Read Mapper Reference Caching

Mapping reads using an index of the reference genome can be substantially faster than mapping reads to the reference directly, especially for large genomes. Generating a reference index can take some time, so the first time a mapping is run using a particular reference genome, the index that is created is cached in the system tmp folder, where it is used by subsequent mapping jobs involving that reference.

Reference indexes are not removed as part of a CLC software shutdown or restart, but may be removed for other reasons, in which case, the next time a mapping job is run using that reference genome, the index will be rebuilt. Examples of reasons that indexes could be removed include that the system tmp is cleared, or that the maximum space allowed for reference index files is exceeded, in which case, the oldest indexes are removed.

The default space limit for index files is 16 GB.

The reference cache size can be changed by creating a file called readmapper.properties, with an entry referencecachesize = <size in bytes>, for example
referencecachesize = 8589934592

A copy of this file should then be placed into the settings folder in the following locations: