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Abort on non-zero blastcmd exit code #213

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Merged
tseemann merged 2 commits into from
Dec 4, 2025
Merged

Abort on non-zero blastcmd exit code #213

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1c67286
Abort on non-zero blastcmd exit code
SamStudio8 Dec 9, 2024
03afa8f
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SamStudio8 Dec 9, 2024
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13 changes: 10 additions & 3 deletions bin/abricate
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Original file line number Diff line number Diff line change
Expand Up @@ -121,12 +121,13 @@ for my $file (@ARGV) {
: "blastx -task blastx-fast -seg no"
;

my $cmd = "(any2fasta -q -u \Q$file\E |"
. " $blastcmd -db \Q$db_path\E -outfmt '$format' -num_threads $threads"
my $cmd = "bash -c 'set -euo pipefail;"
. " any2fasta -q -u \Q$file\E |"
. " $blastcmd -db \Q$db_path\E -outfmt \"$format\" -num_threads $threads"
. " -evalue 1E-20 -culling_limit $CULL"
. " -max_target_seqs 10000" # https://github.com/tseemann/abricate/issues/135
# . " -max_target_seqs ".$dbinfo->{SEQUENCES} # Issue #76
. ")"
. "'"
;

msg("Running: $cmd") if $debug;
Expand Down Expand Up @@ -183,6 +184,12 @@ for my $file (@ARGV) {
];
}
close BLAST;
# Check the exit status of BLAST handle and abort
my $exitcode = $? >> 8;
if ($exitcode != 0) {
msg("Command exited with non-zero exit code $exitcode. Aborting Abricate.");
exit($exitcode);
}

msg("Found", scalar(@hit), "genes in $file");

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