fix: differentiation between stdout and stderr upon job submission, might fix #157

Author: cmeesters

snakemake_executor_plugin_slurm/__init__.py

@@ -217,20 +217,27 @@ def run_job(self, job: JobExecutorInterface):
 
         self.logger.debug(f"sbatch call: {call}")
         try:
-            out = subprocess.check_output(
-                call, shell=True, text=True, stderr=subprocess.STDOUT
-            ).strip()
+            process = subprocess.Popen(call, hell=True, text=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+            out, err = process.communicate()
+            if process.returncode != 0:
+                raise subprocess.CalledProcessError(
+                    process.returncode, call, output=err
+                )
         except subprocess.CalledProcessError as e:
             raise WorkflowError(
                 f"SLURM job submission failed. The error message was {e.output}"
             )
+        if err: # any other error message?
+            raise WorkflowError(
+                f"SLURM job submission failed. The error message was {err}"
+            )
 
         # multicluster submissions yield submission infos like
         # "Submitted batch job <id> on cluster <name>" by default, but with the
         # --parsable option it simply yields "<id>;<name>".
         # To extract the job id we split by semicolon and take the first element
         # (this also works if no cluster name was provided)
-        slurm_jobid = out.split(";")[0]
+        slurm_jobid = out.strip().split(";")[0]
         slurm_logfile = slurm_logfile.replace("%j", slurm_jobid)
         self.logger.info(
             f"Job {job.jobid} has been submitted with SLURM jobid {slurm_jobid} "