嘗試使用PBS運行腳本時出現open3錯誤::客戶端

Question

我試圖讓下面的perl腳本工作。首先，讀取fastq文件，然後使用該文件通過多個程序進行分析。

代碼：

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); 

} 

然而，試圖通過Linux命令行來執行時，它使此錯誤消息：

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 

該錯誤消息指向這一段代碼在PBS客戶端模塊：

#------------------------------------------------------------------- 
# 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>; 
} 
#------------------------------------------------------------------- 

任何人都知道這意味着什麼？

編輯
經過一番調查似乎這行失敗：$client -> qsub($job); ，但我不知道爲什麼。任何想法我做錯了什麼？

---

最後編輯：

所以，我們終於發現了問題的真正原因。事實證明，我們所做的最新安裝PBS::Client出了問題。所以我們回到了一個較舊的版本，問題就此消失了！

Answer 1

該模塊生成一個腳本，然後嘗試執行它，但沒有使其可執行。解決方法：

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; 
}