
Evaluating output
Again you will need to transfer files back to your local computer to visualize the differences. The same exact compression command will work as the folder name is the same. In doing so you need to be careful where you transfer that file on your local computer such that you don't overwrite the previously transferred files. Maybe add a _polymode to the directory you are transferring to as we did in our command above. Again help with SCP can be found here.
...
As already noted, the run will take ~3 ~2.5 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.
...
Additional tutorials dealing with breseq
Error correction
Additional information on analyzing the output
...
This tutorial was substantially reformatted from the most recent version found here. Our thanks to the previous instructors.