From 8a8fed427cb46ab5cc78db11ad34d6d34d9e1817 Mon Sep 17 00:00:00 2001
From: stxue1 <122345910+stxue1@users.noreply.github.com>
Date: Tue, 3 Sep 2024 10:21:05 -0700
Subject: [PATCH] add stdout=subprocess.PIPE to subprocess.run (#5078)

---
 src/toil/batchSystems/lsf.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/toil/batchSystems/lsf.py b/src/toil/batchSystems/lsf.py
index 5d44029af4..fe41cfb687 100644
--- a/src/toil/batchSystems/lsf.py
+++ b/src/toil/batchSystems/lsf.py
@@ -138,7 +138,7 @@ def coalesce_job_exit_codes(self, batch_job_id_list: list) -> list:
                 logger.debug("Getting coalesced job exit codes via bjobs")
                 bjobs_records = self.parseBjobs(
                     subprocess.run(
-                        args, check=False, stderr=subprocess.STDOUT, encoding="utf-8"
+                        args, check=False, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, encoding="utf-8"
                     ).stdout
                 )
                 if bjobs_records: