--- a/gene_family_phylogeny_builder.py	Fri May 05 09:33:40 2017 -0400
+++ b/gene_family_phylogeny_builder.py	Fri May 05 09:33:46 2017 -0400
@@ -1,6 +1,5 @@
 #!/usr/bin/env python
 import argparse
-import subprocess
 
 import utils
 
@@ -15,12 +14,12 @@
 parser.add_argument('--method', dest='method', help='Protein clustering method')
 parser.add_argument('--min_orthogroup_size', dest='min_orthogroup_size', type=int, help='Minimum number of sequences in orthogroup alignments')
 parser.add_argument('--num_threads', dest='num_threads', type=int, help='Number of threads to use for execution')
-parser.add_argument('--orthogroup_aln', dest='orthogroup_aln', help="Input dataset files_path")
+parser.add_argument('--orthogroup_aln', dest='orthogroup_aln', help='Input dataset files_path')
 parser.add_argument('--output', dest='output', help='Output for phylogenetic trees')
 parser.add_argument('--output_dir', dest='output_dir', help='output.files_path')
 parser.add_argument('--rooting_order', dest='rooting_order', default=None, help='Rooting order configuration for rooting trees')
 parser.add_argument('--scaffold', dest='scaffold', help='Orthogroups or gene families proteins scaffold')
-parser.add_argument('--sequence_type', dest='sequence_type', help="Sequence type used in the phylogenetic inference")
+parser.add_argument('--sequence_type', dest='sequence_type', help='Sequence type used in the phylogenetic inference')
 parser.add_argument('--tree_inference', dest='tree_inference', help='Phylogenetic trees inference method')
 
 args = parser.parse_args()
@@ -41,9 +40,10 @@
 cmd += ' --scaffold %s' % args.scaffold
 cmd += ' --sequence_type %s' % args.sequence_type
 cmd += ' --tree_inference %s' % args.tree_inference
+
 # Run the command.
-proc = subprocess.Popen(args=cmd, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True)
-rc = proc.wait()
-utils.check_execution_errors(rc, proc.stderr)
+utils.run_command(cmd)
+
+# Handle outputs.
 utils.move_directory_files(OUTPUT_DIR, args.output_dir)
 utils.write_html_output(args.output, 'Phylogenetic trees', args.output_dir)