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

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;
}