bugfix

proost · Jun 14, 2016 · 5c79ec3 · 5c79ec3
1 parent 0b943ce
commit 5c79ec3
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/pipeline/orthology.py b/pipeline/orthology.py
@@ -16,7 +16,7 @@ def run_orthofinder(self):
         orthofinder_dir = self.dp['GLOBAL']['orthofinder_output']
         orthofinder_cores = self.cp['TOOLS']['orthofinder_cores']
 
-        os.makedirs(os.path.dirname(orthofinder_dir), exist_ok=True)
+        os.makedirs(orthofinder_dir, exist_ok=True)
 
         filename, jobname = self.write_submission_script("orthofinder_%d",
                                                          self.python_module + ' ' +
@@ -26,6 +26,7 @@ def run_orthofinder(self):
                                                          "orthofinder_%d.sh")
 
         for g in self.genomes:
+            print('çopying', self.dp[g]['protein_fasta'], 'to', os.path.join(orthofinder_dir, g + '.fasta'))
             copy(self.dp[g]['protein_fasta'], os.path.join(orthofinder_dir, g + '.fasta'))
 
         subprocess.call(["qsub", "-pe", "cores", orthofinder_cores, "-v", "fasta_dir=" + orthofinder_dir + ",num_cores=" + orthofinder_cores, filename])