From 92eeffe6e0ef17e747f45bbc4d00ffbe26887d8a Mon Sep 17 00:00:00 2001
From: Silvio Waschina <32539757+Waschina@users.noreply.github.com>
Date: Mon, 20 Oct 2025 10:05:09 +0200
Subject: [PATCH 1/2] Bug fix in prepare.py

In the block that constructs the DIAMOND database, there was a small bug in the logging.

The bug caused that the prepare workflow stopped with

`ERROR: DIAMOND database could not be created.`

without further details on the cause of the error in the log files.

Prepending the `shared.` in calling the function `give_user_feedback` fixes the bug.
---
 CAT_pack/prepare.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CAT_pack/prepare.py b/CAT_pack/prepare.py
index 392790a..f009882 100644
--- a/CAT_pack/prepare.py
+++ b/CAT_pack/prepare.py
@@ -115,7 +115,7 @@ def make_diamond_database(
 
     try:
         message = "Running command: {0}".format(" ".join(command))
-        give_user_feedback(message, log_file, quiet)
+        shared.give_user_feedback(message, log_file, quiet)
 
         subprocess.check_call(command)
     except:

From 1bed396648fc4a8612433863829a374092a01ce5 Mon Sep 17 00:00:00 2001
From: Silvio Waschina <32539757+Waschina@users.noreply.github.com>
Date: Mon, 20 Oct 2025 10:44:14 +0200
Subject: [PATCH 2/2] Update prepare.py

In addition to the previous commit:

The same small bug (missing `shared.` prefix in calling `give_user_feedback(...)`) was also there in `make_mmseqs2_database`.
---
 CAT_pack/prepare.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CAT_pack/prepare.py b/CAT_pack/prepare.py
index f009882..a869585 100644
--- a/CAT_pack/prepare.py
+++ b/CAT_pack/prepare.py
@@ -155,7 +155,7 @@ def make_mmseqs2_database(
 
     try:
         message = "Running command: {0}".format(" ".join(command))
-        give_user_feedback(message, log_file, quiet)
+        shared.give_user_feedback(message, log_file, quiet)
 
         subprocess.check_call(command)
     except: