Commit ca577d43 authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
Browse files

Small changes to bsub command creation.

parent 91eb4289
......@@ -378,18 +378,20 @@ sub rescore_gene_matrix_lsf {
my $cmd = qq{$Bin/synteny_rescore.pl $options --index \$LSB_JOBINDEX};
my $pipe = qq{|bsub -J$lsf_name\[1-$num_jobs\] } .
qq{-o $logpath/synteny_rescore.\%I.out } .
qq{-e $logpath/synteny_rescore.\%I.err } .
$self->conf->param('lsf_opt_synteny_rescore');
my $bsub_cmd =
sprintf( "|bsub -J%s[1-%d] "
. "-o %s/synteny_rescore.%%I.out "
. "-e %s/synteny_rescore.%%I.err %s",
$lsf_name, $num_jobs, $logpath, $logpath,
$self->conf()->param('lsf_opt_synteny_rescore') );
# run lsf job array
$self->logger->info("Submitting $num_jobs jobs to lsf.\n");
$self->logger->debug("$cmd\n\n");
local *BSUB;
open BSUB, $pipe or
$self->logger->error("Could not open open pipe to bsub: $!\n");
open( BSUB, $bsub_cmd )
or $self->logger->error("Could not open open pipe to bsub: $!\n");
print BSUB $cmd;
$self->logger->error("Error submitting synteny rescoring jobs: $!\n")
......
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