From c5637d8a0f906a26f662ada11170f1f2ff331b42 Mon Sep 17 00:00:00 2001
From: Jianshu Zhao <jansuechao@gmail.com>
Date: Thu, 24 Jun 2021 15:11:50 -0400
Subject: [PATCH] --phred-offset not recognized

---
 phyloFlash.pl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/phyloFlash.pl b/phyloFlash.pl
index 642dc00..89400a3 100755
--- a/phyloFlash.pl
+++ b/phyloFlash.pl
@@ -1582,7 +1582,7 @@ sub spades_run {
     my $cpus_spades = $cpus > 24 ? 24 : $cpus;
 
     my $return = run_prog_nodie("spades",
-                                "-o $libraryNAME.spades -t $cpus_spades -m 20 -k $kmer "
+                                "-o $libraryNAME.spades -t $cpus_spades -m 20 -k $kmer --phred-offset 33 "
                                 . $args,
                                 $outfiles{"spades_log"}{"filename"},"&1"
                                 );