Timing problem with jobs

Due to the -hold_jid 'ovl_asm parameter passed to qsub, if more than one Celera Assembler jobs are run in parallel from the same user account, the runCA.sge.out.*.sh scripts submitted by qsub from all jobs will hold until all ovl_asm tasks have completed.

This is problematic as multiple jobs spawned by SMRT Portal at the same time will all run with the same user name, such as smrtanalysis. These jobs will be all be waiting for the job with the longest ovl_asm tasks to complete before proceeding. This unnecessarily prolonging analysis.

The sgeName= parameter solves this issue for the default use case where no external \*.spec file is specified. However, to run multiple CA jobs in parallel with externally specified *.spec files, you need to remember to add or modify the sgeName= parameter in the *.spec file to be different for each job running in parallel.