diff --git a/blast_on_cluster.py b/blast_on_cluster.py index 93430ef..da7948e 100644 --- a/blast_on_cluster.py +++ b/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)