From b095c05f2621092420653e0de4d1f7cae1ba93ea Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Thu, 7 Mar 2019 16:30:04 -0600
Subject: [PATCH] Remove extra bwa command.
---
workflow/scripts/pool_and_psuedoreplicate.py | 3 ---
1 file changed, 3 deletions(-)
diff --git a/workflow/scripts/pool_and_psuedoreplicate.py b/workflow/scripts/pool_and_psuedoreplicate.py
index 0f2c295..f3d702f 100644
--- a/workflow/scripts/pool_and_psuedoreplicate.py
+++ b/workflow/scripts/pool_and_psuedoreplicate.py
@@ -153,9 +153,6 @@ def self_psuedoreplication(tag_file, prefix, paired):
logger.info("Running psuedo with %s", psuedo_command)
subprocess.check_call(shlex.split(psuedo_command))
- logger.info("Running bwa with %s", bwa_command)
- subprocess.check_call(shlex.split(bwa_command), stdout=sai_file)
-
# Convert read pairs to reads into standard tagAlign file
--
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