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Updated psi-cd-hit-local.pl #92

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Updated psi-cd-hit-local.pl #92

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12 changes: 6 additions & 6 deletions psi-cd-hit/psi-cd-hit-local.pl
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
#!/usr/bin/env perl
#!/usr/bin/perl -w
################################################################################
######### PSI-cd-hit written by Weizhong Li at http://cd-hit.org
################################################################################
Expand Down Expand Up @@ -1195,9 +1195,9 @@ sub run_batch_blast3_multi {
if ($exec_mode eq "qsub") {
for ($j=0; $j<$num_qsub; $j++) {
my $t = "psi-cd-hit-$j";
my $cmd = `qsub -N $t $remote_sh_script $j`; #### pass $j to qsub command
my $cmd = `qsub -N $t $remote_sh_script -v para=$j`; #### pass $j to qsub command
my $qsub_id = 0;
if ($cmd =~ /(\d+)/) { $qsub_id = $1;} else {die "can not submit qsub job and return a id\n";}
if ($cmd =~ /(\d+)/) { $qsub_id = $1;} else {die "can not submit qsub job and return a id: $cmd\n";}
print LOG "qsub querying $j, PID $qsub_id\n";
$qsub_ids{$qsub_id} = 1;
}
Expand Down Expand Up @@ -1348,7 +1348,7 @@ sub write_remote_sh_script {
print RESH <<EOD;
$local_sh

para=\$1
para=\${para:-\$1}
cd $pwd
EOD

Expand All @@ -1372,7 +1372,7 @@ sub write_remote_perl_script {

open(REPERL, "> $remote_perl_script") || die;
print REPERL <<EOD;
#!/usr/bin/env perl
#!/usr/bin/perl
\$host = shift;
\$instance = shift;
\$arg = shift;
Expand Down Expand Up @@ -1451,7 +1451,7 @@ sub wait_blast_out {
sub SGE_qstat_xml_query {
my ($i, $j, $k, $cmd, $ll);
%qstat_xml_data = (); #### global
$cmd = `qstat -f -xml`;
$cmd = `qstat -f -x`;
if ($cmd =~ /<queue_info/) { #### dummy
$qstat_xml_data{"NULL"}= ["NULL","NULL"];
}
Expand Down