Added redirect for stderr.

Author: icwells

bin/parallelCodeML.py

@@ -101,19 +101,19 @@ def parallelize(ap, outdir, finished, completed, multiple, cpu, ctl,
 				makeCtl(gene, outfile, tempctl, treefile, ctl)
 				os.chdir(wd)
 				# Call CodeML
-				with open(wd + "codemlLog.txt", "w") as tmpout:
+				with open("codemlLog.txt", "w") as tmpout:
 					cm = Popen(split(ap + "paml/bin/codeml " + tempctl),
-									shell = True, stdout = tmpout)
+							shell = True, stdout = tmpout, stderr = tmpout)
 					cm.wait()
 		elif multiple == False:
 			# Make control file
 			treefile = wd + filename + ""
 			makeCtl(gene, outfile, tempctl, treefile, ctl)
 			# Call CodeML for all files
 			os.chdir(wd)
-			with open(wd + "codemlLog.txt", "w") as tmpout:
+			with open("codemlLog.txt", "w") as tmpout:
 				cm = Popen(split(ap + "paml/bin/codeml " + tempctl),
-								shell = True, stdout = tmpout)
+						shell = True, stdout = tmpout, stderr = tmpout)
 				cm.wait()
 		with open(finished, "a") as fin:
 			# Append gene id to list when done