Editing CrocoBLAST:UserManual (section)

== 3.2 Pausing, stopping, and resuming ==
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 interrupt the execution in a controlled way, waiting for all currently active fragments to finish, you should use the "pause" command. In about 5 seconds (in case you did not manually set a fragment size; otherwise it can take more, or less time), your CrocoBLAST processes will all be interrupted and all your progress, from the finished fragments and from the ones that were active when the "pause" command was sent, will be saved.

To immediately interrupt CrocoBLAST execution, freeing up the memory and cores you should use the command "stop". Although this option also saves your progress, performing the stop command will make you lose the progress of the fragments currently being aligned (which typically corresponds to 5 seconds of execution in case you did not manually set a fragment size).
To pause or stop you just type the corresponding command as given below:

# <code>crocoblast -pause</code>
# <code>crocoblast -stop</code>

To resume the CrocoBLAST jobs all you need to do is to perform the "run" command as described in examples "3.1.1" and "3.1.2"

CrocoBLAST will then automatically detect the current state of each job in the queue, and continue from where it left off, resuming the first job on the queue from whichever state it was.