Commit d7f22081 authored by Sebastien Moretti's avatar Sebastien Moretti
Browse files

Since centos7 update --exhaustive option looks to turn into an infinite loop

parent a0731858
......@@ -64,7 +64,7 @@ my $exonerate_exe = 'exonerate'; # Exonerate 1.0 because current parser on
################## Option management
my ($msa, $revtrans, $pep, $hideBOJ, $run_name, $template, $lim) = ('', 0, 0, 0, '', '', 0);
my ($cache, $cleancache) = ('update', 'update');#TODO Finish to implement
my ($cache, $cleancache) = ('update', 'update'); #TODO Finish to implement
my ($debug, $tmp) = (0, 0);
my ($db, $species, $local, $giga) = ($blast_param->{'db1'}, $blast_param->{'species'}, 0, 0);
my %opts = ('msa|in=s' => \$msa, # Input sequences
......@@ -1079,7 +1079,8 @@ sub runExonerate{
}
else{
# Exonerate prot - short genomic or short RNA
system("$exonerate_exe --showquerygff --showtargetgff --model protein2genome --bestn 1 --percent 75 --exhaustive -q $cache/$date.$order.fas -t $cache/$gis[$b].fas >$cache/$date.$order.exon 2>>$cache/$date.ExonerateError");
# system("$exonerate_exe --showquerygff --showtargetgff --model protein2genome --bestn 1 --percent 75 --exhaustive -q $cache/$date.$order.fas -t $cache/$gis[$b].fas >$cache/$date.$order.exon 2>>$cache/$date.ExonerateError");
system("$exonerate_exe --showquerygff --showtargetgff --model protein2genome --bestn 1 --percent 75 -q $cache/$date.$order.fas -t $cache/$gis[$b].fas >$cache/$date.$order.exon 2>>$cache/$date.ExonerateError"); # Since centos7 update --exhaustive option looks to turn into an infinite loop!
}
my $targetNT = $gis[$b];
......
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