vcftools not ouputting log file when run from perl

I am running 325 vcftools commands to generate Fst values, which obviously needs to be automated.

An example:

vcftools --vcf big.vcf --weir-fst-pop pop_lists/pop1.txt --weir-fst-pop pop_lists/pop2.txt  --out weir_fst_results/pop1_vs_pop2

and when I run this job, it works fine when I run it one by one by the command line, i.e. there are two files:

pop1_vs_pop2.log

and

pop1_vs_pop2.weir.fst

I need to get the Fst values from the log file.

The problem is that the log files are not generated when I run from my perl script, even though the commands executed are identical.

This sounds so trivial, but if it’s not producing the log file, I’m wasting my time.

How can I get vcftools to produce the log file when executing from a script? why isn’t vcftools producing the log file?

Perhaps there is a way of calculating this that doesn’t involve using vcftools?

the script to run them:

sub execute {
    my $command = shift;
    print "Executing: $commandn";
    if (system($command) != 0) {
        say "$command failed.";
        die
    }
}

my @pop = list_regex_files('^[A-Y]{3}.txt$', 'ethnicity_lists');
my $outdir="weir_fst_results";
if (not -d $outdir) {
    mkdir $outdir
}
my $vcf="big.vcf";
if (not -e $vcf) {
    say "$vcf doesn't exist.";
    die
}
foreach my $pop1 (0..$#pop) {
    my $label1;
    if ($pop[$pop1] =~ m/^ethnicity_lists/([A-Y]{3}).txt$/) {
      $label1 = $1
   } else {
      say "$pop[$pop1] failed regex.";
      die;
   }
    foreach my $pop2 (($pop1+1)..$#pop) {
        my $label2;
        if ($pop[$pop2] =~ m/^ethnicity_lists/([A-Y]{3}).txt$/) {
            $label2 = $1
        } else {
            say "$pop[$pop2] failed regex.";
            die;
        }
        my $out_prefix = "weir_fst_results/$label1" . "_vs_$label2";
        my $cmd = "vcftools --vcf $vcf ";
        $cmd .= "--weir-fst-pop $pop[$pop1] --weir-fst-pop $pop[$pop2] ";
        $cmd .= " --out $out_prefix > $out_prefix.out";
        execute($cmd);
    }
}

If I try to execute each comparison in a separate directory, with a separate nohup command, unfortunately all command output is still routed to the source nohup.out, and then the log file is empty, which defeats the purpose of running this.