5.3. Why is the total memory used for my read mapping more than specified as the maximum for the java process?
There are three phases when running a read mapping job:
- a pre-processing phase
- a computational phase
- a post-processing phase.
The pre- and post-processing phases are part of the CLC java process, and are thus subject to the heap size restrictions you place on java using the Xmx setting in the vmoptions file. How to alter this setting in the Workbench is described in our manual here:
The computational phase, however, is run via a native binary. It is thus not subject to any java-related settings and will use the amount of memory it needs.
The system requirements for the Workbench are provided on our website (see link below). The information includes a guide to the amount of memory required for running mappings against certain sample genomes. The amount of memory required is linked with the size of the genome you are mapping to.