--- a/bin/SeqSero2_package.py	Mon Apr 27 12:36:27 2020 -0400
+++ b/bin/SeqSero2_package.py	Mon Apr 27 19:39:25 2020 -0400
@@ -1233,14 +1233,20 @@
     xmlfile="NA"
   return xmlfile,new_fasta
 
-def judge_subspecies(fnameA):
+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)
+  samid_strcmd = "python " + dirpath + "/../SalmID.py -i "+fnameA
+  #subprocess.check_call(samid_strcmd + " > Salmidoutput.txt",shell=True)
+  print(samid_strcmd)
+  salmID_output=subprocess.Popen(samid_strcmd,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE)
   out, err = salmID_output.communicate()
+  print(err)
+  print(out)
   out=out.decode("utf-8")
   file=open("data_log.txt","a")
   file.write(out)
   file.close()
+  
   salm_species_scores=out.split("\n")[1].split("\t")[6:]
   salm_species_results=out.split("\n")[0].split("\t")[6:]
   max_score=0
@@ -1258,6 +1264,7 @@
     prediction="-"
   return prediction
 
+
 def judge_subspecies_Kmer(Special_dict):
   #seqsero2 -k;
   max_score=0
@@ -1361,7 +1368,7 @@
           file.close()
           Final_list_passed=[x for x in Final_list if float(x[0].split("_cov_")[1].split("_")[0])>=0.9 and (x[1]>=int(x[0].split("__")[1]) or x[1]>=int(x[0].split("___")[1].split("_")[3]) or x[1]>1000)]
           O_choice,fliC_choice,fljB_choice,special_gene_list,contamination_O,contamination_H,Otypes_uniq,H1_cont_stat_list,H2_cont_stat_list=predict_O_and_H_types(Final_list,Final_list_passed,new_fasta) #predict O, fliC and fljB
-        subspecies=judge_subspecies(fnameA) #predict subspecies
+        subspecies=judge_subspecies(fnameA,dirpath) #predict subspecies
         ###output
         predict_form,predict_sero,star,star_line,claim=seqsero_from_formula_to_serotypes(O_choice,fliC_choice,fljB_choice,special_gene_list,subspecies)
         claim="" #04132019, disable claim for new report requirement

--- a/seqsero2.xml	Mon Apr 27 12:36:27 2020 -0400
+++ b/seqsero2.xml	Mon Apr 27 19:39:25 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="seqsero2v110" name="SeqSero2 v1.1.0" version="2">
+<tool id="seqsero2v110" name="SeqSero2 v1.1.0" version="3">
     <description>Salmonella serotype prediction</description>
     <requirements>
       <requirement type="package" version="3.6">python</requirement>