Editing CrocoBLAST:Job management (section)

==Execution==
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Say you have ''created one or more BLAST jobs'' and are ready to start munching some sequences. It's easy:

<code>
CrocoBLAST -run
</code>

This tells CrocoBLAST to take the input file, break it into little fragments, and submit each fragment for sequence alignment as soon as a core becomes free. This means that, if your computer has only one core, the alignment will start only after fragmentation of the input file is complete. However, if your computer has two cores (or one core that supports multi-threading), the alignment will start as soon as at least one fragment has been generated, which means immediately. The alignment of each fragment runs as an independent thread. The more threads you can run simultaneously, the faster your job will finish. This depends on the number and type of cores your computer has.

When you run CrocoBLAST without any additional options, you will make the most efficient use of your computational resources, as CrocoBLAST will figure out how to best parallelize the calculation on your machine. Nonetheless, if you want to limit the number of threads running simultaneously, you may do so:

<code>
CrocoBLAST -run --num_threads <span style="color:orange">number_of_threads</span>
</code>

Similarly, you can easily stop or pause the execution at any time. The difference between ''pause'' and ''stop'' rests with how long you are willing to wait before your computational resources become available, and how much partial output you need. To immediately kill a CrocoBLAST job and free up the memory and cores:

<code>
CrocoBLAST -stop
</code>

On the other hand, if you are more interested in the output:

<code>
CrocoBLAST -pause
</code>

This lets CrocoBLAST know that no new threads should be initiated, and the output produced by each running thread will be incorporated in the partial results as soon as the thread finishes. Therefore, you will have to wait until all running threads have completed. Depending on the type of BLAST program you are running, the size of the database, and the similarity between your input sequences and the sequences in the database, you may have to wait a considerable amount of time. However, this will ensure that you can resume the calculation at a later time. To resume, simply tell CrocoBLAST to start munching. 

<code>
CrocoBLAST -run
</code>

It will automatically detect the current state of each job in the queue, and continue from where it left off, unless you have made changes to the queue in the meantime. While CrocoBLAST operates with the concept of queue, it is important to note that only one job is active at any given time. You can check the current state of the CrocoBLAST queue:

<code>
CrocoBLAST -status
</code>

This will provide you with information regarding which jobs are queued, with full details regarding the job ID and BLAST setup, as well as a description about the progress of the alignment. The progress of each job is described in three main directions: fragmentation of the input file, alignment, and assembly of results. 
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