Merge branch 'SW-961-fix-pipelinecontrol-2' into 'master'

SW-961: Log stderr but do not use it as output to parse. Unfortunately, slurm...

Closes SW-961

See merge request !423

MAC/Services/src/PipelineControl.py

@@ -102,15 +102,17 @@ def runCommand(cmdline, input=None):
         cmdline,
         stdin=subprocess.PIPE if input else None,
         stdout=subprocess.PIPE,
-        stderr=subprocess.STDOUT,
+        stderr=subprocess.PIPE,
         shell=True,
         universal_newlines=True
     )
 
     # Feed input and wait for termination
     logger.debug("runCommand input: %s", input)
-    stdout, _ = communicate_returning_strings(proc, input)
+    stdout, stderr = communicate_returning_strings(proc, input)
     logger.debug("runCommand output: %s", stdout)
+    if stderr:
+        logger.warn("runCommand stderr output: %s", stderr)
 
     # Check exit status, bail on error
     if proc.returncode != 0: