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A bunch of progress messages will stream by during the breseq run which would clutter the screen if not for the redirection to the log.txt file. The & at the end of the line tells the system to run the previous command in the background which will enable you to still type and execute other commands while breseq runs. The output text details several steps in a pipeline that combines the steps of mapping (using SSAHA2), variant calling, annotating mutations, etc. You can examine them by peeking in the log.txt file as your job runs using tail -f log.txt. The -f option means to "follow" the file and keep giving you output from it as it gets bigger. To stop the tailing command hit ctrl-c which is the keyboard interrupt signal. While breseq is running lets look at what the different parts of the command are actually doing:
| part | puprose |
|---|---|
| -j 2448 | Use 24 48 processors (the max available on lonestar5 nodes) |
| -r lambda.gbk | Use the lambda.gbk file as the reference to identify specific mutations |
| lambda_mixed_population.fastq | breseq assumes any argument not preceded by a - option to be an input fastq file to be used for mapping |
| &> log.txt | redirect the output and error to the file log.txt |
| & | run the preceding command in the background |
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