# HG changeset patch
# User estrain
# Date 1567878142 14400
# Node ID 95764a93ed88d9a5e57a99b96812c04fcf80ec52
# Parent  b2b1d018b90dce73db469f06e9d83db77689f243
Uploaded

diff -r b2b1d018b90d -r 95764a93ed88 SeqSero2_package.py
--- a/SeqSero2_package.py	Sat Sep 07 13:42:11 2019 -0400
+++ b/SeqSero2_package.py	Sat Sep 07 13:42:22 2019 -0400
@@ -1214,7 +1214,7 @@
 
 def judge_subspecies(fnameA,dirpath):
   #seqsero2 -a; judge subspecies on just forward raw reads fastq
-  salmID_output=subprocess.Popen(dirpath+"/SalmID.py -i "+fnameA,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE)
+  salmID_output=subprocess.Popen("/SalmID.py -i "+fnameA,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE)
   out, err = salmID_output.communicate()
   out=out.decode("utf-8")
   err=err.decode("utf-8")