Actually, I ran this: 


open INP,"< $ARGV[0]"
        or die "Cannot open file: $!";

$file = "$ARGV[1]";

open OUT, "> $file"
        or die "Cannot open file: $!";

@out = `/home/applications/samtools-0.1.7a/samtools view -bS $ARGV[0] 
+2>&1`;

print OUT @out;

close INP;
close OUT;

[download]

And I was able to produce a non-empty file. Unfortunately, it got truncated somehow. Is it because of my use of backticks?

In reply to Re: Running an external command by Eldan Aranye
in thread Running an external command by Eldan Aranye

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