Save state after ancestral step.

Author: trvrb

augur/src/H1N1pdm_process.py

@@ -145,6 +145,7 @@ def run(self, steps, viruses_per_month=50, raxml_time_limit = 1.0):
 		if 'ancestral' in steps:
 			print "--- Infer ancestral sequences " + time.strftime("%H:%M:%S") + " ---"
 			self.infer_ancestral()  # -> every node has a sequence
+			self.dump()
 		if 'refine' in steps:
 			print "--- Tree refine at " + time.strftime("%H:%M:%S") + " ---"
 			self.refine()

augur/src/H3N2_process.py

@@ -260,6 +260,7 @@ def run(self, steps, viruses_per_month=50, raxml_time_limit = 1.0):
 		if 'ancestral' in steps:
 			print "--- Infer ancestral sequences " + time.strftime("%H:%M:%S") + " ---"
 			self.infer_ancestral()  # -> every node has a sequence
+			self.dump()
 		if 'refine' in steps:
 			print "--- Tree refine at " + time.strftime("%H:%M:%S") + " ---"
 			self.refine()

augur/src/Vic_process.py

@@ -160,6 +160,7 @@ def run(self, steps, viruses_per_month=50, raxml_time_limit = 1.0):
 		if 'ancestral' in steps:
 			print "--- Infer ancestral sequences " + time.strftime("%H:%M:%S") + " ---"
 			self.infer_ancestral()  # -> every node has a sequence
+			self.dump()
 		if 'refine' in steps:
 			print "--- Tree refine at " + time.strftime("%H:%M:%S") + " ---"
 			self.refine()

augur/src/Yam_process.py

@@ -179,6 +179,7 @@ def run(self, steps, viruses_per_month=50, raxml_time_limit = 1.0):
 		if 'ancestral' in steps:
 			print "--- Infer ancestral sequences " + time.strftime("%H:%M:%S") + " ---"
 			self.infer_ancestral()  # -> every node has a sequence
+			self.dump()
 		if 'refine' in steps:
 			print "--- Tree refine at " + time.strftime("%H:%M:%S") + " ---"
 			self.refine()