From 558741c1d4e5a270e38a15a200c7975d67ef3232 Mon Sep 17 00:00:00 2001
From: Brant Faircloth <brant@faircloth-lab.org>
Date: Fri, 22 May 2015 11:12:44 -0500
Subject: [PATCH] Raxml zombie process

Some alignments will cause raxml to enter a zombie state for unknown
reasons.  Adding a random seed to the '-p' option appears to fix this.
---
 sate/tools.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/sate/tools.py b/sate/tools.py
index 8919f51..025f0a0 100644
--- a/sate/tools.py
+++ b/sate/tools.py
@@ -26,6 +26,7 @@
 import time
 import platform
 import shutil
+import random
 
 from alignment import Alignment
 from sate import get_logger, GLOBAL_DEBUG, SATE_SYSTEM_PATHS_CFGFILE, DEFAULT_MAX_MB
@@ -794,6 +795,7 @@ def create_job(self, alignment, starting_tree=None, name='default', **kwargs):
                 '-n', name,
                 '-q', parfn,
                 '-s', seqfn,
+                '-p', str(random.randint(1,1000000000)),
                 # '-M', # Branch length estimates per partition
                 ]
         #x = open(parfn).readlines()