From fac5996b9536f4e58ee8160f257409e4c69e28a9 Mon Sep 17 00:00:00 2001 From: Ryan Routsong Date: Mon, 12 Aug 2024 15:31:36 -0400 Subject: [PATCH] fix: pass threads to mash sketch --- drep/d_cluster/compare_utils.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/drep/d_cluster/compare_utils.py b/drep/d_cluster/compare_utils.py index f995ff5..87f4184 100644 --- a/drep/d_cluster/compare_utils.py +++ b/drep/d_cluster/compare_utils.py @@ -29,12 +29,12 @@ def __init__(self, locations, number, sketch_folder, genome_names, no_create=Fal if not os.path.exists(self.chunk_folder): os.makedirs(self.chunk_folder) - def gen_sketch_cmds(self, mash_exe, MASH_s): + def gen_sketch_cmds(self, mash_exe, MASH_s, p): cmds = [] for location, name in zip(self.genome_locations, self.genome_names): file = os.path.join(self.chunk_folder, name) if not os.path.isfile(file + '.msh'): - cmd = [mash_exe, 'sketch', location, '-s', str(MASH_s), '-o', + cmd = [mash_exe, 'sketch', location, '-p', str(p), '-s', str(MASH_s), '-o', file] cmds.append(cmd) return cmds @@ -170,7 +170,7 @@ def run_mash_on_genome_chunks(genome_chunks, mash_exe, sketch_folder, MASH_folde # Step 1) Create Mash sketches cmds = [] for GC in genome_chunks: - cmds += GC.gen_sketch_cmds(mash_exe, MASH_s) + cmds += GC.gen_sketch_cmds(mash_exe, MASH_s, p) if (not dry) & (len(cmds) > 0): drep.thread_cmds(cmds, logdir=logdir, t=int(p))