diff --git a/test/scripts/test_checkm.py b/test/scripts/test_checkm.py
index 37706f1..1831b6c 100755
--- a/test/scripts/test_checkm.py
+++ b/test/scripts/test_checkm.py
@@ -7,45 +7,43 @@
 import errno
 
 if len(sys.argv) == 1:
-	print "Please provide a filename"
-	sys.exit()
+    print "Please provide a filename"
+    sys.exit()
 
 # output file
 outfile = sys.argv[1]
 
 if not os.path.dirname(outfile) == '':
-	if not os.path.exists(os.path.dirname(outfile)):
-		try:
-			os.makedirs(os.path.dirname(outfile))
-		except OSError as exc: # Guard against race condition
-			if exc.errno != errno.EEXIST:
-				raise
+    if not os.path.exists(os.path.dirname(outfile)):
+        try:
+            os.makedirs(os.path.dirname(outfile))
+        except OSError as exc: # Guard against race condition
+            if exc.errno != errno.EEXIST:
+                raise
 
 f = open(outfile, 'w+')
 
 # try to run checkM
 try:
-	p1 = subprocess.Popen(['checkm'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+    p1 = subprocess.Popen(['checkm'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
 
-	# Run the command
-	checkm = p1.communicate()
-	output = checkm[0]
-	error  = checkm[1]
+    # Run the command
+    checkm = p1.communicate()
+    output = checkm[0]
+    error  = checkm[1]
 except OSError as o:
-	f.write('OSError: make sure checkM is installed properly' + '\n')
-	f.close()
-	sys.exit()
+    f.write('OSError: make sure checkM is installed properly' + '\n')
+    f.close()
+    sys.exit()
 except:
- 	f.write('Unexpected error: unable to run checkM' + '\n')
-	f.close()
-	sys.exit()
+    f.write('Unexpected error: unable to run checkM' + '\n')
+    f.close()
+    sys.exit()
 
 # if we're still here, check error and print
 if error == '':
-	f.write('CheckM ran without problems' + '\n')
-else :
-	f.write('CheckM ran with some errors: ' + error + '\n')
+    f.write('CheckM ran without problems' + '\n')
+else:
+    f.write('CheckM ran with some errors: ' + error + '\n')
 
 f.close()
-
-
diff --git a/test/scripts/test_checkm_plus.py b/test/scripts/test_checkm_plus.py
index ef2520f..574c8a8 100755
--- a/test/scripts/test_checkm_plus.py
+++ b/test/scripts/test_checkm_plus.py
@@ -7,46 +7,43 @@
 import errno
 
 if len(sys.argv) == 1:
-	print("Please provide a filename")
-	sys.exit()
+    print("Please provide a filename")
+    sys.exit()
 
 # output file
 outfile = sys.argv[1]
 
 if not os.path.dirname(outfile) == '':
-	if not os.path.exists(os.path.dirname(outfile)):
-		try:
-			os.makedirs(os.path.dirname(outfile))
-		except OSError as exc: # Guard against race condition
-			if exc.errno != errno.EEXIST:
-				raise
+    if not os.path.exists(os.path.dirname(outfile)):
+        try:
+            os.makedirs(os.path.dirname(outfile))
+        except OSError as exc: # Guard against race condition
+            if exc.errno != errno.EEXIST:
+                raise
 
 f = open(outfile, 'w+')
 
 # try to run add_tax.py
 try:
-	p1 = subprocess.Popen(['scripts/add_tax.py'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+    p1 = subprocess.Popen(['scripts/add_tax.py'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
 
-	# Run the command
-	addtax = p1.communicate()
-	output = addtax[0]
-	error  = addtax[1]
+    # Run the command
+    addtax = p1.communicate()
+    output = addtax[0]
+    error  = addtax[1]
 except OSError as o:
-	f.write('OSError: is scripts/add_tax.py in your PATH?' + '\n')
-	f.close()
-	sys.exit()
+    f.write('OSError: is scripts/add_tax.py in your PATH?' + '\n')
+    f.close()
+    sys.exit()
 except:
-	f.write('Unexpected error: unable to run scripts/add_tax.py' + '\n')
-	f.close()
-	sys.exit()
+    f.write('Unexpected error: unable to run scripts/add_tax.py' + '\n')
+    f.close()
+    sys.exit()
 
 # if we're still here, check error and print
 if error.decode(sys.stdout.encoding) == '':
-	f.write('scripts/add_tax.py ran without problems' + '\n')
+    f.write('scripts/add_tax.py ran without problems' + '\n')
 else:
-	f.write('scripts/add_tax.py ran with some errors: ' + error.decode(sys.stdout.encoding) + '\n')
+    f.write('scripts/add_tax.py ran with some errors: ' + error.decode(sys.stdout.encoding) + '\n')
 	
-
 f.close()
-
-
diff --git a/test/scripts/test_diamond.py b/test/scripts/test_diamond.py
index aef7a6e..ddf480a 100755
--- a/test/scripts/test_diamond.py
+++ b/test/scripts/test_diamond.py
@@ -7,46 +7,43 @@
 import errno
 
 if len(sys.argv) == 1:
-	print("Please provide a filename")
-	sys.exit()
+    print("Please provide a filename")
+    sys.exit()
 
 # output file
 outfile = sys.argv[1]
 
 if not os.path.dirname(outfile) == '':
-	if not os.path.exists(os.path.dirname(outfile)):
-		try:
-			os.makedirs(os.path.dirname(outfile))
-		except OSError as exc: # Guard against race condition
-			if exc.errno != errno.EEXIST:
-				raise
+    if not os.path.exists(os.path.dirname(outfile)):
+        try:
+            os.makedirs(os.path.dirname(outfile))
+        except OSError as exc: # Guard against race condition
+            if exc.errno != errno.EEXIST:
+                raise
 
 f = open(outfile, 'w+')
 
 # try to run checkM
 try:
-	p1 = subprocess.Popen(['diamond','help'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+    p1 = subprocess.Popen(['diamond','help'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
 
-	# Run the command
-	allout = p1.communicate()
-	output = allout[0]
-	error  = allout[1]
+    # Run the command
+    allout = p1.communicate()
+    output = allout[0]
+    error  = allout[1]
 except OSError as o:
-	f.write('OSError: make sure DIAMOND is installed properly' + '\n')
-	f.close()
-	sys.exit()
+    f.write('OSError: make sure DIAMOND is installed properly' + '\n')
+    f.close()
+    sys.exit()
 except:
-	f.write('Unexpected error: unable to run DIAMOND' + '\n')
-	f.close()
-	sys.exit()
+    f.write('Unexpected error: unable to run DIAMOND' + '\n')
+    f.close()
+    sys.exit()
 
 # if we're still here, check error and print
 if error.decode(sys.stdout.encoding) == '':
-	f.write('DIAMOND ran without problems' + '\n')
-else :
-	f.write('DIAMOND ran with some errors: ' + error.decode(sys.stdout.encoding) + '\n')
+    f.write('DIAMOND ran without problems' + '\n')
+else:
+    f.write('DIAMOND ran with some errors: ' + error.decode(sys.stdout.encoding) + '\n')
 	
-
 f.close()
-
-
diff --git a/test/scripts/test_diamond_bin_summary_plus.py b/test/scripts/test_diamond_bin_summary_plus.py
index 54d9306..fdabeaf 100755
--- a/test/scripts/test_diamond_bin_summary_plus.py
+++ b/test/scripts/test_diamond_bin_summary_plus.py
@@ -7,45 +7,43 @@
 import errno
 
 if len(sys.argv) == 1:
-	print("Please provide a filename")
-	sys.exit()
+    print("Please provide a filename")
+    sys.exit()
 
 # output file
 outfile = sys.argv[1]
 
 if not os.path.dirname(outfile) == '':
-	if not os.path.exists(os.path.dirname(outfile)):
-		try:
-			os.makedirs(os.path.dirname(outfile))
-		except OSError as exc: # Guard against race condition
-			if exc.errno != errno.EEXIST:
-				raise
+    if not os.path.exists(os.path.dirname(outfile)):
+        try:
+            os.makedirs(os.path.dirname(outfile))
+        except OSError as exc: # Guard against race condition
+            if exc.errno != errno.EEXIST:
+                raise
 
 f = open(outfile, 'w+')
 
 # try to run checkM
 try:
-	p1 = subprocess.Popen(['scripts/add_tax_diamond.py'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+    p1 = subprocess.Popen(['scripts/add_tax_diamond.py'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
 
-	# Run the command
-	allout = p1.communicate()
-	output = allout[0]
-	error  = allout[1]
+    # Run the command
+    allout = p1.communicate()
+    output = allout[0]
+    error  = allout[1]
 except OSError as o:
-	f.write('OSError: is scripts/add_tax_diamond.py in your PATH?' + '\n')
-	f.close()
-	sys.exit()
+    f.write('OSError: is scripts/add_tax_diamond.py in your PATH?' + '\n')
+    f.close()
+    sys.exit()
 except:
-	f.write('Unexpected error: unable to run scripts/add_tax_diamond.py' + '\n')
-	f.close()
-	sys.exit()
+    f.write('Unexpected error: unable to run scripts/add_tax_diamond.py' + '\n')
+    f.close()
+    sys.exit()
 
 # if we're still here, check error and print
 if error.decode(sys.stdout.encoding) == '':
-	f.write('scripts/add_tax_diamond.py ran without problems' + '\n')
-else :
-	f.write('scripts/add_tax_diamond.py ran with some errors: ' + error.decode(sys.stdout.encoding) + '\n')
+    f.write('scripts/add_tax_diamond.py ran without problems' + '\n')
+else:
+    f.write('scripts/add_tax_diamond.py ran with some errors: ' + error.decode(sys.stdout.encoding) + '\n')
 	
 f.close()
-
-
diff --git a/test/scripts/test_diamond_report.py b/test/scripts/test_diamond_report.py
index c00afcb..f2dc9f2 100755
--- a/test/scripts/test_diamond_report.py
+++ b/test/scripts/test_diamond_report.py
@@ -7,45 +7,43 @@
 import errno
 
 if len(sys.argv) == 1:
-	print("Please provide a filename")
-	sys.exit()
+    print("Please provide a filename")
+    sys.exit()
 
 # output file
 outfile = sys.argv[1]
 
 if not os.path.dirname(outfile) == '':
-	if not os.path.exists(os.path.dirname(outfile)):
-		try:
-			os.makedirs(os.path.dirname(outfile))
-		except OSError as exc: # Guard against race condition
-			if exc.errno != errno.EEXIST:
-				raise
+    if not os.path.exists(os.path.dirname(outfile)):
+        try:
+            os.makedirs(os.path.dirname(outfile))
+        except OSError as exc: # Guard against race condition
+            if exc.errno != errno.EEXIST:
+                raise
 
 f = open(outfile, 'w+')
 
 # try to run checkM
 try:
-	p1 = subprocess.Popen(['scripts/diamond_report.pl'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+    p1 = subprocess.Popen(['scripts/diamond_report.pl'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
 
-	# Run the command
-	allout = p1.communicate()
-	output = allout[0]
-	error  = allout[1]
+    # Run the command
+    allout = p1.communicate()
+    output = allout[0]
+    error  = allout[1]
 except OSError as o:
-	f.write('OSError: is scripts/diamond_report.pl in your PATH?' + '\n')
-	f.close()
-	sys.exit()
+    f.write('OSError: is scripts/diamond_report.pl in your PATH?' + '\n')
+    f.close()
+    sys.exit()
 except:
-	f.write('Unexpected error: unable to run scripts/diamond_report.pl - is BioPerl installed?' + '\n')
-	f.close()
-	sys.exit()
+    f.write('Unexpected error: unable to run scripts/diamond_report.pl - is BioPerl installed?' + '\n')
+    f.close()
+    sys.exit()
 
 # if we're still here, check error and print
 if error.decode(sys.stdout.encoding) == '':
-	f.write('scripts/diamond_report.pl ran without problems' + '\n')
-else :
-	f.write('scripts/diamond_report.pl ran with some errors: ' + error.decode(sys.stdout.encoding) + '\n')
-	
-f.close()
-
+    f.write('scripts/diamond_report.pl ran without problems' + '\n')
+else:
+    f.write('scripts/diamond_report.pl ran with some errors: ' + error.decode(sys.stdout.encoding) + '\n')
 
+f.close()
diff --git a/test/scripts/test_pfam_scan.py b/test/scripts/test_pfam_scan.py
index 10173b6..2520c5c 100755
--- a/test/scripts/test_pfam_scan.py
+++ b/test/scripts/test_pfam_scan.py
@@ -7,47 +7,45 @@
 import errno
 
 if len(sys.argv) == 1:
-	print("Please provide a filename")
-	sys.exit()
+    print("Please provide a filename")
+    sys.exit()
 
 # output file
 outfile = sys.argv[1]
 
 if not os.path.dirname(outfile) == '':
-	if not os.path.exists(os.path.dirname(outfile)):
-		try:
-			os.makedirs(os.path.dirname(outfile))
-		except OSError as exc: # Guard against race condition
-			if exc.errno != errno.EEXIST:
-				raise
+    if not os.path.exists(os.path.dirname(outfile)):
+        try:
+            os.makedirs(os.path.dirname(outfile))
+        except OSError as exc: # Guard against race condition
+            if exc.errno != errno.EEXIST:
+                raise
 
 f = open(outfile, 'w+')
 
 # try to run checkM
 try:
-	p1 = subprocess.Popen(['pfam_scan.pl', '-h'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+    p1 = subprocess.Popen(['pfam_scan.pl', '-h'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
 
-	# Run the command
-	allout = p1.communicate()
-	output = allout[0]
-	error  = allout[1]
+    # Run the command
+    allout = p1.communicate()
+    output = allout[0]
+    error  = allout[1]
 except OSError as o:
-	f.write('OSError: is pfam_scan.pl installed and in your PATH?' + '\n')
-	f.close()
-	sys.exit()
+    f.write('OSError: is pfam_scan.pl installed and in your PATH?' + '\n')
+    f.close()
+    sys.exit()
 except:
-	f.write('Unexpected error: unable to run pfam_scan.pl' + '\n')
-	f.close()
-	sys.exit()
+    f.write('Unexpected error: unable to run pfam_scan.pl' + '\n')
+    f.close()
+    sys.exit()
 
 teststr = error.decode(sys.stdout.encoding)
 
 # if we're still here, check error and print
 if teststr[1:29] == 'pfam_scan.pl: search a FASTA':
-	f.write('pfam_scan.pl ran without problems' + '\n')
-else :
-	f.write('pfam_scan.pl ran with some errors: ' + error.decode(sys.stdout.encoding) + '\n')
-	
-f.close()
-
+    f.write('pfam_scan.pl ran without problems' + '\n')
+else:
+    f.write('pfam_scan.pl ran with some errors: ' + error.decode(sys.stdout.encoding) + '\n')
 
+f.close()
diff --git a/test/scripts/test_phylophlan.py b/test/scripts/test_phylophlan.py
index 81308b2..36b78e8 100755
--- a/test/scripts/test_phylophlan.py
+++ b/test/scripts/test_phylophlan.py
@@ -7,8 +7,8 @@
 import errno
 
 if len(sys.argv) == 1:
-	print("Please provide a filename")
-	sys.exit()
+    print("Please provide a filename")
+    sys.exit()
 
 # output file
 outfile = sys.argv[1]
@@ -44,10 +44,7 @@
 # if we're still here, check error and print
 if error == '':
     f.write('phylophlan ran without problems' + '\n')
-else :
+else:
     f.write('phylophlan ran with some errors: ' + str(error) + '\n')
 	
-
 f.close()
-
-
diff --git a/test/scripts/test_prodigal.py b/test/scripts/test_prodigal.py
index 42f565e..e1c78b3 100755
--- a/test/scripts/test_prodigal.py
+++ b/test/scripts/test_prodigal.py
@@ -7,46 +7,43 @@
 import errno
 
 if len(sys.argv) == 1:
-	print("Please provide a filename")
-	sys.exit()
+    print("Please provide a filename")
+    sys.exit()
 
 # output file
 outfile = sys.argv[1]
 
 if not os.path.dirname(outfile) == '':
-	if not os.path.exists(os.path.dirname(outfile)):
-		try:
-			os.makedirs(os.path.dirname(outfile))
-		except OSError as exc: # Guard against race condition
-			if exc.errno != errno.EEXIST:
-				raise
+    if not os.path.exists(os.path.dirname(outfile)):
+        try:
+            os.makedirs(os.path.dirname(outfile))
+        except OSError as exc: # Guard against race condition
+            if exc.errno != errno.EEXIST:
+                raise
 
 f = open(outfile, 'w+')
 
 # try to run checkM
 try:
-	p1 = subprocess.Popen(['prodigal','-v'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+    p1 = subprocess.Popen(['prodigal','-v'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
 
-	# Run the command
-	allout = p1.communicate()
-	output = allout[0]
-	error  = allout[1]
+    # Run the command
+    allout = p1.communicate()
+    output = allout[0]
+    error  = allout[1]
 except OSError as o:
-	f.write('OSError: make sure prodigal is installed properly' + '\n')
-	f.close()
-	sys.exit()
+    f.write('OSError: make sure prodigal is installed properly' + '\n')
+    f.close()
+    sys.exit()
 except:
-	f.write('Unexpected error: unable to run prodigal' + '\n')
-	f.close()
-	sys.exit()
+    f.write('Unexpected error: unable to run prodigal' + '\n')
+    f.close()
+    sys.exit()
 
 # if we're still here, check error and print
 if error.decode(sys.stdout.encoding)[1:16] == 'Prodigal V2.6.3':
-	f.write('prodigal ran without problems' + '\n')
-else :
-	f.write('prodigal ran with some errors: ' + error.decode(sys.stdout.encoding) + '\n')
-	
+    f.write('prodigal ran without problems' + '\n')
+else:
+    f.write('prodigal ran with some errors: ' + error.decode(sys.stdout.encoding) + '\n')
 
 f.close()
-
-
diff --git a/test/scripts/test_sourmash.py b/test/scripts/test_sourmash.py
index 6f8bc75..598dbf7 100755
--- a/test/scripts/test_sourmash.py
+++ b/test/scripts/test_sourmash.py
@@ -7,46 +7,43 @@
 import errno
 
 if len(sys.argv) == 1:
-	print("Please provide a filename")
-	sys.exit()
+    print("Please provide a filename")
+    sys.exit()
 
 # output file
 outfile = sys.argv[1]
 
 if not os.path.dirname(outfile) == '':
-	if not os.path.exists(os.path.dirname(outfile)):
-		try:
-			os.makedirs(os.path.dirname(outfile))
-		except OSError as exc: # Guard against race condition
-			if exc.errno != errno.EEXIST:
-				raise
+    if not os.path.exists(os.path.dirname(outfile)):
+        try:
+            os.makedirs(os.path.dirname(outfile))
+        except OSError as exc: # Guard against race condition
+            if exc.errno != errno.EEXIST:
+                raise
 
 f = open(outfile, 'w+')
 
 # try to run checkM
 try:
-	p1 = subprocess.Popen(['sourmash','-h'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+    p1 = subprocess.Popen(['sourmash','-h'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
 
-	# Run the command
-	allout = p1.communicate()
-	output = allout[0]
-	error  = allout[1]
+    # Run the command
+    allout = p1.communicate()
+    output = allout[0]
+    error  = allout[1]
 except OSError as o:
-	f.write('OSError: make sure sourmash is installed properly' + '\n')
-	f.close()
-	sys.exit()
+    f.write('OSError: make sure sourmash is installed properly' + '\n')
+    f.close()
+    sys.exit()
 except:
-	f.write('Unexpected error: unable to run sourmash' + '\n')
-	f.close()
-	sys.exit()
+    f.write('Unexpected error: unable to run sourmash' + '\n')
+    f.close()
+    sys.exit()
 
 # if we're still here, check error and print
 if error.decode(sys.stdout.encoding) == '== This is sourmash version 4.1.1. ==':
-	f.write('Sourmash ran without problems' + '\n')
-else :
-	f.write('Sourmash ran with some errors: ' + error.decode(sys.stdout.encoding) + '\n')
-	
+    f.write('Sourmash ran without problems' + '\n')
+else:
+    f.write('Sourmash ran with some errors: ' + error.decode(sys.stdout.encoding) + '\n')
 
 f.close()
-
-