I don't know what particular error causes the problem you described, but the code is very hard to read (no indenting at all) and misses basic sanity measures (such as use strict; use warnings;).

Without any data files it's basically impossible for us to debug.

However there are some lines that look very suspicious to me:

open $file1 = "executable_$Fld[0]";
open $file2 = "not_executable_$Fld[0]";
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What do you think these lines do? I've never seen that idiom before.