# HG changeset patch
# User estrain
# Date 1567882090 14400
# Node ID 7c51eb2396a9ed39a6eb9648a396675c3df19a5c
# Parent  564ca9d912261c6813ccc0ce1b7d453d94b6bcb0
Uploaded

diff -r 564ca9d91226 -r 7c51eb2396a9 SeqSero2_package.py
--- a/SeqSero2_package.py	Sat Sep 07 14:27:42 2019 -0400
+++ b/SeqSero2_package.py	Sat Sep 07 14:48:10 2019 -0400
@@ -1214,7 +1214,8 @@
 
 def judge_subspecies(fnameA,dirpath):
   #seqsero2 -a; judge subspecies on just forward raw reads fastq
-  salmID_output=subprocess.Popen("python SalmID.py -i "+fnameA,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE)
+  #salmID_output=subprocess.Popen("python SalmID.py -i "+fnameA,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE)
+  salmID_output=subprocess.Popen("python "+ dirpath + "/SalmID.py -i "+fnameA,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE)
   salmID_output2=subprocess.Popen("ls",shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE)
   out, err = salmID_output.communicate()
   out2, err2 = salmID_output2.communicate()