added traces to try to find out why Staph1N long regression test fails in CI...

added traces to try to find out why Staph1N long regression test fails in CI and doesn't when it runs on the cluster

non-regression-tests/common.py

@@ -75,6 +75,7 @@ def check_class(filename,expected_class):
         f=open(filename,"r")
         cl=f.read()
         if (cl!=expected_class):
+            print "found ",cl," instead of: ",expected_class
             return K_WRONG_CLASS
         f.close()
     os.remove(filename)

non-regression-tests/run_StaphN1_long.sh

@@ -2,5 +2,5 @@
 DATA_PATH=./data
 
 echo "running PhageTerm on Staph1N genome and a dataset with a minimum 50x coverage"
-python ../PhageTerm.py -f "$DATA_PATH/R1_1M_READS_EACH_PHAGE(1).fastq.4" -p "$DATA_PATH/R2_1M_READS_EACH_PHAGE(1).fastq.4" -r $DATA_PATH/Staph1N_assembly.fasta
-python check_Staph1N_class.py
\ No newline at end of file
+python ../PhageTerm.py --nrt -f "$DATA_PATH/R1_1M_READS_EACH_PHAGE(1).fastq.4" -p "$DATA_PATH/R2_1M_READS_EACH_PHAGE(1).fastq.4" -r $DATA_PATH/Staph1N_assembly.fasta
+python check_Staph1N_class.py