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Commit 1a1a8bcf authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
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Add memory resources to job waiting for exonerate to finish. Required

by farm3.
parent b2061450
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...@@ -379,7 +379,7 @@ sub rescore_gene_matrix_lsf { ...@@ -379,7 +379,7 @@ sub rescore_gene_matrix_lsf {
my $cmd = qq{$Bin/synteny_rescore.pl $options --index \$LSB_JOBINDEX}; my $cmd = qq{$Bin/synteny_rescore.pl $options --index \$LSB_JOBINDEX};
my $bsub_cmd = my $bsub_cmd =
sprintf( "|bsub -J%s[1-%d] " sprintf( "|bsub -J '%s[1-%d]' "
. "-o %s/synteny_rescore.%%I.out " . "-o %s/synteny_rescore.%%I.out "
. "-e %s/synteny_rescore.%%I.err %s", . "-e %s/synteny_rescore.%%I.err %s",
$lsf_name, $num_jobs, $logpath, $logpath, $lsf_name, $num_jobs, $logpath, $logpath,
...@@ -401,7 +401,9 @@ sub rescore_gene_matrix_lsf { ...@@ -401,7 +401,9 @@ sub rescore_gene_matrix_lsf {
# submit dependent job to monitor finishing of jobs # submit dependent job to monitor finishing of jobs
$self->logger->info("Waiting for jobs to finish...\n", 0, 'stamped'); $self->logger->info("Waiting for jobs to finish...\n", 0, 'stamped');
my $dependent_job = qq{bsub -K -w "ended($lsf_name)" -q small } . my $dependent_job =
qq{bsub -K -w "ended($lsf_name)" -q small } .
qq{-M 100 -R 'select[mem>100]' -R 'rusage[mem=100]' } .
qq{-o $logpath/synteny_rescore_depend.out /bin/true}; qq{-o $logpath/synteny_rescore_depend.out /bin/true};
system($dependent_job) == 0 or system($dependent_job) == 0 or
......
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