Redirect stderr to /dev/null of lsf conf queries (#3751)

Author: juanesarango

src/toil/batchSystems/lsfHelper.py

@@ -22,6 +22,7 @@
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 # SOFTWARE.
 import fnmatch
+import logging
 import os
 import re
 import subprocess
@@ -37,6 +38,8 @@
 DEFAULT_RESOURCE_UNITS = "MB"
 LSF_JSON_OUTPUT_MIN_VERSION = "10.1.0.2"
 
+logger = logging.getLogger(__name__)
+
 
 def find(basedir, string):
     """
@@ -109,8 +112,9 @@ def apply_bparams(fn):
     """
     cmd = ["bparams", "-a"]
     try:
-        output = subprocess.check_output(cmd).decode('utf-8')
-    except:
+        output = subprocess.check_output(cmd, stderr=subprocess.STDOUT).decode('utf-8')
+    except subprocess.CalledProcessError as exc:
+        logger.debug(exc.output.decode('utf-8'))
         return None
     return fn(output.split("\n"))
 
@@ -121,8 +125,9 @@ def apply_lsadmin(fn):
     """
     cmd = ["lsadmin", "showconf", "lim"]
     try:
-        output = subprocess.check_output(cmd).decode('utf-8')
-    except:
+        output = subprocess.check_output(cmd, stderr=subprocess.STDOUT).decode('utf-8')
+    except subprocess.CalledProcessError as exc:
+        logger.debug(exc.output.decode('utf-8'))
         return None
     return fn(output.split("\n"))