# HG changeset patch
# User estrain
# Date 1567879008 14400
# Node ID 4e1596ee5c94a5e05a376d89c047e06feddcf22c
# Parent  f8c06e3b0fb919fd21ad6575c56ca393a2a9df83
Uploaded

diff -r f8c06e3b0fb9 -r 4e1596ee5c94 SeqSero2_package.py
--- a/SeqSero2_package.py	Sat Sep 07 13:51:19 2019 -0400
+++ b/SeqSero2_package.py	Sat Sep 07 13:56:48 2019 -0400
@@ -1215,15 +1215,21 @@
 def judge_subspecies(fnameA,dirpath):
   #seqsero2 -a; judge subspecies on just forward raw reads fastq
   salmID_output=subprocess.Popen("./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:]