diff --git a/pkgs/clan-cli/clan_cli/cmd.py b/pkgs/clan-cli/clan_cli/cmd.py
index cafff882..5650cc70 100644
--- a/pkgs/clan-cli/clan_cli/cmd.py
+++ b/pkgs/clan-cli/clan_cli/cmd.py
@@ -25,7 +25,10 @@ def handle_output(process: subprocess.Popen, log: Log) -> tuple[str, str]:
     stdout_buf = b""
     stderr_buf = b""
 
-    while len(rlist) != 0:
+    # Note: We need to read till the process is done, otherwise we might block
+    # forever because the process might be waiting for us to read from the pipe
+    # before it can continue and will block in the write call.
+    while True:
         r, _, _ = select.select(rlist, [], [], 0)
 
         def handle_fd(fd: IO[Any] | None) -> bytes:
@@ -33,7 +36,6 @@ def handle_output(process: subprocess.Popen, log: Log) -> tuple[str, str]:
                 read = os.read(fd.fileno(), 4096)
                 if len(read) != 0:
                     return read
-                rlist.remove(fd)
             return b""
 
         ret = handle_fd(process.stdout)
@@ -48,6 +50,11 @@ def handle_output(process: subprocess.Popen, log: Log) -> tuple[str, str]:
             sys.stderr.buffer.write(ret)
             sys.stderr.flush()
         stderr_buf += ret
+
+        # Check if the process is still running
+        if process.poll() is not None:
+            break
+
     return stdout_buf.decode("utf-8"), stderr_buf.decode("utf-8")
 
 
diff --git a/pkgs/clan-cli/clan_cli/secrets/generate.py b/pkgs/clan-cli/clan_cli/secrets/generate.py
index 46813a60..27d815bd 100644
--- a/pkgs/clan-cli/clan_cli/secrets/generate.py
+++ b/pkgs/clan-cli/clan_cli/secrets/generate.py
@@ -1,10 +1,9 @@
 import argparse
 import logging
 import os
-import subprocess
 import sys
 
-from clan_cli.errors import ClanError
+from clan_cli.cmd import Log, run
 
 from ..machines.machines import Machine
 
@@ -17,15 +16,14 @@ def generate_secrets(machine: Machine) -> None:
     env["PYTHONPATH"] = ":".join(sys.path)  # TODO do this in the clanCore module
 
     print(f"generating secrets... {machine.generate_secrets}")
-    proc = subprocess.run(
+    run(
         [machine.generate_secrets],
         env=env,
+        error_msg="failed to generate secrets",
+        log=Log.BOTH,
     )
 
-    if proc.returncode != 0:
-        raise ClanError("failed to generate secrets")
-    else:
-        print("successfully generated secrets")
+    print("successfully generated secrets")
 
 
 def generate_command(args: argparse.Namespace) -> None: