Time limits on UnifiedGenotyper (UG)
I'm currently having problems with UG not gracefully quitting and creating a valid truncated bcf/vcf file using the -maxRuntime and -maxRuntimeUnits options.
To test I have set -maxRuntime 1 -maxRuntimeUnits MINUTES and the process has run for a few days already!
I have two questions that may help resolve this problem:
1. Are actual real life minutes being measured or CPU minutes?
- How often is the runtime checked? (i.e. exceedsRuntimeLimit function called). As it appears that each of the jobs that are running over the time limit are stuck on a particular site and if it gets called after each site/interval is called then this may explain why it may be going over the time limit.