open3-error when trying to run a script using PBS::Client - perl

Question

I'm trying to get the following perl script to work. First, a fastq-file is read, this file is then used to be analysed by a number of programs.
Code:
use warnings;
use PBS::Client;
$directory = $ARGV[0];
opendir(DIR, $directory);
#files=();
while ($file = readdir(DIR)) {
push(#files, $file);
}
closedir(DIR);
#fastq_files = grep(/fastq/, #files);
$client = PBS::Client->new();
foreach $fastq (#fastq_files){
#commands = ();
$wd = "/store/www/labresults_QC/snRNA_sequence_analyser/".$ARGV[0];
$name = $fastq."_process_map";
$queue = "system";
$wallt = "72:00:00";
chomp($fastq);
$fastq =~ /.+[^\.fastq]/;
push (#commands, "/opt/fastx_toolkit-0.0.13.2/bin/fastq_quality_filter -q 30 -p 80 -i " . $fastq . " -o ";
push (#commands, "/opt/fastx_toolkit-0.0.13.2/bin/fastx_clipper -i " . $& . "_qc.fastq -o " . $& . "_qc_clipped.fastq -v -l 15 -a TGGAATTCTCGGGTGCCAAGG -Q33\n");
push (#commands, "/opt/fastx_toolkit-0.0.13.2/bin/fastx_collapser -i " . $& . "_qc_clipped.fastq -o " . $& . "_qc_clipped_collapse.fa -v -Q33\n");
push (#commands, "/opt/bowtie-1.0.0/bowtie -f /opt/genomes/9606/GRCh37/bowtie/GRCh37 " . $& . "_qc_clipped_collapse.fa " . $& . "_mapped.sam -k 100 -n 0 -l 25 --best");
$job = PBS::Client::Job -> new(
wd => $wd,
queue => $queue,
name => $name,
wallt => $wallt,
cmd => [[#commands]]);
$client -> qsub($job);
}
However, when trying to execute through a Linux commandline, it gives this error message:
open3: exec of /store/www/labresults_QC/snRNA_sequence_analyser/data/data_raw/test_run/n8XyeYIkfv failed at /store/bin/perl_libs/lib/perl5//PBS/Client.pm line 150
The error message points to this piece of code in the PBS Client module:
#-------------------------------------------------------------------
# Thanks to Sander Hulst
sub call_qsub
{
my #args = #_;
# If the qsub command fails, for instance, pbs_server is not running,
# PBS::Client's qsub should not silently ignore. Disable any reaper
# functions so the exit code can be captured
use Symbol qw(gensym);
use IPC::Open3;
my $stdout = gensym();
my $stderr = gensym();
{
local $SIG{CHLD} = sub{};
my $pid = open3(gensym, $stdout, $stderr, #args); # This is line 150
waitpid($pid,0);
}
confess <$stderr> if ($?);
return <$stdout>;
}
#-------------------------------------------------------------------
Anyone got a clue what this means?
EDIT
After some investigation it seems that this line is failing: $client -> qsub($job);
but I don't know why. Any ideas what I'm doing wrong?
FINAL EDIT:
So, we finally found the real cause of the problem. It turned out something went wrong in the latest installation of PBS::Client we did. So we reverted to an older version, and the problem was gone!

Answer 1

The module generates a script then tries to execute it without having made it executable. Workaround:
use PBS::Client qw( );
BEGIN {
my $orig_genScript = \&PBS::Client::genScript;
my $new_genScript = sub {
my $script_qfn = $orig_genScript->(#_);
chmod(0700, $script_qfn) or die $!;
return $script_qfn;
};
no warnings 'redefine';
*PBS::Client::genScript = $new_genScript;
}