add stdout=subprocess.PIPE to subprocess.run (#5078)

DataBiosphere · Sep 3, 2024 · 8a8fed4 · 8a8fed4
1 parent f23b1d3
commit 8a8fed4
Showing 1 changed file with 1 addition and 1 deletion.
diff --git 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: