tools/gatk: when determining gatk version, ignore stderr output to av…

…oid Picked up _JAVA_OPTIONS message
broadinstitute · Feb 7, 2020 · 6fe46aa · 6fe46aa
1 parent fca68ca
commit 6fe46aa
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/tools/gatk.py b/tools/gatk.py
@@ -93,7 +93,8 @@ def _get_tool_version(self):
                 self.install_and_get_path(), '--version'
             ]
 
-        self.tool_version = util.misc.run_and_print(cmd, buffered=False, silent=True).stdout.decode("utf-8").strip()
+        self.tool_version = util.misc.run_and_print(cmd, buffered=False, silent=True,
+                                                    stderr=subprocess.DEVNULL).stdout.decode("utf-8").strip()
 
     def ug(self, inBam, refFasta, outVcf, options=None, JVMmemory=None, threads=None):
         options = options or ["--min_base_quality_score", 15, "-ploidy", 4]