You can't put named options after the positional ones, try 
-t sur -o results out20111_23866.sorted SUR_P1023866.sorted

[download]


-pete
"Worry is like a rocking chair. It gives you something to do, but it doesn't get you anywhere."

In reply to Re: handling scripts options by dreadpiratepeter
in thread handling scripts options by gyre007

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