From f9c5d152f983c34d95079d557ea56b6a1f545be0 Mon Sep 17 00:00:00 2001
From: ddepanis <ddepanis@mi.fu-berlin.de>
Date: Sun, 26 May 2024 20:03:48 +0000
Subject: [PATCH] Update README.md

---
 README.md | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index c8c3f10..0dd0a88 100644
--- a/README.md
+++ b/README.md
@@ -369,8 +369,6 @@ nohup snakemake --profile SUBMIT_CONFIG/slurm/ &
 ```
 
 ---
-
-
 ## More Useful Tips
 
 The user can directly override any of the Snakemake parameters (and paths) set in the respective configuration files through the command line when executing GEP. For example, to override the values in the sample configuration [GEP/configuration/config.yaml](configuration/config.yaml) for the path to the main results folder without having to edit the document itself:
@@ -398,6 +396,16 @@ snakemake --profile SUBMIT_CONFIG/default/ --until <ruleName>
 
 In such cases all files that this rule depends on will be run, but final PDF reports will not be created.
 
+---
+## Known issues
+
+There is a known merqury issue where png k-mer plots are not generated, making the pieline to fail. If this happens to you, please use this fix:
+1. Go to the gep installation folder.
+2. Run the following command:
+```
+VAR=$(grep merqury .snakemake/conda/*.yaml | awk -F'[:/.]' '{print $4}'); sed -i '/function check_module()/,/^}/s/echo \$?/echo 1/' .snakemake/conda/${VAR}/share/merqury/util/util.sh
+```
+
 ### ERGA Assembly Reports
 
 If you are evaluating a pre-curation and post-curation steps, you can obtain the yaml file automatically filled to produce an ERGA Assembly Report (EAR). Please run like this:
-- 
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