From 605b45b1fe4c933c850cf2c9080ffb8f10b4ad20 Mon Sep 17 00:00:00 2001
From: "Z.-L. Deng" <dawnmsg@gmail.com>
Date: Sun, 13 Mar 2022 18:03:36 +0100
Subject: [PATCH 1/4] Update README.md

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 9f0d24e..0fd5d90 100644
--- a/README.md
+++ b/README.md
@@ -29,7 +29,7 @@ Note: you can skip this step if you don't use GPU
 #### Using pip
 
 ```shell
-pip install -c bioconda ribodetector
+pip install ribodetector
 ```
 
 #### Using conda

From 132841ddce4556a3f0d0e0b7d7753f32595fd46c Mon Sep 17 00:00:00 2001
From: "Z.-L. Deng" <dawnmsg@gmail.com>
Date: Fri, 8 Apr 2022 15:19:58 +0200
Subject: [PATCH 2/4] Update README.md

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 0fd5d90..268f512 100644
--- a/README.md
+++ b/README.md
@@ -156,7 +156,7 @@ optional arguments:
   --chunk_size CHUNK_SIZE
                         chunk_size * threads reads to process per thread.(default: 
                         1024)
-                        When chunk_size=1024 and threads=20, each process will load 
+                        For 20M PE100 reads, when chunk_size=1024 and threads=20, each process will load 
                         1024 reads, in total consumming ~20G memory.
   -v, --version         show program's version number and exit
 ```

From 44e135e3bdf89de0f591d1694523a9a6ac41ec83 Mon Sep 17 00:00:00 2001
From: "Z.-L. Deng" <dawnmsg@gmail.com>
Date: Fri, 8 Apr 2022 15:26:35 +0200
Subject: [PATCH 3/4] Update README.md

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index 268f512..788df8e 100644
--- a/README.md
+++ b/README.md
@@ -161,6 +161,7 @@ optional arguments:
   -v, --version         show program's version number and exit
 ```
 
+**Note**: RiboDetector uses multiprocessing with shared memory, thus the memory use of a single process indicated in `htop` or `top` is actually the total memory used by RiboDector. Some job submission system like SGE mis-calculated the total memory use by adding up the memory use of all process. If you see this do not worry it will cause out of memory issue. 
 
 <!-- ### Benchmarks
 

From 5a21f50258708610c45998e5e3622bb2f06938fc Mon Sep 17 00:00:00 2001
From: "Z.-L. Deng" <dawnmsg@gmail.com>
Date: Thu, 21 Apr 2022 17:40:47 +0200
Subject: [PATCH 4/4] Update README.md

---
 README.md | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index 788df8e..41cd92d 100644
--- a/README.md
+++ b/README.md
@@ -154,10 +154,8 @@ optional arguments:
   -t THREADS, --threads THREADS
                         number of threads to use. (default: 10)
   --chunk_size CHUNK_SIZE
-                        chunk_size * threads reads to process per thread.(default: 
-                        1024)
-                        For 20M PE100 reads, when chunk_size=1024 and threads=20, each process will load 
-                        1024 reads, in total consumming ~20G memory.
+                        chunk_size * 1024 reads to load each time.
+                        When chunk_size=1000 and threads=20, consumming ~20G memory, better to be multiples of the number of threads.
   -v, --version         show program's version number and exit
 ```