update and fixes (first version that works)

blast_on_cluster.py

@@ -17,7 +17,7 @@
 module load biotools/ncbi-blast-2.3.0+
 date
 hostname
-blastp -outfmt 6 -evalue 0.001 -query ${q} -db ${db} -out ${o} -num_threads {t}
+blastp -outfmt 6 -evalue 0.001 -query ${q} -db ${db} -out ${o} -num_threads ${t}
 date
 """
 
@@ -42,7 +42,7 @@ def write_template(filename=None):
     return filename
 
 
-def execute_command_on_cluster(submission_script, cmd, threads=1):
+def execute_command_on_cluster(submission_script, cmd, threads=3):
     """
     Parses blastp command reported by OrthoFinder and submits an equivalent job to the cluster
 
@@ -56,8 +56,8 @@ def execute_command_on_cluster(submission_script, cmd, threads=1):
     query, db, output = cmd_args[6], cmd_args[8], cmd_args[10]
 
     qsub_cmd = ['qsub',
-                '-pe', 'cores', str(threads),
-                '-v', 'q=%s,db=%s,out=%s,t=%d' % (query, db, output, threads),
+                '-pe', 'cores', str(threads+1),
+                '-v', 'q=%s,db=%s,o=%s,t=%d' % (query, db, output, threads),
                 submission_script]
 
     print(qsub_cmd)