Print errors to STDERR

[Jeltje]

I know this is true for rnaseq_cgl and ProTECT (filed a ticket there, too): when the program exits with an error, it is printed to STDOUT. The same is true for warnings. This makes it harder to find the problem (there's a lot of log output) and it also doesn't seem to be good practice.

[hannes-ucsc]

All errors should be logged logging package, not printed, and logging should be configured to write to sys.stderr. This might be a Toil issue, actually, but before we go down that route, I would like this issue to be verified.

[jvivian]

In all production pipelines there is now only use of job.fileStore.logToMaster