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Code Block
languagebash
titleCommands to copy the input data from the first breseq run to a new folder, and rerun breseq on the same fastq and reference file in polymorphism mode. Since this copy command is between 2 scratch locations i doubt there will be issues with it, but remember to restart an idev node if you experience difficulties
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.

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