--- a/conifer3/conifer.py	Fri Mar 17 08:57:10 2017 -0400
+++ b/conifer3/conifer.py	Fri Mar 17 09:02:01 2017 -0400
@@ -40,9 +40,9 @@
 		probe_fn = str(args.probes[0])
 		probes = cf.loadProbeList(probe_fn)
 		num_probes = len(probes)
-        print '[INIT] Successfully read in %s probes from %s' % (str(num_probes), probe_fn)
+		print '[INIT] Successfully read in %d probes from %s' % (num_probes, probe_fn)
 	except IOError as e: 
-        print '[ERROR] Cannot read probes file: ', probe_fn
+		print '[ERROR] Cannot read probes file: ', probe_fn
 		sys.exit(0)
 	
 	try: 
@@ -50,7 +50,7 @@
 		h5file_out = openFile(svd_outfile_fn, mode='w')
 		probe_group = h5file_out.createGroup("/","probes","probes")
 	except IOError as e: 
-        print '[ERROR] Cannot open SVD output file for writing: ', svd_outfile_fn
+		print '[ERROR] Cannot open SVD output file for writing: ', svd_outfile_fn
 		sys.exit(0)
 	
 	if args.write_svals != "":
@@ -65,7 +65,7 @@
 			from matplotlib.lines import Line2D
 			from matplotlib.patches import Rectangle
 		except:
-            print "[ERROR] One or more of the required modules for plotting cannot be loaded! Are matplotlib and pylab installed?"
+			print "[ERROR] One or more of the required modules for plotting cannot be loaded! Are matplotlib and pylab installed?"
 			sys.exit(0)
 		
 		plt.gcf().clear()
@@ -78,10 +78,10 @@
 		print '[ERROR] Cannot find any files in RPKM directory (or directory path is incorrect): ', rpkm_dir
 		sys.exit(0)
 	elif len(rpkm_files) == 1:
-        print '[ERROR] Found only 1 RPKM file (sample). CoNIFER requires multiple samples (8 or more) to run. Exiting.'
+		print '[ERROR] Found only 1 RPKM file (sample). CoNIFER requires multiple samples (8 or more) to run. Exiting.'
 		sys.exit(0)
 	elif len(rpkm_files) < 8:
-        print '[WARNING] Only found %d samples... this is less than the recommended minimum, and CoNIFER may not analyze this dataset correctly!' % len(rpkm_files)
+		print '[WARNING] Only found %d samples... this is less than the recommended minimum, and CoNIFER may not analyze this dataset correctly!' % len(rpkm_files)
 	elif len(rpkm_files) <= int(args.svd):
 		print '[ERROR] The number of SVD values specified (%d) must be less than the number of samples (%d). Either add more samples to the analysis or reduce the --svd parameter! Exiting.' % (len(rpkm_files), int(args.svd))
 		sys.exit(0)