diff --git a/taxon_filter.py b/taxon_filter.py index 6745ca5c7..f5e106a72 100755 --- a/taxon_filter.py +++ b/taxon_filter.py @@ -193,7 +193,7 @@ def lastal_chunked_fastq( lastal_out = mkstempfname('.lastal') with open(lastal_out, 'wt') as outf: - cmd = [lastal_path, '-Q1'] + cmd = [lastal_path, '-Q1', '-P0'] cmd.extend( [ '-n', max_gapless_alignments_per_position, '-l', min_length_for_initial_matches, '-L',