diff --git a/swh/graph/luigi/utils.py b/swh/graph/luigi/utils.py
--- a/swh/graph/luigi/utils.py
+++ b/swh/graph/luigi/utils.py
@@ -6,30 +6,59 @@
 from pathlib import Path
 from typing import Dict
 
+LOGBACK_CONF = b"""\
+<configuration>
+  <appender name="STDERR" class="ch.qos.logback.core.ConsoleAppender">
+    <target>System.err</target>
+    <encoder>
+      <pattern>%d{HH:mm:ss.SSS} [%thread] %-5level %logger{36} %msg%n</pattern>
+    </encoder>
+  </appender>
+
+  <root level="debug">
+    <appender-ref ref="STDERR" />
+  </root>
+</configuration>
+"""
+"""Overrides the default config, to log to stderr instead of stdout"""
+
 
 def run_script(script: str, output_path: Path) -> None:
     import os
     import subprocess
+    import tempfile
 
     from ..config import check_config
 
     conf: Dict = {}  # TODO: configurable
 
-    conf = check_config(conf)
-    env = {
-        **os.environ.copy(),
-        "JAVA_TOOL_OPTIONS": conf["java_tool_options"],
-        "CLASSPATH": conf["classpath"],
-    }
-
     output_path.parent.mkdir(parents=True, exist_ok=True)
 
     tmp_output_path = Path(f"{output_path}.tmp")
 
-    with tmp_output_path.open("wb") as tmp_output:
-        subprocess.run(
-            ["bash", "-c", f"{script.strip()}"], stdout=tmp_output, env=env, check=True
-        )
+    conf = check_config(conf)
+
+    with tempfile.NamedTemporaryFile(prefix="logback_", suffix=".xml") as logback_conf:
+        logback_conf.write(LOGBACK_CONF)
+
+        java_tool_options = [
+            "-Dlogback.configurationFile={logback_conf}",
+            conf["java_tool_options"],
+        ]
+
+        env = {
+            **os.environ.copy(),
+            "JAVA_TOOL_OPTIONS": " ".join(java_tool_options),
+            "CLASSPATH": conf["classpath"],
+        }
+
+        with tmp_output_path.open("wb") as tmp_output:
+            subprocess.run(
+                ["bash", "-c", f"{script.strip()}"],
+                stdout=tmp_output,
+                env=env,
+                check=True,
+            )
 
     # Atomically write the output file
     tmp_output_path.replace(output_path)