You might try to change the backtick you used here 

@out = `/home/applications/samtools-0.1.7a/samtools view -bS $ARGV[0]`

[download]
to using system("...") instead.
check perldoc -q "backtick", it could be of help.

In reply to Re: Trapping diagnostic messages by 2teez
in thread Trapping diagnostic messages by Eldan Aranye

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