Editing CrocoBLAST:UserManual (section)

==3.1. Running==
Say you have ''created one or more BLAST jobs'' and are ready to BLAST them. All you need to do is:

{| class="wikitable" border="1" style="margin: 1em auto 1em auto;" width="650px"
 |- 
 |<!--Col1-->'''a)''' Select the “Manage BLAST jobs” tab.
 |<!--Col2-->'''b)''' (Optional) Select the number of threads to be used.
 |-
 |<!--Col1-->[[File:CrocoBLAST RunQueue1.png|800x800px]]
 |<!--Col2-->[[File:CrocoBLAST RunQueue2.png|800x800px]]
 |- style="background: #313131;"
 |
 |
 |-
 |<!--Col1-->'''c)''' Click on the “Run queue” button.
 |<!--Col2-->'''d)''' You can now inspect the progress of the Jobs on your queue until they finish.
 |-
 |<!--Col1-->[[File:CrocoBLAST RunQueue3.png|800x800px]]
 |<!--Col2-->[[File:CrocoBLAST RunQueue4.png|800x800px]]
 |}

In case you do not set the number of threads, CrocoBLAST will detect how many threads your computer has and assign all of them to CrocoBLAST. That is a good option if you want to dedicated all the computer resources for achieving maximum performance, and if no other intense calculations or programs will be running concurrently to CrocoBLAST on the assigned computer.

Assigning a specific number of threads is useful if you are using a shared computer that concurrently runs different calculations or programs, has several users, or if you were allowed by the manager of a server to use only a certain number of threads in that computer. 

The "Run queue" commands tells CrocoBLAST to sequentially run '''all jobs in queue''' by in small fragments, assigned to all available cores and reassigned as soon as core becomes free until all fragments of all jobs are finished.

The execution process is divided into:
   "Fragmenting", when the input file is fragmented into smaller parts;
   "Aligning", when the input file is being aligned using BLAST against the specified database;
   "Assembling", when the output files corresponding to all fragments are merged together in a final output identical to that of BLAST. 
Each step has its own progress bar and time estimation.

If CrocoBLAST was assigned a single thread, each step runs sequentially after the previous one is finished. However, if you are running CrocoBLAST with several threads, the Alignment will start as soon as a certain number of fragments have been generated, which usually happens in a few seconds, and both stages run concurrently. Similarly, given that more than 1 thread was assigned to CrocoBLAST, the assembling stage will start as soon as the fragmenting stage finishes, running concurrently with the alignment stage.