From 51da5cdd891a30e910749d13ba59a9972333f8bd Mon Sep 17 00:00:00 2001 From: Ryan Wick Date: Thu, 28 Sep 2017 14:10:22 +1000 Subject: [PATCH] Use different Bowtie preset to avoid potential crash --- unicycler/pilon_func.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/unicycler/pilon_func.py b/unicycler/pilon_func.py index d4e11936..232436fe 100644 --- a/unicycler/pilon_func.py +++ b/unicycler/pilon_func.py @@ -112,7 +112,7 @@ def get_insert_size_range(graph, args, polish_dir): # Perform the alignment with Bowtie2. bowtie2_command = [args.bowtie2_path, '-1', args.short1, '-2', args.short2, - '-x', fasta_filename, '--local', '--fast-local', + '-x', fasta_filename, '--fast', '--threads', str(args.threads), '-I', '0', '-X', '5000', '-S', sam_filename] log.log(dim(' ' + ' '.join(bowtie2_command)), 2) try: