I think problem is in the:

    my $line = 1 |  0.116 0.088 0.173 0.624;
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I don't understand what do you mean? Followning code works correctly:

     my $line = "0.116 0.088 0.173 0.624";
     my @prob = $line =~ m/(\b0\.[0-9][0-9][0-9])/g;
     print $prob[0], "\n";
     print $prob[1], "\n";
     print $prob[2], "\n";
     print $prob[3], "\n";
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SV* sv_bless(SV* sv, HV* stash);