Iqtree

shimbalama · Dec 12, 2018 · d69c15c · d69c15c
1 parent 78c8954
commit d69c15c
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/lab_modules.py b/lab_modules.py
@@ -11,12 +11,12 @@
 def main():
     pass
 
-def call_iqtree_with_SNP_aln(args, d_count):
+def call_iqtree_with_SNP_aln(args, d_count, query):
 
     constants=','.join([str(d_count.get('A')), str(d_count.get('C')),
            str(d_count.get('G')), str(d_count.get('T'))])
-    print ('constants',constants)
-    call(['nice', 'iqtree', '-s', args.out + '_trimmed_SNP.aln',
+    print ('constants', query, constants)
+    call(['nice', 'iqtree', '-s', query + '_trimmed_SNP.aln', '-nt', str(args.threads),
           '-m', 'GTR+G', '-bb', '1000', '-czb', '-fconst', constants])