--- a/SeqSero2_package.py	Sat Sep 07 14:52:06 2019 -0400
+++ b/SeqSero2_package.py	Sat Sep 07 14:52:22 2019 -0400
@@ -1214,25 +1214,13 @@
 
 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 "+ 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()
   out=out.decode("utf-8")
-  out2=out2.decode("utf-8")
   err=err.decode("utf-8")
-  err2=err2.decode("utf-8")
   file=open("data_log.txt","a")
   file.write(out)
   file.close()
-  print("dirpath " + str(dirpath))
-  print("SalmID File" + str(out))
-  print("SalmID File" + str(out2))
-  print("SalmID Err File" + str(err))
-  print("SalmID Err File" + str(err2))
-  print("SalmID 1 "+str(out.split("\n")[1]))
-  print("SalmID 0 "+str(out.split("\n")[0]))
   salm_species_scores=out.split("\n")[1].split("\t")[6:]
   salm_species_results=out.split("\n")[0].split("\t")[6:]
   max_score=0