diff --git a/bin/split_fasta.py b/bin/split_fasta.py
index d85b394..dbec63f 100755
--- a/bin/split_fasta.py
+++ b/bin/split_fasta.py
@@ -36,11 +36,11 @@ def log(string, newline_before=False):
         if line.startswith('>'):
 
             # new sequence
-            seq_name = line.strip().split()[0][1:]
+            seq_name = line.strip()[1:]
             assert seq_name != '', f'Empty header in file: {fasta_file}'
             
             # sanitize
-            seq_name = seq_name.replace('/', '_').replace(':', '_').replace('|','_')
+            seq_name = seq_name.replace(' ', '_').replace('/', '_').replace(':', '_').replace('|','_')
 
             # handle duplicates
             if seq_name in sequence_names:
@@ -59,7 +59,10 @@ def log(string, newline_before=False):
             log(f'Writing {outfile}')
             outfh = open(outfile, 'w')
             outfh.write(f'>{seq_name}\n')
-            
+
+        elif line in ['\n','\r\n']:
+            continue
+
         else:
             # write rest of lines (and fix windows line endings)
             outfh.write(line.replace('\r',''))