dépendance entre les jobs lancés depuis perl

[karaudrey88]

Bonjour,
J'ai commencé un script perl qui lance plusieurs jobs a l'aide d'un qsub sur un cluster. Mais certains calculs doivent être finis avant que les autres commencent. J'ai commencé a mettre des dependances, mais j'ai une erreur que je ne comprend pas. Quelqu'un pourrait il m'aider?
Voici le début de mon code

Code :

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#!/usr/bin/perl
 
use strict;
use warnings;
 
use Getopt::Long;
my(%extract_jobs_id,$gtf,$submit,$hold_jid);
GetOptions(	"gtf:s" => \$gtf,
		"submit:s" => \$submit);
$submit ||= "no";
if (!defined $gtf) {
	die "Error : missing gtf file\n";
}
my (@gtf_files);
if (!defined $gtf) {
	die "Error : define input gtf file(s) with -gtf file1.gtf[,file2.gtf]\n";
} else {
	@gtf_files = split(",",$gtf);
}
foreach my $gtf (@gtf_files) {
	#create a directory for each bam
	my @nn=split(/\./,$gtf); 
	my $prefix=$nn[0];
	my $command = "mkdir $prefix";
	qx{$command};
 
 
	#generate qsub file and launch it
	my $qsuboutfile = "$prefix\_transcripts_extraction.qsub";
	open (QSUB,">$prefix/$qsuboutfile")or die "\nError : $qsuboutfile file could not be created: $!\n";
	print QSUB qq(#!/bin/bash
#\$ -S /bin/bash
#\$ -m e
#\$ -o $qsuboutfile.out
#\$ -e $qsuboutfile.err
#\$ -cwd
#\$ -q unlimitq
 
 
# command(s):
hostname >&2
awk '/ transcript_id "CUFF.*"/' ../$prefix.transcripts.gtf > $prefix\_news_exons.gtf
#sed -e "s/^Chr//" $prefix\_news_exons.gtf > $prefix\_news_exons_corrige.gtf
gffread -w $prefix\_new_transcrits.fa -g ../Danio_rerio.Zv9.69.dna.toplevel.fa $prefix\_news_exons.gtf
#gffread -w $prefix\_new_transcrits.fa -g ../Danio_rerio.Zv9.69.dna.toplevel.fa $prefix\_news_exons_corrige.gtf
);
 
	close QSUB;
 
	#launch qsub job if asked
		my $jobid;
		if ($submit eq "yes") {
			my $dependencies = "";
			if (defined $hold_jid) {
				$dependencies = "-hold_jid $hold_jid";
			}
			my $instruction = "cd $prefix/; qsub $dependencies $qsuboutfile | awk '{print \$3}' ";
			$jobid=qx{$instruction};
			chomp $jobid;
 
			print STDERR ".";
		} else {
			$extract_jobs_id{$gtf} = "";
		}
 
 
 
	if ($submit eq "yes") {
		print STDERR "\n";
	}
	if ($submit eq "yes") {
		print STDERR "scriptR";
	}
	my @blast_jobs;
 
	my $fisher_test = "$prefix\_stats.R";
	open (ROUT,">$prefix\_stats.txt") or die "\nError : $fisher_test file could not be created: $!\n";
	print ROUT qq(##read input files
mydata <- read.table("$prefix\_stats.txt")
pdf (file=paste ("$prefix\_stats.pdf"),paper="a4")
layout(matrix(1:4, 2, 2))
hist(mydata\$V4,xlab="exons length",ylab="frequency",col="blue",main="mean size of exons in transcripts")
hist(mydata\$V2,xlab="transcripts length",ylab="frequency",col="blue",main="length of transcripts")
hist(mydata\$V3,xlab="exons number",ylab="frequency",col="blue",main="number of exons in transcripts")
dev.off()
);
	close ROUT;
 
	my $qsuboutfile2 = "$prefix\_blast.qsub";
	open (QSUB,">$prefix/$qsuboutfile2")or die "\nError : $qsuboutfile2 file could not be created: $!\n";
	print QSUB qq(#!/bin/bash
#\$ -S /bin/bash
#\$ -m e
#\$ -o $qsuboutfile2.out
#\$ -e $qsuboutfile2.err
#\$ -cwd
#\$ -q unlimitq
 
# command(s):
#hostname >&2
blastall -p blastx -d nr -i $prefix\_new_transcrits.fa -e 0.00001 -o $prefix\_new_transcrits.blast 
stat_1.pl -gtf_file  -| stat_2.pl $prefix\_news_exons.gtf > $prefix\_stats.txt
);
	close QSUB;
 
	#launch qsub job if asked
	if ($submit eq "yes") {
		my $dependencies = "-hold_jid $extract_jobs_id{$gtf}";
		my $instruction = "cd $prefix/;qsub $dependencies $qsuboutfile2 | awk '{print \$3}'";
	$jobid=qx{$instruction};
	chomp $jobid;
	push (@blast_jobs,$jobid);
	print STDERR ".";
	} else {
		push (@blast_jobs,"");
		}

Et voici l'erreur générée

scriptRUse of uninitialized value within %extract_jobs_id in concatenation (.) or string at /home/kbarrilliot/bin/annotation.pl line 108.
qsub: ERROR! invalid option argument "-hold_jid,"

[Gardyen]

l'erreur te dit tout simplement que ta valeur ligne 108 $extract_jobs_id{$gtf} n'est pas définie quand tu crées ta commande.
En fait, tu n'initialises ta valeur que si submit est à 'no', pour 'yes' tu ne fais rien, d'où le message