From c54b7af8a2a2df64d1b1f1a98c4d70e54b615ff0 Mon Sep 17 00:00:00 2001
From: "Brian P. Walenz" <thebri@gmail.com>
Date: Tue, 11 Apr 2017 15:48:52 -0400
Subject: [PATCH] Run './alignGFA.sh' for small jobs, not just 'alignGFA.sh'.

---
 src/pipelines/canu/Consensus.pm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/pipelines/canu/Consensus.pm b/src/pipelines/canu/Consensus.pm
index 6cd1a3c02..21e7869f2 100644
--- a/src/pipelines/canu/Consensus.pm
+++ b/src/pipelines/canu/Consensus.pm
@@ -668,7 +668,7 @@ sub alignGFA ($) {
     emitStage($asm, "alignGFA", $attempt);
 
     if (getGlobal("genomeSize") < 40000000) {
-        if (runCommand("$path", "alignGFA.sh")) {
+        if (runCommand("$path", "./alignGFA.sh")) {
             caExit("failed to align contigs", "./$asm.contigs.aligned.gfa.err");
         }
     } else {