Try adding '.exe' after the 'java' part. Ie:

my $out = system(
    "/users/sophix/Desktop/prottest3/prottest3/java.exe"
    . " -jar prottest-3.0.jar -i $name.aa -t $name.trees -o $name.out"
+ 
    . "-all -verbose -all-matrices -threads 3 -G -F -all-distributions
+ -ncat 4"
);

[download]
Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
"Science is about questioning the status quo. Questioning authority".
In the absence of evidence, opinion is indistinguishable from prejudice.

In reply to Re: Calling Java using system() by BrowserUk
in thread Calling Java using system() by sophix

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