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Commit b2061450 authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
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Farm3 seems to require memory resources on the job that waits on the

small queue for exonerate to finish.  Also added spaces after -R and -J
switches.
parent 0b16a1cd
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......@@ -490,7 +490,7 @@ sub run_exonerate {
$self->logger->debug("$exonerate_job\n\n");
my $bsub_cmd = sprintf(
"|bsub -J%s[1-%d]%%%d -o %s/exonerate.%%I.out %s",
"|bsub -J '%s[1-%d]%%%d' -o %s/exonerate.%%I.out %s",
$lsf_name,
$num_jobs,
$self->conf()->param('exonerate_concurrent_jobs') || 200,
......@@ -509,7 +509,9 @@ sub run_exonerate {
# submit dependent job to monitor finishing of exonerate jobs
$self->logger->info("Waiting for exonerate 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 $logpath/exonerate_depend.out /bin/true};
system($dependent_job) == 0 or
......
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