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Issue #5 - skip over unreadable files
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tseemann committed Jul 9, 2017
1 parent a0583a1 commit 0184a09
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4 changes: 4 additions & 0 deletions bin/abricate
Original file line number Diff line number Diff line change
Expand Up @@ -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"
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