Adds --seed option in bowtie2 execution

biobakery · Jul 26, 2021 · 55746e6 · 55746e6
1 parent bb964cc
commit 55746e6
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/metaphlan/metaphlan.py b/metaphlan/metaphlan.py
@@ -386,7 +386,7 @@ def run_bowtie2(fna_in, outfmt6_out, bowtie2_db, preset, nproc, min_mapq_val, fi
         else:
             readin = subp.Popen([read_fastx, '-l', str(read_min_len)], stdin=sys.stdin, stdout=subp.PIPE, stderr=subp.PIPE)
 
-        bowtie2_cmd = [exe if exe else 'bowtie2', "--quiet", "--no-unal", "--{}".format(preset),
+        bowtie2_cmd = [exe if exe else 'bowtie2', "--seed", "1992", "--quiet", "--no-unal", "--{}".format(preset),
                        "-S", "-", "-x", bowtie2_db]
 
         if int(nproc) > 1: