--- a/gene_family_integrator.py	Fri Apr 07 16:30:51 2017 -0400
+++ b/gene_family_integrator.py	Mon Apr 10 11:30:34 2017 -0400
@@ -8,7 +8,7 @@
 
 parser = argparse.ArgumentParser()
 parser.add_argument('--orthogroup_faa', dest='orthogroup_faa', help="Directory of input fasta datasets")
-parser.add_argument('--scaffold', dest='scaffold', default='mode', help='Orthogroups or gene families proteins scaffold')
+parser.add_argument('--scaffold', dest='scaffold', help='Orthogroups or gene families proteins scaffold')
 parser.add_argument('--method', dest='method', help='Protein clustering method')
 parser.add_argument('--orthogroup_fna', dest='orthogroup_fna', default=None, help='Use correspong coding sequences')
 parser.add_argument('--output', dest='output', help="Output dataset")
@@ -27,5 +27,5 @@
 proc = subprocess.Popen(args=cmd, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True)
 rc = proc.wait()
 utils.check_execution_errors(rc, proc.stderr)
-utils.move_directory_files(OUTPUT_DIR, args.output_dir)
+utils.move_directory_files(os.path.join(OUTPUT_DIR, 'orthogroups_fasta'), args.output_dir)
 utils.write_html_output(args.output, 'Integrated gene family sequences', args.output_dir)