I see this post has been sleeping for a while ... I'm sorry to have to revive it. We have some mac's that are exhibiting the same issues.
Mac 1 (MBP, 10.10.3, Java6, Java8u45, CP 2,1,2 #13a6470), pipeline 1, Works
Mac 2 (MP, 10.10.3, Java6, Java8u45, CP 2,1,2 #13a6470), pipeline 1, Works
Mac 3 (MBP, 10.9.5, Java6, Java7, CP 2,1,2 #13a6470), pipeline 1, Fails
Mac 3 (MBP, 10.9.x, Java6, Java7, CP 2.1.2 # latest build ), pipeline 1, Fails
The pipeline is loaded OK, Test mode works OK, when you click analyze we see the workers start and there was an error about wanting to clear the contents of the sqliteDB via the ExportToDatabase module (which is the third to last after SaveImages). Immediately we see this grey window pop up giving two options, terminate or open console. The console merely said, CellProfiler has terminated.
We’ve tried the suggestion to remove the config files but no luck. Any other suggestions to try?