diff --git a/bwameth.py b/bwameth.py
index 908492a..bb0d0a9 100755
--- a/bwameth.py
+++ b/bwameth.py
@@ -72,8 +72,10 @@ def convert_reads(fq1s, fq2s, out=sys.stdout):
         sys.stderr.write("converting reads in %s,%s\n" % (fq1, fq2))
         fq1 = nopen(fq1)
 
+        #examines first five lines to detect if this is an interleaved fastq file
         first_five = list(islice(fq1, 5))
         fq1.seek(0)
+
         r1_header = first_five[0]
         r2_header = first_five[-1]
 
@@ -82,6 +84,8 @@ def convert_reads(fq1s, fq2s, out=sys.stdout):
         else:
             already_interleaved = False
 
+        q1_iter = izip(*[fq1] * 4)
+
         if fq2 != "NA":
             fq2 = nopen(fq2)
             q2_iter = izip(*[fq2] * 4)
@@ -92,8 +96,6 @@ def convert_reads(fq1s, fq2s, out=sys.stdout):
                 sys.stderr.write("WARNING: running bwameth in single-end mode\n")
             q2_iter = repeat((None, None, None, None))
 
-        q1_iter = izip(*[fq1] * 4)
-
         lt80 = 0
 
         if already_interleaved: