From Array Suite Wiki

The number of threads to use for a particular module. The more threads that are allocated, the faster the algorithm will run. If ParallelJobNumber is set for an alignment module, this is the # of threads that will be used for each process.

Note: only alignment related, such as RNA-Seq, DNA-Seq and fusion alignment, (oalign) jobs are parallelized, running the same sample on multiple threads. In these cases, ParallelJobNumber and ThreadNumber or ThreadNumberPerJob should be set. Other jobs such as mutation, raw data QC, (osummary) jobs are only parallelized among samples, running one sample on one thread. In these cases, either ParallelJobNumber or ThreadNumber can be used. If ThreadNumber is used, it is actually equal to ParallelJobNumber since osummary jobs are single thread job.

The oshell default value is 4.

ThreadNumberPerJob has the same meaning.