From 0184a09d0f69293f4944ddd2d7415430a50b4539 Mon Sep 17 00:00:00 2001
From: Torsten Seemann <torsten.seemann@gmail.com>
Date: Sun, 9 Jul 2017 10:35:41 +1000
Subject: [PATCH] Issue #5 - skip over unreadable files

---
 bin/abricate | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/bin/abricate b/bin/abricate
index 48df330..b738a15 100755
--- a/bin/abricate
+++ b/bin/abricate
@@ -93,6 +93,10 @@ for my $file (@ARGV) {
   my %seen;
   my @hit;
   msg("Processing: $file");
+  if (! -r $file) {
+    msg("WARNING: '$file' does not exist, or is unreadable");
+    next FILE;
+  }
   my $cmd = "(gzip -d -c -f \Q$file\E | seqret -auto -filter -osformat2 fasta |"
           . " blastn -db \Q$db_path\E -outfmt '$format'"
           . " -task blastn -evalue 1E-20 -dust no -max_target_seqs 10000 -perc_identity $minid"